Contributing to Cellucid (Python)#

Contributions are welcome — code, docs, bug reports, design feedback, and reproducible examples all matter.

This file focuses on cellucid-python (the Python package + CLI), but also helps you route issues/PRs to the correct repo in the Cellucid ecosystem.

By participating, you agree to follow the project’s Code of Conduct:

  • CODE_OF_CONDUCT.md

If you’re reporting a security issue, please follow:

  • SECURITY.md

Which repo should I contribute to?#

Cellucid is split by responsibility:

Repo

What it is

Contribute here when you…

cellucid

Web app (UI + state + WebGL rendering)

are fixing UI bugs, rendering/performance, figure export, sessions, or community annotation frontend

cellucid-python (this repo)

Python package + CLI (prepare, serve, show_anndata, hooks) + Sphinx docs

are fixing Python/CLI bugs, prepare() (Cellucid-ready AnnData), server endpoints, Jupyter hooks, or docs on ReadTheDocs

cellucid-r

R package writing the same Cellucid-ready AnnData from R

are changing the R writer (cellucid_prepare) or adding R-side docs/tests

cellucid-annotation

GitHub repo template for community annotation

are changing the repo schema/validation/workflows

cellucid-datasets

The published demo catalog

are correcting a published generation or its catalog entry

cellucid-demo-custom-datasets

Worked example of publishing your own datasets

are changing that guide or its synthetic examples

If you’re not sure where a bug belongs, open an issue in the repo you’re currently using and include:

  • how you loaded data (.h5ad/.zarr, prepared with prepare() or not, vs remote server vs Jupyter),

  • the UI environment (hosted app vs local app vs Jupyter iframe),

  • and the smallest reproduction you can share.

Fast paths (pick your contribution type)#

I want to report a bug#

Please include:

  • Cellucid version (python -c "import cellucid; print(cellucid.__version__)" if available)

  • Python version + OS

  • how you loaded data (.h5ad / .zarr, prepared or not / remote server / Jupyter)

  • exact steps to reproduce (click-by-click or code)

  • expected vs actual behavior

  • logs:

    • Python server logs (if using cellucid serve)

    • browser console logs (if UI bug; enable debug with localStorage.setItem('CELLUCID_DEBUG','true') and reload)

I want to contribute docs only#

Docs live under cellucid-python/docs/ and use Sphinx + MyST.

Fast workflow:

  1. Edit the relevant .md (or notebook) under docs/

  2. Build docs locally (see “Build docs” below)

  3. Submit a PR

I want to add/modify Python code#

Fast workflow:

  1. Create a dev environment (see “Development setup”)

  2. Make a small, focused change

  3. Add/adjust tests when behavior changes

  4. Run ruff, mypy, and pytest

  5. Submit a PR with a clear “what/why/how to verify”

Development setup (cellucid-python)#

Prerequisites#

  • Python 3.11 through 3.14

  • Git

Recommended:

  • a clean virtual environment (venv/conda)

Clone#

git clone https://github.com/theislab/cellucid-python.git
cd cellucid-python

Install (editable + dev extras)#

Using venv:

python -m venv .venv
source .venv/bin/activate  # Windows: .venv\Scripts\activate
python -m pip install --upgrade pip
python -m pip install -e ".[dev,docs]"

This installs:

  • runtime deps (numpy/pandas/scipy/anndata/etc.)

  • dev tooling (pytest/ruff/mypy/pre-commit)

  • docs tooling (sphinx/myst-nb/pydata-sphinx-theme/etc.)

Code quality checks#

Formatting + lint (Ruff)#

This repo uses Ruff for formatting and linting.

ruff format .
ruff check .

If you want Ruff to auto-fix what it can:

ruff check . --fix

Type checking (mypy)#

mypy src/cellucid

Notes:

  • The mypy config is intentionally pragmatic (ignore_missing_imports = true).

  • If you add new public APIs, prefer adding type hints even if the internal implementation stays flexible.

Tests#

Run the test suite:

pytest

Useful variants:

pytest -v --tb=short
pytest --cov=cellucid

Guidelines:

  • Add tests when you change behavior (especially for edge cases and error messages).

  • Prefer small synthetic inputs over large real datasets (privacy + speed).

Build docs (Sphinx + MyST)#

Docs live in cellucid-python/docs/.

Build HTML:

make -C docs html

Or explicitly:

sphinx-build -b html docs docs/_build/html

Open:

  • cellucid-python/docs/_build/html/index.html

Doc-writing expectations (especially important for Cellucid):

  • Write for mixed audiences: wet lab users, computational users, and developers.

  • Prefer “layered” pages:

    • fast path (click-by-click / copy-paste)

    • practical path (parameters, performance)

    • deep path (design rationale, edge cases)

  • Always include edge cases + troubleshooting for anything that can fail.

PR guidelines (what makes a good PR here)#

Scope and clarity#

  • Keep PRs small and focused (one feature/bugfix at a time).

  • Include a short “Why?” and “How to verify?” in the PR description.

User-facing changes#

If your change affects user-visible behavior:

  • update docs and/or CLI help text

  • add/adjust tests

  • update CHANGELOG.md if it’s a user-facing change worth calling out

Data privacy#

Do not attach private datasets or patient-derived data to issues/PRs. If you need a reproduction:

  • reduce to a tiny synthetic dataset, or

  • provide a script that generates a minimal failing example.

Troubleshooting (common contributor problems)#

pip install -e ".[dev,docs]" fails#

Common causes:

  • old pip (upgrade first)

  • environment mixing (conda + system Python)

Fix:

  • create a fresh environment and retry

  • run python -m pip install --upgrade pip before installing

ruff/mypy/pytest aren’t found#

Cause:

  • dev extras not installed (or you forgot to activate your env).

Fix:

  • activate your env and reinstall dev extras:

    • python -m pip install -e ".[dev]"

Docs build fails on notebooks#

Common causes:

  • missing optional doc dependencies

  • notebook execution errors (if notebooks are executed during build)

Fix:

  • install docs extras: python -m pip install -e ".[docs]"

  • run the failing page’s code cells locally and fix the root error

Thanks#

Thank you for improving Cellucid — contributions here directly improve how quickly people can explore and trust their single-cell results.