Copier update (misc version bumps) (#74)

Pull in upstream template changes

<!-- This is an auto-generated comment: release notes by coderabbit.ai
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## Summary by CodeRabbit

* **New Features**
  * Added optional Claude CLI integration support.
  * Added control over Python version management during setup.

* **Chores**
  * Updated development dependencies and tools to latest versions.
  * Refreshed pre-commit hook configurations and exclusion patterns.
  * Updated documentation branding references.
  * Minor text corrections throughout configuration files.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

Copier update (fix get values CI job) (#72)

Pull in upstream template changes

Copier update (pre-commit bumps) (#71)

Pull in upstream template changes

<!-- This is an auto-generated comment: release notes by coderabbit.ai
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## Summary by CodeRabbit

* **Documentation**
* Clarified install instructions on where to source and place the setup
script.

* **Chores**
* Upgraded developer tooling versions (uv, pnpm, Pulumi, FastAPI,
Uvicorn, and frontend utilities).
  * Hardened installer with timeouts and retry logic.
* Added JSON Schema checks for GitHub workflows; broadened Prettier
exclusions.
  * Updated lint settings to ignore docstrings for magic methods.
* Disabled credential persistence in checkout steps across workflows and
updated tagging action version.
  * Added optional debugging to display full GitHub context.
* Adjusted security tooling to ignore a benign template-injection case.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

Copier update (bump pytest-cov) (#70)

## Why is this change necessary?

Pull in upstream changes



 ## How is this change tested?
Downstream repos

 ## Other
Also resolves
#58
by conditionally including those workflows

<!-- This is an auto-generated comment: release notes by coderabbit.ai
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## Summary by CodeRabbit

- New Features
- Added a CLI flag to generate lock files without installing
dependencies (--only-create-lock).

- Documentation
  - Updated README to reflect the new lock-generation flag.

- Chores
- Bumped tool and library versions (e.g., uv, copier, pytest plugins,
Pulumi, PyInstaller, ESLint, GraphQL codegen, Tailwind).
  - Updated devcontainer tooling to use newer versions.
  - Refreshed template context with latest dependency versions.

- Tests/Quality
- Expanded linter/type-checker exclusions to ignore generated code
(GraphQL/OpenAPI), reducing noise and false positives in checks.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

Copier update (github action versions) (#66)

## Why is this change necessary?
Keep up to date


 ## How does this change address the issue?
Pulls in upstream changes


 ## What side effects does this change have?
None


 ## How is this change tested?
downstream repo


 ## Other
also addresses
#63
and
#67

<!-- This is an auto-generated comment: release notes by coderabbit.ai
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## Summary by CodeRabbit

- New Features
- CI tooling: optional skip for SSM Plugin install and Windows support
for SSM Plugin.
  - Reusable Docker build workflow now exposes an artifact-name output.

- Chores
- Bumped many devcontainer extensions, tooling, dependencies, and GitHub
Action versions.
  - Removed obsolete manual dependency setup script.
  - Pre-commit workflow: added concurrency mutex.
- Publish flow: stricter import verification and changed PyPI install
timing/flags.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

Fix read contents CI permissions (#61)

## Why is this change necessary?
Read contents permission is lost when redefining permissions explicitly,
so any private repos fail to be able to checkout code


 ## How does this change address the issue?
explicitly grants read contents permission wherever permissions are
redefined and it's needed


 ## What side effects does this change have?
none


 ## How is this change tested?
downstream repo

Add support for SSM Port forwarding (#60)

## Why is this change necessary?
Some libraries need it


 ## How does this change address the issue?
Flip the flag in the template to allow using it


 ## What side effects does this change have?
Another question in the template


 ## How is this change tested?
Downstream repo


 ## Other
Pulled in some other misc upstream template changes

Copier update (Apple Silicon compatibility) (#59)

Pull in upstream template changes

Copier update (misc version bumps) (#56)

Pull in upstream changes

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

- New Features
  - None.

- Refactor
- Devcontainer now uses a workspace-relative Ruff configuration path for
easier portability.

- Chores
- Updated template/tooling versions in project context: Pulumi, Pulumi
AWS, boto3, Nuxt (to v4), added nuxt-icon, ESLint v9, Zod v4, and Apollo
(Nuxt) alpha.
- Pre-commit now excludes generated GraphQL files from end-of-file
fixes.
  - Bumped internal template version reference.

- Tests/Documentation/Style/Bug Fixes
  - No changes.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

Fix publish job permissions (#55)

## Why is this change necessary?
The publish job is currently missing permission to push the git tag

https://github.com/LabAutomationAndScreening/pyalab/actions/runs/16704553688/job/47280840075


 ## How does this change address the issue?
Adds permission


 ## What side effects does this change have?
None


 ## How is this change tested?
Can't until after merge


 ## Other
Also handled
#54
Also bumped up the sleep time for PyPI index to populate since there
have been cases where 60s was not enough

<!-- This is an auto-generated comment: release notes by coderabbit.ai
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## Summary by CodeRabbit

* **Chores**
* Increased wait time before package installation from PyPI registries
to improve reliability.
* Enhanced confirmation step to display the Python version before
importing the installed package.
  * Updated workflow permissions to support git tag creation.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->