Install pyopenms in build-push-notebooks workflow

[poshul]

Since we now use a separate script we need to actually call it.

Summary by CodeRabbit

• Chores
  • CI workflows now run an additional Python setup script during dependency installation, adding installation of a Python component.
  • Impact: improved reproducibility of the build and more complete dependency setup in continuous integration.

_{✏️ Tip: You can customize this high-level summary in your review settings.}

[coderabbitai]

📝 Walkthrough

Walkthrough

Added a step to two GitHub Actions workflows to run python3 docs/install_pyopenms.py during the dependency installation phase, executing an additional setup script after upgrading pip and installing requirements.

Changes

Cohort / File(s)	Summary
CI workflows .github/workflows/build-push-notebooks.yaml, .github/workflows/test-pr-sphinx.yml	Both workflow files now run python3 docs/install_pyopenms.py as part of the dependency installation step (after pip/jupyter/requirements installation). Verify CI runner has required system deps and that the script exits appropriately.

Suggested reviewers

• matteopilz

Poem

🐰 A small script hops into the CI tree,
Installing PyOpenMS so builds run with glee,
Pip prances forward, dependencies in tune,
Rabbits cheer softly beneath the CI moon.

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The pull request title directly matches the main objective: it specifies installing pyopenms in the build-push-notebooks workflow, which aligns with the PR description and the changes made.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch poshul-patch-5

---

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ Share

• X
• Mastodon
• Reddit
• LinkedIn

_{Comment @coderabbitai help to get the list of available commands and usage tips.}