Updated Pyccel internal ND_Arrays to work with nvcc compiler

.dict_custom.txt

@@ -106,5 +106,6 @@ Valgrind
 variadic
 subclasses
 oneAPI
+Cuda
 getter
 setter

.github/CODEOWNERS

@@ -0,0 +1,6 @@
+# These owners will be the default owners for everything in
+# the repo. Unless a later match takes precedence,
+# @global-owner1 and @global-owner2 will be requested for
+# review when someone opens a pull request.
+*       @EmilyBourne @bauom
+

.github/actions/coverage_install/action.yml

@@ -15,7 +15,7 @@ runs:
     - name: Directory Creation
       run: |
         INSTALL_DIR=$(cd tests; python -c "import pyccel; print(pyccel.__path__[0])")
-        SITE_DIR=$(python -c 'import sysconfig; print(sysconfig.get_paths()["purelib"])')
+        SITE_DIR=$(dirname ${INSTALL_DIR})
         echo -e "import coverage; coverage.process_startup()" > ${SITE_DIR}/pyccel_cov.pth
         echo -e "[run]\nparallel = True\nsource = ${INSTALL_DIR}\ndata_file = $(pwd)/.coverage\n[report]\ninclude = ${INSTALL_DIR}/*\n[xml]\noutput = cobertura.xml" > .coveragerc
         echo "SITE_DIR=${SITE_DIR}" >> $GITHUB_ENV

.github/actions/linux_install/action.yml

@@ -9,22 +9,22 @@ runs:
       shell: bash
     - name: Install fortran
       run:
-        sudo apt-get install gfortran
+        sudo apt-get install -y gfortran
       shell: bash
     - name: Install LaPack
       run:
-        sudo apt-get install libblas-dev liblapack-dev
+        sudo apt-get install -y libblas-dev liblapack-dev
       shell: bash
     - name: Install MPI
       run: |
-        sudo apt-get install libopenmpi-dev openmpi-bin
+        sudo apt-get install -y libopenmpi-dev openmpi-bin
         echo "MPI_OPTS=--oversubscribe" >> $GITHUB_ENV
       shell: bash
     - name: Install OpenMP
       run:
-        sudo apt-get install libomp-dev libomp5
+        sudo apt-get install -y libomp-dev libomp5
       shell: bash
     - name: Install Valgrind
       run:
-        sudo apt-get install valgrind
+        sudo apt-get install -y valgrind
       shell: bash

.github/actions/pytest_parallel/action.yml

@@ -10,8 +10,8 @@ runs:
   steps:
     - name: Test with pytest
       run: |
-        mpiexec -n 4 ${MPI_OPTS} python -m pytest epyccel/test_parallel_epyccel.py -v -m parallel -rXx
-        #mpiexec -n 4 ${MPI_OPTS} python -m pytest epyccel -v -m parallel -rXx
+        mpiexec -n 4 ${MPI_OPTS} python -m pytest epyccel/test_parallel_epyccel.py -v -m "parallel and not cuda" -rXx
+        #mpiexec -n 4 ${MPI_OPTS} python -m pytest epyccel -v -m "parallel and not cuda" -rXx
       shell: ${{ inputs.shell_cmd }}
       working-directory: ./tests
 

.github/actions/pytest_run/action.yml

@@ -51,13 +51,13 @@ runs:
       working-directory: ./tests
       id: pytest_3
     - name: Test Fortran translations
-      run: python -m pytest -n auto -rX ${FLAGS} -m "not (parallel or xdist_incompatible) and not (c or python) ${{ inputs.pytest_mark }}" --ignore=symbolic --ignore=ndarrays 2>&1 | tee s4_outfile.out
+      run: python -m pytest -n auto -rX ${FLAGS} -m "not (parallel or xdist_incompatible) and not (c or python or cuda) ${{ inputs.pytest_mark }}" --ignore=symbolic --ignore=ndarrays 2>&1 | tee s4_outfile.out
       shell: ${{ inputs.shell_cmd }}
       working-directory: ./tests
       id: pytest_4
     - name: Test multi-file Fortran translations
       run: |
-        python -m pytest -rX ${FLAGS} -m "xdist_incompatible and not parallel and not (c or python) ${{ inputs.pytest_mark }}" --ignore=symbolic --ignore=ndarrays 2>&1 | tee s5_outfile.out
+        python -m pytest -rX ${FLAGS} -m "xdist_incompatible and not parallel and not (c or python or cuda) ${{ inputs.pytest_mark }}" --ignore=symbolic --ignore=ndarrays 2>&1 | tee s5_outfile.out
         pyccel-clean
       shell: ${{ inputs.shell_cmd }}
       working-directory: ./tests

.github/actions/pytest_run_cuda/action.yml

@@ -0,0 +1,24 @@
+name: 'Pyccel pytest commands generating Cuda'
+inputs:
+  shell_cmd:
+    description: 'Specifies the shell command (different for anaconda)'
+    required: false
+    default: "bash"
+
+runs:
+  using: "composite"
+  steps:
+    - name: Ccuda tests with pytest
+      run: |
+        # Catch exit 5 (no tests found)
+        python -m pytest -rX ${FLAGS} -m "not (xdist_incompatible or parallel) and cuda ${{ inputs.pytest_mark }}" --ignore=symbolic --ignore=ndarrays 2>&1 | tee s1_outfile.out
+        pyccel-clean
+      shell: ${{ inputs.shell_cmd }}
+      working-directory: ./tests
+    - name: Final step
+      if: always()
+      id: status
+      run:
+        python ci_tools/json_pytest_output.py -t "Cuda Test Summary" --tests "Cuda tests:${{ steps.pytest_1.outcome }}:tests/s1_outfile.out"
+
+      shell: ${{ inputs.shell_cmd }}

.github/actions/python_install/action.yml

@@ -0,0 +1,17 @@
+name: 'Python installation commands'
+
+runs:
+  using: "composite"
+  steps:
+    - name: Install python
+      run:
+        sudo apt-get -y install python3-dev
+      shell: bash
+    - name: python as python3
+      run:
+        sudo apt-get -y install python-is-python3
+      shell: bash
+    - name: Install Pip
+      run:
+        sudo apt-get -y install python3-pip
+      shell: bash

.github/workflows/anaconda_linux.yml

@@ -16,7 +16,7 @@ on:
         required: false
         type: string
   push:
-    branches: devel
+    branches: [devel, main]
 
 env:
   COMMIT: ${{ inputs.ref || github.event.ref }}
@@ -28,7 +28,7 @@ env:
 jobs:
   Python_version_picker:
     runs-on: ubuntu-latest
-    if: github.event_name != 'push' || github.repository == 'pyccel/pyccel'
+    if: github.event_name != 'push' || github.repository == 'pyccel/pyccel-cuda'
     outputs:
       python_version: ${{ steps.set-python_version.outputs.python_version }}
     steps:

.github/workflows/anaconda_windows.yml

@@ -16,7 +16,7 @@ on:
         required: false
         type: string
   push:
-    branches: devel
+    branches: [devel, main]
 
 env:
   COMMIT: ${{ inputs.ref || github.event.ref }}
@@ -28,7 +28,7 @@ env:
 jobs:
   Python_version_picker:
     runs-on: windows-latest
-    if: github.event_name != 'push' || github.repository == 'pyccel/pyccel'
+    if: github.event_name != 'push' || github.repository == 'pyccel/pyccel-cuda'
     outputs:
       python_version: ${{ steps.set-python_version.outputs.python_version }}
     steps:

.github/workflows/coverage_collect.yml

@@ -0,0 +1,67 @@
+name: Unit test coverage collection
+
+on:
+  workflow_call:
+    inputs:
+      python_version:
+        required: true
+        type: string
+      ref:
+        required: false
+        type: string
+      cuda_result:
+        required: true
+        type: string
+
+jobs:
+  CoverageChecker:
+
+    runs-on: ubuntu-latest
+    name: Unit tests
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          ref: ${{ inputs.ref }}
+      - name: Set up Python ${{ inputs.python_version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ inputs.python_version }}
+      - name: Install dependencies
+        uses: ./.github/actions/linux_install
+      - name: Install coverage
+        run: |
+            python -m pip install --upgrade pip
+            python -m pip install coverage
+        shell: bash
+      - name: Collect coverage information
+        uses: actions/download-artifact@v3
+        with:
+          name: coverage-artifact
+      - name: Rename coverage file
+        run: mv .coverage .coverage.linux
+      - name: Collect coverage information
+        uses: actions/download-artifact@v3
+        if: ${{ inputs.cuda_result }} == 'success'
+        with:
+          name: cuda-coverage-artifact
+      - name: Rename coverage file
+        if: ${{ inputs.cuda_result }} == 'success'
+        run: mv .coverage .coverage.cuda
+      - name: Generate coverage report
+        run: |
+            echo -e "[paths]\nsource =\n   $(pwd)/pyccel\n   */site-packages/pyccel\n[xml]\noutput = cobertura.xml" > .coveragerc
+            coverage combine
+            coverage xml
+      - name: Run codacy-coverage-reporter
+        uses: codacy/codacy-coverage-reporter-action@master
+        continue-on-error: True
+        with:
+          project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
+          coverage-reports: cobertura.xml
+      - name: Save code coverage xml report
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-artifact-xml
+          path: cobertura.xml
+          retention-days: 1

.github/workflows/cuda.yml

@@ -0,0 +1,83 @@
+name: Cuda unit tests
+
+on:
+  workflow_dispatch:
+    inputs:
+      python_version:
+        required: false
+        type: string
+      ref:
+        required: false
+        type: string
+      check_run_id:
+        required: false
+        type: string
+      pr_repo:
+        required: false
+        type: string
+  push:
+    branches: [devel, main]
+
+env:
+  COMMIT: ${{ inputs.ref || github.event.ref }}
+  PEM: ${{ secrets.BOT_PEM }}
+  GITHUB_RUN_ID: ${{ github.run_id }}
+  GITHUB_CHECK_RUN_ID: ${{ inputs.check_run_id }}
+  PR_REPO: ${{ inputs.pr_repo || github.repository }}
+
+jobs:
+  Cuda:
+
+    runs-on: ubuntu-20.04
+    name: Unit tests
+
+    container: nvidia/cuda:11.7.1-devel-ubuntu20.04
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          ref: ${{ env.COMMIT }}
+          repository: ${{ env.PR_REPO }}
+      - name: Prepare docker
+        run: |
+          apt update && apt install sudo
+          TZ=Europe/France
+          ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
+          DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends tzdata
+        shell: bash
+      - name: Install python (setup-python action doesn't work with containers)
+        uses: ./.github/actions/python_install
+      - name: "Setup"
+        id: token
+        run: |
+          pip install jwt requests
+          python ci_tools/setup_check_run.py cuda
+      - name: CUDA Version
+        run: nvcc --version # cuda install check
+      - name: Install dependencies
+        uses: ./.github/actions/linux_install
+      - name: Install Pyccel with tests
+        run: |
+            PATH=${PATH}:$HOME/.local/bin
+            echo "PATH=${PATH}" >> $GITHUB_ENV
+            python -m pip install --upgrade pip
+            python -m pip install --user .[test]
+        shell: bash
+      - name: Coverage install
+        uses: ./.github/actions/coverage_install
+      - name: Ccuda tests with pytest
+        id: cuda_pytest
+        uses: ./.github/actions/pytest_run_cuda
+      - name: Collect coverage information
+        continue-on-error: True
+        uses: ./.github/actions/coverage_collection
+      - name: Save code coverage report
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-artifact
+          path: .coverage
+          retention-days: 1
+      - name: "Post completed"
+        if: always()
+        run:
+          python ci_tools/complete_check_run.py ${{ steps.cuda_pytest.outcome }}
+

.github/workflows/intel.yml

@@ -16,7 +16,7 @@ on:
         required: false
         type: string
   push:
-    branches: devel
+    branches: [devel, main]
 
 env:
   COMMIT: ${{ inputs.ref || github.event.ref }}
@@ -29,7 +29,7 @@ env:
 jobs:
   Python_version_picker:
     runs-on: ubuntu-latest
-    if: github.event_name != 'push' || github.repository == 'pyccel/pyccel'
+    if: github.event_name != 'push' || github.repository == 'pyccel/pyccel-cuda'
     outputs:
       python_version: ${{ steps.set-python_version.outputs.python_version }}
     steps:

.github/workflows/linux.yml

@@ -16,7 +16,7 @@ on:
         required: false
         type: string
   push:
-    branches: devel
+    branches: [devel, main]
 
 env:
   COMMIT: ${{ inputs.ref || github.event.ref }}
@@ -28,7 +28,7 @@ env:
 jobs:
   matrix_prep:
     runs-on: ubuntu-latest
-    if: github.event_name != 'push' || github.repository == 'pyccel/pyccel'
+    if: github.event_name != 'push' || github.repository == 'pyccel/pyccel-cuda'
     outputs:
       matrix: ${{ steps.set-matrix.outputs.matrix }}
     steps:

.github/workflows/macosx.yml

@@ -16,7 +16,7 @@ on:
         required: false
         type: string
   push:
-    branches: devel
+    branches: [devel, main]
 
 env:
   COMMIT: ${{ inputs.ref || github.event.ref }}
@@ -28,7 +28,7 @@ env:
 jobs:
   Python_version_picker:
     runs-on: macos-latest
-    if: github.event_name != 'push' || github.repository == 'pyccel/pyccel'
+    if: github.event_name != 'push' || github.repository == 'pyccel/pyccel-cuda'
     outputs:
       python_version: ${{ steps.set-python_version.outputs.python_version }}
     steps:

.github/workflows/pickle.yml

@@ -19,7 +19,7 @@ on:
         required: false
         type: string
   push:
-    branches: devel
+    branches: [devel, main]
 
 env:
   COMMIT: ${{ inputs.ref || github.event.ref }}
@@ -31,7 +31,7 @@ env:
 jobs:
   Python_version_picker:
     runs-on: ubuntu-latest
-    if: github.event_name != 'push' || github.repository == 'pyccel/pyccel'
+    if: github.event_name != 'push' || github.repository == 'pyccel/pyccel-cuda'
     outputs:
       python_version: ${{ steps.set-matrix.outputs.python_version }}
       matrix: ${{ steps.set-matrix.outputs.matrix }}

.github/workflows/pickle_wheel.yml

@@ -16,7 +16,7 @@ on:
         required: false
         type: string
   push:
-    branches: devel
+    branches: [devel, main]
 
 env:
   COMMIT: ${{ inputs.ref || github.event.ref }}
@@ -28,7 +28,7 @@ env:
 jobs:
   Python_version_picker:
     runs-on: ubuntu-latest
-    if: github.event_name != 'push' || github.repository == 'pyccel/pyccel'
+    if: github.event_name != 'push' || github.repository == 'pyccel/pyccel-cuda'
     outputs:
       python_version: ${{ steps.set-python_version.outputs.python_version }}
     steps: