Python package for evaluating neuron segmentations in terms of the number of splits and merges
Project description
aind-segmentation-evaluation
Python package for evaluating neuron segmentations in terms of the number of splits and merges.
Installation
To use the software, in the root directory, run
pip install -e .
To develop the code, run
pip install -e .[dev]
To install this package from PyPI, run
pip install aind-segmentation-evaluation
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 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 .
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
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/html
More info on sphinx installation can be found here.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for aind_segmentation_evaluation-0.0.22.tar.gz
Algorithm | Hash digest | |
---|---|---|
SHA256 | 9c31bd6561c804c7a62138f2926e895f6dd54cb8ed6a14d471ff49cccafa9d1d |
|
MD5 | 39a7cc8e4bcf00378cd6502197b9c574 |
|
BLAKE2b-256 | 51836317a3efdcd78b42b7e43ef99f02f3e7e0819fe4019b4475d67f33d47b40 |
Hashes for aind_segmentation_evaluation-0.0.22-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | d261a8a5b49056aff3a0636c6ab624704a9d824839ea51e29f8e15941a1cff1b |
|
MD5 | 2fb21f0179fe4fbd2f7bc6b5685798be |
|
BLAKE2b-256 | d23a1668934b90ff8812f33539ab8fa9418a988da5d4bf0ee67884d41221ff4c |