D-SCRIPT/CHANGELOG.md

To Do

• Expand test suite to include function unittests (maximize coverage)
• Add multi-gpu support (issue #6)
• support for loading embeddings on the fly to reduce memory usage (issue #11)

v0

v0.2

v0.2.1

• Add biopython to setup.py

v0.2.0

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

v0.1

v0.1.9: 2022-03-07 -- Minor bug fixes

• Updated model loading on new version to handle re-named parameters
• Updated cpu-only loading during prediction with map_location

v0.1.8: 2022-02-08 -- Finalized training bug fix

• Resolve #24 by fixing training
• Can now run dscript train --train data/pairs/human_train.tsv --test data/pairs/human_test.tsv --embedding /afs/csail/u/s/samsl/Work/databases/STRING/homo.sapiens/human_nonRed.h5 --output [output] --save-prefix [prefix] --device 0 to replicate paper results
• Updated code formatting with black and pre-commit

v0.1.7-dev9: 2022-02-07 -- Update training code to be clean again

• Following previous update, addresses #24 by fixing model training while maintaining preferred API and command line usage

v0.1.7-dev1: 2021-12-16 -- Major overhaul in training

• Fixed significant bug in how training was run by reverting to older code
• Should address issue #24: unable to replicate paper results
• To do: code cleaning to bring up to formatting standards while maintaining performance

v0.1.6: 2021-09-06 -- Bug Fix - Augmentation and proper defaults

• Augmentation fix in v0.1.5 was bugged still and would throw an error, now resets index
• Change --use-w and --augment to --no-w and --no-augment with store false

v0.1.5: 2021-06-23 -- Bug Fix - Augment and Documentation

• Updated package level imports
• Updated documentation
• Fixed issue #13: improper augmentation of data
• Fixed issue #12: overwrites cmap data sets if they already exist

v0.1.4: 2021-03-05 -- Bug Fix - Typo in ContactModule.forward()

• Fixed issue #7: bug which would crash contact module if called directly

v0.1.3: 2021-02-17 -- Bug Fix - Pairs too large for GPU

• Fixed issues #3, #4
• Basic logging system implemented to report skipped pairs
• Fixed wrong variable name in loading from sequence file
• Updated documentation

v0.1.2: 2020-11-30 -- Bug Fix - Eval Mode

• Model should be put into eval() mode before prediction or evaluation, and when new models are downloaded - this makes the output deterministic by disabling dropout layers

v0.1.1: 2020-11-18 -- First Beta Release