Contributing#

Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given.

You can contribute in many ways:

Types of Contributions#

Report Bugs#

If you are reporting a bug, please include:

Your operating system name and version.
Any details about your local setup that might be helpful in troubleshooting.
Detailed steps to reproduce the bug.

Fix Bugs#

Look through the GitHub issues for bugs. Anything tagged with “bug” and “help wanted” is open to whoever wants to implement it.

Implement Features#

Look through the GitHub issues for features. Anything tagged with “enhancement” and “help wanted” is open to whoever wants to implement it.

Write Documentation#

AutomatedCellularImageAnalysis could always use more documentation, whether as part of the official AutomatedCellularImageAnalysis docs, in docstrings, or even on the web in blog posts, articles, and such.

Submit Feedback#

The best way to send feedback is to file an issue at SMLCI/acia-core#issues.

If you are proposing a feature:

Explain in detail how it would work.
Keep the scope as narrow as possible, to make it easier to implement.
Remember that this is a volunteer-driven project, and that contributions are welcome :)

Get Started!#

Ready to contribute? Here’s how to set up acia for local development.

Fork the acia repo on GitHub (SMLCI/acia-core).

Clone your fork locally:

$ git clone git@github.com:your_name_here/acia-core.git

Install your local copy in editable mode with the dev extras:
```
$ cd acia-core/
$ pip install -e ".[dev]"
```
Create a branch for local development:
```
$ git checkout -b name-of-your-bugfix-or-feature
```
Now you can make your changes locally.
When you’re done, check that your changes pass linting, formatting and the tests (the same checks CI runs):
```
$ ruff check acia tests
$ ruff format --check acia tests
$ pytest                      # fast suite; integration tests are deselected
```
Heavy integration tests (external data, trackastra/laptrack, ffmpeg) are marked @pytest.mark.integration and run separately:
```
$ pytest -m integration
```
Add a short entry under ## [Unreleased] in CHANGELOG.md describing your change.

Commit your changes and push your branch to GitHub:

$ git add .
$ git commit -m "Your detailed description of your changes."
$ git push origin name-of-your-bugfix-or-feature

Submit a pull request through the GitHub website.

Pull Request Guidelines#

Before you submit a pull request, check that it meets these guidelines:

The pull request should include tests.
If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring, and add the feature to the list in README.md and an entry under [Unreleased] in CHANGELOG.md.
The pull request should work for Python 3.10, 3.11, 3.12 and 3.13. The CI workflow (.github/workflows/ci.yml) runs lint, type-checks and the test matrix on every push and pull request.

Tips#

To run a subset of tests:

$ pytest tests.test_acia

Releasing#

Releases are automated. A maintainer triggers them from GitHub:

Make sure CHANGELOG.md has the changes for this release under ## [Unreleased].
Go to Actions → Release → Run workflow and choose the bump level (patch / minor / major). Use dry_run first to preview.

The release.yml workflow then, in one run:

runs bump-my-version to update pyproject.toml and acia/__init__.py, promote the [Unreleased] changelog section to a dated version, and create the vX.Y.Z commit and tag,
builds the sdist + wheel and publishes them to PyPI via OIDC trusted publishing (no stored token), and
creates a GitHub Release using the new changelog section as the notes.

Documentation is published to GitHub Pages automatically on every push to the default branch via docs.yml.

Travis will then deploy to PyPI if tests pass.