WIP

.flake8

@@ -1,2 +1,25 @@
 [flake8]
-exclude = .git,__pycache__,build,dist,versioneer.py,bidsonym/_version.py,docs/source/conf.py
+max-line-length = 79
+
+ignore =
+    # these rules don't play well with black
+    # whitespace before ':'
+    E203,
+    # line break before binary operator
+    W503,
+    E241,E305,W504,W605,E731
+
+exclude =
+    .git,
+    .github,
+    .pytest_cache,
+    pycrostates.egg-info,
+    setup.py,
+    docs/source/conf.py,
+    versioneer.py,
+    _version.py
+
+per-file-ignores =
+    # __init__.py files are allowed to have unused imports and lines-too-long
+    */__init__.py:F401
+    */**/__init__.py:F401,E501

.github/workflows/build.yml

@@ -0,0 +1,60 @@
+name: build
+# https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#concurrency
+# https://docs.github.com/en/developers/webhooks-and-events/events/github-event-types#pullrequestevent
+# workflow name, PR number (empty on push), push ref (empty on PR)
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+on:
+  pull_request:
+  push:
+    branches: [main, master]
+  workflow_dispatch:
+
+jobs:
+  build:
+    timeout-minutes: 30
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu]
+        python-version: [3.8, 3.9, "3.10", "3.11"]
+    name: ${{ matrix.os }} - ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}-latest
+    defaults:
+      run:
+        shell: bash
+
+    env:
+      SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL : "True"
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+      - name: Setup Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: 'x64'
+      - name: Install dependencies
+        run: |
+          python -m pip install --progress-bar off --upgrade pip setuptools wheel
+          python -m pip install --progress-bar off .[build]
+      - name: Test package install
+        run: python -c "import bidsonym; print(bidsonym.__version__)"
+      - name: Remove package install
+        run: python -m pip uninstall -y bidsonym
+      - name: Build package
+        run: python -m build
+      - name: Install sdist
+        run: pip install ./dist/*.tar.gz
+      - name: Test sdist install
+        run: python -c "import bidsonym; print(bidsonym.__version__)"
+      - name: Remove sdist install
+        run: python -m pip uninstall -y bidsonym
+      - name: Install wheel
+        run: pip install ./dist/*.whl
+      - name: Test wheel install
+        run: python -c "import bidsonym; print(bidsonym.__version__)"
+      - name: Remove wheel install
+        run: python -m pip uninstall -y bidsonym

.github/workflows/code-style.yml

@@ -0,0 +1,49 @@
+name: style
+# https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#concurrency
+# https://docs.github.com/en/developers/webhooks-and-events/events/github-event-types#pullrequestevent
+# workflow name, PR number (empty on push), push ref (empty on PR)
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+on:
+  pull_request:
+  push:
+    branches: [main, master]
+  workflow_dispatch:
+
+jobs:
+  style:
+    timeout-minutes: 10
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+      - name: Setup Python 3.9
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+          architecture: 'x64'
+      - name: Install dependencies
+        run: |
+          python -m pip install --progress-bar off --upgrade pip setuptools wheel
+          python -m pip install --progress-bar off .[style]
+      - name: Run flake8
+        uses: py-actions/flake8@v2
+        with:
+          path: "bidsonym"
+      - name: Run isort
+        uses: isort/isort-action@master
+      - name: Run black
+        uses: psf/black@stable
+        with:
+          options: "--check --verbose"
+      - name: Run codespell
+        uses: codespell-project/actions-codespell@master
+        with:
+          check_filenames: true
+          check_hidden: true
+          skip: ./.git,./build,./.github,*.bib
+      - name: Run pydocstyle
+        run: pydocstyle .
+      - name: Run bibclean
+        run: bibclean-check docs/references.bib

.github/workflows/docker.yml

@@ -0,0 +1,52 @@
+name: Docker
+# https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#concurrency
+# https://docs.github.com/en/developers/webhooks-and-events/events/github-event-types#pullrequestevent
+# workflow name, PR number (empty on push), push ref (empty on PR)
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+on:
+  pull_request:
+  push:
+    branches: [main, master]
+  workflow_dispatch:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Make script executable
+        run: chmod +x ./generate_images.sh
+
+      - name: Generate docker file
+        run: ./generate_images.sh
+
+      - name: Log in to Docker Hub
+        uses: docker/[email protected]
+        with:
+          username: gitopsfcbg
+          password: ${{ secrets.CAMPUSBIOTECH_PROD_FLUXCD_DOCKERHUB }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/[email protected]
+        with:
+          images: docker.io/fcbg/${{ github.event.repository.name }}
+
+      - name: Build and push Docker image
+        uses: docker/[email protected]
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+
+      - name: Upload Dockerfile
+        uses: actions/upload-artifact@v3
+        with:
+          name: dockerfile
+          path: Dockerfile

.github/workflows/test.yml

@@ -0,0 +1,42 @@
+name: test
+# https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#concurrency
+# https://docs.github.com/en/developers/webhooks-and-events/events/github-event-types#pullrequestevent
+# workflow name, PR number (empty on push), push ref (empty on PR)
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+on:
+  pull_request:
+  push:
+    branches: [main, master]
+  workflow_dispatch:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Make script executable
+        run: chmod +x ./generate_images.sh
+
+      - name: Generate docker file
+        run: ./generate_images.sh
+
+      - name: Build Docker image
+        run: docker build -t bidsonym_tests .
+
+      - name: Setup Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+          architecture: 'x64'
+      - name: Install test dependencies
+        run: |
+          python -m pip install --progress-bar off --upgrade pip setuptools wheel
+          python -m pip install --progress-bar off docker pytest
+          python -m pip install --progress-bar off .[build]
+      - name: Test
+        run: pytest bidsonym

.gitignore

@@ -1,3 +1,5 @@
+.DS_Store
+
 # Created by .ignore support plugin (hsz.mobi)
 
 # pycharm project settings

AUTHORS.rst

@@ -13,3 +13,4 @@ Contributors
 
 * Kirstie Whitaker 
 * Jean-Baptiste Poline
+* Victor Férat