https://github.com/allencellmodeling/geneselection
only the best genes
https://github.com/allencellmodeling/geneselection
Last synced: 4 months ago
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only the best genes
- Host: GitHub
- URL: https://github.com/allencellmodeling/geneselection
- Owner: AllenCellModeling
- License: mit
- Created: 2018-11-29T22:55:06.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2020-06-16T22:58:47.000Z (almost 5 years ago)
- Last Synced: 2025-01-02T23:14:19.840Z (5 months ago)
- Language: Python
- Size: 10.5 MB
- Stars: 0
- Watchers: 4
- Forks: 2
- Open Issues: 9
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Geneselection
[](https://www.travis-ci.com/AllenCellModeling/geneselection)
[](https://geneselection.readthedocs.io/en/latest/?badge=latest)
[](https://codecov.io/gh/donovanr/plasticnet)
## Installation
We use [Conda](https://conda.io/) to manage the development environment, with dependencies listed in [.environment.yml](../master/.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 [email protected]:AllenCellModeling/geneselection.git
cd geneselection
conda env create -f .environment.yml
conda activate gsel
conda develop .
pre-commit install
```
## Development
We use:
- [GitHub](https://github.com) for code hosting and issue tracking
- [Travis CI](https://travis-ci.org/) for testing
- [Read the Docs](https://readthedocs.org/) for auto-generating and publishing the documentation
- [pre-commit hooks](https://git-scm.com/book/en/v2/Customizing-Git-Git-Hooks) for formatting and linting
### Travis
The Travis configuration is in [.travis.yml](../master/.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](http://www.sphinx-doc.org/) + [autodoc](http://www.sphinx-doc.org/en/master/usage/quickstart.html#autodoc) lives in [docs/source/conf.py](../master/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](../master/.pre-commit-config.yaml).
The pre-commit hooks we use are:
- [Black](https://black.readthedocs.io/en/stable/) for formatting, with the default settings
- [Flake8](http://flake8.pycqa.org/en/latest/) for linting, with configurations in [.flake8](../master/.flake8)