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Developer Documentation

To set up pytopotoolbox for development, first make sure you have set up Git, fork the repository on GitHub then use git clone https://github.com/$YOUR_USERNAME/pytopotoolbox to download your fork of the repository, where you have replaced $YOUR_USERNAME with your GitHub username.

To ensure you have a development environment that is consistent with other developers and with our continuous integration and testing setup, it is a good idea to set up a virtual environment in Python. You can then install the developer environment by running

pip install -r requirements.txt .

within the top-level directory of the repository.

Now you can make changes within pytopotoolbox. To rebuild pytopotoolbox after making changes, you'll need to run

pip install .

You can run the tests with

python -m pytest

and the linter and type checks with

pylint --rcfile=pyproject.toml src/topotoolbox
mypy --ignore-missing-imports src/topotoolbox

It is a good idea to run the linter and type checks before making a pull request to pytopotoolbox, because failing lints or type checks will cause a test failure that must be fixed before your contribution can be accepted.

Development environment on Windows

pytopotoolbox requires C/C++ files to be compiled. If you are developing on Windows, there are a few extra steps to ensure that you have access to the Windows C/C++ toolchain.

  1. Install the Developer Command Prompt for VS 2022.
    • Scroll down to 'All Downloads'
    • open 'Tools for Visual Studio'
    • download 'Build Tools for Visual Studio 2022'
    • install it while including the 'Desktop development with C++' workload
  2. To ensure the compiler is working with 64-bit architecture, that is necessary for python, open 'x64 Native Tools Command Prompt for VS 2022' instead of the 'Developer Command Prompt' that defaults to 32-bit architecture.
  3. In the opened command prompt, navigate to the pytopotoolbox directory and follow the instructions above for installing the development environment.