Merge pull request #478 from sbmlteam/development

Pull develop into branch

Author: luciansmith

.github/workflows/brief.yml

@@ -9,6 +9,8 @@ on:
         - "VERSION.txt"
         - "!.github/**"
         - ".github/workflows/brief.yml"
+
+
 env:
   BUILD_TYPE: Release
 
@@ -103,6 +105,7 @@ jobs:
         shell: bash
         run: |
           brew install check swig ccache
+          brew install --cask mono-mdk
           echo PYTHON_LINKING_OPTION="-DPYTHON_USE_DYNAMIC_LOOKUP=ON" >> "${GITHUB_ENV}"
 
       ### setup ccache, not on Windows ###

.github/workflows/extensive.yml

@@ -138,8 +138,15 @@ jobs:
         if: matrix.platform == 'ubuntu-latest'
         shell: bash
         run: |
-          sudo apt-get update
+          # add mono using instructions from: https://www.mono-project.com/download/stable/#download-lin
+          sudo apt install ca-certificates gnupg
+          sudo gpg --homedir /tmp --no-default-keyring --keyring /usr/share/keyrings/mono-official-archive-keyring.gpg --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 3FA7E0328081BFF6A14DA29AA6A19B38D3D831EF
+          echo "deb [signed-by=/usr/share/keyrings/mono-official-archive-keyring.gpg] https://download.mono-project.com/repo/ubuntu stable-focal main" | sudo tee /etc/apt/sources.list.d/mono-official-stable.list
+          sudo apt update
+          sudo apt install -y mono-devel
+        
           sudo apt-get install -y check libxerces-c-dev expat ccache
+          
           echo PYTHON_LINKING_OPTION="-DPYTHON_USE_DYNAMIC_LOOKUP=ON" >> "${GITHUB_ENV}"
           git clone https://github.com/libexpat/libexpat
           cmake -G Ninja -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DEXPAT_BUILD_TESTS=OFF -DEXPAT_BUILD_TOOLS=OFF -DEXPAT_BUILD_EXAMPLES=OFF -DEXPAT_SHARED_LIBS=OFF -DCMAKE_INSTALL_PREFIX=./dependencies -B libexpat -S libexpat/expat 
@@ -153,6 +160,7 @@ jobs:
         shell: bash
         run: |
           brew install check swig xerces-c expat ccache
+          brew install --cask mono-mdk
           echo PYTHON_LINKING_OPTION="-DPYTHON_USE_DYNAMIC_LOOKUP=ON" >> "${GITHUB_ENV}"
 
       - name: Unix R options

CMakeLists.txt

@@ -1,6 +1,6 @@
 ###############################################################################
 #
-# Description       : CMake build script for libSBML
+# Description       : CMake build script for libSBML 
 # Original author(s): Frank Bergmann <fbergman@caltech.edu>
 # Organization      : California Institute of Technology
 #
@@ -595,6 +595,10 @@ if(WITH_CSHARP)
         endif()
     endif()
 
+    if(NOT CSHARP_COMPILER)
+      message(FATAL_ERROR "CSHARP_COMPILER is not found, please ensure that gmcs, csc, or mcs is installed.")
+    endif()
+
 endif(WITH_CSHARP)
 
 
@@ -640,14 +644,14 @@ endif(WITH_CHECK)
 # documentation to be installed in PREFIX/${MISC_PREFIX}.
 #
 
-set( MISC_PREFIX )
+
 if(UNIX OR CYGWIN)
     set(PATH_SEP "/")
     set(FILE_SEP ":")
-    set( MISC_PREFIX "${CMAKE_INSTALL_DATADIR}/libsbml/" )
+    set(MISC_PREFIX "${CMAKE_INSTALL_DATADIR}/libsbml/" CACHE PATH "bindings, examples and documentation path")
     set(LIBSBML_LIBRARY sbml)
 else()
-    set( MISC_PREFIX ".\\" )
+    set(MISC_PREFIX ".\\" CACHE PATH "bindings, examples and documentation path")
     set(PATH_SEP "\\")
     set(FILE_SEP ";")
     if(MINGW)

CMakeModules/FindZLIB.cmake

@@ -1,4 +1,4 @@
-# Copyright (C) 2022 by Pedro Mendes, Rector and Visitors of the 
+# Copyright (C) 2022 - 2025 by Pedro Mendes, Rector and Visitors of the 
 # University of Virginia, University of Heidelberg, and University 
 # of Connecticut School of Medicine. 
 # All rights reserved. 
@@ -31,38 +31,43 @@ if (NOT (ZLIB_INCLUDE_DIR AND ZLIB_LIBRARY) OR NOT ZLIB_FOUND)
     find_path(ZLIB_INCLUDE_DIR zlib.h zlib/zlib.h
 	    PATHS $ENV{ZLIB_DIR}/include
 	          $ENV{ZLIB_DIR}
-            ${${_PROJECT_DEPENDENCY_DIR}}/include
+	          ${${_PROJECT_DEPENDENCY_DIR}}/include
 	          ~/Library/Frameworks
 	          /Library/Frameworks
 	          /sw/include        # Fink
 	          /opt/local/include # MacPorts
 	          /opt/csw/include   # Blastwave
 	          /opt/include
 	          /usr/freeware/include
-            NO_DEFAULT_PATH)
+	          CMAKE_FIND_ROOT_PATH_BOTH
+	          NO_DEFAULT_PATH)
 
     if (NOT ZLIB_INCLUDE_DIR)
-        find_path(ZLIB_INCLUDE_DIR zlib.h zlib/zlib.h)
+        find_path(ZLIB_INCLUDE_DIR zlib.h zlib/zlib.h
+        CMAKE_FIND_ROOT_PATH_BOTH )
     endif ()
 
     find_library(ZLIB_LIBRARY 
-	    NAMES zdll.lib z zlib.lib libzlib zlib libzlib.a 
+	    NAMES zdll.lib z zlib.lib libzlib zlib libzlib.a libzdll.a
 	    PATHS $ENV{ZLIB_DIR}/lib
 	          $ENV{ZLIB_DIR}/lib-dbg
 	          $ENV{ZLIB_DIR}
-            ${${_PROJECT_DEPENDENCY_DIR}}/${CMAKE_INSTALL_LIBDIR}
-            ${${_PROJECT_DEPENDENCY_DIR}}
+              ${${_PROJECT_DEPENDENCY_DIR}}/${CMAKE_INSTALL_LIBDIR}
+              ${${_PROJECT_DEPENDENCY_DIR}}/lib
+              ${${_PROJECT_DEPENDENCY_DIR}}
 	          ~/Library/Frameworks
 	          /Library/Frameworks
 	          /sw/lib        # Fink
 	          /opt/local/lib # MacPorts
 	          /opt/csw/lib   # Blastwave
 	          /opt/lib
 	          /usr/freeware/lib64
+              CMAKE_FIND_ROOT_PATH_BOTH
              NO_DEFAULT_PATH)
 
     if (NOT ZLIB_LIBRARY)
-        find_library(ZLIB_LIBRARY NAMES zdll.lib z zlib.lib libzlib zlib libzlib.a)
+        find_library(ZLIB_LIBRARY NAMES zdll.lib z zlib.lib libzlib zlib libzlib.a libzdll.a
+        CMAKE_FIND_ROOT_PATH_BOTH )
     endif ()
 
     if (NOT WIN32)
@@ -76,24 +81,22 @@ if (NOT (ZLIB_INCLUDE_DIR AND ZLIB_LIBRARY) OR NOT ZLIB_FOUND)
             set(ZLIB_VERSION ${PC_ZLIB_VERSION} CACHE STRING "Zlib Version found" )
         endif (PC_ZLIB_FOUND)
     endif (NOT WIN32)
-
+    
+    
     # make sure that we have a valid zip library
+    if (ZLIB_CHECK_FOR_SYMBOLS)
     file(TO_CMAKE_PATH "${ZLIB_LIBRARY}" LIBZ_CMAKE_PATH)
-    include (CheckLibraryExists)
-    check_library_exists("${LIBZ_CMAKE_PATH}" "gzopen" "" LIBZ_CMAKE_PATH)
-    if(NOT LIBZ_FOUND_SYMBOL)
-        # this is odd, but on windows this check always fails! must be a
-        # bug in the current cmake version so for now only issue this
-        # warning on linux
-        if(UNIX)
-            message(WARNING
-"The chosen zlib library does not appear to be valid because it is
-missing certain required symbols. Please check that ${LIBZ_LIBRARY} is
-the correct zlib library. For details about the error, please see
-${LIBSBML_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeError.log")
-        endif()
+    include(CheckLibraryExists)
+    check_library_exists("${LIBZ_CMAKE_PATH}" "gzopen" "" LIBZ_FOUND_SYMBOL)
+
+    if(NOT LIBZ_FOUND_SYMBOL AND UNIX)
+        message(WARNING
+                "The chosen zlib library does not appear to be valid because it is
+    missing certain required symbols. Please check that ${ZLIB_LIBRARY} is
+    the correct zlib library. For details about the error, please see
+    CMakeError.log or CMakeConfigureLog.yaml in the build directory.")
     endif()
-
+    endif() # Check for symbols
 
     mark_as_advanced(ZLIB_INCLUDE_DIR ZLIB_LIBRARY)
 

NEWS.txt

@@ -1,7 +1,31 @@
            libSBML NEWS -- History of user-visible changes
 
 ====================================================================
-5.20.4
+5.21.1 (2026-03-05)
+====================================================================
+
+This release fixes an issue with the python bindings in the pip 
+package `python-libsbml`.
+
+====================================================================
+5.21.0 (2026-01-09)
+====================================================================
+
+This release further improves the ODE to Reaction converter, 
+improves the ASTNode::derivative function to support all allowed 
+math constructs, and resolves a number of build and stability 
+issues.
+
+====================================================================
+5.20.5 (2025-05-05)
+====================================================================
+
+This release adds support for retrieving / setting notes via Markdown 
+(using the 3rdParty libraries html2md and maddy). Additionally, a 
+number of stability and build issues were resolved.
+
+====================================================================
+5.20.4 (2024-08-07)
 ====================================================================
 
 This is mostly a bug fix release enhancing stability and improving 
@@ -13,7 +37,7 @@ performance when validating models. Main points:
 
 
 ====================================================================
-5.20.2
+5.20.2 (2023-09-21)
 ====================================================================
 
 This is mostly a bug fix release enhancing stability when validating

README.md

@@ -4,9 +4,9 @@ libSBML<img width="22%" align="right" src=".graphics/libsbml-logo-and-name.svg">
 LibSBML is an open-source library for working with SBML (the Systems Biology Markup Language).  It is written in C++ and provides language bindings for many other programming languages.
 
 [![License](https://img.shields.io/badge/License-LGPL-blue.svg?style=flat-square)](https://www.gnu.org/licenses/old-licenses/lgpl-2.1.en.html)
-[![Stable release](https://img.shields.io/badge/Stable_release-5.19.0-brightgreen.svg?style=flat-square)](https://sourceforge.net/projects/sbml/files/libsbml/5.19.0/stable/)
-[![Experimental release](https://img.shields.io/badge/Experimental_release-5.19.0-b44e88.svg?style=flat-square)](https://sourceforge.net/projects/sbml/files/libsbml/5.19.0/experimental/)
-[![Pivotal Tracker](https://img.shields.io/badge/Project_management-Pivotal-d07a3e.svg?style=flat-square)](https://www.pivotaltracker.com/n/projects/248655)
+[![Stable release](https://img.shields.io/badge/Stable_release-5.21.0-brightgreen.svg?style=flat-square)](https://github.com/sbmlteam/libsbml/releases/tag/v5.21.0)
+[![Experimental release](https://img.shields.io/badge/Experimental_release-5.21.0-b44e88.svg?style=flat-square)](https://github.com/sbmlteam/libsbml/releases/tag/v5.21.0)
+[![GitHub Issues or Pull Requests](https://img.shields.io/github/issues/sbmlteam/libsbml)](https://github.com/sbmlteam/libsbml/issues)
 [![Discussion](https://img.shields.io/badge/Discussion-libsbml--development-lightgray.svg?style=flat-square)](https://groups.google.com/g/libsbml-development)
 [![Nightly build](https://img.shields.io/github/workflow/status/sbmlteam/libsbml/Nightly%20build%20(binaries)?label=Nightly%20build&style=flat-square)](https://github.com/sbmlteam/libsbml/actions/workflows/store-artefact.yml)
 

VERSION.txt

@@ -1 +1 @@
-5.20.4
+5.21.1

configure

@@ -1,7 +1,7 @@
 #! /bin/sh
 # From configure.ac Revision.
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.72 for libSBML 5.20.4.
+# Generated by GNU Autoconf 2.72 for libSBML 5.21.1.
 #
 # Report bugs to <libsbml-team@googlegroups.com>.
 #
@@ -759,8 +759,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='libSBML'
 PACKAGE_TARNAME='libsbml'
-PACKAGE_VERSION='5.20.4'
-PACKAGE_STRING='libSBML 5.20.4'
+PACKAGE_VERSION='5.21.1'
+PACKAGE_STRING='libSBML 5.21.1'
 PACKAGE_BUGREPORT='libsbml-team@googlegroups.com'
 PACKAGE_URL='http://sbml.org/Software/libSBML'
 
@@ -1655,7 +1655,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-'configure' configures libSBML 5.20.4 to adapt to many kinds of systems.
+'configure' configures libSBML 5.21.1 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1721,7 +1721,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of libSBML 5.20.4:";;
+     short | recursive ) echo "Configuration of libSBML 5.21.1:";;
    esac
   cat <<\_ACEOF
 
@@ -1878,7 +1878,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-libSBML configure 5.20.4
+libSBML configure 5.21.1
 generated by GNU Autoconf 2.72
 
 Copyright (C) 2023 Free Software Foundation, Inc.
@@ -2494,7 +2494,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by libSBML $as_me 5.20.4, which was
+It was created by libSBML $as_me 5.21.1, which was
 generated by GNU Autoconf 2.72.  Invocation command line was
 
   $ $0$ac_configure_args_raw
@@ -3497,19 +3497,19 @@ ac_config_headers="$ac_config_headers src/sbml/common/libsbml-package.h"
 ac_config_headers="$ac_config_headers src/sbml/common/libsbml-namespace.h"
 
 
-LIBSBML_VERSION_NUMERIC=52004
+LIBSBML_VERSION_NUMERIC=52101
 
 
 
 LIBSBML_MAJOR_VERSION=5
 
 
 
-LIBSBML_MINOR_VERSION=20
+LIBSBML_MINOR_VERSION=21
 
 
 
-LIBSBML_REVISION_VERSION=4
+LIBSBML_REVISION_VERSION=1
 
 
 
@@ -29224,7 +29224,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by libSBML $as_me 5.20.4, which was
+This file was extended by libSBML $as_me 5.21.1, which was
 generated by GNU Autoconf 2.72.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -29289,7 +29289,7 @@ ac_cs_config_escaped=`printf "%s\n" "$ac_cs_config" | sed "s/^ //; s/'/'\\\\\\\\
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config='$ac_cs_config_escaped'
 ac_cs_version="\\
-libSBML config.status 5.20.4
+libSBML config.status 5.21.1
 configured by $0, generated by GNU Autoconf 2.72,
   with options \\"\$ac_cs_config\\"