v0.1.0a1

What's Changed

• Added pyproject.toml with project metadata and dev dependencies by @siddharth7113 in #22
• Added ruff settings and pre-commit hook by @satvshr in #33
• Basic CI by @fkiraly in #36
• [ENH] PseAAC encoding algorithm by @satvshr in #29
• [ENH] Added architecture to support loaders along with a loader for PFOA by @satvshr in #62
• [ENH] AptaMCTS optimizer with docstrings and tests by @NennoMP in #56
• [ENH] Added 1GNH and its loader, standardized loader tests by @satvshr in #67
• [ENH] Readme and release content by @fkiraly in #69
• [ENH] Structure to String helper function by @satvshr in #61
• [ENH] doctest runs as individual pytest tests by @fkiraly in #83
• [BUG] Doctests for PSeAAC fix by @satvshr in #91
• [ENH] Fix example failures in MCTS, Fix tests structure inconsistencies by @NennoMP in #89
• [MNT] Dependabot: Bump actions/checkout from 4 to 5 by @dependabot[bot] in #94
• [ENH] AptaNet algorithm by @satvshr in #30
• [BUG} Solves ruff errors for non-UNIX systems. by @satvshr in https://github.com//pull/96
• [ENH] Add a helper function to convert pdb to Structure and add a loader to use datasets from the Protein Data Bank by @satvshr in #78
• [DOC] Fix typos by @szepeviktor in #107
• [ENH] AptaTrans: neural network and pipeline by @NennoMP in #63
• [DOC] example notebook for AptaNet by @satvshr in #68
• Make PSeAAC more configurable by @NennoMP in #126
• [DOC] AptaNet and AptaNet notebook doc fixes by @satvshr in #132
• [MNT] Dependabot: Bump actions/setup-python from 5 to 6 by @dependabot[bot] in #133
• [ENH] CI test to run jupyter notebooks by @satvshr in #74
• [DOC] Add the __all__ and __author__ tags for all files authored by me by @satvshr in #100
• [MNT] Dependabot: Bump actions/setup-python from 5 to 6 by @dependabot[bot] in #135
• [ENH] Fix PSeAAC discrepancies and optimize the algorithm by @satvshr in #137
• [ENH] regression version of AptaNet - AptaNetRegressor by @satvshr in #116
• [BUG] AptaNet notebook and test fixes by @satvshr in #142
• Add lightning wrapper for AptaTrans by @NennoMP in #130
• [ENH] Make AptaNet compatible with MCTS by @NennoMP in #121
• [ENH] Move reconstruction from experiments to MCTS and fix MCTS' tests by @NennoMP in #168
• [ENH] AptaTrans: training code and training schema by @NennoMP in #92
• [ENH] Generalized PSeAAC by @satvshr in #60
• [ENH] Renaming utils by @satvshr in #176
• [BUG] AptaTrans bug fixes: shapes mismatch in pretraining, add masking in encoders by @NennoMP in #178
• Reorganize aptamer experiments to separate modules by @NennoMP in #181
• [ENH] Add test step and metrics' logs in AptaTrans lightning wrappers by @NennoMP in #183
• [ENH] pdb to String loader using SEQREQ records by @satvshr in #148
• AptaTrans jupyter notebook by @NennoMP in #146
• [ENH] Benchmarking framework by @satvshr in #114
• [ENH] simple in-memory representation for pdb files by @fkiraly in #187
• [ENH] loaders for concrete toy data files based on #187 by @fkiraly in #188
• [ENH] aptacom database loader by @rpgv in #158
• [FEATURE] Add cells for saving model weights in AptaTrans notebook, optimizer memory footprint of lightning training by @NennoMP in #193
• [ENH] transformations interface by @fkiraly in #189
• [MNT] Dependabot: Bump actions/checkout from 5 to 6 by @dependabot[bot] in #199
• [ENH] pdb to String loader using UniProt id by @satvshr in #186
• [DOC] improve aptacom loader docstrings by @fkiraly in #192
• Bug/212 docstring examples failing with cuda by @NennoMP in #213
• [BUG] Remove .DS_Store files and add it to .gitignore by @satvshr in #207
• [BUG] AptaNetPipeline failing tests by @satvshr in #217
• [INVALID] AptaNet tests no longer fail on python version 3.13 by @satvshr in #219
• tutorial notebook on how to finetune AptaNet components by @prashantpandeygit in #227
• [ENH] hugging face loader by @satvshr in #155
• [ENH] Update AptaNet notebook to use AptaTrans data and a pdb for prediction by @satvshr in #153
• add py 3.14 to CI by @prashantpandeygit in #229
• fix: remove redundant inits from _loaders/init.py (resolves #225) by @Dreamstick9 in #233
• Add ValueError when AptaTransPipeline receives a too small depth value by @NennoMP in #220
• Refactor docstrings by @NennoMP in #222
• fix(mcts): correct sequence length handling by @FrankOHara43 in #247
• [ENH] Add 5NU7 and 1BRQ by @satvshr in #198
• [ENH] Remove Structure support for packaged pdbs by @satvshr in #209
• [BUG] pdb sequences returned from MoleculeLoader are wrong by @satvshr in #203
• [ENH] Get rid of load_hf_dataset and replace it with load_hf_to_dataset by @satvshr in #204
• Adding policy about PR and usage examples/ directory by @siddharth7113 in #257
• [ENH] Replace seq_id with chain_id in MoleculeLoader by @kajal-jotwani in #258
• fix(utils): use os.path.basename for PDB structure ID by @tkshsbcue in #245
• fix(aptanet): check pipeline consistency for non deterministic estimators by @FrankOHara43 in #251
• Adding HF_TOKEN in CI by @siddharth7113 in #261
• Reduce logging duplication in AptaTransLightning by @Tarun-goswamii in #241
• Prepare release 0.1.0a1 by @siddharth7113 in #267

New Contributors

• @siddharth7113 made their first contribution in #22
• @satvshr made their first contribution in #33
• @fkiraly made their first contribution in #36
• @NennoMP made their first contribution in #56
• @dependabot[bot] made their first contribution in #94
• @szepeviktor made their first contribution in #107
• @rpgv made their first contribution in #158
• @prashantpandeygit made their first contribution in #227
• @Dreamstick9 made their first contribution in #233
• @FrankOHara43 made their first contribution in #247
• @kajal-jotwani made their first contribution in #258
• @tkshsbcue made their first contribution in #245
• @Tarun-goswamii made their first contribution in #241

Full Changelog: https://github.com/gc-os-ai/pyaptamer/commits/v0.1.0a1