Test to merge hugues caps dataset in maelys caps output

.github/dependabot.yaml

@@ -0,0 +1,7 @@
+version: 2
+
+updates:
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: weekly

.github/workflows/lint.yaml

@@ -1,25 +1,20 @@
 name: 'Lint codebase'
+
 on:
   pull_request:
-    branches:
-      - dev
+    branches: [ "dev", "refactoring" ]
   push:
-    branches:
-      - dev
+    branches: [ "dev", "refactoring" ]
+
+permissions:
+  contents: read
+
 jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: '3.8'
-      - name: Install environment
-        run: |
-          python -m ensurepip
-          python -m pip install poetry
-          make env
-      - name: Lint code with black
-        run: make lint.black
-      - name: Lint code with isort
-        run: make lint.isort
+          python-version: '3.x'
+      - uses: pre-commit/[email protected]

.github/workflows/publish.yaml

@@ -0,0 +1,27 @@
+name: publish
+
+on:
+  release:
+    types: [ published ]
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+      - name: Build distribution
+        run: pipx run build
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/test.yml

@@ -0,0 +1,29 @@
+name: Test
+
+on:
+  push:
+    branches: ["dev", "refactoring"]
+  pull_request:
+    branches: ["dev", "refactoring"]
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    name: Test on ${{ matrix.os }} with Python ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ['3.8', '3.9', '3.10', '3.11']
+    steps:
+      - uses: actions/checkout@v4
+      - uses: snok/install-poetry@v1
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: poetry
+      - name: Run unit tests
+        run: make test

.github/workflows/test_cli.yml

@@ -0,0 +1,49 @@
+name: CLI Tests
+
+on:
+  push:
+    branches: ["dev", "refactoring"]
+  pull_request:
+    branches: ["dev", "refactoring"]
+    types: [opened, synchronize, reopened, ready_for_review]
+
+permissions:
+  contents: read
+
+concurrency:
+  group: '${{ github.workflow }} @ ${{ github.event.pull_request.head.label || github.head_ref || github.ref }}'
+  cancel-in-progress: true
+
+env:
+  POETRY_VERSION: '1.8.3'
+  PYTHON_VERSION: '3.11'
+
+jobs:
+  test-cli:
+    if: github.event.pull_request.draft == false
+    runs-on:
+      - self-hosted
+      - Linux
+      - ubuntu
+      - cpu
+    steps:
+      - uses: actions/checkout@v4
+      - uses: snok/install-poetry@v1
+        with:
+          version: ${{ env.POETRY_VERSION }}
+          virtualenvs-create: false
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+      - name: Run CLI tests
+        run: |
+          source /builds/miniconda3/etc/profile.d/conda.sh
+          make env.conda
+          conda activate "${{ github.workspace }}"/env
+          make install
+          cd tests
+          poetry run pytest \
+          --junitxml=./test-reports/test_cli_report.xml \
+          --disable-warnings \
+          --verbose \
+          test_cli.py

.github/workflows/test_generate.yml

@@ -0,0 +1,54 @@
+name: Generate Tests
+
+on:
+  push:
+    branches: ["dev", "refactoring"]
+  pull_request:
+    branches: ["dev", "refactoring"]
+    types: [opened, synchronize, reopened, ready_for_review]
+
+permissions:
+  contents: read
+
+concurrency:
+  group: '${{ github.workflow }} @ ${{ github.event.pull_request.head.label || github.head_ref || github.ref }}'
+  cancel-in-progress: true
+
+env:
+  POETRY_VERSION: '1.8.3'
+  PYTHON_VERSION: '3.11'
+
+jobs:
+  test-generate:
+    if: github.event.pull_request.draft == false
+    runs-on:
+      - self-hosted
+      - Linux
+      - ubuntu
+      - cpu
+    steps:
+      - uses: actions/checkout@v4
+      - uses: snok/install-poetry@v1
+        with:
+          version: ${{ env.POETRY_VERSION }}
+          virtualenvs-create: false
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+      - name: Run tests for generate task
+        run: |
+          source /builds/miniconda3/etc/profile.d/conda.sh
+          make env.conda
+          conda activate "${{ github.workspace }}"/env
+          make install
+          cd tests
+          poetry run pytest \
+          --junitxml=./test-reports/test_generate_report.xml \
+          --disable-warnings \
+          --verbose \
+          --basetemp=$HOME/tmp/generate \
+          --input_data_directory=/mnt/data/data_ci \
+          test_generate.py
+      - name: Cleaning
+        run: |
+          rm -rf $HOME/tmp/generate

.github/workflows/test_interpret.yml

@@ -0,0 +1,54 @@
+name: Interpretation Tests (GPU)
+
+on:
+  push:
+    branches: ["dev", "refactoring"]
+  pull_request:
+    branches: ["dev", "refactoring"]
+    types: [opened, synchronize, reopened, ready_for_review]
+
+permissions:
+  contents: read
+
+concurrency:
+  group: '${{ github.workflow }} @ ${{ github.event.pull_request.head.label || github.head_ref || github.ref }}'
+  cancel-in-progress: true
+
+env:
+  POETRY_VERSION: '1.8.3'
+  PYTHON_VERSION: '3.11'
+
+jobs:
+  test-interpret-gpu:
+    if: github.event.pull_request.draft == false
+    runs-on:
+      - self-hosted
+      - Linux
+      - ubuntu
+      - gpu
+    steps:
+      - uses: actions/checkout@v4
+      - uses: snok/install-poetry@v1
+        with:
+          version: ${{ env.POETRY_VERSION }}
+          virtualenvs-create: false
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+      - name: Run tests for Interpret task on GPU
+        run: |
+          source "${HOME}/miniconda3/etc/profile.d/conda.sh"
+          make env.conda
+          conda activate "${{ github.workspace }}"/env
+          make install
+          cd tests
+          poetry run pytest \
+          --junitxml=./test-reports/test_interpret_report.xml \
+          --disable-warnings \
+          --verbose \
+          --basetemp=$HOME/actions_runner_workdir/interpret \
+          --input_data_directory=/mnt/data/clinicadl_data_ci/data_ci \
+          test_interpret.py
+      - name: Cleaning
+        run: |
+          rm -rf $HOME/actions_runner_workdir/interpret/*

.github/workflows/test_predict.yml

@@ -0,0 +1,54 @@
+name: Predict Tests
+
+on:
+  push:
+    branches: ["dev", "refactoring"]
+  pull_request:
+    branches: ["dev", "refactoring"]
+    types: [opened, synchronize, reopened, ready_for_review]
+
+permissions:
+  contents: read
+
+concurrency:
+  group: '${{ github.workflow }} @ ${{ github.event.pull_request.head.label || github.head_ref || github.ref }}'
+  cancel-in-progress: true
+
+env:
+  POETRY_VERSION: '1.8.3'
+  PYTHON_VERSION: '3.11'
+
+jobs:
+  test-predict:
+    if: github.event.pull_request.draft == false
+    runs-on:
+      - self-hosted
+      - Linux
+      - ubuntu
+      - cpu
+    steps:
+      - uses: actions/checkout@v4
+      - uses: snok/install-poetry@v1
+        with:
+          version: ${{ env.POETRY_VERSION }}
+          virtualenvs-create: false
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+      - name: Run tests for predict task
+        run: |
+          source /builds/miniconda3/etc/profile.d/conda.sh
+          make env.conda
+          conda activate "${{ github.workspace }}"/env
+          make install
+          cd tests
+          poetry run pytest \
+          --junitxml=./test-reports/test_predict_report.xml \
+          --disable-warnings \
+          --verbose \
+          --basetemp=$HOME/tmp/predict \
+          --input_data_directory=/mnt/data/data_ci \
+          test_predict.py
+      - name: Cleaning
+        run: |
+          rm -rf $HOME/tmp/predict/*

.github/workflows/test_prepare_data.yml

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+name: Prepare data Tests
+
+on:
+  push:
+    branches: ["dev", "refactoring"]
+  pull_request:
+    branches: ["dev", "refactoring"]
+    types: [opened, synchronize, reopened, ready_for_review]
+
+permissions:
+  contents: read
+
+concurrency:
+  group: '${{ github.workflow }} @ ${{ github.event.pull_request.head.label || github.head_ref || github.ref }}'
+  cancel-in-progress: true
+
+env:
+  POETRY_VERSION: '1.8.3'
+  PYTHON_VERSION: '3.11'
+
+jobs:
+  test-prepare-data:
+    if: github.event.pull_request.draft == false
+    runs-on:
+      - self-hosted
+      - Linux
+      - ubuntu
+      - cpu
+    steps:
+      - uses: actions/checkout@v4
+      - uses: snok/install-poetry@v1
+        with:
+          version: ${{ env.POETRY_VERSION }}
+          virtualenvs-create: false
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+      - name: Run tests for prepare data task
+        run: |
+          source /builds/miniconda3/etc/profile.d/conda.sh
+          make env.conda
+          conda activate "${{ github.workspace }}"/env
+          make install
+          cd tests
+          poetry run pytest \
+          --junitxml=./test-reports/test_prepare_data_report.xml \
+          --disable-warnings \
+          --verbose \
+          --basetemp=$HOME/tmp/prepare_data \
+          --input_data_directory=/mnt/data/data_ci \
+          test_prepare_data.py
+      - name: Cleaning
+        run: |
+          rm -rf $HOME/tmp/prepare_data/*