mirror of https://github.com/KosinskiLab/AlphaPulldown.git synced 2026-06-04 14:14:24 +08:00

Files

Dima fff63051b4 Tests (#600 )

* 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

2026-04-01 14:13:35 +02:00

2.3 KiB

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Release Readiness

This branch has broad maintained test coverage, but the protection is layered.

Always-on CI

GitHub Actions runs:

test/unit
test/integration
coverage collection and reporting
Python 3.10 and 3.11

These lanes continuously protect:

feature creation wiring and CLI dispatch
fold parsing and object construction
AF2 backend helper behavior
AF3 backend helper behavior
script entrypoint and wrapper argument handling
post-prediction and ModelCIF integration paths
CPU-safe AlphaLink helper logic

Explicitly-run validation

The following are intentionally outside default CI and must be run explicitly when a change touches them:

test/cluster/check_alphafold2_predictions.py
test/cluster/check_alphafold3_predictions.py
test/cluster/check_alphalink_predictions.py
manual or cluster-backed GPU/Slurm smoke runs

Release-critical examples include:

AF3 wrapper output isolation for combined JSON folds
MMseqs-generated .a3m and .pkl / .pkl.xz feature artifacts
AF3 species pairing regressions for issue #588
AF2 and AF3 dimer inference quality checks such as ipTM > 0.6

Not Continuously Protected

The following areas are only partially protected, optional, or report-only:

test/cluster workflows
test/alphalink workflows beyond CPU-safe helper tests
legacy scenarios still parked under test/outdated
analysis-pipeline utilities and some deeper ModelCIF internals
Python 3.8, which is still advertised in packaging but is not exercised by GitHub Actions

The coverage artifact is useful as an audit input, but it does not prove workflow correctness by itself. In particular, python test/tools/check_function_coverage.py --report-only highlights functions that were never executed in CI and should be treated as follow-up audit items, not automatic release blockers.

Practical Release Gate

Before a final release, the expected evidence is:

PR smoke-tests and coverage are green.
AF3 JSON wrapper regressions are green.
Issue #588 MMseqs/AF3 pairing regressions are green.
Manual or cluster-backed AF2 and AF3 dimer runs from MMseqs features complete successfully with acceptable confidence.

If those gates are green, the branch is in good release shape even though some heavyweight workflows are still validated outside default CI.

2.3 KiB Raw Blame History