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strainFlye development documentation

Thanks for your interest in improving strainFlye's code!

Setting up a development environment

Assuming that you already have conda installed, the following installation instructions should work for most Linux or macOS systems. (However, please feel free to open an issue if you encounter any problems.)

First, you should fork strainFlye; this will make contributing your changes back up to the main branch easier.

After this, the following instructions should work (assuming that conda is installed):

# Clone your fork of strainFlye's source code
git clone https://github.com/your-github-username-goes-here/strainFlye.git

# Create and activate a conda environment based on the "environment.yml" file
# (by default, it'll be named "strainflye")
cd strainFlye
conda env create -f environment.yml
conda activate strainflye

# Install strainFlye from the cloned source in "editable mode"
pip install -e .[dev]

Sidenote: using mamba instead of conda

You may prefer to create the environment using mamba instead of conda, since mamba can be much faster. As of writing, probably the easiest way to do this is to create an empty environment and then update it based on environment.yml.

Sidenote: installing LJA in order to use strainFlye smooth assemble

If you want to work on strainFlye smooth assemble then you may also want to install LJA, as is discussed in the strainFlye README. (That said: as of writing strainFlye's tests do not rely on LJA being installed, so this step is optional.)

Development commands

strainFlye's Makefile, in the root of its repository, provides a few useful commands for development. These are described here. All of these commands assume that strainFlye has been installed as described above, that Make is installed, and that you are running these commands from the root of strainFlye's repository.

Running tests

strainFlye uses pytest and pytest-cov to run its automated tests. You can run these tests using:

make test

Thanks to our use of pytest-cov, this command will create a few formats of coverage report after running:

  1. it'll display a summary on the terminal,
  2. it'll create an XML file in the root of strainFlye's repository that is useful for passing coverage information to CodeCov,
  3. and it'll create a directory in the root of strainFlye's repository called htmlcov.

The last of these (htmlcov) is probably the most useful for local development.

Linting, style-checking, and auto-formatting

strainFlye uses flake8 to lint and style-check its source code, and black to auto-format its source code.

To run linting and style-checking, you can use the following command:

make stylecheck

To auto-format the source code:

make style

Note that, in some rare cases, flake8 and black can disagree. If you run into trouble trying to get the style-checking to pass (or with other development steps), feel free to open an issue in this repository.