LGAR-C workflow for automated tests (#15)

* Test Lgar=C in standalone mode

* Add ngen integration

* Change trigger name

* Add conditional for removing LGAR-C dir

* Fix a bug in ngen_integration.yaml

* Fix realization path

* Move some data file into appropriate dir

* Add sft test

* Revise workflow file

* Fix a path error in realization files

* Fix a bug in workflow file

* Fix a sft file path name error

* Add SMP test

* Removing potentially unnecessary libs builds

* Removing buid PET submodule

* Re-order the various tests in standalone runs

.github/workflows/build_and_run_tests.yml

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+# Test changes that have been pushed to the master branch
+
+name: Testing and Validation
+
+# Controls when the action will run.
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+  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: Build and Run Unittest
+      run: |
+        mkdir build && cd build
+        cmake ../ -DUNITTEST=ON
+        make && cd ../tests
+        ./run_unittest.sh && cd ..
+
+    - name: Build and Run Synthetic Tests
+      run: |
+        if [ -d "./build/" ]
+        then
+          rm -rf build
+        fi
+        mkdir build && cd build
+        cmake ../ -DSTANDALONE=ON
+        make && cd ../tests
+        ./run_synthetic.sh 0
+        ./run_synthetic.sh 1
+        ./run_synthetic.sh 2
+
+    - name: Build and Run Standalone
+      run: |
+        if [ -d "./build/" ]
+        then
+          rm -rf build
+        fi
+        mkdir build && cd build
+        cmake ../ -DSTANDALONE=ON
+        make && cd ..
+        ./build/lasam_standalone configs/config_lasam_Phillipsburg.txt
+        ./build/lasam_standalone configs/config_lasam_Bushland.txt

.github/workflows/ngen_integration.yaml

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+# Test ngen-lgar-c integration
+
+name: Ngen Integration Tests
+
+# Controls when the action will run.
+on:
+  push:
+    branches: [ master, dev, notreal ]
+  pull_request:
+    branches: [ master, 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_lgar-c:
+    # 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 LGAR-C
+      - name: Checkout the commit
+        uses: actions/checkout@v4
+
+      - name: Build the LGAR-C Library
+        run: |
+          cmake -B cmake_build -S . -DNGEN=ON
+          make -C cmake_build
+
+      - name: Save LGAR-C to a Temp Directory
+        run: |
+          # Move files to a temporary directory
+          mkdir ${{runner.temp}}/lgar
+          mv ./* ${{runner.temp}}/lgar
+
+      # Checkout and build the SoilMoistureProfiles
+      - name: Checkout the commit
+        uses: actions/checkout@v4
+        with:
+          repository: noaa-owp/soilmoistureprofiles
+
+      - name: Build the SMP Library
+        run: |
+          cmake -B cmake_build -S . -DNGEN=ON
+          make -C cmake_build
+
+      - name: Save SoilMoistureProfile to a Temp Directory
+        run: |
+          # Move files to a temporary directory
+          mkdir ${{runner.temp}}/smp
+          mv ./* ${{runner.temp}}/smp
+
+      # 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/soilfreezethaw
+
+      - name: Build the SFT Library
+        run: |
+          cmake -B cmake_build -S . -DNGEN=ON
+          make -C cmake_build
+
+      - name: Save SoilFreezeThaw to a Temp Directory
+        run: |
+          # Move files to a temporary directory
+          mkdir ${{runner.temp}}/sft
+          mv ./* ${{runner.temp}}/sft
+
+      # 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 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'
+        timeout-minutes: 15
+
+      - name: Move LGAR-C File Including cmake_build to Appropriate Directory
+        run: |
+          if [ -d "./extern/LGAR-C/" ]
+          then
+            rm -rf extern/LGAR-C
+          fi
+          mkdir extern/LGAR-C
+          mv ${{runner.temp}}/lgar/* extern/LGAR-C
+
+      - name: Move SFT Files Including cmake_build to Appropriate Directory
+        run: |
+          rm -rf extern/SoilFreezeThaw/SoilFreezeThaw/*
+          mv ${{runner.temp}}/sft/* extern/SoilFreezeThaw/SoilFreezeThaw
+
+      - name: Move SMP Files Including cmake_build to Appropriate Directory
+        run: |
+          rm -rf extern/SoilMoistureProfiles/SoilMoistureProfiles/*
+          mv ${{runner.temp}}/smp/* extern/SoilMoistureProfiles/SoilMoistureProfiles
+
+      - name: Run Ngen Test with LASAM
+        run: |
+          # Run ngen with sft, smp, and lasam
+          mv ${{ steps.ngen_id1.outputs.build-dir }} ./ngen-build/
+          cp extern/LGAR-C/data/vG_default_params.dat data/
+          inputfile='extern/LGAR-C/realizations/realization_config_lasam_ngenCI.json'
+          ./ngen-build/ngen ./data/catchment_data.geojson "cat-27" ./data/nexus_data.geojson "nex-26" $inputfile
+
+      - name: Run Ngen Test with SFT and SMP
+        run: |
+          inputfile='extern/LGAR-C/realizations/realization_config_lasam_sft_ngenCI.json'
+          ./ngen-build/ngen ./data/catchment_data.geojson "cat-27" ./data/nexus_data.geojson "nex-26" $inputfile
+
+      - name: Run Ngen Test with SMP
+        run: |
+          inputfile='extern/LGAR-C/realizations/realization_config_lasam_smp_ngenCI.json'
+          ./ngen-build/ngen ./data/catchment_data.geojson "cat-27" ./data/nexus_data.geojson "nex-26" $inputfile

realizations/realization_config_lasam_ngenCI.json

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+{
+    "time": {
+	"start_time": "2016-10-01 00:00:00",
+        "end_time": "2017-08-09 11:00:00",
+        "output_interval": 3600
+    },
+    "catchments": {
+        "cat-27": {
+            "formulations": [
+                {
+		    "name": "bmi_multi",
+                    "params": {
+			"model_type_name": "bmi_multi_lasam",
+			"forcing_file": "",
+			"init_config": "",
+			"allow_exceed_end_time": true,
+			"main_output_variable": "total_discharge",
+			"output_variables" : [
+			    "precipitation",
+			    "potential_evapotranspiration",
+			    "actual_evapotranspiration",
+			    "surface_runoff",
+			    "giuh_runoff",
+			    "soil_storage",
+			    "total_discharge",
+			    "infiltration",
+			    "percolation"
+			],
+			"modules": [
+			    {
+				"name": "bmi_c++",
+				"params": {
+                                    "model_type_name": "bmi_c++_sloth",
+                                    "library_file": "./extern/sloth/cmake_build/libslothmodel",
+                                    "init_config": "/dev/null",
+                                    "allow_exceed_end_time": true,
+                                    "main_output_variable": "z",
+                                    "uses_forcing_file": false,
+                                    "model_params": {
+					"soil_temperature_profile(1,double,K,node)" : 275.15
+                                    }
+				}
+                            },
+			    {
+				"name": "bmi_c++",
+				"params": {
+				    "model_type_name": "bmi_lasam",
+				    "library_file": "./extern/LGAR-C/cmake_build/liblasambmi",
+				    "init_config": "./extern/LGAR-C/configs/config_lasam_Phillipsburg.txt",
+				    "allow_exceed_end_time": true,
+				    "main_output_variable": "precipitation_rate",
+				    "variables_names_map" : {
+					"precipitation_rate" : "P",
+					"potential_evapotranspiration_rate" : "PET"
+				    },
+				    "output_variables" : [
+					"precipitation",
+					"potential_evapotranspiration",
+					"actual_evapotranspiration",
+					"surface_runoff",
+					"giuh_runoff",
+					"soil_storage",
+					"total_discharge",
+					"infiltration",
+					"percolation"
+				    ],
+				    "uses_forcing_file": false
+				}
+			    }
+			],
+			"uses_forcing_file": false
+		    }
+		}
+            ],
+            "forcing": {
+		"path" : "./extern/LGAR-C/forcing/forcing_data_resampled_uniform_Phillipsburg.csv"
+            }
+        }
+    }
+}