Deeprank2

Main changes

Refactor

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

Features

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

Fix

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

Docs

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

Performances

- perf: features.contact by DaniBodor in https://github.com/DeepRank/deeprank-core/pull/220
- perf: suppress warnings in pytest and from PDBParser by DaniBodor in https://github.com/DeepRank/deeprank-core/pull/249
- perf: add try except clause to `_preprocess_one_query` method of `QueryCollection` class by gcroci2 in https://github.com/DeepRank/deeprank-core/pull/264
- perf: improve `process` speed for residue based graph building by cbaakman in https://github.com/DeepRank/deeprank-core/pull/274
- perf: add `cuda` and `ngpu` parameters to the `Trainer` class by gcroci2 in https://github.com/DeepRank/deeprank-core/pull/311
- perf: accelerate indexing of HDF5 files by joyceljy in https://github.com/DeepRank/deeprank-core/pull/362

Style

- style: restructure deeprank2 package and subpackages by gcroci2 in https://github.com/DeepRank/deeprank-core/pull/240
- style: reorganize features/contact.py by DaniBodor in https://github.com/DeepRank/deeprank-core/pull/260
- style: add .vscode settings.json by DaniBodor in https://github.com/DeepRank/deeprank-core/pull/404

Test

- test: make sure that the grid orientation is as in the original deeprank for `ProteinProteinInterfaceAtomicQuery` by cbaakman in https://github.com/DeepRank/deeprank-core/pull/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 https://github.com/DeepRank/deeprank-core/pull/339
- test: improve `utils/test_graph.py` module by gcroci2 in https://github.com/DeepRank/deeprank-core/pull/420

CI

- ci: do not close stale issues or PRs by DaniBodor in https://github.com/DeepRank/deeprank-core/pull/327
- ci: remove incorrect message for stale branches by DaniBodor in https://github.com/DeepRank/deeprank-core/pull/415
- ci: automatically check markdown links by DaniBodor in https://github.com/DeepRank/deeprank-core/pull/433

New Contributors

- joyceljy made their first contribution in https://github.com/DeepRank/deeprank-core/pull/361
- ntxxt made their first contribution in https://github.com/DeepRank/deeprank-core/pull/413

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

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

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

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