Merge develop into 36-add-badges - #68
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Add a comment header for Quarto and ignore docs/.quarto/ (and ensure docs/_site/ remains ignored). This prevents Quarto build artifacts and generated site files from being tracked.
Expanded the .gitignore with a Python template from https://github.com/github/gitignore/blob/main/Python.gitignore
Rename and reconfigure the Quarto docs site for the Reactix project: update website metadata (title, description, site and repo URLs), add metadata-files and navbar entries, and restructure the sidebar into sections (Get started, Examples, API, Development). Add quartodoc API generation settings (package, parser, dir, sidebar, css, sections), update theme and HTML format options (light/dark themes, CSS, toc-depth, code-copy, code-overflow, smooth-scroll), and change execution settings (freeze auto, echo true, suppress warnings/messages). Remove legacy Kinetix-specific values and old Jupyter kernel config.
Add docs/contributing.qmd: a CONTRIBUTING guide that explains how to get help, report issues, share examples, and follow community guidelines. Includes step-by-step instructions for contributing code (fork, branch, tests, PR against develop), contact links (email, GitHub Discussions), and a pointer to the developer-guide for detailed developer guidelines.
Ignore the Quarto freeze output by adding docs/_freeze/ to .gitignore. This keeps generated freeze artifacts out of version control alongside existing Quarto ignores (docs/.quarto/ and docs/_site/).
Also, replace the API reference section block with an href/text entry for a direct link, and set quartodoc.title to "API reference".
Add docs/developer-guide.qmd with contributor-facing instructions. It covers development setup (editable install and deps), pre-PR checks (tests, Ruff, formatters), documentation workflow (Quarto, quartodoc, local build/preview), converting example notebooks, updating the API reference, and publishing to GitHub Pages via Actions or manually.
Adds .github/workflows/docs.yml to build and publish the documentation. The workflow triggers on pushes to main and manual dispatch, checks out the repo, sets up Python 3.13, installs Quarto and project dev/docs dependencies, runs quartodoc to build the API reference, renders the site with Quarto, and deploys the generated site to the gh-pages branch using peaceiris/actions-gh-pages. Permissions are set to allow writing repository contents.
…github-action Add GitHub Actions coverage workflow
Remove archived docs in docsarchive/docs
Instead of having standalone rhs functions for each system, the rhs is defined as a method in the respective system class. The `_rhs` function then only needs to call the method of the system object.
Otherwise, it does not render correctly when the font is not installed.
Clarify JAX GPU support status in README. Add an API reference link to the project documentation and update the notebooks section to include a link to the example notebooks on the documentation site.
Clarify JAX GPU support and update documentation links
…ing in MC sampling in transport_with_pymc.ipynb
Add logo to the repository
edvinskis
marked this pull request as ready for review
July 20, 2026 13:52
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