Dependencies

.github/workflows/buildAllThirdPartyLibrariesExceptLLVMClang.yml

@@ -0,0 +1,11 @@
+name: Build all third-party libraries except LLVM+Clang
+
+on:
+  workflow_dispatch:
+
+jobs:
+  build-all-third-party-libraries-except-llvm-clang:
+    name: Build all third-party libraries except LLVM+Clang
+    uses: ./.github/workflows/buildThirdPartyLibrary.yml
+    with:
+      third_party_library_name: ALL

.github/workflows/buildThirdPartyLibrary.yml

@@ -72,13 +72,16 @@ jobs:
         uses: ilammy/msvc-dev-cmd@v1
         with:
           arch: ${{ matrix.arch }}
-      - name: Configure libOpenCOR (only when building LLVM+Clang)
+      - name: Configure libOpenCOR (for LLVM+Clang)
         if: ${{ inputs.third_party_library_name == 'LLVMClang' }}
         shell: bash
         run: cmake -G Ninja -S . -B build -DBUILD_TYPE=${{ matrix.build_type }} -DONLY_BUILD_THIRD_PARTY_LIBRARIES=ON -DPREBUILT_LLVMCLANG=OFF
-      - name: Configure libOpenCOR (only when NOT building LLVM+Clang)
-        if: ${{ inputs.third_party_library_name != 'LLVMClang' }}
+      - name: Configure libOpenCOR (for a specific third-party library except LLVM+Clang)
+        if: ${{ inputs.third_party_library_name != 'ALL' && inputs.third_party_library_name != 'LLVMClang' }}
         run: cmake -G Ninja -S . -B build -DBUILD_TYPE=${{ matrix.build_type }} -DONLY_BUILD_THIRD_PARTY_LIBRARIES=ON -DPREBUILT_${{ inputs.third_party_library_name }}=OFF
+      - name: Configure libOpenCOR (for all third-party libraries except LLVM+Clang)
+        if: ${{ inputs.third_party_library_name == 'ALL' }}
+        run: cmake -G Ninja -S . -B build -DBUILD_TYPE=${{ matrix.build_type }} -DONLY_BUILD_THIRD_PARTY_LIBRARIES=ON -DPREBUILT_LIBCELLML=OFF -DPREBUILT_LIBCOMBINE=OFF -DPREBUILT_LIBCURL=OFF -DPREBUILT_LIBNUML=OFF -DPREBUILT_LIBSBML=OFF -DPREBUILT_LIBSEDML=OFF -DPREBUILT_LIBSSH2=OFF -DPREBUILT_LIBXML2=OFF -DPREBUILT_OPENSSL=OFF -DPREBUILT_SUNDIALS=OFF -DPREBUILT_ZIPPER=OFF -DPREBUILT_ZLIB=OFF
       - name: Upload library artifact
         if: ${{ !startsWith(github.ref, 'refs/tags/v') }}
         uses: actions/upload-artifact@v4
@@ -109,8 +112,12 @@ jobs:
           cache_key: webassembly
       - name: Install Emscripten
         run: brew install emscripten
-      - name: Configure libOpenCOR
+      - name: Configure libOpenCOR (for a specific third-party library)
+        if: ${{ inputs.third_party_library_name != 'ALL' }}
         run: cmake -G Ninja -S . -B build -DBUILD_TYPE=Release -DJAVASCRIPT_BINDINGS=ON -DONLY_BUILD_THIRD_PARTY_LIBRARIES=ON -DPREBUILT_${{ inputs.third_party_library_name }}=OFF
+      - name: Configure libOpenCOR (for all third-party libraries except LLVM+Clang)
+        if: ${{ inputs.third_party_library_name == 'ALL' }}
+        run: cmake -G Ninja -S . -B build -DBUILD_TYPE=Release -DJAVASCRIPT_BINDINGS=ON -DONLY_BUILD_THIRD_PARTY_LIBRARIES=ON -DPREBUILT_LIBCELLML=OFF -DPREBUILT_LIBCOMBINE=OFF -DPREBUILT_LIBCURL=OFF -DPREBUILT_LIBNUML=OFF -DPREBUILT_LIBSBML=OFF -DPREBUILT_LIBSEDML=OFF -DPREBUILT_LIBSSH2=OFF -DPREBUILT_LIBXML2=OFF -DPREBUILT_OPENSSL=OFF -DPREBUILT_SUNDIALS=OFF -DPREBUILT_ZIPPER=OFF -DPREBUILT_ZLIB=OFF
       - name: Build WebAssembly
         run: cmake --build build
       - name: Upload WebAssembly artifact

VERSION.txt

@@ -1 +1 @@
-0.20260529.0
+0.20260529.1

cmake/packaging/patch.in.cmake

@@ -7,7 +7,7 @@ file(READ ${CMAKE_FILE} FILE_CONTENTS)
 # entry to those needed system libraries or remove the INTERFACE_LINK_LIBRARIES entry altogether.
 
 if(WIN32)
-    string(REGEX REPLACE "INTERFACE_LINK_LIBRARIES[^\n]*\n" "INTERFACE_LINK_LIBRARIES \"$<LINK_ONLY:crypt32.lib>;$<LINK_ONLY:version.lib>;$<LINK_ONLY:wldap32.lib>;$<LINK_ONLY:ws2_32.lib>\"\n" FILE_CONTENTS "${FILE_CONTENTS}")
+    string(REGEX REPLACE "INTERFACE_LINK_LIBRARIES[^\n]*\n" "INTERFACE_LINK_LIBRARIES \"$<LINK_ONLY:bcrypt.lib>;$<LINK_ONLY:crypt32.lib>;$<LINK_ONLY:iphlpapi.lib>;$<LINK_ONLY:version.lib>;$<LINK_ONLY:wldap32.lib>;$<LINK_ONLY:ws2_32.lib>\"\n" FILE_CONTENTS "${FILE_CONTENTS}")
 elseif(APPLE)
     string(REGEX REPLACE "INTERFACE_LINK_LIBRARIES[^\n]*\n" "INTERFACE_LINK_LIBRARIES \"-framework CoreFoundation;-framework SystemConfiguration;$<LINK_ONLY:ldap>\"\n" FILE_CONTENTS "${FILE_CONTENTS}")
 else()

src/3rdparty/CMakeLists.txt

@@ -20,7 +20,11 @@ include(packages)
 
 set(PACKAGES libCellML libCOMBINE libNuML libSBML libSEDML libxml2 LLVMClang SUNDIALS zipper zlib)
 
-if(NOT EMSCRIPTEN)
+if(EMSCRIPTEN OR ONLY_BUILD_JAVASCRIPT_THIRD_PARTY_LIBRARIES)
+    set(WASM_MODE TRUE)
+endif()
+
+if(NOT WASM_MODE)
     list(APPEND PACKAGES libcurl libssh2 OpenSSL)
 endif()
 
@@ -48,7 +52,7 @@ set(DEPENDENT_PACKAGES_TO_BUILD "" CACHE INTERNAL "Dependent packages to be buil
 
 check_dependent_packages(libxml2 libCellML libSBML)
 
-if(EMSCRIPTEN)
+if(WASM_MODE)
     check_dependent_packages(zlib libCellML libCOMBINE zipper)
 else()
     check_dependent_packages(OpenSSL libcurl libssh2)
@@ -58,7 +62,7 @@ endif()
 check_dependent_packages(libSBML libCOMBINE libNuML libSEDML)
 check_dependent_packages(libNuML libSEDML)
 
-if(NOT EMSCRIPTEN)
+if(NOT WASM_MODE)
     check_dependent_packages(libssh2 libcurl)
 endif()
 
@@ -77,7 +81,7 @@ endif()
 check_required_packages(libSBML libxml2)
 check_required_packages(libNuML libSBML)
 
-if(NOT EMSCRIPTEN)
+if(NOT WASM_MODE)
     check_required_packages(libssh2 OpenSSL)
 endif()
 
@@ -86,7 +90,7 @@ check_required_packages(zipper zlib)
 check_required_packages(libCellML libxml2 zlib)
 check_required_packages(libCOMBINE libSBML libxml2 zipper zlib)
 
-if(NOT EMSCRIPTEN)
+if(NOT WASM_MODE)
     check_required_packages(libcurl libssh2 OpenSSL zlib)
 endif()
 
@@ -106,7 +110,7 @@ list(SORT PACKAGES_TO_ADD)
 
 add_package(libxml2)
 
-if(NOT EMSCRIPTEN)
+if(NOT WASM_MODE)
     add_package(OpenSSL)
 endif()
 
@@ -115,7 +119,7 @@ add_package(zlib)
 add_package(libSBML) # Requires libxml2.
 add_package(libNuML) # Requires libSBML.
 
-if(NOT EMSCRIPTEN)
+if(NOT WASM_MODE)
     add_package(libssh2) # Requires OpenSSL and zlib.
 endif()
 
@@ -126,7 +130,7 @@ add_package(zipper) # Requires zlib.
 add_package(libCellML) # Requires libxml2 and zlib.
 add_package(libCOMBINE) # Requires libSBML, libxml2, zipper, and zlib.
 
-if(NOT EMSCRIPTEN)
+if(NOT WASM_MODE)
     add_package(libcurl) # Requires libssh2, OpenSSL, and zlib.
 endif()
 

src/3rdparty/OpenSSL/CMakeLists.txt

@@ -13,9 +13,9 @@
 # limitations under the License.
 
 set(PACKAGE_NAME OpenSSL)
-set(PACKAGE_VERSION 3.5.0)
+set(PACKAGE_VERSION 3.5.6)
 set(PACKAGE_REPOSITORY openssl)
-set(RELEASE_TAG openssl-3.5.0)
+set(RELEASE_TAG openssl-3.5.6)
 set(INSTALL_DIR ${PREBUILT_DIR}/${PACKAGE_NAME})
 
 # Either retrieve or build our package.
@@ -26,42 +26,42 @@ if(LIBOPENCOR_PREBUILT_OPENSSL)
             if(INTEL_MODE)
                 retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                  ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                 ac4440ae3dba3415322fc833bef87b8b4d1b082b)
+                                 1480b47efd53e2a84f5ecf34e007af01bf2b5d1c)
             else()
                 retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                  ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                 cd571c829ce744dbfc82bb1998f4d566b289cf93)
+                                 c3a283735c3fd379b10f91a8fcab5b6bbd1b3b14)
             endif()
         else()
             if(INTEL_MODE)
                 retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                  ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                 ed9489d5ed226ed79ac2d1042a4a22bcdc899a8c)
+                                 c123dc0705360eeadc4186608c041ba7c25cd34c)
             else()
                 retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                  ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                 dec6518c275c9f72aeeea068328ac86f0b87fb82)
+                                 24ca17237784250e8e1a436a7675f087c5f94bf8)
             endif()
         endif()
     elseif(APPLE)
         if(INTEL_MODE)
             retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                              ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                             67f37a19f38abf06220619074ee880ca63b4a804)
+                             3b3a4e534bc0ca067b6c4ba20e16d4d7b3df5364)
         else()
             retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                              ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                             8c5d0afbbd2dfe2120502b728e8e5e9ff8f69ecc)
+                             f03c6b2b4ffc795ae8cdb459a4ee19324c4c910b)
         endif()
     else()
         if(INTEL_MODE)
             retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                              ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                             934a9c39cd923b2466f83066952b17295b8dadf5)
+                             5d413c062d210d51e2b8bc7d43b77e8551524035)
         else()
             retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                              ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                             cc6a2de4b58b0b717e0684534c17ba5c90e6e7ab)
+                             505270e090d7eba089b553c5939801f3e468acd7)
         endif()
     endif()
 else()

src/3rdparty/SUNDIALS/CMakeLists.txt

@@ -13,9 +13,9 @@
 # limitations under the License.
 
 set(PACKAGE_NAME SUNDIALS)
-set(PACKAGE_VERSION v7.3.0)
+set(PACKAGE_VERSION v7.7.0)
 set(PACKAGE_REPOSITORY sundials)
-set(RELEASE_TAG v7.3.0)
+set(RELEASE_TAG v7.7.0)
 set(INSTALL_DIR ${PREBUILT_DIR}/${PACKAGE_NAME})
 
 # Either retrieve or build our package.
@@ -24,49 +24,49 @@ if(LIBOPENCOR_PREBUILT_SUNDIALS)
     if(EMSCRIPTEN)
         retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                          ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                         3ce480076a375ac68b84e3a395805b1304f65ca3)
+                         d51821a5f6edf151e72e53ad9edb700022e44b98)
     else()
         if(WIN32)
             if(RELEASE_MODE)
                 if(INTEL_MODE)
                     retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                      ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                     6c3758026f18435d2ddba98ea6cdca03b720a905)
+                                     ea5e25fbe26a8f1309f9c9424e688abe626700c5)
                 else()
                     retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                      ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                     6bccea22078cac44357cb8c2c70138f1c68837fc)
+                                     9526d5b7723b31f77f8c68ed8a8e356ae7029503)
                 endif()
             else()
                 if(INTEL_MODE)
                     retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                      ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                     0d62d71b789f05270852adb1b280711088304dfd)
+                                     a84a217438bd69c61ba7649ccf54ea3def6f0cdb)
                 else()
                     retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                      ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                     bed457c4b5430aa40a97fa2f403acba8648dadbe)
+                                     0ce0997d40fec38b3f2a6ecea7f39a29a66bef79)
                 endif()
             endif()
         elseif(APPLE)
             if(INTEL_MODE)
                 retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                  ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                 23db2411afd00e339667c7d8761d12dfd43e7c1a)
+                                 0cfb4f6722c19acd12935b9d2a2f9dbea9e44cba)
             else()
                 retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                  ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                 d889bfbf95f76518048523b0a59ca925f73b5b6b)
+                                 6e36a58950250682f16117715d780adb1a9588f5)
             endif()
         else()
             if(INTEL_MODE)
                 retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                  ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                 6b736ecb5d7bac1f54e75b81f2b733c49fc654d7)
+                                 e4501231ad79082f46c031a34c2da1c50d6e7db3)
             else()
                 retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                  ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                 d8e6b1ed20c2fa2557333e0c281e8e4ad622b09b)
+                                 68ca5feee035f3a958225fdaaea6bfab3bae7aa2)
             endif()
         endif()
     endif()

src/3rdparty/libSBML/CMakeLists.txt

@@ -13,9 +13,9 @@
 # limitations under the License.
 
 set(PACKAGE_NAME libSBML)
-set(PACKAGE_VERSION 5.20.5)
+set(PACKAGE_VERSION 5.21.0)
 set(PACKAGE_REPOSITORY libsbml)
-set(RELEASE_TAG v5.20.5)
+set(RELEASE_TAG v5.21.0)
 set(INSTALL_DIR ${PREBUILT_DIR}/${PACKAGE_NAME})
 
 # Either retrieve or build our package.
@@ -28,55 +28,66 @@ if(LIBOPENCOR_PREBUILT_LIBSBML)
     if(EMSCRIPTEN)
         retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                          ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                         7af6669df81bb9ee61ddbca4970d46ae4dbabeee)
+                         54f84ef32f6a70cb7cbe6ffc4251d7762ec3c755)
     else()
         if(WIN32)
             if(RELEASE_MODE)
                 if(INTEL_MODE)
                     retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                      ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                     0ff9f19b3840bf61e7654b5d5cfbebf5af77b718)
+                                     27876adefeba2d0e38da978e6c425f7b303a42a6)
                 else()
                     retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                      ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                     a37af3f1fde2c1f8156e995be154a37eb368e85c)
+                                     ffc13b7e8a0e1ebf410579c09d80a212f4c69998)
                 endif()
             else()
                 if(INTEL_MODE)
                     retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                      ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                     8ccc19c239357bebdd7e7e81a1e80449ee6d81d5)
+                                     c880538369168005bcd80daea453c7b32d95661e)
                 else()
                     retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                      ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                     e729dd13b6bb861644ba801903d9def7b6272f35)
+                                     d12c16ff4a2b8c667160ca8cb2378e332e089bb1)
                 endif()
             endif()
         elseif(APPLE)
             if(INTEL_MODE)
                 retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                  ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                 052aa4d544d1e93cc4530fcfdec68b39879f4878)
+                                 b0fbee2b7a45a35b3cb6751352e56bfc8f111bba)
             else()
                 retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                  ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                 3e0ea2ce2b20189e83aa85c1cc6a45200526875b)
+                                 f3199a109ee56ea2e467ee34c6aca824d63363bb)
             endif()
         else()
             if(INTEL_MODE)
                 retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                  ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                 00358806e25d038071f620c04af8c052c06aafcc)
+                                 3c936c1696294b602aa39dad9a6a255866c2f9bd)
             else()
                 retrieve_package(${PACKAGE_NAME} ${PACKAGE_VERSION}
                                  ${PACKAGE_REPOSITORY} ${RELEASE_TAG}
-                                 6978faf32f2c04d30d4973ae01c83262ae6d4693)
+                                 762d5c39d46a55fc894522ba99ad53c22a3ea1b3)
             endif()
         endif()
     endif()
 elseif(NOT ONLY_BUILD_JAVASCRIPT_THIRD_PARTY_LIBRARIES)
     # Build our package.
 
+    # libSBML's FindLIBXML.cmake unconditionally probes ZLIB. Pre-seed the ZLIB variables so that FindZLIB.cmake can
+    # succeed even when zlib is not available (on Windows and with Emscripten), while still keeping zlib disabled for
+    # libSBML itself.
+
+    set(ZLIB_ARGS
+        -DWITH_ZLIB=OFF
+        -DZLIB_FOUND=TRUE
+        -DZLIB_INCLUDE_DIR=${CMAKE_CURRENT_BINARY_DIR}
+        -DZLIB_LIBRARY=${CMAKE_CURRENT_BINARY_DIR}/zlib.not.used
+    )
+
     build_package(${PACKAGE_NAME}
         URL
             https://github.com/opencor/${PACKAGE_REPOSITORY}/archive/refs/tags/${RELEASE_TAG}.tar.gz
@@ -91,7 +102,7 @@ elseif(NOT ONLY_BUILD_JAVASCRIPT_THIRD_PARTY_LIBRARIES)
             -DWITH_BZIP2=OFF
             -DWITH_CPP_NAMESPACE=ON
             -DWITH_SWIG=OFF
-            -DWITH_ZLIB=OFF
+            ${ZLIB_ARGS}
     )
 
     # Patch some of our CMake configuration files.