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Recent Releases of DeepRank2

DeepRank2 - v3.1.0

What's Changed

  • ci: move ruff settings to separate toml file by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/642
  • ci: improve release workflow by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/621
  • ci: add action for releasing new docker image and testing it by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/640
  • fix: dockerfile image build by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/637
  • tutorials: avoid error messages in tutorial by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/636

Full Changelog: https://github.com/DeepRank/deeprank2/compare/v3.0.5...v3.1.0

Scientific Software - Peer-reviewed - Python
Published by gcroci2 over 1 year ago

DeepRank2 - v3.0.5

What's Changed

  • build: simplify docker installation and improve the manual one by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/615
  • build: make dependencies versions more reliable by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/616
  • ci: update ruff and fix linting rules by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/624
  • docs: clarify usage of output column generated by the exporter by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/618
  • docs: clarify tutorials usage by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/620
  • docs: rename paper folder to joss by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/623
  • docs: improve structure and add modules by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/625
  • docs: clean up docstrings by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/628
  • docs: add doc strings to the neural networks architectures by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/630
  • style: make torch.nn imports more uniform by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/626

Full Changelog: https://github.com/DeepRank/deeprank2/compare/v3.0.4...v3.0.5

Scientific Software - Peer-reviewed - Python
Published by gcroci2 over 1 year ago

DeepRank2 - v3.0.4

What's Changed

  • ci: simplify lint action by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/612
  • ci: restore PyPI installation by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/611

Full Changelog: https://github.com/DeepRank/deeprank2/compare/v3.0.3...v3.0.4

Scientific Software - Peer-reviewed - Python
Published by gcroci2 over 1 year ago

DeepRank2 - v3.0.3

What's Changed

  • fix: OSError when retrieving source code for lambda functions by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/606
  • docs: improve handling pypi packaging contents and add NOTICE by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/601

Full Changelog: https://github.com/DeepRank/deeprank2/compare/v3.0.2...v3.0.3

Scientific Software - Peer-reviewed - Python
Published by gcroci2 over 1 year ago

DeepRank2 - v3.0.2

What's Changed

  • fix: update requirements.txt by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/589
  • ci: move PyPI deps installation to conda by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/565
  • ci: add action for testing the tutorials' notebooks by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/587
  • ci: set default shell for fixing the workflows by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/598
  • docs: update README.md with JOSS badge by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/579
  • docs: add docstring for _check_pdb function of features/secondary_structure.py by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/588
  • docs: clarify queries' usage by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/586
  • docs: add OPLS ref to the docs by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/594
  • paper: add affiliation and corresponding author correction by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/580
  • style: update ruff by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/584

Full Changelog: https://github.com/DeepRank/deeprank2/compare/v3.0.1...v3.0.2

Scientific Software - Peer-reviewed - Python
Published by gcroci2 almost 2 years ago

DeepRank2 - v3.0.1

What's Changed

  • fix: testcuda in `testtrainer.py::TestTrainer` by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/572
  • fix: features transform in Trainer._save_model internal method by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/573
  • fix: typo by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/568
  • docs: fix error message structure by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/564
  • docs: add RSD badge by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/569
  • docs: bump readthedocs-sphinx-search from 0.1.1 to 0.3.2 in /docs by @dependabot in https://github.com/DeepRank/deeprank2/pull/567
  • ci: adapting ruff by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/563
  • paper: add minor fixes for acceptance by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/571

Full Changelog: https://github.com/DeepRank/deeprank2/compare/v3.0.0...v3.0.1

Scientific Software - Peer-reviewed - Python
Published by gcroci2 about 2 years ago

DeepRank2 - v3.0.0

What's Changed

  • refactor: Query classes and related code by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/492
  • refactor: unify buildgraph.py and build_graph functions for atom and residue level graphs by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/507
  • feature: separate max edge distance from interaction radius throughout by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/504
  • feature: improve Trainer and DeeprankDataset logic for production testing by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/515
  • build: switch to conda dssp installation by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/549
  • ci: implement ruff by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/554
  • ci: add GitHub action for testing the latest package version released on PyPi by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/560
  • docs: add Dockerfile and .yml for building conda env by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/528
  • docs: implement minor suggestions for JOSS paper by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/538

Full Changelog: https://github.com/DeepRank/deeprank2/compare/v2.1.2...v3.0.0

Scientific Software - Peer-reviewed - Python
Published by gcroci2 about 2 years ago

DeepRank2 - v2.1.2

What's Changed

  • Update CITATION.cff by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/531
  • fix: handle cases in which losses are nan during the training by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/535

Full Changelog: https://github.com/DeepRank/deeprank2/compare/v2.1.1...v2.1.2

Scientific Software - Peer-reviewed - Python
Published by gcroci2 about 2 years ago

DeepRank2 - v2.1.1

What's Changed

  • docs: Clarify Pytorch Geometric in README installation by @DarioMarzella in https://github.com/DeepRank/deeprank2/pull/508
  • Joss review 5983 jnwei by @jnwei in https://github.com/DeepRank/deeprank2/pull/523
  • fix: installation bug due to missing domain files by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/525

New Contributors

  • @DarioMarzella made their first contribution in https://github.com/DeepRank/deeprank2/pull/508
  • @jnwei made their first contribution in https://github.com/DeepRank/deeprank2/pull/523

Full Changelog: https://github.com/DeepRank/deeprank2/compare/v2.1.0...v2.1.1

Scientific Software - Peer-reviewed - Python
Published by gcroci2 over 2 years ago

DeepRank2 - v2.1.0

What's Changed

Fix * fix: check only 1 pssm for variant queries by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/430 * fix: pdb files with underscore in the filename gives unexpected query ids by @joyceljy in https://github.com/DeepRank/deeprank2/pull/447 * fix: dataset_train inheritance warnings by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/461 * fix: cast hse feature to float64 by @DanLep97 in https://github.com/DeepRank/deeprank2/pull/465 * fix: readthedocs after deeprank2 renaming by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/472 * fix: force scipy version for fixing deeprank2 installation by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/478 * fix: warning messages for invalid data in test_dataset.py by @joyceljy in https://github.com/DeepRank/deeprank2/pull/442 * fix: make scipy 1.11.2 work by @cbaakman in https://github.com/DeepRank/deeprank2/pull/482

Refactor * refactor: inherit information from training set for valid/test sets by @joyceljy in https://github.com/DeepRank/deeprank2/pull/446 * refactor: rename deeprankcore to deeprank2 by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/469

Build * build: improve installation making use of pyproject.toml file only and setuptools by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/491

CI * CI: decrease sensitivity of test_graph_augmented_write_as_grid_to_hdf5 by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/445 * CI: fewer triggers by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/457

Docs * docs: update README.md by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/443 * docs: create tutorial README by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/455 * docs: improve installation instructions by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/452 * docs: add tutorials for PPIs by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/434 * docs: add tutorials for variants by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/459 * docs: minor improvements to install instructions by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/484 * docs: type hinting and docstrings in molstruct by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/497 * docs: joss paper by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/423 * docs: clarify ppi scoring metrics and add doc strings and tests by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/498 * docs: add performances table for deeprank2 by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/493

Style * style: auto-scrape trailing whitespace upon save in VS code by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/483

Full Changelog: https://github.com/DeepRank/deeprank2/compare/v2.0.0...v2.1.0

Scientific Software - Peer-reviewed - Python
Published by gcroci2 over 2 years ago

DeepRank2 - v2.0.0

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 deeprankcore.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 inDeeprankDataset 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 deeprankcore.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 deeprankcore 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

Scientific Software - Peer-reviewed - Python
Published by gcroci2 over 2 years ago

DeepRank2 - v1.0.0

See CHANGELOG.md

Scientific Software - Peer-reviewed - Python
Published by gcroci2 over 3 years ago

DeepRank2 - v0.2.0

See CHANGELOG.md

Scientific Software - Peer-reviewed - Python
Published by gcroci2 over 3 years ago

DeepRank2 - v0.1.1

First release on PyPI

Scientific Software - Peer-reviewed - Python
Published by gcroci2 over 3 years ago

DeepRank2 - First pre-release

Scientific Software - Peer-reviewed - Python
Published by gcroci2 over 3 years ago