add libzip submodule to source build it as static lib on all platforms

Author: jcschaff

.github/workflows/cd.yml

@@ -71,7 +71,6 @@ jobs:
         run: |
           brew install boost
           brew install hdf5
-          brew install libzip
           brew install ninja
 
           brew install llvm
@@ -91,7 +90,6 @@ jobs:
         run: |
           brew install boost
           brew install hdf5
-          brew install libzip
           brew install ninja
 
           brew install llvm
@@ -119,7 +117,6 @@ jobs:
             mingw-w64-clang-x86_64-cmake
             mingw-w64-clang-x86_64-boost
             mingw-w64-clang-x86_64-hdf5
-            mingw-w64-clang-x86_64-libzip
             mingw-w64-clang-x86_64-zlib
             mingw-w64-clang-x86_64-libaec
 
@@ -129,7 +126,6 @@ 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

.github/workflows/pip.yml

@@ -37,7 +37,6 @@ jobs:
       run: |
         brew install boost
         brew install hdf5
-          brew install libzip
         brew install ninja
         
         brew install llvm
@@ -57,7 +56,6 @@ jobs:
       run: |
         brew install boost
         brew install hdf5
-        brew install libzip
         brew install ninja
         
         brew install llvm
@@ -85,7 +83,6 @@ jobs:
           mingw-w64-clang-x86_64-cmake
           mingw-w64-clang-x86_64-boost
           mingw-w64-clang-x86_64-hdf5
-          mingw-w64-clang-x86_64-libzip
           mingw-w64-clang-x86_64-zlib
           mingw-w64-clang-x86_64-libaec
           mingw-w64-clang-x86_64-python-pip-tools
@@ -136,9 +133,9 @@ 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_28_x86_64 \
            /bin/bash -c \
-           "yum install -y boost-devel hdf5-devel libzip-devel ninja-build && \
+           "yum install -y boost-devel hdf5-devel ninja-build && \
            /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"
@@ -148,9 +145,9 @@ 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_28_x86_64 \
            /bin/bash -c \
-           "yum install -y boost-devel hdf5-devel libzip-devel ninja-build && \
+           "yum install -y boost-devel hdf5-devel ninja-build && \
            /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"
@@ -160,9 +157,9 @@ 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_28_x86_64 \
            /bin/bash -c \
-           "yum install -y boost-devel hdf5-devel libzip-devel ninja-build && \
+           "yum install -y boost-devel hdf5-devel ninja-build && \
            /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"
@@ -172,9 +169,9 @@ 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_28_x86_64 \
            /bin/bash -c \
-           "yum install -y boost-devel hdf5-devel libzip-devel ninja-build && \
+           "yum install -y boost-devel hdf5-devel ninja-build && \
            /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"

.gitmodules

@@ -5,3 +5,6 @@
 [submodule "libzippp"]
 	path = libzippp
 	url = https://github.com/ctabin/libzippp.git
+[submodule "extern/libzip"]
+	path = extern/libzip
+	url = https://github.com/nih-at/libzip.git

CMakeLists.txt

@@ -129,8 +129,6 @@ include(GetGitRevisionDescription)
 git_describe(GIT_DESCRIBE ALLOW_LOOKING_ABOVE_CMAKE_SOURCE_DIR)
 
 include (FindZLIB)
-include (FindLIBZIP)
-
 
 if (NOT OPTION_TARGET_PYTHON_BINDING)
 	set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
@@ -201,6 +199,8 @@ add_subdirectory(VCellMessaging)
 
 add_subdirectory(VCellZipUtils)
 
+add_subdirectory(extern/libzip)
+
 add_subdirectory(libzippp)
 
 add_subdirectory(ExpressionParser)

bridgeVCellSmoldyn/CMakeLists.txt

@@ -5,7 +5,7 @@ file (GLOB HEADER_FILES *.h)
 file (GLOB SOURCE_FILES ${CMAKE_CURRENT_SOURCE_DIR}/*.cpp)
 list(REMOVE_ITEM SOURCE_FILES ${VCELL_SMOL_MAIN}) 
 
-add_library(vcellsmoldynbridge ${HEADER_FILES} ${SOURCE_FILES})
+add_library(vcellsmoldynbridge STATIC ${HEADER_FILES} ${SOURCE_FILES})
 target_link_libraries(vcellsmoldynbridge vcell smoldyn_static)
 target_include_directories(vcellsmoldynbridge PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
 target_compile_definitions(vcellsmoldynbridge PUBLIC -DVCELL_HYBRID -DVCELL -D_CRT_SECURE_NO_WARNINGS)