separating build into docker and gcc (#54)

* separating build into docker and gcc

* fixing pages build

* run tests in serial

* not running tests in parallel for focker

* making sure memcheck happens

.github/workflows/docker.yml

@@ -0,0 +1,50 @@
+name: Docker
+
+on: [push, pull_request]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  docker-build-and-test:
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+    name: Build and Test - ${{ matrix.dockerfile }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        dockerfile:
+          - Dockerfile
+          - Dockerfile.coverage
+          - Dockerfile.memcheck
+          - Dockerfile.mpi
+          - Dockerfile.mpi.memcheck
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+        with:
+          submodules: recursive
+
+      - name: Build Docker image
+        run: docker build -t tuvx -f docker/${{ matrix.dockerfile }} .
+
+      - name: Run tests in container
+        if: matrix.dockerfile != 'Dockerfile.coverage'
+        run: docker run --name test-container -t tuvx bash -c 'make test ARGS="--rerun-failed --output-on-failure"'
+
+      - name: Run coverage tests in container
+        if: matrix.dockerfile == 'Dockerfile.coverage'
+        run: docker run --name test-container -t tuvx bash -c 'make coverage ARGS="--rerun-failed --output-on-failure"'
+
+      - name: Copy coverage from container
+        if: matrix.dockerfile == 'Dockerfile.coverage'
+        run: docker cp test-container:build/coverage.info .
+
+      - name: Upload coverage report
+        if: matrix.dockerfile == 'Dockerfile.coverage'
+        uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: coverage.info

.github/workflows/gh-pages.yml

@@ -54,7 +54,7 @@ jobs:
 
           # create two copies of the documentaiton
           # 1. the frozen version, represented as vX.X in the version switcher
-          docker build -t tuvx -f Dockerfile.docs .
+          docker build -t tuvx -f docker/Dockerfile.docs .
           id=$(docker create tuvx)
           docker cp $id:/build/docs/sphinx tmpdocs
           docker rm -v $id
@@ -63,7 +63,7 @@ jobs:
 
           # 2. stable, represented as vX.X (stable) in the version switcher
           # edit conf.py to produce a version string that looks like vX.X (stable)
-          docker build -t tuvx -f Dockerfile.docs --build-arg SUFFIX=" (stable)" .
+          docker build -t tuvx -f docker/Dockerfile.docs --build-arg SUFFIX=" (stable)" .
           id=$(docker create tuvx)
           docker cp $id:/build/docs/sphinx tmpdocs
           docker rm -v $id
@@ -84,7 +84,7 @@ jobs:
           !contains(github.ref, env.DEFAULT_BRANCH)
         run: |
           set -x
-          docker build -t tuvx -f Dockerfile.docs .
+          docker build -t tuvx -f docker/Dockerfile.docs .
           id=$(docker create tuvx)
           docker cp $id:/build/docs/sphinx tmpdocs
           docker rm -v $id

.github/workflows/ubuntu.yml

@@ -0,0 +1,35 @@
+name: Ubuntu
+
+on: [ push, pull_request ]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  gcc:
+    runs-on: ubuntu-latest
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+    strategy:
+      matrix:
+        gcc_version: [11, 12, 13]
+    env:
+      FC: gfortran-${{ matrix.gcc_version }}
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        submodules: recursive
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y libnetcdf-dev netcdf-bin libnetcdff-dev
+    - name: Install python dependencies
+      run: pip install numpy scipy
+    - name: Run Cmake 
+      run: cmake -S . -B build 
+    - name: Build
+      run: cmake --build build --parallel
+    - name: Run tests
+      run: |
+        cd build
+        ctest --rerun-failed --output-on-failure . --verbose

CMakeLists.txt

@@ -31,7 +31,7 @@ option(ENABLE_MPI "Enable MPI parallel support" OFF)
 cmake_dependent_option(ENABLE_OPENMP "Enable OpenMP support" OFF "ENABLE_MPI" OFF)
 option(ENABLE_TESTS "Build tests" ON)
 option(ENABLE_COVERAGE "Enable code coverage output" OFF)
-option(ENABLE_MEMCHECK "Enable memory checking in tests" ON)
+option(ENABLE_MEMCHECK "Enable memory checking in tests" OFF)
 option(ENABLE_NC_CONFIG "Use nc-config to determine NetCDF libraries" OFF)
 option(BUILD_DOCS "Build the documentation" OFF)
 

README.md

@@ -5,7 +5,8 @@
 Tropospheric ultraviolet-extended (TUV-x): A photolysis rate calculator
 
 [![License](https://img.shields.io/github/license/NCAR/tuv-x.svg)](https://github.com/NCAR/tuv-x/blob/main/LICENSE)
-[![CI Status](https://github.com/NCAR/tuv-x/actions/workflows/test.yml/badge.svg)](https://github.com/NCAR/tuv-x/actions/workflows/test.yml)
+[![Ubuntu](https://github.com/NCAR/tuv-x/actions/workflows/ubuntu.yml/badge.svg)](https://github.com/NCAR/tuv-x/actions/workflows/ubuntu.yml)
+[![Docker](https://github.com/NCAR/tuv-x/actions/workflows/docker.yml/badge.svg)](https://github.com/NCAR/tuv-x/actions/workflows/docker.yml)
 [![codecov](https://codecov.io/gh/NCAR/tuv-x/branch/main/graph/badge.svg?token=H46AAEAQF9)](https://codecov.io/gh/NCAR/tuv-x)
 [![DOI](https://zenodo.org/badge/396946468.svg)](https://zenodo.org/badge/latestdoi/396946468)
 [![](https://img.shields.io/badge/Contribute%20with-Gitpod-908a85?logo=gitpod)](https://gitpod.io/#https://github.com/NCAR/tuv-x)

Dockerfile → docker/Dockerfile

@@ -27,7 +27,6 @@ COPY . /tuv-x/
 RUN mkdir /build \
       && cd /build \
       && cmake -D CMAKE_BUILD_TYPE=release \
-               -D ENABLE_MEMCHECK=OFF \
                /tuv-x \
       && make install -j 8
 

docker/Dockerfile.memcheck

@@ -0,0 +1,32 @@
+FROM fedora:37
+
+RUN dnf -y update \
+    && dnf -y install \
+        gcc-fortran \
+        gcc-c++ \
+        gcc \
+        gdb \
+        git \
+        netcdf-fortran-devel \
+        cmake \
+        make \
+        lcov \
+        valgrind \
+        python3 \
+        python3-pip \
+        lapack-devel \
+        yaml-cpp-devel \
+    && dnf clean all
+
+RUN pip3 install numpy scipy
+
+# build the tuv-x tool
+COPY . /tuv-x/
+RUN mkdir /build \
+      && cd /build \
+      && cmake \
+            -DENABLE_MEMCHECK:BOOL=TRUE \
+        /tuv-x \
+      && make -j 8
+
+WORKDIR /build

Dockerfile.mpi → docker/Dockerfile.mpi

@@ -42,7 +42,6 @@ RUN mkdir build \
                -D CMAKE_CXX_COMPILER=/usr/lib64/openmpi/bin/mpicxx \
                -D ENABLE_OPENMP:BOOL=TRUE \
                -D ENABLE_MPI:BOOL=TRUE \
-               -D ENABLE_MEMCHECK:BOOL=FALSE \
                ../tuv-x \
       && make -j 8