See CHANGELOG.md for full details.
| Version | Date | Summary |
|---|---|---|
| v0.7.0 | 04/02/2026 | New codeocean_utils module for attaching dataset-catalog records to capsules/pipelines |
| v0.6.0 | 03/18/2026 | New pairwise/cell-typing/spot-filter modules; major HCRDataset and filters.py additions |
| v0.5.1 | 02/23/2026 | metrics_base_path, spot_filters.py, comprehensive ROI filtering pipeline |
| v0.4.0 | 10/16/2025 | Tile overlap, ROI filtering, linear unmixing, neuroglancer links, saveable_plot |
| v0.3.8 | 08/11/2025 | Cell info loading improvements, metrics paths, error handling |
To use the software, in the root directory, run
pip install -e .To develop the code, run
pip install -e .[dev]There are several libraries used to run linters, check documentation, and run tests.
- Please test your changes using the coverage library, which will run the tests and log a coverage report:
coverage run -m unittest discover && coverage report- Use interrogate to check that modules, methods, etc. have been documented thoroughly:
interrogate .- Use flake8 to check that code is up to standards (no unused imports, etc.):
flake8 .- Use black to automatically format the code into PEP standards:
black .- Use isort to automatically sort import statements:
isort .For internal members, please create a branch. For external members, please fork the repository and open a pull request from the fork. We'll primarily use Angular style for commit messages. Roughly, they should follow the pattern:
<type>(<scope>): <short summary>
where scope (optional) describes the packages affected by the code changes and type (mandatory) is one of:
- build: Changes that affect build tools or external dependencies (example scopes: pyproject.toml, setup.py)
- ci: Changes to our CI configuration files and scripts (examples: .github/workflows/ci.yml)
- docs: Documentation only changes
- feat: A new feature
- fix: A bugfix
- perf: A code change that improves performance
- refactor: A code change that neither fixes a bug nor adds a feature
- test: Adding missing tests or correcting existing tests