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refactor: move AF3 ModelCIF and storage helpers beside the AF3 outputs - #662
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utils/af3_modelcif.py, used only by the AF3 output writer, moves unchanged to folding_backend/alphafold3_modelcif.py. The AF3 half of utils/post_modelling.py (the ranking_scores.csv ledger reader, the best sample it names and the --storage_mode presets) moves to folding_backend/alphafold3_storage.py, which, like post_modelling, imports no AlphaFold 3. post_modelling keeps the AF2 pickle presets and the shared compress_file. Nothing outside AlphaPulldown imports either old path (checked AlphaPulldownSnakemake and AlphaJudge). Tests follow the code; the expensive- test gate tracks the new ModelCIF path. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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The AF3 Dockerfile's test stage still named test/unit/test_af3_modelcif.py, renamed in the previous commit, so the image build failed there. A unit test now checks that every test file and test an image Dockerfile runs exists, so a rename fails in seconds in the unit suite rather than after the image build. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Follow-up to #658–#661: two AF3-only helpers that lived in
utils/move next to the AF3 output writer. No behaviour change.utils/af3_modelcif.py→folding_backend/alphafold3_modelcif.py, byte-for-byte (a pure rename in git). Onlyalphafold3_outputs.pyuses it.utils/post_modelling.py→folding_backend/alphafold3_storage.py: theranking_scores.csvledger reader, the best sample it names, and the--storage_modepresets. Likepost_modelling, it imports no AlphaFold 3.post_modellingkeeps the AF2 pickle presets and the sharedcompress_file.Nothing outside AlphaPulldown imports either old path (checked AlphaPulldownSnakemake and AlphaJudge), so there are no compatibility aliases. The tests follow the code (
test_alphafold3_modelcif.py,test_alphafold3_storage.py), and the expensive-test gate intest/cluster/code_changes.pytracks the new ModelCIF path.The AF3 image's build-time test stage names the ModelCIF test by path, so the first push failed
build-alphafold3-container. It now runs the renamed file, and a new unit test checks that every test file and test an image Dockerfile runs exists. Such a rename now fails in seconds in the unit suite.Verification
main. AF2 image: 946 passed, 26 skipped. AF3 image: 1017 passed, 15 skipped. The same pre-existing environmental failures.🤖 Generated with Claude Code