Commit History
10 days ago
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Install Diffusers from main, pin the current Diffusers weights, add wordmark and project page link
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docs: public install instructions and public Diffusers revision
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Point maintainer instructions at the public RosettaCommons/RFD4-Proteina repository
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Make run_examples.py run again against current Diffusers
`run_examples.py` takes a `--checkpoint` and runs against whatever Diffusers is installed, so it has to track the current pipeline API. It had stopped: * `pipe(features, ...)` passed the whole feature mapping positionally, where the first parameter is `padding_mask`. The same mistake was fixed in the README earlier; these scripts were missed. * `partial_t={"bb_ca": ..., "local_latents": ...}` is now two arguments, `partial_t_bb_ca` and `partial_t_local_latents`. * `coords_nm` is read by name, so it belongs with the arguments rather than in `conditioning_features`. Without it, partial diffusion and inverse folding raise "partial and inverse generation require clean coords_nm". A full run ignores it, so passing it always is correct for every task. The README's own `required` list had the same hole, and is corrected with it. * `TASKS` listed `antibody_design` and `nanobody`, whose inputs this repository does not ship -- the manifest lists them under `excluded` -- so the d…0a34f04 -
Call the pipeline the way its signature actually reads
Every example in this README passed the whole feature mapping as the first positional argument, `pipe(features, ...)`. That argument is `padding_mask`. `RFD4ProteinaPipeline.__call__` takes the masks and molecule tensors as arguments and the annotations separately as `conditioning_features`, so the examples would bind a dict where a tensor belongs and fail. Three call sites, all now matching the pipeline's own documentation: split the features into the five the pipeline takes by name and pass the rest as conditioning. Two of the three predate the batching example added alongside this; that one inherited the mistake from them. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>fda521e
11 days ago
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Document and test RFD4's batching contract for several designs
No change to how write_cif indexes anything. RFD4 replicates at collate time -- datapipes/collate.py does `[sample for sample in samples for _ in range(num_replicates)]` -- so every per-row quantity already has one row per design by the time anything reads it, and the export loop in proteina.py reads row i of each. write_cif already did the same thing, and keeping it that way is the point: this package indexes the way RFD4 indexes. What was missing was saying so, and testing it. The README example replicated with `repeat`, which tiles; an input's designs sit together, so it must be `repeat_interleave`, and the difference is invisible for one input and wrong for more than one. It now also shows `num_designs_per_prompt` alongside the replication, since a pipeline repeating its input internally still leaves the caller to replicate the features it passes back in. Tests cover one and three designs with replicated features, that unreplicated features raise IndexError on the second design r…33517d4 -
Restore the README sections the previous commit overwrote
82eed95 copied a local working tree over the repository and reverted 105 lines of README that had landed in 5ab5b72 in between: the Hub metadata header, the install and authenticate section, the custom-block walkthrough and the downloadable example catalog. That was a clobber, not a decision. This restores 5ab5b72's README and re-applies the only change 82eed95 meant to make to it, the AtomWorks 3.0.4 note. No other file was affected: block.py, LICENSE-APACHE, examples/manifest.json and examples/inputs/ were never copied over and survived. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>2a6de75 -
Take RFD4 5248e9a1, fix a stale vocabulary, require AtomWorks 3.0.4
The vendored modules are re-stamped to RFD4 5248e9a15a18. Across those ten upstream commits not one vendored module changed, so the only thing in the copy that moved is its provenance header. What did move is package data nothing was checking. RFD4 gave the `UNK` row of the checkpoint vocabulary a backbone -- "N CA C - O" where this package still shipped an empty row -- in "filter backbone-capable UNK before refolding" (#740). `resources/aa_rna_dna_glycan_ncaa.yaml` is copied verbatim from the RFD4 repository but is not a module, so it carries no provenance commit and the coverage guard could not see it. check_vendored.py now compares it byte for byte through a VERBATIM_DATA table, which a tamper test exercises. That gap is worth stating plainly: a UNK residue was being featurized with no atom37 slots at all, where upstream gives it four. None of the ten snapshot inputs contains a UNK residue, so the feature snapshot reported no change -- the one real change in this release was invis…82eed95 -
Add modular CIF helper and non-antibody Studio input catalog
Verified signatureAdditive helper, pinned example runner and CPU tests. Existing preprocessing source, model weights and repository visibility are unchanged.5ab5b72
12 days ago
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Vendor the whole RFD4 datapipe instead of an inference-only fork
The `_cif` modules were a hand-curated inference subset of the RFD4 datapipe, which meant every release turned into archaeology: decide which differences were deliberate, which were drift, and which were someone re-wrapping a docstring. Upstream never had two pipelines -- its `build_design_validation_pipeline` is `build_design_train_pipeline(is_inference=True)` -- so the fork was maintaining a split the flag already made for us. The modules are now vendored unedited, training paths included, and `prepare_cif` calls the upstream builder rather than keeping its own transform list. Recorded divergences drop from 24 to 11, and all 11 are packaging rather than behaviour: the DDP logger becomes plain `logging`, and two data files are read from this package instead of a repository checkout. This lands two batches of behaviour change: * Reconciliation against native main. `canonical_polymer_ordering` now treats non-canonical amino acids as protein, so their backbone linkages carry an or…73d658a -
Support the unified 147-class release: atomworks 3.0.3, chirality frames, encoder features
Verified signaturePins atomworks[ml]==3.0.3 and migrates AnnotateCovalentModifications to its API, matching the RFD4 inference datapipe (reassign_modified_residue=False, atomize_modified_residue=False). A pin bump alone fails: the 3.0.1 signature this package called no longer exists. Adds the features the unified checkpoint needs. AddChiralityFeature and the chirals helper are replaced with the RFD4 repository's current versions, which emit chiral_frame_atoms, chiral_slot_owner and tetrahedral_vertices and cover E/Z double-bond stereochemistry; without them noise_align_chirality cannot run. ground_truth_element and incident_bond_type_counts are added for the autoencoder encoder, which partial diffusion and inverse folding go through. Re-pins every vendored module to RFD4-Proteina 63ae4ff0cc26 (they recorded 0e05aece) and adds tools/check_vendored.py, which reports when a vendored source moves upstream. Verified against the previous behaviour: all 675 previously emitted tensors are bit-identical acros…38584dd
15 days ago
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Add the annotated-CIF preparation and export package for the Diffusers RFD4-Proteina pipeline
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README metadata: this is a companion package, not a Diffusers model
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README metadata: this is a companion package, not a Diffusers model
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Add the annotated-CIF preparation and export package for the Diffusers RFD4-Proteina pipeline
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