v3.1.0

What's Changed

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

Full Changelog: v3.0.5...v3.1.0

v3.0.5

What's Changed

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

Full Changelog: v3.0.4...v3.0.5

v3.0.4

What's Changed

• ci: simplify lint action by @DaniBodor in #612
• ci: restore PyPI installation by @gcroci2 in #611

Full Changelog: v3.0.3...v3.0.4

v3.0.3

What's Changed

• fix: OSError when retrieving source code for lambda functions by @gcroci2 in #606
• docs: improve handling pypi packaging contents and add NOTICE by @gcroci2 in #601

Full Changelog: v3.0.2...v3.0.3

v3.0.2

What's Changed

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

Full Changelog: v3.0.1...v3.0.2

v3.0.1

What's Changed

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

Full Changelog: v3.0.0...v3.0.1

v3.0.0

What's Changed

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

Full Changelog: v2.1.2...v3.0.0

v2.1.2

What's Changed

• Update CITATION.cff by @DaniBodor in #531
• fix: handle cases in which losses are nan during the training by @gcroci2 in #535

Full Changelog: v2.1.1...v2.1.2

v2.1.1

What's Changed

• docs: Clarify Pytorch Geometric in README installation by @DarioMarzella in #508
• Joss review 5983 jnwei by @jnwei in #523
• fix: installation bug due to missing domain files by @gcroci2 in #525

New Contributors

• @DarioMarzella made their first contribution in #508
• @jnwei made their first contribution in #523

Full Changelog: v2.1.0...v2.1.1

v2.1.0

What's Changed

Fix

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

Refactor

• refactor: inherit information from training set for valid/test sets by @joyceljy in #446
• refactor: rename deeprankcore to deeprank2 by @gcroci2 in #469

Build

• build: improve installation making use of pyproject.toml file only and setuptools by @gcroci2 in #491

CI

• CI: decrease sensitivity of test_graph_augmented_write_as_grid_to_hdf5 by @DaniBodor in #445
• CI: fewer triggers by @DaniBodor in #457

Docs

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

Style

• style: auto-scrape trailing whitespace upon save in VS code by @DaniBodor in #483

Full Changelog: v2.0.0...v2.1.0