[Documentation] Refactor documentation

[jan-janssen]

Summary by CodeRabbit

• Documentation

  • Reorganized documentation navigation links and updated notebook references in the main README and table of contents.

• Chores

  • Updated CI/CD pipeline configuration to execute the reorganized documentation notebooks.

[coderabbitai]

📝 Walkthrough

Walkthrough

Notebook references are being updated across CI configuration, README navigation, and documentation table of contents. The developer notebook is updated from 4 to 5, while integration notebooks are updated from 5 to 4 versions in their respective locations.

Changes

Cohort / File(s)	Summary
CI Pipeline .github/workflows/pipeline.yml	Updated notebook execution targets: 4-developer.ipynb → 5-developer.ipynb in notebooks job; 5-1-gpaw.ipynb and 5-2-quantum-espresso.ipynb → 4-1-gpaw.ipynb and 4-2-quantum-espresso.ipynb in notebooks_integration job.
Documentation Navigation README.md, docs/_toc.yml	Updated internal documentation links and JupyterBook TOC entries to reflect new notebook versions: Developer docs 4-developer → 5-developer; Application docs 5-1-* and 5-2-* → 4-1-* and 4-2-*.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~8 minutes

Possibly related PRs

• Add integration tests for application notebooks #619 — Directly modifies the same files (.github/workflows/pipeline.yml, README.md, docs/_toc.yml) with identical notebook version swaps across CI and documentation.
• Execute notebooks individually #617 — Updates CI pipeline notebook execution commands in .github/workflows/pipeline.yml with per-notebook papermill invocations related to the same integration notebooks.

Poem

🐰 Five hops forward, four back again,
Notebooks shuffled by clever pen,
From pipelines to docs they now reside,
With fresh numbers, our burrow's pride! ✨

🚥 Pre-merge checks | ✅ 2 | ❌ 1

❌ Failed checks (1 inconclusive)

Check name	Status	Explanation	Resolution
Title check	❓ Inconclusive	The title '[Documentation] Refactor documentation' is vague and generic, using non-descriptive terms that don't convey the specific nature of the changes (notebook renaming/reordering).	Use a more descriptive title that reflects the actual changes, such as '[Documentation] Update notebook references and paths' or '[Documentation] Rename and reorder notebook references'.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch notebook-renaming

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[Copilot]

Pull request overview

Note

Copilot was unable to run its full agentic suite in this review.

Refactors documentation structure by renumbering/reordering notebook-based pages and updating all corresponding links and CI notebook execution steps to match.

Changes:

• Update Jupyter Book TOC entries to point to renumbered notebooks (GPAW/Quantum Espresso and Developer docs).
• Update README documentation links to match the new published doc URLs.
• Update GitHub Actions workflow to execute the renumbered notebooks in CI.

Reviewed changes

Copilot reviewed 3 out of 6 changed files in this pull request and generated no comments.

File	Description
docs/_toc.yml	Updates the documentation table-of-contents to reference renumbered notebook pages.
README.md	Adjusts rendered documentation links to match the new page names/paths.
.github/workflows/pipeline.yml	Aligns CI papermill execution with renamed/renumbered notebooks.

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[coderabbitai]

🧹 Nitpick comments (1)

.github/workflows/pipeline.yml (1)

201-202: Parameterize pseudo_dir path to reduce CI environment coupling.

The notebook hardcodes pseudo_dir="/home/runner/work/executorlib/executorlib/tests/integration" (line 58), which only works in the GitHub Actions runner environment. Parameterize this path by: (1) adding a parameters cell to the notebook with pseudo_dir = None as a default, and (2) updating the workflow to pass the path via papermill, e.g., flux start papermill notebooks/4-2-quantum-espresso.ipynb notebooks/4-2-quantum-espresso-out.ipynb -k python3 -p pseudo_dir "${GITHUB_WORKSPACE}/tests/integration".

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In @.github/workflows/pipeline.yml around lines 201 - 202, The notebook
hardcodes pseudo_dir and the workflow invokes papermill without passing it,
causing CI coupling; add a parameters cell in
notebooks/4-2-quantum-espresso.ipynb (and notebooks/4-1-gpaw.ipynb if
applicable) that defines pseudo_dir = None as the default parameter, then update
the workflow flux start papermill commands to pass the workspace path via
papermill -p pseudo_dir "${GITHUB_WORKSPACE}/tests/integration" (e.g., modify
the flux start papermill invocation for notebooks/4-2-quantum-espresso.ipynb to
include -p pseudo_dir "${GITHUB_WORKSPACE}/tests/integration") so the notebook
reads the injected path instead of the hardcoded "/home/runner/..." value.

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Nitpick comments:
In @.github/workflows/pipeline.yml:
- Around line 201-202: The notebook hardcodes pseudo_dir and the workflow
invokes papermill without passing it, causing CI coupling; add a parameters cell
in notebooks/4-2-quantum-espresso.ipynb (and notebooks/4-1-gpaw.ipynb if
applicable) that defines pseudo_dir = None as the default parameter, then update
the workflow flux start papermill commands to pass the workspace path via
papermill -p pseudo_dir "${GITHUB_WORKSPACE}/tests/integration" (e.g., modify
the flux start papermill invocation for notebooks/4-2-quantum-espresso.ipynb to
include -p pseudo_dir "${GITHUB_WORKSPACE}/tests/integration") so the notebook
reads the injected path instead of the hardcoded "/home/runner/..." value.

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ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 397d1763-448c-484a-aa78-80c043143254

📥 Commits

Reviewing files that changed from the base of the PR and between cddbd83 and f97026f.

📒 Files selected for processing (6)

• .github/workflows/pipeline.yml
• README.md
• docs/_toc.yml
• notebooks/4-1-gpaw.ipynb
• notebooks/4-2-quantum-espresso.ipynb
• notebooks/5-developer.ipynb

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 94.15%. Comparing base (cddbd83) to head (f97026f).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #973   +/-   ##
=======================================
  Coverage   94.15%   94.15%           
=======================================
  Files          39       39           
  Lines        2089     2089           
=======================================
  Hits         1967     1967           
  Misses        122      122           

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