Makefile Reference

The project root Makefile defines build, test, formatting, release, and utility commands. Run make help to see all targets inline.

Quick Reference

Category	Target	Description
Installation	install	Install from pip with basic extras (dlpacker, pippack, colabdesign, thermompnn, test) and optional extras (rfdiffusion_cpu, esm2)
	install-no-dept	Install from pip with no dependencies (--no-dependencies)
	install-pytorch-cpu-mac	Install PyTorch 2.3 CPU build for macOS (PyPI default index)
	install-pytorch-cpu-non-mac	Install PyTorch 2.3 CPU build for Linux/Windows (PyPI --index-url https://download.pytorch.org/whl/cpu)
	install-dgl-linux	Install DGL <=2.4.0 (Linux, pip with https://data.dgl.ai/wheels/torch-2.3/repo.html)
	install-dgl-win	Install DGL for Windows/macOS (pip with https://data.dgl.ai/wheels/repo.html; version <=2.2.1 as noted in help)
	reinstall	Clean, reformat, remove local config, then pip install . -U
	install-pymol-plugin	Copy the package manager startup script to ~/.pymol/startup/
Testing	test	Run the test suite ($(PYTEST_CASES_PATH)) in an isolated temp directory
	all-test	Run all three test phases in sequence (fast parallel, serial, slow serial) and combine coverage
	fast-test	Run fast tests in parallel with xdist (-n 4 -m "not serial")
	serial-test	Run serial tests (-m "(serial and not very_slow) or bootstrap")
	slow-test	Run slow serial tests (-m "(serial and very_slow) or bootstrap")
	kw-test	Run tests filtered by keyword (-k PYTEST_KW); supports single and multi-keyword expressions
	kw-test-pdb	Run keyword-filtered tests under pdb (-s -v --pdb)
	macos-rosetta-test	Run UI tests against the macOS PyMOL.app incentive installation (Rosetta)
Formatting	black	Reformat code with all pre-commit hooks (pre-commit run --all-files); stages black, isort, autoflake, pyupgrade, autopep8
Release	tag	Bump version: extract old/new versions from __init__.py diff, insert dated changelog section, commit, create annotated tag
	license-update	Apply GPL-3.0 license header to all .py files
	license-check	Check license headers are present (python tools/license_notice.py --check)
Translation/UI	compile-ui	Compile .ts translation files to .qm binaries
	translate	Stage translation generation using tools/translate.sh
	upload-gists	Upload the PyMOL installer script, entry UI, and extras JSON to GitHub Gist
Dev tools	reverse	Generate class and package SVGs using pyreverse + dot
	memray	Profile memory under pytest, output flamegraph HTML (leak detection)
	memray-live	Profile memory in live terminal mode with memray run --live
	clean	Remove build artifacts, caches, coverage files, temp directories, and test outputs
	help	Print all available targets and their descriptions
Setup	setup-display-gha	Install X11 libraries and start Xvfb for headless Qt testing on GitHub Actions / CircleCI
	prepare-test	Install pytest, coverage, and server-test dependencies (celery, docker, Flask, SQLAlchemy)

Usage Notes

• Temporary test directory: All test targets run inside tmp-test-dir-with-unique-name/ to ensure the installed package is tested, not the source tree. The conftest resolves REPO_DIR via os.path.dirname(__file__) and TEST_ROOT via os.path.abspath(".") relative to CWD, which fails outside this directory.
• PYTEST_KW: The keyword test target reads the PYTEST_KW variable. For multiple keywords use double quotes: make kw-test PYTEST_KW='"citable or citation"'.
• Condatest environment: Most targets expect a conda environment with PyMOL and the scientific stack installed. See the CI workflows for the full setup sequence.
• Platform awareness: PyTorch CPU wheels differ by platform (install-pytorch-cpu-mac vs install-pytorch-cpu-non-mac). DGL wheels also diverge between Linux and Windows/macOS.
• black exit code: The exit code of make black is advisory. Pre-commit hooks may leave the code with improved syntax and style regardless of the exit code.