This version is compatible with the pipeline feature in Code Ocean.
Tool for whole brain cell couting using dask and cellfinder in the cloud.
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
To generate the rst files source files for documentation, run
sphinx-apidoc -o doc_template/source/ src Then to create the documentation HTML files, run
sphinx-build -b html doc_template/source/ doc_template/build/htmlMore info on sphinx installation can be found here.