ProteinWorkshop

What's Changed

• Improved TFN and MACE implementation by @chaitjo in https://github.com/a-r-j/ProteinWorkshop/pull/38
• Reduce number of layers for TFN model by @chaitjo in https://github.com/a-r-j/ProteinWorkshop/pull/40
• Add preliminary ESM baseline by @amorehead in https://github.com/a-r-j/ProteinWorkshop/pull/33
• Add configs and optional post embedding MLP for ESM encoder by @chaitjo in https://github.com/a-r-j/ProteinWorkshop/pull/41
• Bump gevent from 23.9.0.post1 to 23.9.1 by @dependabot in https://github.com/a-r-j/ProteinWorkshop/pull/42
• Add fix for scheduler initialization with FoldComp datasets by @amorehead in https://github.com/a-r-j/ProteinWorkshop/pull/43
• Update available encoders by @chaitjo in https://github.com/a-r-j/ProteinWorkshop/pull/46
• Update sequence encoder title by @chaitjo in https://github.com/a-r-j/ProteinWorkshop/pull/47
• Wire up argument for create_example_batch by @amorehead in https://github.com/a-r-j/ProteinWorkshop/pull/50
• Add UMAP embedding visualisation script by @amorehead in https://github.com/a-r-j/ProteinWorkshop/pull/55
• Fix tuple iteration in the ProteinDataset's process method by @amorehead in https://github.com/a-r-j/ProteinWorkshop/pull/52
• Fix minor virtual angle feature documentation by @chaitjo in https://github.com/a-r-j/ProteinWorkshop/pull/63
• Linting and updates by @a-r-j in https://github.com/a-r-j/ProteinWorkshop/pull/53
• Version bump for 0.2.5 release by @a-r-j in https://github.com/a-r-j/ProteinWorkshop/pull/64
• Fix orientation batching by @amorehead in https://github.com/a-r-j/ProteinWorkshop/pull/58

Full Changelog: https://github.com/a-r-j/ProteinWorkshop/compare/v0.2.4...v0.2.5

What's Changed

• Update checksums and fnames in download script #27 by @a-r-j in https://github.com/a-r-j/ProteinWorkshop/pull/28
• Fix W&B run name setting by @chaitjo in https://github.com/a-r-j/ProteinWorkshop/pull/30
• [fix] typo by @Croydon-Brixton in https://github.com/a-r-j/ProteinWorkshop/pull/31
• Fix paths for new directory structure by @chaitjo in https://github.com/a-r-j/ProteinWorkshop/pull/32
• Standardize poetry in README.md, and fix up docs by @amorehead in https://github.com/a-r-j/ProteinWorkshop/pull/35
• Bump gitpython from 3.1.32 to 3.1.35 by @dependabot in https://github.com/a-r-j/ProteinWorkshop/pull/36
• Release v0.2.4 by @a-r-j in https://github.com/a-r-j/ProteinWorkshop/pull/37

New Contributors

• @dependabot made their first contribution in https://github.com/a-r-j/ProteinWorkshop/pull/36

Full Changelog: https://github.com/a-r-j/ProteinWorkshop/compare/v0.2.3...v0.2.4

What's Changed

• Fix small notebook typos by @amorehead in https://github.com/a-r-j/ProteinWorkshop/pull/26
• Patch overwrite attributes in dataloaders by @a-r-j in https://github.com/a-r-j/ProteinWorkshop/pull/25

Full Changelog: https://github.com/a-r-j/ProteinWorkshop/compare/v0.2.2...v0.2.3

• Fixes raw data download triggered by absence of PDB when using pre-processed datasets (#24)
• Fixes bug where batches created from in_memory=True data were not correctly formatted (#24)
• Consistently exposes the overwrite argument for datamodules to users (#24)
• Fixes bug where downloading FoldComp datasets into directories with the same name as the dataset throws an error (#24)
• Increments graphein dependency to 1.7.3 (#24)

What's Changed

• Raw files hotfix #23 by @a-r-j in https://github.com/a-r-j/ProteinWorkshop/pull/24

Full Changelog: https://github.com/a-r-j/ProteinWorkshop/compare/v0.2.1...v0.2.2

What's Changed

• Minor docs corrections by @a-r-j in https://github.com/a-r-j/ProteinWorkshop/pull/17
• Add sanity check for CLI install by @a-r-j in https://github.com/a-r-j/ProteinWorkshop/pull/20
• Add a simple hyperlink in the README to point to the GitHub repository by @amorehead in https://github.com/a-r-j/ProteinWorkshop/pull/21
• Correct ENV var detection #18 by @a-r-j in https://github.com/a-r-j/ProteinWorkshop/pull/19
• Bump version strings for 0.2.1 release by @a-r-j in https://github.com/a-r-j/ProteinWorkshop/pull/22

Full Changelog: https://github.com/a-r-j/ProteinWorkshop/compare/v0.2.0...v0.2.1

Initial public release with PyPI distribution and CLI.