Developer guide

This guide is for people working on MolClusters itself: fixing bugs, adding analyses, changing what it computes.

• Development setup: clone, install, run the checks.
• Architecture: the modules, what each owns, and how a run flows through them.
• The tracking algorithm: how cluster ids are assigned, in the detail needed to change it.
• Adding a built-in analysis: the registry and the conventions an analysis follows.
• Changing the report format: versioning and the reader.
• Testing: the test suite, its fixtures, and the units tests.
• Commits and releases: commit messages, branches, what counts as a breaking change, and how a release is cut.
• Writing the docs: this site, and how to build and publish it.

Pull requests are welcome; for larger changes, please open an issue first to discuss them.