Merge branch 'master' into move-clustering-algos

.github/workflows/pytest-core-nompi.yml

@@ -11,127 +11,128 @@ on:
       - master
 
 jobs:
-  ci-linux:
+  pytest:
     name: ${{ matrix.name }}
-    runs-on: ubuntu-16.04
+    runs-on: "${{ matrix.os }}"
 
     env:
-      DEVITO_ARCH: "gcc-${{ matrix.gcc-version }}"
+      DEVITO_ARCH: "${{ matrix.arch }}"
       DEVITO_OPENMP: ${{ matrix.openmp }}
       DEVITO_BACKEND: "core"
       OMP_NUM_THREADS: 2
-      CC: "gcc-${{ matrix.gcc-version }}"
-      CXX: "g++-${{ matrix.gcc-version }}"
       PYTHON_VERSION: "${{ matrix.python-version }}"
+      TESTS: "tests/"
 
     strategy:
       # Prevent all build to stop if a single one fails
       fail-fast: false
 
       matrix:
         name: [
-           py36-gcc49-openmp,
-           py37-gcc5-openmp,
-           py38-gcc6-openmp,
-           py36-gcc7-openmp,
-           py37-gcc7-noopenmp,
-           py37-gcc8-openmp,
-           py38-gcc9-openmp
+           pytest-ubuntu-py36-gcc49-omp,
+           pytest-ubuntu-py37-gcc5-omp,
+           pytest-ubuntu-py38-gcc6-omp,
+           pytest-ubuntu-py36-gcc7-omp,
+           pytest-ubuntu-py37-gcc7-noomp,
+           pytest-ubuntu-py37-gcc8-omp,
+           pytest-ubuntu-py38-gcc9-omp,
+           pytest-osx-py37-clang-omp,
+           pytest-docker-py36-gcc-omp
         ]
         include:
-            - name: py36-gcc49-openmp
-              python-version: 3.6
-              gcc-version: 4.9
-              openmp: 1
-
-            - name: py37-gcc5-openmp
-              python-version: 3.7
-              gcc-version: 5
-              openmp: 1
-
-            - name: py38-gcc6-openmp
-              python-version: 3.8
-              gcc-version: 6
-              openmp: 1
-
-            - name: py36-gcc7-openmp
-              python-version: 3.6
-              gcc-version: 7
-              openmp: 1
-
-            - name: py37-gcc7-noopenmp
-              python-version: 3.7
-              gcc-version: 7
-              openmp: 0
-
-            - name: py37-gcc8-openmp
-              python-version: 3.7
-              gcc-version: 8
-              openmp: 1
-
-            - name: py38-gcc9-openmp
-              python-version: 3.8
-              gcc-version: 9
-              openmp: 1
+        - name: pytest-ubuntu-py36-gcc49-omp
+          python-version: 3.6
+          os: ubuntu-16.04
+          arch: "gcc-4.9"
+          openmp: 1
+
+        - name: pytest-ubuntu-py37-gcc5-omp
+          python-version: 3.7
+          os: ubuntu-16.04
+          arch: "gcc-5"
+          openmp: 1
+
+        - name: pytest-ubuntu-py38-gcc6-omp
+          python-version: 3.8
+          os: ubuntu-16.04
+          arch: "gcc-6"
+          openmp: 1
+
+        - name: pytest-ubuntu-py36-gcc7-omp
+          python-version: 3.6
+          os: ubuntu-16.04
+          arch: "gcc-7"
+          openmp: 1
+
+        - name: pytest-ubuntu-py37-gcc7-noomp
+          python-version: 3.7
+          os: ubuntu-16.04
+          arch: "gcc-7"
+          openmp: 0
+
+        - name: pytest-ubuntu-py37-gcc8-omp
+          python-version: 3.7
+          os: ubuntu-16.04
+          arch: "gcc-8"
+          openmp: 1
+
+        - name: pytest-ubuntu-py38-gcc9-omp
+          python-version: 3.8
+          os: ubuntu-16.04
+          arch: "gcc-9"
+          openmp: 1
+
+        - name: pytest-osx-py37-clang-omp
+          python-version: 3.7
+          os: macos-latest
+          arch: "osx"
+          openmp: 0
+
+        - name: pytest-docker-py36-gcc-omp
+          python-version: 3.6
+          os: ubuntu-16.04
+          arch: "gcc"
+          openmp: 1
 
     steps:
     - name: Checkout devito
       uses: actions/checkout@v1
 
     - name: Set up Python ${{ matrix.python-version }}
+      if: matrix.name != 'pytest-docker-py36-gcc-omp'
       uses: actions/setup-python@v1
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install GCC ${{ matrix.gcc-version }}
-      run : |
-        sudo apt-get install -y g++-${{ matrix.gcc-version }}
-
-    - name: Install dependencies
+    - name: Build docker image
+      if: matrix.name == 'pytest-docker-py36-gcc-omp'
       run: |
-        pip install --upgrade pip
-        pip install -e .
-
-    - name: Test with pytest
-      run: |
-        pytest --cov --cov-config=.coveragerc --cov-report=xml tests/
-
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v1.0.5
-      with:
-        token: ${{ secrets.CODECOV_TOKEN }}
-        name: ${{ matrix.name }}
-
-  # OSX
-  ci-osx:
-    name: py37-clang-osx
-    runs-on: macos-latest
+          docker build . --file docker/Dockerfile --tag devito_img
+          echo "::set-env name=RUN_CMD::docker run --rm --name testrun devito_img"
 
-    env:
-      DEVITO_ARCH: "osx"
-      DEVITO_OPENMP: 0
-      DEVITO_BACKEND: "core"
-
-    steps:
-    - name: Checkout devito
-      uses: actions/checkout@v1
+    - name: Install GCC ${{ matrix.arch }}
+      if: runner.os == 'linux'
+      run : |
+        sudo apt-get install -y ${{ matrix.arch }}
 
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v1
-      with:
-        python-version: 3.7
+    - name: Reduce number of tests for OSX
+      if: runner.os == 'macOS'
+      run : |
+        echo "::set-env name=TESTS::tests/test_operator.py"
 
     - name: Install dependencies
+      if: matrix.name != 'pytest-docker-py36-gcc-omp'
       run: |
         pip install --upgrade pip
         pip install -e .
 
     - name: Test with pytest
       run: |
-        pytest --cov --cov-config=.coveragerc --cov-report=xml tests/test_operator.py
+        $RUN_CMD pytest -m "not parallel" --cov --cov-config=.coveragerc --cov-report=xml $TESTS
 
     - name: Upload coverage to Codecov
+      if: matrix.name != 'pytest-docker-py36-gcc-omp'
       uses: codecov/codecov-action@v1.0.5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
-        name: "py37-clang-osx"
+        name: ${{ matrix.name }}

.github/workflows/pytest-yask.yml

@@ -43,7 +43,6 @@ jobs:
 
     - name: Install yask
       run : |
-        sudo apt-get update
         sudo apt-get install -y swig
         make compiler-api
         pip install -e .

.github/workflows/tutorials.yml

@@ -0,0 +1,105 @@
+name: Jupyter Notebooks
+
+on:
+  # Trigger the workflow on push or pull request,
+  # but only for the master branch
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  tutorials:
+    name: ${{ matrix.name }}
+    runs-on: ${{ matrix.os }}
+
+    env:
+      DEVITO_ARCH: "${{ matrix.compiler }}"
+      DEVITO_OPENMP: ${{ matrix.openmp }}
+      DEVITO_BACKEND: "core"
+      PYTHON_VERSION: "3.7"
+      RUN_CMD: ""
+
+    strategy:
+      # Prevent all build to stop if a single one fails
+      fail-fast: false
+      matrix:
+        name: [
+          tutos-ubuntu-gcc-py37,
+          tutos-osx-gcc-py37,
+          tutos-osx-clang-py37,
+          tutos-docker-gcc-py36
+          ]
+
+        include:
+          - name: tutos-ubuntu-gcc-py37
+            os: ubuntu-16.04
+            compiler: gcc-7
+            openmp: 1
+
+          - name: tutos-osx-gcc-py37
+            os: macos-latest
+            compiler: gcc-9
+            openmp: 1
+
+          - name: tutos-osx-clang-py37
+            os: macos-latest
+            compiler: clang
+            openmp: 0
+
+          - name: tutos-docker-gcc-py36
+            os: ubuntu-latest
+            compiler: gcc
+            openmp: 1
+
+    steps:
+    - name: Checkout devito
+      uses: actions/checkout@v1
+
+    - name: Set up Python 3.7
+      if: matrix.name != 'tutos-docker-gcc-py36'
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.7
+
+    - name: Install compilers for OSX
+      if: runner.os == 'macOS'
+      run: |
+        if [ "${{ matrix.compiler }}" = "gcc-9" ]; then
+          brew install gcc
+        else
+          sudo xcode-select -s /Applications/Xcode_11.app/Contents/Developer
+        fi
+        # dask error on osx, skip dask tuto
+        echo "::set-env name=SKIP::--deselect=examples/seismic/tutorials/04_dask.ipynb"
+
+    - name: Build docker image
+      if: matrix.name == 'tutos-docker-gcc-py36'
+      run: |
+          docker build . --file docker/Dockerfile --tag devito_img
+          echo "::set-env name=RUN_CMD::docker run --rm --name testrun devito_img"
+
+    - name: Install dependencies
+      if: matrix.name != 'tutos-docker-gcc-py36'
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e .
+        pip install matplotlib
+
+    - name: Seismic notebooks
+      run: |
+        $RUN_CMD py.test --nbval $SKIP examples/seismic/tutorials/
+
+    - name: CFD notebooks
+      run: |
+        $RUN_CMD py.test --nbval examples/cfd
+
+    - name: User api notebooks
+      run: |
+        $RUN_CMD py.test --nbval examples/userapi
+
+    - name: User api notebooks
+      run: |
+        $RUN_CMD py.test --nbval examples/compiler

docker/Dockerfile

@@ -1,8 +1,8 @@
 FROM python:3.6
 
-RUN apt-get update && apt-get install -y -q \ 
-    mpich \ 
-    libmpich-dev 
+RUN apt-get update && apt-get install -y -q \
+    mpich \
+    libmpich-dev
 
 ADD ./requirements.txt /app/requirements.txt
 ADD ./requirements-optional.txt /app/requirements-optional.txt
@@ -16,6 +16,7 @@ RUN python3 -m venv /venv && \
 ADD ./devito /app/devito
 ADD ./tests /app/tests
 ADD ./examples /app/examples
+COPY setup.cfg /app/
 
 ADD docker/run-jupyter.sh /jupyter
 ADD docker/run-tests.sh /tests
@@ -31,7 +32,7 @@ RUN chmod +x \
 WORKDIR /app
 
 ENV DEVITO_ARCH="gcc"
-ENV DEVITO_OPENMP="0"
+ENV DEVITO_OPENMP="1"
 
 EXPOSE 8888
 ENTRYPOINT ["/docker-entrypoint.sh"]

tests/test_environment.py

@@ -29,4 +29,4 @@ def test_python_version():
     # Installed version
     i_ver = platform.python_version()
 
-    assert i_ver.startswith(e_ver)
+    assert e_ver is None or i_ver.startswith(e_ver)