Merge pull request #646 from DeepRank/edit-changelog

docs: update CHANGELOG.md

Author: gcroci2

CHANGELOG.md

@@ -1,185 +1,13 @@
-# Change Log
+# Changelog
 
-## 2.0.0
+This project's full changelog is maintained in the GitHub releases page.
 
-### Main changes
+For a comprehensive list of changes, new features, and bug fixes, please visit: https://github.com/DeepRank/deeprank2/releases.
 
-#### Refactor
+This page includes:
 
-- 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
 
-#### 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
-
-## 1.0.0
-
-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
-
-## 0.2.0
-
-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
-
-## 0.1.1
-
-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
+For any questions or to report issues, please use the [GitHub issues page](https://github.com/DeepRank/deeprank2/issues).