Installation

Requirements: git, conda. Creates the biobb_md conda environment and install the package:

git clone https://github.com/NBDsoftware/biobb_md_workflows.git
cd biobb_md_workflows
export KEY_MODELLER="HERE YOUR MODELLER KEY"   # only for academic use
conda env create -f environment.yml
conda activate biobb_md

This exposes the four workflow commands (protein_preparation, ligand_parameterization, md_gromacs, traj_postprocessing).

Releasing (maintainers)

Every version string in the repo (pyproject.toml, the three conda env files, CITATION.cff, docs/conf.py) is generated — do not edit them by hand. Instead:

  1. Describe the changes under ## [Unreleased] in CHANGELOG.md as you work.

  2. Actions ▸ Release (1/2) prepare ▸ Run workflow, branch master, version e.g. 0.2.0 (no leading v). This rewrites the version everywhere, renames [Unreleased] to the new version, and pushes a release/0.2.0 branch. The job summary links you to the PR.

  3. Open that PR (keep the title release: 0.2.0) and merge it.

  4. Release (2/2) publish then fires automatically: it tags the release commit and publishes the GitHub Release, using that CHANGELOG section as the notes.

It is split in two because master requires pull requests, so the version change cannot be pushed to it directly.