fix(ci): use --skip flag for dynamic versioning workaround

[KedoKudo]

Summary

Work around the circular dependency between pixi lock files and dynamic git-based versioning (versioningit).

The Problem:

• Lock file contains version computed from git state (e.g., 0.2.0.dev291+g<commit_hash>)
• Committing lock file changes git state → new commit hash → new version
• CI with --locked fails because versions don't match
• This is a chicken-and-egg problem: you cannot commit a lock file that references its own commit

The Solution:
Use pixi's --skip flag (added in v0.51.0) to skip the local editable package during locked install, then install it separately with pip:

- uses: prefix-dev/[email protected]
  with:
    run-install: false

- run: pixi install --frozen --skip ${{ env.PKG_NAME }}

- run: pixi run pip install --no-deps -e .

This preserves lock file integrity for all external dependencies while allowing the local package version to float.

Changes:

• Updated .github/workflows/test_and_deploy.yaml with the workaround for all jobs
• Added comprehensive documentation in README.md under "Known issues" explaining the problem and solution

References

• Pixi PR #3092: Add --skip flag
• This is a known issue affecting all lock file-based package managers (pixi, poetry, pdm, uv) when combined with dynamic versioning tools

Test plan

• CI passes with the new workflow
• Verify the workaround is applied to all relevant jobs (tests, conda-build, publish, pypi-publish)

🤖 Generated with Claude Code

[peterfpeterson]

I think you can skip installing altogether for the conda package and upload conda package jobs

[peterfpeterson]

I understand better now. Thanks