Update layout.html #233
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Update layout.html #233
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MMathisLab commented Mar 5, 2025
MMathisLab commented - I believe this was the missing part for the plotly loading... lets see!
- I believe this was the missing part for the plotly loading... lets see!
CeliaBenquet pushed a commit to CeliaBenquet/CEBRA that referenced this pull request Apr 23, 2025
MMathisLab added a commit that referenced this pull request May 23, 2025
* first proposal for batching in tranform method * first running version of padding with batched inference * start tests * add pad_before_transform to fit function and add support for convolutional models in _transform * remove print statements * first passing test * add support for hybrid models * rewrite transform in sklearn API * baseline version of a torch.Datset * move batching logic outside solver * move functionality to base file in solver and separate in functions * add test_select_model for single session * add checks and test for _process_batch * add test_select_model for multisession * make self.num_sessions compatible with single session training * improve test_batched_transform_singlesession * make it work with small batches * make test with multisession work * change to torch padding * add argument to sklearn api * add torch padding to _transform * convert to torch if numpy array as inputs * add distinction between pad with data and pad with zeros and modify test accordingly * differentiate between data padding and zero padding * remove float16 * change argument position * clean test * clean test * Fix warning * Improve modularity remove duplicate code and todos * Add tests to solver * Remove unused import in solver/utils * Fix test plot * Add some coverage * Fix save/load * Remove duplicate configure_for in multi dataset * Make save/load cleaner * Fix codespell errors * Fix docs compilation errors * Fix formatting * Fix extra docs errors * Fix offset in docs * Remove attribute ref * Add review updates * apply ruff auto-fixes * Concatenate last batches for batched inference (#200) * Concatenate last to batches for batched inference * Add test case * Fix linting errors in tests (#188) * apply auto-fixes * Fix linting errors in tests/ * Fix version check * Fix `scikit-learn` reference in conda environment files (#195) * Add support for new __sklearn_tags__ (#205) * Add support for new __sklearn_tags__ * fix inheritance order * Add more tests * fix added test * Update workflows to actions/setup-python@v5, actions/cache@v4 (#212) * Fix deprecation warning force_all_finite -> ensure_all_finite for sklearn>=1.6 (#206) * Add tests to check legacy model loading (#214) * Add improved goodness of fit implementation (#190) * Started implementing improved goodness of fit implementation * add tests and improve implementation * Fix examples * Fix docstring error * Handle batch size = None for goodness of fit computation * adapt GoF implementation * Fix docstring tests * Update docstring for goodness_of_fit_score Co-authored-by: Célia Benquet <32598028+CeliaBenquet@users.noreply.github.com> * add annotations to goodness_of_fit_history Co-authored-by: Célia Benquet <32598028+CeliaBenquet@users.noreply.github.com> * fix typo Co-authored-by: Célia Benquet <32598028+CeliaBenquet@users.noreply.github.com> * improve err message Co-authored-by: Célia Benquet <32598028+CeliaBenquet@users.noreply.github.com> * make numerical test less conversative * Add tests for exception handling * fix tests --------- Co-authored-by: Célia Benquet <32598028+CeliaBenquet@users.noreply.github.com> * Support numpy 2, upgrade tests to support torch 2.6 (#221) * Drop numpy constraint * Implement workaround for pytables * better error message * pin numpy only for python 3.9 * update dependencies * Upgrade torch version * Fix based on python version * Add support for torch.load with weights_only=True * Implement safe loading for torch models starting in torch 2.6 * Fix windows specs * fix docstring * Revert changes to loading logic * Release 0.5.0rc1 (#189) * Make bump_version script runnable on MacOS * Bump version to 0.5.0rc1 * fix minor formatting issues * remove commented code --------- Co-authored-by: Mackenzie Mathis <mathis@rowland.harvard.edu> * Fix pypi action (#222) * force packaging upgrade to 24.2 for twine * Bump version to 0.5.0rc2 * remove universal compatibility option * revert tag * adapt files to new wheel name due to py3 * Update base.py (#224) This is a lazy solution to #223 * Change max consistency value to 100 instead of 99 (#227) * Change text consistency max from 99 to 100 * Update cebra/integrations/matplotlib.py --------- Co-authored-by: Mackenzie Mathis <mackenzie.mathis@epfl.ch> Co-authored-by: Steffen Schneider <steffen@bethgelab.org> * Update assets.py --> force check for parent dir (#230) Update assets.py - mkdir was failing in 0.5.0rc1; attempt to fix * User docs minor edit (#229) * user note added to usage.rst - link added * Update usage.rst - more detailed note on the effect of temp. * Update usage.rst - add in temp to demo model - testout put thanks @stes * Update docs/source/usage.rst Co-authored-by: Steffen Schneider <stes@hey.com> * Update docs/source/usage.rst Co-authored-by: Steffen Schneider <stes@hey.com> * Update docs/source/usage.rst Co-authored-by: Steffen Schneider <stes@hey.com> --------- Co-authored-by: Steffen Schneider <stes@hey.com> * General Doc refresher (#232) * Update installation.rst - python 3.9+ * Update index.rst * Update figures.rst * Update index.rst -typo fix * Update usage.rst - update suggestion on data split * Update docs/source/usage.rst Co-authored-by: Steffen Schneider <stes@hey.com> * Update usage.rst - indent error fixed * Update usage.rst - changed infoNCE to new GoF * Update usage.rst - finx numpy() doctest * Update usage.rst - small typo fix (label) * Update usage.rst --------- Co-authored-by: Steffen Schneider <stes@hey.com> * render plotly in our docs, show code/doc version (#231) * Update layout.html (#233) * Update conf.py (#234) - adding link to new notebook icon * Refactoring setup.cfg (#228) * Home page landing update (#235) * website refresh * v0.5.0 (#238) * Upgrade docs build (#241) * Improve build setup for docs * update pydata theme options * Add README for docs folder * Fix demo notebook build * Finish build setup * update git workflow * add timeout to workflow * add timeout also to docs build * switch build back to sphinx for gh actions * attempt to fix build workflow * update to sphinx-build * fix build workflow * fix indent error * fix build system * revert demos to main * increase timeout to 30 * Allow indexing of the cebra docs (#242) * Allow indexing of the cebra docs * Fix docs workflow * Fix broken docs coverage workflows (#246) * Add xCEBRA implementation (AISTATS 2025) (#225) * Add multiobjective solver and regularized training (#783) * Add multiobjective solver and regularized training * Add example for multiobjective training * Add jacobian regularizer and SAM * update license headers * add api draft for multiobjective training * add all necessary modules to run the complete xcebra pipeline * add notebooks to reproduce xcebra pipeline * add first working notebook * add notebook with hybrid learning * add notebook with creation of synthetic data * add notebook with hybrid training * add plot with R2 for different parts of the embedding * add new API * update api wrapper with more checks and messages * add tests and notebook with new api * merge xcebra into attribution * separate xcebra dataset from cebra * some minor refactoring of cebra dataset * separate xcebra loader from cebra * remove xcebra distributions from cebra * minor refactoring with distributions * separate xcebra criterions from cebra * minor refactoring on criterion * separate xcebra models/criterions/layers from cebra * refactoring multiobjective * more refactoring... * separate xcebra solvers from cebra * more refactoring * move xcebra to its own package * move more files into xcebra package * more files and remove changes with the registry * remove unncessary import * add folder structure * move back distributions * add missing init * remove wrong init * make loader and dataset run with new imports * making it run! * make attribution run * Run pre-commit * move xcebra repo one level up * update gitignore and add __init__ from data * add init to distributions * add correct init for attribution pacakge * add correct init for model package * fix remaining imports * fix tests * add examples back to xcebra repo * update imports from graphs_xcebra * add setup.py to create a package * update imports of graph_xcebra * update notebooks * Formatting code for submission Co-authored-by: Rodrigo Gonzalez <gonlairo@gmail.com> * move test into xcebra * Add README * move distributions back to main package * clean up examples * adapt tests * Add LICENSE * add train/eval notebook again * add notebook with clean results * rm synthetic data * change name from xcebra to regcl * change names of modules and adapt imports * change name from graphs_xcebra to synthetic_data * Integrate into CEBRA * Fix remaining imports and make notebook runnable * Add dependencies, add version flag * Remove synthetic data files * reset dockerfile, move vmf * apply pre-commit * Update notice * add some docstrings * Apply license headers * add new scd notebook * add notebook with scd --------- Co-authored-by: Steffen Schneider <stes@hey.com> * Fix tests * bump version * update dockerfile * fix progress bar * remove outdated test * rename models * Apply fixes to pass ruff tests * Fix typos * Update license headers, fix additional ruff errors * remove unused comment * rename regcl in codebase * change regcl name in dockerfile * Improve attribution module * Fix imports name naming * add basic integration test * temp disable of binary check * Add legacy multiobjective model for backward compat * add synth import back in * Fix docstrings and type annot in cebra/models/jacobian_regularizer.py * add xcebra to tests * add missing cvxpy dep * fix docstrings * more docstrings to fix attr error * Improve build setup for docs * update pydata theme options * Add README for docs folder * Fix demo notebook build * Finish build setup * update git workflow * Move demo notebooks to CEBRA-demos repo See AdaptiveMotorControlLab/CEBRA-demos#28 * revert unneeded changes in solver * formatting in solver * further minimize solver diff * Revert unneeded updates to the solver * fix citation * fix docs build, missing refs * remove file dependency from xcebra int test * remove unneeded change in registry * update gitignore * update docs * exclude some assets * include binary file check again * add timeout to workflow * add timeout also to docs build * switch build back to sphinx for gh actions * pin sphinx version in setup.cfg * attempt workflow fix * attempt to fix build workflow * update to sphinx-build * fix build workflow * fix indent error * fix build system * revert demos to main * adapt workflow for testing * bump version to 0.6.0rc1 * format imports * docs writing * enable build on dev branch * fix some review comments * extend multiobjective docs * Set version to alpha * make tempdir platform independent * Remove ratinabox and ephysiopy as deps * Apply review comments * Update Makefile - setting coverage threshold to 80% to not delay good code being made public. In the near future this can be fixed and raised again to 90%. --------- Co-authored-by: Steffen Schneider <stes@hey.com> Co-authored-by: Steffen Schneider <steffen.schneider@helmholtz-munich.de> Co-authored-by: Mackenzie Mathis <mathis@rowland.harvard.edu> * start tests * remove print statements * first passing test * move functionality to base file in solver and separate in functions * add test_select_model for multisession * remove float16 * Improve modularity remove duplicate code and todos * Add tests to solver * Fix save/load * Fix extra docs errors * Add review updates * apply ruff auto-fixes * fix linting errors * Run isort, ruff, yapf * Fix gaussian mixture dataset import * Fix all tests but xcebra tests * Fix pytorch API usage example * Make xCEBRA compatible with the batched inference & padding in solver * Add some tests on transform() with xCEBRA * Add some docstrings and typings and clean unnecessary changes * Implement review comments * Fix sklearn test * Add name in NOTE Co-authored-by: Steffen Schneider <steffen@bethgelab.org> * Implement reviews on tests and typing * Fix import errors * Add select_model to aux solvers * Fix docs error * Add tests on the private functions in base solver * Update tests and duplicate code based on review --------- Co-authored-by: Rodrigo <gonlairo@gmail.com> Co-authored-by: Steffen Schneider <stes@hey.com> Co-authored-by: Mackenzie Mathis <mathis@rowland.harvard.edu> Co-authored-by: Steffen Schneider <steffen.schneider@helmholtz-munich.de> Co-authored-by: Ícaro <icarosadero@proton.me> Co-authored-by: Mackenzie Mathis <mackenzie.mathis@epfl.ch> Co-authored-by: Steffen Schneider <steffen@bethgelab.org> Co-authored-by: Rodrigo González Laiz <31796689+gonlairo@users.noreply.github.com>
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