LORIS-MRI tooling configuration (#1170)

* add pyproject.toml

* keep flake8 (for now)

* double type checking

* Use Pyright as main type checker

* remove comment

* test

* test

* change configuration

* add python environment variables

* try factorization

* test

* test

* test

* test

* remove temporary things

* test ruff error

* ruff output github

* further test errors

* test pyright output github

* test

* test

* test

* change comment

* remove test errors

* test

---------

Co-authored-by: Maxime Mulder <[email protected]>

.github/actions/setup-python/action.yml

@@ -0,0 +1,23 @@
+name: Set up Python
+input:
+inputs:
+  python-version:
+    required: true
+
+runs:
+  using: composite
+
+  steps:
+  - name: Set up the Python environment
+    uses: actions/setup-python@v5
+    with:
+      python-version: ${{ matrix.python-version }}
+      cache: 'pip'
+
+  - name: Install Python dependencies
+    run: pip install -r python/requirements.txt
+    shell: bash
+
+  - name: Set up environment variables
+    run: echo PYTHONPATH=$PYTHONPATH:/`pwd`/python:/`pwd`/python/react-series-data-viewer >> $GITHUB_ENV
+    shell: bash

.github/workflows/python-checks.yml

@@ -0,0 +1,73 @@
+name: Python checks
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  ruff:
+    name: "Ruff"
+    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 Ruff
+      run: ruff check --output-format=github
+
+  pyright-strict:
+    name: "Pyright strict"
+    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 }}
+
+      # 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]})
+
+  pyrigh-global:
+    name: "Pyright global"
+    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]})

pyproject.toml

@@ -0,0 +1,26 @@
+[tool.ruff]
+include = ["python/**/*.py"]
+exclude = ["python/react-series-data-viewer"]
+line-length = 120
+preview = true
+
+[tool.ruff.lint]
+ignore = ["E202", "E203", "E221", "E241", "E251", "E272"]
+# TODO: Select "F", "I", "N", "UP" and format the codebase accordingly.
+select = ["E", "W"]
+
+# The strict type checking configuration is used to type check only the modern (typed) modules. An
+# additional basic type checking configuration to type check legacy modules can be found in the
+# `test` directory.
+
+[tool.pyright]
+include = [
+    "python/lib/db",
+    "python/lib/exception",
+    "python/lib/validate_subject_ids.py"
+]
+typeCheckingMode = "strict"
+reportMissingTypeStubs = "none"
+
+[tool.pytest.ini-options]
+testpaths = ["python/tests"]

python/requirements.txt

@@ -1,5 +1,4 @@
 boto3
-flake8
 google
 mat73
 matplotlib
@@ -13,7 +12,10 @@ nose
 numpy
 protobuf>=3.0.0
 pybids==0.17.0
+pyright
+pytest
 python-dateutil
+ruff
 scikit-learn
 scipy
 sqlalchemy>=2.0.0

test/pyrightconfig.json

@@ -0,0 +1,7 @@
+{
+    "include": ["../python"],
+    "exclude": ["../python/react-series-data-viewer"],
+    "typeCheckingMode": "off",
+    "reportDeprecated": "warning",
+    "reportMissingImports": "error"
+}