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CONTRIBUTING.md

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Contributing

You are cordially invited to contribute to the further development of pyrepseq! There are various ways of contributing (improving documentation, fixing bugs, and extending functionality) all of which are very welcome.

Simply hack away and open a Pull request. Alternatively open an issue if you want to discuss your idea first.

Installing pyrepseq in a development environment

You will want to install pyrepseq from the latest version of the source code. To do this, first use a tool like venv or conda to create a new development environment, and activate it. Then, clone this repository, and from within the project root directory, run:

$ pip install -e ".[dev]"

What this is doing

  1. By pip installing the current directory (.), you are install pyrepseq from the source code you just cloned, and not from the PyPI server.
  2. You will want to directly link the pyrepseq source code you are editing to your environment's install of pyrepseq, so that all changes you make to the source code are reflected in real time in your install. The "editable" flag (-e) ensures that this is the case.
  3. You will want to install some development dependencies along with pyrepseq itself, such as pytest, sphinx, etc. This is done by specifying the dev extras group.

Unit testing

The module comes with a number of unit tests to increase robustness. To make sure your new code does not break any existing functionality, you can run the unittest by typing pytest in the top-level directory.