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Major refactor - #118

Merged

tjduigna merged 411 commits into

mainfrom

major_refactor

Oct 9, 2026

Merged

Major refactor#118
tjduigna merged 411 commits into
mainfrom
major_refactor

This pull request is big! We're only showing the most recent 250 commits

Commits on Aug 13, 2026
- docs(data): describe linked apo release columns
  Ninjani
  committed
  130297f
- fix(loader): align batch collation with dataset items
  Ninjani
  committed
  6d043a8
- feat(core): add release table query API
  Ninjani
  committed
  6e8b527
- chore: mypy fixes
  OleinikovasV
  committed
  50754a8
- refactor(scoring): slim holo scores and repair packed shards
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  committed
  e7b5acd
- refactor(clustering): publish only set-cover clusters
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  c13701a
- fix(index): preserve annotation query safeguards
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  committed
  0ae47ce
- fix(clustering): validate Tanimoto score coverage
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  committed
  7a6c419
- refactor(core): remove legacy archive unpacking
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  committed
  96cb583
Commits on Aug 14, 2026
- refactor(data): remove retired splits and publish MMP pairs
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  2a281c9
- fix(data): MMP pairs
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  2124b94
- refactor(docs): generate reference tables from release metadata
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  e248419
- fix(docs): execute notebooks and escape table metadata
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  committed
  02c6eea
- feat(core): add protein interface reconstruction API
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  c5b565e
- fix(core): add reisdue index checks
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  a405448
- docs: add & to PLINDER full form
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  committed
  0e8bd37
- docs(data): document ligand and protein-interface access
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  committed
  2bf4ea7
- fix(pipeline): complete end-to-end scoring workflow
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  committed
  993c6b9
- refactor(index): separate entry metadata from ligand annotations
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  committed
  0f81fca
- fix(pipeline): handle empty ligand archive shards
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  committed
  e3ec9c1
Commits on Aug 15, 2026
- docs(data): move entry fields to metadata descriptions
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  committed
  0b0f58e
- docs(data): validate release table schemas
  Ninjani
  committed
  b2f13c5
- lint(clustering): apply formatter
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  committed
  445f9a5
- fix(annotations): preserve oligomer ligands
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  committed
  f03c975
- fix(docs): reject stale interface cluster columns
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  committed
  89707b6
- fix(annotations): compute entry validation before export
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  committed
  29ce749
- lint(scoring)
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  committed
  cf3a82f
- docs(data): correct table and interface references
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  committed
  9e28472
- fix(docs): remove splits for now
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  committed
  cbcf831
- docs: update pipeline.md
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  committed
  ccb4ecc
- feat: add lightweight linked apo scoring
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  28d014c
- fix: preserve predicted scoring metrics
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  committed
  569004a
Commits on Aug 16, 2026
- fix: accept unavailable validation metrics
  Ninjani
  committed
  f59bbb7
- fix: reconstructed mmCIF chain IDs
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  committed
  ecd4fe9
- fix: score custom assembly chain IDs
  Ninjani
  committed
  d2bc849
Commits on Aug 17, 2026
- chore: mute the docs before v3
  OleinikovasV
  committed
  404d922
- Retain complete ligand pair similarity scores
  Ninjani
  committed
  3b80780
Commits on Aug 18, 2026
- Allow plinder_link to score protein FASTA queries
  Ninjani
  committed
  eb7bc8a
- Publish complete similarity scores and PLI identity
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  committed
  759d448
- feat: biotite filter heavy
  OleinikovasV
  committed
  02b3fe2
Commits on Aug 19, 2026
- Fix clean-checkout structure test fixtures
  Ninjani
  committed
  3c71b04
- Expose custom scoring only as a Python API
  Ninjani
  committed
  4f33c85
- feat(index): pick tables to join based on columns requested
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  committed
  0f68657
- refactor(index): split system validation from ligand annotations
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  committed
  3f72bb4
- fix(index): join pocket membership to system validation
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  committed
  055c1d9
- refactor(data): remove duplicate ligand SMILES column
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  committed
  3fd142e
- docs: split the column reference by tabl
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  committed
  dde9fb6
- test: update ligand SMILES
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  committed
  5cf6aee
- refactor(data): move cluster columns to other query tables
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  committed
  cf595d3
- docs: describe the release data layout
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  committed
  c27b0a1
- fix(data): preserve annotation index on staging failure
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  committed
  0e0f886
- docs: correct score fields and chain join keys
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  committed
  a97fe82
- docs: add the getting started guide
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  7b46997
- docs: api
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  committed
  f390786
- docs: defer outdated evaluation and loader pages
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  committed
  4ab8671
- docs: fix legacy page handling and release paths
  Ninjani
  committed
  abe0122
- chore: cleanup bird_id and stale cofactors.json
  OleinikovasV
  committed
  4a99ad0
Commits on Aug 20, 2026
- fix(core): accept numpy values in table filters
  Ninjani
  committed
  891e9f2
- feat(scoring): support subsetting PLINDER entry targets
  Ninjani
  committed
  13fd110
- fix(scoring): restrict entry subsets to scoreable chains
  Ninjani
  committed
  6de6e9f
- docs: expand the Python API reference
  Ninjani
  committed
  85114ad
- docs: update the dataset reference
  Ninjani
  committed
  2f18c33
- upgrade sanitize.py patch
  OleinikovasV
  committed
  43185c8
- docs: reorganize notebooks
  Ninjani
  committed
  a64a17a
- fix(annotations): preserve author residue numbering
  Ninjani
  committed
  f1ba6aa
- feat(data): add ligand pocket residue table
  Ninjani
  committed
  e71b5e2
- test(eval): update ligand SMILES fixture
  Ninjani
  committed
  54cd136
- Merge custom scoring database packaging fixes
  Ninjani
  committed
  482f472
- chore: remove deprecated set_structure kwarg warning
  OleinikovasV
  committed
  4533763
- chore: sanitize comment
  OleinikovasV
  committed
  86efb1f
- fix(data): include interaction-only pocket residues
  Ninjani
  committed
  9147abc
- fix(ci): align test image with current dependencies
  Ninjani
  committed
  814c80b
- fix(annotations): preserve connected composite ligand smiles
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  committed
  be41f80
- fix(data): make annotation collation order
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  committed
  67a73b7
Commits on Aug 21, 2026
- feat: get latest BindingDB
  OleinikovasV
  committed
  f8c3e6b
Commits on Aug 26, 2026
- feat: improved local stereocheck for E/Z and @/@@
  OleinikovasV
  committed
  9a1f3dc
Commits on Aug 27, 2026
- fix: consistent ligand handling, improved stereo check, covalent-SDF saving
  OleinikovasV
  committed
  7fc14b7
Commits on Sep 7, 2026
- fix: cif_bond consistency checking, avoid overbonding + chore: numpydoc
  OleinikovasV
  committed
  a089591
Commits on Sep 8, 2026
Commits on Sep 10, 2026
Commits on Sep 11, 2026
- fix(ingest): retain cryo-EM reconstruction resolution
  Ninjani
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  27f21cb
- fix(ingest): isolate chain and system validation failures
  Ninjani
  committed
  10ffa18
- feat(ingest): expose assembly and interaction failure diagnostics
  Ninjani
  committed
  b2fddb3
- fix(ingest): preserve unknown unresolved atom counts
  Ninjani
  committed
  bb3e6b9
- fix(ingest): include MHFP6 scoring in segmented ligand builds
  Ninjani
  committed
  855e962
- fix(ingest): respect annotation threshold overrides
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  d585539
- feat(ingest): record validation settings
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  3b9eef7
- fix(ingest): distinguish linker failures from
  Ninjani
  committed
  c2900ae
- fix(ingest): record unsupported MMP chemistry without aborting
  Ninjani
  committed
  06a4c4f
- refactor(ingest): remove obsolete annotation runners
  Ninjani
  committed
  131d0eb
- feat(ingest): add native protein sequence clustering
  Ninjani
  committed
  32322ab
- feat(ingest): add native protein structure clustering
  Ninjani
  committed
  4352185
- refactor(ingest): simplify protein clustering
  Ninjani
  committed
  ef8d816
- feat: CCD ligand DBs stage (components, ECFP4, MMP fragments, Rascal PARITY-like scores with composite assembly from mono matches); drop no-op RemoveAllHs in CCD conv.
  OleinikovasV
  committed
  214dbf3
- Merge remote-tracking branch 'origin/major_refactor' into major_refactor
  OleinikovasV
  committed
  f3348bf
- refactor(ingest): remove obsolete helpers and redundant checks
  Ninjani
  committed
  c384461
- feat(data): expose protein cluster tables through the release API
  Ninjani
  committed
  642e047
- chore: lint, format
  OleinikovasV
  committed
  4adb233
- fix(ingest): refresh interface representatives before scoring plans
  Ninjani
  committed
  0d6e2c8
- Merge origin/major_refactor with ingest updates
  Ninjani
  committed
  bc7d9bb
- chore: rm dates.csv patch
  OleinikovasV
  committed
  0571649
- fix(ingest): retain unknown-residue chains without structure
  Ninjani
  committed
  00cb8c7
- fix(ingest): include CCD databases in segmented ligand builds
  Ninjani
  committed
  9328632
- fix(ingest): include CCD scoring settings in cache manifest
  Ninjani
  committed
  9eb813b
- fix(ingest): refresh cached entries missing chain modification annotations
  Ninjani
  committed
  1c373a2
- fix(ingest): refresh cached ligand and entry
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  committed
  1fd1f54
- fix(ingest): support metadata
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  committed
  1f80bc9
- chore: cleanup
  OleinikovasV
  committed
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Commits on Sep 12, 2026
- fix(ingest): preserve apo chains without unnecessary ligand spatial work
  Ninjani
  committed
  34d1b4a
- Merge origin/major_refactor with ingest fixes
  Ninjani
  committed
  07efb1a
- feat(ingest): plan incremental updates from PDB snapshots
  Ninjani
  committed
  7dcf77f
- feat(ingest): prepare incremental entry updates safely
  Ninjani
  committed
  a4a5afe
- refactor: consolidate shared helpers and remove unused code
  Ninjani
  committed
  f859f3b
- fix(ingest): simplify incremental updates and support ligand-free changes
  Ninjani
  committed
  a6f7f8b
- feat(ingest): update canonical ligand archives
  Ninjani
  committed
  3e5fa48
- chore(ingest): reset format counters for the
  Ninjani
  committed
  348826c
- feat(ingest): add resumable weekly release updates
  Ninjani
  committed
  d14e112
- fix(ingest): invalidate changed release score caches
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  committed
  37d57ec
- fix(ingest): preserve direct Foldseek coordinate inputs
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  101fb8e
- refactor: remove unused legacy code
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  7a029af
- refactor: consolidate annotation queries
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  950fd13
- refactor: simplify similarity score queries
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  de067fa
- fix: preserve score query inputs
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  committed
  78dcd2f
- fix: reject scalar ligand ID strings
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  committed
  bc7203d
- chore: refresh code quality tooling
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  committed
  5cf7cae
- fix: preserve coordinate dtypes and CI typing
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Commits on Sep 21, 2026
- merge: sync major_refactor with main (Cloudflare R2 migration)
  OleinikovasV
  committed
  e59d8da
- feat(ingest): record protein contacts per assembly chain
  Ninjani
  committed
  8e524e7
- fix(ingest): drop clashing polymer symmetry copies
  Ninjani
  committed
  5f7672d
- perf(clustering): share directed-cover work across thresholds
  Ninjani
  committed
  c035372
- feat(data): link apo chains to protein interfaces
  Ninjani
  committed
  07f0270
- refactor(data): remove obsolete compatibility paths
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  committed
  219b0ab
- fix(scoring): distinguish unchecked ligand shape comparability
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  9315433
- chore:lint
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  559b1fb
- feat: directional RascalParity score
  OleinikovasV
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- Keep temporary search databases on local scratch
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- Publish compact protein similarity scores
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Commits on Sep 22, 2026
- chore: case-insensitive macOS test_ligand_sdf_pairing
  OleinikovasV
  committed
  6346304
- Compress published alignment residue mappings
  Ninjani
  committed
  d066d88
- Add chain residue overlap queries
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  committed
  7ceea82
- Publish optional full-chain alignment CIGARs
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  committed
  4b7c05c
- Use 32 CPUs for protein search stages
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  88a9644
- Define ligand pocket residues by neighboring contacts
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  3fe09bf
- Keep Metaflow ingest aligned with current pipeline
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  c6356b3
- Skip Voronota for assemblies without interfaces or ligand pockets
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  committed
  38a220a
Commits on Sep 23, 2026
- Fix BindingDB affinity matching (issue #94)
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  committed
  96548b8
- Merge remote-tracking branch 'origin/major_refactor' into feat/simple-evaluation
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  committed
  17be040
- chore:lint
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  committed
  65be511
Commits on Sep 29, 2026
- Handle unsupported CCD chemistry and make PARITY scoring optional
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  committed
  ea01d65
- Handle conjugated alkene stereo in MHFP6 fingerprints
  Ninjani
  committed
  8e0e5ff
- Reuse Foldseek database for protein structure clustering
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  committed
  dd321d2
- Read public score alignments from CIGAR shards
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  committed
  e0eaab1
- Fix ingest stage order and CLI override handling
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  committed
  c6ec8b5
- Reuse pocket alignments and cached ligand features during scoring
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  committed
  ac20f75
- Check Foldseek source manifests in parallel
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  committed
  4965cbc
Commits on Sep 30, 2026
- Update ligand affinity tables for changed entries
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  committed
  3abe8b2
- chore: format
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  committed
  9ebd10b
- Support weekly search and per-backend E-values
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  committed
  c9b8f60
- make compact score artifacts and speed up representative covers
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  committed
  8c5331c
- Fix shadowed custom search hits and remove unused PLI metric
  Ninjani
  committed
  e676730
- Keep weekly entry and ligand archive updates consistent
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  committed
  f1d4276
- Update weekly searches and assign changed entries to clusters
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  committed
  20e2c49
- Document compact scores and weekly cluster assignments
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  f113772
- Fix weekly cluster arithmetic and targeted interface score repair
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  committed
  74c4efc
- Fix CI data dependencies and private API docs
  Ninjani
  committed
  8de4819
- fix: serve the 2026-09 release from R2 without a release-number prefix
  tjduigna
  committed
  18d4312
- fix: accept any YYYY-MM release stamp on R2 and drop legacy 2024-06/v2
  tjduigna
  committed
  b975dd3
- ci: drop Docker and run tests directly on the runner
  tjduigna
  committed
  9fe285d
Commits on Oct 1, 2026
Commits on Oct 2, 2026
- build: stop committing uv.lock; resolve from pyproject.toml in CI
  tjduigna
  committed
  e0a3aae
- Merge remote-tracking branch 'origin/drop-docker' into release-date-prefix
  tjduigna
  committed
  ee23388
- ci: install docs builds without uv.lock
  tjduigna
  committed
  8996f82
- build: move the release version script to the repo root
  tjduigna
  committed
  e2f654b
- Merge remote-tracking branch 'origin/drop-docker' into release-date-prefix
  tjduigna
  committed
  355e52b
- Fix overlapping assembly copies and interface clustering
  Ninjani
  committed
  bfb2eae
- Fix weekly release repair and update planning
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  committed
  4024193
- Add monomer search and precomputed protein similarities
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  committed
  d0da6e3
- Separate public release artifacts from working ingest
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  committed
  08eab08
- Fix release packaging and weekly update edge cases
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  committed
  0e940ec
Commits on Oct 3, 2026
- Fix duplicate sequence ID columns in custom chain scores
  Ninjani
  committed
  7cc72ee
Commits on Oct 4, 2026
Commits on Oct 8, 2026
- fix: serve releases directly from the Cameo file server
  tjduigna
  committed
  3473710
Commits on Oct 9, 2026
- update docs
  Ninjani
  committed
  facb939
- Merge pull request #126 from plinder-org/release-date-prefix
  tjduigna
  authored
  e6add68
- Remove Metaflow and fix release cutover control paths
  tjduigna
  committed
  1ad218e

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