Merge branch '_so_push' into _so_main_push

Fixes ReDoS vulnerability in pydantic email validation regex.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

.gitignore

@@ -8,3 +8,4 @@ __pycache__
 package
 stack_orchestrator/data/build_tag.txt
 /build
+.worktrees

.pebbles/config.json

@@ -0,0 +1,3 @@
+{
+  "prefix": "so"
+}

.pebbles/events.jsonl

@@ -0,0 +1,15 @@
+{"type":"create","timestamp":"2026-03-08T06:56:07.080584539Z","issue_id":"so-076","payload":{"description":"Currently laconic-so maps one stack to one deployment to one pod. All containers\nin a stack's compose files become containers in a single k8s pod. This means:\n\n- Can't upgrade doublezero without restarting agave-validator\n- Can't restart monitoring without disrupting the validator\n- Can't independently scale or lifecycle-manage components\n\nThe fix is stack composition. A meta-stack (e.g. biscayne-stack) composes\nsub-stacks (agave, doublezero, agave-monitoring), each becoming its own\nk8s Deployment with independent lifecycle.","priority":"2","title":"Stack composition: deploy multiple stacks into one kind cluster","type":"epic"}}
+{"type":"create","timestamp":"2026-03-08T06:56:07.551986919Z","issue_id":"so-ab0","payload":{"description":"Add laconic-so deployment prepare that creates cluster infrastructure without pods. Already implemented, needs review.","priority":"2","title":"deployment prepare command","type":"task"}}
+{"type":"create","timestamp":"2026-03-08T06:56:07.884418759Z","issue_id":"so-04f","payload":{"description":"deployment stop on ANY deployment deletes the shared kind cluster. Should only delete its own namespace.","priority":"2","title":"deployment stop should not destroy shared cluster","type":"bug"}}
+{"type":"create","timestamp":"2026-03-08T06:56:08.253520249Z","issue_id":"so-370","payload":{"description":"Allow stack.yml to reference sub-stacks. Each sub-stack becomes its own k8s Deployment sharing namespace and PVs.","priority":"2","title":"Add stacks: field to stack.yml for composition","type":"task"}}
+{"type":"create","timestamp":"2026-03-08T06:56:08.646764337Z","issue_id":"so-f7c","payload":{"description":"Create three independent stacks from the monolithic agave-stack. Each gets its own compose file and independent lifecycle.","priority":"2","title":"Split agave-stack into agave + doublezero + monitoring","type":"task"}}
+{"type":"rename","timestamp":"2026-03-08T06:56:14.499990161Z","issue_id":"so-ab0","payload":{"new_id":"so-076.1"}}
+{"type":"dep_add","timestamp":"2026-03-08T06:56:14.499992031Z","issue_id":"so-076.1","payload":{"dep_type":"parent-child","depends_on":"so-076"}}
+{"type":"rename","timestamp":"2026-03-08T06:56:14.786407752Z","issue_id":"so-04f","payload":{"new_id":"so-076.2"}}
+{"type":"dep_add","timestamp":"2026-03-08T06:56:14.786409842Z","issue_id":"so-076.2","payload":{"dep_type":"parent-child","depends_on":"so-076"}}
+{"type":"rename","timestamp":"2026-03-08T06:56:15.058959714Z","issue_id":"so-370","payload":{"new_id":"so-076.3"}}
+{"type":"dep_add","timestamp":"2026-03-08T06:56:15.058961364Z","issue_id":"so-076.3","payload":{"dep_type":"parent-child","depends_on":"so-076"}}
+{"type":"rename","timestamp":"2026-03-08T06:56:15.410080785Z","issue_id":"so-f7c","payload":{"new_id":"so-076.4"}}
+{"type":"dep_add","timestamp":"2026-03-08T06:56:15.410082305Z","issue_id":"so-076.4","payload":{"dep_type":"parent-child","depends_on":"so-076"}}
+{"type":"dep_add","timestamp":"2026-03-08T06:56:16.313585082Z","issue_id":"so-076.3","payload":{"dep_type":"blocks","depends_on":"so-076.2"}}
+{"type":"dep_add","timestamp":"2026-03-08T06:56:16.567629422Z","issue_id":"so-076.4","payload":{"dep_type":"blocks","depends_on":"so-076.3"}}

CLAUDE.md

@@ -8,6 +8,7 @@ NEVER assume your hypotheses are true without evidence
 
 ALWAYS clearly state when something is a hypothesis
 ALWAYS use evidence from the systems your interacting with to support your claims and hypotheses
+ALWAYS run `pre-commit run --all-files` before committing changes
 
 ## Key Principles
 
@@ -43,6 +44,76 @@ This project follows principles inspired by literate programming, where developm
 
 This approach treats the human-AI collaboration as a form of **conversational literate programming** where understanding emerges through dialogue before code implementation.
 
+## External Stacks Preferred
+
+When creating new stacks for any reason, **use the external stack pattern** rather than adding stacks directly to this repository.
+
+External stacks follow this structure:
+
+```
+my-stack/
+└── stack-orchestrator/
+    ├── stacks/
+    │   └── my-stack/
+    │       ├── stack.yml
+    │       └── README.md
+    ├── compose/
+    │   └── docker-compose-my-stack.yml
+    └── config/
+        └── my-stack/
+            └── (config files)
+```
+
+### Usage
+
+```bash
+# Fetch external stack
+laconic-so fetch-stack github.com/org/my-stack
+
+# Use external stack
+STACK_PATH=~/cerc/my-stack/stack-orchestrator/stacks/my-stack
+laconic-so --stack $STACK_PATH deploy init --output spec.yml
+laconic-so --stack $STACK_PATH deploy create --spec-file spec.yml --deployment-dir deployment
+laconic-so deployment --dir deployment start
+```
+
+### Examples
+
+- `zenith-karma-stack` - Karma watcher deployment
+- `urbit-stack` - Fake Urbit ship for testing
+- `zenith-desk-stack` - Desk deployment stack
+
+## Architecture: k8s-kind Deployments
+
+### One Cluster Per Host
+One Kind cluster per host by design. Never request or expect separate clusters.
+
+- `create_cluster()` in `helpers.py` reuses any existing cluster
+- `cluster-id` in deployment.yml is an identifier, not a cluster request
+- All deployments share: ingress controller, etcd, certificates
+
+### Stack Resolution
+- External stacks detected via `Path(stack).exists()` in `util.py`
+- Config/compose resolution: external path first, then internal fallback
+- External path structure: `stack_orchestrator/data/stacks/<name>/stack.yml`
+
+### Secret Generation Implementation
+- `GENERATE_TOKEN_PATTERN` in `deployment_create.py` matches `$generate:type:length$`
+- `_generate_and_store_secrets()` creates K8s Secret
+- `cluster_info.py` adds `envFrom` with `secretRef` to containers
+- Non-secret config written to `config.env`
+
+### Repository Cloning
+`setup-repositories --git-ssh` clones repos defined in stack.yml's `repos:` field. Requires SSH agent.
+
+### Key Files (for codebase navigation)
+- `repos/setup_repositories.py`: `setup-repositories` command (git clone)
+- `deployment_create.py`: `deploy create` command, secret generation
+- `deployment.py`: `deployment start/stop/restart` commands
+- `deploy_k8s.py`: K8s deployer, cluster management calls
+- `helpers.py`: `create_cluster()`, etcd cleanup, kind operations
+- `cluster_info.py`: K8s resource generation (Deployment, Service, Ingress)
+
 ## Insights and Observations
 
 ### Design Principles

README.md

@@ -71,6 +71,59 @@ The various [stacks](/stack_orchestrator/data/stacks) each contain instructions
 - [laconicd with console and CLI](stack_orchestrator/data/stacks/fixturenet-laconic-loaded)
 - [kubo (IPFS)](stack_orchestrator/data/stacks/kubo)
 
+## Deployment Types
+
+- **compose**: Docker Compose on local machine
+- **k8s**: External Kubernetes cluster (requires kubeconfig)
+- **k8s-kind**: Local Kubernetes via Kind - one cluster per host, shared by all deployments
+
+## External Stacks
+
+Stacks can live in external git repositories. Required structure:
+
+```
+<repo>/
+  stack_orchestrator/data/
+    stacks/<stack-name>/stack.yml
+    compose/docker-compose-<pod-name>.yml
+  deployment/spec.yml
+```
+
+## Deployment Commands
+
+```bash
+# Create deployment from spec
+laconic-so --stack <path> deploy create --spec-file <spec.yml> --deployment-dir <dir>
+
+# Start (creates cluster on first run)
+laconic-so deployment --dir <dir> start
+
+# GitOps restart (git pull + redeploy, preserves data)
+laconic-so deployment --dir <dir> restart
+
+# Stop
+laconic-so deployment --dir <dir> stop
+```
+
+## spec.yml Reference
+
+```yaml
+stack: stack-name-or-path
+deploy-to: k8s-kind
+network:
+  http-proxy:
+    - host-name: app.example.com
+      routes:
+        - path: /
+          proxy-to: service-name:port
+  acme-email: admin@example.com
+config:
+  ENV_VAR: value
+  SECRET_VAR: $generate:hex:32$   # Auto-generated, stored in K8s Secret
+volumes:
+  volume-name:
+```
+
 ## Contributing
 
 See the [CONTRIBUTING.md](/docs/CONTRIBUTING.md) for developer mode install.

TODO.md

@@ -7,6 +7,25 @@ We need an "update stack" command in stack orchestrator and cleaner documentatio
 
 **Context**: Currently, `deploy init` generates a spec file and `deploy create` creates a deployment directory. The `deployment update` command (added by Thomas Lackey) only syncs env vars and restarts - it doesn't regenerate configurations. There's a gap in the workflow for updating stack configurations after initial deployment.
 
+## Bugs
+
+### `deploy create` doesn't auto-generate volume mappings for new pods
+
+When a new pod is added to `stack.yml` (e.g. `monitoring`), `deploy create`
+does not generate default host path mappings in spec.yml for the new pod's
+volumes. The deployment then fails at scheduling because the PVCs don't exist.
+
+**Expected**: `deploy create` enumerates all volumes from all compose files
+in the stack and generates default host paths for any that aren't already
+mapped in the spec.yml `volumes:` section.
+
+**Actual**: Only volumes already in spec.yml get PVs. New volumes are silently
+missing, causing `FailedScheduling: persistentvolumeclaim not found`.
+
+**Workaround**: Manually add volume entries to spec.yml and create host dirs.
+
+**Files**: `deployment_create.py` (`_write_config_file`, volume handling)
+
 ## Architecture Refactoring
 
 ### Separate Deployer from Stack Orchestrator CLI

docs/cli.md

@@ -65,3 +65,71 @@ Force full rebuild of packages:
 ```
 $ laconic-so build-npms --include <package-name> --force-rebuild
 ```
+
+## deploy
+
+The `deploy` command group manages persistent deployments. The general workflow is `deploy init` to generate a spec file, then `deploy create` to create a deployment directory from the spec, then runtime commands like `deploy up` and `deploy down`.
+
+### deploy init
+
+Generate a deployment spec file from a stack definition:
+```
+$ laconic-so --stack <stack-name> deploy init --output <spec-file>
+```
+
+Options:
+- `--output` (required): write spec file here
+- `--config`: provide config variables for the deployment
+- `--config-file`: provide config variables in a file
+- `--kube-config`: provide a config file for a k8s deployment
+- `--image-registry`: provide a container image registry url for this k8s cluster
+- `--map-ports-to-host`: map ports to the host (`any-variable-random`, `localhost-same`, `any-same`, `localhost-fixed-random`, `any-fixed-random`)
+
+### deploy create
+
+Create a deployment directory from a spec file:
+```
+$ laconic-so --stack <stack-name> deploy create --spec-file <spec-file> --deployment-dir <dir>
+```
+
+Update an existing deployment in-place (preserving data volumes and env file):
+```
+$ laconic-so --stack <stack-name> deploy create --spec-file <spec-file> --deployment-dir <dir> --update
+```
+
+Options:
+- `--spec-file` (required): spec file to use
+- `--deployment-dir`: target directory for deployment files
+- `--update`: update an existing deployment directory, preserving data volumes and env file. Changed files are backed up with a `.bak` suffix. The deployment's `config.env` and `deployment.yml` are also preserved.
+- `--network-dir`: network configuration supplied in this directory
+- `--initial-peers`: initial set of persistent peers
+
+### deploy up
+
+Start a deployment:
+```
+$ laconic-so deployment --dir <deployment-dir> up
+```
+
+### deploy down
+
+Stop a deployment:
+```
+$ laconic-so deployment --dir <deployment-dir> down
+```
+Use `--delete-volumes` to also remove data volumes.
+
+### deploy ps
+
+Show running services:
+```
+$ laconic-so deployment --dir <deployment-dir> ps
+```
+
+### deploy logs
+
+View service logs:
+```
+$ laconic-so deployment --dir <deployment-dir> logs
+```
+Use `-f` to follow and `-n <count>` to tail.

docs/deployment_patterns.md

@@ -0,0 +1,202 @@
+# Deployment Patterns
+
+## GitOps Pattern
+
+For production deployments, we recommend a GitOps approach where your deployment configuration is tracked in version control.
+
+### Overview
+
+- **spec.yml is your source of truth**: Maintain it in your operator repository
+- **Don't regenerate on every restart**: Run `deploy init` once, then customize and commit
+- **Use restart for updates**: The restart command respects your git-tracked spec.yml
+
+### Workflow
+
+1. **Initial setup**: Run `deploy init` once to generate a spec.yml template
+2. **Customize and commit**: Edit spec.yml with your configuration (hostnames, resources, etc.) and commit to your operator repo
+3. **Deploy from git**: Use the committed spec.yml for deployments
+4. **Update via git**: Make changes in git, then restart to apply
+
+```bash
+# Initial setup (run once)
+laconic-so --stack my-stack deploy init --output spec.yml
+
+# Customize for your environment
+vim spec.yml  # Set hostname, resources, etc.
+
+# Commit to your operator repository
+git add spec.yml
+git commit -m "Add my-stack deployment configuration"
+git push
+
+# On deployment server: deploy from git-tracked spec
+laconic-so deploy create \
+  --spec-file /path/to/operator-repo/spec.yml \
+  --deployment-dir my-deployment
+
+laconic-so deployment --dir my-deployment start
+```
+
+### Updating Deployments
+
+When you need to update a deployment:
+
+```bash
+# 1. Make changes in your operator repo
+vim /path/to/operator-repo/spec.yml
+git commit -am "Update configuration"
+git push
+
+# 2. On deployment server: pull and restart
+cd /path/to/operator-repo && git pull
+laconic-so deployment --dir my-deployment restart
+```
+
+The `restart` command:
+- Pulls latest code from the stack repository
+- Uses your git-tracked spec.yml (does NOT regenerate from defaults)
+- Syncs the deployment directory
+- Restarts services
+
+### Anti-patterns
+
+**Don't do this:**
+```bash
+# BAD: Regenerating spec on every deployment
+laconic-so --stack my-stack deploy init --output spec.yml
+laconic-so deploy create --spec-file spec.yml ...
+```
+
+This overwrites your customizations with defaults from the stack's `commands.py`.
+
+**Do this instead:**
+```bash
+# GOOD: Use your git-tracked spec
+git pull  # Get latest spec.yml from your operator repo
+laconic-so deployment --dir my-deployment restart
+```
+
+## Private Registry Authentication
+
+For deployments using images from private container registries (e.g., GitHub Container Registry), configure authentication in your spec.yml:
+
+### Configuration
+
+Add a `registry-credentials` section to your spec.yml:
+
+```yaml
+registry-credentials:
+  server: ghcr.io
+  username: your-org-or-username
+  token-env: REGISTRY_TOKEN
+```
+
+**Fields:**
+- `server`: The registry hostname (e.g., `ghcr.io`, `docker.io`, `gcr.io`)
+- `username`: Registry username (for GHCR, use your GitHub username or org name)
+- `token-env`: Name of the environment variable containing your API token/PAT
+
+### Token Environment Variable
+
+The `token-env` pattern keeps credentials out of version control. Set the environment variable when running `deployment start`:
+
+```bash
+export REGISTRY_TOKEN="your-personal-access-token"
+laconic-so deployment --dir my-deployment start
+```
+
+For GHCR, create a Personal Access Token (PAT) with `read:packages` scope.
+
+### Ansible Integration
+
+When using Ansible for deployments, pass the token from a credentials file:
+
+```yaml
+- name: Start deployment
+  ansible.builtin.command:
+    cmd: laconic-so deployment --dir {{ deployment_dir }} start
+  environment:
+    REGISTRY_TOKEN: "{{ lookup('file', '~/.credentials/ghcr_token') }}"
+```
+
+### How It Works
+
+1. laconic-so reads the `registry-credentials` config from spec.yml
+2. Creates a Kubernetes `docker-registry` secret named `{deployment}-registry`
+3. The deployment's pods reference this secret for image pulls
+
+## Cluster and Volume Management
+
+### Stopping Deployments
+
+The `deployment stop` command has two important flags:
+
+```bash
+# Default: stops deployment, deletes cluster, PRESERVES volumes
+laconic-so deployment --dir my-deployment stop
+
+# Explicitly delete volumes (USE WITH CAUTION)
+laconic-so deployment --dir my-deployment stop --delete-volumes
+```
+
+### Volume Persistence
+
+Volumes persist across cluster deletion by design. This is important because:
+- **Data survives cluster recreation**: Ledger data, databases, and other state are preserved
+- **Faster recovery**: No need to re-sync or rebuild data after cluster issues
+- **Safe cluster upgrades**: Delete and recreate cluster without data loss
+
+**Only use `--delete-volumes` when:**
+- You explicitly want to start fresh with no data
+- The user specifically requests volume deletion
+- You're cleaning up a test/dev environment completely
+
+### Shared Cluster Architecture
+
+In kind deployments, multiple stacks share a single cluster:
+- First `deployment start` creates the cluster
+- Subsequent deployments reuse the existing cluster
+- `deployment stop` on ANY deployment deletes the shared cluster
+- Other deployments will fail until cluster is recreated
+
+To stop a single deployment without affecting the cluster:
+```bash
+laconic-so deployment --dir my-deployment stop --skip-cluster-management
+```
+
+## Volume Persistence in k8s-kind
+
+k8s-kind has 3 storage layers:
+
+- **Docker Host**: The physical server running Docker
+- **Kind Node**: A Docker container simulating a k8s node
+- **Pod Container**: Your workload
+
+For k8s-kind, volumes with paths are mounted from Docker Host → Kind Node → Pod via extraMounts.
+
+| spec.yml volume | Storage Location | Survives Pod Restart | Survives Cluster Restart |
+|-----------------|------------------|---------------------|-------------------------|
+| `vol:` (empty)  | Kind Node PVC    | ✅ | ❌ |
+| `vol: ./data/x` | Docker Host      | ✅ | ✅ |
+| `vol: /abs/path`| Docker Host      | ✅ | ✅ |
+
+**Recommendation**: Always use paths for data you want to keep. Relative paths
+(e.g., `./data/rpc-config`) resolve to `$DEPLOYMENT_DIR/data/rpc-config` on the
+Docker Host.
+
+### Example
+
+```yaml
+# In spec.yml
+volumes:
+  rpc-config: ./data/rpc-config  # Persists to $DEPLOYMENT_DIR/data/rpc-config
+  chain-data: ./data/chain       # Persists to $DEPLOYMENT_DIR/data/chain
+  temp-cache:                    # Empty = Kind Node PVC (lost on cluster delete)
+```
+
+### The Antipattern
+
+Empty-path volumes appear persistent because they survive pod restarts (data lives
+in Kind Node container). However, this data is lost when the kind cluster is
+recreated. This "false persistence" has caused data loss when operators assumed
+their data was safe.

pyproject.toml

@@ -25,7 +25,7 @@ dependencies = [
     "click>=8.1.6",
     "PyYAML>=6.0.1",
     "ruamel.yaml>=0.17.32",
-    "pydantic==1.10.9",
+    "pydantic==1.10.13",
     "tomli==2.0.1",
     "validators==0.22.0",
     "kubernetes>=28.1.0",

requirements.txt

@@ -6,7 +6,7 @@ python-on-whales>=0.64.0
 click>=8.1.6
 PyYAML>=6.0.1
 ruamel.yaml>=0.17.32
-pydantic==1.10.9
+pydantic==1.10.13
 tomli==2.0.1
 validators==0.22.0
 kubernetes>=28.1.0

setup.py

@@ -1,12 +1,12 @@
 # See
 # https://medium.com/nerd-for-tech/how-to-build-and-distribute-a-cli-tool-with-python-537ae41d9d78
-from setuptools import setup, find_packages
+from setuptools import find_packages, setup
 
-with open("README.md", "r", encoding="utf-8") as fh:
+with open("README.md", encoding="utf-8") as fh:
     long_description = fh.read()
-with open("requirements.txt", "r", encoding="utf-8") as fh:
+with open("requirements.txt", encoding="utf-8") as fh:
     requirements = fh.read()
-with open("stack_orchestrator/data/version.txt", "r", encoding="utf-8") as fh:
+with open("stack_orchestrator/data/version.txt", encoding="utf-8") as fh:
     version = fh.readlines()[-1].strip(" \n")
 setup(
     name="laconic-stack-orchestrator",

stack_orchestrator/base.py

@@ -15,9 +15,11 @@
 
 import os
 from abc import ABC, abstractmethod
-from stack_orchestrator.deploy.deploy import get_stack_status
+
 from decouple import config
 
+from stack_orchestrator.deploy.deploy import get_stack_status
+
 
 def get_stack(config, stack):
     if stack == "package-registry":

stack_orchestrator/build/build_containers.py

@@ -22,17 +22,19 @@
 # allow re-build of either all or specific containers
 
 import os
-import sys
-from decouple import config
 import subprocess
-import click
+import sys
 from pathlib import Path
-from stack_orchestrator.opts import opts
+
-from stack_orchestrator.util import include_exclude_check, stack_is_external, error_exit
+import click
+from decouple import config
+
 from stack_orchestrator.base import get_npm_registry_url
 from stack_orchestrator.build.build_types import BuildContext
-from stack_orchestrator.build.publish import publish_image
 from stack_orchestrator.build.build_util import get_containers_in_scope
+from stack_orchestrator.build.publish import publish_image
+from stack_orchestrator.opts import opts
+from stack_orchestrator.util import error_exit, include_exclude_check, stack_is_external
 
 # TODO: find a place for this
 #    epilog="Config provided either in .env or settings.ini or env vars:
@@ -59,9 +61,7 @@ def make_container_build_env(
     container_build_env.update({"CERC_SCRIPT_DEBUG": "true"} if debug else {})
     container_build_env.update({"CERC_FORCE_REBUILD": "true"} if force_rebuild else {})
     container_build_env.update(
-        {"CERC_CONTAINER_EXTRA_BUILD_ARGS": extra_build_args}
+        {"CERC_CONTAINER_EXTRA_BUILD_ARGS": extra_build_args} if extra_build_args else {}
-        if extra_build_args
-        else {}
     )
     docker_host_env = os.getenv("DOCKER_HOST")
     if docker_host_env:
@@ -81,12 +81,8 @@ def process_container(build_context: BuildContext) -> bool:
 
     # Check if this is in an external stack
     if stack_is_external(build_context.stack):
-        container_parent_dir = Path(build_context.stack).parent.parent.joinpath(
+        container_parent_dir = Path(build_context.stack).parent.parent.joinpath("container-build")
-            "container-build"
+        temp_build_dir = container_parent_dir.joinpath(build_context.container.replace("/", "-"))
-        )
-        temp_build_dir = container_parent_dir.joinpath(
-            build_context.container.replace("/", "-")
-        )
         temp_build_script_filename = temp_build_dir.joinpath("build.sh")
         # Now check if the container exists in the external stack.
         if not temp_build_script_filename.exists():
@@ -104,18 +100,13 @@ def process_container(build_context: BuildContext) -> bool:
         build_command = build_script_filename.as_posix()
     else:
         if opts.o.verbose:
-            print(
+            print(f"No script file found: {build_script_filename}, " "using default build script")
-                f"No script file found: {build_script_filename}, "
-                "using default build script"
-            )
         repo_dir = build_context.container.split("/")[1]
         # TODO: make this less of a hack -- should be specified in
         # some metadata somewhere. Check if we have a repo for this
         # container. If not, set the context dir to container-build subdir
         repo_full_path = os.path.join(build_context.dev_root_path, repo_dir)
-        repo_dir_or_build_dir = (
+        repo_dir_or_build_dir = repo_full_path if os.path.exists(repo_full_path) else build_dir
-            repo_full_path if os.path.exists(repo_full_path) else build_dir
-        )
         build_command = (
             os.path.join(build_context.container_build_dir, "default-build.sh")
             + f" {default_container_tag} {repo_dir_or_build_dir}"
@@ -159,9 +150,7 @@ def process_container(build_context: BuildContext) -> bool:
     default=False,
     help="Publish the built images in the specified image registry",
 )
-@click.option(
+@click.option("--image-registry", help="Specify the image registry for --publish-images")
-    "--image-registry", help="Specify the image registry for --publish-images"
-)
 @click.pass_context
 def command(
     ctx,
@@ -185,14 +174,9 @@ def command(
 
     if local_stack:
         dev_root_path = os.getcwd()[0 : os.getcwd().rindex("stack-orchestrator")]
-        print(
+        print(f"Local stack dev_root_path (CERC_REPO_BASE_DIR) overridden to: " f"{dev_root_path}")
-            f"Local stack dev_root_path (CERC_REPO_BASE_DIR) overridden to: "
-            f"{dev_root_path}"
-        )
     else:
-        dev_root_path = os.path.expanduser(
+        dev_root_path = os.path.expanduser(config("CERC_REPO_BASE_DIR", default="~/cerc"))
-            config("CERC_REPO_BASE_DIR", default="~/cerc")
-        )
 
     if not opts.o.quiet:
         print(f"Dev Root is: {dev_root_path}")
@@ -230,10 +214,7 @@ def command(
             else:
                 print(f"Error running build for {build_context.container}")
                 if not opts.o.continue_on_error:
-                    error_exit(
+                    error_exit("container build failed and --continue-on-error " "not set, exiting")
-                        "container build failed and --continue-on-error "
-                        "not set, exiting"
-                    )
                     sys.exit(1)
                 else:
                     print(

stack_orchestrator/build/build_npms.py

@@ -18,15 +18,17 @@
 # env vars:
 # CERC_REPO_BASE_DIR defaults to ~/cerc
 
+import importlib.resources
 import os
 import sys
-from shutil import rmtree, copytree
+from shutil import copytree, rmtree
-from decouple import config
+
 import click
-import importlib.resources
+from decouple import config
-from python_on_whales import docker, DockerException
+from python_on_whales import DockerException, docker
+
 from stack_orchestrator.base import get_stack
-from stack_orchestrator.util import include_exclude_check, get_parsed_stack_config
+from stack_orchestrator.util import get_parsed_stack_config, include_exclude_check
 
 builder_js_image_name = "cerc/builder-js:local"
 
@@ -70,14 +72,9 @@ def command(ctx, include, exclude, force_rebuild, extra_build_args):
 
     if local_stack:
         dev_root_path = os.getcwd()[0 : os.getcwd().rindex("stack-orchestrator")]
-        print(
+        print(f"Local stack dev_root_path (CERC_REPO_BASE_DIR) overridden to: " f"{dev_root_path}")
-            f"Local stack dev_root_path (CERC_REPO_BASE_DIR) overridden to: "
-            f"{dev_root_path}"
-        )
     else:
-        dev_root_path = os.path.expanduser(
+        dev_root_path = os.path.expanduser(config("CERC_REPO_BASE_DIR", default="~/cerc"))
-            config("CERC_REPO_BASE_DIR", default="~/cerc")
-        )
 
     build_root_path = os.path.join(dev_root_path, "build-trees")
 
@@ -94,9 +91,7 @@ def command(ctx, include, exclude, force_rebuild, extra_build_args):
     # See: https://stackoverflow.com/a/20885799/1701505
     from stack_orchestrator import data
 
-    with importlib.resources.open_text(
+    with importlib.resources.open_text(data, "npm-package-list.txt") as package_list_file:
-        data, "npm-package-list.txt"
-    ) as package_list_file:
         all_packages = package_list_file.read().splitlines()
 
     packages_in_scope = []
@@ -132,8 +127,7 @@ def command(ctx, include, exclude, force_rebuild, extra_build_args):
         build_command = [
             "sh",
             "-c",
-            "cd /workspace && "
+            "cd /workspace && " f"build-npm-package-local-dependencies.sh {npm_registry_url}",
-            f"build-npm-package-local-dependencies.sh {npm_registry_url}",
         ]
         if not dry_run:
             if verbose:
@@ -151,9 +145,7 @@ def command(ctx, include, exclude, force_rebuild, extra_build_args):
             envs.update({"CERC_SCRIPT_DEBUG": "true"} if debug else {})
             envs.update({"CERC_FORCE_REBUILD": "true"} if force_rebuild else {})
             envs.update(
-                {"CERC_CONTAINER_EXTRA_BUILD_ARGS": extra_build_args}
+                {"CERC_CONTAINER_EXTRA_BUILD_ARGS": extra_build_args} if extra_build_args else {}
-                if extra_build_args
-                else {}
             )
             try:
                 docker.run(
@@ -176,16 +168,10 @@ def command(ctx, include, exclude, force_rebuild, extra_build_args):
             except DockerException as e:
                 print(f"Error executing build for {package} in container:\n {e}")
                 if not continue_on_error:
-                    print(
+                    print("FATAL Error: build failed and --continue-on-error " "not set, exiting")
-                        "FATAL Error: build failed and --continue-on-error "
-                        "not set, exiting"
-                    )
                     sys.exit(1)
                 else:
-                    print(
+                    print("****** Build Error, continuing because " "--continue-on-error is set")
-                        "****** Build Error, continuing because "
-                        "--continue-on-error is set"
-                    )
 
         else:
             print("Skipped")
@@ -203,10 +189,7 @@ def _ensure_prerequisites():
     # Tell the user how to build it if not
     images = docker.image.list(builder_js_image_name)
     if len(images) == 0:
-        print(
+        print(f"FATAL: builder image: {builder_js_image_name} is required " "but was not found")
-            f"FATAL: builder image: {builder_js_image_name} is required "
-            "but was not found"
-        )
         print(
             "Please run this command to create it: "
             "laconic-so --stack build-support build-containers"

stack_orchestrator/build/build_types.py

@@ -16,7 +16,6 @@
 
 from dataclasses import dataclass
 from pathlib import Path
-from typing import Mapping
 
 
 @dataclass
@@ -24,5 +23,5 @@ class BuildContext:
     stack: str
     container: str
     container_build_dir: Path
-    container_build_env: Mapping[str, str]
+    container_build_env: dict[str, str]
     dev_root_path: str

stack_orchestrator/build/build_util.py

@@ -30,9 +30,7 @@ def get_containers_in_scope(stack: str):
         # See: https://stackoverflow.com/a/20885799/1701505
         from stack_orchestrator import data
 
-        with importlib.resources.open_text(
+        with importlib.resources.open_text(data, "container-image-list.txt") as container_list_file:
-            data, "container-image-list.txt"
-        ) as container_list_file:
             containers_in_scope = container_list_file.read().splitlines()
 
     if opts.o.verbose:

stack_orchestrator/build/build_webapp.py

@@ -23,20 +23,19 @@
 
 import os
 import sys
-
-from decouple import config
-import click
 from pathlib import Path
+
+import click
+from decouple import config
+
 from stack_orchestrator.build import build_containers
-from stack_orchestrator.deploy.webapp.util import determine_base_container, TimedLogger
 from stack_orchestrator.build.build_types import BuildContext
+from stack_orchestrator.deploy.webapp.util import TimedLogger, determine_base_container
 
 
 @click.command()
 @click.option("--base-container")
-@click.option(
+@click.option("--source-repo", help="directory containing the webapp to build", required=True)
-    "--source-repo", help="directory containing the webapp to build", required=True
-)
 @click.option(
     "--force-rebuild",
     is_flag=True,
@@ -64,13 +63,10 @@ def command(ctx, base_container, source_repo, force_rebuild, extra_build_args, t
     if local_stack:
         dev_root_path = os.getcwd()[0 : os.getcwd().rindex("stack-orchestrator")]
         logger.log(
-            f"Local stack dev_root_path (CERC_REPO_BASE_DIR) overridden to: "
+            f"Local stack dev_root_path (CERC_REPO_BASE_DIR) overridden to: " f"{dev_root_path}"
-            f"{dev_root_path}"
         )
     else:
-        dev_root_path = os.path.expanduser(
+        dev_root_path = os.path.expanduser(config("CERC_REPO_BASE_DIR", default="~/cerc"))
-            config("CERC_REPO_BASE_DIR", default="~/cerc")
-        )
 
     if verbose:
         logger.log(f"Dev Root is: {dev_root_path}")

stack_orchestrator/build/fetch_containers.py

@@ -13,19 +13,19 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with this program.  If not, see <http:#www.gnu.org/licenses/>.
 
-import click
-from dataclasses import dataclass
 import json
 import platform
+from dataclasses import dataclass
+
+import click
+import requests
 from python_on_whales import DockerClient
 from python_on_whales.components.manifest.cli_wrapper import ManifestCLI, ManifestList
 from python_on_whales.utils import run
-import requests
-from typing import List
 
-from stack_orchestrator.opts import opts
-from stack_orchestrator.util import include_exclude_check, error_exit
 from stack_orchestrator.build.build_util import get_containers_in_scope
+from stack_orchestrator.opts import opts
+from stack_orchestrator.util import error_exit, include_exclude_check
 
 # Experimental fetch-container command
 
@@ -55,7 +55,7 @@ def _local_tag_for(container: str):
 # $ curl -u "my-username:my-token" -X GET \
 #   "https://<container-registry-hostname>/v2/cerc-io/cerc/test-container/tags/list"
 # {"name":"cerc-io/cerc/test-container","tags":["202402232130","202402232208"]}
-def _get_tags_for_container(container: str, registry_info: RegistryInfo) -> List[str]:
+def _get_tags_for_container(container: str, registry_info: RegistryInfo) -> list[str]:
     # registry looks like: git.vdb.to/cerc-io
     registry_parts = registry_info.registry.split("/")
     url = f"https://{registry_parts[0]}/v2/{registry_parts[1]}/{container}/tags/list"
@@ -68,16 +68,15 @@ def _get_tags_for_container(container: str, registry_info: RegistryInfo) -> List
         tag_info = response.json()
         if opts.o.debug:
             print(f"container tags list: {tag_info}")
-        tags_array = tag_info["tags"]
+        tags_array: list[str] = tag_info["tags"]
         return tags_array
     else:
         error_exit(
-            f"failed to fetch tags from image registry, "
+            f"failed to fetch tags from image registry, " f"status code: {response.status_code}"
-            f"status code: {response.status_code}"
         )
 
 
-def _find_latest(candidate_tags: List[str]):
+def _find_latest(candidate_tags: list[str]):
     # Lex sort should give us the latest first
     sorted_candidates = sorted(candidate_tags)
     if opts.o.debug:
@@ -86,8 +85,8 @@ def _find_latest(candidate_tags: List[str]):
 
 
 def _filter_for_platform(
-    container: str, registry_info: RegistryInfo, tag_list: List[str]
+    container: str, registry_info: RegistryInfo, tag_list: list[str]
-) -> List[str]:
+) -> list[str]:
     filtered_tags = []
     this_machine = platform.machine()
     # Translate between Python and docker platform names
@@ -151,15 +150,9 @@ def _add_local_tag(remote_tag: str, registry: str, local_tag: str):
     default=False,
     help="Overwrite a locally built image, if present",
 )
-@click.option(
+@click.option("--image-registry", required=True, help="Specify the image registry to fetch from")
-    "--image-registry", required=True, help="Specify the image registry to fetch from"
+@click.option("--registry-username", required=True, help="Specify the image registry username")
-)
+@click.option("--registry-token", required=True, help="Specify the image registry access token")
-@click.option(
-    "--registry-username", required=True, help="Specify the image registry username"
-)
-@click.option(
-    "--registry-token", required=True, help="Specify the image registry access token"
-)
 @click.pass_context
 def command(
     ctx,

stack_orchestrator/build/publish.py

@@ -14,6 +14,7 @@
 # along with this program.  If not, see <http:#www.gnu.org/licenses/>.
 
 from datetime import datetime
+
 from python_on_whales import DockerClient
 
 from stack_orchestrator.opts import opts

stack_orchestrator/constants.py

@@ -44,3 +44,4 @@ unlimited_memlock_key = "unlimited-memlock"
 runtime_class_key = "runtime-class"
 high_memlock_runtime = "high-memlock"
 high_memlock_spec_filename = "high-memlock-spec.json"
+acme_email_key = "acme-email"

stack_orchestrator/data/compose/docker-compose-test.yml

@@ -8,6 +8,8 @@ services:
       CERC_TEST_PARAM_2: "CERC_TEST_PARAM_2_VALUE"
       CERC_TEST_PARAM_3: ${CERC_TEST_PARAM_3:-FAILED}
     volumes:
+      - ../config/test/script.sh:/opt/run.sh
+      - ../config/test/settings.env:/opt/settings.env
       - test-data-bind:/data
       - test-data-auto:/data2
       - test-config:/config:ro

stack_orchestrator/data/config/mainnet-eth-keycloak/scripts/keycloak-mirror/keycloak-mirror.py

@@ -2,12 +2,11 @@
 
 import argparse
 import os
+import random
 import sys
+from subprocess import Popen
 
 import psycopg
-import random
-
-from subprocess import Popen
 from fabric import Connection
 
 
@@ -27,27 +26,19 @@ def dump_src_db_to_file(db_host, db_port, db_user, db_password, db_name, file_na
 def establish_ssh_tunnel(ssh_host, ssh_port, ssh_user, db_host, db_port):
     local_port = random.randint(11000, 12000)
     conn = Connection(host=ssh_host, port=ssh_port, user=ssh_user)
-    fw = conn.forward_local(
+    fw = conn.forward_local(local_port=local_port, remote_port=db_port, remote_host=db_host)
-        local_port=local_port, remote_port=db_port, remote_host=db_host
-    )
     return conn, fw, local_port
 
 
 def load_db_from_file(db_host, db_port, db_user, db_password, db_name, file_name):
-    connstr = "host=%s port=%s user=%s password=%s sslmode=disable dbname=%s" % (
+    connstr = f"host={db_host} port={db_port} user={db_user} password={db_password} sslmode=disable dbname={db_name}"
-        db_host,
-        db_port,
-        db_user,
-        db_password,
-        db_name,
-    )
     with psycopg.connect(connstr) as conn:
         with conn.cursor() as cur:
             print(
                 f"Importing from {file_name} to {db_host}:{db_port}/{db_name}... ",
                 end="",
             )
-            cur.execute(open(file_name, "rt").read())
+            cur.execute(open(file_name).read())
             print("DONE")
 
 
@@ -60,9 +51,7 @@ if __name__ == "__main__":
     parser.add_argument("--src-dbpw", help="DB password", required=True)
     parser.add_argument("--src-dbname", help="dbname", default="keycloak")
 
-    parser.add_argument(
+    parser.add_argument("--dst-file", help="Destination filename", default="keycloak-mirror.sql")
-        "--dst-file", help="Destination filename", default="keycloak-mirror.sql"
-    )
 
     parser.add_argument("--live-import", help="run the import", action="store_true")
 

stack_orchestrator/data/config/test/script.sh

@@ -0,0 +1,3 @@
+#!/bin/sh
+
+echo "Hello"

stack_orchestrator/data/config/test/settings.env

@@ -0,0 +1 @@
+ANSWER=42

stack_orchestrator/data/container-build/cerc-fixturenet-eth-genesis/genesis/accounts/mnemonic_to_csv.py

@@ -1,7 +1,8 @@
-from web3.auto import w3
-import ruamel.yaml as yaml
 import sys
 
+import ruamel.yaml as yaml
+from web3.auto import w3
+
 w3.eth.account.enable_unaudited_hdwallet_features()
 
 testnet_config_path = "genesis-config.yaml"
@@ -11,8 +12,6 @@ if len(sys.argv) > 1:
 with open(testnet_config_path) as stream:
     data = yaml.safe_load(stream)
 
-for key, value in data["el_premine"].items():
+for key, _value in data["el_premine"].items():
-    acct = w3.eth.account.from_mnemonic(
+    acct = w3.eth.account.from_mnemonic(data["mnemonic"], account_path=key, passphrase="")
-        data["mnemonic"], account_path=key, passphrase=""
+    print(f"{key},{acct.address},{acct.key.hex()}")
-    )
-    print("%s,%s,%s" % (key, acct.address, acct.key.hex()))

stack_orchestrator/data/container-build/cerc-test-container/Dockerfile

@@ -1,9 +1,6 @@
-FROM ubuntu:latest
+FROM alpine:latest
 
-RUN apt-get update && export DEBIAN_FRONTEND=noninteractive && export DEBCONF_NOWARNINGS="yes" && \
+RUN apk add --no-cache nginx
-    apt-get install -y software-properties-common && \
-    apt-get install -y nginx && \
-    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 EXPOSE 80
 

stack_orchestrator/data/container-build/cerc-test-container/run.sh

@@ -1,4 +1,4 @@
-#!/usr/bin/env bash
+#!/usr/bin/env sh
 set -e
 
 if [ -n "$CERC_SCRIPT_DEBUG" ]; then
@@ -8,14 +8,14 @@ fi
 echo "Test container starting"
 
 DATA_DEVICE=$(df | grep "/data$" | awk '{ print $1 }')
-if [[ -n "$DATA_DEVICE" ]]; then
+if [ -n "$DATA_DEVICE" ]; then
   echo "/data: MOUNTED dev=${DATA_DEVICE}"
 else
   echo "/data: not mounted"
 fi
 
 DATA2_DEVICE=$(df | grep "/data2$" | awk '{ print $1 }')
-if [[ -n "$DATA_DEVICE" ]]; then
+if [ -n "$DATA_DEVICE" ]; then
   echo "/data2: MOUNTED dev=${DATA2_DEVICE}"
 else
   echo "/data2: not mounted"
@@ -23,7 +23,7 @@ fi
 
 # Test if the container's filesystem is old (run previously) or new
 for d in /data /data2; do
-  if [[ -f "$d/exists" ]];
+  if [ -f "$d/exists" ];
   then
       TIMESTAMP=`cat $d/exists`
       echo "$d filesystem is old, created: $TIMESTAMP"
@@ -52,7 +52,7 @@ fi
 if [ -d "/config" ]; then
   echo "/config: EXISTS"
   for f in /config/*; do
-    if [[ -f "$f" ]] || [[ -L "$f" ]]; then
+    if [ -f "$f" ] || [ -L "$f" ]; then
       echo "$f:"
       cat "$f"
       echo ""
@@ -64,4 +64,4 @@ else
 fi
 
 # Run nginx which will block here forever
-/usr/sbin/nginx -g "daemon off;"
+nginx -g "daemon off;"

stack_orchestrator/data/k8s/components/ingress/ingress-caddy-kind-deploy.yaml

@@ -93,6 +93,7 @@ rules:
       - get
       - create
       - update
+      - delete
 ---
 apiVersion: rbac.authorization.k8s.io/v1
 kind: ClusterRoleBinding

stack_orchestrator/data/stacks/mainnet-blast/deploy/commands.py

@@ -16,13 +16,14 @@
 
 from pathlib import Path
 from shutil import copy
+
 import yaml
 
 
 def create(context, extra_args):
     # Our goal here is just to copy the json files for blast
     yml_path = context.deployment_dir.joinpath("spec.yml")
-    with open(yml_path, "r") as file:
+    with open(yml_path) as file:
         data = yaml.safe_load(file)
 
     mount_point = data["volumes"]["blast-data"]

stack_orchestrator/data/stacks/mainnet-eth/deploy/commands.py

@@ -27,8 +27,6 @@ def setup(ctx):
 def create(ctx, extra_args):
     # Generate the JWT secret and save to its config file
     secret = token_hex(32)
-    jwt_file_path = ctx.deployment_dir.joinpath(
+    jwt_file_path = ctx.deployment_dir.joinpath("data", "mainnet_eth_config_data", "jwtsecret")
-        "data", "mainnet_eth_config_data", "jwtsecret"
-    )
     with open(jwt_file_path, "w+") as jwt_file:
         jwt_file.write(secret)

stack_orchestrator/data/stacks/mainnet-laconic/deploy/commands.py

@@ -13,22 +13,23 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with this program.  If not, see <http:#www.gnu.org/licenses/>.
 
-from stack_orchestrator.util import get_yaml
+import os
+import re
+import sys
+from enum import Enum
+from pathlib import Path
+from shutil import copyfile, copytree
+
+import tomli
 from stack_orchestrator.deploy.deploy_types import (
     DeployCommandContext,
     LaconicStackSetupCommand,
 )
+from stack_orchestrator.deploy.deploy_util import VolumeMapping, run_container_command
 from stack_orchestrator.deploy.deployment_context import DeploymentContext
 from stack_orchestrator.deploy.stack_state import State
-from stack_orchestrator.deploy.deploy_util import VolumeMapping, run_container_command
 from stack_orchestrator.opts import opts
-from enum import Enum
+from stack_orchestrator.util import get_yaml
-from pathlib import Path
-from shutil import copyfile, copytree
-import os
-import sys
-import tomli
-import re
 
 default_spec_file_content = ""
 
@@ -80,9 +81,7 @@ def _copy_gentx_files(network_dir: Path, gentx_file_list: str):
         gentx_file_path = Path(gentx_file)
         copyfile(
             gentx_file_path,
-            os.path.join(
+            os.path.join(network_dir, "config", "gentx", os.path.basename(gentx_file_path)),
-                network_dir, "config", "gentx", os.path.basename(gentx_file_path)
-            ),
         )
 
 
@@ -91,7 +90,7 @@ def _remove_persistent_peers(network_dir: Path):
     if not config_file_path.exists():
         print("Error: config.toml not found")
         sys.exit(1)
-    with open(config_file_path, "r") as input_file:
+    with open(config_file_path) as input_file:
         config_file_content = input_file.read()
         persistent_peers_pattern = '^persistent_peers = "(.+?)"'
         replace_with = 'persistent_peers = ""'
@@ -110,7 +109,7 @@ def _insert_persistent_peers(config_dir: Path, new_persistent_peers: str):
     if not config_file_path.exists():
         print("Error: config.toml not found")
         sys.exit(1)
-    with open(config_file_path, "r") as input_file:
+    with open(config_file_path) as input_file:
         config_file_content = input_file.read()
         persistent_peers_pattern = r'^persistent_peers = ""'
         replace_with = f'persistent_peers = "{new_persistent_peers}"'
@@ -129,7 +128,7 @@ def _enable_cors(config_dir: Path):
     if not config_file_path.exists():
         print("Error: config.toml not found")
         sys.exit(1)
-    with open(config_file_path, "r") as input_file:
+    with open(config_file_path) as input_file:
         config_file_content = input_file.read()
         cors_pattern = r"^cors_allowed_origins = \[]"
         replace_with = 'cors_allowed_origins = ["*"]'
@@ -142,13 +141,11 @@ def _enable_cors(config_dir: Path):
     if not app_file_path.exists():
         print("Error: app.toml not found")
         sys.exit(1)
-    with open(app_file_path, "r") as input_file:
+    with open(app_file_path) as input_file:
         app_file_content = input_file.read()
         cors_pattern = r"^enabled-unsafe-cors = false"
         replace_with = "enabled-unsafe-cors = true"
-        app_file_content = re.sub(
+        app_file_content = re.sub(cors_pattern, replace_with, app_file_content, flags=re.MULTILINE)
-            cors_pattern, replace_with, app_file_content, flags=re.MULTILINE
-        )
     with open(app_file_path, "w") as output_file:
         output_file.write(app_file_content)
 
@@ -158,7 +155,7 @@ def _set_listen_address(config_dir: Path):
     if not config_file_path.exists():
         print("Error: config.toml not found")
         sys.exit(1)
-    with open(config_file_path, "r") as input_file:
+    with open(config_file_path) as input_file:
         config_file_content = input_file.read()
         existing_pattern = r'^laddr = "tcp://127.0.0.1:26657"'
         replace_with = 'laddr = "tcp://0.0.0.0:26657"'
@@ -172,7 +169,7 @@ def _set_listen_address(config_dir: Path):
     if not app_file_path.exists():
         print("Error: app.toml not found")
         sys.exit(1)
-    with open(app_file_path, "r") as input_file:
+    with open(app_file_path) as input_file:
         app_file_content = input_file.read()
         existing_pattern1 = r'^address = "tcp://localhost:1317"'
         replace_with1 = 'address = "tcp://0.0.0.0:1317"'
@@ -192,10 +189,7 @@ def _phase_from_params(parameters):
     phase = SetupPhase.ILLEGAL
     if parameters.initialize_network:
         if parameters.join_network or parameters.create_network:
-            print(
+            print("Can't supply --join-network or --create-network " "with --initialize-network")
-                "Can't supply --join-network or --create-network "
-                "with --initialize-network"
-            )
             sys.exit(1)
         if not parameters.chain_id:
             print("--chain-id is required")
@@ -207,26 +201,17 @@ def _phase_from_params(parameters):
         phase = SetupPhase.INITIALIZE
     elif parameters.join_network:
         if parameters.initialize_network or parameters.create_network:
-            print(
+            print("Can't supply --initialize-network or --create-network " "with --join-network")
-                "Can't supply --initialize-network or --create-network "
-                "with --join-network"
-            )
             sys.exit(1)
         phase = SetupPhase.JOIN
     elif parameters.create_network:
         if parameters.initialize_network or parameters.join_network:
-            print(
+            print("Can't supply --initialize-network or --join-network " "with --create-network")
-                "Can't supply --initialize-network or --join-network "
-                "with --create-network"
-            )
             sys.exit(1)
         phase = SetupPhase.CREATE
     elif parameters.connect_network:
         if parameters.initialize_network or parameters.join_network:
-            print(
+            print("Can't supply --initialize-network or --join-network " "with --connect-network")
-                "Can't supply --initialize-network or --join-network "
-                "with --connect-network"
-            )
             sys.exit(1)
         phase = SetupPhase.CONNECT
     return phase
@@ -341,8 +326,7 @@ def setup(
         output3, status3 = run_container_command(
             command_context,
             "laconicd",
-            f"laconicd cometbft show-validator "
+            f"laconicd cometbft show-validator " f"--home {laconicd_home_path_in_container}",
-            f"--home {laconicd_home_path_in_container}",
             mounts,
         )
         print(f"Node validator address: {output3}")
@@ -361,23 +345,16 @@ def setup(
             # Copy it into our network dir
             genesis_file_path = Path(parameters.genesis_file)
             if not os.path.exists(genesis_file_path):
-                print(
+                print(f"Error: supplied genesis file: {parameters.genesis_file} " "does not exist.")
-                    f"Error: supplied genesis file: {parameters.genesis_file} "
-                    "does not exist."
-                )
                 sys.exit(1)
             copyfile(
                 genesis_file_path,
-                os.path.join(
+                os.path.join(network_dir, "config", os.path.basename(genesis_file_path)),
-                    network_dir, "config", os.path.basename(genesis_file_path)
-                ),
             )
         else:
             # We're generating the genesis file
             # First look in the supplied gentx files for the other nodes' keys
-            other_node_keys = _get_node_keys_from_gentx_files(
+            other_node_keys = _get_node_keys_from_gentx_files(parameters.gentx_address_list)
-                parameters.gentx_address_list
-            )
             # Add those keys to our genesis, with balances we determine here (why?)
             outputk = None
             for other_node_key in other_node_keys:
@@ -398,8 +375,7 @@ def setup(
             output1, status1 = run_container_command(
                 command_context,
                 "laconicd",
-                f"laconicd genesis collect-gentxs "
+                f"laconicd genesis collect-gentxs " f"--home {laconicd_home_path_in_container}",
-                f"--home {laconicd_home_path_in_container}",
                 mounts,
             )
             if options.debug:
@@ -416,8 +392,7 @@ def setup(
         output2, status1 = run_container_command(
             command_context,
             "laconicd",
-            f"laconicd genesis validate-genesis "
+            f"laconicd genesis validate-genesis " f"--home {laconicd_home_path_in_container}",
-            f"--home {laconicd_home_path_in_container}",
             mounts,
         )
         print(f"validate-genesis result: {output2}")
@@ -452,9 +427,7 @@ def create(deployment_context: DeploymentContext, extra_args):
         sys.exit(1)
     # Copy the network directory contents into our deployment
     # TODO: change this to work with non local paths
-    deployment_config_dir = deployment_context.deployment_dir.joinpath(
+    deployment_config_dir = deployment_context.deployment_dir.joinpath("data", "laconicd-config")
-        "data", "laconicd-config"
-    )
     copytree(config_dir_path, deployment_config_dir, dirs_exist_ok=True)
     # If supplied, add the initial persistent peers to the config file
     if extra_args[1]:
@@ -465,9 +438,7 @@ def create(deployment_context: DeploymentContext, extra_args):
     _set_listen_address(deployment_config_dir)
     # Copy the data directory contents into our deployment
     # TODO: change this to work with non local paths
-    deployment_data_dir = deployment_context.deployment_dir.joinpath(
+    deployment_data_dir = deployment_context.deployment_dir.joinpath("data", "laconicd-data")
-        "data", "laconicd-data"
-    )
     copytree(data_dir_path, deployment_data_dir, dirs_exist_ok=True)
 
 

stack_orchestrator/data/stacks/test/deploy/commands.py

@@ -13,12 +13,13 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with this program.  If not, see <http:#www.gnu.org/licenses/>.
 
-from stack_orchestrator.util import get_yaml
+from pathlib import Path
+
 from stack_orchestrator.deploy.deploy_types import DeployCommandContext
+from stack_orchestrator.deploy.deploy_util import VolumeMapping, run_container_command
 from stack_orchestrator.deploy.deployment_context import DeploymentContext
 from stack_orchestrator.deploy.stack_state import State
-from stack_orchestrator.deploy.deploy_util import VolumeMapping, run_container_command
+from stack_orchestrator.util import get_yaml
-from pathlib import Path
 
 default_spec_file_content = """config:
     test-variable-1: test-value-1

stack_orchestrator/deploy/compose/deploy_docker.py

@@ -14,12 +14,13 @@
 # along with this program.  If not, see <http:#www.gnu.org/licenses/>.
 
 from pathlib import Path
-from typing import Optional
+
 from python_on_whales import DockerClient, DockerException
+
 from stack_orchestrator.deploy.deployer import (
     Deployer,
-    DeployerException,
     DeployerConfigGenerator,
+    DeployerException,
 )
 from stack_orchestrator.deploy.deployment_context import DeploymentContext
 from stack_orchestrator.opts import opts
@@ -32,10 +33,10 @@ class DockerDeployer(Deployer):
     def __init__(
         self,
         type: str,
-        deployment_context: Optional[DeploymentContext],
+        deployment_context: DeploymentContext | None,
         compose_files: list,
-        compose_project_name: Optional[str],
+        compose_project_name: str | None,
-        compose_env_file: Optional[str],
+        compose_env_file: str | None,
     ) -> None:
         self.docker = DockerClient(
             compose_files=compose_files,
@@ -53,21 +54,21 @@ class DockerDeployer(Deployer):
             try:
                 return self.docker.compose.up(detach=detach, services=services)
             except DockerException as e:
-                raise DeployerException(e)
+                raise DeployerException(e) from e
 
     def down(self, timeout, volumes, skip_cluster_management):
         if not opts.o.dry_run:
             try:
                 return self.docker.compose.down(timeout=timeout, volumes=volumes)
             except DockerException as e:
-                raise DeployerException(e)
+                raise DeployerException(e) from e
 
-    def update(self):
+    def update_envs(self):
         if not opts.o.dry_run:
             try:
                 return self.docker.compose.restart()
             except DockerException as e:
-                raise DeployerException(e)
+                raise DeployerException(e) from e
 
     def status(self):
         if not opts.o.dry_run:
@@ -75,23 +76,21 @@ class DockerDeployer(Deployer):
                 for p in self.docker.compose.ps():
                     print(f"{p.name}\t{p.state.status}")
             except DockerException as e:
-                raise DeployerException(e)
+                raise DeployerException(e) from e
 
     def ps(self):
         if not opts.o.dry_run:
             try:
                 return self.docker.compose.ps()
             except DockerException as e:
-                raise DeployerException(e)
+                raise DeployerException(e) from e
 
     def port(self, service, private_port):
         if not opts.o.dry_run:
             try:
-                return self.docker.compose.port(
+                return self.docker.compose.port(service=service, private_port=private_port)
-                    service=service, private_port=private_port
-                )
             except DockerException as e:
-                raise DeployerException(e)
+                raise DeployerException(e) from e
 
     def execute(self, service, command, tty, envs):
         if not opts.o.dry_run:
@@ -100,7 +99,7 @@ class DockerDeployer(Deployer):
                     service=service, command=command, tty=tty, envs=envs
                 )
             except DockerException as e:
-                raise DeployerException(e)
+                raise DeployerException(e) from e
 
     def logs(self, services, tail, follow, stream):
         if not opts.o.dry_run:
@@ -109,7 +108,7 @@ class DockerDeployer(Deployer):
                     services=services, tail=tail, follow=follow, stream=stream
                 )
             except DockerException as e:
-                raise DeployerException(e)
+                raise DeployerException(e) from e
 
     def run(
         self,
@@ -118,10 +117,14 @@ class DockerDeployer(Deployer):
         user=None,
         volumes=None,
         entrypoint=None,
-        env={},
+        env=None,
-        ports=[],
+        ports=None,
         detach=False,
     ):
+        if ports is None:
+            ports = []
+        if env is None:
+            env = {}
         if not opts.o.dry_run:
             try:
                 return self.docker.run(
@@ -136,9 +139,9 @@ class DockerDeployer(Deployer):
                     publish_all=len(ports) == 0,
                 )
             except DockerException as e:
-                raise DeployerException(e)
+                raise DeployerException(e) from e
 
-    def run_job(self, job_name: str, release_name: Optional[str] = None):
+    def run_job(self, job_name: str, release_name: str | None = None):
         # release_name is ignored for Docker deployments (only used for K8s/Helm)
         if not opts.o.dry_run:
             try:
@@ -155,9 +158,7 @@ class DockerDeployer(Deployer):
                 )
 
                 if not job_compose_file.exists():
-                    raise DeployerException(
+                    raise DeployerException(f"Job compose file not found: {job_compose_file}")
-                        f"Job compose file not found: {job_compose_file}"
-                    )
 
                 if opts.o.verbose:
                     print(f"Running job from: {job_compose_file}")
@@ -175,7 +176,7 @@ class DockerDeployer(Deployer):
                 return job_docker.compose.run(service=job_name, remove=True, tty=True)
 
             except DockerException as e:
-                raise DeployerException(e)
+                raise DeployerException(e) from e
 
 
 class DockerDeployerConfigGenerator(DeployerConfigGenerator):

stack_orchestrator/deploy/deploy.py

@@ -15,36 +15,37 @@
 
 # Deploys the system components using a deployer (either docker-compose or k8s)
 
-import hashlib
 import copy
+import hashlib
 import os
+import subprocess
 import sys
 from dataclasses import dataclass
 from importlib import resources
-from typing import Optional
-import subprocess
-import click
 from pathlib import Path
+
+import click
+
 from stack_orchestrator import constants
-from stack_orchestrator.opts import opts
-from stack_orchestrator.util import (
-    get_stack_path,
-    include_exclude_check,
-    get_parsed_stack_config,
-    global_options2,
-    get_dev_root_path,
-    stack_is_in_deployment,
-    resolve_compose_file,
-)
-from stack_orchestrator.deploy.deployer import DeployerException
-from stack_orchestrator.deploy.deployer_factory import getDeployer
 from stack_orchestrator.deploy.compose.deploy_docker import DockerDeployer
 from stack_orchestrator.deploy.deploy_types import ClusterContext, DeployCommandContext
+from stack_orchestrator.deploy.deployer import DeployerException
+from stack_orchestrator.deploy.deployer_factory import getDeployer
 from stack_orchestrator.deploy.deployment_context import DeploymentContext
 from stack_orchestrator.deploy.deployment_create import create as deployment_create
 from stack_orchestrator.deploy.deployment_create import init as deployment_init
 from stack_orchestrator.deploy.deployment_create import setup as deployment_setup
 from stack_orchestrator.deploy.k8s import k8s_command
+from stack_orchestrator.opts import opts
+from stack_orchestrator.util import (
+    get_dev_root_path,
+    get_parsed_stack_config,
+    get_stack_path,
+    global_options2,
+    include_exclude_check,
+    resolve_compose_file,
+    stack_is_in_deployment,
+)
 
 
 @click.group()
@@ -52,9 +53,7 @@ from stack_orchestrator.deploy.k8s import k8s_command
 @click.option("--exclude", help="don't start these components")
 @click.option("--env-file", help="env file to be used")
 @click.option("--cluster", help="specify a non-default cluster name")
-@click.option(
+@click.option("--deploy-to", help="cluster system to deploy to (compose or k8s or k8s-kind)")
-    "--deploy-to", help="cluster system to deploy to (compose or k8s or k8s-kind)"
-)
 @click.pass_context
 def command(ctx, include, exclude, env_file, cluster, deploy_to):
     """deploy a stack"""
@@ -93,7 +92,7 @@ def command(ctx, include, exclude, env_file, cluster, deploy_to):
 
 def create_deploy_context(
     global_context,
-    deployment_context: Optional[DeploymentContext],
+    deployment_context: DeploymentContext | None,
     stack,
     include,
     exclude,
@@ -116,9 +115,7 @@ def create_deploy_context(
 
     # For helm chart deployments, skip compose file loading
     if is_helm_chart_deployment:
-        cluster_context = ClusterContext(
+        cluster_context = ClusterContext(global_context, cluster, [], [], [], None, env_file)
-            global_context, cluster, [], [], [], None, env_file
-        )
     else:
         cluster_context = _make_cluster_context(
             global_context, stack, include, exclude, cluster, env_file
@@ -134,9 +131,7 @@ def create_deploy_context(
     return DeployCommandContext(stack, cluster_context, deployer)
 
 
-def up_operation(
+def up_operation(ctx, services_list, stay_attached=False, skip_cluster_management=False):
-    ctx, services_list, stay_attached=False, skip_cluster_management=False
-):
     global_context = ctx.parent.parent.obj
     deploy_context = ctx.obj
     cluster_context = deploy_context.cluster_context
@@ -182,8 +177,14 @@ def status_operation(ctx):
     ctx.obj.deployer.status()
 
 
-def update_operation(ctx):
+def prepare_operation(ctx, skip_cluster_management=False):
-    ctx.obj.deployer.update()
+    ctx.obj.deployer.prepare(
+        skip_cluster_management=skip_cluster_management,
+    )
+
+
+def update_envs_operation(ctx):
+    ctx.obj.deployer.update_envs()
 
 
 def ps_operation(ctx):
@@ -203,8 +204,7 @@ def ps_operation(ctx):
                         print(f"{port_mapping}", end="")
                     else:
                         print(
-                            f"{mapping[0]['HostIp']}:{mapping[0]['HostPort']}"
+                            f"{mapping[0]['HostIp']}:{mapping[0]['HostPort']}" f"->{port_mapping}",
-                            f"->{port_mapping}",
                             end="",
                         )
                     comma = ", "
@@ -254,11 +254,11 @@ def logs_operation(ctx, tail: int, follow: bool, extra_args: str):
     logs_stream = ctx.obj.deployer.logs(
         services=services_list, tail=tail, follow=follow, stream=True
     )
-    for stream_type, stream_content in logs_stream:
+    for _stream_type, stream_content in logs_stream:
         print(stream_content.decode("utf-8"), end="")
 
 
-def run_job_operation(ctx, job_name: str, helm_release: Optional[str] = None):
+def run_job_operation(ctx, job_name: str, helm_release: str | None = None):
     global_context = ctx.parent.parent.obj
     if not global_context.dry_run:
         print(f"Running job: {job_name}")
@@ -278,9 +278,7 @@ def up(ctx, extra_args):
 
 
 @command.command()
-@click.option(
+@click.option("--delete-volumes/--preserve-volumes", default=False, help="delete data volumes")
-    "--delete-volumes/--preserve-volumes", default=False, help="delete data volumes"
-)
 @click.argument("extra_args", nargs=-1)  # help: command: down<service1> <service2>
 @click.pass_context
 def down(ctx, delete_volumes, extra_args):
@@ -380,14 +378,10 @@ def _make_cluster_context(ctx, stack, include, exclude, cluster, env_file):
     else:
         # See:
         # https://stackoverflow.com/questions/25389095/python-get-path-of-root-project-structure
-        compose_dir = (
+        compose_dir = Path(__file__).absolute().parent.parent.joinpath("data", "compose")
-            Path(__file__).absolute().parent.parent.joinpath("data", "compose")
-        )
 
     if cluster is None:
-        cluster = _make_default_cluster_name(
+        cluster = _make_default_cluster_name(deployment, compose_dir, stack, include, exclude)
-            deployment, compose_dir, stack, include, exclude
-        )
     else:
         _make_default_cluster_name(deployment, compose_dir, stack, include, exclude)
 
@@ -404,9 +398,7 @@ def _make_cluster_context(ctx, stack, include, exclude, cluster, env_file):
         if stack_config is not None:
             # TODO: syntax check the input here
             pods_in_scope = stack_config["pods"]
-            cluster_config = (
+            cluster_config = stack_config["config"] if "config" in stack_config else None
-                stack_config["config"] if "config" in stack_config else None
-            )
     else:
         pods_in_scope = all_pods
 
@@ -428,43 +420,29 @@ def _make_cluster_context(ctx, stack, include, exclude, cluster, env_file):
         if include_exclude_check(pod_name, include, exclude):
             if pod_repository is None or pod_repository == "internal":
                 if deployment:
-                    compose_file_name = os.path.join(
+                    compose_file_name = os.path.join(compose_dir, f"docker-compose-{pod_path}.yml")
-                        compose_dir, f"docker-compose-{pod_path}.yml"
-                    )
                 else:
                     compose_file_name = resolve_compose_file(stack, pod_name)
             else:
                 if deployment:
-                    compose_file_name = os.path.join(
+                    compose_file_name = os.path.join(compose_dir, f"docker-compose-{pod_name}.yml")
-                        compose_dir, f"docker-compose-{pod_name}.yml"
-                    )
                     pod_pre_start_command = pod.get("pre_start_command")
                     pod_post_start_command = pod.get("post_start_command")
-                    script_dir = compose_dir.parent.joinpath(
+                    script_dir = compose_dir.parent.joinpath("pods", pod_name, "scripts")
-                        "pods", pod_name, "scripts"
-                    )
                     if pod_pre_start_command is not None:
-                        pre_start_commands.append(
+                        pre_start_commands.append(os.path.join(script_dir, pod_pre_start_command))
-                            os.path.join(script_dir, pod_pre_start_command)
-                        )
                     if pod_post_start_command is not None:
-                        post_start_commands.append(
+                        post_start_commands.append(os.path.join(script_dir, pod_post_start_command))
-                            os.path.join(script_dir, pod_post_start_command)
-                        )
                 else:
                     # TODO: fix this code for external stack with scripts
                     pod_root_dir = os.path.join(
                         dev_root_path, pod_repository.split("/")[-1], pod["path"]
                     )
-                    compose_file_name = os.path.join(
+                    compose_file_name = os.path.join(pod_root_dir, f"docker-compose-{pod_name}.yml")
-                        pod_root_dir, f"docker-compose-{pod_name}.yml"
-                    )
                     pod_pre_start_command = pod.get("pre_start_command")
                     pod_post_start_command = pod.get("post_start_command")
                     if pod_pre_start_command is not None:
-                        pre_start_commands.append(
+                        pre_start_commands.append(os.path.join(pod_root_dir, pod_pre_start_command))
-                            os.path.join(pod_root_dir, pod_pre_start_command)
-                        )
                     if pod_post_start_command is not None:
                         post_start_commands.append(
                             os.path.join(pod_root_dir, pod_post_start_command)
@@ -508,9 +486,7 @@ def _run_command(ctx, cluster_name, command):
     command_env["CERC_SO_COMPOSE_PROJECT"] = cluster_name
     if ctx.debug:
         command_env["CERC_SCRIPT_DEBUG"] = "true"
-    command_result = subprocess.run(
+    command_result = subprocess.run(command_file, shell=True, env=command_env, cwd=command_dir)
-        command_file, shell=True, env=command_env, cwd=command_dir
-    )
     if command_result.returncode != 0:
         print(f"FATAL Error running command: {command}")
         sys.exit(1)
@@ -567,9 +543,7 @@ def _orchestrate_cluster_config(ctx, cluster_config, deployer, container_exec_en
                         # "It returned with code 1"
                         if "It returned with code 1" in str(error):
                             if ctx.verbose:
-                                print(
+                                print("Config export script returned an error, re-trying")
-                                    "Config export script returned an error, re-trying"
-                                )
                         # If the script failed to execute
                         # (e.g. the file is not there) then we get:
                         # "It returned with code 2"

stack_orchestrator/deploy/deploy_types.py

@@ -13,8 +13,9 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with this program.  If not, see <http:#www.gnu.org/licenses/>.
 
-from typing import List, Mapping, Optional
+from collections.abc import Mapping
 from dataclasses import dataclass
+
 from stack_orchestrator.command_types import CommandOptions
 from stack_orchestrator.deploy.deployer import Deployer
 
@@ -23,19 +24,19 @@ from stack_orchestrator.deploy.deployer import Deployer
 class ClusterContext:
     # TODO: this should be in its own object not stuffed in here
     options: CommandOptions
-    cluster: Optional[str]
+    cluster: str | None
-    compose_files: List[str]
+    compose_files: list[str]
-    pre_start_commands: List[str]
+    pre_start_commands: list[str]
-    post_start_commands: List[str]
+    post_start_commands: list[str]
-    config: Optional[str]
+    config: str | None
-    env_file: Optional[str]
+    env_file: str | None
 
 
 @dataclass
 class DeployCommandContext:
     stack: str
     cluster_context: ClusterContext
-    deployer: Optional[Deployer]
+    deployer: Deployer | None
 
 
 @dataclass

stack_orchestrator/deploy/deploy_util.py

@@ -13,15 +13,16 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with this program.  If not, see <http:#www.gnu.org/licenses/>.
 
-from typing import List, Any
+from typing import Any
+
 from stack_orchestrator.deploy.deploy_types import DeployCommandContext, VolumeMapping
+from stack_orchestrator.opts import opts
 from stack_orchestrator.util import (
     get_parsed_stack_config,
-    get_yaml,
     get_pod_list,
+    get_yaml,
     resolve_compose_file,
 )
-from stack_orchestrator.opts import opts
 
 
 def _container_image_from_service(stack: str, service: str):
@@ -32,7 +33,7 @@ def _container_image_from_service(stack: str, service: str):
     yaml = get_yaml()
     for pod in pods:
         pod_file_path = resolve_compose_file(stack, pod)
-        parsed_pod_file = yaml.load(open(pod_file_path, "r"))
+        parsed_pod_file = yaml.load(open(pod_file_path))
         if "services" in parsed_pod_file:
             services = parsed_pod_file["services"]
             if service in services:
@@ -45,7 +46,7 @@ def _container_image_from_service(stack: str, service: str):
 def parsed_pod_files_map_from_file_names(pod_files):
     parsed_pod_yaml_map: Any = {}
     for pod_file in pod_files:
-        with open(pod_file, "r") as pod_file_descriptor:
+        with open(pod_file) as pod_file_descriptor:
             parsed_pod_file = get_yaml().load(pod_file_descriptor)
             parsed_pod_yaml_map[pod_file] = parsed_pod_file
     if opts.o.debug:
@@ -53,7 +54,7 @@ def parsed_pod_files_map_from_file_names(pod_files):
     return parsed_pod_yaml_map
 
 
-def images_for_deployment(pod_files: List[str]):
+def images_for_deployment(pod_files: list[str]):
     image_set = set()
     parsed_pod_yaml_map = parsed_pod_files_map_from_file_names(pod_files)
     # Find the set of images in the pods
@@ -69,7 +70,7 @@ def images_for_deployment(pod_files: List[str]):
     return image_set
 
 
-def _volumes_to_docker(mounts: List[VolumeMapping]):
+def _volumes_to_docker(mounts: list[VolumeMapping]):
     # Example from doc: [("/", "/host"), ("/etc/hosts", "/etc/hosts", "rw")]
     result = []
     for mount in mounts:
@@ -79,7 +80,7 @@ def _volumes_to_docker(mounts: List[VolumeMapping]):
 
 
 def run_container_command(
-    ctx: DeployCommandContext, service: str, command: str, mounts: List[VolumeMapping]
+    ctx: DeployCommandContext, service: str, command: str, mounts: list[VolumeMapping]
 ):
     deployer = ctx.deployer
     if deployer is None:

stack_orchestrator/deploy/deployer.py

@@ -15,7 +15,6 @@
 
 from abc import ABC, abstractmethod
 from pathlib import Path
-from typing import Optional
 
 
 class Deployer(ABC):
@@ -28,7 +27,7 @@ class Deployer(ABC):
         pass
 
     @abstractmethod
-    def update(self):
+    def update_envs(self):
         pass
 
     @abstractmethod
@@ -59,16 +58,23 @@ class Deployer(ABC):
         user=None,
         volumes=None,
         entrypoint=None,
-        env={},
+        env=None,
-        ports=[],
+        ports=None,
         detach=False,
     ):
         pass
 
     @abstractmethod
-    def run_job(self, job_name: str, release_name: Optional[str] = None):
+    def run_job(self, job_name: str, release_name: str | None = None):
         pass
 
+    def prepare(self, skip_cluster_management):
+        """Create cluster infrastructure (namespace, PVs, services) without starting pods.
+
+        Only supported for k8s deployers. Compose deployers raise an error.
+        """
+        raise DeployerException("prepare is only supported for k8s deployments")
+
 
 class DeployerException(Exception):
     def __init__(self, *args: object) -> None:

stack_orchestrator/deploy/deployer_factory.py

@@ -14,14 +14,14 @@
 # along with this program.  If not, see <http:#www.gnu.org/licenses/>.
 
 from stack_orchestrator import constants
-from stack_orchestrator.deploy.k8s.deploy_k8s import (
-    K8sDeployer,
-    K8sDeployerConfigGenerator,
-)
 from stack_orchestrator.deploy.compose.deploy_docker import (
     DockerDeployer,
     DockerDeployerConfigGenerator,
 )
+from stack_orchestrator.deploy.k8s.deploy_k8s import (
+    K8sDeployer,
+    K8sDeployerConfigGenerator,
+)
 
 
 def getDeployerConfigGenerator(type: str, deployment_context):
@@ -44,10 +44,7 @@ def getDeployer(
             compose_project_name,
             compose_env_file,
         )
-    elif (
+    elif type == type == constants.k8s_deploy_type or type == constants.k8s_kind_deploy_type:
-        type == type == constants.k8s_deploy_type
-        or type == constants.k8s_kind_deploy_type
-    ):
         return K8sDeployer(
             type,
             deployment_context,

stack_orchestrator/deploy/deployment.py

@@ -13,26 +13,28 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with this program.  If not, see <http:#www.gnu.org/licenses/>.
 
-import click
+import subprocess
-from pathlib import Path
 import sys
+from pathlib import Path
+
+import click
+
 from stack_orchestrator import constants
-from stack_orchestrator.deploy.images import push_images_operation
 from stack_orchestrator.deploy.deploy import (
-    up_operation,
+    create_deploy_context,
     down_operation,
-    ps_operation,
-    port_operation,
-    status_operation,
-)
-from stack_orchestrator.deploy.deploy import (
     exec_operation,
     logs_operation,
-    create_deploy_context,
+    port_operation,
-    update_operation,
+    prepare_operation,
+    ps_operation,
+    status_operation,
+    up_operation,
+    update_envs_operation,
 )
 from stack_orchestrator.deploy.deploy_types import DeployCommandContext
 from stack_orchestrator.deploy.deployment_context import DeploymentContext
+from stack_orchestrator.deploy.images import push_images_operation
 
 
 @click.group()
@@ -112,7 +114,7 @@ def up(ctx, stay_attached, skip_cluster_management, extra_args):
 )
 @click.option(
     "--skip-cluster-management/--perform-cluster-management",
-    default=False,
+    default=True,
     help="Skip cluster initialization/tear-down (only for kind-k8s deployments)",
 )
 @click.argument("extra_args", nargs=-1)  # help: command: up <service1> <service2>
@@ -123,14 +125,33 @@ def start(ctx, stay_attached, skip_cluster_management, extra_args):
     up_operation(ctx, services_list, stay_attached, skip_cluster_management)
 
 
-# TODO: remove legacy up command since it's an alias for stop
 @command.command()
-@click.option(
-    "--delete-volumes/--preserve-volumes", default=False, help="delete data volumes"
-)
 @click.option(
     "--skip-cluster-management/--perform-cluster-management",
     default=False,
+    help="Skip cluster initialization (only for kind-k8s deployments)",
+)
+@click.pass_context
+def prepare(ctx, skip_cluster_management):
+    """Create cluster infrastructure without starting pods.
+
+    Sets up the kind cluster, namespace, PVs, PVCs, ConfigMaps, Services,
+    and Ingresses — everything that 'start' does EXCEPT creating the
+    Deployment resource. No pods will be scheduled.
+
+    Use 'start --skip-cluster-management' afterward to create the Deployment
+    and start pods when ready.
+    """
+    ctx.obj = make_deploy_context(ctx)
+    prepare_operation(ctx, skip_cluster_management)
+
+
+# TODO: remove legacy up command since it's an alias for stop
+@command.command()
+@click.option("--delete-volumes/--preserve-volumes", default=False, help="delete data volumes")
+@click.option(
+    "--skip-cluster-management/--perform-cluster-management",
+    default=True,
     help="Skip cluster initialization/tear-down (only for kind-k8s deployments)",
 )
 @click.argument("extra_args", nargs=-1)  # help: command: down <service1> <service2>
@@ -144,12 +165,10 @@ def down(ctx, delete_volumes, skip_cluster_management, extra_args):
 
 # stop is the preferred alias for down
 @command.command()
-@click.option(
+@click.option("--delete-volumes/--preserve-volumes", default=False, help="delete data volumes")
-    "--delete-volumes/--preserve-volumes", default=False, help="delete data volumes"
-)
 @click.option(
     "--skip-cluster-management/--perform-cluster-management",
-    default=False,
+    default=True,
     help="Skip cluster initialization/tear-down (only for kind-k8s deployments)",
 )
 @click.argument("extra_args", nargs=-1)  # help: command: down <service1> <service2>
@@ -208,11 +227,11 @@ def status(ctx):
     status_operation(ctx)
 
 
-@command.command()
+@command.command(name="update-envs")
 @click.pass_context
-def update(ctx):
+def update_envs(ctx):
     ctx.obj = make_deploy_context(ctx)
-    update_operation(ctx)
+    update_envs_operation(ctx)
 
 
 @command.command()
@@ -228,3 +247,162 @@ def run_job(ctx, job_name, helm_release):
 
     ctx.obj = make_deploy_context(ctx)
     run_job_operation(ctx, job_name, helm_release)
+
+
+@command.command()
+@click.option("--stack-path", help="Path to stack git repo (overrides stored path)")
+@click.option("--spec-file", help="Path to GitOps spec.yml in repo (e.g., deployment/spec.yml)")
+@click.option("--config-file", help="Config file to pass to deploy init")
+@click.option(
+    "--force",
+    is_flag=True,
+    default=False,
+    help="Skip DNS verification",
+)
+@click.option(
+    "--expected-ip",
+    help="Expected IP for DNS verification (if different from egress)",
+)
+@click.pass_context
+def restart(ctx, stack_path, spec_file, config_file, force, expected_ip):
+    """Pull latest code and restart deployment using git-tracked spec.
+
+    GitOps workflow:
+    1. Operator maintains spec.yml in their git repository
+    2. This command pulls latest code (including updated spec.yml)
+    3. If hostname changed, verifies DNS routes to this server
+    4. Syncs deployment directory with the git-tracked spec
+    5. Stops and restarts the deployment
+
+    Data volumes are always preserved. The cluster is never destroyed.
+
+    Stack source resolution (in order):
+    1. --stack-path argument (if provided)
+    2. stack-source field in deployment.yml (if stored)
+    3. Error if neither available
+
+    Note: spec.yml should be maintained in git, not regenerated from
+    commands.py on each restart. Use 'deploy init' only for initial
+    spec generation, then customize and commit to your operator repo.
+    """
+    from stack_orchestrator.deploy.deployment_create import create_operation
+    from stack_orchestrator.deploy.dns_probe import verify_dns_via_probe
+    from stack_orchestrator.util import get_parsed_deployment_spec, get_yaml
+
+    deployment_context: DeploymentContext = ctx.obj
+
+    # Get current spec info (before git pull)
+    current_spec = deployment_context.spec
+    current_http_proxy = current_spec.get_http_proxy()
+    current_hostname = current_http_proxy[0]["host-name"] if current_http_proxy else None
+
+    # Resolve stack source path
+    if stack_path:
+        stack_source = Path(stack_path).resolve()
+    else:
+        # Try to get from deployment.yml
+        deployment_file = deployment_context.deployment_dir / constants.deployment_file_name
+        deployment_data = get_yaml().load(open(deployment_file))
+        stack_source_str = deployment_data.get("stack-source")
+        if not stack_source_str:
+            print("Error: No stack-source in deployment.yml and --stack-path not provided")
+            print("Use --stack-path to specify the stack git repository location")
+            sys.exit(1)
+        stack_source = Path(stack_source_str)
+
+    if not stack_source.exists():
+        print(f"Error: Stack source path does not exist: {stack_source}")
+        sys.exit(1)
+
+    print("=== Deployment Restart ===")
+    print(f"Deployment dir: {deployment_context.deployment_dir}")
+    print(f"Stack source: {stack_source}")
+    print(f"Current hostname: {current_hostname}")
+
+    # Step 1: Git pull (brings in updated spec.yml from operator's repo)
+    print("\n[1/4] Pulling latest code from stack repository...")
+    git_result = subprocess.run(["git", "pull"], cwd=stack_source, capture_output=True, text=True)
+    if git_result.returncode != 0:
+        print(f"Git pull failed: {git_result.stderr}")
+        sys.exit(1)
+    print(f"Git pull: {git_result.stdout.strip()}")
+
+    # Determine spec file location
+    # Priority: --spec-file argument > repo's deployment/spec.yml > deployment dir
+    # Stack path is like: repo/stack_orchestrator/data/stacks/stack-name
+    # So repo root is 4 parents up
+    repo_root = stack_source.parent.parent.parent.parent
+    if spec_file:
+        # Spec file relative to repo root
+        spec_file_path = repo_root / spec_file
+    else:
+        # Try standard GitOps location in repo
+        gitops_spec = repo_root / "deployment" / "spec.yml"
+        if gitops_spec.exists():
+            spec_file_path = gitops_spec
+        else:
+            # Fall back to deployment directory
+            spec_file_path = deployment_context.deployment_dir / "spec.yml"
+
+    if not spec_file_path.exists():
+        print(f"Error: spec.yml not found at {spec_file_path}")
+        print("For GitOps, add spec.yml to your repo at deployment/spec.yml")
+        print("Or specify --spec-file with path relative to repo root")
+        sys.exit(1)
+
+    print(f"Using spec: {spec_file_path}")
+
+    # Parse spec to check for hostname changes
+    new_spec_obj = get_parsed_deployment_spec(str(spec_file_path))
+    new_http_proxy = new_spec_obj.get("network", {}).get("http-proxy", [])
+    new_hostname = new_http_proxy[0]["host-name"] if new_http_proxy else None
+
+    print(f"Spec hostname: {new_hostname}")
+
+    # Step 2: DNS verification (only if hostname changed)
+    if new_hostname and new_hostname != current_hostname:
+        print(f"\n[2/4] Hostname changed: {current_hostname} -> {new_hostname}")
+        if force:
+            print("DNS verification skipped (--force)")
+        else:
+            print("Verifying DNS via probe...")
+            if not verify_dns_via_probe(new_hostname):
+                print(f"\nDNS verification failed for {new_hostname}")
+                print("Ensure DNS is configured before restarting.")
+                print("Use --force to skip this check.")
+                sys.exit(1)
+    else:
+        print("\n[2/4] Hostname unchanged, skipping DNS verification")
+
+    # Step 3: Sync deployment directory with spec
+    print("\n[3/4] Syncing deployment directory...")
+    deploy_ctx = make_deploy_context(ctx)
+    create_operation(
+        deployment_command_context=deploy_ctx,
+        spec_file=str(spec_file_path),
+        deployment_dir=str(deployment_context.deployment_dir),
+        update=True,
+        network_dir=None,
+        initial_peers=None,
+    )
+
+    # Reload deployment context with updated spec
+    deployment_context.init(deployment_context.deployment_dir)
+    ctx.obj = deployment_context
+
+    # Stop deployment
+    print("\n[4/4] Restarting deployment...")
+    ctx.obj = make_deploy_context(ctx)
+    down_operation(ctx, delete_volumes=False, extra_args_list=[], skip_cluster_management=True)
+
+    # Namespace deletion wait is handled by _ensure_namespace() in
+    # the deployer — no fixed sleep needed here.
+
+    # Start deployment
+    up_operation(ctx, services_list=None, stay_attached=False, skip_cluster_management=True)
+
+    print("\n=== Restart Complete ===")
+    print("Deployment restarted with git-tracked configuration.")
+    if new_hostname and new_hostname != current_hostname:
+        print(f"\nNew hostname: {new_hostname}")
+        print("Caddy will automatically provision TLS certificate.")

stack_orchestrator/deploy/deployment_context.py

@@ -18,9 +18,9 @@ import os
 from pathlib import Path
 
 from stack_orchestrator import constants
-from stack_orchestrator.util import get_yaml
-from stack_orchestrator.deploy.stack import Stack
 from stack_orchestrator.deploy.spec import Spec
+from stack_orchestrator.deploy.stack import Stack
+from stack_orchestrator.util import get_yaml
 
 
 class DeploymentContext:
@@ -58,7 +58,7 @@ class DeploymentContext:
         self.stack.init_from_file(self.get_stack_file())
         deployment_file_path = self.get_deployment_file()
         if deployment_file_path.exists():
-            obj = get_yaml().load(open(deployment_file_path, "r"))
+            obj = get_yaml().load(open(deployment_file_path))
             self.id = obj[constants.cluster_id_key]
         # Handle the case of a legacy deployment with no file
         # Code below is intended to match the output from _make_default_cluster_name()
@@ -75,7 +75,7 @@ class DeploymentContext:
             raise ValueError(f"File is not inside deployment directory: {file_path}")
 
         yaml = get_yaml()
-        with open(file_path, "r") as f:
+        with open(file_path) as f:
             yaml_data = yaml.load(f)
 
         modifier_func(yaml_data)

stack_orchestrator/deploy/deployment_create.py

@@ -13,38 +13,44 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with this program.  If not, see <http:#www.gnu.org/licenses/>.
 
-import click
+import base64
-from importlib import util
+import filecmp
+import json
 import os
-from pathlib import Path
-from typing import List
 import random
-from shutil import copy, copyfile, copytree
+import re
-from secrets import token_hex
 import sys
+import tempfile
+from importlib import util
+from pathlib import Path
+from secrets import token_hex
+from shutil import copy, copyfile, copytree, rmtree
+
+import click
+
 from stack_orchestrator import constants
-from stack_orchestrator.opts import opts
-from stack_orchestrator.util import (
-    get_stack_path,
-    get_parsed_deployment_spec,
-    get_parsed_stack_config,
-    global_options,
-    get_yaml,
-    get_pod_list,
-    get_pod_file_path,
-    pod_has_scripts,
-    get_pod_script_paths,
-    get_plugin_code_paths,
-    error_exit,
-    env_var_map_from_file,
-    resolve_config_dir,
-    get_job_list,
-    get_job_file_path,
-)
-from stack_orchestrator.deploy.spec import Spec
 from stack_orchestrator.deploy.deploy_types import LaconicStackSetupCommand
 from stack_orchestrator.deploy.deployer_factory import getDeployerConfigGenerator
 from stack_orchestrator.deploy.deployment_context import DeploymentContext
+from stack_orchestrator.deploy.spec import Spec
+from stack_orchestrator.opts import opts
+from stack_orchestrator.util import (
+    env_var_map_from_file,
+    error_exit,
+    get_job_file_path,
+    get_job_list,
+    get_parsed_deployment_spec,
+    get_parsed_stack_config,
+    get_plugin_code_paths,
+    get_pod_file_path,
+    get_pod_list,
+    get_pod_script_paths,
+    get_stack_path,
+    get_yaml,
+    global_options,
+    pod_has_scripts,
+    resolve_config_dir,
+)
 
 
 def _make_default_deployment_dir():
@@ -60,7 +66,7 @@ def _get_ports(stack):
         pod_file_path = get_pod_file_path(stack, parsed_stack, pod)
         if pod_file_path is None:
             continue
-        parsed_pod_file = yaml.load(open(pod_file_path, "r"))
+        parsed_pod_file = yaml.load(open(pod_file_path))
         if "services" in parsed_pod_file:
             for svc_name, svc in parsed_pod_file["services"].items():
                 if "ports" in svc:
@@ -96,7 +102,7 @@ def _get_named_volumes(stack):
         pod_file_path = get_pod_file_path(stack, parsed_stack, pod)
         if pod_file_path is None:
             continue
-        parsed_pod_file = yaml.load(open(pod_file_path, "r"))
+        parsed_pod_file = yaml.load(open(pod_file_path))
         if "volumes" in parsed_pod_file:
             volumes = parsed_pod_file["volumes"]
             for volume in volumes.keys():
@@ -126,9 +132,7 @@ def _create_bind_dir_if_relative(volume, path_string, compose_dir):
         absolute_path.mkdir(parents=True, exist_ok=True)
     else:
         if not path.exists():
-            print(
+            print(f"WARNING: mount path for volume {volume} does not exist: {path_string}")
-                f"WARNING: mount path for volume {volume} does not exist: {path_string}"
-            )
 
 
 # See:
@@ -145,9 +149,7 @@ def _fixup_pod_file(pod, spec, compose_dir):
                     volume_spec = spec_volumes[volume]
                     if volume_spec:
                         volume_spec_fixedup = (
-                            volume_spec
+                            volume_spec if Path(volume_spec).is_absolute() else f".{volume_spec}"
-                            if Path(volume_spec).is_absolute()
-                            else f".{volume_spec}"
                         )
                         _create_bind_dir_if_relative(volume, volume_spec, compose_dir)
                         # this is Docker specific
@@ -322,10 +324,7 @@ def _get_mapped_ports(stack: str, map_recipe: str):
                         else:
                             print("Error: bad map_recipe")
             else:
-                print(
+                print(f"Error: --map-ports-to-host must specify one of: " f"{port_map_recipes}")
-                    f"Error: --map-ports-to-host must specify one of: "
-                    f"{port_map_recipes}"
-                )
                 sys.exit(1)
     return ports
 
@@ -350,9 +349,7 @@ def _parse_config_variables(variable_values: str):
 
 @click.command()
 @click.option("--config", help="Provide config variables for the deployment")
-@click.option(
+@click.option("--config-file", help="Provide config variables in a file for the deployment")
-    "--config-file", help="Provide config variables in a file for the deployment"
-)
 @click.option("--kube-config", help="Provide a config file for a k8s deployment")
 @click.option(
     "--image-registry",
@@ -366,9 +363,7 @@ def _parse_config_variables(variable_values: str):
     "localhost-same, any-same, localhost-fixed-random, any-fixed-random",
 )
 @click.pass_context
-def init(
+def init(ctx, config, config_file, kube_config, image_registry, output, map_ports_to_host):
-    ctx, config, config_file, kube_config, image_registry, output, map_ports_to_host
-):
     stack = global_options(ctx).stack
     deployer_type = ctx.obj.deployer.type
     deploy_command_context = ctx.obj
@@ -415,13 +410,9 @@ def init_operation(
     else:
         # Check for --kube-config supplied for non-relevant deployer types
         if kube_config is not None:
-            error_exit(
+            error_exit(f"--kube-config is not allowed with a {deployer_type} deployment")
-                f"--kube-config is not allowed with a {deployer_type} deployment"
-            )
         if image_registry is not None:
-            error_exit(
+            error_exit(f"--image-registry is not allowed with a {deployer_type} deployment")
-                f"--image-registry is not allowed with a {deployer_type} deployment"
-            )
     if default_spec_file_content:
         spec_file_content.update(default_spec_file_content)
     config_variables = _parse_config_variables(config)
@@ -465,27 +456,181 @@ def init_operation(
             else:
                 volume_descriptors[named_volume] = f"./data/{named_volume}"
         if volume_descriptors:
-            spec_file_content["volumes"] = volume_descriptors
+            # Merge with existing volumes from stack init()
+            # init() volumes take precedence over compose defaults
+            orig_volumes = spec_file_content.get("volumes", {})
+            spec_file_content["volumes"] = {**volume_descriptors, **orig_volumes}
         if configmap_descriptors:
             spec_file_content["configmaps"] = configmap_descriptors
 
     if opts.o.debug:
-        print(
+        print(f"Creating spec file for stack: {stack} with content: {spec_file_content}")
-            f"Creating spec file for stack: {stack} with content: {spec_file_content}"
-        )
 
     with open(output, "w") as output_file:
         get_yaml().dump(spec_file_content, output_file)
 
 
-def _write_config_file(spec_file: Path, config_env_file: Path):
+# Token pattern: $generate:hex:32$ or $generate:base64:16$
+GENERATE_TOKEN_PATTERN = re.compile(r"\$generate:(\w+):(\d+)\$")
+
+
+def _generate_and_store_secrets(config_vars: dict, deployment_name: str):
+    """Generate secrets for $generate:...$ tokens and store in K8s Secret.
+
+    Called by `deploy create` - generates fresh secrets and stores them.
+    Returns the generated secrets dict for reference.
+    """
+    from kubernetes import client
+    from kubernetes import config as k8s_config
+
+    secrets = {}
+    for name, value in config_vars.items():
+        if not isinstance(value, str):
+            continue
+        match = GENERATE_TOKEN_PATTERN.search(value)
+        if not match:
+            continue
+
+        secret_type, length = match.group(1), int(match.group(2))
+        if secret_type == "hex":
+            secrets[name] = token_hex(length)
+        elif secret_type == "base64":
+            secrets[name] = base64.b64encode(os.urandom(length)).decode()
+        else:
+            secrets[name] = token_hex(length)
+
+    if not secrets:
+        return secrets
+
+    # Store in K8s Secret
+    try:
+        k8s_config.load_kube_config()
+    except Exception:
+        # Fall back to in-cluster config if available
+        try:
+            k8s_config.load_incluster_config()
+        except Exception:
+            print("Warning: Could not load kube config, secrets will not be stored in K8s")
+            return secrets
+
+    v1 = client.CoreV1Api()
+    secret_name = f"{deployment_name}-generated-secrets"
+    namespace = "default"
+
+    secret_data = {k: base64.b64encode(v.encode()).decode() for k, v in secrets.items()}
+    k8s_secret = client.V1Secret(
+        metadata=client.V1ObjectMeta(name=secret_name), data=secret_data, type="Opaque"
+    )
+
+    try:
+        v1.create_namespaced_secret(namespace, k8s_secret)
+        num_secrets = len(secrets)
+        print(f"Created K8s Secret '{secret_name}' with {num_secrets} secret(s)")
+    except client.exceptions.ApiException as e:
+        if e.status == 409:  # Already exists
+            v1.replace_namespaced_secret(secret_name, namespace, k8s_secret)
+            num_secrets = len(secrets)
+            print(f"Updated K8s Secret '{secret_name}' with {num_secrets} secret(s)")
+        else:
+            raise
+
+    return secrets
+
+
+def create_registry_secret(spec: Spec, deployment_name: str) -> str | None:
+    """Create K8s docker-registry secret from spec + environment.
+
+    Reads registry configuration from spec.yml and creates a Kubernetes
+    secret of type kubernetes.io/dockerconfigjson for image pulls.
+
+    Args:
+        spec: The deployment spec containing image-registry config
+        deployment_name: Name of the deployment (used for secret naming)
+
+    Returns:
+        The secret name if created, None if no registry config
+    """
+    from kubernetes import client
+    from kubernetes import config as k8s_config
+
+    registry_config = spec.get_image_registry_config()
+    if not registry_config:
+        return None
+
+    server = registry_config.get("server")
+    username = registry_config.get("username")
+    token_env = registry_config.get("token-env")
+
+    if not all([server, username, token_env]):
+        return None
+
+    # Type narrowing for pyright - we've validated these aren't None above
+    assert token_env is not None
+    token = os.environ.get(token_env)
+    if not token:
+        print(f"Warning: Registry token env var '{token_env}' not set, " "skipping registry secret")
+        return None
+
+    # Create dockerconfigjson format (Docker API uses "password" field for tokens)
+    auth = base64.b64encode(f"{username}:{token}".encode()).decode()
+    docker_config = {"auths": {server: {"username": username, "password": token, "auth": auth}}}
+
+    # Secret name derived from deployment name
+    secret_name = f"{deployment_name}-registry"
+
+    # Load kube config
+    try:
+        k8s_config.load_kube_config()
+    except Exception:
+        try:
+            k8s_config.load_incluster_config()
+        except Exception:
+            print("Warning: Could not load kube config, registry secret not created")
+            return None
+
+    v1 = client.CoreV1Api()
+    namespace = "default"
+
+    k8s_secret = client.V1Secret(
+        metadata=client.V1ObjectMeta(name=secret_name),
+        data={".dockerconfigjson": base64.b64encode(json.dumps(docker_config).encode()).decode()},
+        type="kubernetes.io/dockerconfigjson",
+    )
+
+    try:
+        v1.create_namespaced_secret(namespace, k8s_secret)
+        print(f"Created registry secret '{secret_name}' for {server}")
+    except client.exceptions.ApiException as e:
+        if e.status == 409:  # Already exists
+            v1.replace_namespaced_secret(secret_name, namespace, k8s_secret)
+            print(f"Updated registry secret '{secret_name}' for {server}")
+        else:
+            raise
+
+    return secret_name
+
+
+def _write_config_file(spec_file: Path, config_env_file: Path, deployment_name: str | None = None):
     spec_content = get_parsed_deployment_spec(spec_file)
-    # Note: we want to write an empty file even if we have no config variables
+    config_vars = spec_content.get("config", {}) or {}
+
+    # Generate and store secrets in K8s if deployment_name provided and tokens exist
+    if deployment_name and config_vars:
+        has_generate_tokens = any(
+            isinstance(v, str) and GENERATE_TOKEN_PATTERN.search(v) for v in config_vars.values()
+        )
+        if has_generate_tokens:
+            _generate_and_store_secrets(config_vars, deployment_name)
+
+    # Write non-secret config to config.env (exclude $generate:...$ tokens)
     with open(config_env_file, "w") as output_file:
-        if "config" in spec_content and spec_content["config"]:
-            config_vars = spec_content["config"]
         if config_vars:
             for variable_name, variable_value in config_vars.items():
+                # Skip variables with generate tokens - they go to K8s Secret
+                if isinstance(variable_value, str) and GENERATE_TOKEN_PATTERN.search(
+                    variable_value
+                ):
+                    continue
                 output_file.write(f"{variable_name}={variable_value}\n")
 
 
@@ -495,17 +640,20 @@ def _write_kube_config_file(external_path: Path, internal_path: Path):
     copyfile(external_path, internal_path)
 
 
-def _copy_files_to_directory(file_paths: List[Path], directory: Path):
+def _copy_files_to_directory(file_paths: list[Path], directory: Path):
     for path in file_paths:
         # Using copy to preserve the execute bit
         copy(path, os.path.join(directory, os.path.basename(path)))
 
 
-def _create_deployment_file(deployment_dir: Path):
+def _create_deployment_file(deployment_dir: Path, stack_source: Path | None = None):
     deployment_file_path = deployment_dir.joinpath(constants.deployment_file_name)
     cluster = f"{constants.cluster_name_prefix}{token_hex(8)}"
+    deployment_content = {constants.cluster_id_key: cluster}
+    if stack_source:
+        deployment_content["stack-source"] = str(stack_source)
     with open(deployment_file_path, "w") as output_file:
-        output_file.write(f"{constants.cluster_id_key}: {cluster}\n")
+        get_yaml().dump(deployment_content, output_file)
 
 
 def _check_volume_definitions(spec):
@@ -513,17 +661,25 @@ def _check_volume_definitions(spec):
         for volume_name, volume_path in spec.get_volumes().items():
             if volume_path:
                 if not os.path.isabs(volume_path):
+                    # For k8s-kind: allow relative paths, they'll be resolved
+                    # by _make_absolute_host_path() during kind config generation
+                    if not spec.is_kind_deployment():
+                        deploy_type = spec.get_deployment_type()
                         raise Exception(
-                        f"Relative path {volume_path} for volume {volume_name} not "
+                            f"Relative path {volume_path} for volume "
-                        f"supported for deployment type {spec.get_deployment_type()}"
+                            f"{volume_name} not supported for {deploy_type}"
                         )
 
 
 @click.command()
-@click.option(
+@click.option("--spec-file", required=True, help="Spec file to use to create this deployment")
-    "--spec-file", required=True, help="Spec file to use to create this deployment"
-)
 @click.option("--deployment-dir", help="Create deployment files in this directory")
+@click.option(
+    "--update",
+    is_flag=True,
+    default=False,
+    help="Update existing deployment directory, preserving data volumes and env file",
+)
 @click.option(
     "--helm-chart",
     is_flag=True,
@@ -536,13 +692,21 @@ def _check_volume_definitions(spec):
 @click.argument("extra_args", nargs=-1, type=click.UNPROCESSED)
 @click.pass_context
 def create(
-    ctx, spec_file, deployment_dir, helm_chart, network_dir, initial_peers, extra_args
+    ctx,
+    spec_file,
+    deployment_dir,
+    update,
+    helm_chart,
+    network_dir,
+    initial_peers,
+    extra_args,
 ):
     deployment_command_context = ctx.obj
     return create_operation(
         deployment_command_context,
         spec_file,
         deployment_dir,
+        update,
         helm_chart,
         network_dir,
         initial_peers,
@@ -556,35 +720,34 @@ def create_operation(
     deployment_command_context,
     spec_file,
     deployment_dir,
+    update=False,
     helm_chart=False,
     network_dir=None,
     initial_peers=None,
     extra_args=(),
 ):
-    parsed_spec = Spec(
+    parsed_spec = Spec(os.path.abspath(spec_file), get_parsed_deployment_spec(spec_file))
-        os.path.abspath(spec_file), get_parsed_deployment_spec(spec_file)
-    )
     _check_volume_definitions(parsed_spec)
     stack_name = parsed_spec["stack"]
     deployment_type = parsed_spec[constants.deploy_to_key]
 
-    stack_file = get_stack_path(stack_name).joinpath(constants.stack_file_name)
-    parsed_stack = get_parsed_stack_config(stack_name)
     if opts.o.debug:
         print(f"parsed spec: {parsed_spec}")
+
     if deployment_dir is None:
         deployment_dir_path = _make_default_deployment_dir()
     else:
         deployment_dir_path = Path(deployment_dir)
-    if deployment_dir_path.exists():
-        error_exit(f"{deployment_dir_path} already exists")
-    os.mkdir(deployment_dir_path)
-    # Copy spec file and the stack file into the deployment dir
-    copyfile(spec_file, deployment_dir_path.joinpath(constants.spec_file_name))
-    copyfile(stack_file, deployment_dir_path.joinpath(constants.stack_file_name))
 
-    # Create deployment.yml with cluster-id
+    if deployment_dir_path.exists():
-    _create_deployment_file(deployment_dir_path)
+        if not update:
+            error_exit(f"{deployment_dir_path} already exists")
+        if opts.o.debug:
+            print(f"Updating existing deployment at {deployment_dir_path}")
+    else:
+        if update:
+            error_exit(f"--update requires that {deployment_dir_path} already exists")
+        os.mkdir(deployment_dir_path)
 
     # Branch to Helm chart generation flow if --helm-chart flag is set
     if deployment_type == "k8s" and helm_chart:
@@ -595,75 +758,203 @@ def create_operation(
         generate_helm_chart(stack_name, spec_file, deployment_dir_path)
         return  # Exit early for helm chart generation
 
-    # Existing deployment flow continues unchanged
+    # Resolve stack source path for restart capability
-    # Copy any config varibles from the spec file into an env file suitable for compose
+    stack_source = get_stack_path(stack_name)
-    _write_config_file(
+
-        spec_file, deployment_dir_path.joinpath(constants.config_file_name)
+    if update:
+        # Sync mode: write to temp dir, then copy to deployment dir with backups
+        temp_dir = Path(tempfile.mkdtemp(prefix="deployment-sync-"))
+        try:
+            # Write deployment files to temp dir
+            # (skip deployment.yml to preserve cluster ID)
+            _write_deployment_files(
+                temp_dir,
+                Path(spec_file),
+                parsed_spec,
+                stack_name,
+                deployment_type,
+                include_deployment_file=False,
+                stack_source=stack_source,
             )
-    # Copy any k8s config file into the deployment dir
+
+            # Copy from temp to deployment dir, excluding data volumes
+            # and backing up changed files.
+            # Exclude data/* to avoid touching user data volumes.
+            # Exclude config file to preserve deployment settings
+            # (XXX breaks passing config vars from spec)
+            exclude_patterns = ["data", "data/*", constants.config_file_name]
+            _safe_copy_tree(temp_dir, deployment_dir_path, exclude_patterns=exclude_patterns)
+        finally:
+            # Clean up temp dir
+            rmtree(temp_dir)
+    else:
+        # Normal mode: write directly to deployment dir
+        _write_deployment_files(
+            deployment_dir_path,
+            Path(spec_file),
+            parsed_spec,
+            stack_name,
+            deployment_type,
+            include_deployment_file=True,
+            stack_source=stack_source,
+        )
+
+    # Delegate to the stack's Python code
+    # The deploy create command doesn't require a --stack argument so we need
+    # to insert the stack member here.
+    deployment_command_context.stack = stack_name
+    deployment_context = DeploymentContext()
+    deployment_context.init(deployment_dir_path)
+    # Call the deployer to generate any deployer-specific files (e.g. for kind)
+    deployer_config_generator = getDeployerConfigGenerator(deployment_type, deployment_context)
+    # TODO: make deployment_dir_path a Path above
+    if deployer_config_generator is not None:
+        deployer_config_generator.generate(deployment_dir_path)
+    call_stack_deploy_create(deployment_context, [network_dir, initial_peers, *extra_args])
+
+
+def _safe_copy_tree(src: Path, dst: Path, exclude_patterns: list[str] | None = None):
+    """
+    Recursively copy a directory tree, backing up changed files with .bak suffix.
+
+    :param src: Source directory
+    :param dst: Destination directory
+    :param exclude_patterns: List of path patterns to exclude (relative to src)
+    """
+    if exclude_patterns is None:
+        exclude_patterns = []
+
+    def should_exclude(path: Path) -> bool:
+        """Check if path matches any exclude pattern."""
+        rel_path = path.relative_to(src)
+        for pattern in exclude_patterns:
+            if rel_path.match(pattern):
+                return True
+        return False
+
+    def safe_copy_file(src_file: Path, dst_file: Path):
+        """Copy file, backing up destination if it differs."""
+        if dst_file.exists() and not dst_file.is_dir() and not filecmp.cmp(src_file, dst_file):
+            os.rename(dst_file, f"{dst_file}.bak")
+        copy(src_file, dst_file)
+
+    # Walk the source tree
+    for src_path in src.rglob("*"):
+        if should_exclude(src_path):
+            continue
+
+        rel_path = src_path.relative_to(src)
+        dst_path = dst / rel_path
+
+        if src_path.is_dir():
+            dst_path.mkdir(parents=True, exist_ok=True)
+        else:
+            dst_path.parent.mkdir(parents=True, exist_ok=True)
+            safe_copy_file(src_path, dst_path)
+
+
+def _write_deployment_files(
+    target_dir: Path,
+    spec_file: Path,
+    parsed_spec: Spec,
+    stack_name: str,
+    deployment_type: str,
+    include_deployment_file: bool = True,
+    stack_source: Path | None = None,
+):
+    """
+    Write deployment files to target directory.
+
+    :param target_dir: Directory to write files to
+    :param spec_file: Path to spec file
+    :param parsed_spec: Parsed spec object
+    :param stack_name: Name of stack
+    :param deployment_type: Type of deployment
+    :param include_deployment_file: Whether to create deployment.yml (skip for update)
+    :param stack_source: Path to stack source (git repo) for restart capability
+    """
+    stack_file = get_stack_path(stack_name).joinpath(constants.stack_file_name)
+    parsed_stack = get_parsed_stack_config(stack_name)
+
+    # Copy spec file and the stack file into the target dir
+    copyfile(spec_file, target_dir.joinpath(constants.spec_file_name))
+    copyfile(stack_file, target_dir.joinpath(constants.stack_file_name))
+
+    # Create deployment file if requested
+    if include_deployment_file:
+        _create_deployment_file(target_dir, stack_source=stack_source)
+
+    # Copy any config variables from the spec file into an env file suitable for compose
+    # Use stack_name as deployment_name for K8s secret naming
+    # Extract just the name part if stack_name is a path ("path/to/stack" -> "stack")
+    deployment_name = Path(stack_name).name.replace("_", "-")
+    _write_config_file(spec_file, target_dir.joinpath(constants.config_file_name), deployment_name)
+
+    # Copy any k8s config file into the target dir
     if deployment_type == "k8s":
         _write_kube_config_file(
             Path(parsed_spec[constants.kube_config_key]),
-            deployment_dir_path.joinpath(constants.kube_config_filename),
+            target_dir.joinpath(constants.kube_config_filename),
         )
-    # Copy the pod files into the deployment dir, fixing up content
+
+    # Copy the pod files into the target dir, fixing up content
     pods = get_pod_list(parsed_stack)
-    destination_compose_dir = deployment_dir_path.joinpath("compose")
+    destination_compose_dir = target_dir.joinpath("compose")
-    os.mkdir(destination_compose_dir)
+    os.makedirs(destination_compose_dir, exist_ok=True)
-    destination_pods_dir = deployment_dir_path.joinpath("pods")
+    destination_pods_dir = target_dir.joinpath("pods")
-    os.mkdir(destination_pods_dir)
+    os.makedirs(destination_pods_dir, exist_ok=True)
     yaml = get_yaml()
+
     for pod in pods:
         pod_file_path = get_pod_file_path(stack_name, parsed_stack, pod)
         if pod_file_path is None:
             continue
-        parsed_pod_file = yaml.load(open(pod_file_path, "r"))
+        parsed_pod_file = yaml.load(open(pod_file_path))
         extra_config_dirs = _find_extra_config_dirs(parsed_pod_file, pod)
         destination_pod_dir = destination_pods_dir.joinpath(pod)
-        os.mkdir(destination_pod_dir)
+        os.makedirs(destination_pod_dir, exist_ok=True)
         if opts.o.debug:
             print(f"extra config dirs: {extra_config_dirs}")
         _fixup_pod_file(parsed_pod_file, parsed_spec, destination_compose_dir)
         with open(
-            destination_compose_dir.joinpath("docker-compose-%s.yml" % pod), "w"
+            destination_compose_dir.joinpath(f"docker-compose-{pod}.yml"), "w"
         ) as output_file:
             yaml.dump(parsed_pod_file, output_file)
+
         # Copy the config files for the pod, if any
         config_dirs = {pod}
         config_dirs = config_dirs.union(extra_config_dirs)
         for config_dir in config_dirs:
             source_config_dir = resolve_config_dir(stack_name, config_dir)
             if os.path.exists(source_config_dir):
-                destination_config_dir = deployment_dir_path.joinpath(
+                destination_config_dir = target_dir.joinpath("config", config_dir)
-                    "config", config_dir
+                copytree(source_config_dir, destination_config_dir, dirs_exist_ok=True)
-                )
+
-                # If the same config dir appears in multiple pods, it may already have
-                # been copied
-                if not os.path.exists(destination_config_dir):
-                    copytree(source_config_dir, destination_config_dir)
         # Copy the script files for the pod, if any
         if pod_has_scripts(parsed_stack, pod):
             destination_script_dir = destination_pod_dir.joinpath("scripts")
-            os.mkdir(destination_script_dir)
+            os.makedirs(destination_script_dir, exist_ok=True)
             script_paths = get_pod_script_paths(parsed_stack, pod)
             _copy_files_to_directory(script_paths, destination_script_dir)
+
         if parsed_spec.is_kubernetes_deployment():
             for configmap in parsed_spec.get_configmaps():
                 source_config_dir = resolve_config_dir(stack_name, configmap)
                 if os.path.exists(source_config_dir):
-                    destination_config_dir = deployment_dir_path.joinpath(
+                    destination_config_dir = target_dir.joinpath("configmaps", configmap)
-                        "configmaps", configmap
+                    copytree(source_config_dir, destination_config_dir, dirs_exist_ok=True)
-                    )
-                    copytree(
-                        source_config_dir, destination_config_dir, dirs_exist_ok=True
-                    )
         else:
+            # TODO:
+            # This is odd - looks up config dir that matches a volume name,
+            # then copies as a mount dir?
+            # AFAICT not used by or relevant to any existing stack - roy
+
             # TODO: We should probably only do this if the volume is marked :ro.
             for volume_name, volume_path in parsed_spec.get_volumes().items():
                 source_config_dir = resolve_config_dir(stack_name, volume_name)
                 # Only copy if the source exists and is _not_ empty.
                 if os.path.exists(source_config_dir) and os.listdir(source_config_dir):
-                    destination_config_dir = deployment_dir_path.joinpath(volume_path)
+                    destination_config_dir = target_dir.joinpath(volume_path)
                     # Only copy if the destination exists and _is_ empty.
                     if os.path.exists(destination_config_dir) and not os.listdir(
                         destination_config_dir
@@ -674,43 +965,24 @@ def create_operation(
                             dirs_exist_ok=True,
                         )
 
-    # Copy the job files into the deployment dir (for Docker deployments)
+    # Copy the job files into the target dir (for Docker deployments)
     jobs = get_job_list(parsed_stack)
     if jobs and not parsed_spec.is_kubernetes_deployment():
-        destination_compose_jobs_dir = deployment_dir_path.joinpath("compose-jobs")
+        destination_compose_jobs_dir = target_dir.joinpath("compose-jobs")
-        os.mkdir(destination_compose_jobs_dir)
+        os.makedirs(destination_compose_jobs_dir, exist_ok=True)
         for job in jobs:
             job_file_path = get_job_file_path(stack_name, parsed_stack, job)
             if job_file_path and job_file_path.exists():
-                parsed_job_file = yaml.load(open(job_file_path, "r"))
+                parsed_job_file = yaml.load(open(job_file_path))
                 _fixup_pod_file(parsed_job_file, parsed_spec, destination_compose_dir)
                 with open(
-                    destination_compose_jobs_dir.joinpath(
+                    destination_compose_jobs_dir.joinpath(f"docker-compose-{job}.yml"),
-                        "docker-compose-%s.yml" % job
-                    ),
                     "w",
                 ) as output_file:
                     yaml.dump(parsed_job_file, output_file)
                 if opts.o.debug:
                     print(f"Copied job compose file: {job}")
 
-    # Delegate to the stack's Python code
-    # The deploy create command doesn't require a --stack argument so we need
-    # to insert the stack member here.
-    deployment_command_context.stack = stack_name
-    deployment_context = DeploymentContext()
-    deployment_context.init(deployment_dir_path)
-    # Call the deployer to generate any deployer-specific files (e.g. for kind)
-    deployer_config_generator = getDeployerConfigGenerator(
-        deployment_type, deployment_context
-    )
-    # TODO: make deployment_dir_path a Path above
-    if deployer_config_generator is not None:
-        deployer_config_generator.generate(deployment_dir_path)
-    call_stack_deploy_create(
-        deployment_context, [network_dir, initial_peers, *extra_args]
-    )
-
 
 # TODO: this code should be in the stack .py files but
 # we haven't yet figured out how to integrate click across
@@ -719,18 +991,14 @@ def create_operation(
 @click.option("--node-moniker", help="Moniker for this node")
 @click.option("--chain-id", help="The new chain id")
 @click.option("--key-name", help="Name for new node key")
-@click.option(
+@click.option("--gentx-files", help="List of comma-delimited gentx filenames from other nodes")
-    "--gentx-files", help="List of comma-delimited gentx filenames from other nodes"
-)
 @click.option(
     "--gentx-addresses",
     type=str,
     help="List of comma-delimited validator addresses for other nodes",
 )
 @click.option("--genesis-file", help="Genesis file for the network")
-@click.option(
+@click.option("--initialize-network", is_flag=True, default=False, help="Initialize phase")
-    "--initialize-network", is_flag=True, default=False, help="Initialize phase"
-)
 @click.option("--join-network", is_flag=True, default=False, help="Join phase")
 @click.option("--connect-network", is_flag=True, default=False, help="Connect phase")
 @click.option("--create-network", is_flag=True, default=False, help="Create phase")

stack_orchestrator/deploy/dns_probe.py

@@ -0,0 +1,158 @@
+# Copyright © 2024 Vulcanize
+# SPDX-License-Identifier: AGPL-3.0
+
+"""DNS verification via temporary ingress probe."""
+
+import secrets
+import socket
+import time
+
+import requests
+from kubernetes import client
+
+
+def get_server_egress_ip() -> str:
+    """Get this server's public egress IP via ipify."""
+    response = requests.get("https://api.ipify.org", timeout=10)
+    response.raise_for_status()
+    result: str = response.text.strip()
+    return result
+
+
+def resolve_hostname(hostname: str) -> list[str]:
+    """Resolve hostname to list of IP addresses."""
+    try:
+        _, _, ips = socket.gethostbyname_ex(hostname)
+        return ips
+    except socket.gaierror:
+        return []
+
+
+def verify_dns_simple(hostname: str, expected_ip: str | None = None) -> bool:
+    """Simple DNS verification - check hostname resolves to expected IP.
+
+    If expected_ip not provided, uses server's egress IP.
+    Returns True if hostname resolves to expected IP.
+    """
+    resolved_ips = resolve_hostname(hostname)
+    if not resolved_ips:
+        print(f"DNS FAIL: {hostname} does not resolve")
+        return False
+
+    if expected_ip is None:
+        expected_ip = get_server_egress_ip()
+
+    if expected_ip in resolved_ips:
+        print(f"DNS OK: {hostname} -> {resolved_ips} (includes {expected_ip})")
+        return True
+    else:
+        print(f"DNS WARN: {hostname} -> {resolved_ips} (expected {expected_ip})")
+        return False
+
+
+def create_probe_ingress(hostname: str, namespace: str = "default") -> str:
+    """Create a temporary ingress for DNS probing.
+
+    Returns the probe token that the ingress will respond with.
+    """
+    token = secrets.token_hex(16)
+
+    networking_api = client.NetworkingV1Api()
+
+    # Create a simple ingress that Caddy will pick up
+    ingress = client.V1Ingress(
+        metadata=client.V1ObjectMeta(
+            name="laconic-dns-probe",
+            annotations={
+                "kubernetes.io/ingress.class": "caddy",
+                "laconic.com/probe-token": token,
+            },
+        ),
+        spec=client.V1IngressSpec(
+            rules=[
+                client.V1IngressRule(
+                    host=hostname,
+                    http=client.V1HTTPIngressRuleValue(
+                        paths=[
+                            client.V1HTTPIngressPath(
+                                path="/.well-known/laconic-probe",
+                                path_type="Exact",
+                                backend=client.V1IngressBackend(
+                                    service=client.V1IngressServiceBackend(
+                                        name="caddy-ingress-controller",
+                                        port=client.V1ServiceBackendPort(number=80),
+                                    )
+                                ),
+                            )
+                        ]
+                    ),
+                )
+            ]
+        ),
+    )
+
+    networking_api.create_namespaced_ingress(namespace=namespace, body=ingress)
+    return token
+
+
+def delete_probe_ingress(namespace: str = "default"):
+    """Delete the temporary probe ingress."""
+    networking_api = client.NetworkingV1Api()
+    try:
+        networking_api.delete_namespaced_ingress(name="laconic-dns-probe", namespace=namespace)
+    except client.exceptions.ApiException:
+        pass  # Ignore if already deleted
+
+
+def verify_dns_via_probe(
+    hostname: str, namespace: str = "default", timeout: int = 30, poll_interval: int = 2
+) -> bool:
+    """Verify DNS by creating temp ingress and probing it.
+
+    This definitively proves that traffic to the hostname reaches this cluster.
+
+    Args:
+        hostname: The hostname to verify
+        namespace: Kubernetes namespace for probe ingress
+        timeout: Total seconds to wait for probe to succeed
+        poll_interval: Seconds between probe attempts
+
+    Returns:
+        True if probe succeeds, False otherwise
+    """
+    # First check DNS resolves at all
+    if not resolve_hostname(hostname):
+        print(f"DNS FAIL: {hostname} does not resolve")
+        return False
+
+    print(f"Creating probe ingress for {hostname}...")
+    create_probe_ingress(hostname, namespace)
+
+    try:
+        # Wait for Caddy to pick up the ingress
+        time.sleep(3)
+
+        # Poll until success or timeout
+        probe_url = f"http://{hostname}/.well-known/laconic-probe"
+        start_time = time.time()
+        last_error = None
+
+        while time.time() - start_time < timeout:
+            try:
+                response = requests.get(probe_url, timeout=5)
+                # For now, just verify we get a response from this cluster
+                # A more robust check would verify a unique token
+                if response.status_code < 500:
+                    print(f"DNS PROBE OK: {hostname} routes to this cluster")
+                    return True
+            except requests.RequestException as e:
+                last_error = e
+
+            time.sleep(poll_interval)
+
+        print(f"DNS PROBE FAIL: {hostname} - {last_error}")
+        return False
+
+    finally:
+        print("Cleaning up probe ingress...")
+        delete_probe_ingress(namespace)

stack_orchestrator/deploy/images.py

@@ -13,15 +13,14 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with this program.  If not, see <http:#www.gnu.org/licenses/>.
 
-from typing import Set
 
 from python_on_whales import DockerClient
 
 from stack_orchestrator import constants
-from stack_orchestrator.opts import opts
-from stack_orchestrator.deploy.deployment_context import DeploymentContext
 from stack_orchestrator.deploy.deploy_types import DeployCommandContext
 from stack_orchestrator.deploy.deploy_util import images_for_deployment
+from stack_orchestrator.deploy.deployment_context import DeploymentContext
+from stack_orchestrator.opts import opts
 
 
 def _image_needs_pushed(image: str):
@@ -32,9 +31,7 @@ def _image_needs_pushed(image: str):
 def _remote_tag_for_image(image: str, remote_repo_url: str):
     # Turns image tags of the form: foo/bar:local into remote.repo/org/bar:deploy
     major_parts = image.split("/", 2)
-    image_name_with_version = (
+    image_name_with_version = major_parts[1] if 2 == len(major_parts) else major_parts[0]
-        major_parts[1] if 2 == len(major_parts) else major_parts[0]
-    )
     (image_name, image_version) = image_name_with_version.split(":")
     if image_version == "local":
         return f"{remote_repo_url}/{image_name}:deploy"
@@ -63,18 +60,14 @@ def add_tags_to_image(remote_repo_url: str, local_tag: str, *additional_tags):
 
     docker = DockerClient()
     remote_tag = _remote_tag_for_image(local_tag, remote_repo_url)
-    new_remote_tags = [
+    new_remote_tags = [_remote_tag_for_image(tag, remote_repo_url) for tag in additional_tags]
-        _remote_tag_for_image(tag, remote_repo_url) for tag in additional_tags
-    ]
     docker.buildx.imagetools.create(sources=[remote_tag], tags=new_remote_tags)
 
 
 def remote_tag_for_image_unique(image: str, remote_repo_url: str, deployment_id: str):
     # Turns image tags of the form: foo/bar:local into remote.repo/org/bar:deploy
     major_parts = image.split("/", 2)
-    image_name_with_version = (
+    image_name_with_version = major_parts[1] if 2 == len(major_parts) else major_parts[0]
-        major_parts[1] if 2 == len(major_parts) else major_parts[0]
-    )
     (image_name, image_version) = image_name_with_version.split(":")
     if image_version == "local":
         # Salt the tag with part of the deployment id to make it unique to this
@@ -91,24 +84,20 @@ def push_images_operation(
 ):
     # Get the list of images for the stack
     cluster_context = command_context.cluster_context
-    images: Set[str] = images_for_deployment(cluster_context.compose_files)
+    images: set[str] = images_for_deployment(cluster_context.compose_files)
     # Tag the images for the remote repo
     remote_repo_url = deployment_context.spec.obj[constants.image_registry_key]
     docker = DockerClient()
     for image in images:
         if _image_needs_pushed(image):
-            remote_tag = remote_tag_for_image_unique(
+            remote_tag = remote_tag_for_image_unique(image, remote_repo_url, deployment_context.id)
-                image, remote_repo_url, deployment_context.id
-            )
             if opts.o.verbose:
                 print(f"Tagging {image} to {remote_tag}")
             docker.image.tag(image, remote_tag)
     # Run docker push commands to upload
     for image in images:
         if _image_needs_pushed(image):
-            remote_tag = remote_tag_for_image_unique(
+            remote_tag = remote_tag_for_image_unique(image, remote_repo_url, deployment_context.id)
-                image, remote_repo_url, deployment_context.id
-            )
             if opts.o.verbose:
                 print(f"Pushing image {remote_tag}")
             docker.image.push(remote_tag)

stack_orchestrator/deploy/k8s/cluster_info.py

@@ -13,32 +13,31 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with this program.  If not, see <http:#www.gnu.org/licenses/>.
 
-import os
 import base64
+import os
+from typing import Any
 
 from kubernetes import client
-from typing import Any, List, Optional, Set
 
-from stack_orchestrator.opts import opts
+from stack_orchestrator.deploy.deploy_types import DeployEnvVars
-from stack_orchestrator.util import env_var_map_from_file
+from stack_orchestrator.deploy.deploy_util import (
+    images_for_deployment,
+    parsed_pod_files_map_from_file_names,
+)
+from stack_orchestrator.deploy.images import remote_tag_for_image_unique
 from stack_orchestrator.deploy.k8s.helpers import (
+    envs_from_compose_file,
+    envs_from_environment_variables_map,
+    get_kind_pv_bind_mount_path,
+    merge_envs,
     named_volumes_from_pod_files,
+    translate_sidecar_service_names,
     volume_mounts_for_service,
     volumes_for_pod_files,
 )
-from stack_orchestrator.deploy.k8s.helpers import get_kind_pv_bind_mount_path
+from stack_orchestrator.deploy.spec import ResourceLimits, Resources, Spec
-from stack_orchestrator.deploy.k8s.helpers import (
+from stack_orchestrator.opts import opts
-    envs_from_environment_variables_map,
+from stack_orchestrator.util import env_var_map_from_file
-    envs_from_compose_file,
-    merge_envs,
-)
-from stack_orchestrator.deploy.deploy_util import (
-    parsed_pod_files_map_from_file_names,
-    images_for_deployment,
-)
-from stack_orchestrator.deploy.deploy_types import DeployEnvVars
-from stack_orchestrator.deploy.spec import Spec, Resources, ResourceLimits
-from stack_orchestrator.deploy.images import remote_tag_for_image_unique
 
 DEFAULT_VOLUME_RESOURCES = Resources({"reservations": {"storage": "2Gi"}})
 
@@ -51,7 +50,7 @@ DEFAULT_CONTAINER_RESOURCES = Resources(
 
 
 def to_k8s_resource_requirements(resources: Resources) -> client.V1ResourceRequirements:
-    def to_dict(limits: Optional[ResourceLimits]):
+    def to_dict(limits: ResourceLimits | None):
         if not limits:
             return None
 
@@ -71,7 +70,7 @@ def to_k8s_resource_requirements(resources: Resources) -> client.V1ResourceRequi
 
 class ClusterInfo:
     parsed_pod_yaml_map: Any
-    image_set: Set[str] = set()
+    image_set: set[str] = set()
     app_name: str
     environment_variables: DeployEnvVars
     spec: Spec
@@ -79,14 +78,12 @@ class ClusterInfo:
     def __init__(self) -> None:
         pass
 
-    def int(self, pod_files: List[str], compose_env_file, deployment_name, spec: Spec):
+    def int(self, pod_files: list[str], compose_env_file, deployment_name, spec: Spec):
         self.parsed_pod_yaml_map = parsed_pod_files_map_from_file_names(pod_files)
         # Find the set of images in the pods
         self.image_set = images_for_deployment(pod_files)
         # Filter out None values from env file
-        env_vars = {
+        env_vars = {k: v for k, v in env_var_map_from_file(compose_env_file).items() if v}
-            k: v for k, v in env_var_map_from_file(compose_env_file).items() if v
-        }
         self.environment_variables = DeployEnvVars(env_vars)
         self.app_name = deployment_name
         self.spec = spec
@@ -123,9 +120,9 @@ class ClusterInfo:
                         service = client.V1Service(
                             metadata=client.V1ObjectMeta(
                                 name=(
-                                    f"{self.app_name}-nodeport-"
+                                    f"{self.app_name}-nodeport-" f"{pod_port}-{protocol.lower()}"
-                                    f"{pod_port}-{protocol.lower()}"
+                                ),
-                                )
+                                labels={"app": self.app_name},
                             ),
                             spec=client.V1ServiceSpec(
                                 type="NodePort",
@@ -143,9 +140,7 @@ class ClusterInfo:
                         nodeports.append(service)
         return nodeports
 
-    def get_ingress(
+    def get_ingress(self, use_tls=False, certificate=None, cluster_issuer="letsencrypt-prod"):
-        self, use_tls=False, certificate=None, cluster_issuer="letsencrypt-prod"
-    ):
         # No ingress for a deployment that has no http-proxy defined, for now
         http_proxy_info_list = self.spec.get_http_proxy()
         ingress = None
@@ -160,9 +155,7 @@ class ClusterInfo:
             tls = (
                 [
                     client.V1IngressTLS(
-                        hosts=certificate["spec"]["dnsNames"]
+                        hosts=certificate["spec"]["dnsNames"] if certificate else [host_name],
-                        if certificate
-                        else [host_name],
                         secret_name=certificate["spec"]["secretName"]
                         if certificate
                         else f"{self.app_name}-tls",
@@ -208,7 +201,9 @@ class ClusterInfo:
 
             ingress = client.V1Ingress(
                 metadata=client.V1ObjectMeta(
-                    name=f"{self.app_name}-ingress", annotations=ingress_annotations
+                    name=f"{self.app_name}-ingress",
+                    labels={"app": self.app_name},
+                    annotations=ingress_annotations,
                 ),
                 spec=spec,
             )
@@ -233,12 +228,14 @@ class ClusterInfo:
             return None
 
         service_ports = [
-            client.V1ServicePort(port=p, target_port=p, name=f"port-{p}")
+            client.V1ServicePort(port=p, target_port=p, name=f"port-{p}") for p in sorted(ports_set)
-            for p in sorted(ports_set)
         ]
 
         service = client.V1Service(
-            metadata=client.V1ObjectMeta(name=f"{self.app_name}-service"),
+            metadata=client.V1ObjectMeta(
+                name=f"{self.app_name}-service",
+                labels={"app": self.app_name},
+            ),
             spec=client.V1ServiceSpec(
                 type="ClusterIP",
                 ports=service_ports,
@@ -283,9 +280,7 @@ class ClusterInfo:
                 volume_name=k8s_volume_name,
             )
             pvc = client.V1PersistentVolumeClaim(
-                metadata=client.V1ObjectMeta(
+                metadata=client.V1ObjectMeta(name=f"{self.app_name}-{volume_name}", labels=labels),
-                    name=f"{self.app_name}-{volume_name}", labels=labels
-                ),
                 spec=spec,
             )
             result.append(pvc)
@@ -302,9 +297,7 @@ class ClusterInfo:
                 continue
 
             if not cfg_map_path.startswith("/") and self.spec.file_path is not None:
-                cfg_map_path = os.path.join(
+                cfg_map_path = os.path.join(os.path.dirname(str(self.spec.file_path)), cfg_map_path)
-                    os.path.dirname(str(self.spec.file_path)), cfg_map_path
-                )
 
             # Read in all the files at a single-level of the directory.
             # This mimics the behavior of
@@ -313,14 +306,12 @@ class ClusterInfo:
             for f in os.listdir(cfg_map_path):
                 full_path = os.path.join(cfg_map_path, f)
                 if os.path.isfile(full_path):
-                    data[f] = base64.b64encode(open(full_path, "rb").read()).decode(
+                    data[f] = base64.b64encode(open(full_path, "rb").read()).decode("ASCII")
-                        "ASCII"
-                    )
 
             spec = client.V1ConfigMap(
                 metadata=client.V1ObjectMeta(
                     name=f"{self.app_name}-{cfg_map_name}",
-                    labels={"configmap-label": cfg_map_name},
+                    labels={"app": self.app_name, "configmap-label": cfg_map_name},
                 ),
                 binary_data=data,
             )
@@ -352,6 +343,10 @@ class ClusterInfo:
                 continue
 
             if not os.path.isabs(volume_path):
+                # For k8s-kind, allow relative paths:
+                # - PV uses /mnt/{volume_name} (path inside kind node)
+                # - extraMounts resolve the relative path to Docker Host
+                if not self.spec.is_kind_deployment():
                     print(
                         f"WARNING: {volume_name}:{volume_path} is not absolute, "
                         "cannot bind volume."
@@ -373,20 +368,53 @@ class ClusterInfo:
             pv = client.V1PersistentVolume(
                 metadata=client.V1ObjectMeta(
                     name=f"{self.app_name}-{volume_name}",
-                    labels={"volume-label": f"{self.app_name}-{volume_name}"},
+                    labels={
+                        "app": self.app_name,
+                        "volume-label": f"{self.app_name}-{volume_name}",
+                    },
                 ),
                 spec=spec,
             )
             result.append(pv)
         return result
 
+    def _any_service_has_host_network(self):
+        for pod_name in self.parsed_pod_yaml_map:
+            pod = self.parsed_pod_yaml_map[pod_name]
+            for svc in pod.get("services", {}).values():
+                if svc.get("network_mode") == "host":
+                    return True
+        return False
+
+    def _resolve_container_resources(
+        self, container_name: str, service_info: dict, global_resources: Resources
+    ) -> Resources:
+        """Resolve resources for a container using layered priority.
+
+        Priority: spec per-container > compose deploy.resources
+        > spec global > DEFAULT
+        """
+        # 1. Check spec.yml for per-container override
+        per_container = self.spec.get_container_resources_for(container_name)
+        if per_container:
+            return per_container
+
+        # 2. Check compose service_info for deploy.resources
+        deploy_block = service_info.get("deploy", {})
+        compose_resources = deploy_block.get("resources", {}) if deploy_block else {}
+        if compose_resources:
+            return Resources(compose_resources)
+
+        # 3. Fall back to spec.yml global (already resolved with DEFAULT fallback)
+        return global_resources
+
     # TODO: put things like image pull policy into an object-scope struct
-    def get_deployment(self, image_pull_policy: Optional[str] = None):
+    def get_deployment(self, image_pull_policy: str | None = None):
         containers = []
         services = {}
-        resources = self.spec.get_container_resources()
+        global_resources = self.spec.get_container_resources()
-        if not resources:
+        if not global_resources:
-            resources = DEFAULT_CONTAINER_RESOURCES
+            global_resources = DEFAULT_CONTAINER_RESOURCES
         for pod_name in self.parsed_pod_yaml_map:
             pod = self.parsed_pod_yaml_map[pod_name]
             services = pod["services"]
@@ -409,9 +437,7 @@ class ClusterInfo:
                             port_str = port_str.split(":")[-1]
                         port = int(port_str)
                         container_ports.append(
-                            client.V1ContainerPort(
+                            client.V1ContainerPort(container_port=port, protocol=protocol)
-                                container_port=port, protocol=protocol
-                            )
                         )
                     if opts.o.debug:
                         print(f"image: {image}")
@@ -426,6 +452,10 @@ class ClusterInfo:
                     if "environment" in service_info
                     else self.environment_variables.map
                 )
+                # Translate docker-compose service names to localhost for sidecars
+                # All services in the same pod share the network namespace
+                sibling_services = [s for s in services.keys() if s != service_name]
+                merged_envs = translate_sidecar_service_names(merged_envs, sibling_services)
                 envs = envs_from_environment_variables_map(merged_envs)
                 if opts.o.debug:
                     print(f"Merged envs: {envs}")
@@ -438,21 +468,30 @@ class ClusterInfo:
                     if self.spec.get_image_registry() is not None
                     else image
                 )
-                volume_mounts = volume_mounts_for_service(
+                volume_mounts = volume_mounts_for_service(self.parsed_pod_yaml_map, service_name)
-                    self.parsed_pod_yaml_map, service_name
-                )
                 # Handle command/entrypoint from compose file
                 # In docker-compose: entrypoint -> k8s command, command -> k8s args
                 container_command = None
                 container_args = None
                 if "entrypoint" in service_info:
                     entrypoint = service_info["entrypoint"]
-                    container_command = (
+                    container_command = entrypoint if isinstance(entrypoint, list) else [entrypoint]
-                        entrypoint if isinstance(entrypoint, list) else [entrypoint]
-                    )
                 if "command" in service_info:
                     cmd = service_info["command"]
                     container_args = cmd if isinstance(cmd, list) else cmd.split()
+                # Add env_from to pull secrets from K8s Secret
+                secret_name = f"{self.app_name}-generated-secrets"
+                env_from = [
+                    client.V1EnvFromSource(
+                        secret_ref=client.V1SecretEnvSource(
+                            name=secret_name,
+                            optional=True,  # Don't fail if no secrets
+                        )
+                    )
+                ]
+                container_resources = self._resolve_container_resources(
+                    container_name, service_info, global_resources
+                )
                 container = client.V1Container(
                     name=container_name,
                     image=image_to_use,
@@ -460,23 +499,25 @@ class ClusterInfo:
                     command=container_command,
                     args=container_args,
                     env=envs,
+                    env_from=env_from,
                     ports=container_ports if container_ports else None,
                     volume_mounts=volume_mounts,
                     security_context=client.V1SecurityContext(
                         privileged=self.spec.get_privileged(),
-                        capabilities=client.V1Capabilities(
+                        capabilities=client.V1Capabilities(add=self.spec.get_capabilities())
-                            add=self.spec.get_capabilities()
-                        )
                         if self.spec.get_capabilities()
                         else None,
                     ),
-                    resources=to_k8s_resource_requirements(resources),
+                    resources=to_k8s_resource_requirements(container_resources),
                 )
                 containers.append(container)
-        volumes = volumes_for_pod_files(
+        volumes = volumes_for_pod_files(self.parsed_pod_yaml_map, self.spec, self.app_name)
-            self.parsed_pod_yaml_map, self.spec, self.app_name
+        registry_config = self.spec.get_image_registry_config()
-        )
+        if registry_config:
-        image_pull_secrets = [client.V1LocalObjectReference(name="laconic-registry")]
+            secret_name = f"{self.app_name}-registry"
+            image_pull_secrets = [client.V1LocalObjectReference(name=secret_name)]
+        else:
+            image_pull_secrets = []
 
         annotations = None
         labels = {"app": self.app_name}
@@ -532,6 +573,7 @@ class ClusterInfo:
                     )
                 )
 
+        use_host_network = self._any_service_has_host_network()
         template = client.V1PodTemplateSpec(
             metadata=client.V1ObjectMeta(annotations=annotations, labels=labels),
             spec=client.V1PodSpec(
@@ -541,6 +583,8 @@ class ClusterInfo:
                 affinity=affinity,
                 tolerations=tolerations,
                 runtime_class_name=self.spec.get_runtime_class(),
+                host_network=use_host_network or None,
+                dns_policy=("ClusterFirstWithHostNet" if use_host_network else None),
             ),
         )
         spec = client.V1DeploymentSpec(

stack_orchestrator/deploy/k8s/deploy_k8s.py

@@ -12,42 +12,41 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with this program.  If not, see <http:#www.gnu.org/licenses/>.
 
+import time
 from datetime import datetime, timezone
-
 from pathlib import Path
+from typing import Any, cast
+
 from kubernetes import client, config
 from kubernetes.client.exceptions import ApiException
-from typing import Any, Dict, List, Optional, cast
 
 from stack_orchestrator import constants
 from stack_orchestrator.deploy.deployer import Deployer, DeployerConfigGenerator
+from stack_orchestrator.deploy.deployment_context import DeploymentContext
+from stack_orchestrator.deploy.k8s.cluster_info import ClusterInfo
 from stack_orchestrator.deploy.k8s.helpers import (
+    connect_registry_to_kind_network,
+    containers_in_pod,
     create_cluster,
     destroy_cluster,
-    load_images_into_kind,
+    ensure_local_registry,
-)
+    generate_high_memlock_spec_json,
-from stack_orchestrator.deploy.k8s.helpers import (
+    generate_kind_config,
     install_ingress_for_kind,
+    is_ingress_running,
+    local_registry_image,
+    log_stream_from_string,
+    pods_in_deployment,
+    push_images_to_local_registry,
     wait_for_ingress_in_kind,
 )
-from stack_orchestrator.deploy.k8s.helpers import (
-    pods_in_deployment,
-    containers_in_pod,
-    log_stream_from_string,
-)
-from stack_orchestrator.deploy.k8s.helpers import (
-    generate_kind_config,
-    generate_high_memlock_spec_json,
-)
-from stack_orchestrator.deploy.k8s.cluster_info import ClusterInfo
 from stack_orchestrator.opts import opts
-from stack_orchestrator.deploy.deployment_context import DeploymentContext
 from stack_orchestrator.util import error_exit
 
 
 class AttrDict(dict):
     def __init__(self, *args, **kwargs):
-        super(AttrDict, self).__init__(*args, **kwargs)
+        super().__init__(*args, **kwargs)
         self.__dict__ = self
 
 
@@ -95,7 +94,7 @@ class K8sDeployer(Deployer):
     core_api: client.CoreV1Api
     apps_api: client.AppsV1Api
     networking_api: client.NetworkingV1Api
-    k8s_namespace: str = "default"
+    k8s_namespace: str
     kind_cluster_name: str
     skip_cluster_management: bool
     cluster_info: ClusterInfo
@@ -112,6 +111,7 @@ class K8sDeployer(Deployer):
     ) -> None:
         self.type = type
         self.skip_cluster_management = False
+        self.k8s_namespace = "default"  # Will be overridden below if context exists
         # TODO: workaround pending refactoring above to cope with being
         # created with a null deployment_context
         if deployment_context is None:
@@ -119,6 +119,8 @@ class K8sDeployer(Deployer):
         self.deployment_dir = deployment_context.deployment_dir
         self.deployment_context = deployment_context
         self.kind_cluster_name = compose_project_name
+        # Use deployment-specific namespace for resource isolation and easy cleanup
+        self.k8s_namespace = f"laconic-{compose_project_name}"
         self.cluster_info = ClusterInfo()
         self.cluster_info.int(
             compose_files,
@@ -139,15 +141,238 @@ class K8sDeployer(Deployer):
         else:
             # Get the config file and pass to load_kube_config()
             config.load_kube_config(
-                config_file=self.deployment_dir.joinpath(
+                config_file=self.deployment_dir.joinpath(constants.kube_config_filename).as_posix()
-                    constants.kube_config_filename
-                ).as_posix()
             )
         self.core_api = client.CoreV1Api()
         self.networking_api = client.NetworkingV1Api()
         self.apps_api = client.AppsV1Api()
         self.custom_obj_api = client.CustomObjectsApi()
 
+    def _ensure_namespace(self):
+        """Create the deployment namespace if it doesn't exist.
+
+        If the namespace exists but is terminating (e.g., from a prior
+        down() call), wait for deletion to complete before creating a
+        fresh namespace.  K8s rejects resource creation in a terminating
+        namespace with 403 Forbidden, so proceeding without waiting
+        causes PVC/ConfigMap creation failures.
+        """
+        if opts.o.dry_run:
+            print(f"Dry run: would create namespace {self.k8s_namespace}")
+            return
+
+        self._wait_for_namespace_deletion()
+
+        try:
+            self.core_api.read_namespace(name=self.k8s_namespace)
+            if opts.o.debug:
+                print(f"Namespace {self.k8s_namespace} already exists")
+        except ApiException as e:
+            if e.status == 404:
+                # Create the namespace
+                ns = client.V1Namespace(
+                    metadata=client.V1ObjectMeta(
+                        name=self.k8s_namespace,
+                        labels={"app": self.cluster_info.app_name},
+                    )
+                )
+                self.core_api.create_namespace(body=ns)
+                if opts.o.debug:
+                    print(f"Created namespace {self.k8s_namespace}")
+            else:
+                raise
+
+    def _wait_for_namespace_deletion(self):
+        """Block until the namespace is fully deleted, if it is terminating.
+
+        Polls every 2s for up to 120s.  If the namespace does not exist
+        (404) or is active, returns immediately.
+        """
+        deadline = time.monotonic() + 120
+        while True:
+            try:
+                ns = self.core_api.read_namespace(name=self.k8s_namespace)
+            except ApiException as e:
+                if e.status == 404:
+                    return  # Gone — ready to create
+                raise
+
+            phase = ns.status.phase if ns.status else None
+            if phase != "Terminating":
+                return  # Active or unknown — proceed
+
+            if time.monotonic() > deadline:
+                error_exit(
+                    f"Namespace {self.k8s_namespace} still terminating "
+                    f"after 120s — cannot proceed"
+                )
+
+            if opts.o.debug:
+                print(f"Namespace {self.k8s_namespace} is terminating, " f"waiting for deletion...")
+            time.sleep(2)
+
+    def _delete_namespace(self):
+        """Delete the deployment namespace and all resources within it."""
+        if opts.o.dry_run:
+            print(f"Dry run: would delete namespace {self.k8s_namespace}")
+            return
+        try:
+            self.core_api.delete_namespace(name=self.k8s_namespace)
+            if opts.o.debug:
+                print(f"Deleted namespace {self.k8s_namespace}")
+        except ApiException as e:
+            if e.status == 404:
+                if opts.o.debug:
+                    print(f"Namespace {self.k8s_namespace} not found")
+            else:
+                raise
+
+    def _ensure_config_map(self, cfg_map):
+        """Create or replace a ConfigMap (idempotent)."""
+        try:
+            resp = self.core_api.create_namespaced_config_map(
+                body=cfg_map, namespace=self.k8s_namespace
+            )
+            if opts.o.debug:
+                print(f"ConfigMap created: {resp}")
+        except ApiException as e:
+            if e.status == 409:
+                existing = self.core_api.read_namespaced_config_map(
+                    name=cfg_map.metadata.name, namespace=self.k8s_namespace
+                )
+                cfg_map.metadata.resource_version = existing.metadata.resource_version
+                resp = self.core_api.replace_namespaced_config_map(
+                    name=cfg_map.metadata.name,
+                    namespace=self.k8s_namespace,
+                    body=cfg_map,
+                )
+                if opts.o.debug:
+                    print(f"ConfigMap updated: {resp}")
+            else:
+                raise
+
+    def _ensure_deployment(self, deployment):
+        """Create or replace a Deployment (idempotent)."""
+        try:
+            resp = cast(
+                client.V1Deployment,
+                self.apps_api.create_namespaced_deployment(
+                    body=deployment, namespace=self.k8s_namespace
+                ),
+            )
+            if opts.o.debug:
+                print("Deployment created:")
+        except ApiException as e:
+            if e.status == 409:
+                existing = self.apps_api.read_namespaced_deployment(
+                    name=deployment.metadata.name,
+                    namespace=self.k8s_namespace,
+                )
+                deployment.metadata.resource_version = existing.metadata.resource_version
+                resp = cast(
+                    client.V1Deployment,
+                    self.apps_api.replace_namespaced_deployment(
+                        name=deployment.metadata.name,
+                        namespace=self.k8s_namespace,
+                        body=deployment,
+                    ),
+                )
+                if opts.o.debug:
+                    print("Deployment updated:")
+            else:
+                raise
+        if opts.o.debug:
+            meta = resp.metadata
+            spec = resp.spec
+            if meta and spec and spec.template.spec:
+                containers = spec.template.spec.containers
+                img = containers[0].image if containers else None
+                print(f"{meta.namespace} {meta.name} {meta.generation} {img}")
+
+    def _ensure_service(self, service, kind: str = "Service"):
+        """Create or replace a Service (idempotent).
+
+        Services have immutable fields (spec.clusterIP) that must be
+        preserved from the existing object on replace.
+        """
+        try:
+            resp = self.core_api.create_namespaced_service(
+                namespace=self.k8s_namespace, body=service
+            )
+            if opts.o.debug:
+                print(f"{kind} created: {resp}")
+        except ApiException as e:
+            if e.status == 409:
+                existing = self.core_api.read_namespaced_service(
+                    name=service.metadata.name, namespace=self.k8s_namespace
+                )
+                service.metadata.resource_version = existing.metadata.resource_version
+                if existing.spec.cluster_ip:
+                    service.spec.cluster_ip = existing.spec.cluster_ip
+                resp = self.core_api.replace_namespaced_service(
+                    name=service.metadata.name,
+                    namespace=self.k8s_namespace,
+                    body=service,
+                )
+                if opts.o.debug:
+                    print(f"{kind} updated: {resp}")
+            else:
+                raise
+
+    def _ensure_ingress(self, ingress):
+        """Create or replace an Ingress (idempotent)."""
+        try:
+            resp = self.networking_api.create_namespaced_ingress(
+                namespace=self.k8s_namespace, body=ingress
+            )
+            if opts.o.debug:
+                print(f"Ingress created: {resp}")
+        except ApiException as e:
+            if e.status == 409:
+                existing = self.networking_api.read_namespaced_ingress(
+                    name=ingress.metadata.name, namespace=self.k8s_namespace
+                )
+                ingress.metadata.resource_version = existing.metadata.resource_version
+                resp = self.networking_api.replace_namespaced_ingress(
+                    name=ingress.metadata.name,
+                    namespace=self.k8s_namespace,
+                    body=ingress,
+                )
+                if opts.o.debug:
+                    print(f"Ingress updated: {resp}")
+            else:
+                raise
+
+    def _clear_released_pv_claim_refs(self):
+        """Patch any Released PVs for this deployment to clear stale claimRefs.
+
+        After a namespace is deleted, PVCs are cascade-deleted but
+        cluster-scoped PVs survive in Released state with claimRefs
+        pointing to the now-deleted PVC UIDs.  New PVCs cannot bind
+        to these PVs until the stale claimRef is removed.
+        """
+        try:
+            pvs = self.core_api.list_persistent_volume(
+                label_selector=f"app={self.cluster_info.app_name}"
+            )
+        except ApiException:
+            return
+
+        for pv in pvs.items:
+            phase = pv.status.phase if pv.status else None
+            if phase == "Released" and pv.spec and pv.spec.claim_ref:
+                pv_name = pv.metadata.name
+                if opts.o.debug:
+                    old_ref = pv.spec.claim_ref
+                    print(
+                        f"Clearing stale claimRef on PV {pv_name} "
+                        f"(was {old_ref.namespace}/{old_ref.name})"
+                    )
+                self.core_api.patch_persistent_volume(
+                    name=pv_name,
+                    body={"spec": {"claimRef": None}},
+                )
+
     def _create_volume_data(self):
         # Create the host-path-mounted PVs for this deployment
         pvs = self.cluster_info.get_pvs()
@@ -156,24 +381,29 @@ class K8sDeployer(Deployer):
                 print(f"Sending this pv: {pv}")
             if not opts.o.dry_run:
                 try:
-                    pv_resp = self.core_api.read_persistent_volume(
+                    pv_resp = self.core_api.read_persistent_volume(name=pv.metadata.name)
-                        name=pv.metadata.name
-                    )
                     if pv_resp:
                         if opts.o.debug:
                             print("PVs already present:")
                             print(f"{pv_resp}")
                         continue
-                except:  # noqa: E722
+                except ApiException as e:
-                    pass
+                    if e.status != 404:
+                        raise
 
                 pv_resp = self.core_api.create_persistent_volume(body=pv)
                 if opts.o.debug:
                     print("PVs created:")
                     print(f"{pv_resp}")
 
+        # After PV creation/verification, clear stale claimRefs on any
+        # Released PVs so that new PVCs can bind to them.
+        if not opts.o.dry_run:
+            self._clear_released_pv_claim_refs()
+
         # Figure out the PVCs for this deployment
         pvcs = self.cluster_info.get_pvcs()
+        pvc_errors = []
         for pvc in pvcs:
             if opts.o.debug:
                 print(f"Sending this pvc: {pvc}")
@@ -188,15 +418,27 @@ class K8sDeployer(Deployer):
                             print("PVCs already present:")
                             print(f"{pvc_resp}")
                         continue
-                except:  # noqa: E722
+                except ApiException as e:
-                    pass
+                    if e.status != 404:
+                        raise
 
+                try:
                     pvc_resp = self.core_api.create_namespaced_persistent_volume_claim(
                         body=pvc, namespace=self.k8s_namespace
                     )
                     if opts.o.debug:
                         print("PVCs created:")
                         print(f"{pvc_resp}")
+                except ApiException as e:
+                    pvc_name = pvc.metadata.name
+                    print(f"Error creating PVC {pvc_name}: {e.reason}")
+                    pvc_errors.append(pvc_name)
+
+        if pvc_errors:
+            error_exit(
+                f"Failed to create PVCs: {', '.join(pvc_errors)}. "
+                f"Check namespace state and PV availability."
+            )
 
         # Figure out the ConfigMaps for this deployment
         config_maps = self.cluster_info.get_configmaps()
@@ -204,50 +446,35 @@ class K8sDeployer(Deployer):
             if opts.o.debug:
                 print(f"Sending this ConfigMap: {cfg_map}")
             if not opts.o.dry_run:
-                cfg_rsp = self.core_api.create_namespaced_config_map(
+                self._ensure_config_map(cfg_map)
-                    body=cfg_map, namespace=self.k8s_namespace
-                )
-                if opts.o.debug:
-                    print("ConfigMap created:")
-                    print(f"{cfg_rsp}")
 
     def _create_deployment(self):
-        # Process compose files into a Deployment
+        """Create the k8s Deployment resource (which starts pods)."""
         deployment = self.cluster_info.get_deployment(
             image_pull_policy=None if self.is_kind() else "Always"
         )
-        # Create the k8s objects
+        if self.is_kind():
+            self._rewrite_local_images(deployment)
         if opts.o.debug:
             print(f"Sending this deployment: {deployment}")
         if not opts.o.dry_run:
-            deployment_resp = cast(
+            self._ensure_deployment(deployment)
-                client.V1Deployment,
-                self.apps_api.create_namespaced_deployment(
-                    body=deployment, namespace=self.k8s_namespace
-                ),
-            )
-            if opts.o.debug:
-                print("Deployment created:")
-                meta = deployment_resp.metadata
-                spec = deployment_resp.spec
-                if meta and spec and spec.template.spec:
-                    ns = meta.namespace
-                    name = meta.name
-                    gen = meta.generation
-                    containers = spec.template.spec.containers
-                    img = containers[0].image if containers else None
-                    print(f"{ns} {name} {gen} {img}")
 
-        service = self.cluster_info.get_service()
+    def _rewrite_local_images(self, deployment):
-        if opts.o.debug:
+        """Rewrite local container images to use the local registry.
-            print(f"Sending this service: {service}")
+
-        if service and not opts.o.dry_run:
+        Images built locally (listed in stack.yml containers) are pushed to
-            service_resp = self.core_api.create_namespaced_service(
+        localhost:5001 by push_images_to_local_registry(). The k8s pod spec
-                namespace=self.k8s_namespace, body=service
+        must reference them at that address so containerd pulls from the
-            )
+        local registry instead of trying to find them in its local store.
-            if opts.o.debug:
+        """
-                print("Service created:")
+        local_containers = self.deployment_context.stack.obj.get("containers", [])
-                print(f"{service_resp}")
+        if not local_containers:
+            return
+        containers = deployment.spec.template.spec.containers or []
+        for container in containers:
+            if any(c in container.image for c in local_containers):
+                container.image = local_registry_image(container.image)
 
     def _find_certificate_for_host_name(self, host_name):
         all_certificates = self.custom_obj_api.list_namespaced_custom_object(
@@ -279,187 +506,134 @@ class K8sDeployer(Deployer):
                     if before < now < after:
                         # Check the status is Ready
                         for condition in status.get("conditions", []):
-                            if "True" == condition.get(
+                            if "True" == condition.get("status") and "Ready" == condition.get(
-                                "status"
+                                "type"
-                            ) and "Ready" == condition.get("type"):
+                            ):
                                 return cert
         return None
 
     def up(self, detach, skip_cluster_management, services):
+        self._setup_cluster_and_namespace(skip_cluster_management)
+        self._create_infrastructure()
+        self._create_deployment()
+
+    def _setup_cluster_and_namespace(self, skip_cluster_management):
+        """Create kind cluster (if needed) and namespace.
+
+        Shared by up() and prepare().
+        """
         self.skip_cluster_management = skip_cluster_management
         if not opts.o.dry_run:
             if self.is_kind() and not self.skip_cluster_management:
-                # Create the kind cluster
+                ensure_local_registry()
-                create_cluster(
+                kind_config = str(self.deployment_dir.joinpath(constants.kind_config_filename))
-                    self.kind_cluster_name,
+                actual_cluster = create_cluster(self.kind_cluster_name, kind_config)
-                    str(self.deployment_dir.joinpath(constants.kind_config_filename)),
+                if actual_cluster != self.kind_cluster_name:
-                )
+                    self.kind_cluster_name = actual_cluster
-                # Ensure the referenced containers are copied into kind
+                connect_registry_to_kind_network(self.kind_cluster_name)
-                load_images_into_kind(
+                local_containers = self.deployment_context.stack.obj.get("containers", [])
-                    self.kind_cluster_name, self.cluster_info.image_set
+                if local_containers:
-                )
+                    local_images = {
+                        img
+                        for img in self.cluster_info.image_set
+                        if any(c in img for c in local_containers)
+                    }
+                    if local_images:
+                        push_images_to_local_registry(local_images)
             self.connect_api()
+            self._ensure_namespace()
             if self.is_kind() and not self.skip_cluster_management:
-                # Configure ingress controller (not installed by default in kind)
+                if not is_ingress_running():
-                install_ingress_for_kind()
+                    install_ingress_for_kind(self.cluster_info.spec.get_acme_email())
-                # Wait for ingress to start
-                # (deployment provisioning will fail unless this is done)
                     wait_for_ingress_in_kind()
-                # Create RuntimeClass if unlimited_memlock is enabled
                 if self.cluster_info.spec.get_unlimited_memlock():
                     _create_runtime_class(
                         constants.high_memlock_runtime,
                         constants.high_memlock_runtime,
                     )
-
         else:
             print("Dry run mode enabled, skipping k8s API connect")
 
+    def _create_infrastructure(self):
+        """Create PVs, PVCs, ConfigMaps, Services, Ingresses, NodePorts.
+
+        Everything except the Deployment resource (which starts pods).
+        Shared by up() and prepare().
+        """
+        from stack_orchestrator.deploy.deployment_create import create_registry_secret
+
+        create_registry_secret(self.cluster_info.spec, self.cluster_info.app_name)
+
         self._create_volume_data()
-        self._create_deployment()
+
+        # Create the ClusterIP service (paired with the deployment)
+        service = self.cluster_info.get_service()
+        if service and not opts.o.dry_run:
+            if opts.o.debug:
+                print(f"Sending this service: {service}")
+            self._ensure_service(service)
 
         http_proxy_info = self.cluster_info.spec.get_http_proxy()
-        # Note: we don't support tls for kind (enabling tls causes errors)
         use_tls = http_proxy_info and not self.is_kind()
         certificate = (
             self._find_certificate_for_host_name(http_proxy_info[0]["host-name"])
             if use_tls
             else None
         )
-        if opts.o.debug:
+        if opts.o.debug and certificate:
-            if certificate:
             print(f"Using existing certificate: {certificate}")
 
-        ingress = self.cluster_info.get_ingress(
+        ingress = self.cluster_info.get_ingress(use_tls=use_tls, certificate=certificate)
-            use_tls=use_tls, certificate=certificate
-        )
         if ingress:
             if opts.o.debug:
                 print(f"Sending this ingress: {ingress}")
             if not opts.o.dry_run:
-                ingress_resp = self.networking_api.create_namespaced_ingress(
+                self._ensure_ingress(ingress)
-                    namespace=self.k8s_namespace, body=ingress
+        elif opts.o.debug:
-                )
-                if opts.o.debug:
-                    print("Ingress created:")
-                    print(f"{ingress_resp}")
-        else:
-            if opts.o.debug:
             print("No ingress configured")
 
-        nodeports: List[client.V1Service] = self.cluster_info.get_nodeports()
+        nodeports: list[client.V1Service] = self.cluster_info.get_nodeports()
         for nodeport in nodeports:
             if opts.o.debug:
                 print(f"Sending this nodeport: {nodeport}")
             if not opts.o.dry_run:
-                nodeport_resp = self.core_api.create_namespaced_service(
+                self._ensure_service(nodeport, kind="NodePort")
-                    namespace=self.k8s_namespace, body=nodeport
-                )
-                if opts.o.debug:
-                    print("NodePort created:")
-                    print(f"{nodeport_resp}")
 
-    def down(self, timeout, volumes, skip_cluster_management):  # noqa: C901
+    def prepare(self, skip_cluster_management):
+        """Create cluster infrastructure without starting pods.
+
+        Sets up kind cluster, namespace, PVs, PVCs, ConfigMaps, Services,
+        Ingresses, and NodePorts — everything that up() does EXCEPT creating
+        the Deployment resource.
+        """
+        self._setup_cluster_and_namespace(skip_cluster_management)
+        self._create_infrastructure()
+        print("Cluster infrastructure prepared (no pods started).")
+
+    def down(self, timeout, volumes, skip_cluster_management):
         self.skip_cluster_management = skip_cluster_management
         self.connect_api()
-        # Delete the k8s objects
 
+        # PersistentVolumes are cluster-scoped (not namespaced), so delete by label
         if volumes:
-            # Create the host-path-mounted PVs for this deployment
-            pvs = self.cluster_info.get_pvs()
-            for pv in pvs:
-                if opts.o.debug:
-                    print(f"Deleting this pv: {pv}")
             try:
-                    pv_resp = self.core_api.delete_persistent_volume(
+                pvs = self.core_api.list_persistent_volume(
-                        name=pv.metadata.name
+                    label_selector=f"app={self.cluster_info.app_name}"
                 )
+                for pv in pvs.items:
                     if opts.o.debug:
-                        print("PV deleted:")
+                        print(f"Deleting PV: {pv.metadata.name}")
-                        print(f"{pv_resp}")
+                    try:
+                        self.core_api.delete_persistent_volume(name=pv.metadata.name)
                     except ApiException as e:
                         _check_delete_exception(e)
+            except ApiException as e:
+                if opts.o.debug:
+                    print(f"Error listing PVs: {e}")
 
-            # Figure out the PVCs for this deployment
+        # Delete the deployment namespace - this cascades to all namespaced resources
-            pvcs = self.cluster_info.get_pvcs()
+        # (PVCs, ConfigMaps, Deployments, Services, Ingresses, etc.)
-            for pvc in pvcs:
+        self._delete_namespace()
-                if opts.o.debug:
-                    print(f"Deleting this pvc: {pvc}")
-                try:
-                    pvc_resp = self.core_api.delete_namespaced_persistent_volume_claim(
-                        name=pvc.metadata.name, namespace=self.k8s_namespace
-                    )
-                    if opts.o.debug:
-                        print("PVCs deleted:")
-                        print(f"{pvc_resp}")
-                except ApiException as e:
-                    _check_delete_exception(e)
-
-        # Figure out the ConfigMaps for this deployment
-        cfg_maps = self.cluster_info.get_configmaps()
-        for cfg_map in cfg_maps:
-            if opts.o.debug:
-                print(f"Deleting this ConfigMap: {cfg_map}")
-            try:
-                cfg_map_resp = self.core_api.delete_namespaced_config_map(
-                    name=cfg_map.metadata.name, namespace=self.k8s_namespace
-                )
-                if opts.o.debug:
-                    print("ConfigMap deleted:")
-                    print(f"{cfg_map_resp}")
-            except ApiException as e:
-                _check_delete_exception(e)
-
-        deployment = self.cluster_info.get_deployment()
-        if opts.o.debug:
-            print(f"Deleting this deployment: {deployment}")
-        if deployment and deployment.metadata and deployment.metadata.name:
-            try:
-                self.apps_api.delete_namespaced_deployment(
-                    name=deployment.metadata.name, namespace=self.k8s_namespace
-                )
-            except ApiException as e:
-                _check_delete_exception(e)
-
-        service = self.cluster_info.get_service()
-        if opts.o.debug:
-            print(f"Deleting service: {service}")
-        if service and service.metadata and service.metadata.name:
-            try:
-                self.core_api.delete_namespaced_service(
-                    namespace=self.k8s_namespace, name=service.metadata.name
-                )
-            except ApiException as e:
-                _check_delete_exception(e)
-
-        ingress = self.cluster_info.get_ingress(use_tls=not self.is_kind())
-        if ingress and ingress.metadata and ingress.metadata.name:
-            if opts.o.debug:
-                print(f"Deleting this ingress: {ingress}")
-            try:
-                self.networking_api.delete_namespaced_ingress(
-                    name=ingress.metadata.name, namespace=self.k8s_namespace
-                )
-            except ApiException as e:
-                _check_delete_exception(e)
-        else:
-            if opts.o.debug:
-                print("No ingress to delete")
-
-        nodeports: List[client.V1Service] = self.cluster_info.get_nodeports()
-        for nodeport in nodeports:
-            if opts.o.debug:
-                print(f"Deleting this nodeport: {nodeport}")
-            if nodeport.metadata and nodeport.metadata.name:
-                try:
-                    self.core_api.delete_namespaced_service(
-                        namespace=self.k8s_namespace, name=nodeport.metadata.name
-                    )
-                except ApiException as e:
-                    _check_delete_exception(e)
-        else:
-            if opts.o.debug:
-                print("No nodeport to delete")
 
         if self.is_kind() and not self.skip_cluster_management:
             # Destroy the kind cluster
@@ -498,7 +672,7 @@ class K8sDeployer(Deployer):
                 return
 
             cert = cast(
-                Dict[str, Any],
+                dict[str, Any],
                 self.custom_obj_api.get_namespaced_custom_object(
                     group="cert-manager.io",
                     version="v1",
@@ -514,7 +688,7 @@ class K8sDeployer(Deployer):
                 if lb_ingress:
                     ip = lb_ingress[0].ip or "?"
             cert_status = cert.get("status", {})
-            tls = "notBefore: %s; notAfter: %s; names: %s" % (
+            tls = "notBefore: {}; notAfter: {}; names: {}".format(
                 cert_status.get("notBefore", "?"),
                 cert_status.get("notAfter", "?"),
                 ingress.spec.tls[0].hosts,
@@ -555,9 +729,7 @@ class K8sDeployer(Deployer):
                     if c.ports:
                         for prt in c.ports:
                             ports[str(prt.container_port)] = [
-                                AttrDict(
+                                AttrDict({"HostIp": pod_ip, "HostPort": prt.container_port})
-                                    {"HostIp": pod_ip, "HostPort": prt.container_port}
-                                )
                             ]
 
                 ret.append(
@@ -597,7 +769,7 @@ class K8sDeployer(Deployer):
                 log_data = ""
                 for container in containers:
                     container_log = self.core_api.read_namespaced_pod_log(
-                        k8s_pod_name, namespace="default", container=container
+                        k8s_pod_name, namespace=self.k8s_namespace, container=container
                     )
                     container_log_lines = container_log.splitlines()
                     for line in container_log_lines:
@@ -608,7 +780,7 @@ class K8sDeployer(Deployer):
                 log_data = "******* No logs available ********\n"
         return log_stream_from_string(log_data)
 
-    def update(self):
+    def update_envs(self):
         self.connect_api()
         ref_deployment = self.cluster_info.get_deployment()
         if not ref_deployment or not ref_deployment.metadata:
@@ -619,9 +791,7 @@ class K8sDeployer(Deployer):
 
         deployment = cast(
             client.V1Deployment,
-            self.apps_api.read_namespaced_deployment(
+            self.apps_api.read_namespaced_deployment(name=ref_name, namespace=self.k8s_namespace),
-                name=ref_name, namespace=self.k8s_namespace
-            ),
         )
         if not deployment.spec or not deployment.spec.template:
             return
@@ -660,14 +830,14 @@ class K8sDeployer(Deployer):
         user=None,
         volumes=None,
         entrypoint=None,
-        env={},
+        env=None,
-        ports=[],
+        ports=None,
         detach=False,
     ):
         # We need to figure out how to do this -- check why we're being called first
         pass
 
-    def run_job(self, job_name: str, helm_release: Optional[str] = None):
+    def run_job(self, job_name: str, helm_release: str | None = None):
         if not opts.o.dry_run:
             from stack_orchestrator.deploy.k8s.helm.job_runner import run_helm_job
 
@@ -709,13 +879,9 @@ class K8sDeployerConfigGenerator(DeployerConfigGenerator):
             # Must be done before generate_kind_config() which references it.
             if self.deployment_context.spec.get_unlimited_memlock():
                 spec_content = generate_high_memlock_spec_json()
-                spec_file = deployment_dir.joinpath(
+                spec_file = deployment_dir.joinpath(constants.high_memlock_spec_filename)
-                    constants.high_memlock_spec_filename
-                )
                 if opts.o.debug:
-                    print(
+                    print(f"Creating high-memlock spec for unlimited memlock: {spec_file}")
-                        f"Creating high-memlock spec for unlimited memlock: {spec_file}"
-                    )
                 with open(spec_file, "w") as output_file:
                     output_file.write(spec_content)
 

stack_orchestrator/deploy/k8s/helm/chart_generator.py

@@ -16,21 +16,21 @@
 from pathlib import Path
 
 from stack_orchestrator import constants
-from stack_orchestrator.opts import opts
-from stack_orchestrator.util import (
-    get_parsed_stack_config,
-    get_pod_list,
-    get_pod_file_path,
-    get_job_list,
-    get_job_file_path,
-    error_exit,
-)
 from stack_orchestrator.deploy.k8s.helm.kompose_wrapper import (
     check_kompose_available,
-    get_kompose_version,
     convert_to_helm_chart,
+    get_kompose_version,
+)
+from stack_orchestrator.opts import opts
+from stack_orchestrator.util import (
+    error_exit,
+    get_job_file_path,
+    get_job_list,
+    get_parsed_stack_config,
+    get_pod_file_path,
+    get_pod_list,
+    get_yaml,
 )
-from stack_orchestrator.util import get_yaml
 
 
 def _wrap_job_templates_with_conditionals(chart_dir: Path, jobs: list) -> None:
@@ -88,7 +88,7 @@ def _post_process_chart(chart_dir: Path, chart_name: str, jobs: list) -> None:
     # Fix Chart.yaml
     chart_yaml_path = chart_dir / "Chart.yaml"
     if chart_yaml_path.exists():
-        chart_yaml = yaml.load(open(chart_yaml_path, "r"))
+        chart_yaml = yaml.load(open(chart_yaml_path))
 
         # Fix name
         chart_yaml["name"] = chart_name
@@ -108,9 +108,7 @@ def _post_process_chart(chart_dir: Path, chart_name: str, jobs: list) -> None:
         _wrap_job_templates_with_conditionals(chart_dir, jobs)
 
 
-def generate_helm_chart(
+def generate_helm_chart(stack_path: str, spec_file: str, deployment_dir_path: Path) -> None:
-    stack_path: str, spec_file: str, deployment_dir_path: Path
-) -> None:
     """
     Generate a self-sufficient Helm chart from stack compose files using Kompose.
 
@@ -152,7 +150,7 @@ def generate_helm_chart(
         error_exit(f"Deployment file not found: {deployment_file}")
 
     yaml = get_yaml()
-    deployment_config = yaml.load(open(deployment_file, "r"))
+    deployment_config = yaml.load(open(deployment_file))
     cluster_id = deployment_config.get(constants.cluster_id_key)
     if not cluster_id:
         error_exit(f"cluster-id not found in {deployment_file}")
@@ -219,10 +217,7 @@ def generate_helm_chart(
     # 5. Create chart directory and invoke Kompose
     chart_dir = deployment_dir_path / "chart"
 
-    print(
+    print(f"Converting {len(compose_files)} compose file(s) to Helm chart " "using Kompose...")
-        f"Converting {len(compose_files)} compose file(s) to Helm chart "
-        "using Kompose..."
-    )
 
     try:
         output = convert_to_helm_chart(
@@ -304,9 +299,7 @@ Edit the generated template files in `templates/` to customize:
 
     # Count generated files
     template_files = (
-        list((chart_dir / "templates").glob("*.yaml"))
+        list((chart_dir / "templates").glob("*.yaml")) if (chart_dir / "templates").exists() else []
-        if (chart_dir / "templates").exists()
-        else []
     )
     print(f"  Files:    {len(template_files)} template(s) generated")
 

stack_orchestrator/deploy/k8s/helm/job_runner.py

@@ -13,12 +13,12 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with this program.  If not, see <http:#www.gnu.org/licenses/>.
 
+import json
+import os
 import subprocess
 import tempfile
-import os
-import json
 from pathlib import Path
-from typing import Optional
+
 from stack_orchestrator.util import get_yaml
 
 
@@ -40,18 +40,19 @@ def get_release_name_from_chart(chart_dir: Path) -> str:
         raise Exception(f"Chart.yaml not found: {chart_yaml_path}")
 
     yaml = get_yaml()
-    chart_yaml = yaml.load(open(chart_yaml_path, "r"))
+    chart_yaml = yaml.load(open(chart_yaml_path))
 
     if "name" not in chart_yaml:
         raise Exception(f"Chart name not found in {chart_yaml_path}")
 
-    return chart_yaml["name"]
+    name: str = chart_yaml["name"]
+    return name
 
 
 def run_helm_job(
     chart_dir: Path,
     job_name: str,
-    release: Optional[str] = None,
+    release: str | None = None,
     namespace: str = "default",
     timeout: int = 600,
     verbose: bool = False,
@@ -94,9 +95,7 @@ def run_helm_job(
         print(f"Running job '{job_name}' from helm chart: {chart_dir}")
 
     # Use helm template to render the job manifest
-    with tempfile.NamedTemporaryFile(
+    with tempfile.NamedTemporaryFile(mode="w", suffix=".yaml", delete=False) as tmp_file:
-        mode="w", suffix=".yaml", delete=False
-    ) as tmp_file:
         try:
             # Render job template with job enabled
             # Use --set-json to properly handle job names with dashes
@@ -116,9 +115,7 @@ def run_helm_job(
             if verbose:
                 print(f"Running: {' '.join(helm_cmd)}")
 
-            result = subprocess.run(
+            result = subprocess.run(helm_cmd, check=True, capture_output=True, text=True)
-                helm_cmd, check=True, capture_output=True, text=True
-            )
             tmp_file.write(result.stdout)
             tmp_file.flush()
 
@@ -139,9 +136,7 @@ def run_helm_job(
                 "-n",
                 namespace,
             ]
-            subprocess.run(
+            subprocess.run(kubectl_apply_cmd, check=True, capture_output=True, text=True)
-                kubectl_apply_cmd, check=True, capture_output=True, text=True
-            )
 
             if verbose:
                 print(f"Job {actual_job_name} created, waiting for completion...")
@@ -164,7 +159,7 @@ def run_helm_job(
 
         except subprocess.CalledProcessError as e:
             error_msg = e.stderr if e.stderr else str(e)
-            raise Exception(f"Job failed: {error_msg}")
+            raise Exception(f"Job failed: {error_msg}") from e
         finally:
             # Clean up temp file
             if os.path.exists(tmp_file.name):

stack_orchestrator/deploy/k8s/helm/kompose_wrapper.py

@@ -13,10 +13,9 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with this program.  If not, see <http:#www.gnu.org/licenses/>.
 
-import subprocess
 import shutil
+import subprocess
 from pathlib import Path
-from typing import List, Optional
 
 
 def check_kompose_available() -> bool:
@@ -37,9 +36,7 @@ def get_kompose_version() -> str:
     if not check_kompose_available():
         raise Exception("kompose not found in PATH")
 
-    result = subprocess.run(
+    result = subprocess.run(["kompose", "version"], capture_output=True, text=True, timeout=10)
-        ["kompose", "version"], capture_output=True, text=True, timeout=10
-    )
 
     if result.returncode != 0:
         raise Exception(f"Failed to get kompose version: {result.stderr}")
@@ -53,7 +50,7 @@ def get_kompose_version() -> str:
 
 
 def convert_to_helm_chart(
-    compose_files: List[Path], output_dir: Path, chart_name: Optional[str] = None
+    compose_files: list[Path], output_dir: Path, chart_name: str | None = None
 ) -> str:
     """
     Invoke kompose to convert Docker Compose files to a Helm chart.
@@ -71,8 +68,7 @@ def convert_to_helm_chart(
     """
     if not check_kompose_available():
         raise Exception(
-            "kompose not found in PATH. "
+            "kompose not found in PATH. " "Install from: https://kompose.io/installation/"
-            "Install from: https://kompose.io/installation/"
         )
 
     # Ensure output directory exists
@@ -95,9 +91,7 @@ def convert_to_helm_chart(
 
     if result.returncode != 0:
         raise Exception(
-            f"Kompose conversion failed:\n"
+            f"Kompose conversion failed:\n" f"Command: {' '.join(cmd)}\n" f"Error: {result.stderr}"
-            f"Command: {' '.join(cmd)}\n"
-            f"Error: {result.stderr}"
         )
 
     return result.stdout

stack_orchestrator/deploy/k8s/helpers.py

@@ -13,18 +13,64 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with this program.  If not, see <http:#www.gnu.org/licenses/>.
 
-from kubernetes import client, utils, watch
 import os
-from pathlib import Path
-import subprocess
 import re
-from typing import Set, Mapping, List, Optional, cast
+import subprocess
+from collections.abc import Mapping
+from pathlib import Path
+from typing import cast
 
-from stack_orchestrator.util import get_k8s_dir, error_exit
+import yaml
-from stack_orchestrator.opts import opts
+from kubernetes import client, utils, watch
+from kubernetes.client.exceptions import ApiException
+
+from stack_orchestrator import constants
 from stack_orchestrator.deploy.deploy_util import parsed_pod_files_map_from_file_names
 from stack_orchestrator.deploy.deployer import DeployerException
-from stack_orchestrator import constants
+from stack_orchestrator.opts import opts
+from stack_orchestrator.util import error_exit, get_k8s_dir
+
+
+def is_host_path_mount(volume_name: str) -> bool:
+    """Check if a volume name is a host path mount (starts with /, ., or ~)."""
+    return volume_name.startswith(("/", ".", "~"))
+
+
+def sanitize_host_path_to_volume_name(host_path: str) -> str:
+    """Convert a host path to a valid k8s volume name.
+
+    K8s volume names must be lowercase, alphanumeric, with - allowed.
+    E.g., '../config/test/script.sh' -> 'host-path-config-test-script-sh'
+    """
+    # Remove leading ./ or ../
+    clean_path = re.sub(r"^\.+/", "", host_path)
+    # Replace path separators and dots with hyphens
+    name = re.sub(r"[/.]", "-", clean_path)
+    # Remove any non-alphanumeric characters except hyphens
+    name = re.sub(r"[^a-zA-Z0-9-]", "", name)
+    # Convert to lowercase
+    name = name.lower()
+    # Remove leading/trailing hyphens and collapse multiple hyphens
+    name = re.sub(r"-+", "-", name).strip("-")
+    # Prefix with 'host-path-' to distinguish from named volumes
+    return f"host-path-{name}"
+
+
+def resolve_host_path_for_kind(host_path: str, deployment_dir: Path) -> Path:
+    """Resolve a host path mount (relative to compose file) to absolute path.
+
+    Compose files are in deployment_dir/compose/, so '../config/foo'
+    resolves to deployment_dir/config/foo.
+    """
+    # The path is relative to the compose directory
+    compose_dir = deployment_dir.joinpath("compose")
+    resolved = compose_dir.joinpath(host_path).resolve()
+    return resolved
+
+
+def get_kind_host_path_mount_path(sanitized_name: str) -> str:
+    """Get the path inside the kind node where a host path mount will be available."""
+    return f"/mnt/{sanitized_name}"
 
 
 def get_kind_cluster():
@@ -33,9 +79,7 @@ def get_kind_cluster():
     Uses `kind get clusters` to find existing clusters.
     Returns the cluster name or None if no cluster exists.
     """
-    result = subprocess.run(
+    result = subprocess.run("kind get clusters", shell=True, capture_output=True, text=True)
-        "kind get clusters", shell=True, capture_output=True, text=True
-    )
     if result.returncode != 0:
         return None
 
@@ -54,19 +98,246 @@ def _run_command(command: str):
     return result
 
 
+def _get_etcd_host_path_from_kind_config(config_file: str) -> str | None:
+    """Extract etcd host path from kind config extraMounts."""
+    import yaml
+
+    try:
+        with open(config_file) as f:
+            config = yaml.safe_load(f)
+    except Exception:
+        return None
+
+    nodes = config.get("nodes", [])
+    for node in nodes:
+        extra_mounts = node.get("extraMounts", [])
+        for mount in extra_mounts:
+            if mount.get("containerPath") == "/var/lib/etcd":
+                host_path: str | None = mount.get("hostPath")
+                return host_path
+    return None
+
+
+def _clean_etcd_keeping_certs(etcd_path: str) -> bool:
+    """Clean persisted etcd, keeping only TLS certificates.
+
+    When etcd is persisted and a cluster is recreated, kind tries to install
+    resources fresh but they already exist. Instead of trying to delete
+    specific stale resources (blacklist), we keep only the valuable data
+    (caddy TLS certs) and delete everything else (whitelist approach).
+
+    The etcd image is distroless (no shell), so we extract the statically-linked
+    etcdctl binary and run it from alpine which has shell support.
+
+    Returns True if cleanup succeeded, False if no action needed or failed.
+    """
+    db_path = Path(etcd_path) / "member" / "snap" / "db"
+    # Check existence using docker since etcd dir is root-owned
+    check_cmd = (
+        f"docker run --rm -v {etcd_path}:/etcd:ro alpine:3.19 " "test -f /etcd/member/snap/db"
+    )
+    check_result = subprocess.run(check_cmd, shell=True, capture_output=True)
+    if check_result.returncode != 0:
+        if opts.o.debug:
+            print(f"No etcd snapshot at {db_path}, skipping cleanup")
+        return False
+
+    if opts.o.debug:
+        print(f"Cleaning persisted etcd at {etcd_path}, keeping only TLS certs")
+
+    etcd_image = "gcr.io/etcd-development/etcd:v3.5.9"
+    temp_dir = "/tmp/laconic-etcd-cleanup"
+
+    # Whitelist: prefixes to KEEP - everything else gets deleted.
+    # Must include core cluster resources (kubernetes service, kube-system
+    # secrets) or kindnet panics on restart — KUBERNETES_SERVICE_HOST is
+    # injected from the kubernetes ClusterIP service in default namespace.
+    keep_prefixes = [
+        "/registry/secrets/caddy-system",
+        "/registry/services/specs/default/kubernetes",
+        "/registry/services/endpoints/default/kubernetes",
+    ]
+    keep_prefixes_str = " ".join(keep_prefixes)
+
+    # The etcd image is distroless (no shell). We extract the statically-linked
+    # etcdctl binary and run it from alpine which has shell + jq support.
+    cleanup_script = f"""
+        set -e
+        ALPINE_IMAGE="alpine:3.19"
+
+        # Cleanup previous runs
+        docker rm -f laconic-etcd-cleanup 2>/dev/null || true
+        docker rm -f etcd-extract 2>/dev/null || true
+        docker run --rm -v /tmp:/tmp $ALPINE_IMAGE rm -rf {temp_dir}
+
+        # Create temp dir
+        docker run --rm -v /tmp:/tmp $ALPINE_IMAGE mkdir -p {temp_dir}
+
+        # Extract etcdctl binary (it's statically linked)
+        docker create --name etcd-extract {etcd_image}
+        docker cp etcd-extract:/usr/local/bin/etcdctl /tmp/etcdctl-bin
+        docker rm etcd-extract
+        docker run --rm -v /tmp/etcdctl-bin:/src:ro -v {temp_dir}:/dst $ALPINE_IMAGE \
+            sh -c "cp /src /dst/etcdctl && chmod +x /dst/etcdctl"
+
+        # Copy db to temp location
+        docker run --rm \
+            -v {etcd_path}:/etcd:ro \
+            -v {temp_dir}:/tmp-work \
+            $ALPINE_IMAGE cp /etcd/member/snap/db /tmp-work/etcd-snapshot.db
+
+        # Restore snapshot
+        docker run --rm -v {temp_dir}:/work {etcd_image} \
+            etcdutl snapshot restore /work/etcd-snapshot.db \
+                --data-dir=/work/etcd-data --skip-hash-check 2>/dev/null
+
+        # Start temp etcd (runs the etcd binary, no shell needed)
+        docker run -d --name laconic-etcd-cleanup \
+            -v {temp_dir}/etcd-data:/etcd-data \
+            -v {temp_dir}:/backup \
+            {etcd_image} etcd \
+                --data-dir=/etcd-data \
+                --listen-client-urls=http://0.0.0.0:2379 \
+                --advertise-client-urls=http://localhost:2379
+
+        sleep 3
+
+        # Use alpine with extracted etcdctl to run commands (alpine has shell + jq)
+        # Export whitelisted keys (caddy TLS certs + core cluster services)
+        docker run --rm \
+            -v {temp_dir}:/backup \
+            --network container:laconic-etcd-cleanup \
+            $ALPINE_IMAGE sh -c '
+                apk add --no-cache jq >/dev/null 2>&1
+                echo "[]" > /backup/all-kvs.json
+                for prefix in {keep_prefixes_str}; do
+                    /backup/etcdctl get --prefix "$prefix" -w json 2>/dev/null \
+                        | jq ".kvs // []" >> /backup/all-kvs.json || true
+                done
+                jq -s "add" /backup/all-kvs.json \
+                    | jq "{{kvs: .}}" > /backup/kept.json 2>/dev/null \
+                    || echo "{{}}" > /backup/kept.json
+            '
+
+        # Delete ALL registry keys
+        docker run --rm \
+            -v {temp_dir}:/backup \
+            --network container:laconic-etcd-cleanup \
+            $ALPINE_IMAGE /backup/etcdctl del --prefix /registry
+
+        # Restore kept keys using jq
+        docker run --rm \
+            -v {temp_dir}:/backup \
+            --network container:laconic-etcd-cleanup \
+            $ALPINE_IMAGE sh -c '
+                apk add --no-cache jq >/dev/null 2>&1
+                jq -r ".kvs[] | @base64" /backup/kept.json 2>/dev/null | \
+                while read encoded; do
+                    key=$(echo $encoded | base64 -d | jq -r ".key" | base64 -d)
+                    val=$(echo $encoded | base64 -d | jq -r ".value" | base64 -d)
+                    echo "$val" | /backup/etcdctl put "$key"
+                done
+            ' || true
+
+        # Save cleaned snapshot
+        docker exec laconic-etcd-cleanup \
+            etcdctl snapshot save /etcd-data/cleaned-snapshot.db
+
+        docker stop laconic-etcd-cleanup
+        docker rm laconic-etcd-cleanup
+
+        # Restore to temp location first to verify it works
+        docker run --rm \
+            -v {temp_dir}/etcd-data/cleaned-snapshot.db:/data/db:ro \
+            -v {temp_dir}:/restore \
+            {etcd_image} \
+            etcdutl snapshot restore /data/db --data-dir=/restore/new-etcd \
+            --skip-hash-check 2>/dev/null
+
+        # Create timestamped backup of original (kept forever)
+        TIMESTAMP=$(date +%Y%m%d-%H%M%S)
+        docker run --rm -v {etcd_path}:/etcd $ALPINE_IMAGE \
+            cp -a /etcd/member /etcd/member.backup-$TIMESTAMP
+
+        # Replace original with cleaned version
+        docker run --rm -v {etcd_path}:/etcd -v {temp_dir}:/tmp-work $ALPINE_IMAGE \
+            sh -c "rm -rf /etcd/member && mv /tmp-work/new-etcd/member /etcd/member"
+
+        # Cleanup temp files (but NOT the timestamped backup in etcd_path)
+        docker run --rm -v /tmp:/tmp $ALPINE_IMAGE rm -rf {temp_dir}
+        rm -f /tmp/etcdctl-bin
+    """
+
+    result = subprocess.run(cleanup_script, shell=True, capture_output=True, text=True)
+    if result.returncode != 0:
+        if opts.o.debug:
+            print(f"Warning: etcd cleanup failed: {result.stderr}")
+        return False
+
+    if opts.o.debug:
+        print("Cleaned etcd, kept only TLS certificates")
+    return True
+
+
 def create_cluster(name: str, config_file: str):
+    """Create or reuse the single kind cluster for this host.
+
+    There is only one kind cluster per host by design. Multiple deployments
+    share this cluster. If a cluster already exists, it is reused.
+
+    Args:
+        name: Cluster name (used only when creating the first cluster)
+        config_file: Path to kind config file (used only when creating)
+
+    Returns:
+        The name of the cluster being used
+    """
+    existing = get_kind_cluster()
+    if existing:
+        print(f"Using existing cluster: {existing}")
+        return existing
+
+    # Clean persisted etcd, keeping only TLS certificates
+    etcd_path = _get_etcd_host_path_from_kind_config(config_file)
+    if etcd_path:
+        _clean_etcd_keeping_certs(etcd_path)
+
+    print(f"Creating new cluster: {name}")
     result = _run_command(f"kind create cluster --name {name} --config {config_file}")
     if result.returncode != 0:
         raise DeployerException(f"kind create cluster failed: {result}")
+    return name
 
 
 def destroy_cluster(name: str):
     _run_command(f"kind delete cluster --name {name}")
 
 
+def is_ingress_running() -> bool:
+    """Check if the Caddy ingress controller is already running in the cluster."""
+    try:
+        core_v1 = client.CoreV1Api()
+        pods = core_v1.list_namespaced_pod(
+            namespace="caddy-system",
+            label_selector=(
+                "app.kubernetes.io/name=caddy-ingress-controller,"
+                "app.kubernetes.io/component=controller"
+            ),
+        )
+        for pod in pods.items:
+            if pod.status and pod.status.container_statuses:
+                if pod.status.container_statuses[0].ready is True:
+                    if opts.o.debug:
+                        print("Caddy ingress controller already running")
+                    return True
+        return False
+    except ApiException:
+        return False
+
+
 def wait_for_ingress_in_kind():
     core_v1 = client.CoreV1Api()
-    for i in range(20):
+    for _i in range(20):
         warned_waiting = False
         w = watch.Watch()
         for event in w.stream(
@@ -90,25 +361,119 @@ def wait_for_ingress_in_kind():
     error_exit("ERROR: Timed out waiting for Caddy ingress to become ready")
 
 
-def install_ingress_for_kind():
+def install_ingress_for_kind(acme_email: str = ""):
     api_client = client.ApiClient()
     ingress_install = os.path.abspath(
-        get_k8s_dir().joinpath(
+        get_k8s_dir().joinpath("components", "ingress", "ingress-caddy-kind-deploy.yaml")
-            "components", "ingress", "ingress-caddy-kind-deploy.yaml"
-        )
     )
     if opts.o.debug:
         print("Installing Caddy ingress controller in kind cluster")
-    utils.create_from_yaml(api_client, yaml_file=ingress_install)
+
+    # Template the YAML with email before applying
+    with open(ingress_install) as f:
+        yaml_content = f.read()
+
+    if acme_email:
+        yaml_content = yaml_content.replace('email: ""', f'email: "{acme_email}"')
+        if opts.o.debug:
+            print(f"Configured Caddy with ACME email: {acme_email}")
+
+    # Apply templated YAML
+    yaml_objects = list(yaml.safe_load_all(yaml_content))
+    utils.create_from_yaml(api_client, yaml_objects=yaml_objects)
+
+    # Patch ConfigMap with ACME email if provided
+    if acme_email:
+        if opts.o.debug:
+            print(f"Configuring ACME email: {acme_email}")
+        core_api = client.CoreV1Api()
+        configmap = core_api.read_namespaced_config_map(
+            name="caddy-ingress-controller-configmap", namespace="caddy-system"
+        )
+        configmap.data["email"] = acme_email
+        core_api.patch_namespaced_config_map(
+            name="caddy-ingress-controller-configmap",
+            namespace="caddy-system",
+            body=configmap,
+        )
 
 
-def load_images_into_kind(kind_cluster_name: str, image_set: Set[str]):
+LOCAL_REGISTRY_NAME = "kind-registry"
-    for image in image_set:
+LOCAL_REGISTRY_HOST_PORT = 5001
+LOCAL_REGISTRY_CONTAINER_PORT = 5000
+
+
+def ensure_local_registry():
+    """Ensure a persistent local registry container is running.
+
+    The registry survives kind cluster recreates — images pushed to it
+    remain available without re-pushing. After ensuring the registry is
+    running, connects it to the kind Docker network so kind nodes can
+    pull from it.
+    """
+    # Check if registry container exists (running or stopped)
+    check = subprocess.run(
+        f"docker inspect {LOCAL_REGISTRY_NAME}",
+        shell=True,
+        capture_output=True,
+    )
+    if check.returncode != 0:
+        # Create the registry container
         result = _run_command(
-            f"kind load docker-image {image} --name {kind_cluster_name}"
+            f"docker run -d --restart=always"
+            f" -p {LOCAL_REGISTRY_HOST_PORT}:{LOCAL_REGISTRY_CONTAINER_PORT}"
+            f" --name {LOCAL_REGISTRY_NAME} registry:2"
         )
         if result.returncode != 0:
-            raise DeployerException(f"kind load docker-image failed: {result}")
+            raise DeployerException(f"Failed to start local registry: {result}")
+        print(f"Started local registry on port {LOCAL_REGISTRY_HOST_PORT}")
+    else:
+        # Ensure it's running (may have been stopped)
+        _run_command(f"docker start {LOCAL_REGISTRY_NAME}")
+        if opts.o.debug:
+            print("Local registry already exists, ensured running")
+
+
+def connect_registry_to_kind_network(kind_cluster_name: str):
+    """Connect the local registry to the kind Docker network.
+
+    Idempotent — silently succeeds if already connected.
+    """
+    network = "kind"
+    result = subprocess.run(
+        f"docker network connect {network} {LOCAL_REGISTRY_NAME}",
+        shell=True,
+        capture_output=True,
+    )
+    if result.returncode != 0 and b"already exists" not in result.stderr:
+        raise DeployerException(
+            f"Failed to connect registry to kind network: " f"{result.stderr.decode()}"
+        )
+
+
+def push_images_to_local_registry(image_set: set[str]):
+    """Tag and push images to the local registry.
+
+    Near-instant compared to kind load (shared filesystem, layer dedup).
+    """
+    for image in image_set:
+        registry_image = local_registry_image(image)
+        tag_result = _run_command(f"docker tag {image} {registry_image}")
+        if tag_result.returncode != 0:
+            raise DeployerException(f"docker tag failed for {image}: {tag_result}")
+        push_result = _run_command(f"docker push {registry_image}")
+        if push_result.returncode != 0:
+            raise DeployerException(f"docker push failed for {registry_image}: {push_result}")
+        if opts.o.debug:
+            print(f"Pushed {registry_image} to local registry")
+
+
+def local_registry_image(image: str) -> str:
+    """Rewrite an image reference to use the local registry.
+
+    e.g. laconicnetwork/agave:local -> localhost:5001/laconicnetwork/agave:local
+    """
+    return f"localhost:{LOCAL_REGISTRY_HOST_PORT}/{image}"
 
 
 def pods_in_deployment(core_api: client.CoreV1Api, deployment_name: str):
@@ -124,11 +489,9 @@ def pods_in_deployment(core_api: client.CoreV1Api, deployment_name: str):
     return pods
 
 
-def containers_in_pod(core_api: client.CoreV1Api, pod_name: str) -> List[str]:
+def containers_in_pod(core_api: client.CoreV1Api, pod_name: str) -> list[str]:
-    containers: List[str] = []
+    containers: list[str] = []
-    pod_response = cast(
+    pod_response = cast(client.V1Pod, core_api.read_namespaced_pod(pod_name, namespace="default"))
-        client.V1Pod, core_api.read_namespaced_pod(pod_name, namespace="default")
-    )
     if opts.o.debug:
         print(f"pod_response: {pod_response}")
     if not pod_response.spec or not pod_response.spec.containers:
@@ -151,7 +514,7 @@ def named_volumes_from_pod_files(parsed_pod_files):
         parsed_pod_file = parsed_pod_files[pod]
         if "volumes" in parsed_pod_file:
             volumes = parsed_pod_file["volumes"]
-            for volume, value in volumes.items():
+            for volume, _value in volumes.items():
                 # Volume definition looks like:
                 # 'laconicd-data': None
                 named_volumes.append(volume)
@@ -177,21 +540,26 @@ def volume_mounts_for_service(parsed_pod_files, service):
                         for mount_string in volumes:
                             # Looks like: test-data:/data
                             # or test-data:/data:ro or test-data:/data:rw
+                            # or ../config/file.sh:/opt/file.sh (host path mount)
                             if opts.o.debug:
                                 print(f"mount_string: {mount_string}")
                             mount_split = mount_string.split(":")
                             volume_name = mount_split[0]
                             mount_path = mount_split[1]
-                            mount_options = (
+                            mount_options = mount_split[2] if len(mount_split) == 3 else None
-                                mount_split[2] if len(mount_split) == 3 else None
+                            # For host path mounts, use sanitized name
-                            )
+                            if is_host_path_mount(volume_name):
+                                k8s_volume_name = sanitize_host_path_to_volume_name(volume_name)
+                            else:
+                                k8s_volume_name = volume_name
                             if opts.o.debug:
                                 print(f"volume_name: {volume_name}")
+                                print(f"k8s_volume_name: {k8s_volume_name}")
                                 print(f"mount path: {mount_path}")
                                 print(f"mount options: {mount_options}")
                             volume_device = client.V1VolumeMount(
                                 mount_path=mount_path,
-                                name=volume_name,
+                                name=k8s_volume_name,
                                 read_only="ro" == mount_options,
                             )
                             result.append(volume_device)
@@ -200,8 +568,12 @@ def volume_mounts_for_service(parsed_pod_files, service):
 
 def volumes_for_pod_files(parsed_pod_files, spec, app_name):
     result = []
+    seen_host_path_volumes = set()  # Track host path volumes to avoid duplicates
+
     for pod in parsed_pod_files:
         parsed_pod_file = parsed_pod_files[pod]
+
+        # Handle named volumes from top-level volumes section
         if "volumes" in parsed_pod_file:
             volumes = parsed_pod_file["volumes"]
             for volume_name in volumes.keys():
@@ -216,10 +588,33 @@ def volumes_for_pod_files(parsed_pod_files, spec, app_name):
                     claim = client.V1PersistentVolumeClaimVolumeSource(
                         claim_name=f"{app_name}-{volume_name}"
                     )
+                    volume = client.V1Volume(name=volume_name, persistent_volume_claim=claim)
+                    result.append(volume)
+
+        # Handle host path mounts from service volumes
+        if "services" in parsed_pod_file:
+            services = parsed_pod_file["services"]
+            for service_name in services:
+                service_obj = services[service_name]
+                if "volumes" in service_obj:
+                    for mount_string in service_obj["volumes"]:
+                        mount_split = mount_string.split(":")
+                        volume_source = mount_split[0]
+                        if is_host_path_mount(volume_source):
+                            sanitized_name = sanitize_host_path_to_volume_name(volume_source)
+                            if sanitized_name not in seen_host_path_volumes:
+                                seen_host_path_volumes.add(sanitized_name)
+                                # Create hostPath volume for mount inside kind node
+                                kind_mount_path = get_kind_host_path_mount_path(sanitized_name)
+                                host_path_source = client.V1HostPathVolumeSource(
+                                    path=kind_mount_path, type="FileOrCreate"
+                                )
                                 volume = client.V1Volume(
-                        name=volume_name, persistent_volume_claim=claim
+                                    name=sanitized_name, host_path=host_path_source
                                 )
                                 result.append(volume)
+                                if opts.o.debug:
+                                    print(f"Created hostPath volume: {sanitized_name}")
     return result
 
 
@@ -238,6 +633,27 @@ def _make_absolute_host_path(data_mount_path: Path, deployment_dir: Path) -> Pat
 def _generate_kind_mounts(parsed_pod_files, deployment_dir, deployment_context):
     volume_definitions = []
     volume_host_path_map = _get_host_paths_for_volumes(deployment_context)
+    seen_host_path_mounts = set()  # Track to avoid duplicate mounts
+
+    # Cluster state backup for offline data recovery (unique per deployment)
+    # etcd contains all k8s state; PKI certs needed to decrypt etcd offline
+    deployment_id = deployment_context.id
+    backup_subdir = f"cluster-backups/{deployment_id}"
+
+    etcd_host_path = _make_absolute_host_path(Path(f"./data/{backup_subdir}/etcd"), deployment_dir)
+    volume_definitions.append(
+        f"  - hostPath: {etcd_host_path}\n"
+        f"    containerPath: /var/lib/etcd\n"
+        f"    propagation: HostToContainer\n"
+    )
+
+    pki_host_path = _make_absolute_host_path(Path(f"./data/{backup_subdir}/pki"), deployment_dir)
+    volume_definitions.append(
+        f"  - hostPath: {pki_host_path}\n"
+        f"    containerPath: /etc/kubernetes/pki\n"
+        f"    propagation: HostToContainer\n"
+    )
+
     # Note these paths are relative to the location of the pod files (at present)
     # So we need to fix up to make them correct and absolute because kind assumes
     # relative to the cwd.
@@ -252,27 +668,48 @@ def _generate_kind_mounts(parsed_pod_files, deployment_dir, deployment_context):
                     for mount_string in volumes:
                         # Looks like: test-data:/data
                         # or test-data:/data:ro or test-data:/data:rw
+                        # or ../config/file.sh:/opt/file.sh (host path mount)
                         if opts.o.debug:
                             print(f"mount_string: {mount_string}")
                         mount_split = mount_string.split(":")
                         volume_name = mount_split[0]
                         mount_path = mount_split[1]
+
+                        if is_host_path_mount(volume_name):
+                            # Host path mount - add extraMount for kind
+                            sanitized_name = sanitize_host_path_to_volume_name(volume_name)
+                            if sanitized_name not in seen_host_path_mounts:
+                                seen_host_path_mounts.add(sanitized_name)
+                                # Resolve path relative to compose directory
+                                host_path = resolve_host_path_for_kind(volume_name, deployment_dir)
+                                container_path = get_kind_host_path_mount_path(sanitized_name)
+                                volume_definitions.append(
+                                    f"  - hostPath: {host_path}\n"
+                                    f"    containerPath: {container_path}\n"
+                                    f"    propagation: HostToContainer\n"
+                                )
+                                if opts.o.debug:
+                                    print(f"Added host path mount: {host_path}")
+                        else:
+                            # Named volume
                             if opts.o.debug:
                                 print(f"volume_name: {volume_name}")
                                 print(f"map: {volume_host_path_map}")
                                 print(f"mount path: {mount_path}")
                             if volume_name not in deployment_context.spec.get_configmaps():
-                            if volume_host_path_map[volume_name]:
+                                if (
+                                    volume_name in volume_host_path_map
+                                    and volume_host_path_map[volume_name]
+                                ):
                                     host_path = _make_absolute_host_path(
                                         volume_host_path_map[volume_name],
                                         deployment_dir,
                                     )
-                                container_path = get_kind_pv_bind_mount_path(
+                                    container_path = get_kind_pv_bind_mount_path(volume_name)
-                                    volume_name
-                                )
                                     volume_definitions.append(
                                         f"  - hostPath: {host_path}\n"
                                         f"    containerPath: {container_path}\n"
+                                        f"    propagation: HostToContainer\n"
                                     )
     return (
         ""
@@ -296,8 +733,7 @@ def _generate_kind_port_mappings_from_services(parsed_pod_files):
                         # TODO handle the complex cases
                         # Looks like: 80 or something more complicated
                         port_definitions.append(
-                            f"  - containerPort: {port_string}\n"
+                            f"  - containerPort: {port_string}\n" f"    hostPort: {port_string}\n"
-                            f"    hostPort: {port_string}\n"
                         )
     return (
         ""
@@ -310,9 +746,7 @@ def _generate_kind_port_mappings(parsed_pod_files):
     port_definitions = []
     # Map port 80 and 443 for the Caddy ingress controller (HTTPS support)
     for port_string in ["80", "443"]:
-        port_definitions.append(
+        port_definitions.append(f"  - containerPort: {port_string}\n    hostPort: {port_string}\n")
-            f"  - containerPort: {port_string}\n    hostPort: {port_string}\n"
-        )
     return (
         ""
         if len(port_definitions) == 0
@@ -328,7 +762,11 @@ def _generate_high_memlock_spec_mount(deployment_dir: Path):
     references an absolute path.
     """
     spec_path = deployment_dir.joinpath(constants.high_memlock_spec_filename).resolve()
-    return f"  - hostPath: {spec_path}\n" f"    containerPath: {spec_path}\n"
+    return (
+        f"  - hostPath: {spec_path}\n"
+        f"    containerPath: {spec_path}\n"
+        f"    propagation: HostToContainer\n"
+    )
 
 
 def generate_high_memlock_spec_json():
@@ -502,28 +940,38 @@ def generate_cri_base_json():
     return generate_high_memlock_spec_json()
 
 
-def _generate_containerd_config_patches(
+def _generate_containerd_config_patches(deployment_dir: Path, has_high_memlock: bool) -> str:
-    deployment_dir: Path, has_high_memlock: bool
+    """Generate containerdConfigPatches YAML for containerd configuration.
-) -> str:
-    """Generate containerdConfigPatches YAML for custom runtime handlers.
 
-    This configures containerd to have a runtime handler named 'high-memlock'
+    Includes:
-    that uses a custom OCI base spec with unlimited RLIMIT_MEMLOCK.
+    - Local registry mirror (localhost:5001 -> http://kind-registry:5000)
+    - Custom runtime handler for high-memlock (if enabled)
     """
-    if not has_high_memlock:
+    patches = []
-        return ""
 
+    # Always configure the local registry mirror so kind nodes pull from it
+    registry_plugin = f'plugins."io.containerd.grpc.v1.cri".registry.mirrors."localhost:{LOCAL_REGISTRY_HOST_PORT}"'
+    endpoint = f"http://{LOCAL_REGISTRY_NAME}:{LOCAL_REGISTRY_CONTAINER_PORT}"
+    patches.append(f"    [{registry_plugin}]\n" f'      endpoint = ["{endpoint}"]')
+
+    if has_high_memlock:
         spec_path = deployment_dir.joinpath(constants.high_memlock_spec_filename).resolve()
         runtime_name = constants.high_memlock_runtime
         plugin_path = 'plugins."io.containerd.grpc.v1.cri".containerd.runtimes'
-    return (
+        patches.append(
-        "containerdConfigPatches:\n"
-        "  - |-\n"
             f"    [{plugin_path}.{runtime_name}]\n"
             '      runtime_type = "io.containerd.runc.v2"\n'
-        f'      base_runtime_spec = "{spec_path}"\n'
+            f'      base_runtime_spec = "{spec_path}"'
         )
 
+    if not patches:
+        return ""
+
+    result = "containerdConfigPatches:\n"
+    for patch in patches:
+        result += "  - |-\n" + patch + "\n"
+    return result
+
 
 # Note: this makes any duplicate definition in b overwrite a
 def merge_envs(a: Mapping[str, str], b: Mapping[str, str]) -> Mapping[str, str]:
@@ -531,9 +979,7 @@ def merge_envs(a: Mapping[str, str], b: Mapping[str, str]) -> Mapping[str, str]:
     return result
 
 
-def _expand_shell_vars(
+def _expand_shell_vars(raw_val: str, env_map: Mapping[str, str] | None = None) -> str:
-    raw_val: str, env_map: Optional[Mapping[str, str]] = None
-) -> str:
     # Expand docker-compose style variable substitution:
     # ${VAR} - use VAR value or empty string
     # ${VAR:-default} - use VAR value or default if unset/empty
@@ -558,7 +1004,7 @@ def _expand_shell_vars(
 
 
 def envs_from_compose_file(
-    compose_file_envs: Mapping[str, str], env_map: Optional[Mapping[str, str]] = None
+    compose_file_envs: Mapping[str, str], env_map: Mapping[str, str] | None = None
 ) -> Mapping[str, str]:
     result = {}
     for env_var, env_val in compose_file_envs.items():
@@ -567,9 +1013,49 @@ def envs_from_compose_file(
     return result
 
 
+def translate_sidecar_service_names(
+    envs: Mapping[str, str], sibling_service_names: list[str]
+) -> Mapping[str, str]:
+    """Translate docker-compose service names to localhost for sidecar containers.
+
+    In docker-compose, services can reference each other by name (e.g., 'db:5432').
+    In Kubernetes, when multiple containers are in the same pod (sidecars), they
+    share the same network namespace and must use 'localhost' instead.
+
+    This function replaces service name references with 'localhost' in env values.
+    """
+    import re
+
+    if not sibling_service_names:
+        return envs
+
+    result = {}
+    for env_var, env_val in envs.items():
+        if env_val is None:
+            result[env_var] = env_val
+            continue
+
+        new_val = str(env_val)
+        for service_name in sibling_service_names:
+            # Match service name followed by optional port (e.g., 'db:5432', 'db')
+            # Handle URLs like: postgres://user:pass@db:5432/dbname
+            # and simple refs like: db:5432 or just db
+            pattern = rf"\b{re.escape(service_name)}(:\d+)?\b"
+
+            def _replace_with_localhost(m: re.Match[str]) -> str:
+                port: str = m.group(1) or ""
+                return "localhost" + port
+
+            new_val = re.sub(pattern, _replace_with_localhost, new_val)
+
+        result[env_var] = new_val
+
+    return result
+
+
 def envs_from_environment_variables_map(
-    map: Mapping[str, str]
+    map: Mapping[str, str],
-) -> List[client.V1EnvVar]:
+) -> list[client.V1EnvVar]:
     result = []
     for env_var, env_val in map.items():
         result.append(client.V1EnvVar(env_var, env_val))
@@ -600,17 +1086,13 @@ def generate_kind_config(deployment_dir: Path, deployment_context):
     pod_files = [p for p in compose_file_dir.iterdir() if p.is_file()]
     parsed_pod_files_map = parsed_pod_files_map_from_file_names(pod_files)
     port_mappings_yml = _generate_kind_port_mappings(parsed_pod_files_map)
-    mounts_yml = _generate_kind_mounts(
+    mounts_yml = _generate_kind_mounts(parsed_pod_files_map, deployment_dir, deployment_context)
-        parsed_pod_files_map, deployment_dir, deployment_context
-    )
 
     # Check if unlimited_memlock is enabled
     unlimited_memlock = deployment_context.spec.get_unlimited_memlock()
 
     # Generate containerdConfigPatches for RuntimeClass support
-    containerd_patches_yml = _generate_containerd_config_patches(
+    containerd_patches_yml = _generate_containerd_config_patches(deployment_dir, unlimited_memlock)
-        deployment_dir, unlimited_memlock
-    )
 
     # Add high-memlock spec file mount if needed
     if unlimited_memlock:

stack_orchestrator/deploy/spec.py

@@ -14,19 +14,18 @@
 # along with this program.  If not, see <http:#www.gnu.org/licenses/>.
 
 import typing
-from typing import Optional
-import humanfriendly
-
 from pathlib import Path
 
-from stack_orchestrator.util import get_yaml
+import humanfriendly
+
 from stack_orchestrator import constants
+from stack_orchestrator.util import get_yaml
 
 
 class ResourceLimits:
-    cpus: Optional[float] = None
+    cpus: float | None = None
-    memory: Optional[int] = None
+    memory: int | None = None
-    storage: Optional[int] = None
+    storage: int | None = None
 
     def __init__(self, obj=None):
         if obj is None:
@@ -50,8 +49,8 @@ class ResourceLimits:
 
 
 class Resources:
-    limits: Optional[ResourceLimits] = None
+    limits: ResourceLimits | None = None
-    reservations: Optional[ResourceLimits] = None
+    reservations: ResourceLimits | None = None
 
     def __init__(self, obj=None):
         if obj is None:
@@ -74,9 +73,9 @@ class Resources:
 
 class Spec:
     obj: typing.Any
-    file_path: Optional[Path]
+    file_path: Path | None
 
-    def __init__(self, file_path: Optional[Path] = None, obj=None) -> None:
+    def __init__(self, file_path: Path | None = None, obj=None) -> None:
         if obj is None:
             obj = {}
         self.file_path = file_path
@@ -92,12 +91,24 @@ class Spec:
         return self.obj.get(item, default)
 
     def init_from_file(self, file_path: Path):
-        self.obj = get_yaml().load(open(file_path, "r"))
+        self.obj = get_yaml().load(open(file_path))
         self.file_path = file_path
 
     def get_image_registry(self):
         return self.obj.get(constants.image_registry_key)
 
+    def get_image_registry_config(self) -> dict | None:
+        """Returns registry auth config: {server, username, token-env}.
+
+        Used for private container registries like GHCR. The token-env field
+        specifies an environment variable containing the API token/PAT.
+
+        Note: Uses 'registry-credentials' key to avoid collision with
+        'image-registry' key which is for pushing images.
+        """
+        result: dict[str, str] | None = self.obj.get("registry-credentials")
+        return result
+
     def get_volumes(self):
         return self.obj.get(constants.volumes_key, {})
 
@@ -105,14 +116,46 @@ class Spec:
         return self.obj.get(constants.configmaps_key, {})
 
     def get_container_resources(self):
-        return Resources(
+        return Resources(self.obj.get(constants.resources_key, {}).get("containers", {}))
-            self.obj.get(constants.resources_key, {}).get("containers", {})
+
+    def get_container_resources_for(self, container_name: str) -> Resources | None:
+        """Look up per-container resource overrides from spec.yml.
+
+        Checks resources.containers.<container_name> in the spec. Returns None
+        if no per-container override exists (caller falls back to other sources).
+        """
+        containers_block = self.obj.get(constants.resources_key, {}).get("containers", {})
+        if container_name in containers_block:
+            entry = containers_block[container_name]
+            # Only treat it as a per-container override if it's a dict with
+            # reservations/limits nested inside (not a top-level global key)
+            if isinstance(entry, dict) and ("reservations" in entry or "limits" in entry):
+                return Resources(entry)
+        return None
+
+    def get_container_resources_for(
+        self, container_name: str
+    ) -> typing.Optional[Resources]:
+        """Look up per-container resource overrides from spec.yml.
+
+        Checks resources.containers.<container_name> in the spec. Returns None
+        if no per-container override exists (caller falls back to other sources).
+        """
+        containers_block = self.obj.get(constants.resources_key, {}).get(
+            "containers", {}
         )
+        if container_name in containers_block:
+            entry = containers_block[container_name]
+            # Only treat it as a per-container override if it's a dict with
+            # reservations/limits nested inside (not a top-level global key)
+            if isinstance(entry, dict) and (
+                "reservations" in entry or "limits" in entry
+            ):
+                return Resources(entry)
+        return None
 
     def get_volume_resources(self):
-        return Resources(
+        return Resources(self.obj.get(constants.resources_key, {}).get(constants.volumes_key, {}))
-            self.obj.get(constants.resources_key, {}).get(constants.volumes_key, {})
-        )
 
     def get_http_proxy(self):
         return self.obj.get(constants.network_key, {}).get(constants.http_proxy_key, [])
@@ -135,9 +178,7 @@ class Spec:
     def get_privileged(self):
         return (
             "true"
-            == str(
+            == str(self.obj.get(constants.security_key, {}).get("privileged", "false")).lower()
-                self.obj.get(constants.security_key, {}).get("privileged", "false")
-            ).lower()
         )
 
     def get_capabilities(self):
@@ -164,9 +205,7 @@ class Spec:
             Runtime class name string, or None to use default runtime.
         """
         # Explicit runtime class takes precedence
-        explicit = self.obj.get(constants.security_key, {}).get(
+        explicit = self.obj.get(constants.security_key, {}).get(constants.runtime_class_key, None)
-            constants.runtime_class_key, None
-        )
         if explicit:
             return explicit
 
@@ -179,6 +218,9 @@ class Spec:
     def get_deployment_type(self):
         return self.obj.get(constants.deploy_to_key)
 
+    def get_acme_email(self):
+        return self.obj.get(constants.network_key, {}).get(constants.acme_email_key, "")
+
     def is_kubernetes_deployment(self):
         return self.get_deployment_type() in [
             constants.k8s_kind_deploy_type,

stack_orchestrator/deploy/stack.py

@@ -13,8 +13,9 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with this program.  If not, see <http:#www.gnu.org/licenses/>.
 
-from pathlib import Path
 import typing
+from pathlib import Path
+
 from stack_orchestrator.util import get_yaml
 
 
@@ -26,4 +27,4 @@ class Stack:
         self.name = name
 
     def init_from_file(self, file_path: Path):
-        self.obj = get_yaml().load(open(file_path, "r"))
+        self.obj = get_yaml().load(open(file_path))

stack_orchestrator/deploy/webapp/deploy_webapp.py

@@ -13,23 +13,22 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with this program.  If not, see <http:#www.gnu.org/licenses/>.
 
-import click
 import os
 from pathlib import Path
-from urllib.parse import urlparse
 from tempfile import NamedTemporaryFile
+from urllib.parse import urlparse
+
+import click
 
-from stack_orchestrator.util import error_exit, global_options2
-from stack_orchestrator.deploy.deployment_create import init_operation, create_operation
 from stack_orchestrator.deploy.deploy import create_deploy_context
 from stack_orchestrator.deploy.deploy_types import DeployCommandContext
+from stack_orchestrator.deploy.deployment_create import create_operation, init_operation
+from stack_orchestrator.util import error_exit, global_options2
 
 
 def _fixup_container_tag(deployment_dir: str, image: str):
     deployment_dir_path = Path(deployment_dir)
-    compose_file = deployment_dir_path.joinpath(
+    compose_file = deployment_dir_path.joinpath("compose", "docker-compose-webapp-template.yml")
-        "compose", "docker-compose-webapp-template.yml"
-    )
     # replace "cerc/webapp-container:local" in the file with our image tag
     with open(compose_file) as rfile:
         contents = rfile.read()
@@ -56,9 +55,7 @@ def _fixup_url_spec(spec_file_name: str, url: str):
         wfile.write(contents)
 
 
-def create_deployment(
+def create_deployment(ctx, deployment_dir, image, url, kube_config, image_registry, env_file):
-    ctx, deployment_dir, image, url, kube_config, image_registry, env_file
-):
     # Do the equivalent of:
     # 1. laconic-so --stack webapp-template deploy --deploy-to k8s init \
     #    --output webapp-spec.yml
@@ -94,7 +91,7 @@ def create_deployment(
     # Add the TLS and DNS spec
     _fixup_url_spec(spec_file_name, url)
     create_operation(
-        deploy_command_context, spec_file_name, deployment_dir, False, None, None
+        deploy_command_context, spec_file_name, deployment_dir, False, False, None, None
     )
     # Fix up the container tag inside the deployment compose file
     _fixup_container_tag(deployment_dir, image)
@@ -117,9 +114,7 @@ def command(ctx):
     "--image-registry",
     help="Provide a container image registry url for this k8s cluster",
 )
-@click.option(
+@click.option("--deployment-dir", help="Create deployment files in this directory", required=True)
-    "--deployment-dir", help="Create deployment files in this directory", required=True
-)
 @click.option("--image", help="image to deploy", required=True)
 @click.option("--url", help="url to serve", required=True)
 @click.option("--env-file", help="environment file for webapp")
@@ -127,6 +122,4 @@ def command(ctx):
 def create(ctx, deployment_dir, image, url, kube_config, image_registry, env_file):
     """create a deployment for the specified webapp container"""
 
-    return create_deployment(
+    return create_deployment(ctx, deployment_dir, image, url, kube_config, image_registry, env_file)
-        ctx, deployment_dir, image, url, kube_config, image_registry, env_file
-    )

stack_orchestrator/deploy/webapp/deploy_webapp_from_registry.py

@@ -21,10 +21,10 @@ import sys
 import tempfile
 import time
 import uuid
-import yaml
 
 import click
 import gnupg
+import yaml
 
 from stack_orchestrator.deploy.images import remote_image_exists
 from stack_orchestrator.deploy.webapp import deploy_webapp
@@ -34,16 +34,16 @@ from stack_orchestrator.deploy.webapp.util import (
     TimedLogger,
     build_container_image,
     confirm_auction,
-    push_container_image,
-    file_hash,
-    deploy_to_k8s,
-    publish_deployment,
-    hostname_for_deployment_request,
-    generate_hostname_for_app,
-    match_owner,
-    skip_by_tag,
     confirm_payment,
+    deploy_to_k8s,
+    file_hash,
+    generate_hostname_for_app,
+    hostname_for_deployment_request,
     load_known_requests,
+    match_owner,
+    publish_deployment,
+    push_container_image,
+    skip_by_tag,
 )
 
 
@@ -70,9 +70,7 @@ def process_app_deployment_request(
     logger.log("BEGIN - process_app_deployment_request")
 
     # 1. look up application
-    app = laconic.get_record(
+    app = laconic.get_record(app_deployment_request.attributes.application, require=True)
-        app_deployment_request.attributes.application, require=True
-    )
     assert app is not None  # require=True ensures this
     logger.log(f"Retrieved app record {app_deployment_request.attributes.application}")
 
@@ -84,9 +82,7 @@ def process_app_deployment_request(
         if "allow" == fqdn_policy or "preexisting" == fqdn_policy:
             fqdn = requested_name
         else:
-            raise Exception(
+            raise Exception(f"{requested_name} is invalid: only unqualified hostnames are allowed.")
-                f"{requested_name} is invalid: only unqualified hostnames are allowed."
-            )
     else:
         fqdn = f"{requested_name}.{default_dns_suffix}"
 
@@ -108,8 +104,7 @@ def process_app_deployment_request(
             logger.log(f"Matched DnsRecord ownership: {matched_owner}")
         else:
             raise Exception(
-                "Unable to confirm ownership of DnsRecord %s for request %s"
+                f"Unable to confirm ownership of DnsRecord {dns_lrn} for request {app_deployment_request.id}"
-                % (dns_lrn, app_deployment_request.id)
             )
     elif "preexisting" == fqdn_policy:
         raise Exception(
@@ -144,7 +139,7 @@ def process_app_deployment_request(
         env_filename = tempfile.mktemp()
         with open(env_filename, "w") as file:
             for k, v in env.items():
-                file.write("%s=%s\n" % (k, shlex.quote(str(v))))
+                file.write(f"{k}={shlex.quote(str(v))}\n")
 
     # 5. determine new or existing deployment
     #   a. check for deployment lrn
@@ -153,8 +148,7 @@ def process_app_deployment_request(
         app_deployment_lrn = app_deployment_request.attributes.deployment
     if not app_deployment_lrn.startswith(deployment_record_namespace):
         raise Exception(
-            "Deployment LRN %s is not in a supported namespace"
+            f"Deployment LRN {app_deployment_request.attributes.deployment} is not in a supported namespace"
-            % app_deployment_request.attributes.deployment
         )
 
     deployment_record = laconic.get_record(app_deployment_lrn)
@@ -165,14 +159,14 @@ def process_app_deployment_request(
     # already-unique deployment id
     unique_deployment_id = hashlib.md5(fqdn.encode()).hexdigest()[:16]
     deployment_config_file = os.path.join(deployment_dir, "config.env")
-    deployment_container_tag = "laconic-webapp/%s:local" % unique_deployment_id
+    deployment_container_tag = f"laconic-webapp/{unique_deployment_id}:local"
     app_image_shared_tag = f"laconic-webapp/{app.id}:local"
     #   b. check for deployment directory (create if necessary)
     if not os.path.exists(deployment_dir):
         if deployment_record:
             raise Exception(
-                "Deployment record %s exists, but not deployment dir %s. "
+                f"Deployment record {app_deployment_lrn} exists, but not deployment dir {deployment_dir}. "
-                "Please remove name." % (app_deployment_lrn, deployment_dir)
+                "Please remove name."
             )
         logger.log(
             f"Creating webapp deployment in: {deployment_dir} "
@@ -198,11 +192,7 @@ def process_app_deployment_request(
         )
     # 6. build container (if needed)
     # TODO: add a comment that explains what this code is doing (not clear to me)
-    if (
+    if not deployment_record or deployment_record.attributes.application != app.id or force_rebuild:
-        not deployment_record
-        or deployment_record.attributes.application != app.id
-        or force_rebuild
-    ):
         needs_k8s_deploy = True
         # check if the image already exists
         shared_tag_exists = remote_image_exists(image_registry, app_image_shared_tag)
@@ -224,11 +214,9 @@ def process_app_deployment_request(
             # )
             logger.log("Tag complete")
         else:
-            extra_build_args = []  # TODO: pull from request
+            extra_build_args: list[str] = []  # TODO: pull from request
             logger.log(f"Building container image: {deployment_container_tag}")
-            build_container_image(
+            build_container_image(app, deployment_container_tag, extra_build_args, logger)
-                app, deployment_container_tag, extra_build_args, logger
-            )
             logger.log("Build complete")
             logger.log(f"Pushing container image: {deployment_container_tag}")
             push_container_image(deployment_dir, logger)
@@ -287,9 +275,7 @@ def dump_known_requests(filename, requests, status="SEEN"):
 
 @click.command()
 @click.option("--kube-config", help="Provide a config file for a k8s deployment")
-@click.option(
+@click.option("--laconic-config", help="Provide a config file for laconicd", required=True)
-    "--laconic-config", help="Provide a config file for laconicd", required=True
-)
 @click.option(
     "--image-registry",
     help="Provide a container image registry url for this k8s cluster",
@@ -306,9 +292,7 @@ def dump_known_requests(filename, requests, status="SEEN"):
     is_flag=True,
     default=False,
 )
-@click.option(
+@click.option("--state-file", help="File to store state about previously seen requests.")
-    "--state-file", help="File to store state about previously seen requests."
-)
 @click.option(
     "--only-update-state",
     help="Only update the state file, don't process any requests anything.",
@@ -331,9 +315,7 @@ def dump_known_requests(filename, requests, status="SEEN"):
     help="eg, lrn://laconic/deployments",
     required=True,
 )
-@click.option(
+@click.option("--dry-run", help="Don't do anything, just report what would be done.", is_flag=True)
-    "--dry-run", help="Don't do anything, just report what would be done.", is_flag=True
-)
 @click.option(
     "--include-tags",
     help="Only include requests with matching tags (comma-separated).",
@@ -344,17 +326,13 @@ def dump_known_requests(filename, requests, status="SEEN"):
     help="Exclude requests with matching tags (comma-separated).",
     default="",
 )
-@click.option(
+@click.option("--force-rebuild", help="Rebuild even if the image already exists.", is_flag=True)
-    "--force-rebuild", help="Rebuild even if the image already exists.", is_flag=True
-)
 @click.option(
     "--recreate-on-deploy",
     help="Remove and recreate deployments instead of updating them.",
     is_flag=True,
 )
-@click.option(
+@click.option("--log-dir", help="Output build/deployment logs to directory.", default=None)
-    "--log-dir", help="Output build/deployment logs to directory.", default=None
-)
 @click.option(
     "--min-required-payment",
     help="Requests must have a minimum payment to be processed (in alnt)",
@@ -378,9 +356,7 @@ def dump_known_requests(filename, requests, status="SEEN"):
     help="The directory containing uploaded config.",
     required=True,
 )
-@click.option(
+@click.option("--private-key-file", help="The private key for decrypting config.", required=True)
-    "--private-key-file", help="The private key for decrypting config.", required=True
-)
 @click.option(
     "--registry-lock-file",
     help="File path to use for registry mutex lock",
@@ -435,11 +411,7 @@ def command(  # noqa: C901
         sys.exit(2)
 
     if not only_update_state:
-        if (
+        if not record_namespace_dns or not record_namespace_deployments or not dns_suffix:
-            not record_namespace_dns
-            or not record_namespace_deployments
-            or not dns_suffix
-        ):
             print(
                 "--dns-suffix, --record-namespace-dns, and "
                 "--record-namespace-deployments are all required",
@@ -491,8 +463,7 @@ def command(  # noqa: C901
 
         if min_required_payment and not payment_address:
             print(
-                f"Minimum payment required, but no payment address listed "
+                f"Minimum payment required, but no payment address listed " f"for deployer: {lrn}.",
-                f"for deployer: {lrn}.",
                 file=sys.stderr,
             )
             sys.exit(2)
@@ -557,26 +528,18 @@ def command(  # noqa: C901
                 requested_name = r.attributes.dns
                 if not requested_name:
                     requested_name = generate_hostname_for_app(app)
-                    main_logger.log(
+                    main_logger.log(f"Generating name {requested_name} for request {r_id}.")
-                        "Generating name %s for request %s." % (requested_name, r_id)
-                    )
 
-                if (
+                if requested_name in skipped_by_name or requested_name in requests_by_name:
-                    requested_name in skipped_by_name
+                    main_logger.log(f"Ignoring request {r_id}, it has been superseded.")
-                    or requested_name in requests_by_name
-                ):
-                    main_logger.log(
-                        "Ignoring request %s, it has been superseded." % r_id
-                    )
                     result = "SKIP"
                     continue
 
                 if skip_by_tag(r, include_tags, exclude_tags):
                     r_tags = r.attributes.tags if r.attributes else None
                     main_logger.log(
-                        "Skipping request %s, filtered by tag "
+                        f"Skipping request {r_id}, filtered by tag "
-                        "(include %s, exclude %s, present %s)"
+                        f"(include {include_tags}, exclude {exclude_tags}, present {r_tags})"
-                        % (r_id, include_tags, exclude_tags, r_tags)
                     )
                     skipped_by_name[requested_name] = r
                     result = "SKIP"
@@ -584,8 +547,7 @@ def command(  # noqa: C901
 
                 r_app = r.attributes.application if r.attributes else "unknown"
                 main_logger.log(
-                    "Found pending request %s to run application %s on %s."
+                    f"Found pending request {r_id} to run application {r_app} on {requested_name}."
-                    % (r_id, r_app, requested_name)
                 )
                 requests_by_name[requested_name] = r
             except Exception as e:
@@ -617,17 +579,14 @@ def command(  # noqa: C901
 
         requests_to_check_for_payment = []
         for r in requests_by_name.values():
-            if r.id in cancellation_requests and match_owner(
+            if r.id in cancellation_requests and match_owner(cancellation_requests[r.id], r):
-                cancellation_requests[r.id], r
-            ):
                 main_logger.log(
                     f"Found deployment cancellation request for {r.id} "
                     f"at {cancellation_requests[r.id].id}"
                 )
             elif r.id in deployments_by_request:
                 main_logger.log(
-                    f"Found satisfied request for {r.id} "
+                    f"Found satisfied request for {r.id} " f"at {deployments_by_request[r.id].id}"
-                    f"at {deployments_by_request[r.id].id}"
                 )
             else:
                 if (
@@ -635,8 +594,7 @@ def command(  # noqa: C901
                     and previous_requests[r.id].get("status", "") != "RETRY"
                 ):
                     main_logger.log(
-                        f"Skipping unsatisfied request {r.id} "
+                        f"Skipping unsatisfied request {r.id} " "because we have seen it before."
-                        "because we have seen it before."
                     )
                 else:
                     main_logger.log(f"Request {r.id} needs to processed.")
@@ -650,14 +608,10 @@ def command(  # noqa: C901
                         main_logger.log(f"{r.id}: Auction confirmed.")
                         requests_to_execute.append(r)
                     else:
-                        main_logger.log(
+                        main_logger.log(f"Skipping request {r.id}: unable to verify auction.")
-                            f"Skipping request {r.id}: unable to verify auction."
-                        )
                         dump_known_requests(state_file, [r], status="SKIP")
                 else:
-                    main_logger.log(
+                    main_logger.log(f"Skipping request {r.id}: not handling requests with auction.")
-                        f"Skipping request {r.id}: not handling requests with auction."
-                    )
                     dump_known_requests(state_file, [r], status="SKIP")
             elif min_required_payment:
                 main_logger.log(f"{r.id}: Confirming payment...")
@@ -671,16 +625,12 @@ def command(  # noqa: C901
                     main_logger.log(f"{r.id}: Payment confirmed.")
                     requests_to_execute.append(r)
                 else:
-                    main_logger.log(
+                    main_logger.log(f"Skipping request {r.id}: unable to verify payment.")
-                        f"Skipping request {r.id}: unable to verify payment."
-                    )
                     dump_known_requests(state_file, [r], status="UNPAID")
             else:
                 requests_to_execute.append(r)
 
-        main_logger.log(
+        main_logger.log(f"Found {len(requests_to_execute)} unsatisfied request(s) to process.")
-            "Found %d unsatisfied request(s) to process." % len(requests_to_execute)
-        )
 
         if not dry_run:
             for r in requests_to_execute:
@@ -700,10 +650,8 @@ def command(  # noqa: C901
                         if not os.path.exists(run_log_dir):
                             os.mkdir(run_log_dir)
                         run_log_file_path = os.path.join(run_log_dir, f"{run_id}.log")
-                        main_logger.log(
+                        main_logger.log(f"Directing deployment logs to: {run_log_file_path}")
-                            f"Directing deployment logs to: {run_log_file_path}"
+                        run_log_file = open(run_log_file_path, "w")
-                        )
-                        run_log_file = open(run_log_file_path, "wt")
                         run_reg_client = LaconicRegistryClient(
                             laconic_config,
                             log_file=run_log_file,

stack_orchestrator/deploy/webapp/handle_deployment_auction.py

@@ -12,18 +12,18 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with this program.  If not, see <http:#www.gnu.org/licenses/>.
 
-import sys
 import json
+import sys
 
 import click
 
 from stack_orchestrator.deploy.webapp.util import (
+    AUCTION_KIND_PROVIDER,
     AttrDict,
+    AuctionStatus,
     LaconicRegistryClient,
     TimedLogger,
     load_known_requests,
-    AUCTION_KIND_PROVIDER,
-    AuctionStatus,
 )
 
 
@@ -44,16 +44,13 @@ def process_app_deployment_auction(
 
     # Check auction kind
     if auction.kind != AUCTION_KIND_PROVIDER:
-        raise Exception(
+        raise Exception(f"Auction kind needs to be ${AUCTION_KIND_PROVIDER}, got {auction.kind}")
-            f"Auction kind needs to be ${AUCTION_KIND_PROVIDER}, got {auction.kind}"
-        )
 
     if current_status == "PENDING":
         # Skip if pending auction not in commit state
         if auction.status != AuctionStatus.COMMIT:
             logger.log(
-                f"Skipping pending request, auction {auction_id} "
+                f"Skipping pending request, auction {auction_id} " f"status: {auction.status}"
-                f"status: {auction.status}"
             )
             return "SKIP", ""
 
@@ -115,9 +112,7 @@ def dump_known_auction_requests(filename, requests, status="SEEN"):
 
 
 @click.command()
-@click.option(
+@click.option("--laconic-config", help="Provide a config file for laconicd", required=True)
-    "--laconic-config", help="Provide a config file for laconicd", required=True
-)
 @click.option(
     "--state-file",
     help="File to store state about previously seen auction requests.",
@@ -133,9 +128,7 @@ def dump_known_auction_requests(filename, requests, status="SEEN"):
     help="File path to use for registry mutex lock",
     default=None,
 )
-@click.option(
+@click.option("--dry-run", help="Don't do anything, just report what would be done.", is_flag=True)
-    "--dry-run", help="Don't do anything, just report what would be done.", is_flag=True
-)
 @click.pass_context
 def command(
     ctx,
@@ -198,8 +191,7 @@ def command(
                         continue
 
                     logger.log(
-                        f"Found pending auction request {r.id} for application "
+                        f"Found pending auction request {r.id} for application " f"{application}."
-                        f"{application}."
                     )
 
                 # Add requests to be processed
@@ -209,9 +201,7 @@ def command(
                 result_status = "ERROR"
                 logger.log(f"ERROR: examining request {r.id}: " + str(e))
             finally:
-                logger.log(
+                logger.log(f"DONE: Examining request {r.id} with result {result_status}.")
-                    f"DONE: Examining request {r.id} with result {result_status}."
-                )
                 if result_status in ["ERROR"]:
                     dump_known_auction_requests(
                         state_file,

stack_orchestrator/deploy/webapp/publish_deployment_auction.py

@@ -30,9 +30,7 @@ def fatal(msg: str):
 
 
 @click.command()
-@click.option(
+@click.option("--laconic-config", help="Provide a config file for laconicd", required=True)
-    "--laconic-config", help="Provide a config file for laconicd", required=True
-)
 @click.option(
     "--app",
     help="The LRN of the application to deploy.",

stack_orchestrator/deploy/webapp/publish_webapp_deployer.py

@@ -13,28 +13,24 @@
 # along with this program.  If not, see <http:#www.gnu.org/licenses/>.
 
 import base64
-import click
 import sys
-import yaml
-
 from urllib.parse import urlparse
 
+import click
+import yaml
+
 from stack_orchestrator.deploy.webapp.util import LaconicRegistryClient
 
 
 @click.command()
-@click.option(
+@click.option("--laconic-config", help="Provide a config file for laconicd", required=True)
-    "--laconic-config", help="Provide a config file for laconicd", required=True
-)
 @click.option("--api-url", help="The API URL of the deployer.", required=True)
 @click.option(
     "--public-key-file",
     help="The public key to use.  This should be a binary file.",
     required=True,
 )
-@click.option(
+@click.option("--lrn", help="eg, lrn://laconic/deployers/my.deployer.name", required=True)
-    "--lrn", help="eg, lrn://laconic/deployers/my.deployer.name", required=True
-)
 @click.option(
     "--payment-address",
     help="The address to which payments should be made.  "
@@ -84,9 +80,7 @@ def command(  # noqa: C901
     }
 
     if min_required_payment:
-        webapp_deployer_record["record"][
+        webapp_deployer_record["record"]["minimumPayment"] = f"{min_required_payment}alnt"
-            "minimumPayment"
-        ] = f"{min_required_payment}alnt"
 
     if dry_run:
         yaml.dump(webapp_deployer_record, sys.stdout)

stack_orchestrator/deploy/webapp/registry_mutex.py

@@ -1,6 +1,6 @@
-from functools import wraps
 import os
 import time
+from functools import wraps
 
 # Define default file path for the lock
 DEFAULT_LOCK_FILE_PATH = "/tmp/registry_mutex_lock_file"
@@ -17,7 +17,7 @@ def acquire_lock(client, lock_file_path, timeout):
         try:
             # Check if lock file exists and is potentially stale
             if os.path.exists(lock_file_path):
-                with open(lock_file_path, "r") as lock_file:
+                with open(lock_file_path) as lock_file:
                     timestamp = float(lock_file.read().strip())
 
                 # If lock is stale, remove the lock file
@@ -25,9 +25,7 @@ def acquire_lock(client, lock_file_path, timeout):
                     print(f"Stale lock detected, removing lock file {lock_file_path}")
                     os.remove(lock_file_path)
                 else:
-                    print(
+                    print(f"Lock file {lock_file_path} exists and is recent, waiting...")
-                        f"Lock file {lock_file_path} exists and is recent, waiting..."
-                    )
                     time.sleep(LOCK_RETRY_INTERVAL)
                     continue
 

stack_orchestrator/deploy/webapp/request_webapp_deployment.py

@@ -12,24 +12,24 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with this program.  If not, see <http:#www.gnu.org/licenses/>.
 
+import base64
 import shutil
 import sys
 import tempfile
 from datetime import datetime
 from typing import NoReturn
-import base64
 
-import gnupg
 import click
+import gnupg
 import requests
 import yaml
+from dotenv import dotenv_values
 
 from stack_orchestrator.deploy.webapp.util import (
     AUCTION_KIND_PROVIDER,
     AuctionStatus,
     LaconicRegistryClient,
 )
-from dotenv import dotenv_values
 
 
 def fatal(msg: str) -> NoReturn:
@@ -38,9 +38,7 @@ def fatal(msg: str) -> NoReturn:
 
 
 @click.command()
-@click.option(
+@click.option("--laconic-config", help="Provide a config file for laconicd", required=True)
-    "--laconic-config", help="Provide a config file for laconicd", required=True
-)
 @click.option(
     "--app",
     help="The LRN of the application to deploy.",
@@ -63,9 +61,7 @@ def fatal(msg: str) -> NoReturn:
         "'auto' to use the deployer's minimum required payment."
     ),
 )
-@click.option(
+@click.option("--use-payment", help="The TX id of an existing, unused payment", default=None)
-    "--use-payment", help="The TX id of an existing, unused payment", default=None
-)
 @click.option("--dns", help="the DNS name to request (default is autogenerated)")
 @click.option(
     "--dry-run",
@@ -144,9 +140,7 @@ def command(  # noqa: C901
         # Check auction kind
         auction_kind = auction.kind if auction else None
         if auction_kind != AUCTION_KIND_PROVIDER:
-            fatal(
+            fatal(f"Auction kind needs to be ${AUCTION_KIND_PROVIDER}, got {auction_kind}")
-                f"Auction kind needs to be ${AUCTION_KIND_PROVIDER}, got {auction_kind}"
-            )
 
         # Check auction status
         auction_status = auction.status if auction else None
@@ -163,14 +157,9 @@ def command(  # noqa: C901
         # Get deployer record for all the auction winners
         for auction_winner in auction_winners:
             # TODO: Match auction winner address with provider address?
-            deployer_records_by_owner = laconic.webapp_deployers(
+            deployer_records_by_owner = laconic.webapp_deployers({"paymentAddress": auction_winner})
-                {"paymentAddress": auction_winner}
-            )
             if len(deployer_records_by_owner) == 0:
-                print(
+                print(f"WARNING: Unable to locate deployer for auction winner " f"{auction_winner}")
-                    f"WARNING: Unable to locate deployer for auction winner "
-                    f"{auction_winner}"
-                )
 
             # Take first record with name set
             target_deployer_record = deployer_records_by_owner[0]
@@ -196,9 +185,7 @@ def command(  # noqa: C901
                 gpg = gnupg.GPG(gnupghome=tempdir)
 
                 # Import the deployer's public key
-                result = gpg.import_keys(
+                result = gpg.import_keys(base64.b64decode(deployer_record.attributes.publicKey))
-                    base64.b64decode(deployer_record.attributes.publicKey)
-                )
                 if 1 != result.imported:
                     fatal("Failed to import deployer's public key.")
 
@@ -237,15 +224,9 @@ def command(  # noqa: C901
         if (not deployer) and len(deployer_record.names):
             target_deployer = deployer_record.names[0]
 
-        app_name = (
+        app_name = app_record.attributes.name if app_record and app_record.attributes else "unknown"
-            app_record.attributes.name
-            if app_record and app_record.attributes
-            else "unknown"
-        )
         app_version = (
-            app_record.attributes.version
+            app_record.attributes.version if app_record and app_record.attributes else "unknown"
-            if app_record and app_record.attributes
-            else "unknown"
         )
         deployment_request = {
             "record": {
@@ -273,15 +254,11 @@ def command(  # noqa: C901
                 deployment_request["record"]["payment"] = "DRY_RUN"
             elif "auto" == make_payment:
                 if "minimumPayment" in deployer_record.attributes:
-                    amount = int(
+                    amount = int(deployer_record.attributes.minimumPayment.replace("alnt", ""))
-                        deployer_record.attributes.minimumPayment.replace("alnt", "")
-                    )
             else:
                 amount = make_payment
             if amount:
-                receipt = laconic.send_tokens(
+                receipt = laconic.send_tokens(deployer_record.attributes.paymentAddress, amount)
-                    deployer_record.attributes.paymentAddress, amount
-                )
                 deployment_request["record"]["payment"] = receipt.tx.hash
                 print("Payment TX:", receipt.tx.hash)
         elif use_payment:

stack_orchestrator/deploy/webapp/request_webapp_undeployment.py

@@ -26,12 +26,8 @@ def fatal(msg: str) -> None:
 
 
 @click.command()
-@click.option(
+@click.option("--laconic-config", help="Provide a config file for laconicd", required=True)
-    "--laconic-config", help="Provide a config file for laconicd", required=True
+@click.option("--deployer", help="The LRN of the deployer to process this request.", required=True)
-)
-@click.option(
-    "--deployer", help="The LRN of the deployer to process this request.", required=True
-)
 @click.option(
     "--deployment",
     help="Deployment record (ApplicationDeploymentRecord) id of the deployment.",
@@ -44,9 +40,7 @@ def fatal(msg: str) -> None:
         "'auto' to use the deployer's minimum required payment."
     ),
 )
-@click.option(
+@click.option("--use-payment", help="The TX id of an existing, unused payment", default=None)
-    "--use-payment", help="The TX id of an existing, unused payment", default=None
-)
 @click.option(
     "--dry-run",
     help="Don't publish anything, just report what would be done.",

stack_orchestrator/deploy/webapp/run_webapp.py

@@ -22,6 +22,7 @@
 # all or specific containers
 
 import hashlib
+
 import click
 from dotenv import dotenv_values
 

stack_orchestrator/deploy/webapp/undeploy_webapp_from_registry.py

@@ -21,11 +21,11 @@ import sys
 import click
 
 from stack_orchestrator.deploy.webapp.util import (
-    TimedLogger,
     LaconicRegistryClient,
+    TimedLogger,
+    confirm_payment,
     match_owner,
     skip_by_tag,
-    confirm_payment,
 )
 
 main_logger = TimedLogger(file=sys.stderr)
@@ -40,9 +40,7 @@ def process_app_removal_request(
     delete_names,
     webapp_deployer_record,
 ):
-    deployment_record = laconic.get_record(
+    deployment_record = laconic.get_record(app_removal_request.attributes.deployment, require=True)
-        app_removal_request.attributes.deployment, require=True
-    )
     assert deployment_record is not None  # require=True ensures this
     assert deployment_record.attributes is not None
 
@@ -50,12 +48,10 @@ def process_app_removal_request(
     assert dns_record is not None  # require=True ensures this
     assert dns_record.attributes is not None
 
-    deployment_dir = os.path.join(
+    deployment_dir = os.path.join(deployment_parent_dir, dns_record.attributes.name.lower())
-        deployment_parent_dir, dns_record.attributes.name.lower()
-    )
 
     if not os.path.exists(deployment_dir):
-        raise Exception("Deployment directory %s does not exist." % deployment_dir)
+        raise Exception(f"Deployment directory {deployment_dir} does not exist.")
 
     # Check if the removal request is from the owner of the DnsRecord or
     # deployment record.
@@ -63,9 +59,7 @@ def process_app_removal_request(
 
     # Or of the original deployment request.
     if not matched_owner and deployment_record.attributes.request:
-        original_request = laconic.get_record(
+        original_request = laconic.get_record(deployment_record.attributes.request, require=True)
-            deployment_record.attributes.request, require=True
-        )
         assert original_request is not None  # require=True ensures this
         matched_owner = match_owner(app_removal_request, original_request)
 
@@ -75,8 +69,7 @@ def process_app_removal_request(
         deployment_id = deployment_record.id if deployment_record else "unknown"
         request_id = app_removal_request.id if app_removal_request else "unknown"
         raise Exception(
-            "Unable to confirm ownership of deployment %s for removal request %s"
+            f"Unable to confirm ownership of deployment {deployment_id} for removal request {request_id}"
-            % (deployment_id, request_id)
         )
 
     # TODO(telackey): Call the function directly. The easiest way to build
@@ -124,7 +117,7 @@ def process_app_removal_request(
 
 def load_known_requests(filename):
     if filename and os.path.exists(filename):
-        return json.load(open(filename, "r"))
+        return json.load(open(filename))
     return {}
 
 
@@ -138,9 +131,7 @@ def dump_known_requests(filename, requests):
 
 
 @click.command()
-@click.option(
+@click.option("--laconic-config", help="Provide a config file for laconicd", required=True)
-    "--laconic-config", help="Provide a config file for laconicd", required=True
-)
 @click.option(
     "--deployment-parent-dir",
     help="Create deployment directories beneath this directory",
@@ -153,9 +144,7 @@ def dump_known_requests(filename, requests):
     is_flag=True,
     default=False,
 )
-@click.option(
+@click.option("--state-file", help="File to store state about previously seen requests.")
-    "--state-file", help="File to store state about previously seen requests."
-)
 @click.option(
     "--only-update-state",
     help="Only update the state file, don't process any requests anything.",
@@ -166,12 +155,8 @@ def dump_known_requests(filename, requests):
     help="Delete all names associated with removed deployments.",
     default=True,
 )
-@click.option(
+@click.option("--delete-volumes/--preserve-volumes", default=True, help="delete data volumes")
-    "--delete-volumes/--preserve-volumes", default=True, help="delete data volumes"
+@click.option("--dry-run", help="Don't do anything, just report what would be done.", is_flag=True)
-)
-@click.option(
-    "--dry-run", help="Don't do anything, just report what would be done.", is_flag=True
-)
 @click.option(
     "--include-tags",
     help="Only include requests with matching tags (comma-separated).",
@@ -245,8 +230,7 @@ def command(  # noqa: C901
 
     if min_required_payment and not payment_address:
         print(
-            f"Minimum payment required, but no payment address listed "
+            f"Minimum payment required, but no payment address listed " f"for deployer: {lrn}.",
-            f"for deployer: {lrn}.",
             file=sys.stderr,
         )
         sys.exit(2)
@@ -303,9 +287,7 @@ def command(  # noqa: C901
             continue
         if not r.attributes.deployment:
             r_id = r.id if r else "unknown"
-            main_logger.log(
+            main_logger.log(f"Skipping removal request {r_id} since it was a cancellation.")
-                f"Skipping removal request {r_id} since it was a cancellation."
-            )
         elif r.attributes.deployment in one_per_deployment:
             r_id = r.id if r else "unknown"
             main_logger.log(f"Skipping removal request {r_id} since it was superseded.")
@@ -323,14 +305,12 @@ def command(  # noqa: C901
                 )
             elif skip_by_tag(r, include_tags, exclude_tags):
                 main_logger.log(
-                    "Skipping removal request %s, filtered by tag "
+                    f"Skipping removal request {r.id}, filtered by tag "
-                    "(include %s, exclude %s, present %s)"
+                    f"(include {include_tags}, exclude {exclude_tags}, present {r.attributes.tags})"
-                    % (r.id, include_tags, exclude_tags, r.attributes.tags)
                 )
             elif r.id in removals_by_request:
                 main_logger.log(
-                    f"Found satisfied request for {r.id} "
+                    f"Found satisfied request for {r.id} " f"at {removals_by_request[r.id].id}"
-                    f"at {removals_by_request[r.id].id}"
                 )
             elif r.attributes.deployment in removals_by_deployment:
                 main_logger.log(
@@ -344,8 +324,7 @@ def command(  # noqa: C901
                     requests_to_check_for_payment.append(r)
                 else:
                     main_logger.log(
-                        f"Skipping unsatisfied request {r.id} "
+                        f"Skipping unsatisfied request {r.id} " "because we have seen it before."
-                        "because we have seen it before."
                     )
         except Exception as e:
             main_logger.log(f"ERROR examining {r.id}: {e}")
@@ -370,9 +349,7 @@ def command(  # noqa: C901
     else:
         requests_to_execute = requests_to_check_for_payment
 
-    main_logger.log(
+    main_logger.log(f"Found {len(requests_to_execute)} unsatisfied request(s) to process.")
-        "Found %d unsatisfied request(s) to process." % len(requests_to_execute)
-    )
 
     if not dry_run:
         for r in requests_to_execute:

stack_orchestrator/deploy/webapp/util.py

@@ -22,10 +22,10 @@ import subprocess
 import sys
 import tempfile
 import uuid
-import yaml
-
 from enum import Enum
-from typing import Any, List, Optional, TextIO
+from typing import Any, TextIO
+
+import yaml
 
 from stack_orchestrator.deploy.webapp.registry_mutex import registry_mutex
 
@@ -43,17 +43,17 @@ AUCTION_KIND_PROVIDER = "provider"
 
 class AttrDict(dict):
     def __init__(self, *args: Any, **kwargs: Any) -> None:
-        super(AttrDict, self).__init__(*args, **kwargs)
+        super().__init__(*args, **kwargs)
         self.__dict__ = self
 
     def __getattribute__(self, attr: str) -> Any:
-        __dict__ = super(AttrDict, self).__getattribute__("__dict__")
+        __dict__ = super().__getattribute__("__dict__")
         if attr in __dict__:
-            v = super(AttrDict, self).__getattribute__(attr)
+            v = super().__getattribute__(attr)
             if isinstance(v, dict):
                 return AttrDict(v)
             return v
-        return super(AttrDict, self).__getattribute__(attr)
+        return super().__getattribute__(attr)
 
     def __getattr__(self, attr: str) -> Any:
         # This method is called when attribute is not found
@@ -62,15 +62,13 @@ class AttrDict(dict):
 
 
 class TimedLogger:
-    def __init__(self, id: str = "", file: Optional[TextIO] = None) -> None:
+    def __init__(self, id: str = "", file: TextIO | None = None) -> None:
         self.start = datetime.datetime.now()
         self.last = self.start
         self.id = id
         self.file = file
 
-    def log(
+    def log(self, msg: str, show_step_time: bool = True, show_total_time: bool = False) -> None:
-        self, msg: str, show_step_time: bool = True, show_total_time: bool = False
-    ) -> None:
         prefix = f"{datetime.datetime.utcnow()} - {self.id}"
         if show_step_time:
             prefix += f" - {datetime.datetime.now() - self.last} (step)"
@@ -84,11 +82,11 @@ class TimedLogger:
 
 def load_known_requests(filename):
     if filename and os.path.exists(filename):
-        return json.load(open(filename, "r"))
+        return json.load(open(filename))
     return {}
 
 
-def logged_cmd(log_file: Optional[TextIO], *vargs: str) -> str:
+def logged_cmd(log_file: TextIO | None, *vargs: str) -> str:
     result = None
     try:
         if log_file:
@@ -105,15 +103,14 @@ def logged_cmd(log_file: Optional[TextIO], *vargs: str) -> str:
         raise err
 
 
-def match_owner(
+def match_owner(recordA: AttrDict | None, *records: AttrDict | None) -> str | None:
-    recordA: Optional[AttrDict], *records: Optional[AttrDict]
-) -> Optional[str]:
     if not recordA or not recordA.owners:
         return None
     for owner in recordA.owners:
         for otherRecord in records:
             if otherRecord and otherRecord.owners and owner in otherRecord.owners:
-                return owner
+                result: str | None = owner
+                return result
     return None
 
 
@@ -147,9 +144,7 @@ class LaconicRegistryClient:
             return self.cache["whoami"]
 
         args = ["laconic", "-c", self.config_file, "registry", "account", "get"]
-        results = [
+        results = [AttrDict(r) for r in json.loads(logged_cmd(self.log_file, *args)) if r]
-            AttrDict(r) for r in json.loads(logged_cmd(self.log_file, *args)) if r
-        ]
 
         if len(results):
             self.cache["whoami"] = results[0]
@@ -178,9 +173,7 @@ class LaconicRegistryClient:
             "--address",
             address,
         ]
-        results = [
+        results = [AttrDict(r) for r in json.loads(logged_cmd(self.log_file, *args)) if r]
-            AttrDict(r) for r in json.loads(logged_cmd(self.log_file, *args)) if r
-        ]
         if len(results):
             self.cache["accounts"][address] = results[0]
             return results[0]
@@ -203,9 +196,7 @@ class LaconicRegistryClient:
             "--id",
             id,
         ]
-        results = [
+        results = [AttrDict(r) for r in json.loads(logged_cmd(self.log_file, *args)) if r]
-            AttrDict(r) for r in json.loads(logged_cmd(self.log_file, *args)) if r
-        ]
         self._add_to_cache(results)
         if len(results):
             return results[0]
@@ -216,9 +207,7 @@ class LaconicRegistryClient:
 
     def list_bonds(self):
         args = ["laconic", "-c", self.config_file, "registry", "bond", "list"]
-        results = [
+        results = [AttrDict(r) for r in json.loads(logged_cmd(self.log_file, *args)) if r]
-            AttrDict(r) for r in json.loads(logged_cmd(self.log_file, *args)) if r
-        ]
         self._add_to_cache(results)
         return results
 
@@ -232,12 +221,10 @@ class LaconicRegistryClient:
 
         if criteria:
             for k, v in criteria.items():
-                args.append("--%s" % k)
+                args.append(f"--{k}")
                 args.append(str(v))
 
-        results = [
+        results = [AttrDict(r) for r in json.loads(logged_cmd(self.log_file, *args)) if r]
-            AttrDict(r) for r in json.loads(logged_cmd(self.log_file, *args)) if r
-        ]
 
         # Most recent records first
         results.sort(key=lambda r: r.createTime or "")
@@ -246,7 +233,7 @@ class LaconicRegistryClient:
 
         return results
 
-    def _add_to_cache(self, records: List[AttrDict]) -> None:
+    def _add_to_cache(self, records: list[AttrDict]) -> None:
         if not records:
             return
 
@@ -271,9 +258,7 @@ class LaconicRegistryClient:
 
         args = ["laconic", "-c", self.config_file, "registry", "name", "resolve", name]
 
-        parsed = [
+        parsed = [AttrDict(r) for r in json.loads(logged_cmd(self.log_file, *args)) if r]
-            AttrDict(r) for r in json.loads(logged_cmd(self.log_file, *args)) if r
-        ]
         if parsed:
             self._add_to_cache(parsed)
             return parsed[0]
@@ -303,9 +288,7 @@ class LaconicRegistryClient:
             name_or_id,
         ]
 
-        parsed = [
+        parsed = [AttrDict(r) for r in json.loads(logged_cmd(self.log_file, *args)) if r]
-            AttrDict(r) for r in json.loads(logged_cmd(self.log_file, *args)) if r
-        ]
         if len(parsed):
             self._add_to_cache(parsed)
             return parsed[0]
@@ -356,9 +339,7 @@ class LaconicRegistryClient:
 
         results = None
         try:
-            results = [
+            results = [AttrDict(r) for r in json.loads(logged_cmd(self.log_file, *args)) if r]
-                AttrDict(r) for r in json.loads(logged_cmd(self.log_file, *args)) if r
-            ]
         except:  # noqa: E722
             pass
 
@@ -422,7 +403,7 @@ class LaconicRegistryClient:
             record_file = open(record_fname, "w")
             yaml.dump(record, record_file)
             record_file.close()
-            print(open(record_fname, "r").read(), file=self.log_file)
+            print(open(record_fname).read(), file=self.log_file)
 
             new_record_id = json.loads(
                 logged_cmd(
@@ -573,10 +554,10 @@ def determine_base_container(clone_dir, app_type="webapp"):
 
 
 def build_container_image(
-    app_record: Optional[AttrDict],
+    app_record: AttrDict | None,
     tag: str,
-    extra_build_args: Optional[List[str]] = None,
+    extra_build_args: list[str] | None = None,
-    logger: Optional[TimedLogger] = None,
+    logger: TimedLogger | None = None,
 ) -> None:
     if app_record is None:
         raise ValueError("app_record cannot be None")
@@ -649,9 +630,7 @@ def build_container_image(
             )
             result.check_returncode()
 
-        base_container = determine_base_container(
+        base_container = determine_base_container(clone_dir, app_record.attributes.app_type)
-            clone_dir, app_record.attributes.app_type
-        )
 
         if logger:
             logger.log("Building webapp ...")
@@ -696,7 +675,7 @@ def deploy_to_k8s(deploy_record, deployment_dir, recreate, logger):
         if not deploy_record:
             commands_to_run = ["start"]
         else:
-            commands_to_run = ["update"]
+            commands_to_run = ["update-envs"]
 
     for command in commands_to_run:
         logger.log(f"Running {command} command on deployment dir: {deployment_dir}")
@@ -727,14 +706,12 @@ def publish_deployment(
     if not deploy_record:
         deploy_ver = "0.0.1"
     else:
-        deploy_ver = "0.0.%d" % (
+        deploy_ver = f"0.0.{int(deploy_record.attributes.version.split('.')[-1]) + 1}"
-            int(deploy_record.attributes.version.split(".")[-1]) + 1
-        )
 
     if not dns_record:
         dns_ver = "0.0.1"
     else:
-        dns_ver = "0.0.%d" % (int(dns_record.attributes.version.split(".")[-1]) + 1)
+        dns_ver = f"0.0.{int(dns_record.attributes.version.split('.')[-1]) + 1}"
 
     spec = yaml.full_load(open(os.path.join(deployment_dir, "spec.yml")))
     fqdn = spec["network"]["http-proxy"][0]["host-name"]
@@ -779,13 +756,9 @@ def publish_deployment(
 
         # Set auction or payment id from request
         if app_deployment_request.attributes.auction:
-            new_deployment_record["record"][
+            new_deployment_record["record"]["auction"] = app_deployment_request.attributes.auction
-                "auction"
-            ] = app_deployment_request.attributes.auction
         elif app_deployment_request.attributes.payment:
-            new_deployment_record["record"][
+            new_deployment_record["record"]["payment"] = app_deployment_request.attributes.payment
-                "payment"
-            ] = app_deployment_request.attributes.payment
 
     if webapp_deployer_record:
         new_deployment_record["record"]["deployer"] = webapp_deployer_record.names[0]
@@ -799,9 +772,7 @@ def publish_deployment(
 def hostname_for_deployment_request(app_deployment_request, laconic):
     dns_name = app_deployment_request.attributes.dns
     if not dns_name:
-        app = laconic.get_record(
+        app = laconic.get_record(app_deployment_request.attributes.application, require=True)
-            app_deployment_request.attributes.application, require=True
-        )
         dns_name = generate_hostname_for_app(app)
     elif dns_name.startswith("lrn://"):
         record = laconic.get_record(dns_name, require=True)
@@ -818,7 +789,7 @@ def generate_hostname_for_app(app):
         m.update(app.attributes.repository[0].encode())
     else:
         m.update(app.attributes.repository.encode())
-    return "%s-%s" % (last_part, m.hexdigest()[0:10])
+    return f"{last_part}-{m.hexdigest()[0:10]}"
 
 
 def skip_by_tag(r, include_tags, exclude_tags):
@@ -881,16 +852,13 @@ def confirm_payment(
     pay_denom = "".join([i for i in tx_amount if not i.isdigit()])
     if pay_denom != "alnt":
         logger.log(
-            f"{record.id}: {pay_denom} in tx {tx.hash} is not an expected "
+            f"{record.id}: {pay_denom} in tx {tx.hash} is not an expected " "payment denomination"
-            "payment denomination"
         )
         return False
 
     pay_amount = int("".join([i for i in tx_amount if i.isdigit()]) or "0")
     if pay_amount < min_amount:
-        logger.log(
+        logger.log(f"{record.id}: payment amount {tx.amount} is less than minimum {min_amount}")
-            f"{record.id}: payment amount {tx.amount} is less than minimum {min_amount}"
-        )
         return False
 
     # Check if the payment was already used on a deployment
@@ -914,9 +882,7 @@ def confirm_payment(
         {"deployer": record.attributes.deployer, "payment": tx.hash}, all=True
     )
     if len(used):
-        logger.log(
+        logger.log(f"{record.id}: payment {tx.hash} already used on deployment removal {used}")
-            f"{record.id}: payment {tx.hash} already used on deployment removal {used}"
-        )
         return False
 
     return True
@@ -940,9 +906,7 @@ def confirm_auction(
 
     # Cross check app against application in the auction record
     requested_app = laconic.get_record(record.attributes.application, require=True)
-    auction_app = laconic.get_record(
+    auction_app = laconic.get_record(auction_records_by_id[0].attributes.application, require=True)
-        auction_records_by_id[0].attributes.application, require=True
-    )
     requested_app_id = requested_app.id if requested_app else None
     auction_app_id = auction_app.id if auction_app else None
     if requested_app_id != auction_app_id:

stack_orchestrator/main.py

@@ -15,30 +15,24 @@
 
 import click
 
+from stack_orchestrator import opts, update, version
+from stack_orchestrator.build import build_containers, build_npms, build_webapp, fetch_containers
 from stack_orchestrator.command_types import CommandOptions
-from stack_orchestrator.repos import setup_repositories
+from stack_orchestrator.deploy import deploy, deployment
-from stack_orchestrator.repos import fetch_stack
-from stack_orchestrator.build import build_containers, fetch_containers
-from stack_orchestrator.build import build_npms
-from stack_orchestrator.build import build_webapp
 from stack_orchestrator.deploy.webapp import (
-    run_webapp,
     deploy_webapp,
     deploy_webapp_from_registry,
-    undeploy_webapp_from_registry,
-    publish_webapp_deployer,
-    publish_deployment_auction,
     handle_deployment_auction,
+    publish_deployment_auction,
+    publish_webapp_deployer,
     request_webapp_deployment,
     request_webapp_undeployment,
+    run_webapp,
+    undeploy_webapp_from_registry,
 )
-from stack_orchestrator.deploy import deploy
+from stack_orchestrator.repos import fetch_stack, setup_repositories
-from stack_orchestrator import version
-from stack_orchestrator.deploy import deployment
-from stack_orchestrator import opts
-from stack_orchestrator import update
 
-CONTEXT_SETTINGS = dict(help_option_names=["-h", "--help"])
+CONTEXT_SETTINGS = {"help_option_names": ["-h", "--help"]}
 
 
 @click.group(context_settings=CONTEXT_SETTINGS)

stack_orchestrator/repos/fetch_stack.py

@@ -17,9 +17,9 @@
 # CERC_REPO_BASE_DIR defaults to ~/cerc
 
 
-import click
 import os
 
+import click
 from decouple import config
 from git import exc
 
@@ -36,9 +36,7 @@ from stack_orchestrator.util import error_exit
 @click.pass_context
 def command(ctx, stack_locator, git_ssh, check_only, pull):
     """Optionally resolve then git clone a repository with stack definitions."""
-    dev_root_path = os.path.expanduser(
+    dev_root_path = os.path.expanduser(str(config("CERC_REPO_BASE_DIR", default="~/cerc")))
-        str(config("CERC_REPO_BASE_DIR", default="~/cerc"))
-    )
     if not opts.o.quiet:
         print(f"Dev Root is: {dev_root_path}")
     try:

stack_orchestrator/repos/setup_repositories.py

@@ -16,20 +16,22 @@
 # env vars:
 # CERC_REPO_BASE_DIR defaults to ~/cerc
 
+import importlib.resources
 import os
 import sys
-from decouple import config
-import git
-from git.exc import GitCommandError, InvalidGitRepositoryError
 from typing import Any
-from tqdm import tqdm
+
 import click
-import importlib.resources
+import git
+from decouple import config
+from git.exc import GitCommandError, InvalidGitRepositoryError
+from tqdm import tqdm
+
 from stack_orchestrator.opts import opts
 from stack_orchestrator.util import (
+    error_exit,
     get_parsed_stack_config,
     include_exclude_check,
-    error_exit,
     warn_exit,
 )
 
@@ -86,48 +88,38 @@ def _get_repo_current_branch_or_tag(full_filesystem_repo_path):
     current_repo_branch_or_tag = "***UNDETERMINED***"
     is_branch = False
     try:
-        current_repo_branch_or_tag = git.Repo(
+        current_repo_branch_or_tag = git.Repo(full_filesystem_repo_path).active_branch.name
-            full_filesystem_repo_path
-        ).active_branch.name
         is_branch = True
     except TypeError:
         # This means that the current ref is not a branch, so possibly a tag
         # Let's try to get the tag
         try:
-            current_repo_branch_or_tag = git.Repo(
+            current_repo_branch_or_tag = git.Repo(full_filesystem_repo_path).git.describe(
-                full_filesystem_repo_path
+                "--tags", "--exact-match"
-            ).git.describe("--tags", "--exact-match")
+            )
             # Note that git is asymmetric -- the tag you told it to check out
             # may not be the one you get back here (if there are multiple tags
             # associated with the same commit)
         except GitCommandError:
             # If there is no matching branch or tag checked out, just use the current
             # SHA
-            current_repo_branch_or_tag = (
+            current_repo_branch_or_tag = git.Repo(full_filesystem_repo_path).commit("HEAD").hexsha
-                git.Repo(full_filesystem_repo_path).commit("HEAD").hexsha
-            )
     return current_repo_branch_or_tag, is_branch
 
 
 # TODO: fix the messy arg list here
-def process_repo(
+def process_repo(pull, check_only, git_ssh, dev_root_path, branches_array, fully_qualified_repo):
-    pull, check_only, git_ssh, dev_root_path, branches_array, fully_qualified_repo
-):
     if opts.o.verbose:
         print(f"Processing repo: {fully_qualified_repo}")
     repo_host, repo_path, repo_branch = host_and_path_for_repo(fully_qualified_repo)
     git_ssh_prefix = f"git@{repo_host}:"
     git_http_prefix = f"https://{repo_host}/"
-    full_github_repo_path = (
+    full_github_repo_path = f"{git_ssh_prefix if git_ssh else git_http_prefix}{repo_path}"
-        f"{git_ssh_prefix if git_ssh else git_http_prefix}{repo_path}"
-    )
     repoName = repo_path.split("/")[-1]
     full_filesystem_repo_path = os.path.join(dev_root_path, repoName)
     is_present = os.path.isdir(full_filesystem_repo_path)
     (current_repo_branch_or_tag, is_branch) = (
-        _get_repo_current_branch_or_tag(full_filesystem_repo_path)
+        _get_repo_current_branch_or_tag(full_filesystem_repo_path) if is_present else (None, None)
-        if is_present
-        else (None, None)
     )
     if not opts.o.quiet:
         present_text = (
@@ -140,10 +132,7 @@ def process_repo(
     # Quick check that it's actually a repo
     if is_present:
         if not is_git_repo(full_filesystem_repo_path):
-            print(
+            print(f"Error: {full_filesystem_repo_path} does not contain " "a valid git repository")
-                f"Error: {full_filesystem_repo_path} does not contain "
-                "a valid git repository"
-            )
             sys.exit(1)
         else:
             if pull:
@@ -190,8 +179,7 @@ def process_repo(
 
     if branch_to_checkout:
         if current_repo_branch_or_tag is None or (
-            current_repo_branch_or_tag
+            current_repo_branch_or_tag and (current_repo_branch_or_tag != branch_to_checkout)
-            and (current_repo_branch_or_tag != branch_to_checkout)
         ):
             if not opts.o.quiet:
                 print(f"switching to branch {branch_to_checkout} in repo {repo_path}")
@@ -245,14 +233,9 @@ def command(ctx, include, exclude, git_ssh, check_only, pull, branches):
 
     if local_stack:
         dev_root_path = os.getcwd()[0 : os.getcwd().rindex("stack-orchestrator")]
-        print(
+        print(f"Local stack dev_root_path (CERC_REPO_BASE_DIR) overridden to: " f"{dev_root_path}")
-            f"Local stack dev_root_path (CERC_REPO_BASE_DIR) overridden to: "
-            f"{dev_root_path}"
-        )
     else:
-        dev_root_path = os.path.expanduser(
+        dev_root_path = os.path.expanduser(str(config("CERC_REPO_BASE_DIR", default="~/cerc")))
-            str(config("CERC_REPO_BASE_DIR", default="~/cerc"))
-        )
 
     if not quiet:
         print(f"Dev Root is: {dev_root_path}")
@@ -265,9 +248,7 @@ def command(ctx, include, exclude, git_ssh, check_only, pull, branches):
     # See: https://stackoverflow.com/a/20885799/1701505
     from stack_orchestrator import data
 
-    with importlib.resources.open_text(
+    with importlib.resources.open_text(data, "repository-list.txt") as repository_list_file:
-        data, "repository-list.txt"
-    ) as repository_list_file:
         all_repos = repository_list_file.read().splitlines()
 
     repos_in_scope = []

stack_orchestrator/update.py

@@ -13,16 +13,18 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with this program.  If not, see <http:#www.gnu.org/licenses/>.
 
-import click
 import datetime
 import filecmp
 import os
-from pathlib import Path
-import requests
-import sys
-import stat
 import shutil
+import stat
+import sys
+from pathlib import Path
+
+import click
+import requests
 import validators
+
 from stack_orchestrator.util import get_yaml
 
 
@@ -40,9 +42,7 @@ def _error_exit(s: str):
 
 # Note at present this probably won't work on non-Unix based OSes like Windows
 @click.command()
-@click.option(
+@click.option("--check-only", is_flag=True, default=False, help="only check, don't update")
-    "--check-only", is_flag=True, default=False, help="only check, don't update"
-)
 @click.pass_context
 def command(ctx, check_only):
     """update shiv binary from a distribution url"""
@@ -52,7 +52,7 @@ def command(ctx, check_only):
     if not config_file_path.exists():
         _error_exit(f"Error: Config file: {config_file_path} not found")
     yaml = get_yaml()
-    config = yaml.load(open(config_file_path, "r"))
+    config = yaml.load(open(config_file_path))
     if "distribution-url" not in config:
         _error_exit(f"Error: {config_key} not defined in {config_file_path}")
     distribution_url = config[config_key]
@@ -61,9 +61,7 @@ def command(ctx, check_only):
         _error_exit(f"ERROR: distribution url: {distribution_url} is not valid")
     # Figure out the filename for ourselves
     shiv_binary_path = Path(sys.argv[0])
-    timestamp_filename = (
+    timestamp_filename = f"laconic-so-download-{datetime.datetime.now().strftime('%y%m%d-%H%M%S')}"
-        f"laconic-so-download-{datetime.datetime.now().strftime('%y%m%d-%H%M%S')}"
-    )
     temp_download_path = shiv_binary_path.parent.joinpath(timestamp_filename)
     # Download the file to a temp filename
     if ctx.obj.verbose:

stack_orchestrator/util.py

@@ -13,14 +13,17 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with this program.  If not, see <http:#www.gnu.org/licenses/>.
 
-from decouple import config
 import os.path
 import sys
-import ruamel.yaml
+from collections.abc import Mapping
 from pathlib import Path
+from typing import NoReturn
+
+import ruamel.yaml
+from decouple import config
 from dotenv import dotenv_values
-from typing import Mapping, NoReturn, Optional, Set, List
+
-from stack_orchestrator.constants import stack_file_name, deployment_file_name
+from stack_orchestrator.constants import deployment_file_name, stack_file_name
 
 
 def include_exclude_check(s, include, exclude):
@@ -50,14 +53,9 @@ def get_dev_root_path(ctx):
     if ctx and ctx.local_stack:
         # TODO: This code probably doesn't work
         dev_root_path = os.getcwd()[0 : os.getcwd().rindex("stack-orchestrator")]
-        print(
+        print(f"Local stack dev_root_path (CERC_REPO_BASE_DIR) overridden to: " f"{dev_root_path}")
-            f"Local stack dev_root_path (CERC_REPO_BASE_DIR) overridden to: "
-            f"{dev_root_path}"
-        )
     else:
-        dev_root_path = os.path.expanduser(
+        dev_root_path = os.path.expanduser(str(config("CERC_REPO_BASE_DIR", default="~/cerc")))
-            str(config("CERC_REPO_BASE_DIR", default="~/cerc"))
-        )
     return dev_root_path
 
 
@@ -65,7 +63,7 @@ def get_dev_root_path(ctx):
 def get_parsed_stack_config(stack):
     stack_file_path = get_stack_path(stack).joinpath(stack_file_name)
     if stack_file_path.exists():
-        return get_yaml().load(open(stack_file_path, "r"))
+        return get_yaml().load(open(stack_file_path))
     # We try here to generate a useful diagnostic error
     # First check if the stack directory is present
     if stack_file_path.parent.exists():
@@ -101,10 +99,10 @@ def get_job_list(parsed_stack):
     return result
 
 
-def get_plugin_code_paths(stack) -> List[Path]:
+def get_plugin_code_paths(stack) -> list[Path]:
     parsed_stack = get_parsed_stack_config(stack)
     pods = parsed_stack["pods"]
-    result: Set[Path] = set()
+    result: set[Path] = set()
     for pod in pods:
         if type(pod) is str:
             result.add(get_stack_path(stack))
@@ -191,7 +189,7 @@ def get_job_file_path(stack, parsed_stack, job_name: str):
 def get_pod_script_paths(parsed_stack, pod_name: str):
     pods = parsed_stack["pods"]
     result = []
-    if not type(pods[0]) is str:
+    if type(pods[0]) is not str:
         for pod in pods:
             if pod["name"] == pod_name:
                 pod_root_dir = os.path.join(
@@ -243,7 +241,7 @@ def get_k8s_dir():
 def get_parsed_deployment_spec(spec_file):
     spec_file_path = Path(spec_file)
     try:
-        return get_yaml().load(open(spec_file_path, "r"))
+        return get_yaml().load(open(spec_file_path))
     except FileNotFoundError as error:
         # We try here to generate a useful diagnostic error
         print(f"Error: spec file: {spec_file_path} does not exist")
@@ -293,5 +291,6 @@ def warn_exit(s) -> NoReturn:
     sys.exit(0)
 
 
-def env_var_map_from_file(file: Path) -> Mapping[str, Optional[str]]:
+def env_var_map_from_file(file: Path) -> Mapping[str, str | None]:
-    return dotenv_values(file)
+    result: Mapping[str, str | None] = dotenv_values(file)
+    return result

stack_orchestrator/version.py

@@ -13,8 +13,9 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with this program.  If not, see <http:#www.gnu.org/licenses/>.
 
+from importlib import metadata, resources
+
 import click
-from importlib import resources, metadata
 
 
 @click.command()

tests/database/run-test.sh

@@ -86,7 +86,7 @@ fi
 echo "deploy init test: passed"
 
 # Switch to a full path for the data dir so it gets provisioned as a host bind mounted volume and preserved beyond cluster lifetime
-sed -i "s|^\(\s*db-data:$\)$|\1 ${test_deployment_dir}/data/db-data|" $test_deployment_spec
+sed -i.bak "s|^\(\s*db-data:$\)$|\1 ${test_deployment_dir}/data/db-data|" $test_deployment_spec
 
 $TEST_TARGET_SO --stack ${stack} deploy create --spec-file $test_deployment_spec --deployment-dir $test_deployment_dir
 # Check the deployment dir exists

tests/deploy/run-deploy-test.sh

@@ -34,6 +34,7 @@ mkdir -p $CERC_REPO_BASE_DIR
 # with and without volume removal
 $TEST_TARGET_SO --stack test setup-repositories
 $TEST_TARGET_SO --stack test build-containers
+
 # Test deploy command execution
 $TEST_TARGET_SO --stack test deploy setup $CERC_REPO_BASE_DIR
 # Check that we now have the expected output directory
@@ -85,6 +86,7 @@ else
     exit 1
 fi
 $TEST_TARGET_SO --stack test deploy down --delete-volumes
+
 # Basic test of creating a deployment
 test_deployment_dir=$CERC_REPO_BASE_DIR/test-deployment-dir
 test_deployment_spec=$CERC_REPO_BASE_DIR/test-deployment-spec.yml
@@ -122,6 +124,101 @@ fi
 echo "dbfc7a4d-44a7-416d-b5f3-29842cc47650" > $test_deployment_dir/data/test-config/test_config
 
 echo "deploy create output file test: passed"
+
+# Test sync functionality: update deployment without destroying data
+# First, create a marker file in the data directory to verify it's preserved
+test_data_marker="$test_deployment_dir/data/test-data-bind/sync-test-marker.txt"
+echo "original-data-$(date +%s)" > "$test_data_marker"
+original_marker_content=$(<$test_data_marker)
+
+# Modify a config file in the deployment to differ from source (to test backup)
+test_config_file="$test_deployment_dir/config/test/settings.env"
+test_config_file_original_content=$(<$test_config_file)
+test_config_file_changed_content="ANSWER=69"
+echo "$test_config_file_changed_content" > "$test_config_file"
+
+# Check a config file that matches the source (to test no backup for unchanged files)
+test_unchanged_config="$test_deployment_dir/config/test/script.sh"
+
+# Modify spec file to simulate an update
+sed -i.bak 's/CERC_TEST_PARAM_3:/CERC_TEST_PARAM_3: FASTER/' $test_deployment_spec
+
+# Create/modify config.env to test it isn't overwritten during sync
+config_env_file="$test_deployment_dir/config.env"
+config_env_persistent_content="PERSISTENT_VALUE=should-not-be-overwritten-$(date +%s)"
+echo "$config_env_persistent_content" >> "$config_env_file"
+original_config_env_content=$(<$config_env_file)
+
+# Run sync to update deployment files without destroying data
+$TEST_TARGET_SO --stack test deploy create --spec-file $test_deployment_spec --deployment-dir $test_deployment_dir --update
+
+# Verify config.env was not overwritten
+synced_config_env_content=$(<$config_env_file)
+if [ "$synced_config_env_content" == "$original_config_env_content" ]; then
+    echo "deployment update test: config.env preserved - passed"
+else
+    echo "deployment update test: config.env was overwritten - FAILED"
+    echo "Expected: $original_config_env_content"
+    echo "Got: $synced_config_env_content"
+    exit 1
+fi
+
+# Verify the spec file was updated in deployment dir
+updated_deployed_spec=$(<$test_deployment_dir/spec.yml)
+if [[ "$updated_deployed_spec" == *"FASTER"* ]]; then
+    echo "deployment update test: spec file updated"
+else
+    echo "deployment update test: spec file not updated - FAILED"
+    exit 1
+fi
+
+# Verify changed config file was backed up
+test_config_backup="${test_config_file}.bak"
+if [ -f "$test_config_backup" ]; then
+    backup_content=$(<$test_config_backup)
+    if [ "$backup_content" == "$test_config_file_changed_content" ]; then
+        echo "deployment update test: changed config file backed up - passed"
+    else
+        echo "deployment update test: backup content incorrect - FAILED"
+        exit 1
+    fi
+else
+    echo "deployment update test: backup file not created for changed file - FAILED"
+    exit 1
+fi
+
+# Verify unchanged config file was NOT backed up
+test_unchanged_backup="$test_unchanged_config.bak"
+if [ -f "$test_unchanged_backup" ]; then
+    echo "deployment update test: backup created for unchanged file - FAILED"
+    exit 1
+else
+    echo "deployment update test: no backup for unchanged file - passed"
+fi
+
+# Verify the config file was updated from source
+updated_config_content=$(<$test_config_file)
+if [ "$updated_config_content" == "$test_config_file_original_content" ]; then
+    echo "deployment update test: config file updated from source - passed"
+else
+    echo "deployment update test: config file not updated correctly - FAILED"
+    exit 1
+fi
+
+# Verify the data marker file still exists with original content
+if [ ! -f "$test_data_marker" ]; then
+    echo "deployment update test: data file deleted - FAILED"
+    exit 1
+fi
+synced_marker_content=$(<$test_data_marker)
+if [ "$synced_marker_content" == "$original_marker_content" ]; then
+    echo "deployment update test: data preserved - passed"
+else
+    echo "deployment update test: data corrupted - FAILED"
+    exit 1
+fi
+echo "deployment update test: passed"
+
 # Try to start the deployment
 $TEST_TARGET_SO deployment --dir $test_deployment_dir start
 # Check logs command works

tests/external-stack/run-test.sh

@@ -125,6 +125,49 @@ fi
 echo "dbfc7a4d-44a7-416d-b5f3-29842cc47650" > $test_deployment_dir/data/test-config/test_config
 
 echo "deploy create output file test: passed"
+
+# Test sync functionality: update deployment without destroying data
+# First, create a marker file in the data directory to verify it's preserved
+test_data_marker="$test_deployment_dir/data/test-data/sync-test-marker.txt"
+mkdir -p "$test_deployment_dir/data/test-data"
+echo "external-stack-data-$(date +%s)" > "$test_data_marker"
+original_marker_content=$(<$test_data_marker)
+# Verify deployment file exists and preserve its cluster ID
+original_cluster_id=$(grep "cluster-id:" "$test_deployment_dir/deployment.yml" 2>/dev/null || echo "")
+# Modify spec file to simulate an update
+sed -i.bak 's/CERC_TEST_PARAM_1=PASSED/CERC_TEST_PARAM_1=UPDATED/' $test_deployment_spec
+# Run sync to update deployment files without destroying data
+$TEST_TARGET_SO_STACK deploy create --spec-file $test_deployment_spec --deployment-dir $test_deployment_dir --update
+# Verify the spec file was updated in deployment dir
+updated_deployed_spec=$(<$test_deployment_dir/spec.yml)
+if [[ "$updated_deployed_spec" == *"UPDATED"* ]]; then
+    echo "deploy sync test: spec file updated"
+else
+    echo "deploy sync test: spec file not updated - FAILED"
+    exit 1
+fi
+# Verify the data marker file still exists with original content
+if [ ! -f "$test_data_marker" ]; then
+    echo "deploy sync test: data file deleted - FAILED"
+    exit 1
+fi
+synced_marker_content=$(<$test_data_marker)
+if [ "$synced_marker_content" == "$original_marker_content" ]; then
+    echo "deploy sync test: data preserved - passed"
+else
+    echo "deploy sync test: data corrupted - FAILED"
+    exit 1
+fi
+# Verify cluster ID was preserved (not regenerated)
+new_cluster_id=$(grep "cluster-id:" "$test_deployment_dir/deployment.yml" 2>/dev/null || echo "")
+if [ -n "$original_cluster_id" ] && [ "$original_cluster_id" == "$new_cluster_id" ]; then
+    echo "deploy sync test: cluster ID preserved - passed"
+else
+    echo "deploy sync test: cluster ID not preserved - FAILED"
+    exit 1
+fi
+echo "deploy sync test: passed"
+
 # Try to start the deployment
 $TEST_TARGET_SO deployment --dir $test_deployment_dir start
 # Check logs command works

tests/scripts/run-test-local.sh

@@ -0,0 +1,53 @@
+#!/bin/bash
+# Run a test suite locally in an isolated venv.
+#
+# Usage:
+#   ./tests/scripts/run-test-local.sh <test-script>
+#
+# Examples:
+#   ./tests/scripts/run-test-local.sh tests/webapp-test/run-webapp-test.sh
+#   ./tests/scripts/run-test-local.sh tests/smoke-test/run-smoke-test.sh
+#   ./tests/scripts/run-test-local.sh tests/k8s-deploy/run-deploy-test.sh
+#
+# The script creates a temporary venv, installs shiv, builds the laconic-so
+# package, runs the requested test, then cleans up.
+
+set -euo pipefail
+
+if [ $# -lt 1 ]; then
+  echo "Usage: $0 <test-script> [args...]"
+  exit 1
+fi
+
+TEST_SCRIPT="$1"
+shift
+
+if [ ! -f "$TEST_SCRIPT" ]; then
+  echo "Error: $TEST_SCRIPT not found"
+  exit 1
+fi
+
+REPO_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/../.." && pwd)"
+VENV_DIR=$(mktemp -d /tmp/so-test-XXXXXX)
+
+cleanup() {
+  echo "Cleaning up venv: $VENV_DIR"
+  rm -rf "$VENV_DIR"
+}
+trap cleanup EXIT
+
+cd "$REPO_DIR"
+
+echo "==> Creating venv in $VENV_DIR"
+python3 -m venv "$VENV_DIR"
+source "$VENV_DIR/bin/activate"
+
+echo "==> Installing shiv"
+pip install -q shiv
+
+echo "==> Building laconic-so package"
+./scripts/create_build_tag_file.sh
+./scripts/build_shiv_package.sh
+
+echo "==> Running: $TEST_SCRIPT $*"
+exec "./$TEST_SCRIPT" "$@"