Development¶

Contributions are welcome. The repository is matthiaskoenig/libsbgnpy; development happens against the develop branch via pull requests.

Branch model¶

Two branches are permanent:

• develop is the default branch and the branch everything is integrated into. The documentation on matthiaskoenig.github.io/libsbgnpy is published from it.
• main tracks the latest published release. It is fast-forwarded to the released commit by the sync-main job of the CI-CD workflow after the package went to pypi, so main and the newest version on pypi always agree. Nothing is developed on main and nothing is merged into it by hand.

Work happens on short lived branches off develop, which GitHub deletes after the merge. Releases are tagged on develop, see Release.

Pull requests¶

Neither branch accepts a direct push, every change goes through a pull request against develop. This includes the maintainer, there is no bypass.

A pull request can only be merged once the four required checks are green:

tests aggregates the test matrix into a single job, so the name of the required check stays the same when the matrix changes.

Further rules of a pull request:

• conversations have to be resolved before the merge
• an approval is dismissed when new commits are pushed
• the history stays linear, i.e., a pull request is merged with squash or rebase; merge commits are disabled
• the maintainer is the code owner of the repository (.github/CODEOWNERS) and is requested for review on every pull request. A pull request of a contributor is therefore reviewed and merged by the maintainer, who has the only write access. The rulesets themselves do not require an approval: on a personal repository a ruleset cannot ask for an approval only from somebody else, and requiring one would block the pull requests of the maintainer, who cannot approve their own. Once a second person has write access, a ruleset requiring an approving review of a code owner can be added

Auto-merge is enabled for the repository, so a pull request can be queued and is merged as soon as the checks pass and the required approval is there.

Repository policies¶

The protection is implemented with repository rulesets. They are part of the repository in .github/rulesets/ instead of only living in the web interface, so a change to a policy is reviewed like any other change:

Changing a policy means changing the json and applying it:

.github/rulesets/apply.sh

The script is idempotent: it updates the rulesets which exist and creates the missing ones. It also sets the merge settings of the repository, i.e., auto-merge, delete branch on merge, and squash and rebase as the only merge methods. It needs the github cli authenticated as a user with admin permission on the repository.

Setup development environment¶

Development needs uv and a checkout of the repository:

git clone https://github.com/matthiaskoenig/libsbgnpy.git
cd libsbgnpy

A single sync creates the virtual environment in .venv, installs libsbgnpy into it in editable mode and adds the complete tooling:

uv sync --extra dev

The dev extra contains everything used below, i.e., pytest, ruff, ty, tox, pre-commit, zensical and bump-my-version, so nothing has to be installed separately. The python version is taken from .python-version (currently 3.14); to work against the oldest supported version instead use uv sync --extra dev --python 3.11, which replaces the environment.

The tools are then run either with uv run <command>, which uses the environment without activating it, or from the activated environment:

source .venv/bin/activate        # Linux and macOS
.venv\Scripts\activate           # Windows

The commands in this document are written without the uv run prefix; prepend it if the environment is not activated.

The last step installs the git hook:

uv run pre-commit install          # install the hook, once per checkout
uv run pre-commit run --all-files  # check the current state of the repository

From now on every commit is checked with ruff (lint and format) and ty, i.e., the same checks that run in continuous integration. On a commit only the changed files are looked at, --all-files checks the whole repository and is what a newly added hook should be tried with.

Testing¶

The tests are written with pytest, tox runs them against every supported python version.

The tox environments are named after the interpreter (py3.11 to py3.14, see envlist in tox.ini), a single one is run with

tox r -e py3.14

tox run-parallel

This needs the interpreters to be available, which uv installs with uv python install 3.11 3.12 3.13 3.14. Continuous integration runs the same environments as uvx --with tox-uv tox -e py3.14.

To run the tests directly against the development environment use

pytest                                    # the full suite
pytest tests/test_io.py                   # a single module
pytest tests/test_io.py::test_upconvert   # a single test

tests/data holds the reference maps of the SBGN specifications, one directory per map language. tests/test_data.py reads, writes and validates every one of them, so a change to the bindings or to the io is checked against the whole corpus.

tests/test_examples.py runs every example of examples/ in a temporary working directory, which keeps the examples of the documentation working. The tests of tests/test_image.py query the rendering web service and therefore require network access.

Linting and formatting¶

Linting and formatting use ruff:

ruff check     # lint
ruff format    # format

The generated bindings, libsbgnpy/sbgn.py and libsbgnpy/render.py, are excluded from the docstring rules, see [lint.per-file-ignores] in .ruff.toml; their docstrings are the documentation of the schema.

Type checking¶

Type checking is performed with ty:

tox r -e ty

uvx ty check

The configuration lives in [tool.ty] in pyproject.toml. Warnings are treated as errors, so the codebase is kept free of diagnostics. Suppress an unavoidable diagnostic with a rule specific # ty: ignore[rule-name] rather than a blanket comment.

Documentation¶

The documentation is built with Zensical, the static site generator of the Material for MkDocs authors. The sources are markdown files in docs/, the site is configured in zensical.toml in the repository root. Nothing rendered is committed: the site is built by the documentation workflow on every push and published to matthiaskoenig.github.io/libsbgnpy from the develop branch.

Build the site into site/:

uv run zensical build --clean

For writing, the preview rebuilds on save:

uv run zensical serve

The API reference is rendered from the docstrings by mkdocstrings; a page in docs/api/ only contains the module directive:

# io

::: libsbgnpy.io

Docstrings are therefore the place to document functions and classes, the markdown files provide the narrative around them. Adding a module to the reference means adding such a page and an entry to nav in zensical.toml.

Files for agents¶

Agents and language models read markdown, not rendered html. scripts/llms_txt.py writes the files of the llms.txt convention into the built site, i.e., llms.txt as an annotated index of all pages, llms-full.txt with the complete documentation in a single file, and the markdown of every page next to its html (/io.md for /io/). The markdown of the API reference is generated from the docstrings with inspect, since the pages themselves only contain the mkdocstrings directive.

uv run zensical build --clean
uv run python scripts/llms_txt.py

The documentation workflow runs both steps, so the files are regenerated with every push. docs/robots.txt points crawlers at the sitemap and at these files.

Regenerating the bindings¶

libsbgnpy.sbgn and libsbgnpy.render are generated modules and should not be edited by hand. They are generated from the schemas in src/libsbgnpy/schema/ with xsdata; the current schemas are published with sbgn/libsbgn in the resources folder. The procedure and the manual fixes which are applied afterwards are described in src/libsbgnpy/schema/README.md.

Run ruff format and ruff check --fix afterwards, the generated modules are neither formatted nor on current python syntax.

Work in progress¶

libsbgnpy.oven collects unfinished work: it is not wired into the package, not documented, not part of the public API and not shipped in the release, see [tool.hatch.build] in pyproject.toml. It currently holds the mapping of SBO terms to SBGN glyphs, groundwork for the conversion of SBML to SBGN, see issue #52.

Release¶

A release is made from develop. Since develop only accepts pull requests, the release is prepared on a branch and tagged once that pull request is merged:

1. branch off develop: git switch -c release/x.y.z develop
2. write the release notes for the version in release-notes/x.y.z.md
3. make sure everything passes: tox run-parallel, ruff check, tox r -e ty
4. check the version bump: uvx bump-my-version bump [major|minor|patch] --dry-run -vv
5. bump the version: uvx bump-my-version bump [major|minor|patch], which updates src/libsbgnpy/__init__.py and CITATION.cff and commits. It does not create the tag; a squash or rebase merge would rewrite the commit and leave the tag behind on a commit which is not part of develop
6. push the branch, open the pull request against develop and merge it once the checks are green

7. tag the merged commit on develop and push the tag:

   git switch develop
   git pull
   git tag x.y.z
   git push origin x.y.z
   

   This starts the CI-CD workflow, which runs the test matrix, publishes to pypi, creates the GitHub release from release-notes/x.y.z.md and fast-forwards main to the tagged commit. Check the version before pushing, a tag cannot be moved or deleted afterwards.

8. test the installation from pypi in a fresh environment:

   uv venv --python 3.14
   uv pip install libsbgnpy
   

9. once Zenodo has archived the release, update the citation information: date-released and the version DOI in doi and identifiers of CITATION.cff, and the citation and the bibtex entry of the How to cite section of docs/index.md. bump-my-version only updates the version, neither the date nor the DOI, which are only known after the release. The badges and the README.md carry the concept DOI, which always resolves to the latest version, and stay as they are. These changes go in through a pull request like everything else