feat: new pre-commit hook to update Nextflow manifest version

[Copilot]

Changes

• added ccbr-hooks sync-nextflow-version
• registered it in .pre-commit-hooks.yaml
• added tests for update/skip/error/no-op behavior and improved hook coverage
• updated hook docs in README.md, CHANGELOG.md, and hooks module metadata

Behavior:

• skips when repo-root nextflow.config is absent
• raises an error if nextflow.config exists but repo-root VERSION is missing
• lets manifest.version lookup errors bubble up
• updates manifest.version in nextflow.config from VERSION

Validation:

python -m pytest tests/test_hooks.py --cov=ccbr_tools.hooks.sync_nextflow_version --cov-report=term-missing ✅
pre-commit run --files ...changed files... ✅
codeql_checker ✅ no alerts
secret scan ✅ no secrets

Issues

see CCBR/CCBR_NextflowTemplate#76

Pull request created by AI Agent

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 73.47%. Comparing base (83d7b57) to head (9c986f6).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #193      +/-   ##
==========================================
+ Coverage   72.84%   73.47%   +0.63%     
==========================================
  Files          27       28       +1     
  Lines        1893     1938      +45     
==========================================
+ Hits         1379     1424      +45     
  Misses        514      514              

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[kelly-sovacool]

improve the code coverage https://app.codecov.io/gh/CCBR/Tools/pull/193?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=CCBR

[Copilot]

Pull request overview

Adds a new ccbr-hooks sync-nextflow-version pre-commit hook intended to keep a Nextflow repo’s nextflow.config manifest.version synchronized with the repo-root VERSION file, and wires it into the hooks CLI, hook registry, docs, and tests.

Changes:

• Implement sync-nextflow-version hook (CLI + update_manifest_version() helper) to update manifest.version from VERSION.
• Register the hook in ccbr-hooks and .pre-commit-hooks.yaml.
• Add/extend tests and update README/CHANGELOG/docs metadata to reference the new hook.

Reviewed changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
tests/test_hooks.py	Adds unit tests for manifest updating and CLI behaviors (update/skip/error/no-op), plus CLI help coverage.
src/ccbr_tools/hooks/sync_nextflow_version.py	New hook implementation and helper for updating manifest.version inside nextflow.config.
src/ccbr_tools/hooks/__main__.py	Registers sync-nextflow-version with the ccbr-hooks Click command group.
src/ccbr_tools/hooks/__init__.py	Updates hooks module docstring to include the new hook.
README.md	Updates pre-commit example list to include the new hook.
CHANGELOG.md	Adds changelog entry documenting the new hook.
.pre-commit-hooks.yaml	Registers the hook for pre-commit, scoped to VERSION/nextflow.config changes.