LORIS-MRI tooling configuration (Docker version)

.github/workflows/loristest.yml

@@ -1,8 +1,6 @@
 name: LORIS Test Suite
 
-on:
-  - push
-  - pull_request
+on: workflow_dispatch
 
 jobs:
   docker:

.github/workflows/python-checks.yml

@@ -1,32 +1,73 @@
 name: Python checks
 
-on:
-  - push
-  - pull_request
+on: pull_request
 
 jobs:
+  docker:
+    name: Docker
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12"]
+
+    steps:
+      - name: Check out LORIS-MRI
+        uses: actions/checkout@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Build Docker image
+        id: build-and-push
+        uses: docker/build-push-action@v4
+        with:
+          context: .
+          file: ./test/python.Dockerfile
+          build-args: |
+            PYTHON_VERSION=${{ matrix.python-version }}
+            WORKSPACE=/workspace
+          tags: loris-python:${{ matrix.python-version }}
+          cache-from: type=gha,scope=loris-python-${{ matrix.python-version }}
+          cache-to: type=gha,scope=loris-python-${{ matrix.python-version }}
+          outputs: type=docker,dest=/tmp/loris-python-${{ matrix.python-version }}.tar
+
+      - name: Upload Docker image
+        uses: actions/upload-artifact@v4
+        with:
+          name: loris-python-${{ matrix.python-version }}
+          path: /tmp/loris-python-${{ matrix.python-version }}.tar
+
   ruff:
-    name: "Ruff"
+    name: Ruff
+    needs: docker
     runs-on: ubuntu-latest
 
     strategy:
       matrix:
         python-version: ["3.11", "3.12"]
 
     steps:
-    - name: Check out LORIS-MRI
-      uses: actions/checkout@v4
+      - name: Checkout LORIS-MRI
+        uses: actions/checkout@v4
 
-    - name: Set up Python
-      uses: ./.github/actions/setup-python
-      with:
-        python-version: ${{ matrix.python-version }}
+      - name: Download Docker image
+        uses: actions/download-artifact@v4
+        with:
+          name: loris-python-${{ matrix.python-version }}
+          path: /tmp
 
-    - name: Run Ruff
-      run: ruff check --output-format=github
+      - name: Load Docker image
+        run: docker load -i /tmp/loris-python-${{ matrix.python-version }}.tar
+
+      - name: Run Ruff
+        run: |
+          docker run -v ${{ github.workspace }}:/workspace -w /workspace loris-python:${{ matrix.python-version }} \
+            ruff check --output-format=github
 
   pyright-strict:
-    name: "Pyright strict"
+    name: Pyright strict
+    needs: docker
     runs-on: ubuntu-latest
 
     strategy:
@@ -37,37 +78,43 @@ jobs:
     - name: Check out LORIS-MRI
       uses: actions/checkout@v4
 
-    - name: Set up Python
-      uses: ./.github/actions/setup-python
+    - name: Download Docker image
+      uses: actions/download-artifact@v4
       with:
-        python-version: ${{ matrix.python-version }}
+        name: loris-python-${{ matrix.python-version }}
+        path: /tmp
+
+    - name: Load Docker image
+      run: docker load -i /tmp/loris-python-${{ matrix.python-version }}.tar
 
-      # Like in the other Pyright run, the `jq` arcane is used to translate the errors from JSON to
-      # the GitHub actions format
     - name: Run Pyright
       run: |
-        pyright --outputjson | jq -r '.generalDiagnostics[] | "::error file=\(.file),line=\(.range.start.line),col=\(.range.start.character)::\(.message)"'
-        (exit ${PIPESTATUS[0]})
+        docker run -v ${{ github.workspace }}:/workspace -w /workspace loris-python:${{ matrix.python-version }} bash -c \
+          "set -o pipefail && pyright --outputjson | bash test/pyright_to_github.sh"
 
   pyrigh-global:
-    name: "Pyright global"
+    name: Pyright global
+    needs: docker
     runs-on: ubuntu-latest
 
     strategy:
       matrix:
         python-version: ["3.11", "3.12"]
 
     steps:
-    - name: Check out LORIS-MRI
-      uses: actions/checkout@v4
-
-    - name: Set up Python
-      uses: ./.github/actions/setup-python
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Run Pyright
-      run: |
-        cd test
-        pyright --outputjson | jq -r '.generalDiagnostics[] | "::error file=\(.file),line=\(.range.start.line),col=\(.range.start.character)::\(.message)"'
-        (exit ${PIPESTATUS[0]})
+      - name: Check out LORIS-MRI
+        uses: actions/checkout@v4
+
+      - name: Download Docker image
+        uses: actions/download-artifact@v4
+        with:
+          name: loris-python-${{ matrix.python-version }}
+          path: /tmp
+
+      - name: Load Docker image
+        run: docker load -i /tmp/loris-python-${{ matrix.python-version }}.tar
+
+      - name: Run Pyright
+        run: |
+          docker run -v ${{ github.workspace }}:/workspace -w /workspace loris-python:${{ matrix.python-version }} bash -c \
+            "cd test && set -o pipefail && pyright --outputjson | bash pyright_to_github.sh"

test/pyright_to_github.sh

@@ -0,0 +1,3 @@
+# This is a simple script to format Pyright errors (in JSON format) into GitHub errors, used by CI.
+# TODO: Add formatting for warnings
+jq -r '.generalDiagnostics[] | "::error file=\(.file),line=\(.range.start.line),col=\(.range.start.character)::\(.message)"'

test/python.Dockerfile

@@ -0,0 +1,25 @@
+# This is a minimal Docker image to run static tests on the Python code of LORIS-MRI.
+# It sets up Python and our Python dependencies, but does not configure a full setup
+# to test LORIS-MRI (Perl code, database...).
+
+# Python version to use for the tests
+ARG PYTHON_VERSION=3.11
+
+FROM python:${PYTHON_VERSION}-slim
+
+# Path of the LORIS-MRI repository in the container
+ARG WORKSPACE
+
+RUN apt-get update
+
+# Required for the Python library `mysqlclient`
+RUN apt-get install -y default-libmysqlclient-dev build-essential pkg-config
+
+# Used to format the Pyright errors to the GitHub format
+RUN apt-get install -y jq
+
+COPY ./python/requirements.txt requirements.txt
+
+RUN pip install --no-cache-dir --root-user-action=ignore -r requirements.txt
+
+ENV PYTHONPATH=${WORKSPACE}/python:${WORKSPACE}/python/react-series-data-viewer