Release v2.0.0 · DeepRank/deeprank2

Main changes

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 deeprankcore.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

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: list all submodules imported from deeprankcore.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: 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

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

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

Full Changelog: v1.0.0...v2.0.0