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 <[email protected]> * Add CSV row --------- Signed-off-by: PierreGtch <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: bruAristimunha <[email protected]> Co-authored-by: PierreGtch <[email protected]> Co-authored-by: Pierre Guetschel <[email protected]> * 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 <[email protected]> Signed-off-by: Bru <[email protected]> Co-authored-by: Bru <[email protected]> * [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](pre-commit/pre-commit-hooks@v4.5.0...v4.6.0) - [github.com/psf/black: 24.3.0 → 24.4.2](psf/black@24.3.0...24.4.2) - [github.com/asottile/blacken-docs: 1.16.0 → 1.18.0](adamchainz/blacken-docs@1.16.0...1.18.0) - [github.com/PyCQA/flake8: 7.0.0 → 7.1.0](PyCQA/flake8@7.0.0...7.1.0) - [github.com/astral-sh/ruff-pre-commit: v0.3.5 → v0.5.0](astral-sh/ruff-pre-commit@v0.3.5...v0.5.0) - [github.com/codespell-project/codespell: v2.2.6 → v2.3.0](codespell-project/codespell@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 <[email protected]> * 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 <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: bruAristimunha <[email protected]> * 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 <[email protected]> Signed-off-by: Bru <[email protected]> Co-authored-by: PierreGtch <[email protected]> Co-authored-by: Taha Habib <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Pierre Guetschel <[email protected]> Co-authored-by: Igor Carrara <[email protected]> Co-authored-by: Quentin Barthélemy <[email protected]>
NeuroTechX · Sep 17, 2024 · d2c980d · d2c980d
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diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -1,23 +1,27 @@
 name: Docs
-
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
   cancel-in-progress: true
 
+
 on:
   push:
-    branches: [master, develop]
+    branches: [ master, develop ]
   pull_request:
-    branches: [master, develop]
+    branches: [ master, develop ]
+permissions:
+  contents: write
+  pages: write
+  id-token: write
 
 jobs:
   build_docs:
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: true
       matrix:
-        os: [ubuntu-latest]
-        python-version: ["3.9"]
+        os: [ ubuntu-latest ]
+        python-version: [ "3.9" ]
 
     steps:
       - uses: actions/checkout@v4
@@ -27,7 +31,7 @@ jobs:
           mkdir ~/mne_data
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -37,63 +41,79 @@ jobs:
           virtualenvs-create: true
           virtualenvs-in-project: true
 
-      - name: Cache datasets and docs
-        id: cached-dataset-docs
+      - name: Create/Restore MNE Data Cache
+        id: cache-mne_data
+        uses: actions/cache@v3
+        with:
+          path: ~/mne_data
+          key: ${{ runner.os }}-mne_data
+
+      - name: Cache docs build
+        id: cache-docs
         uses: actions/cache@v3
         with:
-          key: doc-${{ github.head_ref }}-${{ hashFiles('moabb/datasets/**') }}
-          path: |
-            ~/mne_data
-            docs/build
+          key: docs-build-${{ github.run_id }}-${{ github.run_attempt }}
+          path: docs/build
+
+      - name: Load cached venv
+        id: cached-poetry-dependencies
+        uses: actions/cache@v3
+        with:
+          path: .venv
+          key:
+            docsvenv-${{ matrix.os }}-py${{matrix.python-version}}-${{
+            hashFiles('**/pyproject.toml') }}
 
       - name: Install dependencies
-        if: steps.cached-dataset-docs.outputs.cache-hit != 'true'
-        run: poetry install --no-interaction --no-root --with docs --extras deeplearning
+        if: (steps.cached-poetry-dependencies.outputs.cache-hit != 'true')
+        run: poetry install --no-interaction --no-root --with docs --extras deeplearning --extras optuna
 
       - name: Install library
-        run: poetry install --no-interaction --with docs --extras deeplearning
+        run: poetry install --no-interaction --with docs --extras deeplearning --extras optuna
 
       - name: Build docs
         run: |
           cd docs && poetry run make html
 
       # Create an artifact of the html output.
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         with:
           name: DocumentationHTML
           path: docs/build/html/
 
-  deploy_docs:
-    if: ${{ github.ref == 'refs/heads/master' }}
+  deploy_neurotechx:
+    if: ${{ github.ref == 'refs/heads/develop' }}
     needs: build_docs
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest]
+        os: [ ubuntu-latest ]
 
     steps:
       - uses: actions/checkout@v4
 
-      - name: Create local data folder
-        run: |
-          mkdir ~/mne_data
-
-      - name: Cache datasets and docs
-        id: cached-dataset-docs
-        uses: actions/cache@v3
+      - name: Restore cached docs build
+        id: cache-docs
+        uses: actions/cache/restore@v3
         with:
-          key: doc-${{ github.head_ref }}-${{ hashFiles('moabb/datasets/**') }}
-          path: |
-            ~/mne_data
-            docs/build
+          key: docs-build-${{ github.run_id }}-${{ github.run_attempt }}
+          path: docs/build
 
-      - name: Checkout moabb.github.io
-        uses: actions/checkout@v4
+      - name: Check cache hit
+        if: steps.cache-docs.outputs.cache-hit != 'true'
+        run: exit 1
+
+      - name: Deploy Neurotechx Subpage
+        uses: peaceiris/actions-gh-pages@v4
         with:
-          repository: "NeuroTechX/moabb.github.io"
-          path: moabb-ghio
-          token: ${{ secrets.MOABB_GHIO }}
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          deploy_key: ${{ secrets.ACTIONS_DEPLOY_KEY }}
+          external_repository: NeuroTechX/moabb.github.io
+          destination_dir: docs/
+          publish_branch: master
+          publish_dir: ./docs/build/html
+          cname: moabb.neurotechx.com/
 
   deploy_gh_pages:
     if: ${{ github.ref == 'refs/heads/develop' }}
@@ -102,47 +122,28 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest]
+        os: [ ubuntu-latest ]
 
     steps:
       - uses: actions/checkout@v4
 
-      - name: Create local data folder
-        run: |
-          mkdir ~/mne_data
-
-      - name: Cache datasets and docs
-        id: cached-dataset-docs
-        uses: actions/cache@v3
+      - name: Restore cached docs build
+        id: cache-docs
+        uses: actions/cache/restore@v3
         with:
-          key: doc-${{ github.head_ref }}-${{ hashFiles('moabb/datasets/**') }}
-          path: |
-            ~/mne_data
-            docs/build
+          key: docs-build-${{ github.run_id }}-${{ github.run_attempt }}
+          path: docs/build
 
-      - name: Checkout gh pages
-        uses: actions/checkout@v4
-        with:
-          ref: gh-pages
-          path: moabb-ghpages
+      - name: Check cache hit
+        if: steps.cache-docs.outputs.cache-hit != 'true'
+        run: exit 1
 
-      - name: Deploy Neurotechx Subpage
-        uses: peaceiris/actions-gh-pages@v3
+      - name: Deploy gh-pages
+        uses: peaceiris/actions-gh-pages@v4
         with:
-          deploy_key: ${{ secrets.ACTIONS_DEPLOY_KEY }}
-          external_repository: NeuroTechX/moabb.github.io
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          deploy_key: ${{ secrets.MOABB_DEPLOY_KEY_NEW }}
           destination_dir: docs/
-          publish_branch: master
+          publish_branch: gh-pages
           publish_dir: ./docs/build/html
-          cname: moabb.neurotechx.com/
-
-      - name: Deploy on gh-pages
-        run: |
-          git config --global user.email "[email protected]"
-          git config --global user.name "Github Actions"
-          cd ~/work/moabb/moabb/moabb-ghpages
-          rm -Rf docs
-          cp -a ~/work/moabb/moabb/docs/build/html ./docs
-          git add -A
-          git commit -m "GH Actions update of GH pages ($GITHUB_RUN_ID - $GITHUB_RUN_NUMBER)"
-          git push origin gh-pages
+          cname: neurotechx.github.io/moabb/
diff --git a/.github/workflows/test-braindecode.yml b/.github/workflows/test-braindecode.yml
@@ -1,15 +1,13 @@
 name: Test-braindecode
-
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
   cancel-in-progress: true
 
-
 on:
   push:
-    branches: [develop]
+    branches: [ develop ]
   pull_request:
-    branches: [develop]
+    branches: [ develop ]
 
 jobs:
   test:
@@ -18,8 +16,8 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        os: [ubuntu-latest]
-        python-version: ["3.8"]
+        os: [ ubuntu-latest ]
+        python-version: [ "3.8" ]
     defaults:
       run:
         shell: bash
@@ -33,8 +31,21 @@ jobs:
           repository: braindecode/braindecode
           path: braindecode
 
+      - name: Create local data folder
+        if: runner.os != 'Windows'
+        run: |
+          mkdir ~/mne_data
+
+      - name: Create/Restore MNE Data Cache
+        if: runner.os != 'Windows'
+        id: cache-mne_data
+        uses: actions/cache@v3
+        with:
+          path: ~/mne_data
+          key: ${{ runner.os }}-mne_data
+
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -44,22 +55,15 @@ jobs:
           virtualenvs-create: true
           virtualenvs-in-project: true
 
-      - name: Create/Restore MNE Data Cache
-        id: cache-mne_data
-        uses: actions/cache@v3
-        with:
-          path: ~/mne_data
-          key: ${{ runner.os }}-mne
-
       - name: Load cached venv
         if: runner.os != 'Windows'
         id: cached-poetry-dependencies
         uses: actions/cache@v3
         with:
           path: .venv
           key:
-            testvenv-${{ matrix.os }}-py${{matrix.python-version}}-${{
-            hashFiles('**/poetry.lock') }}
+            testvenv-braindecode-${{ matrix.os }}-py${{matrix.python-version}}-${{
+            hashFiles('**/pyproject.toml') }}
 
       - name: Install dependencies
         if: |

diff --git a/.github/workflows/test-devel.yml b/.github/workflows/test-devel.yml
@@ -1,15 +1,13 @@
 name: Test-devel
-
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
   cancel-in-progress: true
 
-
 on:
   push:
-    branches: [develop]
+    branches: [ develop ]
   pull_request:
-    branches: [develop]
+    branches: [ develop ]
 
 jobs:
   test:
@@ -18,16 +16,29 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        os: [ubuntu-latest, windows-latest, macOS-latest]
-        python-version: ["3.9", "3.10"]
+        os: [ ubuntu-latest, windows-latest, macOS-latest ]
+        python-version: [ "3.9", "3.10" ]
     defaults:
       run:
         shell: bash
     steps:
       - uses: actions/checkout@v4
 
+      - name: Create local data folder
+        if: runner.os != 'Windows'
+        run: |
+          mkdir ~/mne_data
+
+      - name: Create/Restore MNE Data Cache
+        if: runner.os != 'Windows'
+        id: cache-mne_data
+        uses: actions/cache@v3
+        with:
+          path: ~/mne_data
+          key: ${{ runner.os }}-mne_data
+
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -45,21 +56,21 @@ jobs:
           path: .venv
           key:
             testvenv-${{ matrix.os }}-py${{matrix.python-version}}-${{
-            hashFiles('**/poetry.lock') }}
+            hashFiles('**/pyproject.toml') }}
 
       - name: Install dependencies
         if: |
           (runner.os != 'Windows') &&
           (steps.cached-poetry-dependencies.outputs.cache-hit != 'true')
-        run: poetry install --no-interaction --no-root --extras deeplearning
+        run: poetry install --no-interaction --no-root --extras deeplearning --extras optuna
 
       - name: Install library (Linux/OSX)
         if: ${{ runner.os != 'Windows' }}
-        run: poetry install --no-interaction --extras deeplearning
+        run: poetry install --no-interaction --extras deeplearning --extras optuna
 
       - name: Install library (Windows)
         if: ${{ runner.os == 'Windows' }}
-        run: poetry install --no-interaction
+        run: poetry install --no-interaction --extras optuna
 
       - name: Run tests
         run: |