Development

Development#

Setting up a development environment#

First clone the GitHub repo and set it as the current directory:

git clone https://github.com/saeyslab/napari-sparrow.git
cd napari-sparrow

Create a conda virtual environment as explained here and install SPArrOW.

conda activate napari-sparrow
pip install -e '.[testing,docs]'

This development environment is supported for:

  • CentOS

  • Ubuntu

  • MacOS with an M1/M2 Pro

  • Windows 11

Testing#

To run unit tests, run the following from the root of the project:

pytest

Continuous integration will automatically run the tests on all pull requests.

Type testing#

Do a type test:

mypy --ignore-missing-imports src/

Automated commit checks#

Install a pre-commit hook to run all configured checks in .pre-commit-config.yaml:

pre-commit install
pre-commit run -a
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