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https://github.com/KosinskiLab/AlphaPulldown.git
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fff63051b4
* Harden MMseqs species ID resolution fallback * Reorganize tests for CPU coverage CI * New * Fix function coverage checker def-line false positives * Expand unit coverage for helper and backend manager utilities * New. * New. * Expand unit coverage for template and post-processing helpers * Expand unit coverage for objects.py edge cases * Publish HTML coverage reports via GitHub Pages * Add CPU unit coverage for AlphaFold3 backend helpers * Reorganize tests and expand backend coverage * Reset shared test flags between cases * Expand AF3 prepare_input unit coverage * Cover AF3 and truemultimer feature creation * Test AF3 multimer MSA translation paths * Cover AF3 duplicate-residue multimer fallback * Cover AF2 resume and postprocess edge paths * Cover AF3 template mmCIF preparation * Test small script entry points * Expand workflow and ModelCIF test coverage * Add backend extras and install guide * Clarify AF3 backend installation path * Stabilize cluster GPU test runners * Document AF3 CMake SQLite hints * Simplify backend installation guide * Align AF3 install with working cluster env * Backfill typing dataclass_transform for AF2 * Pin TensorFlow for cluster installs * Fallback AF2 relax when CUDA OpenMM is unavailable * Raise AF3 default minimum bucket size * Simplify backend cluster installation guide * Fix AF3 wrapper JSON output isolation * Fix AF3 JSON wrapper outputs and MMseqs ID parsing * Fix CI entrypoint stub and Python 3.8 typing * Document release readiness test gates
The active pytest layout is:
test/unitfor fast helper and mocked component teststest/integrationfor CPU-only filesystem, CLI wiring, and module interaction teststest/functionalfor heavier workflow tests that still belong to the main package test treetest/clusterfor Slurm, GPU, or workstation smoke wrappers that are run explicitlytest/outdatedfor legacy tests kept for reference until they are rewritten or deleted
Notes:
pytest.inionly collectsunit,integration, andfunctional.conftest.pyauto-applies markers from the directory layout.test/alphalinknow holds AlphaLink fixture files used by optional tests and cluster smoke runs.test/RELEASE_READINESS.mdtracks which workflows are continuously protected by CI and which still require explicit cluster or manual validation before a release.