Add tutorial on using mne-features in pipeline #762
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| # Here, we closely follow Tutorial 3, but we create pipelines using features | ||
| # extracted using the mne-features library. We instantiate the three different | ||
| # classiciation pipelines to be considered in the analysis. | ||
| # See the mne-features docs to learn more about the available features: | ||
| # https://mne.tools/mne-features/api.html#api-documentation | ||
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| # mne-feature's FeatureExtractor can be used directly in our pipelines | ||
| # as it implements the fit() and transform() methods | ||
| # (note that fit does not have any effect, but it is implemented for compatibility). | ||
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| # We can specify which features we want to extract as a list of strings, see | ||
| # https://mne.tools/mne-features/generated/mne_features.feature_extraction.FeatureExtractor.html#mne_features.feature_extraction.FeatureExtractor |
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More important than commenting on the technical functionality here is explaining in detail exactly what mne-feature will do in this step, and linking with some reference why variance and ptp_amp are important. Linking with some reference, the original mne-features paper has some original citation about this.
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| # | ||
| # The following plot shows a comparison of the three classification pipelines | ||
| # for each subject of each dataset. |
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any comments about the results?
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| This example shows how to evaluate a pipeline constructed using the | ||
| mne-features library |
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You also need to mention that it is necessary to install mne-features outside of moabb, it tells a mini-story telling... moabb is really cool, and we have easy interconnectivity with any library that has a sklearn pipeline.
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It's great to see you here ;) I commented on the tutorial and adjusted the settings so you can view the documentation in the CI. The tutorial has a good start! Basically, you need to populate it with more text/figures/information. If you have any course material that links to the features you chose, it would be very welcome to be mentioned in the tutorial. I am giving you permission to run CI, so you can see when the documentation is generated. You can check the generated documentation here: https://docs.github.com/en/actions/managing-workflow-runs-and-deployments/managing-workflow-runs/downloading-workflow-artifacts but I strongly suggest you run first locally. |
Co-authored-by: Bru <b.aristimunha@gmail.com> Signed-off-by: Alexander de Ranitz <89586187+alexander-de-ranitz@users.noreply.github.com>
…de-ranitz/moabb into tutorial/mne-features
…z/moabb into tutorial/mne-features
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@bruAristimunha Thanks for the feedback! I've added slightly more documentation. However, I'm not sure exactly what kind of additional information would be suitable here. I figured this tutorial would be a minimal working example of how to use mne-features, rather than a tutorial on any specific pipeline/dataset. The pipelines used are only trivial examples and not based on any literature. I looked at the original mne-features paper, but since this focuses on epilepsy detection, opposed to standard BCI approaches (P300/MI/etc.), it does not seem very relevant to include it in a tutorial. Similarly, I would think any mathematical details regarding standard EEG features would deserve their own tutorial, rather than being mixed in with this tutorial which is specifically about combining mne-features and MOABB. Of course, I am new to MOABB and I don't know what your vision is for these tutorials, so please let me know what approach you think is best and what this tutorial should aim for. If you have any concrete suggestions for details/explanations that should be added, I am happy to add them. |
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Ah, I got it. Math is necessary, and we want new tutorials to be better and better. Put the formula and explanation of precisely what is being calculated, like, we are computing this across channels or in the temporal dimensions, or something else. Remember that the formula must be formatted in .rst. It has to be at the same level of detail as the tutorial meeget. I think this will add more paragraphs to the tutorial. References are nice and necessary, but I think Pierre and I can help you with this point. The tutorial should also have the angle changed a little. A little less homework and more tutorials for new users. It is not teaching much, but it is a good start. Just remember that whoever is going to consume this material will be a new user, who possibly doesn't understand much about what brain signals are. You are very close to reaching the level, you just need to go a little beyond. |
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Do you want some extra suggestion @alexander-de-ranitz? |
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I think I get the gist, but a I have a one remaining question: do you have any suggestions on which dataset and pipelines to use to best demonstrate the combination of MOABB and mne-features? I am not familiar with most of the more complex features available in mne-features and I do not have any literature at the ready to point me in the right direction. If you (or @PierreGtch) could give me any suggestions (and/or references) for an insightful combination of dataset and pipeline I will work on the necessary documentation and explanations. |
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@PierreGtch, is all your the question :) |
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For the sake of simplicity, I think you could re-use the pipeline introduced in this tutorial (and reference the tutorial). It's meant for seizure detection, but we could check what it gives on ERP decoding
General rule: it's best to re-use datasets used in other MOABB tutorials to avoid downloading too many datasets when the documentation is built. For example, this tutorial uses the
First thing to do: look at the documentation. If you do this, you will find out that the API page of most non-trivial functions in MNE-features provides a reference to a publication which introduces the function. |
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Hey guys @PierreGtch and @alexander-de-ranitz, I pushed the ""math"" that I was asking, solving the other comments it is fine to merge for me. |
| # References | ||
| # ----------- | ||
| # | ||
| # .. [1] https://mne.tools/mne-features/index.html |
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We use apa reference style...
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| # The following plot shows a comparison of the three classification pipelines | ||
| # for each subject of each dataset. |
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I removed one dataset to speed-up a little the generation
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Hey @alexander-de-ranitz, Do you need help to finish the tutorial? |
Signed-off-by: Alexander de Ranitz <89586187+alexander-de-ranitz@users.noreply.github.com>
The previous description was based on an outdated/wrong figure.
…z/moabb into tutorial/mne-features
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@bruAristimunha I have updated the documentation and reference and it should be complete now. Please let me know if any further additions are needed. |
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Good job @alexander-de-ranitz ! Just minor comments, then we can merge
docs/source/whats_new.rst
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| - Adding :func:`moabb.analysis.plotting.dataset_bubble_plot` plus the corresponding tutorial (:gh:`753` by `Pierre Guetschel`_) | ||
| - Adding :func:`moabb.datasets.utils.plot_all_datasets` and update the tutorial (:gh:`758` by `Pierre Guetschel`_) | ||
| - Improve the dataset model cards in each API page (:gh:`765` by `Pierre Guetschel`_) | ||
| - Adding tutorial on using mne-features (:gh:`762` by `Alexander de Ranitz`_ and `Bruno Aristimunha`_) |
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You can also add your other group members, depending on who actually contributed
| # only the variance performs best. Perhaps this is because the variance is | ||
| # less sensitive to noise than the peak-to-peak amplitude, as the variance | ||
| # is computed over the whole epoch, whereas the peak-to-peak amplitude | ||
| # only considers the two most extreme data points (which could be outliers). |
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| # only considers the two most extreme data points (which could be outliers). | |
| # only considers the two most extreme data points (which could be outliers). | |
| # |
Co-authored-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Signed-off-by: Alexander de Ranitz <89586187+alexander-de-ranitz@users.noreply.github.com>
…z/moabb into tutorial/mne-features
bruAristimunha
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May 8, 2025
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thank you for the contribution @alexander-de-ranitz |
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Congrats @alexander-de-ranitz @LuukNeervens @charlynnvanosch!! 🎉 |
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* [MNT] update to release * [MNT] update to release * [MNT] single readme file * [MNT] typo * Apply suggestions from code review Co-authored-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Signed-off-by: Bru <b.aristimunha@gmail.com> * [MNT] version control * Single readme and contributing webpage * [pre-commit.ci] auto fixes from pre-commit.com hooks * removing docker, no one is using. * removing docker, no one is using. * removing poetry * external example * Hard fix * skipped test to release * V1.2.0 (#713) * [MNT] Sync v1.2.0 (#712) * develop into master v1.1.1 (#645) * Fix workflow cache (#632) * Copy workflow changes from PR #584 * Update whats_new.rst * Remove "always deploy" used for testing * Restore change to pytest instead of unittest * Use mne data cache in tests too * Remove duplicate restore cache (#634) * Fix example Hinss2021 (#636) * Dataset summary in CSV and leaderboard links (#635) * Add summary tables as csv * Change BaseDataset to include the dataset's summary table in the docstring * Try update summary table in doc * Add test for dataset summary table * Fix future annotations * Prepare summary tables before doc * Make build dir if not exist * Add rstate table * Replace tables with CSVs in doc * Add PapersWithCOde column * Fix initial white space * Fix formatting of ints * Remove tables from docstrings * Add missing DemonsP300 row * Update whats_new.rst * Remove Shin2017B leaderboard * Move PWC link outside of docstring table * Add Liu2024 Dataset (#619) * including Liu2024 Dataset * [pre-commit.ci] auto fixes from pre-commit.com hooks * Function data_path * [pre-commit.ci] auto fixes from pre-commit.com hooks * data_infos and get_single_subject_data functions * [pre-commit.ci] auto fixes from pre-commit.com hooks * Data Description * [pre-commit.ci] auto fixes from pre-commit.com hooks * updating get_single_subject fct and data_path & adding encoding fct * [pre-commit.ci] auto fixes from pre-commit.com hooks * Finishing the code * [pre-commit.ci] auto fixes from pre-commit.com hooks * updating docstrings for data_path * Updating dataset_summary and updating the get_single_subject fct to handle the case of existing file in path_electrodes * adapting the return of get_single_subject_data fct * [pre-commit.ci] auto fixes from pre-commit.com hooks * Adding dataset description and preload = True when reading the data in the get_single_subject fct * fix: codespell * fix: changing to static method the encoding * repushing and resolving pre-commit conflicts * [pre-commit.ci] auto fixes from pre-commit.com hooks * fix: changing the mapping * fix: changing the unmatching between the trigger and the events from the csv * ehn: using pylint to improve the code (remove not used variables, and change the module); * modifying the python version in the pre-commit file * adding description to enhancements * adjusting the encoding * adjusting comments and dataset description * solving channels types and names issues & correcting encoding * Correcting the number of trials per class and the total trials * Correcting data description * Adding the possibility to exclude/include break and instructions events * Correcting code to include/exclude instr and break events * Remove table from docstring Signed-off-by: PierreGtch <25532709+PierreGtch@users.noreply.github.com> * Add CSV row --------- Signed-off-by: PierreGtch <25532709+PierreGtch@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: bruAristimunha <a.bruno@aluno.ufabc.edu.br> Co-authored-by: PierreGtch <25532709+PierreGtch@users.noreply.github.com> Co-authored-by: Pierre Guetschel <pierre.guetschel@donders.ru.nl> * Add scripts to publish results on PaperWithCode (#561) * Add scripts to publish results on paperwithcode * Create tasks manually instead (API error 403 forbidden) * Try to create the evaluation first and other things, not working... * Update whats_new.rst * Fix example from API's README; still results in a "403 Forbidden" * Fix task_id * Allow passing multiple results files * Save commands used as comments * Add comment --------- Signed-off-by: PierreGtch <25532709+PierreGtch@users.noreply.github.com> Signed-off-by: Bru <a.bruno@aluno.ufabc.edu.br> Co-authored-by: Bru <a.bruno@aluno.ufabc.edu.br> * [pre-commit.ci] pre-commit autoupdate (#631) * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.5.0...v4.6.0) - [github.com/psf/black: 24.3.0 → 24.4.2](https://github.com/psf/black/compare/24.3.0...24.4.2) - [github.com/asottile/blacken-docs: 1.16.0 → 1.18.0](https://github.com/asottile/blacken-docs/compare/1.16.0...1.18.0) - [github.com/PyCQA/flake8: 7.0.0 → 7.1.0](https://github.com/PyCQA/flake8/compare/7.0.0...7.1.0) - [github.com/astral-sh/ruff-pre-commit: v0.3.5 → 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an issue if the conversion didn't worked and exposed time_out parameter * [pre-commit.ci] auto fixes from pre-commit.com hooks * FIX: italian to eng * EHN: making optuna optional * FIX: fixing the workflow files * FIX: changing the optuna file * FIX: including optuna for the windows --------- Signed-off-by: Bru <a.bruno@aluno.ufabc.edu.br> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: bruAristimunha <a.bruno@aluno.ufabc.edu.br> * correct name (#642) * V1.1.1 (#644) * release 1.1.1 * increase the version * increase the version * removing the poetry.lock * increase version * changing the CITATION.cff * upload versino for artifact * pylock -> pyproject.toml --------- Signed-off-by: PierreGtch <25532709+PierreGtch@users.noreply.github.com> Signed-off-by: Bru <a.bruno@aluno.ufabc.edu.br> Co-authored-by: PierreGtch <25532709+PierreGtch@users.noreply.github.com> Co-authored-by: Taha Habib <95372659+tahatt13@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Pierre Guetschel <pierre.guetschel@donders.ru.nl> Co-authored-by: Igor Carrara <94047258+carraraig@users.noreply.github.com> Co-authored-by: Quentin Barthélemy <q.barthelemy@gmail.com> * V1.2.0 (#708) * [MNT] update to release * [MNT] update to release * [MNT] single readme file * [MNT] typo * Apply suggestions from code review Co-authored-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Signed-off-by: Bru <b.aristimunha@gmail.com> * [MNT] version control * Single readme and contributing webpage * [pre-commit.ci] auto fixes from pre-commit.com hooks * removing docker, no one is using. * removing docker, no one is using. * removing poetry * external example --------- Signed-off-by: Bru <b.aristimunha@gmail.com> Signed-off-by: Bru <a.bruno@aluno.ufabc.edu.br> Co-authored-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Co-authored-by: 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<b.aristimunha@gmail.com> Co-authored-by: PierreGtch <25532709+PierreGtch@users.noreply.github.com> Co-authored-by: Taha Habib <95372659+tahatt13@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Pierre Guetschel <pierre.guetschel@donders.ru.nl> Co-authored-by: Igor Carrara <94047258+carraraig@users.noreply.github.com> Co-authored-by: Quentin Barthélemy <q.barthelemy@gmail.com> * Correct bug when corrupted cache results (#715) * fix: caching incomplete data * fix: correct PR in whatsnew --------- Co-authored-by: Sylvain Chevallier <sylain.chevallier@universite-paris-saclay.fr> Co-authored-by: Bru <a.bruno@aluno.ufabc.edu.br> * [MNT] update the documentation generation (#706) * [EHN] fixing the doc api * [MNT] upgrade the docs dependecies * [MNT] upgrade the docs dependecies * more update in the docs * changing the tutorial order * updating the name to lower case * [EHN] updating the name * [EHN] updating the name * [EHN] updating the tutorial/examples, reordering... * [EHN] updating the readme file * [EHN] updating the readme file * [EHN] centralizing the contributing * [EHN] changing the overview * [EHN] increasing the python * fixing the plot benchmark * fixing issues with doc generation * no plot for the load * replacing dataset * Updating doc string * updating the installation webpage * updating the installation webpage * updating the citation * reducing the number of subject * reducing the number of subject * updating the whats new file * updating the citation * updating the installation * cleaning the deep learning * making the installation webpage better * updating the python version * updating the python version * making more simple and direct the doc * centralizing the api * centralizing the api * fixs * fixs * removing missed word * increasing * more fix in the documentation * order * updating * updating readme * updating readme * updating readme * updating readme * updating the makefile * updating the makefile * centralizing the process * testing something * updating citation in the readme * citation as tab * solving the docs * [EHN] creating the metainformation file to allow lazy loading by default (#688) * [EHN] creating the metainformation file to allow lazy loading by default * [EHN] whats_new file * [EHN] moving to the father class * updating the whats_new.rst file * fixing the tests * [EHN] moving to utils and changing to tests * Apply suggestions from code review Signed-off-by: Bru <b.aristimunha@gmail.com> * mistake with whats_new.rst file --------- Signed-off-by: Bru <b.aristimunha@gmail.com> * [WIP] Adding a A large EEG database with users' profile information for motor imagery Brain-Computer Interface dataset (#404) * Adding a new dataset * [pre-commit.ci] auto fixes from pre-commit.com hooks * Add data loading, update docstring * [pre-commit.ci] auto fixes from pre-commit.com hooks * Update dataset and add example * [pre-commit.ci] auto fixes from pre-commit.com hooks * Update Dreyer 2023 dataset class and example * Remove loading info before db is downloaded * Update dataset session and run naming; update plotting * Add whats_new * Add words to ignore in pre commit config * Add words to ignore in pre commit config * [pre-commit.ci] auto fixes from pre-commit.com hooks * [pre-commit.ci] auto fixes from pre-commit.com hooks * Update docstrings * Update summary table * Rename file to lowercase * rename file to lowercase * Update docstring ref links * Small adjustment on the tutorial * Do not expose the subjects and db_id parameters * playing and cleaning * updating the table * updating the table * fixing the limits * updating the API * updating here * suggestions from the code review * making the example run * Update moabb/datasets/dreyer2023.py Co-authored-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Signed-off-by: Bru <b.aristimunha@gmail.com> * Update moabb/datasets/dreyer2023.py Co-authored-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Signed-off-by: Bru <b.aristimunha@gmail.com> --------- Signed-off-by: Bru <a.bruno@aluno.ufabc.edu.br> Signed-off-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Signed-off-by: Bru <b.aristimunha@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Bru <a.bruno@aluno.ufabc.edu.br> Co-authored-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Co-authored-by: Pierre Guetschel <pierre.guetschel@donders.ru.nl> Co-authored-by: Bru <b.aristimunha@gmail.com> * Removing the Keras sub-module from moabb (#692) * bye keras models * bye keras models * no more keras models * removing the docker and poetry comments * updating the instruction list * updating poetry part * removing keras * removing keras * removing util deep learning from moabb * updating the tests * removing scikeras * removing scikeras * removing more keras * updating import * Updating the whats_new file * bye m2r2 * updating the docs dep * Updating the python version * - to _ * Apply suggestion from the review. * [pre-commit.ci] auto fixes from pre-commit.com hooks * updating the docstring * updating the docs yml file * update to make the review easy * updating config * fixing merging issue * renaming * update whats new file * Apply suggestions from code review Signed-off-by: Bru <b.aristimunha@gmail.com> --------- Signed-off-by: Bru <a.bruno@aluno.ufabc.edu.br> Signed-off-by: Bru <b.aristimunha@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add BEETL data to MOABB for benchmarking (#675) * handle pagination - needed for Stieger2021 ds * [pre-commit.ci] auto fixes from pre-commit.com hooks * add beetl datasets * beetl dataset final eval does now contain labels * added some description to the datasets * add more info to descirption * [pre-commit.ci] auto fixes from pre-commit.com hooks * 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Reverted to default version. * typos * wrong code * fixing the name * fixing the table * updating the whats_new file * updating the whats new file * fixing the tests * Fix the code * updating the braindecode cache * updating the file --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Bru <a.bruno@aluno.ufabc.edu.br> * MNT adjusting the docs (#719) * fixing the doc * trying to fix the lateral bar and failing * more updates on the doc * Update the template * Update `tdlda` dep (#717) * Update tdlda dep * Reactivate plot on toeplitxlda example * [pre-commit.ci] auto fixes from pre-commit.com hooks * Add suggestions from Jan * Update whatsnew --------- Signed-off-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * `BaseBIDSDataset` and `LocalBIDSDataset` (#724) * Add BaseBIDSDataset and LocalBIDSDataset * Update doc * Add test for LocalBIDSDataset * Update test * [pre-commit.ci] auto fixes from pre-commit.com hooks * Update whatsnew * Move list to global variable --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Pick all data channels in filter preprocessing step (#729) * Pick all data channels in filter step * Update whatsnew * [mnt] fix the n2pc (#730) * [mnt] removing the rest session and unit (#731) * Including cross-session splitter (#720) * Including cross-session splitter * playing... * playing and debugging... * playing... * adjusting the splitter * adjuting the splitter * updating the splitter * updating the figures * updating the splitter * updating the splitter * doc string and parameters * doc string and parameters * doc string and parameters * changing the doc's splitter * changing the doc's splitter * more doc string * removing the type * Applying suggestion from code review * [pre-commit.ci] auto fixes from pre-commit.com hooks * returning the within-session modification * [ehn] returing the withinsession bev * [FIX] fixing the tests and including some shuffling using cv * [pre-commit.ci] auto fixes from pre-commit.com hooks * removing visual code * more test and improve the tests * from the code review * Apply suggestions from code review Co-authored-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Signed-off-by: Bru <b.aristimunha@gmail.com> * improve the docstring * FIX the suggestion from code review * [EHN] improve the number of splits * Update moabb/evaluations/splitters.py Co-authored-by: Thomas Moreau <thomas.moreau.2010@gmail.com> Signed-off-by: Bru <b.aristimunha@gmail.com> * [EHN] returning * create some tests * code review * Apply suggestions from code review Co-authored-by: Thomas Moreau <thomas.moreau.2010@gmail.com> Signed-off-by: Bru <b.aristimunha@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks * Code review * type * type * type * Update moabb/evaluations/splitters.py Co-authored-by: Thomas Moreau <thomas.moreau.2010@gmail.com> Signed-off-by: Bru <b.aristimunha@gmail.com> * Apply suggestions from code review Co-authored-by: Thomas Moreau <thomas.moreau.2010@gmail.com> Signed-off-by: Bru <b.aristimunha@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks * [FIX] fixing suggestion --------- Signed-off-by: Bru <a.bruno@aluno.ufabc.edu.br> Signed-off-by: Bru <b.aristimunha@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Co-authored-by: Thomas Moreau <thomas.moreau.2010@gmail.com> * Fix analysis test (#735) * no message * [pre-commit.ci] auto fixes from pre-commit.com hooks * Update test_analysis.py apply Quentin's suggestion * Update whats_new.rst --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Fix seed in permutation test (#736) * Fix seed in permutation test * Fix * [MNT] Updating the doc (#738) * update the template * updating the color * updating to html * testing some solution * update the template * updating the colour * updating * updating the docs * updating the container * updating doc * updating html and css path * Update the range of python versions to allow moabb to work with python 3.13.2 (#740) * Update the range of python versions to allow moabb to work with python 3.13.2. * increase the CI * remove the upper limit * removing the version 3.13 * Re-add python 3.13 testing, correct TestSSVEP_MsetCCA. * increase the pytest version to capture the issue * Update .github/workflows/test.yml Signed-off-by: Bru <b.aristimunha@gmail.com> * Update .github/workflows/test.yml Signed-off-by: Bru <b.aristimunha@gmail.com> --------- Signed-off-by: Bru <b.aristimunha@gmail.com> Co-authored-by: Bru <b.aristimunha@gmail.com> * Updating ci (#742) * update the template * updating the color * updating to html * testing some solution * update the template * updating the colour * updating * updating the docs * updating the container * updating doc * updating html and css path * MNT: returning windows CI * running again * [pre-commit.ci] pre-commit autoupdate (#745) updates: - [github.com/PyCQA/isort: 6.0.0 → 6.0.1](https://github.com/PyCQA/isort/compare/6.0.0...6.0.1) - [github.com/PyCQA/flake8: 7.1.1 → 7.2.0](https://github.com/PyCQA/flake8/compare/7.1.1...7.2.0) - [github.com/astral-sh/ruff-pre-commit: v0.9.5 → v0.11.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.9.5...v0.11.4) - [github.com/adrienverge/yamllint.git: v1.35.1 → v1.37.0](https://github.com/adrienverge/yamllint.git/compare/v1.35.1...v1.37.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Mnt fix doc (#746) * update the template * updating the color * updating to html * testing some solution * update the template * updating the colour * updating * updating the docs * updating the container * updating doc * updating html and css path * [MNT] small doc change * small change on the font size * Including Cross subject splitter (#722) * draft * updating the splitter * whats_new.rst file * Update docs/source/whats_new.rst Signed-off-by: Bru <b.aristimunha@gmail.com> * Update moabb/evaluations/splitters.py Signed-off-by: Bru <b.aristimunha@gmail.com> * Update moabb/evaluations/splitters.py Signed-off-by: Bru <b.aristimunha@gmail.com> * fixing the init * [pre-commit.ci] auto fixes from pre-commit.com hooks * updating the test * final fixes * updating the test * updating the splitter from the code review * Updating the cross-subject * fixing the splitter * code review * Update moabb/evaluations/splitters.py Co-authored-by: Thomas Moreau <thomas.moreau.2010@gmail.com> Signed-off-by: Bru <b.aristimunha@gmail.com> * Update moabb/evaluations/splitters.py Co-authored-by: Thomas Moreau <thomas.moreau.2010@gmail.com> Signed-off-by: Bru <b.aristimunha@gmail.com> * Update moabb/evaluations/splitters.py Co-authored-by: Thomas Moreau <thomas.moreau.2010@gmail.com> Signed-off-by: Bru <b.aristimunha@gmail.com> * Update moabb/evaluations/splitters.py Co-authored-by: Thomas Moreau <thomas.moreau.2010@gmail.com> Signed-off-by: Bru <b.aristimunha@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks * updating the tests --------- Signed-off-by: Bru <b.aristimunha@gmail.com> Signed-off-by: Bru <a.bruno@aluno.ufabc.edu.br> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Thomas Moreau <thomas.moreau.2010@gmail.com> * Fix linux server download issue (#750) (#751) * Fix #750 issue Fix missing download test dataset on linux server. * [pre-commit.ci] auto fixes from pre-commit.com hooks * Update moabb/datasets/schirrmeister2017.py Signed-off-by: Bru <b.aristimunha@gmail.com> * updating whats new file --------- Signed-off-by: Bru <b.aristimunha@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Bru <b.aristimunha@gmail.com> * Dataset bubble plots (#753) * Add bubble plot function * Add doc entry * Add docstring * Add example * fix alphas index and use better colour palette * [pre-commit.ci] auto fixes from pre-commit.com hooks * Update whatsnew * import future annotations (python 3.9) * [pre-commit.ci] auto fixes from pre-commit.com hooks --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add `shape`, `gap` and `size_mode` parameters to `dataset_bubble_plot` (#755) * Add shape and gap parameters * [pre-commit.ci] auto fixes from pre-commit.com hooks * Add size mode parameter * Update example --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Additional fixes for `dataset_bubble_plot` (#756) * Mini fixes * Add possibility to plot a custom dataset * Add test for dataset plot (#757) * Add test * fix table * Update parsing function * Fix paradigm in Shin2017 dataset * [pre-commit.ci] auto fixes from pre-commit.com hooks * Normalize column names * Set gid * [pre-commit.ci] auto fixes from pre-commit.com hooks * Set trials per class in BEETL datasets --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add `plot_all_datasets` function (#758) * Add plot_all_datasets function * Update example * Fix * [pre-commit.ci] auto fixes from pre-commit.com hooks * Update whatsnew * remove lambda --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Fix links in `paper_results.rst` to point to the correct API documentation (#759) * dataset_bubble_plot tight layout (#761) Signed-off-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> * Add `plot_all_datasets` function to doc (#764) * Add datasets overview plot * Add dataset_bubble_plot to API * Add dataset plot to dataset summary page * Move overview image * [pre-commit.ci] auto fixes from pre-commit.com hooks --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Improve the dataset cards (#765) * Simplify code * Rename variables * Allow vertical table * Transfer unit * fix vertical table * Add comments and make the keys bold * [pre-commit.ci] auto fixes from pre-commit.com hooks * Fix presentation rate column for cVEP datasets * Update whatsnew * small hotfix --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: bruAristimunha <b.aristimunha@gmail.com> * Add `plot_datasets_cluster` function (#766) * Add cluster plot * update example * Update doc * [pre-commit.ci] auto fixes from pre-commit.com hooks * future annotations --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [MNT] fix text formatting in example Signed-off-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> * Fix some tests not running in test_datasets (#768) * Use get_dataset_path to set the dataset path in mne.config * Using only pytest with some added fixtures * Replace distutils as it can fail in new python versions * Improve dataset plots (#770) * Improve scaling of dataset plots * Use bbox instead of path_effects for titles * [pre-commit.ci] auto fixes from pre-commit.com hooks --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Creating a tutorial showing how to play with pre-processing steps (#771) * updating the pre-processing * updating the res test * pre-processing steps * including the pre-processing examples * updating the whats news * updating the whats new * updating api * updating * including the references * Apply suggestions from code review Co-authored-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Signed-off-by: Bru <b.aristimunha@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks * Update examples/advanced_examples/plot_pre_processing_steps.py Co-authored-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Signed-off-by: Bru <b.aristimunha@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks * last comments from code review --------- Signed-off-by: Bru <b.aristimunha@gmail.com> Co-authored-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Last mini-change to the dataset plot (#772) * Add tutorial on using mne-features in pipeline (#762) * Add example of using mne-features * Add authors * fixing documentation * Fix title formatting Co-authored-by: Bru <b.aristimunha@gmail.com> Signed-off-by: Alexander de Ranitz <89586187+alexander-de-ranitz@users.noreply.github.com> * fixing * Improve documentation * fix typo * updating to include what I was asking * Update documentation and fix reference * Update whats_new * Fix description of results The previous description was based on an outdated/wrong figure. * Add fellow authors to whats new * Fix typo Co-authored-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Signed-off-by: Alexander de Ranitz <89586187+alexander-de-ranitz@users.noreply.github.com> * Fix whitespace Co-authored-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Signed-off-by: Alexander de Ranitz <89586187+alexander-de-ranitz@users.noreply.github.com> * HOT-FIX of snowballstemmer --------- Signed-off-by: Alexander de Ranitz <89586187+alexander-de-ranitz@users.noreply.github.com> Co-authored-by: bruAristimunha <b.aristimunha@gmail.com> Co-authored-by: Bru <a.bruno@aluno.ufabc.edu.br> Co-authored-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> * Remove keras_eegnet in codecarbon example (#777) * remove keras eegnet from list * add changes to what's new * Update docs/source/whats_new.rst Signed-off-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> --------- Signed-off-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Co-authored-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> * Added a tutorial for the Within session splitter (#776) * Add files via upload Signed-off-by: jellymace <thomas.kooiman@icloud.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks * Updated whats_new.rst with contribution by #776 Signed-off-by: Paul Verhoeven <43268349+PaulusBoskabouter@users.noreply.github.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks * Update and rename tutorial_splitter.py to tutorial_6_within_session_splitter.py Added the naming convention and moved some of the warner.settings in hopes that it's causing the "import not on top of file" error we're getting. Signed-off-by: Paul Verhoeven <43268349+PaulusBoskabouter@users.noreply.github.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks * moving the tutroail to how_to_benchamrk and renaming to stay inline with the naming scheme in the new folder * revertiung name change because we ran into issues * changed the syntax a little to be more in line with existing documentation * Update examples/how_to_benchmark/tutorial_6_within_session_splitter.py Signed-off-by: Bru <b.aristimunha@gmail.com> * Added subject split plot and fixed the sphinx formatting bug. * Fixed mergeconflict on whats_new.rst * Now really fixed whats_new.rst * [pre-commit.ci] auto fixes from pre-commit.com hooks * Fixed the small issues in whats_new and the tutorial. * Added plot of eeg data for a single epoch and 3 channels. * [pre-commit.ci] auto fixes from pre-commit.com hooks * Fixed merge-conflict * [pre-commit.ci] auto fixes from pre-commit.com hooks * Deletion of sg_execution_times.rst file * Reworked and reformatted the markdown * [pre-commit.ci] auto fixes from pre-commit.com hooks * Fixed spelling error. --------- Signed-off-by: jellymace <thomas.kooiman@icloud.com> Signed-off-by: Paul Verhoeven <43268349+PaulusBoskabouter@users.noreply.github.com> Signed-off-by: Bru <a.bruno@aluno.ufabc.edu.br> Signed-off-by: Bru <b.aristimunha@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Paul Verhoeven <43268349+PaulusBoskabouter@users.noreply.github.com> Co-authored-by: Bru <a.bruno@aluno.ufabc.edu.br> Co-authored-by: Bru <b.aristimunha@gmail.com> Co-authored-by: PaulusBoskabouter <paul_2000@hotmail.nl> * Fix regression in `process_pipeline` flag (#774) * updating and hope to fix the regression * updating the whats new * fixing the if * Apply suggestions from code review Co-authored-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Signed-off-by: Bru <b.aristimunha@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks * fix identation * Try fix tests Signed-off-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> * Try fix tests Signed-off-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> * Try fix --------- Signed-off-by: Bru <b.aristimunha@gmail.com> Signed-off-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Co-authored-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Pierre Guetschel <pierre.guetschel@donders.ru.nl> * Including the fix_bad_channels for the :class:`moabb.datasets.Stieger2021` (#783) * Add option to fix bad channels in Stieger2021 dataset * updating the whats new file * update the whats new * Changed channels CB1 and CB2's type from 'misc' to 'eeg' from Wang2016 dataset (#781) * Changed channels CB1 and CB2's type from 'misc' to 'eeg' * fixing whats new file * updating the docstring --------- Co-authored-by: Ulysse Durand <ulysse.durand@ens-lyon.fr> Co-authored-by: Bru <a.bruno@aluno.ufabc.edu.br> Co-authored-by: bruAristimunha <b.aristimunha@gmail.com> * FIX Reduce warnings when building documentation (#784) * FIX Reduce warning when building documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks * Update whats_new.rst with PR number Signed-off-by: Lucas Heck <lucasheck17@gmail.com> --------- Signed-off-by: Lucas Heck <lucasheck17@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * DOC Add function to auto-generate the paper results tables (#785) * Add function to auto-generate results tables * [pre-commit.ci] auto fixes from pre-commit.com hooks * Add dark theme support for fixed column --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Update README.md (#791) * Update README.md Remove unnecessary line. Signed-off-by: lionel kusch <lionel.kusch@grenoble-inp.org> * Update whats_new.rst Signed-off-by: lionel kusch <lionel.kusch@grenoble-inp.org> --------- Signed-off-by: lionel kusch <lionel.kusch@grenoble-inp.org> * Update CONTRIBUTING.md (#792) * Update CONTRIBUTING.md One link in the Contribution was dead. I propose a new one, which seems to direct to a similar source. Signed-off-by: lionel kusch <lionel.kusch@grenoble-inp.org> * Update whats_new.rst Signed-off-by: lionel kusch <lionel.kusch@grenoble-inp.org> --------- Signed-off-by: lionel kusch <lionel.kusch@grenoble-inp.org> Co-authored-by: gcattan <gcattan@hotmail.fr> * Exposing util functions (#788) * exposing the new function * finished * Apply suggestions from code review Co-authored-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Signed-off-by: Bru <b.aristimunha@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks * updating the bids * updating the utils --------- Signed-off-by: Bru <b.aristimunha@gmail.com> Co-authored-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Update CODE_OF_CONDUCT.md (#796) Signed-off-by: Bru <a.bruno@aluno.ufabc.edu.br> * [pre-commit.ci] pre-commit autoupdate (#798) updates: - [github.com/PyCQA/flake8: 7.2.0 → 7.3.0](https://github.com/PyCQA/flake8/compare/7.2.0...7.3.0) - [github.com/astral-sh/ruff-pre-commit: v0.11.4 → v0.12.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.11.4...v0.12.2) - [github.com/adrienverge/yamllint.git: v1.37.0 → v1.37.1](https://github.com/adrienverge/yamllint.git/compare/v1.37.0...v1.37.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Fix: number of trial per class for PHMD_ML dataset (#797) * Update summary_rstate.csv Signed-off-by: gcattan <gcattan@hotmail.fr> * Update whats_new.rst Signed-off-by: gcattan <gcattan@hotmail.fr> --------- Signed-off-by: gcattan <gcattan@hotmail.fr> * A tutorial on how to create and use a MOABB dataset from X y (non continuous, epoched) data (#800) * A new RawEpochParadigm that allows a non continuous dataset in the form of X y to be processed by MOABB. * [pre-commit.ci] auto fixes from pre-commit.com hooks * Better comment section. * [pre-commit.ci] auto fixes from pre-commit.com hooks * small improvement * small improvement * improved comment section * [pre-commit.ci] auto fixes from pre-commit.com hooks * Improved comments and a typo. * [pre-commit.ci] auto fixes from pre-commit.com hooks * Improved description. * [pre-commit.ci] auto fixes from pre-commit.com hooks * Update whats_new.rst * Update tutorial_6_use_an_X_y_dataset.py * moving and renaming --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: gcattan <gcattan@hotmail.fr> Co-authored-by: bruAristimunha <b.aristimunha@gmail.com> * Filterbank tutorial (#787) * Small adjust on the tutorial * updating the whats new file * including in the api * updating the tutorial * updating last things * updating * updating * fixing typo --------- Signed-off-by: Bru <a.bruno@aluno.ufabc.edu.br> * [FIX] Converting the Zhou2016 to allow increase the moabb version (#802) * including notes * updating zhou * updating new utils functions * updating zhou * last things * updating the what's new * Update to pyRiemann 0.8 and mne 1.10 (#789) * Update to pyRiemann 0.8 Signed-off-by: gcattan <gcattan@hotmail.fr> * Update pyproject.toml Signed-off-by: gcattan <gcattan@hotmail.fr> * updating pyproject * updating tutorial to solve the dependecy issue * solving zhou? * trying again * updating again with zhou * updating the pyproject * bye python 3.9 * updating the pyproject * removing dep * Update pyproject.toml Signed-off-by: gcattan <gcattan@hotmail.fr> * Update Zhou2016.py try read_raw_ant Signed-off-by: gcattan <gcattan@hotmail.fr> * Update pyproject.toml Signed-off-by: gcattan <gcattan@hotmail.fr> * Update Zhou2016.py replace list by regex Signed-off-by: gcattan <gcattan@hotmail.fr> * updating .gitignore * changing to another dataset * fixing last tutorial * last adjust * removing the new library dep * reverting examples * updating the examples * updating tutorials 1 * updating the zhou * removing * updating git ignore --------- Signed-off-by: gcattan <gcattan@hotmail.fr> Co-authored-by: Bru <a.bruno@aluno.ufabc.edu.br> Co-authored-by: bruAristimunha <b.aristimunha@gmail.com> * Increased visibility of `LocalBIDSDataset` by adding small description to data summary page (#778) * description data summary file external dataset use * data summary page additions * Delete poetry.lock Signed-off-by: Bru <b.aristimunha@gmail.com> * Apply suggestions from code review Co-authored-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Signed-off-by: Bru <b.aristimunha@gmail.com> * Update docs/source/dataset_summary.rst Signed-off-by: Bru <b.aristimunha@gmail.com> * Delete examples/how_to_benchmark/benchmark/LeftRightImagery/analysis/info.txt Signed-off-by: Bru <b.aristimunha@gmail.com> --------- Signed-off-by: Bru <b.aristimunha@gmail.com> Co-authored-by: Bru <b.aristimunha@gmail.com> Co-authored-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Co-authored-by: Bru <a.bruno@aluno.ufabc.edu.br> * Pre-release 1.3.0 (#803) * Update to pyRiemann 0.8 Signed-off-by: gcattan <gcattan@hotmail.fr> * Update pyproject.toml Signed-off-by: gcattan <gcattan@hotmail.fr> * updating pyproject * updating tutorial to solve the dependecy issue * solving zhou? * trying again * updating again with zhou * updating the pyproject * bye python 3.9 * updating the pyproject * removing dep * Update pyproject.toml Signed-off-by: gcattan <gcattan@hotmail.fr> * Update Zhou2016.py try read_raw_ant Signed-off-by: gcattan <gcattan@hotmail.fr> * Update pyproject.toml Signed-off-by: gcattan <gcattan@hotmail.fr> * Update Zhou2016.py replace list by regex Signed-off-by: gcattan <gcattan@hotmail.fr> * updating .gitignore * changing to another dataset * fixing last tutorial * last adjust * removing the new library dep * reverting examples * updating the examples * updating tutorials 1 * updating the zhou * removing * solving results parallel issue * updating the what's new file * changing the evaluation .utils * open lock everywhere * logger and not print please * solving print vs logging * changing in the logger * more things to improve the tests * solving issue with logger * solving future warning of evaluation * updating for new version * updating the citation --------- Signed-off-by: gcattan <gcattan@hotmail.fr> Co-authored-by: gcattan <gcattan@hotmail.fr> * Update evaluation to use new splitters and include updates (#769) * updating evaluation to use new splitters * cross-subject * including the whats new * updating the whats new * Update docs/source/whats_new.rst Co-authored-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Signed-off-by: Bru <b.aristimunha@gmail.com> * simple fit for everybody * updating the splitter * parallel evaluation now * solving the small issue * updating the evaluation * adjusting in the other evaluation too * updating * updating the evaluations * Apply suggestions from code review Co-authored-by: Thomas Moreau <thomas.moreau.2010@gmail.com> Signed-off-by: Bru <b.aristimunha@gmail.com> * updating base * updating the pyproject * trying to solve this shit... * crazy things here.. * too much things at the same time * reverting * evaluation * including acceptance test * forcing two reference results * reverting small detail * updating the pyproject * upgrading the mne version * solving issue with saving * scoring * fixing import --------- Signed-off-by: Bru <b.aristimunha@gmail.com> Signed-off-by: Bru <a.bruno@aluno.ufabc.edu.br> Co-authored-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Co-authored-by: Thomas Moreau <thomas.moreau.2010@gmail.com> * Add BNCI2003_004 dataset (BCI Competition III Dataset IVa) (#811) * Add BCICIII IVa dataset loader and export * Initial commit * Updated docstring * Added import for BCICIII_IVa * [pre-commit.ci] auto fixes from pre-commit.com hooks * Updated docs * Changed name of class and references * Updated references * Updated reference * [pre-commit.ci] auto fixes from pre-commit.com hooks * Implemented new class and loader functions for BNCI2003_IVa dataset * Imported BNCI2003_IVa class from .bnci * [pre-commit.ci] auto fixes from pre-commit.com hooks * Remove bnci2003.py (moved BNCI2003_IVa to bnci.py) * Removed import from deleted file bnci2003.py * Apply suggestions from code review Signed-off-by: Bru <b.aristimunha@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks * Updated motor imagery table with BNCI2003_IVa dataset * Update moabb/datasets/summary_imagery.csv Signed-off-by: Bru <b.aristimunha@gmail.com> * solving the issue with reading in parallel * updating and fixing the tests * not my day * no parallel test --------- Signed-off-by: Bru <b.aristimunha@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Bru <b.aristimunha@gmail.com> * Add auditory ERP dataset (Kojima2024A) (#807) * add Kojima2024A dataset * add what's new entry for Kojima2024A dataset * merge Kojima2024A parent and child into a single class * add a test for Kojima2024A --------- Signed-off-by: Bru <a.bruno@aluno.ufabc.edu.br> Co-authored-by: Simon Kojima <simon.kojima@inria.fr> Co-authored-by: Bru <a.bruno@aluno.ufabc.edu.br> * [BUG] swap the labels of '17' and '21' (#814) * swap the labels of '17' and '21' * Adding logs on the what's new file * updating the request informations * [pre-commit.ci] auto fixes from pre-commit.com hooks --------- Co-authored-by: Bru <b.aristimunha@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add auditory ERP dataset (Kojima2024B) (#806) * add Kojima2024B datasets * add what's new entry for Kojima2024B_2stream and Kojima2024B_4stream datasets * [pre-commit.ci] auto fixes from pre-commit.com hooks * add note for keep_trial_structure=True option * add a test for Kojima2024B * remove unnecessary comments * show document for convert_subject_to_subject_id method in child class * add _get_run_num_for_task * implement events encoding * add get_data_with_events_info method * Implement Option 1 Add multiclass to P300 Add get_block_rep at dataset level * [pre-commit.ci] auto fixes from pre-commit.com hooks * check for event_id not found * [pre-commit.ci] auto fixes from pre-commit.com hooks * remove debug trace * handle scalar * Update kojima2024b.py Signed-off-by: gcattan <gcattan@hotmail.fr> * update documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks * fix not implemented error in fake vr dataset * [pre-commit.ci] auto fixes from pre-commit.com hooks * remove outdated test * Update moabb/datasets/kojima2024b.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Signed-off-by: gcattan <gcattan@hotmail.fr> * Update moabb/paradigms/p300.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Signed-off-by: gcattan <gcattan@hotmail.fr> * Update kojima2024b.py Signed-off-by: gcattan <gcattan@hotmail.fr> * [pre-commit.ci] auto fixes from pre-commit.com hooks * add task specific data loading option --------- Signed-off-by: Simon Kojima <38077652+simonkojima@users.noreply.github.com> Signed-off-by: gcattan <gcattan@hotmail.fr> Co-authored-by: Simon Kojima <simon.kojima@inria.fr> Co-authored-by: Bru <a.bruno@aluno.ufabc.edu.br> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Gregoire Cattan <gregoire.cattan@ibm.com> Co-authored-by: gcattan <gcattan@hotmail.fr> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#819) updates: - [github.com/pre-commit/pre-commit-hooks: v5.0.0 → v6.0.0](https://github.com/pre-commit/pre-commit-hooks/compare/v5.0.0...v6.0.0) - https://github.com/psf/black → https://github.com/psf/black-pre-commit-mirror - [github.com/psf/black-pre-commit-mirror: 25.1.0 → 25.9.0](https://github.com/psf/black-pre-commit-mirror/compare/25.1.0...25.9.0) - [github.com/asottile/blacken-docs: 1.19.1 → 1.20.0](https://github.com/asottile/blacken-docs/compare/1.19.1...1.20.0) - [github.com/PyCQA/isort: 6.0.1 → 6.1.0](https://github.com/PyCQA/isort/compare/6.0.1...6.1.0) - [github.com/astral-sh/ruff-pre-commit: v0.12.2 → v0.13.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.12.2...v0.13.3) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Fix issues in Dreyer2023 dataset (#828) * fix issue where run6 was not being loaded in Dreyer2023 dataset class * update what's new * fix channel montage * fix interval * update what's new --------- Co-authored-by: Simon Kojima <simon.kojima@inria.fr> * Document pyRiemann 0.9 and numpy 2.0 compatibility update in changelog (#821) * Initial plan * Document pyRiemann 0.9 and numpy 2.0 compatibility update Co-authored-by: bruAristimunha <42702466+bruAristimunha@users.noreply.github.com> * Update whats_new.rst Signed-off-by: gcattan <gcattan@hotmail.fr> --------- Signed-off-by: gcattan <gcattan@hotmail.fr> Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: bruAristimunha <42702466+bruAristimunha@users.noreply.github.com> Co-authored-by: gcattan <gcattan@hotmail.fr> Co-authored-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> * Easier handling of pipelines for benchmark() (#826) * Support for providing the pipelines programmatically and not only from a folder using a separate file per pipeline. * Improved doc section. * updated whats new * [pre-commit.ci] auto fixes from pre-commit.com hooks * small fix * typo fix * Apply suggestions from code review Co-authored-by: Quentin Barthélemy <q.barthelemy@gmail.com> Signed-off-by: Bru <b.aristimunha@gmail.com> --------- Signed-off-by: Bru <b.aristimunha@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Bru <b.aristimunha@gmail.com> Co-authored-by: Quentin Barthélemy <q.barthelemy@gmail.com> Co-authored-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> * Pre-release 1.4.0 (#831) * Release V1.2.0 (#714) * [MNT] update to release * [MNT] update to release * [MNT] single readme file * [MNT] typo * Apply suggestions from code review Co-authored-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Signed-off-by: Bru <b.aristimunha@gmail.com> * [MNT] version control * Single readme and contributing webpage * [pre-commit.ci] auto fixes from pre-commit.com hooks * removing docker, no one is using. * removing docker, no one is using. * removing poetry * external example * Hard fix * skipped test to release * V1.2.0 (#713) * [MNT] Sync v1.2.0 (#712) * develop into master v1.1.1 (#645) * Fix workflow cache (#632) * Copy workflow changes from PR #584 * Update whats_new.rst * Remove "always deploy" used for testing * Restore change to pytest instead of unittest * Use mne data cache in tests too * Remove duplicate restore cache (#634) * Fix example Hinss2021 (#636) * Dataset summary in CSV and leaderboard links (#635) * Add summary tables as csv * Change BaseDataset to include the dataset's summary table in the docstring * Try update summary table in doc * Add test for dataset summary table * Fix future annotations * Prepare summary tables before doc * Make build dir if not exist * Add rstate table * Replace tables with CSVs in doc * Add PapersWithCOde column * Fix initial white space * Fix formatting of ints * Remove tables from docstrings * Add missing DemonsP300 row * Update whats_new.rst * Remove Shin2017B leaderboard * Move PWC link outside of docstring table * Add Liu2024 Dataset (#619) * including Liu2024 Dataset * [pre-commit.ci] auto fixes from pre-commit.com hooks * Function data_path * [pre-commit.ci] auto fixes from pre-commit.com hooks * data_infos and get_single_subject_data functions * [pre-commit.ci] auto fixes from pre-commit.com hooks * Data Description * [pre-commit.ci] auto fixes from pre-commit.com hooks * updating get_single_subject fct and data_path & adding encoding fct * [pre-commit.ci] auto fixes from pre-commit.com hooks * Finishing the code * [pre-commit.ci] auto fixes from pre-commit.com hooks * updating docstrings for data_path * Updating dataset_summary and updating the get_single_subject fct to handle the case of existing file in path_electrodes * adapting the return of get_single_subject_data fct * [pre-commit.ci] auto fixes from pre-commit.com hooks * Adding dataset description and preload = True when reading the data in the get_single_subject fct * fix: codespell * fix: changing to static method the encoding * repushing and resolving pre-commit conflicts * [pre-commit.ci] auto fixes from pre-commit.com hooks * fix: changing the mapping * fix: changing the unmatching between the trigger and the events from the csv * ehn: using pylint to improve the code (remove not used variables, and change the module); * modifying the python version in the pre-commit file * adding description to enhancements * adjusting the encoding * adjusting comments and dataset description * solving channels types and names issues & correcting encoding * Correcting the number of trials per class and the total trials * Correcting data description * Adding the possibility to exclude/include break and instructions events * Correcting code to include/exclude instr and break events * Remove table from docstring Signed-off-by: PierreGtch <25532709+PierreGtch@users.noreply.github.com> * Add CSV row --------- Signed-off-by: PierreGtch <25532709+PierreGtch@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: bruAristimunha <a.bruno@aluno.ufabc.edu.br> Co-authored-by: PierreGtch <25532709+PierreGtch@users.noreply.github.com> Co-authored-by: Pierre Guetschel <pierre.guetschel@donders.ru.nl> * Add scripts to publish results on PaperWithCode (#561) * Add scripts to publish results on paperwithcode * Create tasks manually instead (API error 403 forbidden) * Try to create the evaluation first and other things, not working... * Update whats_new.rst * Fix example from API's README; still results in a "403 Forbidden" * Fix task_id * Allow passing multiple results files * Save commands used as comments * Add comment --------- Signed-off-by: PierreGtch <25532709+PierreGtch@users.noreply.github.com> Signed-off-by: Bru <a.bruno@aluno.ufabc.edu.br> Co-authored-by: Bru <a.bruno@aluno.ufabc.edu.br> * [pre-commit.ci] pre-commit autoupdate (#631) * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.5.0...v4.6.0) - [github.com/psf/black: 24.3.0 → 24.4.2](https://github.com/psf/black/compare/24.3.0...24.4.2) - [github.com/asottile/blacken-docs: 1.16.0 → 1.18.0](https://github.com/asottile/blacken-docs/compare/1.16.0...1.18.0) - [github.com/PyCQA/flake8: 7.0.0 → 7.1.0](https://github.com/PyCQA/flake8/compare/7.0.0...7.1.0) - [github.com/astral-sh/ruff-pre-commit: v0.3.5 → v0.5.0](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.5...v0.5.0) - [github.com/codespell-project/codespell: v2.2.6 → v2.3.0](https://github.com/codespell-project/codespell/compare/v2.2.6...v2.3.0) * FIX: including new word * including --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Bru <a.bruno@aluno.ufabc.edu.br> * Optuna GridSearch (#630) * Optuna * [pre-commit.ci] auto fixes from pre-commit.com hooks * Optuna - Categorical Distibution * [pre-commit.ci] auto fixes from pre-commit.com hooks * Add optuna to dependency and regenerate poetry * Add optuna to dependency and regenerate poetry * Add optuna to dependency and regenerate poetry * Add test on within Session * [pre-commit.ci] auto fixes from pre-commit.com hooks * Add test on within Session * Add test on within Session * ehn: common function with dict * ehn: moving function to util * fix: correcting the what news file. * Add test benchmark and raise an issue if the conversion didn't worked and exposed time_out parameter * [pre-commit.ci] auto fixes from pre-commit.com hooks * FIX: italian to eng * EHN: making optuna optional * FIX: fixing the workflow files * FIX: changing the optuna file * FIX: including optuna for the windows --------- Signed-off-by: Bru <a.bruno@aluno.ufabc.edu.br> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: bruAristimunha <a.bruno@aluno.ufabc.edu.br> * correct name (#642) * V1.1.1 (#644) * release 1.1.1 * increase the version * increase the version * removing the poetry.lock * increase version * changing the CITATION.cff * upload versino for artifact * pylock -> pyproject.toml --------- Signed-off-by: PierreGtch <25532709+PierreGtch@users.noreply.github.com> Signed-off-by: Bru <a.bruno@aluno.ufabc.edu.br> Co-authored-by: PierreGtch <25532709+PierreGtch@users.noreply.github.com> Co-authored-by: Taha Habib <95372659+tahatt13@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Pierre Guetschel <pierre.guetschel@donders.ru.nl> Co-authored-by: Igor Carrara <94047258+carraraig@users.noreply.github.com> Co-authored-by: Quentin Barthélemy <q.barthelemy@gmail.com> * V1.2.0 (#708) * [MNT] update to release * [MNT] update to release * [MNT] single readme file * [MNT] typo * Apply suggestions from code review Co-authored-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Signed-off-by: Bru <b.aristimunha@gmail.com> * [MNT] version control * Single readme and contributing webpage * [pre-commit.ci] auto fixes from pre-commit.com hooks * removing docker, no one is using. * removing docker, no one is using. * removing poetry * external example --------- Signed-off-by: Bru <b.aristimunha@gmail.com> Signed-off-by: Bru <a.bruno@aluno.ufabc.edu.br> Co-authored-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Hard fix * skipped test to release * fixing issue with master * fixing issue with master part 2 --------- Signed-off-by: PierreGtch <25532709+PierreGtch@users.noreply.github.com> Signed-off-by: Bru <a.bruno@aluno.ufabc.edu.br> Signed-off-by: Bru <b.aristimunha@gmail.com> Co-authored-by: PierreGtch <25532709+PierreGtch@users.noreply.github.com> Co-authored-by: Taha Habib <95372659+tahatt13@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Pierre Guetschel <pierre.guetschel@donders.ru.nl> Co-authored-by: Igor Carrara <94047258+carraraig@users.noreply.github.com> Co-authored-by: Quentin Barthélemy <q.barthelemy@gmail.com> * Solving the tdlda situation * renaming --------- Signed-off-by: PierreGtch <25532709+PierreGtch@users.noreply.github.com> Signed-off-by: Bru <a.bruno@aluno.ufabc.edu.br> Signed-off-by: Bru <b.aristimunha@gmail.com> Co-authored-by: PierreGtch <25532709+PierreGtch@users.noreply.github.com> Co-authored-by: Taha Habib <95372659+tahatt13@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Pierre Guetschel <pierre.guetschel@donders.ru.nl> Co-authored-by: Igor Carrara <94047258+carraraig@users.noreply.github.com> Co-authored-by: Quentin Barthélemy <q.barthelemy@gmail.com> --------- Signed-off-by: Bru <b.aristimunha@gmail.com> Signed-off-by: Bru <a.bruno@aluno.ufabc.edu.br> Signed-off-by: PierreGtch <25532709+PierreGtch@users.noreply.github.com> Co-authored-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Taha Habib <95372659+tahatt13@users.noreply.github.com> Co-authored-by: Pierre Guetschel <pierre.guetschel@donders.ru.nl> Co-authored-by: Igor Carrara <94047258+carraraig@users.noreply.github.com> Co-authored-by: Quentin Barthélemy <q.barthelemy@gmail.com> * Fix incomplete merge in pyproject.toml * Skip tests due to network issues with dataverse.harvard.edu (#835) * skip connection * [pre-commit.ci] auto fixes from pre-commit.com hooks --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --------- Signed-off-by: Bru <b.aristimunha@gmail.com> Signed-off-by: Bru <a.bruno@aluno.ufabc.edu.br> Signed-off-by: PierreGtch <25532709+PierreGtch@users.noreply.github.com> Signed-off-by: Pierre Guetschel <25532709+PierreGtch@users.noreply.github.com> Signed-off-by: Alexander de Ranitz <89586187+alexander-de-ranitz@users.noreply.github.com> Signed-off-by: jellymace <thomas.kooiman@icloud.com> Signed-off-by: Paul Verhoeven <43268349+PaulusBoskabouter@users.noreply.github.com> Signed-off-by: Lucas Heck <lucasheck17@gmail.com> Signed-off-by: lionel kusch <lionel.kusch@grenoble-inp.org> Signed-off-by: gcattan <gcattan@hotmail.fr> Signed-off-by: Simon Kojima <38077652+simonkojima@users.noreply.github.com> Co-authored-by: bruAristimunha <a.bruno@aluno.ufabc.edu.br> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Taha Habib <95372659+tahatt13@users.noreply.github.com> Co-authored-by: Igor Carrara <94047258+carraraig@users.noreply.github.com> Co-authored-by: Quentin Barthélemy <q.barthelemy@gmail.com> Co-authored-by: Sylvain Chevallier <sylvain.chevallier@universite-paris-saclay.fr> Co-authored-by: Sylvain Chevallier <sylain.chevallier@universite-paris-saclay.fr> Co-authored-by: Sara Sedlar <sara.sedlar@gmail.com> Co-authored-by: Bru <b.aristimunha@gmail.com> Co-authored-by: Samuel-Boehm <74181211+Samuel-Boehm@users.noreply.github.com> Co-authored-by: Thomas Moreau <thomas.moreau.2010@gmail.com> Co-authored-by: gcattan <gcattan@hotmail.fr> Co-authored-by: Theodore Papadopoulo <Theodore.Papadopoulo@inria.fr> Co-authored-by: Zheyu Yao <44063007+zyao197@users.noreply.github.com> Co-authored-by: Emanuele Frasca <noostale@live.it> Co-authored-by: Lucas Heck <lucasheck17@gmail.com> Co-authored-by: Alexander de Ranitz <89586187+alexander-de-ranitz@users.noreply.github.com> Co-authored-by: Amar Enkhbat <38126496+amar-enkhbat@users.noreply.github.com> Co-authored-by: Thomas Kooiman <thomas.kooiman@icloud.com> Co-authored-by: Paul Verhoeven <43268349+PaulusBoskabouter@users.noreply.github.com> Co-authored-by: PaulusBoskabouter <paul_2000@hotmail.nl> Co-authored-by: Ulysse Durand <61126385+UlysseDurand@users.noreply.github.com> Co-authored-by: Ulysse Durand <ulysse.durand@ens-lyon.fr> Co-authored-by: lionel kusch <lionel.kusch@grenoble-inp.org> Co-authored-by: toncho11 <toncho11@users.noreply.github.com> Co-authored-by: TessvandeVijver <160933114+TessvandeVijver@users.noreply.github.com> Co-authored-by: Griffin Keeler <144262024+griffinkeeler@users.noreply.github.com> Co-authored-by: Simon Kojima <38077652+simonkojima@users.noreply.github.com> Co-authored-by: Simon Kojima <simon.kojima@inria.fr> Co-authored-by: Kosei Nakada <76725154+ponpopon@users.noreply.github.com> Co-authored-by: Gregoire Cattan <gregoire.cattan@ibm.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com> Co-authored-by: bruAristimunha <42702466+bruAristimunha@users.noreply.github.com>
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This tutorial is a minimal example of how to use features from the mne-feature library in a pipeline. This tutorial follows tutorial 3 closely, except for the pipelines used.
This PR is made as part of the advanced BCI course at Radboud University @PierreGtch