Welcome to Elastic Net Gene Selection’s documentation!¶

Elastic Net Gene Selection¶

scRNA-seq gene selection code

Installation¶

First create a conda environment with

conda create -n enetgsel python=3.8
conda activate enetgsel
conda install -c conda-forge fortran-compiler

Then:

Stable Release: pip install elastic_net_gene_selection
Development Head: pip install git+https://github.com/AllenCellModeling/elastic_net_gene_selection.git

Documentation¶

For full package documentation please visit AllenCellModeling.github.io/elastic_net_gene_selection.

Development¶

See CONTRIBUTING.md for information related to developing the code.

The Four Commands You Need To Know¶

pip install -e .[dev]

This will install your package in editable mode with all the required development dependencies (i.e. tox).
make build

This will run tox which will run all your tests in both Python 3.6, Python 3.7, and Python 3.8 as well as linting your code.
make clean

This will clean up various Python and build generated files so that you can ensure that you are working in a clean environment.
make docs

This will generate and launch a web browser to view the most up-to-date documentation for your Python package.

TODO: Additional Optional Setup Steps:¶

Register your project with PyPI:
- Make an account on pypi.org
- Go to your GitHub repository’s settings and under the ``Secrets` tab <https://github.com/AllenCellModeling/elastic_net_gene_selection/settings/secrets>`_, add a secret called PYPI_TOKEN with your password for your PyPI account. Don’t worry, no one will see this password because it will be encrypted.
- Next time you push to the branch: stable, GitHub actions will build and deploy your Python package to PyPI.
- Recommendation: Prior to pushing to ``stable`` it is recommended to install and run ``bumpversion`` as this will, tag a git commit for release and update the ``setup.py`` version number.

**Free software: Allen Institute Software License**