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CRISPR-CARB / nocap

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Network Optimization and Causal Analysis of Perturb-seq

Tests PyPI PyPI - Python Version PyPI - License Documentation Status Codecov status Cookiecutter template from @cthoyt Code style: black Contributor Covenant

Network Optimization and Causal Analysis of Petrurb-seq

💪 Getting Started

TODO show in a very small amount of space the MOST useful thing your package can do. Make it as short as possible! You have an entire set of docs for later.

Command Line Interface

The nocap command line tool is automatically installed. It can be used from the shell with the --help flag to show all subcommands:

nocap --help

TODO show the most useful thing the CLI does! The CLI will have documentation auto-generated by sphinx.

🚀 Installation

The most recent code and data can be installed directly from GitHub with:

pip install git+https://github.com/pnnl-compbio/nocap.git

👐 Contributing

Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved.

👋 Attribution

⚖️ License

The code in this package is licensed under the MIT License.

🍪 Cookiecutter

This package was created with @audreyfeldroy's cookiecutter package using @cthoyt's cookiecutter-snekpack template.

🛠️ For Developers

See developer instructions The final section of the README is for if you want to get involved by making a code contribution. ### Development Installation To install in development mode, use the following: ```bash git clone git+https://github.com/pnnl-compbio/nocap.git cd nocap pip install -e . ``` ### 🥼 Testing After cloning the repository and installing `tox` with `pip install tox`, the unit tests in the `tests/` folder can be run reproducibly with: ```shell tox ``` Additionally, these tests are automatically re-run with each commit in a [GitHub Action](https://github.com/pnnl-compbio/nocap/actions?query=workflow%3ATests). ### 📖 Building the Documentation The documentation can be built locally using the following: ```shell git clone git+https://github.com/pnnl-compbio/nocap.git cd nocap tox -e docs open docs/build/html/index.html ``` The documentation automatically installs the package as well as the `docs` extra specified in the [`setup.cfg`](setup.cfg). `sphinx` plugins like `texext` can be added there. Additionally, they need to be added to the `extensions` list in [`docs/source/conf.py`](docs/source/conf.py). The documentation can be deployed to [ReadTheDocs](https://readthedocs.io) using [this guide](https://docs.readthedocs.io/en/stable/intro/import-guide.html). The [`.readthedocs.yml`](.readthedocs.yml) YAML file contains all the configuration you'll need. You can also set up continuous integration on GitHub to check not only that Sphinx can build the documentation in an isolated environment (i.e., with ``tox -e docs-test``) but also that [ReadTheDocs can build it too](https://docs.readthedocs.io/en/stable/pull-requests.html). ### 📦 Making a Release After installing the package in development mode and installing `tox` with `pip install tox`, the commands for making a new release are contained within the `finish` environment in `tox.ini`. Run the following from the shell: ```shell tox -e finish ``` This script does the following: 1. Uses [Bump2Version](https://github.com/c4urself/bump2version) to switch the version number in the `setup.cfg`, `src/nocap/version.py`, and [`docs/source/conf.py`](docs/source/conf.py) to not have the `-dev` suffix 2. Packages the code in both a tar archive and a wheel using [`build`](https://github.com/pypa/build) 3. Uploads to PyPI using [`twine`](https://github.com/pypa/twine). Be sure to have a `.pypirc` file configured to avoid the need for manual input at this step 4. Push to GitHub. You'll need to make a release going with the commit where the version was bumped. 5. Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can use `tox -e bumpversion -- minor` after.