Welcome to aind-ophys-utils
This repository contains python utility methods for processing optical physiology data. Methods in this repository have simple, standard data interfaces and are generally applicable to optical physiology data. As much as possible think arrays and dataframes rather than complex project-specific data structures.
Installation
pip install aind-ophys-utilsTo use the software from source, clone the repository and in the root directory run
pip install -e .To develop the code in place, run
pip install -e .[dev]Contributing
Linters and testing
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 pytest && 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 .
Pull requests
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
Semantic Release
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) |
Documentation
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.