Merge branch 'develop' into feature/new_ip

Fixes ufs-community#242.

.github/workflows/debug-docs-test_coverage.yml

@@ -0,0 +1,115 @@
+name: debug-docs-test_coverage
+on: [push, pull_request]
+
+defaults:
+  run:
+    shell: bash -exo pipefail {0}
+
+jobs:
+  debug-build-and-test:
+    runs-on: ubuntu-latest
+
+    steps:
+
+    - name: install-dependencies
+      run: |
+          sudo apt-get update
+          sudo apt-get install libmpich-dev
+          sudo apt-get install doxygen
+          sudo apt-get install libpng-dev
+          sudo apt-get install libjpeg-dev
+          sudo apt-get install libnetcdf-dev libnetcdff-dev netcdf-bin pkg-config
+          python3 -m pip install gcovr
+
+    - name: cache-esmf
+      id: cache-esmf
+      uses: actions/cache@v2
+      with:
+        path: ~/esmf
+        key: esmf-8.0.1-${{ runner.os }}
+
+    - name: build-esmf
+      if: steps.cache-esmf.outputs.cache-hit != 'true'
+      run: |
+        pushd ~
+        export ESMF_DIR=~/esmf-ESMF_8_0_1
+        wget https://github.com/esmf-org/esmf/archive/ESMF_8_0_1.tar.gz &> /dev/null
+        tar zxf ESMF_8_0_1.tar.gz
+        cd esmf-ESMF_8_0_1
+        export ESMF_COMM=mpich3
+        export ESMF_INSTALL_BINDIR=bin
+        export ESMF_INSTALL_LIBDIR=lib
+        export ESMF_INSTALL_MODDIR=mod
+        export ESMF_COMPILER=gfortran
+        export ESMF_INSTALL_PREFIX=~/esmf
+        export ESMF_NETCDF=split
+        export ESMF_NETCDF_INCLUDE=/usr/include
+        export ESMF_NETCDF_LIBPATH=/usr/x86_64-linux-gnu
+        make -j2
+        make install
+
+    - name: cache-jasper
+      id: cache-jasper
+      uses: actions/cache@v2
+      with:
+        path: ~/jasper
+        key: jasper-2.0.25-${{ runner.os }}
+
+    - name: build-jasper
+      if: steps.cache-jasper.outputs.cache-hit != 'true'
+      run: |
+        wget https://github.com/jasper-software/jasper/archive/version-2.0.25.tar.gz &> /dev/null
+        tar zxf version-2.0.25.tar.gz
+        cd jasper-version-2.0.25
+        mkdir build-jasper && cd build-jasper
+        cmake .. -DCMAKE_INSTALL_PREFIX=~/jasper
+        make -j2
+        make install
+
+    - name: cache-nceplibs 
+      id: cache-nceplibs
+      uses: actions/cache@v2
+      with:
+        path: ~/nceplibs
+        key: nceplibs-1.3.0-${{ runner.os }}
+
+    - name: build-nceplibs
+      if: steps.cache-nceplibs.outputs.cache-hit != 'true'
+      run: |
+        wget https://github.com/NOAA-EMC/NCEPLIBS/archive/v1.3.0.tar.gz &> /dev/null
+        tar zxf v1.3.0.tar.gz
+        cd NCEPLIBS-1.3.0
+        export ESMFMKFILE=~/esmf/lib/esmf.mk
+        mkdir build && cd build
+        cmake .. -DCMAKE_PREFIX_PATH='~;~/jasper' -DCMAKE_INSTALL_PREFIX='~/nceplibs' -DFLAT=ON
+        make -j2
+       
+    - name: checkout-ufs-utils
+      uses: actions/checkout@v2
+      with: 
+        path: ufs_utils
+
+    - name: build
+      run: |
+        export ESMFMKFILE=~/esmf/lib/esmf.mk
+        cd ufs_utils
+        mkdir build && cd build
+        export CC=mpicc
+        export CXX=mpicxx
+        export FC=mpifort
+        cmake .. -DCMAKE_PREFIX_PATH='~/jasper;~/nceplibs' -DCMAKE_BUILD_TYPE=Debug -DENABLE_DOCS=On -DCMAKE_Fortran_FLAGS="-g -fprofile-arcs -ftest-coverage -O0"
+        make -j2
+
+    - name: test
+      run: |
+        cd ufs_utils/build/tests/chgres_cube/data
+        wget -i files.txt
+        cd ../../..
+        ctest --rerun-failed --output-on-failure
+        export PATH="/home/runner/.local/bin:$PATH"
+        gcovr -r .. --html-details -o test-coverage.html
+
+    - uses: actions/upload-artifact@v2
+      with:
+        name: test-coverage
+        path: ufs_utils/build/*.html