Mlcolvar

Bug fixes + sensitivity analysis

What's Changed
* Fix mamba commands migration issue by EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/98
* Fix bug in CI badge by EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/99
* general split_dataset functions by EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/100
* Add installation info for main page by EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/102
* change register_cmap to register by luigibonati in https://github.com/luigibonati/mlcolvar/pull/107
* remove version check on scipy by luigibonati in https://github.com/luigibonati/mlcolvar/pull/109
* Add sensitivity analysis by luigibonati in https://github.com/luigibonati/mlcolvar/pull/108
* add sensitivity tutorial to doc by luigibonati in https://github.com/luigibonati/mlcolvar/pull/112
* Fix bug unrepresented state. by andrrizzi in https://github.com/luigibonati/mlcolvar/pull/110
* Fix 103: CVs cannot be loaded from checkpoint by andrrizzi in https://github.com/luigibonati/mlcolvar/pull/113
* Add lr_scheduler options by EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/111


**Full Changelog**: https://github.com/luigibonati/mlcolvar/compare/v1.0.1...v1.1.0

Bug fixes and doc improvements

What's Changed
* Fixed path to state file timelagged experiment by EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/82
* added scipy version requirement by luigibonati in https://github.com/luigibonati/mlcolvar/pull/85
* Update doc and readme by luigibonati in https://github.com/luigibonati/mlcolvar/pull/86
* fix citation by luigibonati in https://github.com/luigibonati/mlcolvar/pull/87
* specify dependency version requirement by luigibonati in https://github.com/luigibonati/mlcolvar/pull/89
* Minor fixes by EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/92
* Allow training without validation dataset by luigibonati in https://github.com/luigibonati/mlcolvar/pull/88
* Fix doc by luigibonati in https://github.com/luigibonati/mlcolvar/pull/93


**Full Changelog**: https://github.com/luigibonati/mlcolvar/compare/v1.0.0...v1.0.1

First stable release of `mlcolvar` package. Most of the changes with respect to 0.3.0 are related to documentation and notebooks illustrating tutorials and examples on how to use and expand the library, together with small fixes and enhancements.

What's Changed
* Support for multiple datasets of different size by andrrizzi in https://github.com/luigibonati/mlcolvar/pull/59
* NormalizationInverse class by EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/61
* Codecov_debug by EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/64
* Codecov_improve by EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/65
* Include notebook testing to codecov by EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/70
* Fix AutoEncoder calling pre/postprocessing during training by andrrizzi in https://github.com/luigibonati/mlcolvar/pull/69
* Colab interface for notebooks by EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/71
* Tutorials_fix by EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/62
* Moved notebook tests only to Ubuntu by EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/76
* Chingolin example with TPI-Deep-TDA + minor fix in create_dataset_from_file by EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/77
* Update documentation with contributions and references by luigibonati in https://github.com/luigibonati/mlcolvar/pull/78
* Add section for examples notebooks by luigibonati in https://github.com/luigibonati/mlcolvar/pull/79
* Prepare for pypi release by luigibonati in https://github.com/luigibonati/mlcolvar/pull/80
* fix dependencies in pyproject by luigibonati in https://github.com/luigibonati/mlcolvar/pull/81


**Full Changelog**: https://github.com/luigibonati/mlcolvar/compare/v0.3.0...v1.0.0

First `mlcolvar` release

The library went through a complete refactoring (including being renamed from `mlcvs` to `mlcolvar`) with new structure and APIs.

Main changes
* Pytorch lightning support
* Modular CV structure
* Dict-like datasets
* Many new CVs methods

Pull requests
Only the recent changes are shown in this list:
* First implementation of a Variation Autoencoder CV by andrrizzi in https://github.com/luigibonati/mlcolvar/pull/27
* Change base cv attributes by luigibonati in https://github.com/luigibonati/mlcolvar/pull/32
* change MSE_loss signature from diff to input, target by luigibonati in https://github.com/luigibonati/mlcolvar/pull/37
* add option in ae/vae to compare output of the decoder with a different target by luigibonati in https://github.com/luigibonati/mlcolvar/pull/38
* Improve load_dataframe by luigibonati in https://github.com/luigibonati/mlcolvar/pull/41
* Implement Loss classes, some PEP8 fixes by andrrizzi in https://github.com/luigibonati/mlcolvar/pull/42
* Switch from functional to class losses by andrrizzi in https://github.com/luigibonati/mlcolvar/pull/43
* Add PCA method by luigibonati in https://github.com/luigibonati/mlcolvar/pull/44
* Support for multiple datasets by andrrizzi in https://github.com/luigibonati/mlcolvar/pull/45
* Added reduced_rank to TICA by Pietronvll in https://github.com/luigibonati/mlcolvar/pull/36
* Multi-task CV and various fixes by andrrizzi in https://github.com/luigibonati/mlcolvar/pull/46
* rename library v2 by luigibonati in https://github.com/luigibonati/mlcolvar/pull/49
* Fix device loss by luigibonati in https://github.com/luigibonati/mlcolvar/pull/50
* Rename data objects by luigibonati in https://github.com/luigibonati/mlcolvar/pull/51
* Support for task-specific layers by andrrizzi in https://github.com/luigibonati/mlcolvar/pull/53
* Merge lightning into main by luigibonati in https://github.com/luigibonati/mlcolvar/pull/55
* Add paper experiments by luigibonati in https://github.com/luigibonati/mlcolvar/pull/56
* Code fixes by luigibonati in https://github.com/luigibonati/mlcolvar/pull/58

New Contributors
* andrrizzi made their first contribution in https://github.com/luigibonati/mlcolvar/pull/27
* Pietronvll made their first contribution in https://github.com/luigibonati/mlcolvar/pull/36

**Full Changelog**: https://github.com/luigibonati/mlcolvar/compare/v0.2.2...v0.3.0

What's Changed
* Fix bug in the logging for the tutorials (see 25)

Note that this is the last version that does not use the PyTorch Lightning high-level framework, and in which the module is named `mlcvs`.

**Full Changelog**: https://github.com/luigibonati/mlcvs/compare/v0.2.1...v0.2.2

What's Changed
* Prune the tree: move general functions to base class NNCV by luigibonati in https://github.com/luigibonati/mlcvs/pull/18
* add autoencoder cv by luigibonati in https://github.com/luigibonati/mlcvs/pull/22
* Add CodeQL workflow for GitHub code scanning by lgtm-com in https://github.com/luigibonati/mlcvs/pull/21

New Contributors
* lgtm-com made their first contribution in https://github.com/luigibonati/mlcvs/pull/21

**Full Changelog**: https://github.com/luigibonati/mlcvs/compare/v0.2.0...v0.2.1