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release: AtomWorks 3.0.0 - #116

Merged

nscorley merged 108 commits into

productionfrom

release/atomworks-3-0

Oct 5, 2026

Commits on Dec 1, 2025
- feat: hatch build change
  kierandidi
  committed
  691c67e
- fix: pip wheel
  nscorley
  committed
  82305e1
- fix: pypi release version
  nscorley
  committed
  97d2822
- Merge branch 'production' into staging
  nscorley
  authored
  b4fa5b7
Commits on Mar 19, 2026
- fix: pin requires-python <3.13 due to pyarrow 17.x build failure
  
  daylight-00
  authored and
  nscorley
  committed
  ea325c3
Commits on May 5, 2026
Commits on May 11, 2026
- feat: Add additional annotations for atom arrays in ase_atoms_to_atom_array function to support foundry training
  amorehead
  committed
  46f34ab
Commits on May 12, 2026
- docs(lmdb): clarify ASE atom array loading
  Alex-Abrudan
  committed
  58cb6a6
- Merge pull request #1 from amorehead/amorehead-lmdb-touchup
  amorehead
  authored
  ceeafc8
Commits on May 22, 2026
- fix: enhance get_row_and_index_by_example_id to handle datasets without 'data' attribute, such as the ASELMDBDataset
  amorehead
  committed
  665c246
- refactor: run linting
  amorehead
  committed
  53626ef
Commits on Jun 7, 2026
- Merge origin/staging; resolve pyproject.toml conflict.
  kierandidi
  committed
  9547bb7
Commits on Jun 8, 2026
- Update urllib3 package based on security alert
  Hope Woods
  committed
  8769ecd
- Update tornado due to security risk
  Hope Woods
  committed
  358c4dc
- Update packages to address security risks
  Hope Woods
  committed
  36fae05
- Update formatting
  Hope Woods
  committed
  4ce3a8b
Commits on Jun 9, 2026
- Revert torch dependency version back to 2.2.0 in pyproject.toml
  woodsh17
  authored
  7ba1b58
Commits on Jun 19, 2026
- Merge branch 'production' into feat/add-lmdb-support
  amorehead
  authored
  3ed2df4
Commits on Jun 29, 2026
- Docs: AtomWorks Cookbook
  rclune
  committed
  0ca1bd7
Commits on Jul 17, 2026
- Docs: point version switcher at RosettaCommons Pages
  Kieran Didi
  committed
  643820e
- Docs: deploy archived docs only for tagged releases
  Kieran Didi
  committed
  bc437fd
Commits on Jul 30, 2026
- fix(ml): don't require CCD leaving groups when substituting residues
  benz0id
  committed
  4e463e7
Commits on Aug 8, 2026
- feat: add mmseqs server usage
  r-krishna
  committed
  fc043e7
- remove server tests
  r-krishna
  committed
  f50d629
- remove init
  r-krishna
  committed
  d6c52cb
- chore ruff
  r-krishna
  committed
  bdc64fd
Commits on Aug 13, 2026
- fix(io): write parse cache atomically
  hwendler
  committed
  332dab9
- style(docs): apply make format to conf.py
  hwendler
  committed
  1cce0c9
Commits on Aug 18, 2026
- Apply suggestions from code review
  
  hwendler
  and
  nscorley
  authored
  e87e7fa
- fix(io): map cache suffix to compression; drop redundant cache tests
  
  hwendler
  and
  claude
  committed
  1367359
Commits on Sep 10, 2026
- docs(installation): Add CCD sync to test setup instructions
  Emrys-Merlin
  committed
  2cbb836
Commits on Sep 30, 2026
- chore(release): prepare AtomWorks 3.0 public snapshot
  nscorley
  committed
  df50559
- docs: add AtomWorks 3.0 migration guides
  m1c0l
  committed
  d151847
- docs: fix migration index heading
  m1c0l
  committed
  46b19b3
- docs: focus migration guides on IO changes
  m1c0l
  committed
  50f6050
- docs: remove migration draft scope section
  m1c0l
  committed
  c76d9a6
- fix(ml): adapt canonical residue matching to 3.0 CCD groups
  m1c0l
  committed
  8aec643
- docs: update cookbook recipes for AtomWorks 3.0
  m1c0l
  committed
  eb83eb6
- docs: clarify separate CCD sync for release 3.0
  m1c0l
  committed
  23f9f4d
- Merge pull request #101 from Emrys-Merlin/docs/installation_instructions
  m1c0l
  authored
  1e59a6b
- docs: simplify short migration parser guidance
  m1c0l
  committed
  5b86399
Commits on Oct 1, 2026
Commits on Oct 2, 2026
Commits on Oct 3, 2026
- docs: refresh AtomWorks 3 release README and navigation
  kierandidi
  committed
  eb5cf73
Commits on Oct 4, 2026
- ci: publish AtomWorks from verified version tags
  kierandidi
  committed
  46fcbcc
- ci: run lint on a hosted runner
  kierandidi
  committed
  c135b2f
- ci: expose test helpers to spawned workers
  kierandidi
  committed
  b878415
- build: prepare AtomWorks 3.0.0 metadata
  kierandidi
  committed
  d4a0227
- docs: preserve public analytics and clarify mmJSON inputs
  kierandidi
  committed
  4090824
- docs: name the 2.3 release and use a transparent dark-mode logo
  kierandidi
  committed
  1007121
- release: prepare AtomWorks 2.3.0
  kierandidi
  committed
  12744d5
- fix: retain package sources when rebuilding release wheels
  kierandidi
  committed
  5ea0636
- ci: validate ready PRs through the pull request workflow
  kierandidi
  committed
  04467a8
- Merge branch 'review/aw-23-docs' into ci/public-release-checks
  kierandidi
  committed
  ecbb0b4
- docs: resolve migration guide conflicts with release branch
  nscorley
  committed
  40a8917
- Merge pull request #103 from m1c0l/docs/atomworks-3-migration
  nscorley
  authored
  1e362a2
- chore: name the upcoming release AtomWorks 3.0
  kierandidi
  committed
  64986a0
- chore: name the upcoming release AtomWorks 3.0
  kierandidi
  committed
  e636a9b
- fix: preserve dependency versions during release rename
  kierandidi
  committed
  f92c214
- ci: gate AtomWorks 3 releases on public tests, installed wheels and docs
  kierandidi
  committed
  206fbee
- Merge branch 'review/aw-23-release' into ci/public-release-checks
  kierandidi
  committed
  3bd741f
- Merge branch 'review/aw-23-docs' into ci/public-release-checks
  kierandidi
  committed
  96913df
- feat: sync remaining dev chemistry and ColabFold updates for 3.0
  nscorley
  committed
  b911d9f
- fix: keep core CLI imports independent of optional ML dependencies
  kierandidi
  committed
  38ae3fd
- docs: use the minimal parser preset in the quick start
  kierandidi
  committed
  bbe0273
- Merge remote-tracking branch 'public/release/atomworks-3-0' into ci/public-release-checks
  kierandidi
  committed
  bb08e58
- ci: pin regression inputs and deploy release docs explicitly
  kierandidi
  committed
  fa8778c
- docs: consolidate AtomWorks release and development guidance
  kierandidi
  committed
  7747d8e
- refactor: replace duplicate MSA server client with ColabFold workflow
  nscorley
  committed
  a201fac
- docs: preserve explanatory docstrings and examples
  kierandidi
  committed
  6c419b1
Commits on Oct 5, 2026

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Commits on Jun 19, 2026

Commits on Jun 29, 2026

Commits on Jul 17, 2026

Commits on Jul 30, 2026

Commits on Aug 8, 2026

Commits on Aug 13, 2026

Commits on Aug 18, 2026

Commits on Sep 10, 2026

Commits on Sep 30, 2026

Commits on Oct 1, 2026

Commits on Oct 2, 2026

Commits on Oct 3, 2026

Commits on Oct 4, 2026

Commits on Oct 5, 2026