Merge pull request #1 from NeuralNetworkVerification/master

Merge from master
NeuralNetworkVerification · Jul 30, 2020 · 8170038 · 8170038
2 parents 45a9f8b + 792e8ed
commit 8170038
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diff --git a/.codecov.yml b/.codecov.yml
@@ -0,0 +1,31 @@
+# Check if this file is valid by running in bash:
+# curl -X POST --data-binary @.codecov.yml https://codecov.io/validate
+
+comment: false
+
+ignore:
+  - "**/__init__.py"
+  - "maraboupy/test"
+
+coverage:
+  status:
+    # Make sure the total coverage decreased by at most 1%
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        base: auto
+        paths:
+          - "src"
+          - "maraboupy"
+    # Make sure the new added code is at least 80% covered 
+    patch: 
+      default:
+        target: 80%
+        base: auto
+        paths:
+          - "src"
+          - "maraboupy"
+
+
+
diff --git a/.gitignore b/.gitignore
@@ -19,6 +19,8 @@ tools/boost_1_68_0
 /tools/boost.unzipped
 /tools/boost_1_68_0.tar.gz
 /tools/pybind11-2.3.0
+/tools/OpenBLAS-0.3.9/
+/tools/OpenBLASv0.3.9.tar.gz
 /cpp_interface_example/example.elf
 /src/input_parsers/mps_example/mps.elf
 

diff --git a/.travis.yml b/.travis.yml
@@ -3,14 +3,34 @@ language: cpp
 cache:
   directories:
     - tools/boost_1_68_0
-
+    - $HOME/.pip-cache
+    - /c/Python3
 
 before_install:
-  - PY_CMD=python3
+  - if [ "$TRAVIS_OS_NAME" = "windows" ]; then PY_CMD=/c/Python3/python ; else PY_CMD=python3 ; fi
   - if [ "$TRAVIS_OS_NAME" = "windows" ]; then powershell Start-Process -PassThru -Wait PowerShell -ArgumentList "'-Command Set-MpPreference -DisableArchiveScanning \$true'"    ; fi
   - if [ "$TRAVIS_OS_NAME" = "windows" ]; then powershell Start-Process -PassThru -Wait PowerShell -ArgumentList "'-Command Set-MpPreference -DisableBehaviorMonitoring \$true'" ; fi
   - if [ "$TRAVIS_OS_NAME" = "windows" ]; then powershell Start-Process -PassThru -Wait PowerShell -ArgumentList "'-Command Set-MpPreference -DisableRealtimeMonitoring \$true'" ; fi
 
+addons:
+  apt:
+    packages:
+    - python3
+    - python3-pip
+    - python3-setuptools
+
+install:
+  - if [ "$TRAVIS_COMPILER" = "gcc" ]; then
+      wget https://github.com/linux-test-project/lcov/archive/v1.13.zip;
+      unzip v1.13.zip;
+      export PATH=$PATH:`pwd`/lcov-1.13/bin;
+    fi
+  - if [ "$TRAVIS_OS_NAME" = "windows" ]; then if [[ ! -d "C:\Python3" || ! -f "C:\Python3\python" ]]; then choco install python3 --version=3.5.4 --params "/InstallDir:C:\Python3"; fi fi
+  - $PY_CMD -m pip install --user --upgrade pip
+  - $PY_CMD -m pip install --user --upgrade setuptools
+  - $PY_CMD -m pip install --user wheel
+  - $PY_CMD -m pip install --user -r maraboupy/test_requirements.txt --cache-dir $HOME/.pip-cache --progress-bar off
+
 matrix:
   include:
     - os: linux
@@ -19,31 +39,63 @@ matrix:
       script:
       - mkdir -p build
       - cd build
-      - cmake .. -DRUN_UNIT_TEST=ON -DPYTHON_EXECUTABLE=$(which $PY_CMD)
+      - cmake .. -DRUN_UNIT_TEST=ON -DPYTHON_EXECUTABLE=$(which $PY_CMD) -DCMAKE_BUILD_TYPE=Debug -DCODE_COVERAGE=ON
       - cmake --build . -j 2
       - ctest -L system -j 2
       - ctest -L regress[0-1] -j 2
+      - cd ..
+      - $PY_CMD -m pytest --cov=maraboupy maraboupy/test
 
     - os: linux
       dist: xenial
       compiler: clang
       script:
       - mkdir - p build
       - cd build
-      - cmake .. -DRUN_UNIT_TEST=ON -DPYTHON_EXECUTABLE=$(which $PY_CMD)
+      - cmake .. -DRUN_UNIT_TEST=ON -DPYTHON_EXECUTABLE=$(which $PY_CMD) 
       - cmake --build . -j 2
       - ctest -L system -j 2
       - ctest -L regress0 -j 2
+      - cd ..
+      - $PY_CMD -m pytest maraboupy/test
 
     - os: windows
       script:
-      - choco install python3 --params "/InstallDir:C:\Python3"
       - mkdir -p build
       - cd build
-      - cmake .. -DRUN_UNIT_TEST=ON -DPYTHON_EXECUTABLE=/c/Python3/python -G"Visual Studio 15 2017 Win64"
+      - cmake .. -DRUN_UNIT_TEST=ON -DPYTHON_EXECUTABLE=$(which $PY_CMD) -G"Visual Studio 15 2017 Win64"
       - cmake --build . --config Release
       - ctest -L system -j 2
       - ctest -L regress0 -j 2 # does not work ...
+      - cd ..
+      - cp maraboupy/Release/* maraboupy
+      - $PY_CMD -m pytest maraboupy/test
+
+after_success:
+  - if [ "$TRAVIS_COMPILER" = "gcc" ]; then
+      codecov;
+      lcov --capture --directory . --output-file coverage.info;
+      lcov --remove coverage.info '/usr/*' '*/tools/*' '*.cc' '*/tests/*' '*Test_*.h' --output-file coverage.info;
+      lcov --list coverage.info;
+      bash <(curl -s https://codecov.io/bash) -f coverage.info || echo "Codecov did not collect coverage reports";
+    fi
+
+before_deploy:
+  - if [ "$TRAVIS_COMPILER" = "gcc" ]; then
+      pip install --user -r maraboupy/docs/requirements.txt --progress-bar off;
+      export PYTHONPATH=$PYTHONPATH:`pwd`;
+      make -C maraboupy/docs html;
+      touch maraboupy/docs/_build/html/.nojekyll;
+    fi
+
+deploy:
+  provider: pages
+  skip_cleanup: true
+  github_token: "$GITHUB_PAGES_DEPLOY_TOKEN"
+  local_dir: maraboupy/docs/_build/html
+  on:
+    branch: master
+    condition: $TRAVIS_COMPILER = gcc
 
 notifications:
   email:

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -11,6 +11,10 @@ option(RUN_UNIT_TEST "run unit tests on build" ON)
 option(RUN_REGRESS_TEST "run regression tests on build" OFF)
 option(RUN_SYSTEM_TEST "run system tests on build" OFF)
 option(RUN_MEMORY_TEST "run cxxtest testing with ASAN ON" ON)
+option(RUN_PYTHON_TEST "run python API tests if building with python" OFF)
+option(ENABLE_GUROBI "Enable use the Gurobi optimizer" OFF)
+option(ENABLE_OPENBLAS "Do symbolic bound tighting using blas" ON) # Not available on windows
+option(CODE_COVERAGE "add code coverage" OFF)  # Available only in debug mode
 
 set(DEFAULT_PYTHON_VERSION "3" CACHE STRING "Default Python version 2/3")
 set(PYTHON_VERSIONS_SUPPORTED 2 3)
@@ -33,9 +37,11 @@ set(REGRESS_DIR "${PROJECT_SOURCE_DIR}/regress")
 set(ENGINE_DIR "${SRC_DIR}/engine")
 set(PYBIND11_DIR "${TOOLS_DIR}/pybind11-2.3.0")
 set(BOOST_DIR "${TOOLS_DIR}/boost_1_68_0")
+set(OPENBLAS_DIR "${TOOLS_DIR}/OpenBLAS-0.3.9")
 set(COMMON_DIR "${SRC_DIR}/common")
 set(BASIS_DIR "${SRC_DIR}/basis_factorization")
 
+set(OPENBLAS_LIB openblas)
 
 set(BIN_DIR "${CMAKE_BINARY_DIR}/bin")
 
@@ -64,6 +70,28 @@ if(CTEST_NTHREADS EQUAL 0)
   set(CTEST_NTHREADS 1)
 endif()
 
+# --------------- set build type ----------------------------
+set(BUILD_TYPES Release Debug MinSizeRel RelWithDebInfo)
+
+# Set the default build type to Production
+if(NOT CMAKE_BUILD_TYPE)
+  set(CMAKE_BUILD_TYPE
+      Release CACHE STRING "Options are: Release Debug MinSizeRel RelWithDebInfo" FORCE)
+  # Provide drop down menu options in cmake-gui
+  set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS ${BUILD_TYPES})
+endif()
+message(STATUS "Building ${CMAKE_BUILD_TYPE} build")
+
+
+#-------------------------set code coverage----------------------------------#
+# Allow coverage only in debug mode only in gcc
+if(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU" AND CMAKE_BUILD_TYPE MATCHES Debug)
+  message(STATUS "Building with code coverage")
+  set(COVERAGE_COMPILER_FLAGS "-g -O0 --coverage" CACHE INTERNAL "")
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${COVERAGE_COMPILER_FLAGS}")
+  set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} --coverage")
+endif()
+
 
 # We build a static library that is the core of the project, the link it to the
 # API's (executable and python at the moment)
@@ -151,6 +179,40 @@ endif()
 set(LIBS_INCLUDES ${Boost_INCLUDE_DIRS})
 set(LIBS ${Boost_LIBRARIES})
 
+if (${ENABLE_GUROBI})
+  message(STATUS "Using Gurobi for LP relaxation for bound tightening")
+  if (NOT DEFINED GUROBI_DIR) 
+    set(GUROBI_DIR $ENV{GUROBI_HOME})
+  endif()
+  add_compile_definitions(ENABLE_GUROBI)
+
+  set(GUROBI_LIB1 "gurobi_c++")
+  set(GUROBI_LIB2 "gurobi90")
+
+  add_library(${GUROBI_LIB1} SHARED IMPORTED)
+  set_target_properties(${GUROBI_LIB1} PROPERTIES IMPORTED_LOCATION ${GUROBI_DIR}/lib/libgurobi_c++.a)
+  list(APPEND LIBS ${GUROBI_LIB1})
+  target_include_directories(${GUROBI_LIB1} INTERFACE ${GUROBI_DIR}/include/)
+
+  add_library(${GUROBI_LIB2} SHARED IMPORTED)
+  set_target_properties(${GUROBI_LIB2} PROPERTIES IMPORTED_LOCATION ${GUROBI_DIR}/lib/libgurobi90.so)
+  list(APPEND LIBS ${GUROBI_LIB2})
+  target_include_directories(${GUROBI_LIB2} INTERFACE ${GUROBI_DIR}/include/)
+endif()
+
+if (${ENABLE_OPENBLAS} AND NOT MSVC)
+    message(STATUS "using openblas for matrix multiplication")
+    add_compile_definitions(ENABLE_OPENBLAS)
+    #OpenBLAS
+    if(NOT EXISTS "${OPENBLAS_DIR}/installed/lib/libopenblas.a")
+        execute_process(COMMAND ${TOOLS_DIR}/download_openBLAS.sh)
+    endif()
+
+    add_library(${OPENBLAS_LIB} SHARED IMPORTED)
+    set_target_properties(${OPENBLAS_LIB} PROPERTIES IMPORTED_LOCATION ${OPENBLAS_DIR}/installed/lib/libopenblas.a)
+    list(APPEND LIBS ${OPENBLAS_LIB})
+    target_include_directories(${OPENBLAS_LIB} INTERFACE ${OPENBLAS_DIR}/installed/include)
+endif()
 
 # pthread
 set(THREADS_PREFER_PTHREAD_FLAG ON)
@@ -268,6 +330,22 @@ if (NOT ${TESTS_TO_RUN} STREQUAL "")
     )
 endif()
 
+if (${BUILD_PYTHON} AND ${RUN_PYTHON_TEST})
+    if (MSVC)
+        add_custom_command(
+            TARGET build-tests
+            POST_BUILD
+            COMMAND cp ${PYTHON_API_DIR}/Release/* ${PYTHON_API_DIR}
+        )
+    endif()
+
+    add_custom_command(
+        TARGET build-tests
+        POST_BUILD
+        COMMAND ${PYTHON_EXECUTABLE} -m pytest ${PYTHON_API_DIR}/test
+    )
+endif()
+
 # Add the input parsers
 add_custom_target(build_input_parsers)
 add_dependencies(build_input_parsers ${MPS_PARSER} ${ACAS_PARSER}
@@ -296,3 +374,4 @@ set(MARABOU_VERSION 1.0.+)
 add_definitions("-DGIT_COMMIT_HASH=\"${GIT_COMMIT_HASH}\"")
 add_definitions("-DGIT_BRANCH=\"${GIT_BRANCH}\"")
 add_definitions("-DMARABOU_VERSION=\"${MARABOU_VERSION}\"")
+
diff --git a/COPYING b/COPYING
@@ -4,8 +4,8 @@ affiliations. All rights reserved.
 
 The source code of Marabou is open and available to study, to modify, and to
 redistribute original or modified versions; distribution is under the terms of
-the modified BSD license (reproduced below). Marabou links against Boost which
-is separately licensed under the Boost Software License.
+the modified BSD license (reproduced below). Marabou links against multiple
+third-party libraries, see details below.
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are
@@ -34,4 +34,17 @@ THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-----------------------------------------------------------------------
+-------------------------------------------------------------------------------
+ Third-Party Software
+-------------------------------------------------------------------------------
+
+The Marabou source code includes third-party software which has its own copyright
+and licensing terms, as described below. 
+
+Marabou links (by default) against the following libraries:
+    Boost        Boost Software License     (https://www.boost.org)
+    OpenBlas     BSD license                (https://www.openblas.net) 
+
+Marabou can also be linked (however, by default it is not) against the following libraries:
+  Gurobi                                    (https://www.gurobi.com)
+