[DimaMolod]

Plan item 3 of 3: generate the workflow's inference-flag tables from AlphaPulldown, and enforce them in CI.

Problem

common.smk held hand-copied per-backend flag sets. The test comparing them with AlphaPulldown skipped wherever AlphaPulldown was not importable, which includes every CI run. The sets had drifted before.

Change

• tools/generate_inference_flag_tables.py --source-checkout PATH [--check].
  • Reads FLAGS_BY_BACKEND from an explicit AlphaPulldown checkout by evaluating its syntax tree. Nothing is imported, and no dependencies or submodules are needed.
  • Refuses a source file with uncommitted changes, and records the full commit.
  • Writes a sorted, clearly marked block into common.smk. No runtime imports, network access or schema files.
  • Its --help documents the update procedure: check out the intended revision, regenerate, inspect the diff, run the compatibility tests.
• The first block comes from 2.10.0 (6e7f9869), the release the default containers run. It equals the hand-copied sets exactly: 38, 21 and 38 flags for alphafold2, alphafold3 and alphalink.
• New CI job inference-flag-tables. It reads the recorded commit, checks out that AlphaPulldown revision without submodules, and runs --check. A missing source or any difference fails the job instead of skipping. To make the job required, main needs branch protection, which this repo doesn't have yet. That's a settings change left to the maintainers.

Tests

• Replaced: the hand-copied expected-set test gives way to generator tests on a throwaway git checkout:
  • output is deterministic;
  • --check writes nothing;
  • a removed or renamed flag fails --check;
  • an uncommitted source is refused;
  • a missing source fails rather than skips;
  • common.smk parses with no AlphaPulldown.
• Kept: the behavioural tests (ModelCIF, fast kernels and compile-cache flags on both backends) and the default-container compatibility tests.
• Full suite with Snakemake on PATH, so every dry run executes: 220 passed, none skipped. On main: 213 passed, 1 skipped, the old import-or-skip test.
• Dry runs against main: the AF2 and AF3 fixtures, and AF3 with the unsupported --allow_resume plus a misspelt flag. They produce identical commands, manifests, output targets and warnings. Timestamps, Snakemake's random file-set order and its scheduling notes are normalised out.

When an AlphaPulldown release with AF3 --allow_resume ships, #72 regenerates the block from that release instead of editing the set by hand.

🤖 Generated with Claude Code