Merge branch 'master' into doxygen

.github/workflows/ci.yml

@@ -4,52 +4,86 @@ on:
   push:
     branches:
       - master
-
   pull_request:
 
 jobs:
-
-  # try to build SIPNET on Ubuntu & MacOS
+  # Build and Integration Test
   build:
     strategy:
       fail-fast: false
       matrix:
-        OS:
+        OS: 
           - macos-latest
           - ubuntu-latest
           - ubuntu-20.04
+    runs-on: ${{ matrix.OS }}
+
+    steps:
+      # checkout source code
+      - uses: actions/checkout@v2
+
+      # install doxygen
+      - name: Install Doxygen
+        run:  |
+          if [[ "$RUNNER_OS" == "Linux" ]]; then
+            sudo apt-get install doxygen -y
+          elif [[ "$RUNNER_OS" == "macOS" ]]; then
+            brew install --formula doxygen
+          fi
+        
+      # compile SIPNET
+      - name: compile sipnet
+        run: make
+
+      # remove existing test output file
+      - name: Remove Niwout Output File
+        run: rm Sites/Niwot/niwot.out
+
+      # run single sipnet run
+      - name: Run SIPNET on Sites/Niwot/niwot
+        run: ./sipnet
+
+      # check for correct output of Niwot run
+      - name: Check if niwot.out is generated
+        shell: bash
+        run: |
+          if [ ! -f Sites/Niwot/niwot.out ]; then
+            echo "::error title={No Output}::Test run for Niwot site failed to produce output"
+            exit 1
+          fi
+        
+      # Check if niwot.out has changed 
+      - name: Check whether niwot.out has changed 
+        shell: bash
+        run: |
+          if git diff --exit-code Sites/Niwot/niwot.out; then
+            echo "Success: Niwot.out created and has not changed"
+          else
+            echo "::error title={Output Changed}::The test file niwot.out has changed. This is expected to fail with some changes to SIPNET. When this happens, assess correctness and then update the reference niwot.out."
+            exit 1
+          fi
 
+  # Run Unit Tests
+  test:
+    needs: build
+    strategy:
+      fail-fast: false
+      matrix:
+        OS: 
+          - macos-latest
+          - ubuntu-latest
+          - ubuntu-20.04
     runs-on: ${{ matrix.OS }}
 
     steps:
-    # checkout source code
-    - uses: actions/checkout@v2
-
-    # compile sipnet
-    - name: compile sipnet
-      run: make
-
-    # remove existing test output file
-    - name: Remove Niwout Output File
-      run: rm Sites/Niwot/niwot.out
-
-    # run single sipnet run
-    - name: sipnet on Sites/Niwot/niwot
-      run: ./sipnet
-
-    # check output of test
-    - name: fail if no niwot output exists
-      if: ${{ hashFiles('Sites/Niwot/niwot.out') == '' }}
-      run: |
-        echo "::error title={No Output}::Test run for Niwot site failed to produce output"
-        exit 1
-    # check whether niwot.out has changed
-    - name: Check whether niwot.out has changed 
-      shell: bash
-      run: |
-         if git diff --exit-code Sites/Niwot/niwot.out; then
-           echo "Success: Niwot.out created and has not changed"
-           else
-             echo "::error title={Output Changed}::The test file niwot.out has changed"
-           exit 1
-           fi
+      # checkout source code
+      - uses: actions/checkout@v2
+
+      # compile unit tests
+      - name: compile tests
+        run: make test
+
+      # run tests
+      - name: Run Unit Tests
+        run: make testrun
+

.gitignore

@@ -14,20 +14,6 @@ docs/latex
 .Rproj.user
 .Rhistory
 
-
-# build artifacts and executables
-*.o
-estimate
-sipnet
-subsetData
-transpose
-.doxygen.stamp
-
-# documentation
-docs/html/
-docs/latex/
-
-
 # System-specific files
 .DS_Store
 .Rproj.user

CONTRIBUTING.md

@@ -3,7 +3,7 @@
 
 ## Compiling
 
-SIPNET uses `make` build the model and documentation. There are also miscellaneous targets for running analysis workflows:
+SIPNET uses `make` to build the model and documentation. There are also miscellaneous targets for running analysis workflows:
 
 ```sh
 # build SIPNET executable
@@ -15,3 +15,20 @@ make clean
 # list all make commands
 make help
 ```
+## Testing
+
+SIPNET also uses `make` to build and run its unit tests. This can be done with the following commands:
+```shell
+# Compile tests
+make test
+# Run tests
+make testrun
+# Clean after tests are run
+make testclean
+```
+
+If changes are made to the `modelStructure.h` file and unit tests are failing, try running the update script as shown below. Consider running this script even if unit tests _are not_ failing.
+```shell
+# Run this command from the root directory to update unit test versions of modelStructures.h
+tests/update_model_structures.sh
+```

Makefile

@@ -1,15 +1,16 @@
 CC=gcc
 LD=gcc
+AR=ar
 CFLAGS=-Wall
 LIBLINKS=-lm
 
-ESTIMATE_CFILES=sipnet.c ml-metro5.c ml-metrorun.c paramchange.c runmean.c util.c spatialParams.c namelistInput.c outputItems.c
+ESTIMATE_CFILES=sipnet.c ml-metro5.c ml-metrorun.c paramchange.c runmean.c util.c spatialParams.c namelistInput.c outputItems.c events.c
 ESTIMATE_OFILES=$(ESTIMATE_CFILES:.c=.o)
 
-SENSTEST_CFILES=sipnet.c sensTest.c paramchange.c runmean.c util.c spatialParams.c namelistInput.c outputItems.c
+SENSTEST_CFILES=sipnet.c sensTest.c paramchange.c runmean.c util.c spatialParams.c namelistInput.c outputItems.c events.c
 SENSTEST_OFILES=$(SENSTEST_CFILES:.c=.o)
 
-SIPNET_CFILES=sipnet.c frontend.c runmean.c util.c spatialParams.c namelistInput.c outputItems.c
+SIPNET_CFILES=sipnet.c frontend.c runmean.c util.c spatialParams.c namelistInput.c outputItems.c events.c
 SIPNET_OFILES=$(SIPNET_CFILES:.c=.o)
 
 TRANSPOSE_CFILES=transpose.c util.c
@@ -25,13 +26,9 @@ DOXYFILE = docs/Doxyfile
 DOXYGEN_HTML_DIR = docs/html
 DOXYGEN_LATEX_DIR = docs/latex
 
-# .PHONY indicates target names that are not file names, preventing conflicts if these names are used for filenames
-.PHONY: all clean document estimate sipnet transpose subsetData doxygen
-
 # all: estimate sensTest sipnet transpose subsetData
 all: estimate sipnet transpose subsetData document
 
-
 # Only update docs if source files or Doxyfile have changed
 document: .doxygen.stamp
 
@@ -58,8 +55,45 @@ subsetData: $(SUBSET_DATA_OFILES)
 clean:
 	rm -f $(ESTIMATE_OFILES) $(SIPNET_OFILES) $(TRANSPOSE_OFILES) $(SUBSET_DATA_OFILES) estimate sensTest  sipnet transpose subsetData
 	rm -rf $(DOXYGEN_HTML_DIR) $(DOXYGEN_LATEX_DIR)
-#clean:
-#	rm -f $(ESTIMATE_OFILES) $(SENSTEST_OFILES) $(SIPNET_OFILES) $(TRANSPOSE_OFILES) $(SUBSET_DATA_OFILES) estimate sensTest  sipnet transpose subsetData
+
+# UNIT TESTS
+SIPNET_TEST_DIRS:=$(shell find tests/sipnet -type d -mindepth 1 -maxdepth 1)
+SIPNET_TEST_DIRS_RUN:= $(addsuffix .run, $(SIPNET_TEST_DIRS))
+SIPNET_TEST_DIRS_CLEAN:= $(addsuffix .clean, $(SIPNET_TEST_DIRS))
+SIPNET_LIB=libsipnet.a
+
+$(SIPNET_LIB): $(SIPNET_LIB)($(SIPNET_OFILES))
+	ranlib $(SIPNET_LIB)
+
+test: pretest $(SIPNET_TEST_DIRS) posttest $(SIPNET_LIB)
+
+pretest:
+	cp modelStructures.h modelStructures.orig.h
+
+# The dash in the build command tells make to continue if there are errors, allowing cleanup
+$(SIPNET_TEST_DIRS): pretest $(SIPNET_LIB)
+	cp $@/modelStructures.h modelStructures.h
+	-$(MAKE) -C $@
+
+# This is far from infallible, as model_structures.h will be in a bad place if a test
+# build step fails in a non-catchable way
+posttest: $(SIPNET_TEST_DIRS)
+	mv modelStructures.orig.h modelStructures.h
+
+testrun: $(SIPNET_TEST_DIRS_RUN)
+
+$(SIPNET_TEST_DIRS_RUN):
+	$(MAKE) -C $(basename $@) run
+
+testclean: $(SIPNET_TEST_DIRS_CLEAN)
+	rm -f $(SIPNET_LIB)
+
+$(SIPNET_TEST_DIRS_CLEAN):
+	$(MAKE) -C $(basename $@) clean
+
+.PHONY: all clean document estimate sipnet transpose subsetData doxygen
+	test $(SIPNET_TEST_DIRS) pretest posttest $(SIPNET_LIB) testrun 
+	$(SIPNET_TEST_DIRS_RUN) testclean $(SIPNET_TEST_DIRS_CLEAN)
 
 help:
 	@echo "Available targets:"
@@ -68,7 +102,7 @@ help:
 	@echo "  all         - Builds all components."
 	@echo "  document    - Generate documentation."
 	@echo "  sipnet      - Builds the 'sipnet' executable."
-	@echo "  clean       - Removes compiled files and executables."
+	@echo "  clean       - Removes compiled files, executables, and documentation."
 	@echo "  depend      - Automatically generates dependency information for source files."
 	@echo "  === additional tools ==="
 	@echo "  estimate    - Builds 'estimate' executable to estimate parameters using MCMC."
@@ -80,4 +114,3 @@ depend::
 
 # DO NOT DELETE THIS LINE -- make depend depends on it.
 
-