v0.3

What's Changed

• Feature/more model options by @kellrott in #42
• Use package metadata for version and add test coverage by @Copilot in #45
• feat: Add version flag by @lbeckman314 in #44
• Feature/more model options by @kellrott in #46
• Feature/more model options by @kellrott in #47
• Issues related to HLA2Vec development by @kellrott in #41
• Address review feedback: class renames, registry ordering, mapping cleanup, docs, and style fixes by @Copilot in #50
• [WIP] Feature/factory by @kellrott in #49
• Refactor CsvReader: pandas-style header param, bug fixes, and tests by @Copilot in #52
• Fix NetVAE serialization, weight-access crash, tautological test, and doc inconsistencies by @Copilot in #54
• Claude suggestions for docs by @kellrott in #53
• Encoding Classes by @kellrott in #51
• Add unit tests for get_dataset_nonzero_mask by @Copilot in #56
• Fix type annotations, dead code, VAE objective, and device consistency bugs from PR review by @Copilot in #55
• Switch examples to use factory.save instead of model.save by @Copilot in #57
• [WIP] Develop Merge v0.3 by @kellrott in #48

New Contributors

• @Copilot made their first contribution in #45
• @lbeckman314 made their first contribution in #44

Full Changelog: v0.2...v0.3

v0.2

What's Changed

• Add cli support for embkit by @Exitare in #1
• Create new preprocessing module by @Exitare in #2
• Consolidate VAEs to use base class by @Exitare in #3
• Add unit tests for decoder, encoder and layers by @Exitare in #4
• Implement pairwise comparison layer by @Exitare in #5
• Add github workflow to release a new package based on a new Github Re… by @Exitare in #6
• Add test coverage action by @Exitare in #8
• Update pr action to deal with forked PRs by @Exitare in #9
• Add c-bio commands by @Exitare in #10
• Rename study name to study id by @Exitare in #11
• Update test_c_bio.py by @Exitare in #12
• Create pytorch.py by @briankarlberg in #13
• Add improved return value for unpack function by @Exitare in #14
• Add docs for cbio commands by @Exitare in #16
• GTEx embedding example by @kellrott in #15
• Update loss function documentation by @Exitare in #20
• Add dynamic loss function for VAE by @Exitare in #22
• Distance metrics by @jordan2lee in #21
• Move distance calculations to a separate module by @Exitare in #23
• Update docs by @Exitare in #24
• Add ability to directly pass dataloader class to load/download datasets by @Exitare in #25
• Fix missing file update for data loader by @Exitare in #26
• Create tsp layer & docs by @Exitare in #27
• Hla2vec by @Exitare in #29
• feat: add datasets command by @Exitare in #31
• feat: add new hugo download command by @Exitare in #32
• [WIP] Adding more constrain options to NetVAE elements by @kellrott in #30
• feat: move open_model to a class method. by @Exitare in #34
• add SIF dataset command by @Exitare in #35
• fix: change gtex example from bce loss to mse loss by @Exitare in #36
• fix: net van missing constraints by @Exitare in #37
• VAE alignment by @kellrott in #38
• RNA VAE by @Exitare in #39
• [WIP] hla2vec by @kellrott in #33
• feat: utility functions for hla experiment support by @Exitare in #40

New Contributors

• @briankarlberg made their first contribution in #13
• @jordan2lee made their first contribution in #21

Full Changelog: https://github.com/ohsu-comp-bio/embedding-kit/commits/v0.2