Geneselection

Installation

We use Conda to manage the development environment, with dependencies listed in .environment.yml. If you don't have conda installed and set up for Python 3.x, install it using the instructions on their site, and then install this package with

git clone git@github.com:AllenCellModeling/geneselection.git
cd geneselection
conda env create -f .environment.yml
conda activate gsel
conda develop .
pre-commit install

Development

We use:

• GitHub for code hosting and issue tracking
• Travis CI for testing
• Read the Docs for auto-generating and publishing the documentation
• pre-commit hooks for formatting and linting

Travis

The Travis configuration is in .travis.yml, and doesn't have anything fancy set up.

Tests are run automatically when commits are pushed to GitHub. To run the tests locally, issue pytest in the main project directory.

Read the Docs

Documentation config for Sphinx + autodoc lives in docs/source/conf.py. To get things to build with Read the Docs, you need to set up a virtual environment in the admin options there so that dependencies like numpy can be installed, and point Read the Docs to the docs/source/rtd-requirements.txt file. You should also choose the CPython 3.x interpreter.

Docs are generated automatically when commits are pushed to GitHub. To generate the docs locally, from the main project directory, use

sphinx-build -b html docs/source docs/build

You may have to create docs/build if it doesn't exist yet.

Pre-Commit Hooks

Pre-commit hooks are configured in .pre-commit-config.yaml.

The pre-commit hooks we use are:

• Black for formatting, with the default settings
• Flake8 for linting, with configurations in .flake8