New caps dataset

.github/workflows/lint.yaml

@@ -2,9 +2,9 @@ name: 'Lint codebase'
 
 on:
   pull_request:
-    branches: [ dev ]
+    branches: [ "dev", "refactoring" ]
   push:
-    branches: [ dev ]
+    branches: [ "dev", "refactoring" ]
 
 permissions:
   contents: read

.github/workflows/test.yml

@@ -2,9 +2,9 @@ name: Test
 
 on:
   push:
-    branches: [dev]
+    branches: ["dev", "refactoring"]
   pull_request:
-    branches: [dev]
+    branches: ["dev", "refactoring"]
 
 permissions:
   contents: read

.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

@@ -0,0 +1,54 @@
+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/*

.github/workflows/test_quality_checks.yml

@@ -0,0 +1,54 @@
+name: Quality Check 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-quality-check:
+    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: ${{ env.PYTHON_VERSION }}
+      - name: Run tests for Quality Check
+        run: |
+          source /builds/miniconda3/etc/profile.d/conda.sh
+          make env.conda
+          conda activate "${{ github.workspace }}"/env
+          make install
+          cd tests
+          poetry run pytest \
+          --junitxml=./test-reports/test_quality_check_report.xml \
+          --disable-warnings \
+          --verbose \
+          --basetemp=$HOME/tmp/quality_checks \
+          --input_data_directory=/mnt/data/data_ci \
+          test_qc.py
+      - name: Cleaning
+        run: |
+          rm -rf $HOME/tmp/quality_checks/*