Merge pull request #510 from NeuroTechX/develop

Stable version 1.0.0
NeuroTechX · Oct 23, 2023 · bb31be3 · bb31be3
2 parents 2a0b97f + 0f8b864
commit bb31be3
Show file tree

Hide file tree

Showing 157 changed files with 9,611 additions and 3,509 deletions.
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -16,7 +16,7 @@ jobs:
         python-version: ["3.9"]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Create local data folder
         run: |
@@ -44,10 +44,10 @@ jobs:
 
       - name: Install dependencies
         if: steps.cached-dataset-docs.outputs.cache-hit != 'true'
-        run: poetry install --no-interaction --no-root --with docs,deeplearning
+        run: poetry install --no-interaction --no-root --with docs --extras deeplearning
 
       - name: Install library
-        run: poetry install --no-interaction --with docs,deeplearning
+        run: poetry install --no-interaction --with docs --extras deeplearning
 
       - name: Build docs
         run: |
@@ -69,7 +69,7 @@ jobs:
         os: [ubuntu-latest]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Create local data folder
         run: |
@@ -85,23 +85,12 @@ jobs:
             docs/build
 
       - name: Checkout moabb.github.io
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: "NeuroTechX/moabb.github.io"
           path: moabb-ghio
           token: ${{ secrets.MOABB_GHIO }}
 
-      - name: Deploy on moabb.neurotechx.com
-        run: |
-          git config --global user.email "ci@neurotechx.com"
-          git config --global user.name "Github Actions"
-          cd ~/work/moabb/moabb/moabb-ghio
-          rm -Rf docs
-          cp -a ~/work/moabb/moabb/docs/build/html ./docs
-          git add -A
-          git commit -m "GH Actions update of docs ($GITHUB_RUN_ID - $GITHUB_RUN_NUMBER)"
-          git push origin master
-
   deploy_gh_pages:
     if: ${{ github.ref == 'refs/heads/develop' }}
     needs: build_docs
@@ -112,7 +101,7 @@ jobs:
         os: [ubuntu-latest]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Create local data folder
         run: |
@@ -128,11 +117,21 @@ jobs:
             docs/build
 
       - name: Checkout gh pages
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: gh-pages
           path: moabb-ghpages
 
+      - name: Deploy Neurotechx Subpage
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          deploy_key: ${{ secrets.ACTIONS_DEPLOY_KEY }}
+          external_repository: NeuroTechX/moabb.github.io
+          destination_dir: docs/
+          publish_branch: master
+          publish_dir: ./docs/build/html
+          cname: moabb.neurotechx.com/
+
       - name: Deploy on gh-pages
         run: |
           git config --global user.email "ci@neurotechx.com"
@@ -143,60 +142,3 @@ jobs:
           git add -A
           git commit -m "GH Actions update of GH pages ($GITHUB_RUN_ID - $GITHUB_RUN_NUMBER)"
           git push origin gh-pages
-
-      - name: Deploy to moabb.neurotechx.com/
-        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/develop'}}
-        uses: peaceiris/actions-gh-pages@v3
-        with:
-          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/
-
-      # Previous test with moabb GH pages, official docs point to moabb.github.io
-      ###########################################################################
-      # Since we want the URL to be neurotechx.github.io/docs/ the html output needs to be put in a ./docs subfolder of the publish_dir
-      # - name: Move docs into site folder
-      #   run: |
-      #     mkdir site
-      #     mv docs/build/html site/docs
-
-      # - name: Deploy on moabb gh-pages
-      #   uses: peaceiris/actions-gh-pages@v3
-      #   if: github.ref == 'refs/heads/master'
-      #   with:
-      #     github_token: ${{ secrets.GITHUB_TOKEN }}
-      #     publish_dir: site
-
-      # Using checkout and push actions, not working
-      ##############################################
-      # - name: Install SSH key
-      #   uses: shimataro/ssh-key-action@v2
-      #   with:
-      #     key: ${{ secrets.MOABB_DOCS_SSH }}
-      #     known_hosts: ${{ secrets.KNOWN_HOST_GH }}
-
-      # - name: Checkout moabb.github.io
-      #   uses: actions/checkout@v2
-      #   with:
-      #     repository: "NeuroTechX/moabb.github.io"
-      #     path: moabb-ghio
-      #     fetch-depth: 0
-      #     persist-credentials: false
-
-      # - name: Add html files
-      #   run: |
-      #     cd ~/work/moabb/moabb/moabb-ghio
-      #     rm -Rf docs
-      #     cp -a ~/work/moabb/moabb/docs/build/html ./docs
-      #     git config --global user.email "ci@neurotechx.com"
-      #     git config --global user.name "Github Actions"
-      #     git commit -m "GH Actions update of docs ($GITHUB_RUN_ID - $GITHUB_RUN_NUMBER)" -a
-
-      # - name: Push
-      #   uses: ad-m/github-push-action@master
-      #   with:
-      #     github_token: ${{ secrets.MOABB_GHIO }}
-      #     repository: "NeuroTechX/moabb.github.io"
diff --git a/.github/workflows/test-braindecode.yml b/.github/workflows/test-braindecode.yml
@@ -0,0 +1,76 @@
+name: Test-braindecode
+
+on:
+  push:
+    branches: [develop]
+  pull_request:
+    branches: [develop]
+
+jobs:
+  test:
+    name: dev ${{ matrix.os }}, py-${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: true
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.8"]
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - name: Checkout MOABB
+        uses: actions/checkout@v4
+
+      - name: Checkout Braindecode
+        uses: actions/checkout@v4
+        with:
+          repository: braindecode/braindecode
+          path: braindecode
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+        with:
+          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') }}
+
+      - name: Install dependencies
+        if: |
+          (runner.os != 'Windows') &&
+          (steps.cached-poetry-dependencies.outputs.cache-hit != 'true')
+        run: poetry install --no-interaction --no-root
+
+      - name: Install library
+        run: poetry install --no-interaction
+
+      - 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/
+
+      # poetry run pip install -U https://api.github.com/repos/braindecode/braindecode/zipball/master
diff --git a/.github/workflows/test-devel.yml b/.github/workflows/test-devel.yml
@@ -19,7 +19,7 @@ jobs:
       run:
         shell: bash
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Setup Python
         uses: actions/setup-python@v4
@@ -46,11 +46,11 @@ jobs:
         if: |
           (runner.os != 'Windows') &&
           (steps.cached-poetry-dependencies.outputs.cache-hit != 'true')
-        run: poetry install --no-interaction --no-root --with deeplearning
+        run: poetry install --no-interaction --no-root --extras deeplearning
 
       - name: Install library (Linux/OSX)
         if: ${{ runner.os != 'Windows' }}
-        run: poetry install --no-interaction --with deeplearning
+        run: poetry install --no-interaction --extras deeplearning
 
       - name: Install library (Windows)
         if: ${{ runner.os == 'Windows' }}

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -19,7 +19,7 @@ jobs:
       run:
         shell: bash
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Setup Python
         uses: actions/setup-python@v4
@@ -46,11 +46,11 @@ jobs:
         if: |
           (runner.os != 'Windows') &&
           (steps.cached-poetry-dependencies.outputs.cache-hit != 'true')
-        run: poetry install --no-interaction --no-root --with deeplearning
+        run: poetry install --no-interaction --no-root --extras deeplearning
 
       - name: Install library (Linux/OSX)
         if: ${{ runner.os != 'Windows' }}
-        run: poetry install --no-interaction --with deeplearning
+        run: poetry install --no-interaction --extras deeplearning
 
       - name: Install library (Windows)
         if: ${{ runner.os == 'Windows' }}

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -8,39 +8,90 @@ ci:
   autoupdate_branch: "develop"
   autoupdate_commit_msg: "[pre-commit.ci] pre-commit autoupdate"
   autoupdate_schedule: quarterly
-  skip: []
+  skip: [ ]
   submodules: false
 
+exclude: ".*svg"
+
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0
     hooks:
       - id: check-yaml
       - id: check-json
+      - id: check-executables-have-shebangs
+      - id: check-toml
+      - id: check-docstring-first
       - id: check-added-large-files
       - id: end-of-file-fixer
       - id: trailing-whitespace
       - id: check-case-conflict
       - id: mixed-line-ending
+      - id: end-of-file-fixer
+      - id: check-case-conflict
+      - id: forbid-new-submodules
+      - id: pretty-format-json
+        args: [ "--autofix", "--no-sort-keys", "--indent=4" ]
+
 
   - repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 23.9.1
     hooks:
       - id: black
+        language_version: python3.8
+        args: [ --line-length=90, --target-version=py38 ]
+
+  -   repo: https://github.com/asottile/blacken-docs
+      rev: 1.16.0
+      hooks:
+      -   id: blacken-docs
+          additional_dependencies: [black==23.3.0]
+          exclude: ^.github/
 
   - repo: https://github.com/PyCQA/isort
     rev: 5.12.0
     hooks:
       - id: isort
 
-  - repo: https://github.com/pycqa/flake8
-    rev: 6.0.0
+  - repo: https://github.com/PyCQA/flake8
+    rev: 6.1.0
     hooks:
       - id: flake8
-        additional_dependencies: [flake8-bugbear]
+        additional_dependencies: [
+          'flake8-blind-except',
+          'flake8-docstrings',
+          'flake8-bugbear',
+          'flake8-comprehensions',
+          'flake8-docstrings',
+          'flake8-implicit-str-concat',
+          'pydocstyle>=5.0.0',
+        ]
+        exclude: ^docs/ | ^setup\.py$ |
 
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.0-alpha.6
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.292
     hooks:
-      - id: prettier
-        args: [--print-width=90, --prose-wrap=always]
+      - id: ruff
+        args: [ --fix, --exit-non-zero-on-fix, --ignore, E501 ]
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
+    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
+          - --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
+    hooks:
+      - id: yamllint
+        exclude: >
+          (?x)^(
+            .pre-commit-config.yaml*|
+            .github/workflows/.*|
+
+          )$