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Tutorials_fix#62

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luigibonati merged 113 commits intomainluigibonati/mlcolvar:mainfrom tutorials_fixluigibonati/mlcolvar:tutorials_fixCopy head branch name to clipboardMay 29, 2023

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Commits on May 5, 2023

• Adde mfep to muller-brown + mfep utils to plot

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Commits on May 8, 2023

• First part of new cv tutorial

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Commits on May 9, 2023

• Deleted useless file from paper_experiments folder

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• Merge branch 'develop_trizio' into tutorials_fix

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• Fixed typo in comments in autoencoder cv

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• Added tutorial for new cv implementation

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• Added utils to load mfep to exp_4 notebook

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• Multitasking tutorial first commit

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• Added NormalizationInverse helper class

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• Added to AE CVs method to export the decoder model + inversed normalization

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Commits on May 10, 2023

• Replaced NormalizationInverse with transform.utils.Inverse wrapper class

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• Changed return_decoder_model to get_decoder_model and use Inverse wrapper

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• Added short intro to multitask tutorial

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• Merge branch 'main' into tutorials_fix

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• Added comments to MultitaskCV tutorial

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• Update newCV tutorial

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• Removed mfep utils from mutitask experiment notebook

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Commits on May 12, 2023

• Modified get_decoder_model to get_decoder with normalization switch

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• Edited paper multitask experiment to use get_decoder function

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• Merge pull request #61 from luigibonati/norm_inverse

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Commits on May 15, 2023

• Fixed typos and added @andrrizzi review comments on multitask tutorial

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• Fixed typos, added @andrrizzi review comments, removed repetitions in code cells in newCV tutorial

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Commits on May 18, 2023

• added -e to pip install and remove notebook testing fro debug

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• Kinldy ask conda to install

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• Fix typo in CI.yaml

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• Merge pull request #64 from luigibonati/codecov_debug

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• Added min_max mode to test function

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• Added all activation functions to feedforwrd test

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• Added test_statistics to tests

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• Added tests for plot utils where possible

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• added tests for metrics callbacks utils

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• Added min_max mode to test function

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• Added all activation functions to feedforwrd test

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• Added test_statistics to tests

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• Added tests for plot utils where possible

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• added tests for metrics callbacks utils

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• Merge branch 'codecov_improve' of https://github.com/luigibonati/mlcolvar into codecov_improve

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Commits on May 22, 2023

• added tutorial for implementing CVs from subclassing

  luigibonati

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• added tutorials in doc

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• draft version preprocessing

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Commits on May 23, 2023

• Added sklearn to test environment

  EnricoTrizio

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• Added sklearn to requirements

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• Added test function for utils.fes

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• Fix AutoEncoder calling pre/postprocessing during training

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• Merge pull request #65 from luigibonati/codecov_improve

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Commits on May 24, 2023

• First part of new cv tutorial

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• Deleted useless file from paper_experiments folder

  EnricoTrizio

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• Adde mfep to muller-brown + mfep utils to plot

  EnricoTrizio

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• Fixed typo in comments in autoencoder cv

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• Added tutorial for new cv implementation

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• Added utils to load mfep to exp_4 notebook

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• Multitasking tutorial first commit

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• Added short intro to multitask tutorial

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• Added comments to MultitaskCV tutorial

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• Update newCV tutorial

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• Removed mfep utils from mutitask experiment notebook

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• Fixed typos and added @andrrizzi review comments on multitask tutorial

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• Fixed typos, added @andrrizzi review comments, removed repetitions in code cells in newCV tutorial

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• Merge branch 'tutorials_fix' of https://github.com/luigibonati/mlcolvar into tutorials_fix

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• Remove sklearn from requirements.txt

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• Added back and included in coverage notebooks testing

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• Added verbosity to notebooks testing

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• Shorten training in alanine TICA tutorial

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• Merge pull request #70 from luigibonati/add_back_nb_testing

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• Added colab_setup.sh file

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• Test run on colab setup for TDA tutorial

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• Fixed link for colab_setup file download

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• Edit colab_setup to copy paper experiments data as well

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• Added colab button and setup to notebooks

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• Changed colab setup paths to use colab_setup branch for testing

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Commits on May 25, 2023

• update tutorial subclassing

  luigibonati

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• fixed error for not defined variable in preprocessing tutorial

  EnricoTrizio

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• Added safety check for multiple executions and polished commands

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• Added verbosity to colab setup in notebooks

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• Replaced symlink with actual data files in paper_experiments

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• Added notebook_type argument to colab_setp.sh

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• Updated notebook_type argument for colab_setup.sh for notebooks

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• Merge pull request #69 from luigibonati/fix-autoencoder

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Commits on May 26, 2023

• added pre/post processing tutorial

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• Edit paths to from colab_setup to main branch

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• Merge pull request #71 from luigibonati/colab_setup

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• First part of new cv tutorial

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• Deleted useless file from paper_experiments folder

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• Adde mfep to muller-brown + mfep utils to plot

  EnricoTrizio

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• Fixed typo in comments in autoencoder cv

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• Added tutorial for new cv implementation

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• Added utils to load mfep to exp_4 notebook

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• Multitasking tutorial first commit

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• Added short intro to multitask tutorial

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• Added comments to MultitaskCV tutorial

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• Update newCV tutorial

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• Removed mfep utils from mutitask experiment notebook

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• Fixed typos and added @andrrizzi review comments on multitask tutorial

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• Fixed typos, added @andrrizzi review comments, removed repetitions in code cells in newCV tutorial

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• First part of new cv tutorial

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• Added tutorial for new cv implementation

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• Added utils to load mfep to exp_4 notebook

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• Multitasking tutorial first commit

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• Added short intro to multitask tutorial

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• Added comments to MultitaskCV tutorial

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• Update newCV tutorial

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• Removed mfep utils from mutitask experiment notebook

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• Fixed typos and added @andrrizzi review comments on multitask tutorial

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• Fixed typos, added @andrrizzi review comments, removed repetitions in code cells in newCV tutorial

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• added tutorial for implementing CVs from subclassing

  

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• added tutorials in doc

  

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• draft version preprocessing

  

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• update tutorial subclassing

  

  luigibonati

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• fixed error for not defined variable in preprocessing tutorial

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• added pre/post processing tutorial

  

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• Merge branch 'tutorials_fix' of https://github.com/luigibonati/mlcolvar into tutorials_fix

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Commits on May 29, 2023

• Added colab butons and setup to new adv notebook

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• Moved notebooks testing only to Ubuntu

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