CHANGELOG.md

Change Log

2.0.0

Main changes

Refactor

• refactor: make preprocess use all available feature modules as default by @gcroci2 in #247
• refactor: move preprocess function to QueryDataset class and rename by @gcroci2 in #252
• refactor: save preprocessed data into one .hdf5 file as default by @gcroci2 in #250
• refactor: clean up GraphDataset and Trainer class by @DaniBodor in #255
• refactor: reorganize deeprank2.utils.metrics module by @gcroci2 in #262
• refactor: fix transform_sigmoid logic and move it to GraphDataset class by @gcroci2 in #288
• refactor: add grid dataset class and make the trainer class work with it. by @cbaakman in #294
• refactor: update deprecated dataloader import by @DaniBodor in #310
• refactor: move tests/_utils.py to tests/init.py by @DaniBodor in #322
• refactor: delete all outputs from unit tests after run by @DaniBodor in #324
• refactor: test_contact.py function naming and output by @DaniBodor in #372
• refactor: split test contact.py by @joyceljy in #369
• refactor: change repr of AminoAcid to 3 letter code by @DaniBodor in #384
• refactor: make feature modules and tests uniform and ditch duplicate code by @DaniBodor in #400

Features

• feat: improve amino acid features by @DaniBodor in #272
• feat: add test_size equivalent of val_size to Trainer class by @DaniBodor in #291
• feat: add the option to have a grid box of different x,y and z dimensions by @cbaakman in #292
• feat: add early stopping to Trainer.train by @DaniBodor in #303
• feat: add hist module for plotting raw hdf5 files features distributions by @gcroci2 in #261
• feat: allow for different loss functions other than the default by @DaniBodor in #313
• feat: center the grids as in the old deeprank by @cbaakman in #323
• feat: add data augmentation for grids by @cbaakman in #336
• feat: insert features standardization option inDeeprankDataset children classes by @gcroci2 in #326
• feat: add log transformation option for plotting features' hist by @joyceljy in #389
• feat: add inter-residue contact (IRC) node features by @DaniBodor in #333
• feat: add feature module for secondary structure by @DTRademaker in #387
• feat: use dictionary for flexibly transforming and standardizing features by @joyceljy in #418

Fix

• fix: list all submodules imported from deeprank2.features using pkgutil by @gcroci2 in #263
• fix: let classes argument be also categorical by @gcroci2 in #286
• fix: makes sure that the map_feature function can handle single value features. by @cbaakman in #289
• fix: raise exception for invalid optimizer by @DaniBodor in #307
• fix: num_workers parameter of Dataloader object by @gcroci2 in #319
• fix: gpu usage by @gcroci2 in #334
• fix: gpu and entry_names usage by @gcroci2 in #335
• fix: data generation threading locked by @gcroci2 in #330
• fix: __hash__ circular dependency issue by @cbaakman in #341
• fix: make sure that Grid data also has target values, like graph data by @cbaakman in #347
• fix: change the internal structure of the grid data to match the graph data by @cbaakman in #352
• fix: conflicts in package by @DaniBodor in #386
• fix: correct usage of nonbond energy for close contacts by @DaniBodor in #368
• fix: Incorrect number of datapoints loaded to model by @joyceljy in #397
• fix: pytorch 2.0 by @DaniBodor in #406
• fix: covalent bonds cannot link nodes on separate branches by @DaniBodor in #408
• fix: Trainer error when only dataset_test and pretrained_model are used by @ntxxt in #413
• fix: check PSSMs by @DaniBodor in #401
• fix: only check pssms if conservation module was used by @DaniBodor in #425
• fix: epoch number in test() and test on the correct model by @gcroci2 in #427
• fix: convert list of arrays into arrays before converting to Pytorch tensor by @gcroci2 in #438

Docs

• docs: add verbose arg to QueryCollection class by @gcroci2 in #267
• docs: improve clustering_method description and default value by @gcroci2 in #293
• docs: uniform docstrings format in modules by @joyceljy
• docs: incorrect usage of Union in Optional type hints by @DaniBodor in #370
• docs: improve docs for default exporter and results visualization by @gcroci2 in #414
• docs: update feature documentations by @DaniBodor in #419
• docs: add instructions for GridDataset by @gcroci2 in #421
• docs: fix getstarted hierarchy by @gcroci2 in #422
• docs: update dssp 4 install instructions by @DaniBodor in #437
• docs: change external_distance_cutoff and interface_distance_cutoff to distance_cutoff by @gcroci2 in #246

Performances

• perf: features.contact by @DaniBodor in #220
• perf: suppress warnings in pytest and from PDBParser by @DaniBodor in #249
• perf: add try except clause to _preprocess_one_query method of QueryCollection class by @gcroci2 in #264
• perf: improve process speed for residue based graph building by @cbaakman in #274
• perf: add cuda and ngpu parameters to the Trainer class by @gcroci2 in #311
• perf: accelerate indexing of HDF5 files by @joyceljy in #362

Style

• style: restructure deeprank2 package and subpackages by @gcroci2 in #240
• style: reorganize features/contact.py by @DaniBodor in #260
• style: add .vscode settings.json by @DaniBodor in #404

Test

• test: make sure that the grid orientation is as in the original deeprank for ProteinProteinInterfaceAtomicQuery by @cbaakman in #312
• test: check that the grid for residue-based protein-protein interfaces has the same center and orientation as in the original deeprank. by @cbaakman in #339
• test: improve utils/test_graph.py module by @gcroci2 in #420

CI

• ci: do not close stale issues or PRs by @DaniBodor in #327
• ci: remove incorrect message for stale branches by @DaniBodor in #415
• ci: automatically check markdown links by @DaniBodor in #433

New Contributors

• @joyceljy made their first contribution in #361
• @ntxxt made their first contribution in #413

Full Changelog: https://github.com/DeepRank/deeprank-core/compare/v1.0.0...v2.0.0

1.0.0

Released on Oct 24, 2022

Added

• weight_decay parameter to NeuralNet #155
• Exporter for generating a unique .csv file containing results per epoch #151
• Automatized testing of all available features modules #163
• optimizer parameter to NeuralNet #154
• atom node feature #168

Changed

• index parameter of NeuralNet is now called subset #159
• percent parameter of NeuralNet is now called val_size, and the logic behing it has been improved #183
• Aligned the package to PyTorch high-level frameworks #172
  • NeuralNet is now called Trainer
• Clearer features names #145
• Changed definitions in storage.py #150
• MAX_COVALENT_DISTANCE is now 2.1 instead of 3 #205

Removed

• threshold input parameter from NeuralNet #157

0.2.0

Released on Aug 10, 2022

Added

• Automatic version bumping using bump2version with .bumpversion.cfg #126
• cffconvert.yml to the CI workflow #139
• Integration test for the Machine Learning pipeline #95
• The package now is tested also on Python 3.10 #165

Changed

• Test PyPI package before publishing, by triggering a workflow_dispatch event from the Actions tab on release.yml workflow file #123
• Coveralls is now working again #124
• Wrong Zenodo entry has been corrected #138
• Improved CUDA support (added for data tensors) #132

0.1.1

Released on June 28, 2022

Added

• Graph class #48
• Tensorboard #15
• CI Linting #30
• Name, affiliation and orcid to .zenodo.json #18
• Metrics class #17
• QueryDataset class #53
• Unit tests for NeuralNet class #86
• Error message if you pick the wrong metrics #110
• Unit tests for HDF5Dataset class parameters #82
• Installation from PyPI in the readme #122

Changed

• test_process() does not fail anymore #47
• Tests have been speded up #36
• multiprocessing.Queue has been replaced with multiprocessing.pool.map in PreProcessor #56
• test_preprocess.py does not fail anymore on Mac M1 #74
• It's now possible to pass your own train/test split to NeuralNet class #81
• HDF5Dataset class now is used in the UX #83
• IndexError running NeuralNet.train() has been fixed #89
• pip installation has been fixed
• Repository has been renamed deeprank-core, and the package deeprank2 #101
• The zero-division like error from TensorboardBinaryClassificationExporter has been fixed #112
• h5xplorer is installed through setup.cfg file #121
• Sphinx docs have been fixed #108