add noah-owp-modular workflow (#96)

* add noah-owp-modular workflow

* change master to main and addressing comments

* Remove LD_LIBRARY_PATH for macOS

* add noah-owp-modular workflow

* change master to main and addressing comments

* Remove LD_LIBRARY_PATH for macOS

* Revise build and run

* Use unified build and run codes for Linux & MacOS

* Add make clean

* Fix a configure issue

* Add revised ngen_integration.yaml

* Clean up commit history
Brew install gcc9

Try Homebrew

Try Linux

Try Linux with brew install

* Try Linux style gfortran

* Add a comment on gfortran in macOS

* Remove the re-checkout

* Delete .github/workflows/tmp.md

* update realization.json to include pet

---------

Co-authored-by: JessicaGarrett-NOAA <[email protected]>

.github/workflows/Build_and_Run_Standalone_Test.yml

@@ -0,0 +1,78 @@
+# Test changes that have been pushed to the main branch
+
+name: Testing and Validation
+
+# Controls when the action will run.
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  workflow_dispatch:
+
+#env:
+  # Obtained from https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources
+  # TODO: add something later that can check the runners for hyperthreading
+  #LINUX_NUM_PROC_CORES: 2
+  #MACOS_NUM_PROC_CORES: 3
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # Run general unit tests in linux environment
+  test_unit:
+    # The type of runner that the job will run on
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+      fail-fast: false
+    runs-on: ${{ matrix.os }}
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+    - name: Checkout the commit
+      uses: actions/checkout@v4
+
+    - name: Install NetCDF
+      run: |
+        if [ ${{ runner.os }} == 'Linux' ]
+        then
+          sudo apt-get update
+          sudo apt-get install -y --fix-missing libnetcdf-dev libnetcdff-dev libnetcdf-c++4-1 libnetcdf-c++4-dev
+          echo "NETCDF=/usr" >> $GITHUB_ENV
+        elif [ ${{ runner.os }} == 'macOS' ]
+        then
+          brew install netcdf netcdf-cxx netcdf-fortran
+          echo "LIBRARY_PATH=/usr/local/lib/:$LIBRARY_PATH" >> $GITHUB_ENV
+          echo "LDFLAGS=-L/usr/local/lib" >> $GITHUB_ENV
+          echo "INCLUDE=/usr/local/include" >> $GITHUB_ENV
+          echo "NETCDF=/usr/local" >> $GITHUB_ENV
+        fi
+    
+    # Build and run noah executable
+    # noah-owp-modular's configure system has 5 options serving the need for different computer
+    # servers and OS environment. The numbers 5 is for Linux type computing enviroments.
+    # Using the Linux option for macOS as macOS could not find gfortran in /usr/local/bin/.
+    - name: Configure
+      run: |
+        if [ ${{ runner.os }} == 'Linux' ]
+        then
+          ./configure 5
+        elif [ ${{ runner.os }} == 'macOS' ]
+        then
+          sudo ln -s $(which gfortran-13) /usr/local/bin/gfortran
+          ./configure 5
+        fi
+
+    - name: Build and Run Standalone
+      run: |
+        make clean
+        make
+        cd run
+        ./noah_owp_modular.exe namelist.input
+
+    - name: Build and Run BMI test
+      run: |
+        make clean
+        make testBMI
+        cd test
+        ./noahowp_test.exe ../run/namelist.input

.github/workflows/ngen_integration.yaml

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+# Test ngen-cfe integration
+
+name: Ngen Integration Tests
+
+# Controls when the action will run.
+on:
+  push:
+    branches: [ main, dev, notreal ]
+  pull_request:
+    branches: [ main, dev, notreal ]
+  workflow_dispatch:
+
+env:
+  # Obtained from https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources
+  # TODO: add something later that can check the runners for hyperthreading
+  LINUX_NUM_PROC_CORES: 2
+  MACOS_NUM_PROC_CORES: 3
+  ASAN_OPTIONS: detect_leaks=false
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # Run general unit tests in linux environment
+  test_surfacebmi_plus_cfe:
+    # The type of runner that the job will run on
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+      fail-fast: false
+    runs-on: ${{ matrix.os }}
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+
+      # Checkout and build the noah-owp-modular
+      - name: Checkout the commit
+        uses: actions/checkout@v4
+
+      - name: Save noah-owp-modular to a Temp Directory
+        run: |
+          # Move files to appropriate temporary directory
+          mkdir ${{runner.temp}}/noah-owp-modular
+          mv ./* ${{runner.temp}}/noah-owp-modular
+
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - name: checkout actions in another repo
+        uses: actions/checkout@v4
+        with:
+          repository: noaa-owp/ngen
+
+      - name: Build ISO C Fortran BMI
+        id: submod_build_2
+        uses: ./.github/actions/ngen-submod-build
+        with:
+          mod-dir: "extern/iso_c_fortran_bmi/"
+
+      - name: Build CFE
+        id: submod_build_3
+        uses: ./.github/actions/ngen-submod-build
+        with:
+          mod-dir: "extern/cfe/"
+          targets: "cfebmi"
+
+      - name: Build PET
+        id: submod_build_5
+        uses: ./.github/actions/ngen-submod-build
+        with:
+          mod-dir: "extern/evapotranspiration/evapotranspiration"
+          targets: "petbmi"
+
+      - name: Build SLoTH
+        id: submod_build_6
+        uses: ./.github/actions/ngen-submod-build
+        with:
+          mod-dir: "extern/sloth/"
+          targets: "slothmodel"
+
+      # Build Ngen and save some files
+      - name: Build Ngen
+        id: ngen_id1
+        uses: ./.github/actions/ngen-build
+        with:
+          targets: "ngen"
+          build-cores: ${{ env.LINUX_NUM_PROC_CORES }}
+          #is this required for this test?
+          bmi_c: 'ON'
+          bmi_fortran: 'ON'
+        timeout-minutes: 15
+
+      - name: Prepare to Build noah-owp-modular Library for Ngen
+        run: |
+          # Move files to appropriate directory to build noah-owp-modular library
+          rm -rf extern/noah-owp-modular/noah-owp-modular/*
+          mv ${{runner.temp}}/noah-owp-modular/* extern/noah-owp-modular/noah-owp-modular
+
+      - name: Build Noah-owp-modular Surfacebmi
+        id: submod_build_1
+        uses: ./.github/actions/ngen-submod-build
+        with:
+          mod-dir: " extern/noah-owp-modular/"
+          targets: "surfacebmi"
+
+      - name: Run Ngen Test
+        run: |
+          # Run ngen with NoahOWPModular, CFE & PET
+          mv ${{ steps.ngen_id1.outputs.build-dir }} ./ngen-build/
+          inputfile='data/example_bmi_multi_realization_config_w_noah_pet_cfe.json'
+          ./ngen-build/ngen ./data/catchment_data.geojson "cat-27" ./data/nexus_data.geojson "nex-26" $inputfile