Development¶

Contributions are welcome. The repository is matthiaskoenig/pkpdsim; 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/pkpdsim 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.

Continuous integration is kept small: every workflow cancels its running build when a newer commit of the same branch or pull request arrives, uv caches the packages and the interpreters between runs, dependabot proposes its updates once a month, and the matrix tests only python 3.14. Python 3.13 is tested locally, see Testing, before a pull request is opened.

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/pkpdsim.git
cd pkpdsim

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

uv sync --extra dev

The environment is resolved from uv.lock, which is committed, so local development, including uv run ty check, and the documentation build use the same versions. The tox environments, i.e. the test matrix and the ty check of continuous integration, resolve from pyproject.toml and do not use the lock; the lower bounds in pyproject.toml are what a user of the library installs against. After changing a dependency in pyproject.toml run uv lock: the documentation workflow syncs with uv sync --locked, which fails when pyproject.toml and the lock disagree. uv lock --upgrade moves the lock to the newest releases. Dependabot bumps the locked dependencies as one grouped monthly pull request, with versioning-strategy: lockfile-only, so the lower bounds in pyproject.toml are never raised by it and only ever changed by hand.

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 3.13, 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.

libroadrunner on Linux¶

The interpreters of uv keep libpython, which the extension of libroadrunner links against, outside the search path of the loader on Linux, see Installation. Before running the tests:

export LD_LIBRARY_PATH="$(uv run python -c 'import sys; print(sys.base_prefix)')/lib"

The workflows do the same in .github/actions/setup.

Testing¶

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

The tox environments are named after the interpreter (py3.13 and py3.14, see envlist in tox.ini), a single one is run with

tox r -e py3.14

and the complete matrix, including the ty environment, in parallel with

tox run-parallel

This needs the interpreters to be available, which uv installs with uv python install 3.13 3.14. The tox environments build the wheel and install it, so the tests run against the package as it is published. It is the complete test and is run before a pull request is opened: continuous integration runs only py3.14, on linux, macos and windows, as uvx --with tox-uv tox -e py3.14 -- --durations=15, which lists the slowest tests in the log.

To run the tests directly against the development environment use

pytest                                       # the full suite
pytest -n 0                                  # in one process, e.g. for --pdb
pytest tests/test_package.py                 # a single module
pytest tests/test_package.py::test_version   # a single test

The tests run in parallel, addopts = "-n auto" in pyproject.toml gives pytest-xdist one worker per core; -n 0 on the command line runs everything in one process, which the debugger needs.

Linting and formatting¶

Linting and formatting use ruff:

ruff check     # lint
ruff format    # format

The ruff workflow installs the ruff version locked in uv.lock, so continuous integration and uv run ruff agree.

The docstring rules (D) are enforced for the package, not for tests/ and scripts/, see .ruff.toml; the annotation rules (ANN) hold everywhere.

Type checking¶

Type checking is performed with ty:

tox r -e ty

Or directly in the working tree:

uv run 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/pkpdsim from the develop branch.

Build the site into site/:

uv run zensical build --clean --strict

The build is strict: a broken link or a missing page fails it, in continuous integration as well.

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:

# pkpdsim

::: pkpdsim

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, an entry to nav in zensical.toml and a row to docs/api/index.md.

Snippets of the documentation¶

Every ```python block of the pages follows two rules:

• It runs. The first block of a page is self-contained (its imports, its data, the call and the output it prints) and runs from the root of the repository with warnings as errors. A later block of the same page may be a fragment, but then it names in a comment or in the sentence before it where every object it uses comes from. The output a snippet prints is shown below it as a text block and is pasted from a run, never written by hand.

  tests/docs/test_snippets.py keeps this honest: it runs the blocks of every page in the order they appear and in one namespace per page, in a temporary working directory, in a subprocess with -W error. A fragment which needs what a page cannot provide (a checkout of pkdb_data, a model of a reader) carries the comment # not executed as its first line and is skipped; every other block has to run.

• It is formatted. ruff format formats the code blocks of the markdown files as well, so ruff format --check covers the documentation and a snippet is written the way ruff would write it.

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 (/installation.md for /installation/). 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 --strict
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. Zensical will provide agent context files itself at some point, then this script can go.

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 [dev|major|minor|patch] --dry-run -vv. A development version (x.y.z.devN) is finalized with uvx bump-my-version bump dev, which drops the .devN suffix (0.2.0.dev0 becomes 0.2.0); major, minor and patch start the next development cycle instead (0.2.0.dev0 becomes 1.0.0.dev0, 0.3.0.dev0, 0.2.1.dev0)
5. bump the version: uvx bump-my-version bump [dev|major|minor|patch], which updates src/pkpdsim/__init__.py, CITATION.cff, tests/test_package.py and .bumpversion.toml (its own current_version) and commits. Use dev to release the current development version and major|minor|patch to open the next one. 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 through the trusted publisher of the GitHub environment pypi, creates the GitHub release from release-notes/x.y.z.md and fast-forwards main to the tagged commit. Zenodo archives the GitHub release. 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 pkpdsim
   

9. once Zenodo has archived the release, update the citation information, i.e., date-released and doi in CITATION.cff and the version, date and DOI of the release in the citation of README.md and docs/index.md. bump-my-version only updates the version, not the date and the DOI, which are only known after the release. These changes go in through a pull request like everything else