Merge pull request #6 from virtualcell/unit-test

smoke test for FiniteVolume and Smoldyn

Author: jcschaff

.github/workflows/cd.yml

@@ -1,6 +1,7 @@
 name: CD
 
-on: 
+on:
+  workflow_dispatch:
   pull_request:
   push:
     branches:
@@ -24,6 +25,8 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
+        with:
+          submodules: true
 
       - name: Log in to the Container registry
         uses: docker/login-action@v3
@@ -60,19 +63,24 @@ jobs:
     steps:
       - name: checkout vcell-solvers repo
         uses: actions/checkout@v4
+        with:
+          submodules: true
 
       - name: Install Intel MacOS dependencies
         if: matrix.platform == 'macos-13'
         shell: bash
         run: |
           brew install boost
           brew install hdf5
+          brew install libzip
           brew install ninja
+          brew install libaec
 
           brew install llvm
           echo 'export PATH="/usr/local/opt/llvm/bin:$PATH"' >> /Users/runner/.bash_profile
           source /Users/runner/.bash_profile
-          
+          ln -s $(which gfortran-14) /usr/local/bin/gfortran
+
           gcc --version
           gfortran --version
           cmake --version
@@ -85,7 +93,9 @@ jobs:
         run: |
           brew install boost
           brew install hdf5
+          brew install libzip
           brew install ninja
+          brew install libaec
 
           brew install llvm
           echo 'export PATH="/opt/homebrew/opt/llvm/bin:$PATH"' >> /Users/runner/.bash_profile
@@ -209,7 +219,7 @@ jobs:
           mkdir build
           cd build
 
-          PATH="/c/Program\ Files/LLVM/bin:$PATH"
+          export PATH="/c/Program\ Files/LLVM/bin:$PATH"
 
           cmake \
           -G Ninja \
@@ -232,6 +242,9 @@ jobs:
           echo "working dir is $PWD"
 
           cd build
+          
+          export PATH="/d/a/_temp/msys64/clang64/bin:$PATH"
+          pacman -Sy --noconfirm diffutils
 
           ctest -VV
 
@@ -243,9 +256,7 @@ jobs:
         if: matrix.platform == 'ubuntu-latest'
         run: |
           sudo apt-get update
-          sudo apt-get install -y libboost-all-dev
-          sudo apt-get install -y libhdf5-dev
-          sudo apt-get install -y ninja-build
+          sudo apt-get install -y libboost-all-dev libhdf5-dev libzip-dev libbz2-dev ninja-build
 
           gcc --version
           gfortran --version

.github/workflows/conda.yml

@@ -24,6 +24,9 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
+        with:
+          submodules: true
+
 
       - name: Get conda
         uses: conda-incubator/setup-miniconda@v3.0.4

.github/workflows/pip.yml

@@ -28,18 +28,23 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+      with:
+        submodules: true
 
     - name: Install Intel MacOS dependencies
       if: matrix.platform == 'macos-13'
       shell: bash
       run: |
         brew install boost
         brew install hdf5
+        brew install libzip
         brew install ninja
+        brew install libaec
         
         brew install llvm
         echo 'export PATH="/usr/local/opt/llvm/bin:$PATH"' >> /Users/runner/.bash_profile
         source /Users/runner/.bash_profile
+        ln -s $(which gfortran-14) /usr/local/bin/gfortran
         
         gcc --version
         gfortran --version
@@ -54,7 +59,9 @@ jobs:
       run: |
         brew install boost
         brew install hdf5
+        brew install libzip
         brew install ninja
+        brew install libaec
         
         brew install llvm
         echo 'export PATH="/opt/homebrew/opt/llvm/bin:$PATH"' >> /Users/runner/.bash_profile
@@ -130,9 +137,9 @@ jobs:
 
     - name: Build and install manylinux for python 3.9
       run: |
-        docker run --rm -v $(pwd):/io quay.io/pypa/manylinux2014_x86_64 \
+        docker run --rm -v $(pwd):/io quay.io/pypa/manylinux_2_34_x86_64 \
            /bin/bash -c \
-           "yum install -y boost-devel hdf5-devel ninja-build && \
+           "yum install -y boost-devel hdf5-devel libzip-devel bzip2-devel ninja-build openssl-devel xz-devel && \
            /opt/python/cp39-cp39/bin/pip wheel /io/ -w /io/dist && \
            auditwheel repair /io/dist/*.whl -w /io/dist/"
         echo "keeping only the manylinux wheels, remove those with -linux_x86_64.whl in the name"
@@ -142,9 +149,9 @@ jobs:
 
     - name: Build and install manylinux for python 3.10
       run: |
-        docker run --rm -v $(pwd):/io quay.io/pypa/manylinux2014_x86_64 \
+        docker run --rm -v $(pwd):/io quay.io/pypa/manylinux_2_34_x86_64 \
            /bin/bash -c \
-           "yum install -y boost-devel hdf5-devel ninja-build && \
+           "yum install -y boost-devel hdf5-devel libzip-devel bzip2-devel ninja-build openssl-devel xz-devel && \
            /opt/python/cp310-cp310/bin/pip wheel /io/ -w /io/dist && \
            auditwheel repair /io/dist/*.whl -w /io/dist/"
         echo "keeping only the manylinux wheels, remove those with -linux_x86_64.whl in the name"
@@ -154,9 +161,9 @@ jobs:
 
     - name: Build and install manylinux for python 3.11
       run: |
-        docker run --rm -v $(pwd):/io quay.io/pypa/manylinux2014_x86_64 \
+        docker run --rm -v $(pwd):/io quay.io/pypa/manylinux_2_34_x86_64 \
            /bin/bash -c \
-           "yum install -y boost-devel hdf5-devel ninja-build && \
+           "yum install -y boost-devel hdf5-devel libzip-devel bzip2-devel ninja-build openssl-devel xz-devel && \
            /opt/python/cp311-cp311/bin/pip wheel /io/ -w /io/dist && \
            auditwheel repair /io/dist/*.whl -w /io/dist/"
         echo "keeping only the manylinux wheels, remove those with -linux_x86_64.whl in the name"
@@ -166,9 +173,9 @@ jobs:
 
     - name: Build and install manylinux for python 3.12
       run: |
-        docker run --rm -v $(pwd):/io quay.io/pypa/manylinux2014_x86_64 \
+        docker run --rm -v $(pwd):/io quay.io/pypa/manylinux_2_34_x86_64 \
            /bin/bash -c \
-           "yum install -y boost-devel hdf5-devel ninja-build && \
+           "yum install -y boost-devel hdf5-devel libzip-devel bzip2-devel ninja-build openssl-devel xz-devel && \
            /opt/python/cp312-cp312/bin/pip wheel /io/ -w /io/dist && \
            auditwheel repair /io/dist/*.whl -w /io/dist/"
         echo "keeping only the manylinux wheels, remove those with -linux_x86_64.whl in the name"
@@ -260,4 +267,5 @@ jobs:
       if: ${{ failure() }}
       with:
         github-token: ${{ secrets.GITHUB_TOKEN }}
+        limit-access-to-actor: false
 

.github/workflows/wheels.yml

@@ -115,6 +115,7 @@ jobs:
         sudo apt-get update
         sudo apt-get install -y libboost-all-dev
         sudo apt-get install -y libhdf5-dev
+        sudo apt-get install -y libzip-dev
         sudo apt-get install -y ninja-build
         
         gcc --version

.gitignore

@@ -26,3 +26,5 @@
 tests/__pycache__/
 
 *.whl
+
+VCell/tests/testFiles/output/

.gitmodules

@@ -2,3 +2,6 @@
 	path = extern/pybind11
 	url = ../../pybind/pybind11
 	branch = stable
+[submodule "libzippp"]
+	path = libzippp
+	url = https://github.com/ctabin/libzippp.git

CMakeLists.txt

@@ -11,6 +11,9 @@ option(OPTION_USE_ZLIB "Build with Zlib support" ON)
 option(OPTION_USE_LIBTIFF "Build with LibTiff support" OFF)
 option(OPTION_USE_ICONV "Build with Libiconv support" OFF)
 
+# need to statically link everything for the python bindings and standalone solvers
+set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
+set(BUILD_SHARED_LIBS OFF)
 
 if (OPTION_TARGET_PYTHON_BINDING)
 	project(
@@ -123,11 +126,21 @@ elseif (MINGW)
 endif()
 
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/modules/")
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/libzippp/cmake/")
 
 include(GetGitRevisionDescription)
 git_describe(GIT_DESCRIBE ALLOW_LOOKING_ABOVE_CMAKE_SOURCE_DIR)
 
 include (FindZLIB)
+include (FindLIBZIP)
+
+# help CMake find libzip
+if (APPLE)
+	execute_process(COMMAND brew --prefix libzip OUTPUT_VARIABLE LIBZIP_PREFIX OUTPUT_STRIP_TRAILING_WHITESPACE)
+	set(CMAKE_PREFIX_PATH ${CMAKE_PREFIX_PATH} ${LIBZIP_PREFIX})
+endif()
+find_package(LIBZIP 1.10 REQUIRED)
+
 
 if (NOT OPTION_TARGET_PYTHON_BINDING)
 	set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
@@ -185,15 +198,59 @@ if (LINUX AND OPTION_TARGET_PYTHON_BINDING)
 endif()
 
 #CMakeList.txt that comes with hdf5 switches library name if compiled with debug
+if (APPLE)
+	execute_process(COMMAND brew --prefix libaec OUTPUT_VARIABLE LIBAEC_PREFIX OUTPUT_STRIP_TRAILING_WHITESPACE)
+	set(CMAKE_PREFIX_PATH ${CMAKE_PREFIX_PATH} ${LIBAEC_PREFIX})
+	find_package(libaec REQUIRED)
+endif()
 find_package(HDF5 COMPONENTS HL CXX C)
 set(HDF_VERSION ${HDF5_VERSION})
 ######    ${HDF5_HL_LIBRARIES} ${HDF5_CXX_LIBRARIES}
 
+if (OPTION_TARGET_TESTS)
+	enable_testing()
+	set(LIBZIPPP_BUILD_TESTS ON)
+endif ()
+
 add_subdirectory(VCellMessaging)
 
 add_subdirectory(VCellZipUtils)
 
-add_subdirectory(libzip-1.2.0)
+
+
+
+add_subdirectory(libzippp)
+# Path to the patch file
+set(PATCH_FILE "${CMAKE_SOURCE_DIR}/patches/libzippp_patch.diff")
+# Path to the file to be patched
+set(FILE_TO_PATCH "${CMAKE_SOURCE_DIR}/libzippp/src/libzippp.cpp")
+# Apply the patch
+if (WIN32)
+	add_custom_command(
+			OUTPUT ${FILE_TO_PATCH}
+			COMMAND ${CMAKE_COMMAND} -E echo "Applying patch to libzippp"
+			COMMAND ${CMAKE_COMMAND} -E copy_if_different ${FILE_TO_PATCH} ${FILE_TO_PATCH}.bak
+			COMMAND ${CMAKE_COMMAND} -E touch ${FILE_TO_PATCH}
+			COMMAND git apply ${PATCH_FILE}
+			DEPENDS ${PATCH_FILE}
+			COMMENT "Patching libzippp"
+	)
+else()
+	add_custom_command(
+			OUTPUT ${FILE_TO_PATCH}
+			COMMAND ${CMAKE_COMMAND} -E echo "Applying patch to libzippp"
+			COMMAND ${CMAKE_COMMAND} -E copy_if_different ${FILE_TO_PATCH} ${FILE_TO_PATCH}.bak
+			COMMAND ${CMAKE_COMMAND} -E touch ${FILE_TO_PATCH}
+			COMMAND patch --forward ${FILE_TO_PATCH} < ${PATCH_FILE} | true
+			DEPENDS ${PATCH_FILE}
+			COMMENT "Patching libzippp"
+	)
+endif()
+# Ensure the patch is applied before building the submodule
+add_custom_target(apply_patch ALL DEPENDS ${FILE_TO_PATCH})
+add_dependencies(libzippp apply_patch)
+
+
 
 add_subdirectory(ExpressionParser)
 

Dockerfile

@@ -1,8 +1,17 @@
-FROM ubuntu:22.04 as build
+FROM ubuntu:22.04
 
 RUN apt-get -y update && apt-get install -y apt-utils && \
-    apt-get install -y -qq -o=Dpkg::Use-Pty=0 build-essential gfortran zlib1g-dev \
-    libhdf5-dev ninja-build libcurl4-openssl-dev libboost-all-dev cmake wget python3
+    apt-get install -y -qq -o=Dpkg::Use-Pty=0 build-essential gfortran \
+    libhdf5-dev libzip-dev ninja-build libcurl4-openssl-dev libboost-all-dev libbz2-dev cmake python3
+
+# Install an alternative Fortran compiler
+RUN apt-get install -y gfortran-10
+
+# Set the alternative Fortran compiler as the default
+RUN update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-10 10
+
+# Fix broken dependencies and reconfigure ca-certificates
+RUN apt-get -y update && apt-get install -f && dpkg --configure -a && apt-get clean
 
 COPY . /vcellroot
 
@@ -13,10 +22,13 @@ RUN cmake \
     -G Ninja \
     -DOPTION_TARGET_PYTHON_BINDING=OFF \
     -DOPTION_TARGET_MESSAGING=ON \
-    -DOPTION_TARGET_SMOLDYN_SOLVER=OFF \
+    -DOPTION_TARGET_SMOLDYN_SOLVER=ON \
     -DOPTION_TARGET_FV_SOLVER=ON \
     -DOPTION_TARGET_DOCS=OFF \
     .. && \
     ninja
 
-#RUN ctest
+RUN ctest -VV
+
+WORKDIR /vcellroot/build/bin
+ENV PATH="/vcellroot/build/bin:${PATH}"

VCell/CMakeLists.txt

@@ -243,5 +243,18 @@ endif()
 
 # add google tests
 if (OPTION_TARGET_TESTS)
+	enable_testing()
+	if (MINGW)
+		set(test_fvsolver_exe ${CMAKE_BINARY_DIR}/bin/${EXE_FILE}.exe)
+		set(python_cmd py)
+	else (MINGW)
+		set(test_fvsolver_exe ${CMAKE_BINARY_DIR}/bin/${EXE_FILE})
+		set(python_cmd python3)
+	endif (MINGW)
+	set(test_dir ${CMAKE_CURRENT_SOURCE_DIR}/tests/smoke)
+
+	# smoke test as a python script, for bash test example, see NFsim/tests/smoke
+	add_test(NAME ${EXE_FILE}_smoke COMMAND ${python_cmd} ${test_dir}/smoke.py ${test_fvsolver_exe} WORKING_DIRECTORY ${test_dir})
+
 	add_subdirectory(tests)
 endif()

VCell/src/PostProcessingHdf5Writer.cpp

@@ -208,7 +208,7 @@ void PostProcessingHdf5Writer::writeOutput(SimTool* sim_tool) {
 
 		h5PPFile->flush(H5F_SCOPE_GLOBAL);
 	} catch(H5::Exception error ) {
-		throw error.getDetailMsg();
+		throw std::runtime_error(error.getDetailMsg());
 	}
 }