Skip to content

Latest commit

 

History

History
109 lines (79 loc) · 2.95 KB

CONTRIBUTING.md

File metadata and controls

109 lines (79 loc) · 2.95 KB
Raw

Contributing to genslm

If you are interested in contributing to genslm, your contributions will fall into two categories:

  1. You want to implement a new feature:
    • In general, we accept any features as long as they fit the scope of this package. If you are unsure about this or need help on the design/implementation of your feature, post about it in an issue.
  2. You want to fix a bug:
    • Please post an issue using the Bug template which provides a clear and concise description of what the bug was.

Once you finish implementing a feature or bug-fix, please send a Pull Request to https://github.com/ramanathanlab/genslm.

Developing genslm

To develop genslm on your machine, please follow these instructions:

  1. Clone a copy of genslm from source:
git clone https://github.com/ramanathanlab/genslm
cd genslm
  1. If you already have a genslm from source, update it:
git pull
  1. Install genslm in develop mode:
python -m venv env
source env/bin/activate
pip install -U pip setuptools wheel
pip install -r requirements/dev.txt
pip install -e .

This mode will symlink the Python files from the current local source tree into the Python install. Hence, if you modify a Python file, you do not need to reinstall genslm again and again.

  1. Ensure that you have a working genslm installation by running:
python -c "import genslm; print(genslm.__version__)"
  1. To run dev tools (isort, flake8, black, mypy, coverage, pygount):
make
make mypy
make coverage
make pygount

Unit Testing

To run the test suite:

  1. Build and install genslm from source.
  2. Run the test suite: pytest tests

If contributing, please add a test_<module_name>.py in the tests/ directory in a subdirectory that matches the genslm package directory structure. Inside, test_<module_name>.py implement test functions using pytest.

Building Documentation

To build the documentation:

  1. Build and install genslm from source.
  2. Generate the documentation file via:
cd genslm/docs
make html

The docs are located in genslm/docs/build/html/index.html.

To view the docs run: open genslm/docs/build/html/index.html.

Releasing to PyPI

To release a new version of genslm to PyPI:

  1. Merge the develop branch into the main branch with an updated version number in genslm.__init__.
  2. Make a new release on GitHub with the tag and name equal to the version number with a "v" in front, e.g., v<version-number>.
  3. Build and install genslm from source.
  4. Run the following commands:
python setup.py sdist
twine upload dist/*

Releasing to Docker

To setup the docker container and push to docker hub:

cd requirements
docker login
docker build . -t genslm
docker tag genslm abrace05/genslm
docker push abrace05/genslm

Check that the container runs:

docker run -it --rm abrace05/genslm bash