Merge pull request #7 from mogproject/dev

Dev

.github/workflows/ut.yml

@@ -21,8 +21,10 @@ jobs:
               run: pip install numpy
             - name: Install testing dependencies
               run: pip install pytest pytest-cov mypy coveralls
-            - name: Run unit tests
-              run: make test
+            - name: Install lcov
+              run: sudo apt-get install -y lcov
+            - name: Run unit tests with coverage
+              run: make coverage
             - name: Coveralls
               uses: coverallsapp/github-action@master
               with:

Makefile

@@ -1,10 +1,35 @@
 RM = /bin/rm
 PYTHON=python3
+MKDIR=mkdir
+GCOV=gcov
+LCOV=lcov
+GENHTML=genhtml
+
+ifneq ("$(wildcard /opt/homebrew/bin/g++-12)","")
+export CC=/opt/homebrew/bin/gcc-12
+export CXX=/opt/homebrew/bin/g++-12
+GCOV=/opt/homebrew/bin/gcov-12
+else
+ifneq ("$(wildcard /opt/homebrew/bin/g++-11)","")
+export CC=/opt/homebrew/bin/gcc-11
+export CXX=/opt/homebrew/bin/g++-11
+GCOV=/opt/homebrew/bin/gcov-11
+endif
+endif
+
+CMAKE=cmake
+CMAKE_OPTS=-DCMAKE_C_COMPILER=$(CC) -DCMAKE_CXX_COMPILER=$(CXX)
 
 SRC_CPP=src/main/cpp
 BUILD_DIR=$(PWD)/build
 TEST_BIN_DIR=$(BUILD_DIR)/test
 TEST_EXEC=$(TEST_BIN_DIR)/modular_test
+COV_CPP_DIR=coverage/cpp
+COV_CPP=$(COV_CPP_DIR)/lcov.info
+COV_PY_DIR=coverage/py
+COV_PY=$(COV_PY_DIR)/lcov.info
+COV_HTML=coverage/html
+COV_MERGED=coverage/lcov.info
 
 SRC_PY=src/main/python
 TEST_PY=src/test/python
@@ -19,27 +44,38 @@ PROFILE_ON ?= false
 TRACE_ON ?= false
 
 build:
-	cd $(SRC_CPP) && cmake -S . -B $(BUILD_DIR)/Release -DCMAKE_BUILD_TYPE=Release -DPROFILE_ON=$(PROFILE_ON) -DTRACE_ON=$(TRACE_ON)
-	cd $(SRC_CPP) && cmake --build $(BUILD_DIR)/Release
+	cd $(SRC_CPP) && $(CMAKE) -S . -B $(BUILD_DIR)/Release $(CMAKE_OPTS) -DCMAKE_BUILD_TYPE=Release -DPROFILE_ON=$(PROFILE_ON) -DTRACE_ON=$(TRACE_ON)
+	cd $(SRC_CPP) && $(CMAKE) --build $(BUILD_DIR)/Release
 
 test: test-cpp test-py
 
-test-py:
-	mypy $(SRC_PY)
-	$(PYTHON) -m pytest -x --cov=$(SRC_PY) --cov-report=lcov:./coverage/lcov.info $(PYTEST_OPTS) $(TEST_PY)
-
 test-cpp:
 	@echo "GTEST_FILTER: $(GTEST_FILTER)"
-	cd $(SRC_CPP) && cmake -DBUILD_TESTS=ON -S . -B $(BUILD_DIR)/Debug
-	cd $(SRC_CPP) && cmake --build $(BUILD_DIR)/Debug
+	cd $(SRC_CPP) && $(CMAKE) -DBUILD_TESTS=ON -S . -B $(BUILD_DIR)/Debug $(CMAKE_OPTS)
+	cd $(SRC_CPP) && $(CMAKE) --build $(BUILD_DIR)/Debug
 	$(TEST_EXEC) --output-on-failure $(GTEST_OPTS)
+	$(MKDIR) -p $(COV_CPP_DIR)
+	$(LCOV) --gcov-tool $(GCOV) -d $(TEST_BIN_DIR) -c -o "$(COV_CPP)"
+	$(LCOV) -r "${COV_CPP}" "*/include/*" "*.h" "*/test/*" "*/build*/*" -o "${COV_CPP}"
+
+test-py:
+	mypy $(SRC_PY)
+	$(MKDIR) -p $(COV_PY_DIR)
+	$(PYTHON) -m pytest -x --cov=$(SRC_PY) --cov-report=lcov:$(COV_PY) $(PYTEST_OPTS) $(TEST_PY)
+
+coverage: test
+	$(LCOV) --add-tracefile $(COV_PY) -a $(COV_CPP) -o $(COV_MERGED)
+
+coverage-html: coverage
+	$(GENHTML) -o $(COV_HTML) $(COV_MERGED)
+	open $(COV_HTML)/index.html
 
 clean:
 	@echo "Cleaning..."
-	@$(RM) -rf build/*
+	@$(RM) -rf build/* coverage/*
 	@echo "Cleaning done."
 
 lab:
 	jupyter-lab
 
-.PHONY: build test test-cpp clean lab
+.PHONY: build test test-py test-cpp coverage coverage-html clean lab

README.md

@@ -9,8 +9,8 @@ The code implements the algorithm described in *Simpler, Linear-Time Modular Dec
 ## Dependencies
 
 - C++
-  - gcc version 11 or 12
-  - CMake
+  - gcc version 11 or 12 (Mac: `brew install gcc@12`)
+  - CMake (Mac: `brew install cmake`)
 - Python
   - NetworkX (`pip install networkx`)
   - NumPy (`pip install numpy`)
@@ -19,6 +19,7 @@ The code implements the algorithm described in *Simpler, Linear-Time Modular Dec
 
 - C++
   - GoogleTest (automatically installed during the build process)
+  - lcov (Mac: `brew install lcov`)
 - Python
   - pytest (`pip install pytest`)
   - pytest-cov (`pip install pytest-cov`)

src/main/cpp/CMakeLists.txt

@@ -12,15 +12,6 @@ option(BUILD_TESTS "Build test programs" OFF)
 set(CMAKE_CXX_STANDARD 14)
 set(CMAKE_CXX_STANDARD_REQUIRED True)
 
-# specify compilers on local machine (Mac)
-if (EXISTS /opt/homebrew/bin/g++-12)
-  set(CMAKE_C_COMPILER /opt/homebrew/bin/gcc-12)
-  set(CMAKE_CXX_COMPILER /opt/homebrew/bin/g++-12)
-elseif(EXISTS /opt/homebrew/bin/gcc-11)
-  set(CMAKE_C_COMPILER /opt/homebrew/bin/gcc-11)
-  set(CMAKE_CXX_COMPILER /opt/homebrew/bin/g++-11)
-endif ()
-
 message("Compiler: ${CMAKE_CXX_COMPILER}")
 
 # source files

src/main/python/modular/MDTree.py

@@ -16,7 +16,7 @@ class MDTree:
     Modular decomposition tree for undirected graphs.
     """
 
-    def __init__(self, G: nx.Graph, solver: str = 'naive') -> None:
+    def __init__(self, G: nx.Graph, solver: str = 'linear') -> None:
         assert len(G) > 0, 'graph cannot be empty'
 
         if solver == 'linear':
@@ -73,7 +73,7 @@ def __repr__(self) -> str:
         return repr(self.root)
 
 
-def modular_decomposition(G: nx.Graph, sorted: bool = False, solver: str = 'naive') -> Optional[MDTree]:
+def modular_decomposition(G: nx.Graph, sorted: bool = False, solver: str = 'linear') -> Optional[MDTree]:
     """Alias to the constructor."""
 
     if len(G) == 0:

src/test/cpp/CMakeLists.txt

@@ -19,6 +19,19 @@ set(gtest_force_shared_crt ON CACHE BOOL "" FORCE)
 FetchContent_MakeAvailable(googletest)
 enable_testing()
 
+# Code coverage
+function(add_code_coverage)
+  if(CMAKE_C_COMPILER_ID MATCHES "(Apple)?[Cc]lang" OR CMAKE_CXX_COMPILER_ID MATCHES "(Apple)?[Cc]lang")
+    add_compile_options(-fprofile-instr-generate -fcoverage-mapping)
+    add_link_options(-fprofile-instr-generate -fcoverage-mapping)
+  elseif(CMAKE_C_COMPILER_ID MATCHES "GNU" OR CMAKE_CXX_COMPILER_ID MATCHES "GNU")
+    add_compile_options(-fprofile-arcs -ftest-coverage)
+    link_libraries(gcov)
+  endif()
+endfunction()
+
+add_code_coverage()
+
 # source files
 file(GLOB_RECURSE TEST_SRC
   LIST_DIRECTORIES false