Fork and Workspace Setup#

This guide walks you through cloning, configuring, and working on your local fork of MolSysMT.

1. Fork and Clone#

  1. Fork the uibcdf/MolSysMT repository on GitHub.

  2. Clone your fork locally:

git clone https://github.com/<your-username>/MolSysMT.git
cd MolSysMT

  1. Add the upstream repository as a remote:

git remote add upstream https://github.com/uibcdf/MolSysMT.git
git fetch upstream

2. Setting Up the Development Environment#

We recommend creating an isolated environment using conda, mamba, or micromamba with Python 3.11+:

Using the Automated Bootstrap Script#

The easiest way to configure your environment is using our automated bootstrap tool:

bash devtools/start_dev_env.sh

This script detects your package manager, creates or updates the environment from development_env.yaml, and installs MolSysMT in editable mode.

Manual Installation#

Alternatively, you can create and activate the environment manually:

conda env create -f development_env.yaml -n molsysmt_dev
conda activate molsysmt_dev
pip install --no-deps -e .

3. Verifying the Installation#

Verify that MolSysMT imports cleanly and your development environment is active:

python -c "import molsysmt as msm; print('MolSysMT version:', msm.__version__)"
pytest tests/basic/test_get_form.py

4. Development Workflow and Git Conventions#

When contributing code:

  • Create a feature branch:

    git checkout -b feature/my-improvement upstream/main

  • Verify code style with Ruff:

    ruff check molsysmt

  • Commit messages:

    • Keep messages descriptive and concise.

    • Include [skip ci] in intermediate or documentation-only commits to save CI resources unless triggering the full CI pipeline is required.

    • Never add attribution footers such as Co-Authored-By.