Merge upstream/main: resolve docs workflow and preserve examples #4
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* Add notebooks in docs/examples/, which can each be an executable example as well as documentation * Add mkdocs-ipynb as a plugin, which translates Jupyter notebooks to Markdown for rendering by mkdocs * Add a CI pipeline for running included notebooks, so that they act as a sort of doctest. Each notebook gets its own job, and needs to be added to the CI in `rundocs.yml`--that might be worth changing to simply look at all notebooks
…pynb; preserve local examples
…mples; merge upstream docs additions
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Pull request overview
This PR merges upstream/main documentation workflow changes while preserving local examples and CI configurations. It integrates documentation tooling improvements, adds plotting utilities, enhances docstrings for better API documentation, and includes benchmark data and example notebooks.
Key changes:
- Enhanced MkDocs configuration with new plugins (ipynb) and markdown extensions for better documentation rendering
- New
plot_styling.pymodule providing matplotlib styling utilities - Improved docstrings in core simulation functions with detailed return value documentation
- New GitHub Actions workflow for testing documentation notebooks
- Addition of benchmark results and example data files
Reviewed changes
Copilot reviewed 21 out of 71 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
| mkdocs.yml | Adds ipynb plugin, code copy feature, markdown extensions, and example notebook navigation |
| lyopronto/plot_styling.py | New module with matplotlib axis styling functions for various plot types |
| lyopronto/functions.py | Enhanced docstring with detailed return array column descriptions |
| lyopronto/calc_knownRp.py | Added comprehensive docstring documenting simulation function parameters and outputs |
| lyopronto/init.py | Imports new plot_styling module |
| docs/examples/temperature.txt | Example temperature data file (452 data points) |
| benchmarks/results/*/summary.json | Benchmark summary files with performance metrics |
| benchmarks/results//figures/.png | Benchmark visualization (binary PNG file) |
| benchmarks/results/archive/*.jsonl | Archived benchmark results in JSONL format |
| .github/workflows/rundocs.yml | New workflow to run documentation notebooks as tests using papermill |
| .github/workflows/docs.yml | Adds mkdocs-ipynb dependency and removes redundant git push |
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Merge upstream/main (docs) and resolve incompatibilities: combine docs workflow changes while keeping local examples and CI Python-version handling. Tests pass locally. This PR contains the merge resolution branch 'fix/upstream-incompatibility'.