Merge pull request #613 from NeuroTechX/develop

v1.1.0 in master

.github/workflows/docs.yml

@@ -1,5 +1,9 @@
 name: Docs
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+
 on:
   push:
     branches: [master, develop]

.github/workflows/test-braindecode.yml

@@ -1,5 +1,10 @@
 name: Test-braindecode
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+
+
 on:
   push:
     branches: [develop]
@@ -68,9 +73,8 @@ jobs:
       - name: Install and test braindecode
         run: |
           source $VENV
-          poetry run pip install torch
           cd braindecode
-          poetry run pip install -e .[tests]
-          poetry run pytest test/
+          pip install -e .[tests]
+          pytest test/
 
       # poetry run pip install -U https://api.github.com/repos/braindecode/braindecode/zipball/master

.github/workflows/test-devel.yml

@@ -1,5 +1,10 @@
 name: Test-devel
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+
+
 on:
   push:
     branches: [develop]
@@ -14,7 +19,7 @@ jobs:
       fail-fast: true
       matrix:
         os: [ubuntu-latest, windows-latest, macOS-latest]
-        python-version: ["3.8"]
+        python-version: ["3.9", "3.10"]
     defaults:
       run:
         shell: bash
@@ -59,7 +64,7 @@ jobs:
       - name: Run tests
         run: |
           source $VENV
-          poetry run coverage run -m unittest moabb.tests
+          poetry run coverage run -m pytest moabb/tests
           poetry run coverage xml
 
       - name: Run pipelines

.github/workflows/test.yml

@@ -1,5 +1,10 @@
 name: Test
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+
+
 on:
   push:
     branches: [master]
@@ -14,7 +19,7 @@ jobs:
       fail-fast: true
       matrix:
         os: [ubuntu-latest, windows-latest, macOS-latest]
-        python-version: ["3.8", "3.9"]
+        python-version: ["3.9"]
     defaults:
       run:
         shell: bash
@@ -59,7 +64,7 @@ jobs:
       - name: Run tests
         run: |
           source $VENV
-          poetry run coverage run -m unittest moabb.tests
+          poetry run coverage run -m pytest moabb/tests
           poetry run coverage xml
 
       - name: Run pipelines

.github/workflows/whats-new.yml

@@ -0,0 +1,18 @@
+name: Check What's News Changes
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+
+on:
+  pull_request:
+    types: [ assigned, opened, synchronize, reopened, labeled, unlabeled ]
+    branches:
+      - '*'
+jobs:
+  check-whats-news:
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: tarides/changelog-check-action@v2
+        with:
+          changelog: docs/source/whats_new.rst

.gitignore

@@ -115,3 +115,10 @@ analysis/*
 
 # mac os x stuff
 *DS_store*
+
+# local files generated by doc
+docs/source/auto_*/
+docs/source/generated/
+examples/advanced_examples/Results/
+examples/benchmark/
+examples/results/

.pre-commit-config.yaml

@@ -15,7 +15,7 @@ exclude: ".*svg"
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: check-yaml
       - id: check-json
@@ -35,7 +35,7 @@ repos:
 
 
   - repo: https://github.com/psf/black
-    rev: 23.9.1
+    rev: 24.3.0
     hooks:
       - id: black
         language_version: python3.8
@@ -49,12 +49,12 @@ repos:
           exclude: ^.github/
 
   - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
+    rev: 7.0.0
     hooks:
       - id: flake8
         additional_dependencies: [
@@ -69,7 +69,7 @@ repos:
         exclude: ^docs/ | ^setup\.py$ |
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.292
+    rev: v0.3.5
     hooks:
       - id: ruff
         args: [ --fix, --exit-non-zero-on-fix, --ignore, E501 ]
@@ -79,14 +79,14 @@ repos:
     hooks:
       - id: codespell
         args:
-          - --ignore-words-list=additionals,alle,alot,bund,currenty,datas,farenheit,falsy,fo,haa,hass,iif,incomfort,ines,ist,nam,nd,pres,pullrequests,resset,rime,ser,serie,te,technik,ue,unsecure,withing,zar
+          - --ignore-words-list=additionals,alle,alot,bund,currenty,datas,farenheit,falsy,fo,haa,hass,iif,incomfort,ines,ist,nam,nd,pres,pullrequests,resset,rime,ser,serie,te,technik,ue,unsecure,withing,zar,crate
           - --skip="./.*,*.csv,*.json,*.ambr"
           - --quiet-level=2
         exclude_types: [ csv, json, svg ]
         exclude: ^tests/|generated/
 
   - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.32.0
+    rev: v1.35.1
     hooks:
       - id: yamllint
         exclude: >

CITATION.cff

@@ -30,6 +30,9 @@ authors:
 - family-names: "Schirrmeister"
   given-names: "Robin Tibor"
   orcid: "https://orcid.org/0000-0002-5518-7445"
+- family-names: "Kobler"
+  given-names: "Reinmar"
+  orcid: "https://orcid.org/0000-0003-4007-279X"
 - family-names: "Kalunga"
   given-names: "Emmanuel"
   orcid: "https://orcid.org/0000-0001-7522-5253"
@@ -67,7 +70,7 @@ authors:
   given-names: "Sylvain"
   orcid: "https://orcid.org/0000-0003-3027-8241"
 title: "Mother of all BCI Benchmarks"
-version: 1.0.0
-doi: 10.5281/zenodo.XXXXX
-date-released: 2023-10-12
+version: 1.1.0
+doi: 10.5281/zenodo.10034223
+date-released: 2024-05-30
 url: "https://github.com/NeuroTechX/moabb"

README.md

@@ -12,8 +12,12 @@
 **This is an open science project that may evolve depending on the need of the
 community.**
 
+
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10034224.svg)](https://doi.org/10.5281/zenodo.10034224)
 [![Build Status](https://github.com/NeuroTechX/moabb/workflows/Test/badge.svg)](https://github.com/NeuroTechX/moabb/actions?query=branch%3Amaster)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![codecov](https://codecov.io/gh/NeuroTechX/moabb/graph/badge.svg?token=NwHD3ethB5)](https://codecov.io/gh/NeuroTechX/moabb)
 [![PyPI](https://img.shields.io/pypi/v/moabb?color=blue&style=plastic)](https://img.shields.io/pypi/v/moabb)
 [![Downloads](https://pepy.tech/badge/moabb)](https://pepy.tech/project/moabb)
 
@@ -173,12 +177,6 @@ modify the run_docker.sh script to save in another path beyond the root of the p
 default, the script will save the results in the project's root in the folder `results`,
 the datasets in the folder `dataset` and the output in the folder `output`.
 
-### Troubleshooting
-
-Currently pip install moabb fails when pip version < 21, e.g. with 20.0.2 due to an `idna`
-package conflict. Newer pip versions resolve this conflict automatically. To fix this you
-can upgrade your pip version using: `pip install -U pip` before installing `moabb`.
-
 ## Supported datasets
 
 The list of supported datasets can be found here :
@@ -289,7 +287,29 @@ analyze(results)
 
 ## Citing MOABB and related publications
 
-To cite MOABB, you could use the following paper:
+If you use MOABB in your experiments, please cite this library when
+publishing a paper to increase the visibility of open science initiatives:
+
+```
+Aristimunha, B., Carrara, I., Guetschel, P., Sedlar, S., Rodrigues, P., Sosulski, J., Narayanan, D., Bjareholt, E., Quentin, B., Schirrmeister, R. T.,Kalunga, E., Darmet, L., Gregoire, C., Abdul Hussain, A., Gatti, R., Goncharenko, V., Thielen, J., Moreau, T., Roy, Y., Jayaram, V., Barachant,A., & Chevallier, S.
+Mother of all BCI Benchmarks (MOABB), 2023. DOI: 10.5281/zenodo.10034223.
+```
+and here is the Bibtex version:
+```bibtex
+@software{Aristimunha_Mother_of_all_2023,
+ author = {Aristimunha, Bruno and Carrara, Igor and Guetschel, Pierre and Sedlar, Sara and Rodrigues, Pedro and Sosulski, Jan and Narayanan, Divyesh and Bjareholt, Erik and Quentin, Barthelemy and Schirrmeister, Robin Tibor and Kalunga, Emmanuel and Darmet, Ludovic and Gregoire, Cattan and Abdul Hussain, Ali and Gatti, Ramiro and Goncharenko, Vladislav and Thielen, Jordy and Moreau, Thomas and Roy, Yannick and Jayaram, Vinay and Barachant, Alexandre and Chevallier, Sylvain},
+ doi = {10.5281/zenodo.10034223},
+ title = {{Mother of all BCI Benchmarks}},
+ url = {https://github.com/NeuroTechX/moabb},
+ version = {1.1.0},
+ year = {2023}
+ }
+```
+If you want to cite the scientific contributions of MOABB, you could use the following paper:
+
+> Sylvain Chevallier, Igor Carrara, Bruno Aristimunha, Pierre Guetschel, Sara Sedlar, Bruna Junqueira Lopes, Sébastien Velut, Salim Khazem, Thomas Moreau
+> ["The largest EEG-based BCI reproducibility study for open science: the MOABB benchmark"](https://cnrs.hal.science/hal-04537061/)
+> HAL: hal-04537061.
 
 > Vinay Jayaram and Alexandre Barachant.
 > ["MOABB: trustworthy algorithm benchmarking for BCIs."](http://iopscience.iop.org/article/10.1088/1741-2552/aadea0/meta)

contexts/mi_rh_f.yml

@@ -0,0 +1,5 @@
+MotorImagery:
+  n_classes: 2
+  events:
+    - right_hand
+    - feet

docs/source/README.md

@@ -2,7 +2,7 @@
 
 # <p align="center">Mother of all BCI Benchmarks</p>
 
-<p align="center">
+<p align="center" class="large-text">
   <img src="https://raw.githubusercontent.com/bruAristimunha/moabb/new_theme/docs/source/_static/moabb_logo.svg" width="400" height="400" style="display: block; margin: auto;" />
   Build a comprehensive benchmark of popular Brain-Computer Interface (BCI) algorithms applied on an extensive list of freely available EEG datasets.
 </p>
@@ -12,8 +12,10 @@
 **This is an open science project that may evolve depending on the need of the
 community.**
 
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10034224.svg)](https://doi.org/10.5281/zenodo.10034224)
 [![Build Status](https://github.com/NeuroTechX/moabb/workflows/Test/badge.svg)](https://github.com/NeuroTechX/moabb/actions?query=branch%3Amaster)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![codecov](https://codecov.io/gh/NeuroTechX/moabb/graph/badge.svg?token=NwHD3ethB5)](https://codecov.io/gh/NeuroTechX/moabb)
 [![PyPI](https://img.shields.io/pypi/v/moabb?color=blue&style=plastic)](https://img.shields.io/pypi/v/moabb)
 [![Downloads](https://pepy.tech/badge/moabb)](https://pepy.tech/project/moabb)
 
@@ -66,12 +68,6 @@ First, you could take a look at our [tutorials](./auto_tutorials/index.html) tha
 the most important concepts and use cases. Also, we have a gallery of
 [examples](./auto_examples/index.html) available.
 
-### Troubleshooting
-
-Currently pip install moabb fails when pip version < 21, e.g. with 20.0.2 due to an `idna`
-package conflict. Newer pip versions resolve this conflict automatically. To fix this you
-can upgrade your pip version using: `pip install -U pip` before installing `moabb`.
-
 ## Core Team
 
 This project is under the umbrella of [NeuroTechX][link_neurotechx], the international
@@ -138,8 +134,8 @@ fetch(endpoint)
       const img = document.createElement('img');
       img.src = contributor.avatar_url;
       img.alt = contributor.login;
-      img.style.width = '150px';
-      img.style.height = '150px';
+      img.style.width = '100px';
+      img.style.height = '100px';
       img.style.objectFit = 'cover';
       img.style.borderRadius = '50%';
       link.appendChild(img);
@@ -179,6 +175,41 @@ professional development of any and all of our contributors. If you're looking t
 code, try out working collaboratively, or translate your skills to the digital domain,
 we're here to help.
 
+## Citing MOABB and related publications
+
+If you use MOABB in your experiments, please cite this library when
+publishing a paper to increase the visibility of open science initiatives:
+
+> Aristimunha, B., Carrara, I., Guetschel, P., Sedlar, S., Rodrigues, P., Sosulski, J., Narayanan, D., Bjareholt, E., Quentin, B., Schirrmeister, R. T.,Kalunga, E., Darmet, L., Gregoire, C., Abdul Hussain, A., Gatti, R., Goncharenko, V., Thielen, J., Moreau, T., Roy, Y., Jayaram, V., Barachant,A., & Chevallier, S.
+> Mother of all BCI Benchmarks (MOABB), 2023. DOI: 10.5281/zenodo.10034223.
+
+and here is the Bibtex version:
+
+> @software{Aristimunha_Mother_of_all_2023,
+> author = {Aristimunha, Bruno and Carrara, Igor and Guetschel, Pierre and Sedlar, Sara and Rodrigues, Pedro and Sosulski, Jan and Narayanan, Divyesh and Bjareholt, Erik and Quentin, Barthelemy and Schirrmeister, Robin Tibor and Kalunga, Emmanuel and Darmet, Ludovic and Gregoire, Cattan and Abdul Hussain, Ali and Gatti, Ramiro and Goncharenko, Vladislav and Thielen, Jordy and Moreau, Thomas and Roy, Yannick and Jayaram, Vinay and Barachant, Alexandre and Chevallier, Sylvain},
+> doi = {10.5281/zenodo.10034223},
+> title = {{Mother of all BCI Benchmarks}},
+> url = {https://github.com/NeuroTechX/moabb},
+> version = {1.0.0},
+> year = {2023}
+> }
+
+If you want to cite the scientific contributions of MOABB, you could use the following paper:
+
+> Sylvain Chevallier, Igor Carrara, Bruno Aristimunha, Pierre Guetschel, Sara Sedlar, Bruna Junqueira Lopes, Sébastien Velut, Salim Khazem, Thomas Moreau
+> ["The largest EEG-based BCI reproducibility study for open science: the MOABB benchmark"](https://cnrs.hal.science/hal-04537061/)
+> HAL: hal-04537061.
+
+> Vinay Jayaram and Alexandre Barachant.
+> ["MOABB: trustworthy algorithm benchmarking for BCIs."](http://iopscience.iop.org/article/10.1088/1741-2552/aadea0/meta)
+> Journal of neural engineering 15.6 (2018): 066011.
+> [DOI](https://doi.org/10.1088/1741-2552/aadea0)
+
+If you publish a paper using MOABB, please contact us on [gitter][link_gitter] or open an
+issue, and we will add your paper to the
+[dedicated wiki page](https://github.com/NeuroTechX/moabb/wiki/MOABB-bibliography).
+
+
 ## Contact us
 
 If you want to report a problem or suggest an enhancement, we'd love for you to
@@ -191,11 +222,6 @@ happening on a [regular basis](https://github.com/NeuroTechX/moabb/issues/191),
 the link on the gitter channel. We are also on NeuroTechX Slack channel
 [#moabb][link_neurotechx_signup].
 
-## Thank You!
-
-Thank you so much (Danke schön! Merci beaucoup!) for visiting the project and we do hope
-that you'll join us on this amazing journey to build a comprehensive benchmark of popular
-BCI algorithms applied on an extensive list of freely available EEG datasets.
 
 [link_alex_b]: http://alexandre.barachant.org/
 [link_vinay]: https://www.linkedin.com/in/vinay-jayaram-8635aa25

docs/source/_static/css/custom.css

@@ -0,0 +1,10 @@
+.large-text {
+    font-size: 30px;
+}
+
+.bd-main .bd-content .bd-article-container {
+  max-width: 75em;  /* default is 60em */
+}
+.bd-page-width {
+  max-width: 88em;  /* default is 88rem */
+}

docs/source/_templates/custom-template.html

@@ -0,0 +1,6 @@
+<div class="sidebar-message">
+  If you use moabb, remember to <a href="https://neurotechx.github.io/moabb/#citing-moabb-and-related-publications">cite</a>!
+  The largest BCI EEG benchmark dataset is out!
+  Now available on <a href="https://universite-paris-saclay.hal.science/hal-04537061">pre-print version.</a>
+  Check the result webpage <a href="http://moabb.neurotechx.com/docs/paper_results.html">here</a>.
+</div>