This library is for pythonic access to data stored in the AIND SLIMS deployment. It is not meant to be a generic way to interact with SLIMS, but rather specific to how data is modeled in AIND's SLIMS instance.
To use the software, in the root directory, run
pip install -e .To develop the code, run
pip install -e .[dev]
Requires the pylance extension to be installed for similar functionality.
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
The table below, from semantic release, shows which commit message gets you which release type when semantic-release runs (using the default configuration):
| Commit message | Release type |
|---|---|
fix(pencil): stop graphite breaking when too much pressure applied |
|
feat(pencil): add 'graphiteWidth' option |
|
perf(pencil): remove graphiteWidth optionBREAKING CHANGE: The graphiteWidth option has been removed.The default graphite width of 10mm is always used for performance reasons. |
(Note that the BREAKING CHANGE: token must be in the footer of the commit) |
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.