pySSMF

Installation steps

In order to install pySSMF, you will need a machine with Python3.9 and create a virtual environment.

First, open a terminal, clone, and enter in the folder of this project:

git clone https://github.com/JosePizarro3/pySSMF.git
cd pySSMF

Create the virtual environment specifying the version of Python3.9:

python3.9 -m venv .pyenv
source .pyenv/bin/activate

We recommend using uv for pip installing all packages:

pip install uv

Make sure to have pip upgraded to its latest version:

uv pip install --upgrade pip

Now, install the dependencies in editable mode (this is done by adding the flag -e and it is useful when debugging the code):

uv pip install -e '.[dev]'

The [dev] option will allow to install the optional-dependencies specified in the configuration pyproject.toml file.

Run the tests

You can run local tests using the pytest package:

python -m pytest -sv tests

where the -s and -v options toggle the output verbosity.

Our CI/CD pipeline produces a more comprehensive test report using coverage and coveralls packages. We suggest you to generate your own coverage reports locally by doing:

uv pip install coverage coveralls
python -m pytest --cov=src tests

Run linting and auto-formatting

We use Ruff for auto-formatting our Python modules. This package is included as part of the [dev] dependencies of the project, and can be run in the terminal:

ruff check .
ruff format . --check

Ruff auto-formatting is also a part of the GitHub workflow actions. Make sure that before you make a Pull Request, ruff format . --check runs in your local without any errors otherwise the workflow action will fail.

Using VSCode for debugging

I recommend to use VSCode as your visual editor for debugging. The project comes with a settings.json file which already takes care of formatting everytime you save changes in a file (using Ruff).

You can also create your own personal debugger launch.json. As an example, this is my current debug file:

{
    "version": "0.2.0",
    "configurations": [
        {
            "name": "pySSMF python",
            "type": "debugpy",
            "request": "launch",
            "program": "${workspaceFolder}/debug.py",
            "python": "${workspaceFolder}/.pyenv/bin/python",
            "console": "integratedTerminal",
            "justMyCode": true,
            "env": {
                "PYTHONDONTWRITEBYTECODE": "1"
            }
        },
        {
            "name": "pySSMF pytest",
            "type": "debugpy",
            "request": "launch",
            "module": "pytest",
            "args": [
                "-sv",
                "${workspaceFolder}/tests"
            ],
            "python": "${workspaceFolder}/.pyenv/bin/python",
            "console": "integratedTerminal",
            "justMyCode": true,
            "env": {
                "PYTHONDONTWRITEBYTECODE": "1"
            }
        },
    ]
}

Feel free to modify the relative paths under "program" or "args" respectively.