Contributing

Setting up a development environment

1. Fork the basicsynbio repository.

2. Clone your fork:

   git clone https://github.com/username/basicsynbio.git
   

3. cd into the directory.

4. Using a virtual environment running Python 3.8 or greater install the dependencies:

   pip install -r requirements.txt
   

5. Install the package in editable mode:

   pip install -e .
   

6. Confirm all test pass:

   pytest [--runslow]
   

Making changes

Steps

1. set the upstream repository:

   git remote add upstream https://github.com/LondonBiofoundry/basicsynbio.git
   

2. Pull the latest changes to origin/master:

   git pull upstream master
   

3. Create a new branch for your development:

   git checkout -b dev/foobar
   

4. Make the development then stage and commit:

   git add .
   git commit -m "make this desirable development to basicsynbio"
   

5. Push the development back to GitHub:

   git push origin dev/foobar
   

6. Go to GitHub and create a new Pull Request.

Guidelines for changes

General Guidelines

• Code should be formatted using black.

• New code should have associated tests written using pytest.

• Update the documentation if required. The documentation is formatted using Sphinx and as such all files must be written in reST.

• Update GitHub pages by running make github in the /docsource directory. This implements GitHub Pages as described by Anne Gentle.

• New releases are made online (https://github.com/LondonBiofoundry/basicsynbio/releases). Releases are automatically published to PyPi via the build-publish.yml workflow.

Guidelines for docstrings

• Format docstrings according to the Google Style Guide. This enables automated documentation of the API using sphinx.ext.napoleon.

• Where the same argument is used by multiple methods/functions, the basicsynbio.decorators.addargs2docs() decorator may be used. Associated instances of basicsynbio.decorators.ArgDescription are placed in basicsynbio.main.CommonArgDocs.