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| # Change Log | ||
| # Changelog | ||
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| ## 2.0.0 | ||
| This project's full changelog is maintained in the GitHub releases page. | ||
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| ### Main changes | ||
| For a comprehensive list of changes, new features, and bug fixes, please visit: https://github.com/DeepRank/deeprank2/releases. | ||
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| #### Refactor | ||
| This page includes: | ||
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| - 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 | ||
| - Detailed release notes for each version | ||
| - Summary of changes | ||
| - Links to relevant issues and pull requests | ||
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| #### Features | ||
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| - 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 | ||
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| #### Fix | ||
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| - 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 | ||
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| #### Docs | ||
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| - 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 | ||
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| #### Performances | ||
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| - 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 | ||
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| #### Style | ||
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| - 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 | ||
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| #### Test | ||
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| - 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 | ||
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| #### CI | ||
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| - 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 | ||
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| ### New Contributors | ||
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| - @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 | ||
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| **Full Changelog**: https://github.com/DeepRank/deeprank-core/compare/v1.0.0...v2.0.0 | ||
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| ## 1.0.0 | ||
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| Released on Oct 24, 2022 | ||
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| ### Added | ||
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| - `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 | ||
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| ### Changed | ||
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| - `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 | ||
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| ### Removed | ||
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| - `threshold` input parameter from NeuralNet #157 | ||
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| ## 0.2.0 | ||
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| Released on Aug 10, 2022 | ||
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| ### Added | ||
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| - 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 | ||
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| ### Changed | ||
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| - 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 | ||
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| ## 0.1.1 | ||
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| Released on June 28, 2022 | ||
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| ### Added | ||
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| - 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 | ||
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| ### Changed | ||
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| - `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 | ||
| For any questions or to report issues, please use the [GitHub issues page](https://github.com/DeepRank/deeprank2/issues). |