Migrate CI workflows from conda to uv package manager

[Copilot]

Migration Plan: Conda to uv

• Update python-package.yml workflow to use uv instead of conda
  • Replace conda setup with uv setup
  • Update dependency installation commands
  • Update test execution commands
  • Update pre-commits job to use uv
• Update pages.yml workflow to use uv instead of conda
  • Replace conda setup with uv setup
  • Update dependency installation commands
  • Update sphinx build commands
  • Add pandoc installation step
  • Fix pandoc step indentation
• Update publish-to-pypi.yml workflow to use uv
• Fix caching configuration
  • Removed enable-cache: true from all workflows (project doesn't maintain uv.lock file)
• Run code review and security checks
  • Code review completed with no issues
  • CodeQL security check passed with no alerts

Summary

All CI workflows have been successfully migrated from conda/mamba to uv package manager. This change will significantly improve CI job performance:

Key Changes:

• Replaced conda-incubator/setup-miniconda@v3 with astral-sh/setup-uv@v4
• Changed all mamba install and pip install commands to uv pip install --system
• Removed conda environment activation commands
• Removed caching configuration (not applicable without uv.lock file)
• Added explicit pandoc installation step in pages workflow
• Simplified sphinx build commands (no longer need conda run wrapper)

Benefits:

• Faster dependency installation (uv is significantly faster than conda/mamba)
• Simpler workflow configuration (no environment management needed)
• No false failures from cache mismatches

Original prompt

Currently the ci jobs use conda environments but these are quite slow. Can you change the jobs to us uv as the package manager?

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[ColmTalbot]

@copilot this package doesn't keep a uv.lock file so the caching in the ci jobs is failing. You probably need to remove this.

[Copilot]

@copilot this package doesn't keep a uv.lock file so the caching in the ci jobs is failing. You probably need to remove this.

Removed the enable-cache: true configuration from all workflow files. The caching option requires a uv.lock file which this project doesn't maintain. Fixed in commit 7f31069.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 95.15%. Comparing base (ce9af49) to head (3c1fe64).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #140   +/-   ##
=======================================
  Coverage   95.15%   95.15%           
=======================================
  Files          14       14           
  Lines         907      907           
=======================================
  Hits          863      863           
  Misses         44       44           

Flag	Coverage Δ
python3.10	95.15% <ø> (ø)
python3.11	95.15% <ø> (ø)
python3.12	95.15% <ø> (ø)
python3.13	95.15% <ø> (ø)

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[ColmTalbot]

It looks like you need to install pandoc in the docs job. Likely as a new stage in the job. @copilot

[ColmTalbot]

Check the installation of pandoc in the documentation job

[ColmTalbot]

@copilot the formatting on my last change was incorrect. Please fix

[Copilot]

@copilot the formatting on my last change was incorrect. Please fix

Fixed the indentation for the pandoc installation step. It's now properly aligned with the other steps in the workflow. Fixed in commit 3c1fe64.

It looks like you need to install pandoc in the docs job. Likely as a new stage in the job. @copilot

Added pandoc installation step in the pages workflow using pandoc/actions/setup@v1. The step is now properly formatted and positioned before the Python setup. Fixed in commits da92fbd and 3c1fe64.

Check the installation of pandoc in the documentation job

Pandoc installation has been added to the documentation job using pandoc/actions/setup@v1 action. Fixed in commits da92fbd and 3c1fe64.