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release: AtomWorks 3.0.0 - #116
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…and validate metadata
… update documentation
…_array function to support foundry training
docs(lmdb): clarify ASE atom array loading
…ut 'data' attribute, such as the ASELMDBDataset
Take upstream 2.1.1 and hatch packages layout; local hatch wheel.targets change is superseded.
Adding a 'cookbook' reference for commonly used atomworks functions. Originally created by Rocco Moretti. Updated the io_utils.py file to include the PDB buffer and string converter to the list of API functions.
Keep future release switchers on the repository's current Pages host instead of the retired atomworks-dev URL.
Prevent non-release production pushes from overwriting the latest immutable version directory.
In _map_to_closest_canonical_residue we use a template canonical residue to check if an unwanted residue might be substituted for a canonical. The template canonical residue includes leaving groups, causing it to always fail for residues in a polymer when checking if it subsets the atoms of the residue to be substituted. This fix removes leaving groups from the comparison logic when required and adds regression tests demonstrating both the in-chain and chain-terminus cases.
…61004 feat: sync remaining dev chemistry and ColabFold updates for 3.0
docs: finish MSA CLI and preprocessing documentation for 3.0
nscorley
marked this pull request as ready for review
October 5, 2026 03:05
This was referenced Oct 5, 2026
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AtomWorks 3.0.0
Changes
ParseConfigandPrepareConfigfor parser and AtomArray preparation settings.Migration from 2.x
filename=are deprecated.fix_formal_charges,fix_bond_types, andhydrogen_policy="infer"are removed.OP3, and conditions store target values rather than only masks.mlextra for ML/MSA tools.Short migration guide · Detailed migration guide · MSA documentation
Maintainer notes
release_and_docs.yaml, environmentpypi) and that version3.0.0is unused.v3.0.0to publish the package, GitHub release, and versioned docs. Merging alone does not publish.gh-pages.The failed legacy Ruff run 37257995594 checked old production commit
fcf7af8cthroughpull_request_target, not the release candidate. This PR removes that workflow; use the current CI and release workflow to validate the candidate.