Final version for JOSE with DOIs

Had to add DOIs to citations, now this version should be final.

Final version for JOSE

Final version of repo for JOSE acceptance.

v1.0.1

What's Changed

• Material for M2LINES team meeting on 2021-04-30 by @lesommer in #1
• DA demo merge by @feiyulu in #2
• Save output data and figs, add documentation by @MitchBushuk in #3
• small fixes for demo by @feiyulu in #4
• Add DA Demo slides by @MitchBushuk in #5
• Add pytorch tutorial by @yaniyuval in #6
• reproducible code, adding figures by @yaniyuval in #7
• corrected requirements file by @yaniyuval in #8
• Notebooks for learning DA increments by @adcroft in #9
• Fix some typos in the text by Cheng. by @chzhangudel in #14
• review changes of DA notebook by @William-gregory in #13
• Review for 02type-of-parametrization by @bhouri0412 in #20
• Create jupyter book by @rabernat in #25
• Review 06-Different-ML-models by @Sshamekh in #16
• Set up pre commit by @rabernat in #27
• Add build workflow by @rabernat in #28
• Fix typo in L96 eqn for Y variable by @adconnolly in #30
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #34
• Consolidate version of L96 module by @adcroft in #32
• Automated building by @rabernat in #33
• Standardize kernels by @rabernat in #35
• Strip notebook output by @rabernat in #37
• Fix random forest by @rabernat in #44
• Dollarmath by @breichl in #48
• Change cache behavior by @rabernat in #49
• L96 description and implementation by @bhouri0412 in #31
• Refactor environment creation and caching by @rabernat in #53
• Changes the timeout from 30 secs to 2 mins by @adcroft in #51
• Removes an unused file, LRP_gradient.py by @adcroft in #52
• Removed use of torch_lr_finder from notebooks by @adcroft in #55
• Updated Review for 04Subgrid-parametrization-pytorch by @rabernat in #54
• bibliography structure added - no citation updated in notebooks by @lzampier in #58
• Fix covariance file depend by @adcroft in #57
• Fixes a bad merge in earlier PR by @adcroft in #60
• remove notebooks/gcm-analog-demo.ipynb - content was redundant, chang… by @yaniyuval in #61
• Nn advect refinement by @breichl in #62
• gcm-parameterization-problem checked by @lzampier in #63
• Fixing header levels and bulleting in Neural_network_for_Lorenz96.ipynb by @breichl in #65
• Nn advect markdown by @breichl in #67
• Laure's notebooks by @lzampier in #68
• Merged two DA notebooks to remove need for artifact by @adcroft in #69
• Shows logs, if any by @adcroft in #70
• Removes a notebook used only to generate a figure by @adcroft in #71
• Renamed stored network by @adcroft in #73
• Big reorganization and renaming by @rabernat in #74
• Refactor interpretability notebook, add comments, and add pure Jacobian formulation by @asross in #21
• Added more explanatory cells to L96 two time-scale description by @adcroft in #75
• Remove slide-cells from presentation by @adcroft in #76
• Fixed build errors due to updated dependencies by @shan18 in #79
• fixes #80 by @IamShubhamGupto in #81
• Updating the Two-Timescale System Notebook by @shan18 in #82
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #78
• Rearrange chapters and update table of contents by @dhruvbalwada in #90
• Gcm parameterization notebook update by @shan18 in #84
• Beautify gcm analogue by @IamShubhamGupto in #83
• Beautify Tuning GCM parameterization by @IamShubhamGupto in #85
• Beautify Neural Networks by @IamShubhamGupto in #88
• Update code and documentation of the data assimilation in L96 notebook by @shan18 in #86
• Beautify random forest parameterization by @IamShubhamGupto in #87
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #92
• Reformat code and text in the Using neural networks for L96 parameterization notebook by @shan18 in #93
• Beautify saliency maps by @IamShubhamGupto in #94
• removed build warnings by @IamShubhamGupto in #95
• Update lock file by @shan18 in #96
• Add references by @IamShubhamGupto in #97
• Update references by @IamShubhamGupto in #99
• feature importance notebook by @IamShubhamGupto in #102
• Update the learning da increments by @shan18 in #100
• Intro to Deep Learning by @IamShubhamGupto in #105
• Splitting the Neural Networks notebook and Adding MyST visual elements to the notebooks by @shan18 in #108
• Feature importance by @IamShubhamGupto in #107
• Try Shumbham's pr-preview PR with different account by @dhruvbalwada in #110
• New/sindy eq discovery by @IamShubhamGupto in #111
• Add Equation discovery Introduction Notebook by @shan18 in #112
• Update README and fix output streams to merge into one block by @shan18 in #113
• updated the first few notebooks on gcm analogues and parameterization. by @dhruvbalwada in #114
• Possible title fix by @IamShubhamGupto in #115
• Possible fix for title v2 by @IamShubhamGupto in #117
• Add Constraints notebook by @IamShubhamGupto in #118
• GP notebook import by @IamShubhamGupto in #121
• Fix climatology figure by @NoraLoose in #122
• Fix numba warnings by @IamShubhamGupto in #124
• Introduction of distribution-based error metric by @NoraLoose in #126
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #127
• ignore old notebooks by @IamShubhamGupto in #129
• Reworked some of the neural network notebooks by @dhruvbalwada in #128
• Update _toc.yml by @dhruvbalwada in #132
• Retry PR by @feiyulu in #131
• Added notebook for online training by @dhruvbalwada in #133
• Major restructure by @dhruvbalwada in #134
• imported cnn and resnet by @IamShubhamGupto in #136
• minor text formatting on resnet notebook by @IamShubhamGupto in #137
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #139
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #140
• Updated paper bib and constraints by @dhruvbalwada in #141
• Refresh cache by @IamShubhamGupto in #142
• Force rebuild all notebooks by @IamShubhamGupto in #143
• add closing references by @IamShubhamGupto in #144
• added citations to closing page by @dhruvbalwada in #145
• closing remarks force rebuild page by @IamShubhamGupto in #146
• citation b...

v1.0

What's Changed

• Material for M2LINES team meeting on 2021-04-30 by @lesommer in #1
• DA demo merge by @feiyulu in #2
• Save output data and figs, add documentation by @MitchBushuk in #3
• small fixes for demo by @feiyulu in #4
• Add DA Demo slides by @MitchBushuk in #5
• Add pytorch tutorial by @yaniyuval in #6
• reproducible code, adding figures by @yaniyuval in #7
• corrected requirements file by @yaniyuval in #8
• Notebooks for learning DA increments by @adcroft in #9
• Fix some typos in the text by Cheng. by @chzhangudel in #14
• review changes of DA notebook by @William-gregory in #13
• Review for 02type-of-parametrization by @bhouri0412 in #20
• Create jupyter book by @rabernat in #25
• Review 06-Different-ML-models by @Sshamekh in #16
• Set up pre commit by @rabernat in #27
• Add build workflow by @rabernat in #28
• Fix typo in L96 eqn for Y variable by @adconnolly in #30
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #34
• Consolidate version of L96 module by @adcroft in #32
• Automated building by @rabernat in #33
• Standardize kernels by @rabernat in #35
• Strip notebook output by @rabernat in #37
• Fix random forest by @rabernat in #44
• Dollarmath by @breichl in #48
• Change cache behavior by @rabernat in #49
• L96 description and implementation by @bhouri0412 in #31
• Refactor environment creation and caching by @rabernat in #53
• Changes the timeout from 30 secs to 2 mins by @adcroft in #51
• Removes an unused file, LRP_gradient.py by @adcroft in #52
• Removed use of torch_lr_finder from notebooks by @adcroft in #55
• Updated Review for 04Subgrid-parametrization-pytorch by @rabernat in #54
• bibliography structure added - no citation updated in notebooks by @lzampier in #58
• Fix covariance file depend by @adcroft in #57
• Fixes a bad merge in earlier PR by @adcroft in #60
• remove notebooks/gcm-analog-demo.ipynb - content was redundant, chang… by @yaniyuval in #61
• Nn advect refinement by @breichl in #62
• gcm-parameterization-problem checked by @lzampier in #63
• Fixing header levels and bulleting in Neural_network_for_Lorenz96.ipynb by @breichl in #65
• Nn advect markdown by @breichl in #67
• Laure's notebooks by @lzampier in #68
• Merged two DA notebooks to remove need for artifact by @adcroft in #69
• Shows logs, if any by @adcroft in #70
• Removes a notebook used only to generate a figure by @adcroft in #71
• Renamed stored network by @adcroft in #73
• Big reorganization and renaming by @rabernat in #74
• Refactor interpretability notebook, add comments, and add pure Jacobian formulation by @asross in #21
• Added more explanatory cells to L96 two time-scale description by @adcroft in #75
• Remove slide-cells from presentation by @adcroft in #76
• Fixed build errors due to updated dependencies by @shan18 in #79
• fixes #80 by @IamShubhamGupto in #81
• Updating the Two-Timescale System Notebook by @shan18 in #82
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #78
• Rearrange chapters and update table of contents by @dhruvbalwada in #90
• Gcm parameterization notebook update by @shan18 in #84
• Beautify gcm analogue by @IamShubhamGupto in #83
• Beautify Tuning GCM parameterization by @IamShubhamGupto in #85
• Beautify Neural Networks by @IamShubhamGupto in #88
• Update code and documentation of the data assimilation in L96 notebook by @shan18 in #86
• Beautify random forest parameterization by @IamShubhamGupto in #87
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #92
• Reformat code and text in the Using neural networks for L96 parameterization notebook by @shan18 in #93
• Beautify saliency maps by @IamShubhamGupto in #94
• removed build warnings by @IamShubhamGupto in #95
• Update lock file by @shan18 in #96
• Add references by @IamShubhamGupto in #97
• Update references by @IamShubhamGupto in #99
• feature importance notebook by @IamShubhamGupto in #102
• Update the learning da increments by @shan18 in #100
• Intro to Deep Learning by @IamShubhamGupto in #105
• Splitting the Neural Networks notebook and Adding MyST visual elements to the notebooks by @shan18 in #108
• Feature importance by @IamShubhamGupto in #107
• Try Shumbham's pr-preview PR with different account by @dhruvbalwada in #110
• New/sindy eq discovery by @IamShubhamGupto in #111
• Add Equation discovery Introduction Notebook by @shan18 in #112
• Update README and fix output streams to merge into one block by @shan18 in #113
• updated the first few notebooks on gcm analogues and parameterization. by @dhruvbalwada in #114
• Possible title fix by @IamShubhamGupto in #115
• Possible fix for title v2 by @IamShubhamGupto in #117
• Add Constraints notebook by @IamShubhamGupto in #118
• GP notebook import by @IamShubhamGupto in #121
• Fix climatology figure by @NoraLoose in #122
• Fix numba warnings by @IamShubhamGupto in #124
• Introduction of distribution-based error metric by @NoraLoose in #126
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #127
• ignore old notebooks by @IamShubhamGupto in #129
• Reworked some of the neural network notebooks by @dhruvbalwada in #128
• Update _toc.yml by @dhruvbalwada in #132
• Retry PR by @feiyulu in #131
• Added notebook for online training by @dhruvbalwada in #133
• Major restructure by @dhruvbalwada in #134
• imported cnn and resnet by @IamShubhamGupto in #136
• minor text formatting on resnet notebook by @IamShubhamGupto in #137
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #139
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #140
• Updated paper bib and constraints by @dhruvbalwada in #141
• Refresh cache by @IamShubhamGupto in #142
• Force rebuild all notebooks by @IamShubhamGupto in #143
• add closing references by @IamShubhamGupto in #144
• added citations to closing page by @dhruvbalwada in #145
• closing remarks force rebuild page by @IamShubhamGupto in #146
• citation b...