v0.2.8: 2024-09-16 -- Fix bug with model cuda assignment during prediction

Full Changelog: v0.2.7...v0.2.8

v0.2.7: 2024-09-13 -- HuggingFace Models

What's Changed

• R notebooks added for baseline sequence-based analysis by @kap-devkota in #59
• Add HuggingFace support by @samsledje in #69

Full Changelog: v0.2.6...v0.2.7

v0.2.6b: 2023-08-24 -- Zenodo Release

Release to generate a DOI for the current state of the repository containing TT3D experiments.

What's Changed

• R notebooks added for baseline sequence-based analysis by @kap-devkota in #59
• Python notebooks for baseline structure-based analysis

Full Changelog: v0.2.6...v0.2.6b

v0.2.6: 2023-09-28 -- Add TT3D as a pretrained option

Full Changelog: v0.2.5...v0.2.6

v0.2.5: 2023-07-24 -- Integrating 3Di sequences into prediction

Update predict.py so models trained with --allow_foldseek (Topsy-Turvy 3D) can be used to make predictions, provided that a foldseek_fasta is provided.

v0.2.4

TT3D -- Integrating FoldSeek Structures into Topsy-Turvy training

v0.2.2: 2023-01-20 -- Bug Fixes and Topsy-Turvy

• Resolve #35 to use require_dataset -- can now add multiple .fasta files to the same h5 file
• Update pretrained API and docs to include Topsy-Turvy
• Add retry decorator to get_pretrained if download fails
• Add ability to set a random seed for training
• Update evaluate code to also store metrics in a file

v0.2.1: 2022-06-28 -- Bug Fixes

• Update setup.py to include biopython so that it runs properly on a clean pip install.

v0.2.0: 2022-06-24 -- Integration of Topsy-Turvy

Topsy-Turvy Integration

• Integrate Topsy-Turvy to allow for top-down supervision
• See the GitHub repository
• See the landing page
• To appear at ISMB 2022 and in Bioinformatics as Devkota*, Singh*, Sledzieski, Berger, Cowen, “Topsy-Turvy: integrating a global view into sequence-based PPI prediction”

Bug Fixes and Quality of Life

• Use utils.log function across all commands
• Speed up loading embeddings into memory using parallel processing
• Update fasta.parse and fasta.write to use BioPython SeqIO (better error checking)
• More comprehensive test suite for main commands

v0.1.9 Dealing with pypi and semvar fussiness

This is the same as v0.1.8b0 but it will actually take priority