amici 0.26.0__tar.gz → 0.26.2__tar.gz

{amici-0.26.0/amici.egg-info → amici-0.26.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: amici
-Version: 0.26.0
+Version: 0.26.2
 Summary: Advanced multi-language Interface to CVODES and IDAS
 Author: Jan Hasenauer, AMICI contributors
 Author-email: Fabian Froehlich <froehlichfab@gmail.com>, Daniel Weindl <sci@danielweindl.de>

{amici-0.26.0 → amici-0.26.2}/amici/CMakeLists.txt

@@ -2,12 +2,9 @@
 # Build AMICI library
 #
 cmake_minimum_required(VERSION 3.15)
-cmake_policy(VERSION 3.15...3.27)
-
-# cmake >=3.27
-if(POLICY CMP0144)
-  cmake_policy(SET CMP0144 NEW)
-endif(POLICY CMP0144)
+# When updating the policy version, please also update it in
+# src/CMakeLists.template.cmake
+cmake_policy(VERSION 3.15...3.30)
 
 project(amici)
 
@@ -32,10 +29,11 @@ message(STATUS "CMAKE_INSTALL_PREFIX: ${CMAKE_INSTALL_PREFIX}")
 
 list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
 
-if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
-  # require at least gcc 4.9, otherwise regex wont work properly
-  if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 4.9)
-    message(FATAL_ERROR "GCC version must be at least 4.9!")
+if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU" OR "${CMAKE_CXX_COMPILER_ID}"
+                                                STREQUAL "MINGW")
+  # require at least gcc 9.1 for proper C+17 support, e.g. std::reduce
+  if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 9.1)
+    message(FATAL_ERROR "GCC version must be at least 9.1!")
   endif()
 endif()
 
@@ -143,8 +141,7 @@ else()
   set(VENDORED_SUNDIALS_INSTALL_DIR ${VENDORED_SUNDIALS_BUILD_DIR})
 endif()
 set(SUNDIALS_ROOT "${VENDORED_SUNDIALS_INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}")
-find_package(
-  SUNDIALS REQUIRED CONFIG PATHS "${SUNDIALS_ROOT}/cmake/sundials/")
+find_package(SUNDIALS REQUIRED CONFIG PATHS "${SUNDIALS_ROOT}/cmake/sundials/")
 message(STATUS "Found SUNDIALS: ${SUNDIALS_DIR}")
 
 set(GSL_LITE_INCLUDE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/ThirdParty/gsl")
@@ -373,7 +370,7 @@ export(
 include(CMakePackageConfigHelpers)
 include(version)
 configure_package_config_file(
-  cmake/AmiciConfig.cmake "${CMAKE_CURRENT_BINARY_DIR}/AmiciConfig.cmake"
+  "cmake/AmiciConfig.cmake.in" "${CMAKE_CURRENT_BINARY_DIR}/AmiciConfig.cmake"
   INSTALL_DESTINATION "${CMAKE_INSTALL_LIBDIR}/cmake/Amici")
 write_basic_package_version_file(AmiciConfigVersion.cmake
                                  COMPATIBILITY ExactVersion)

{amici-0.26.0 → amici-0.26.2}/amici/ThirdParty/SuiteSparse/AMD/CMakeLists.txt

@@ -12,10 +12,10 @@
 
 cmake_minimum_required ( VERSION 3.22 )
 
-set ( AMD_DATE "Jan 10, 2024" )
+set ( AMD_DATE "June 20, 2024" )
 set ( AMD_VERSION_MAJOR 3 CACHE STRING "" FORCE )
 set ( AMD_VERSION_MINOR 3 CACHE STRING "" FORCE )
-set ( AMD_VERSION_SUB   1 CACHE STRING "" FORCE )
+set ( AMD_VERSION_SUB   3 CACHE STRING "" FORCE )
 
 message ( STATUS "Building AMD version: v"
     ${AMD_VERSION_MAJOR}.
@@ -49,10 +49,10 @@ endif ( )
 #-------------------------------------------------------------------------------
 
 if ( NOT SUITESPARSE_ROOT_CMAKELISTS )
-    find_package ( SuiteSparse_config 7.5.0
+    find_package ( SuiteSparse_config 7.8.0
         PATHS ${CMAKE_SOURCE_DIR}/../SuiteSparse_config/build NO_DEFAULT_PATH )
     if ( NOT TARGET SuiteSparse::SuiteSparseConfig )
-        find_package ( SuiteSparse_config 7.5.0 REQUIRED )
+        find_package ( SuiteSparse_config 7.8.0 REQUIRED )
     endif ( )
 endif ( )
 
@@ -90,7 +90,8 @@ if ( BUILD_SHARED_LIBS )
         OUTPUT_NAME amd
         SOVERSION ${AMD_VERSION_MAJOR}
         PUBLIC_HEADER "Include/amd.h"
-        WINDOWS_EXPORT_ALL_SYMBOLS ON )
+        WINDOWS_EXPORT_ALL_SYMBOLS ON
+        LINKER_LANGUAGE C )
 
     if ( ${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.25" )
         set_target_properties ( AMD PROPERTIES EXPORT_NO_SYSTEM ON )
@@ -111,9 +112,10 @@ if ( BUILD_STATIC_LIBS )
         C_STANDARD 11
         C_STANDARD_REQUIRED ON
         OUTPUT_NAME amd
-        PUBLIC_HEADER "Include/amd.h" )
+        PUBLIC_HEADER "Include/amd.h"
+        LINKER_LANGUAGE C )
 
-    if ( MSVC )
+    if ( MSVC OR ("${CMAKE_C_SIMULATE_ID}" STREQUAL "MSVC") )
         set_target_properties ( AMD_static PROPERTIES
             OUTPUT_NAME amd_static )
     endif ( )

{amici-0.26.0 → amici-0.26.2}/amici/ThirdParty/SuiteSparse/AMD/Config/amd.h.in

@@ -392,8 +392,8 @@ void amd_version (int version [3]) ;
 
 #define AMD__VERSION SUITESPARSE__VERCODE(@AMD_VERSION_MAJOR@,@AMD_VERSION_MINOR@,@AMD_VERSION_SUB@)
 #if !defined (SUITESPARSE__VERSION) || \
-    (SUITESPARSE__VERSION < SUITESPARSE__VERCODE(7,5,0))
-#error "AMD @AMD_VERSION_MAJOR@.@AMD_VERSION_MINOR@.@AMD_VERSION_SUB@ requires SuiteSparse_config 7.5.0 or later"
+    (SUITESPARSE__VERSION < SUITESPARSE__VERCODE(7,8,0))
+#error "AMD @AMD_VERSION_MAJOR@.@AMD_VERSION_MINOR@.@AMD_VERSION_SUB@ requires SuiteSparse_config 7.8.0 or later"
 #endif
 
 #endif

{amici-0.26.0 → amici-0.26.2}/amici/ThirdParty/SuiteSparse/AMD/Doc/ChangeLog

@@ -1,3 +1,11 @@
+June 20, 2024: version 3.3.3
+
+    * minor update for MATLAB on Windows
+
+Mar 22, 2024: version 3.3.2
+
+    * minor updates to build system
+
 Jan 10, 2024: version 3.3.1
 
     * minor updates to build system

amici-0.26.2/amici/ThirdParty/SuiteSparse/AMD/Doc/amd_version.tex

@@ -0,0 +1,2 @@
+% version of SuiteSparse/AMD
+\date{VERSION 3.3.3, June 20, 2024}

{amici-0.26.0 → amici-0.26.2}/amici/ThirdParty/SuiteSparse/AMD/Include/amd.h

@@ -382,18 +382,18 @@ void amd_version (int version [3]) ;
  * Versions 1.1 and earlier of AMD do not include a #define'd version number.
  */
 
-#define AMD_DATE "Jan 10, 2024"
+#define AMD_DATE "June 20, 2024"
 #define AMD_MAIN_VERSION   3
 #define AMD_SUB_VERSION    3
-#define AMD_SUBSUB_VERSION 1
+#define AMD_SUBSUB_VERSION 3
 
 #define AMD_VERSION_CODE(main,sub) SUITESPARSE_VER_CODE(main,sub)
 #define AMD_VERSION AMD_VERSION_CODE(3,3)
 
-#define AMD__VERSION SUITESPARSE__VERCODE(3,3,1)
+#define AMD__VERSION SUITESPARSE__VERCODE(3,3,3)
 #if !defined (SUITESPARSE__VERSION) || \
-    (SUITESPARSE__VERSION < SUITESPARSE__VERCODE(7,5,0))
-#error "AMD 3.3.1 requires SuiteSparse_config 7.5.0 or later"
+    (SUITESPARSE__VERSION < SUITESPARSE__VERCODE(7,8,0))
+#error "AMD 3.3.3 requires SuiteSparse_config 7.8.0 or later"
 #endif
 
 #endif

{amici-0.26.0 → amici-0.26.2}/amici/ThirdParty/SuiteSparse/BTF/CMakeLists.txt

@@ -12,10 +12,10 @@
 
 cmake_minimum_required ( VERSION 3.22 )
 
-set ( BTF_DATE "Jan 10, 2024" )
+set ( BTF_DATE "Mar 22, 2024" )
 set ( BTF_VERSION_MAJOR 2 CACHE STRING "" FORCE )
 set ( BTF_VERSION_MINOR 3 CACHE STRING "" FORCE )
-set ( BTF_VERSION_SUB   1 CACHE STRING "" FORCE )
+set ( BTF_VERSION_SUB   2 CACHE STRING "" FORCE )
 
 message ( STATUS "Building BTF version: v"
     ${BTF_VERSION_MAJOR}.
@@ -44,10 +44,10 @@ include ( SuiteSparsePolicy )
 #-------------------------------------------------------------------------------
 
 if ( NOT SUITESPARSE_ROOT_CMAKELISTS )
-    find_package ( SuiteSparse_config 7.5.0
+    find_package ( SuiteSparse_config 7.7.0
         PATHS ${CMAKE_SOURCE_DIR}/../SuiteSparse_config/build NO_DEFAULT_PATH )
     if ( NOT TARGET SuiteSparse::SuiteSparseConfig )
-        find_package ( SuiteSparse_config 7.5.0 REQUIRED )
+        find_package ( SuiteSparse_config 7.7.0 REQUIRED )
     endif ( )
 endif ( )
 
@@ -104,7 +104,7 @@ if ( BUILD_STATIC_LIBS )
         OUTPUT_NAME btf
         PUBLIC_HEADER "Include/btf.h" )
 
-    if ( MSVC )
+    if ( MSVC OR ("${CMAKE_C_SIMULATE_ID}" STREQUAL "MSVC") )
         set_target_properties ( BTF_static PROPERTIES
             OUTPUT_NAME btf_static )
     endif ( )

{amici-0.26.0 → amici-0.26.2}/amici/ThirdParty/SuiteSparse/BTF/Config/btf.h.in

@@ -274,8 +274,8 @@ void btf_version (int version [3]) ;
 
 #define BTF__VERSION SUITESPARSE__VERCODE(@BTF_VERSION_MAJOR@,@BTF_VERSION_MINOR@,@BTF_VERSION_SUB@)
 #if !defined (SUITESPARSE__VERSION) || \
-    (SUITESPARSE__VERSION < SUITESPARSE__VERCODE(7,5,0))
-#error "BTF @BTF_VERSION_MAJOR@.@BTF_VERSION_MINOR@.@BTF_VERSION_SUB@ requires SuiteSparse_config 7.5.0 or later"
+    (SUITESPARSE__VERSION < SUITESPARSE__VERCODE(7,7,0))
+#error "BTF @BTF_VERSION_MAJOR@.@BTF_VERSION_MINOR@.@BTF_VERSION_SUB@ requires SuiteSparse_config 7.7.0 or later"
 #endif
 
 #endif

{amici-0.26.0 → amici-0.26.2}/amici/ThirdParty/SuiteSparse/BTF/Doc/ChangeLog

@@ -1,3 +1,7 @@
+Mar 22, 2024: version 2.3.2
+
+    * minor updates to build system
+
 Jan 10, 2024: version 2.3.1
 
     * minor updates to build system

{amici-0.26.0 → amici-0.26.2}/amici/ThirdParty/SuiteSparse/BTF/Include/btf.h

@@ -264,18 +264,18 @@ void btf_version (int version [3]) ;
  *      #endif
  */
 
-#define BTF_DATE "Jan 10, 2024"
+#define BTF_DATE "Mar 22, 2024"
 #define BTF_MAIN_VERSION   2
 #define BTF_SUB_VERSION    3
-#define BTF_SUBSUB_VERSION 1
+#define BTF_SUBSUB_VERSION 2
 
 #define BTF_VERSION_CODE(main,sub) SUITESPARSE_VER_CODE(main,sub)
 #define BTF_VERSION BTF_VERSION_CODE(2,3)
 
-#define BTF__VERSION SUITESPARSE__VERCODE(2,3,1)
+#define BTF__VERSION SUITESPARSE__VERCODE(2,3,2)
 #if !defined (SUITESPARSE__VERSION) || \
-    (SUITESPARSE__VERSION < SUITESPARSE__VERCODE(7,5,0))
-#error "BTF 2.3.1 requires SuiteSparse_config 7.5.0 or later"
+    (SUITESPARSE__VERSION < SUITESPARSE__VERCODE(7,7,0))
+#error "BTF 2.3.2 requires SuiteSparse_config 7.7.0 or later"
 #endif
 
 #endif

{amici-0.26.0 → amici-0.26.2}/amici/ThirdParty/SuiteSparse/CITATION.bib

@@ -474,7 +474,7 @@ keywords = {vertex matching, Graph partitioning, graph coarsening}
 
 @article{10.1145/3519024,
 author = {Lourenco, Christopher and Chen, Jinhao and Moreno-Centeno, Erick and Davis, Timothy A.},
-title = {Algorithm 1XXX: SPEX Left LU, Exactly Solving Sparse Linear Systems via a Sparse Left-Looking Integer-Preserving LU Factorization},
+title = {Algorithm 1021: SPEX Left LU, Exactly Solving Sparse Linear Systems via a Sparse Left-Looking Integer-Preserving LU Factorization},
 year = {2022},
 publisher = {Association for Computing Machinery},
 address = {New York, NY, USA},
@@ -482,9 +482,8 @@ issn = {0098-3500},
 url = {https://doi.org/10.1145/3519024},
 doi = {10.1145/3519024},
 abstract = {SPEX Left LU is a software package for exactly solving unsymmetric sparse linear systems. As a component of the sparse exact (SPEX) software package, SPEX Left LU can be applied to any input matrix, A, whose entries are integral, rational, or decimal, and provides a solution to the system Ax = b which is either exact or accurate to user-specified precision. SPEX Left LU preorders the matrix A with a user-specified fill-reducing ordering and computes a left-looking LU factorization with the special property that each operation used to compute the L and U matrices is integral. Notable additional applications of this package include benchmarking the stability and accuracy of state-of-the-art linear solvers, and determining whether singular-to-double-precision matrices are indeed singular. Computationally, this paper evaluates the impact of several novel pivoting schemes in exact arithmetic, benchmarks the exact iterative solvers within Linbox, and benchmarks the accuracy of MATLAB sparse backslash. Most importantly, it is shown that SPEX Left LU outperforms the exact iterative solvers in run time on easy instances and in stability as the iterative solver fails on a sizeable subset of the tested (both easy and hard) instances. The SPEX Left LU package is written in ANSI C, comes with a MATLAB interface, and is distributed via GitHub, as a component of the SPEX software package, and as a component of SuiteSparse.},
-note = {Just Accepted},
 journal = {ACM Trans. Math. Softw.},
-month = {feb},
+month = {jun},
 keywords = {exact matrix factorization, sparse linear systems, sparse matrix algorithms, exactly solving linear systems, roundoff errors}
 }
 

{amici-0.26.0 → amici-0.26.2}/amici/ThirdParty/SuiteSparse/CMakeLists.txt

@@ -85,6 +85,7 @@ option ( SUITESPARSE_USE_SYSTEM_CAMD "ON: use CAMD libraries installed on the bu
 option ( SUITESPARSE_USE_SYSTEM_CCOLAMD "ON: use CCOLAMD libraries installed on the build system.  OFF (default): Automatically build CCOLAMD as dependency if needed." OFF )
 option ( SUITESPARSE_USE_SYSTEM_GRAPHBLAS "ON: use GraphBLAS libraries installed on the build system.  OFF (default): Automatically build GraphBLAS as dependency if needed." OFF )
 option ( SUITESPARSE_USE_SYSTEM_SUITESPARSE_CONFIG "ON: use SuiteSparse_config libraries installed on the build system.  OFF (default): Automatically build SuiteSparse_config as dependency if needed." OFF )
+option ( SUITESPARSE_USE_SYSTEM_UMFPACK "ON: use UMFPACK libraries installed on the build system.  OFF (default): Automatically build UMFPACK as dependency if needed." OFF )
 
 #-------------------------------------------------------------------------------
 # global variables
@@ -110,7 +111,7 @@ include ( SuiteSparsePolicy )
 
 if ( SUITESPARSE_USE_SYSTEM_GRAPHBLAS )
     list ( REMOVE_ITEM SUITESPARSE_ENABLE_PROJECTS "graphblas" )
-    find_package ( GraphBLAS 9.0.1 REQUIRED )
+    find_package ( GraphBLAS 9.3.1 REQUIRED )
 else ( )
     if ( "lagraph" IN_LIST SUITESPARSE_ENABLE_PROJECTS )
         # LAGraph requires GraphBLAS.
@@ -123,7 +124,7 @@ endif ( )
 
 if ( SUITESPARSE_USE_SYSTEM_BTF )
     list ( REMOVE_ITEM SUITESPARSE_ENABLE_PROJECTS "btf" )
-    find_package ( BTF 2.3.1 REQUIRED )
+    find_package ( BTF 2.3.2 REQUIRED )
 else ( )
     if ( "klu" IN_LIST SUITESPARSE_ENABLE_PROJECTS )
         # KLU requires BTF.
@@ -134,9 +135,22 @@ else ( )
     endif ( )
 endif ( )
 
+if ( SUITESPARSE_USE_SYSTEM_UMFPACK )
+    list ( REMOVE_ITEM SUITESPARSE_ENABLE_PROJECTS "umfpack" )
+    find_package ( UMFPACK 6.3.4 REQUIRED )
+else ( )
+    if ( "paru" IN_LIST SUITESPARSE_ENABLE_PROJECTS )
+        # ParU requires UMFPACK.
+        if ( NOT "umfpack" IN_LIST SUITESPARSE_ENABLE_PROJECTS )
+            message ( STATUS "Adding \"umfpack\" to the list of built targets." )
+            list ( APPEND SUITESPARSE_ENABLE_PROJECTS "umfpack" )
+        endif ( )
+    endif ( )
+endif ( )
+
 if ( SUITESPARSE_USE_SYSTEM_CHOLMOD )
     list ( REMOVE_ITEM SUITESPARSE_ENABLE_PROJECTS "cholmod" )
-    find_package ( CHOLMOD 5.2.0 REQUIRED )
+    find_package ( CHOLMOD 5.3.0 REQUIRED )
 else ( )
     if ( ( KLU_USE_CHOLMOD AND "klu" IN_LIST SUITESPARSE_ENABLE_PROJECTS )
             OR ( UMFPACK_USE_CHOLMOD AND "umfpack" IN_LIST SUITESPARSE_ENABLE_PROJECTS )
@@ -154,7 +168,7 @@ endif ( )
 
 if ( SUITESPARSE_USE_SYSTEM_AMD )
     list ( REMOVE_ITEM SUITESPARSE_ENABLE_PROJECTS "amd" )
-    find_package ( AMD 3.3.1 REQUIRED )
+    find_package ( AMD 3.3.3 REQUIRED )
 else ( )
     if ( "cholmod" IN_LIST SUITESPARSE_ENABLE_PROJECTS
             OR "ldl" IN_LIST SUITESPARSE_ENABLE_PROJECTS
@@ -170,7 +184,7 @@ endif ( )
 
 if ( SUITESPARSE_USE_SYSTEM_COLAMD )
     list ( REMOVE_ITEM SUITESPARSE_ENABLE_PROJECTS "colamd" )
-    find_package ( COLAMD 3.3.2 REQUIRED )
+    find_package ( COLAMD 3.3.4 REQUIRED )
 else ( )
     if ( "cholmod" IN_LIST SUITESPARSE_ENABLE_PROJECTS
             OR "spex" IN_LIST SUITESPARSE_ENABLE_PROJECTS )
@@ -184,7 +198,7 @@ endif ( )
 
 if ( SUITESPARSE_USE_SYSTEM_CAMD )
     list ( REMOVE_ITEM SUITESPARSE_ENABLE_PROJECTS "camd" )
-    find_package ( CAMD 3.3.1 REQUIRED )
+    find_package ( CAMD 3.3.3 REQUIRED )
 else ( )
     if ( CHOLMOD_CAMD AND "cholmod" IN_LIST SUITESPARSE_ENABLE_PROJECTS )
         # CHOLMOD can optionally use CAMD.
@@ -197,7 +211,7 @@ endif ( )
 
 if ( SUITESPARSE_USE_SYSTEM_CCOLAMD )
     list ( REMOVE_ITEM SUITESPARSE_ENABLE_PROJECTS "ccolamd" )
-    find_package ( CCOLAMD 3.3.2 REQUIRED )
+    find_package ( CCOLAMD 3.3.4 REQUIRED )
 else ( )
     if ( CHOLMOD_CAMD AND "cholmod" IN_LIST SUITESPARSE_ENABLE_PROJECTS )
         # CHOLMOD can optionally use CCOLAMD.
@@ -210,7 +224,7 @@ endif ( )
 
 if ( SUITESPARSE_USE_SYSTEM_SUITESPARSE_CONFIG )
     list ( REMOVE_ITEM SUITESPARSE_ENABLE_PROJECTS "suitesparse_config" )
-    find_package ( SuiteSparse_config 7.6.0 REQUIRED )
+    find_package ( SuiteSparse_config 7.8.2 REQUIRED )
 else ( )
     if ( "mongoose" IN_LIST SUITESPARSE_ENABLE_PROJECTS
             OR "amd" IN_LIST SUITESPARSE_ENABLE_PROJECTS

{amici-0.26.0 → amici-0.26.2}/amici/ThirdParty/SuiteSparse/COLAMD/CMakeLists.txt

@@ -11,10 +11,10 @@
 
 cmake_minimum_required ( VERSION 3.22 )
 
-set ( COLAMD_DATE "Jan 20, 2024" )
+set ( COLAMD_DATE "June 20, 2024" )
 set ( COLAMD_VERSION_MAJOR 3 CACHE STRING "" FORCE )
 set ( COLAMD_VERSION_MINOR 3 CACHE STRING "" FORCE )
-set ( COLAMD_VERSION_SUB   2 CACHE STRING "" FORCE )
+set ( COLAMD_VERSION_SUB   4 CACHE STRING "" FORCE )
 
 message ( STATUS "Building COLAMD version: v"
     ${COLAMD_VERSION_MAJOR}.
@@ -43,10 +43,10 @@ include ( SuiteSparsePolicy )
 #-------------------------------------------------------------------------------
 
 if ( NOT SUITESPARSE_ROOT_CMAKELISTS )
-    find_package ( SuiteSparse_config 7.6.0
+    find_package ( SuiteSparse_config 7.8.0
         PATHS ${CMAKE_SOURCE_DIR}/../SuiteSparse_config/build NO_DEFAULT_PATH )
     if ( NOT TARGET SuiteSparse::SuiteSparseConfig )
-        find_package ( SuiteSparse_config 7.6.0 REQUIRED )
+        find_package ( SuiteSparse_config 7.8.0 REQUIRED )
     endif ( )
 endif ( )
 
@@ -104,7 +104,7 @@ if ( BUILD_STATIC_LIBS )
         C_STANDARD_REQUIRED ON
         PUBLIC_HEADER "Include/colamd.h" )
 
-    if ( MSVC )
+    if ( MSVC OR ("${CMAKE_C_SIMULATE_ID}" STREQUAL "MSVC") )
         set_target_properties ( COLAMD_static PROPERTIES
             OUTPUT_NAME colamd_static )
     endif ( )

{amici-0.26.0 → amici-0.26.2}/amici/ThirdParty/SuiteSparse/COLAMD/Config/colamd.h.in

@@ -75,8 +75,8 @@
 
 #define COLAMD__VERSION SUITESPARSE__VERCODE(@COLAMD_VERSION_MAJOR@,@COLAMD_VERSION_MINOR@,@COLAMD_VERSION_SUB@)
 #if !defined (SUITESPARSE__VERSION) || \
-    (SUITESPARSE__VERSION < SUITESPARSE__VERCODE(7,6,0))
-#error "COLAMD @COLAMD_VERSION_MAJOR@.@COLAMD_VERSION_MINOR@.@COLAMD_VERSION_SUB@ requires SuiteSparse_config 7.6.0 or later"
+    (SUITESPARSE__VERSION < SUITESPARSE__VERCODE(7,8,0))
+#error "COLAMD @COLAMD_VERSION_MAJOR@.@COLAMD_VERSION_MINOR@.@COLAMD_VERSION_SUB@ requires SuiteSparse_config 7.8.0 or later"
 #endif
 
 /* ========================================================================== */

{amici-0.26.0 → amici-0.26.2}/amici/ThirdParty/SuiteSparse/COLAMD/Doc/ChangeLog

@@ -1,3 +1,11 @@
+June 20, 2024: version 3.3.4
+
+    * minor update for MATLAB on Windows
+
+Mar 22, 2024: version 3.3.3
+
+    * minor updates to build system
+
 Jan 20, 2024: version 3.3.2
 
     * minor updates to build system

{amici-0.26.0 → amici-0.26.2}/amici/ThirdParty/SuiteSparse/COLAMD/Include/colamd.h

@@ -65,18 +65,18 @@
  * Versions 2.3 and earlier of COLAMD do not include a #define'd version number.
  */
 
-#define COLAMD_DATE "Jan 20, 2024"
+#define COLAMD_DATE "June 20, 2024"
 #define COLAMD_MAIN_VERSION   3
 #define COLAMD_SUB_VERSION    3
-#define COLAMD_SUBSUB_VERSION 2
+#define COLAMD_SUBSUB_VERSION 4
 
 #define COLAMD_VERSION_CODE(main,sub) SUITESPARSE_VER_CODE(main,sub)
 #define COLAMD_VERSION COLAMD_VERSION_CODE(3,3)
 
-#define COLAMD__VERSION SUITESPARSE__VERCODE(3,3,2)
+#define COLAMD__VERSION SUITESPARSE__VERCODE(3,3,4)
 #if !defined (SUITESPARSE__VERSION) || \
-    (SUITESPARSE__VERSION < SUITESPARSE__VERCODE(7,6,0))
-#error "COLAMD 3.3.2 requires SuiteSparse_config 7.6.0 or later"
+    (SUITESPARSE__VERSION < SUITESPARSE__VERCODE(7,8,0))
+#error "COLAMD 3.3.4 requires SuiteSparse_config 7.8.0 or later"
 #endif
 
 /* ========================================================================== */

{amici-0.26.0 → amici-0.26.2}/amici/ThirdParty/SuiteSparse/CONTRIBUTING.md

@@ -6,13 +6,13 @@ you can use the issue tracker on github.com, at
 (https://github.com/DrTimothyAldenDavis/SuiteSparse/issues).
 
 To contribute code, you can submit a pull request.  To do so,
-you must first agree to the Contributor License Agreement
-[`CONTRIBUTOR-LICENSE.txt`](CONTRIBUTOR-LICENSE.txt).
-Print a copy of the txt file (as a PDF), sign and date it,
-and email it to me at DrTimothyAldenDavis@gmail.com.  Pull
-requests will only be included into SuiteSparse after I receive
-your email with the signed PDF.
+you must first agree to the Contributor License
+in the [`Contributor_License`](Contributor_License) folder.
+Sign and date it the PDF, and email it to me at
+DrTimothyAldenDavis@gmail.com.  Pull requests will only be
+included into SuiteSparse after I receive your email with
+the signed PDF.
 
 Do not submit a pull request to the default branch.
-Instead, use the dev or dev2 branches.
+Instead, use the dev2 branch.
 

{amici-0.26.0 → amici-0.26.2}/amici/ThirdParty/SuiteSparse/ChangeLog

@@ -1,3 +1,154 @@
+Aug 20, 2024: version 7.8.2
+
+    * LAGraph 1.1.4: bug fix for LAGraph_MMWrite when matrix is dense
+    * SPEX 3.2.1: release date revised, sync with primary SPEX repo
+    * SuiteSparse_config, Example: modified to reflect the release of
+        LAGraph 1.1.4 and SPEX 3.2.1
+    * ParU 0.3.0: added parameter to ParU_Get
+    * Package versions in this release: (* denotes a new version)
+        SuiteSparse_config 7.8.2    *
+        AMD 3.3.3
+        BTF 2.3.2
+        CAMD 3.3.3
+        CCOLAMD 3.3.4
+        CHOLMOD 5.3.0
+        COLAMD 3.3.4
+        CSparse 4.3.2
+        CXSparse 4.4.1
+        Example 1.8.2               *
+        GraphBLAS 9.3.1
+        KLU 2.3.4
+        LDL 3.3.2
+        LAGraph 1.1.4               *
+        SuiteSparse_Mongoose 3.3.4
+        ParU 0.3.0                  *
+        RBio 4.3.3
+        SPEX 3.2.1                  *
+        SPQR 4.3.4
+        UMFPACK 6.3.4
+
+Aug 12, 2024: version 7.8.1
+
+    * GraphBLAS 9.3.1: bug fix in creation of JIT package
+    * SuiteSparse_config, Example: modified to reflect the release of
+        GraphBLAS 9.3.1
+    * Package versions in this release: (* denotes a new version)
+        SuiteSparse_config 7.8.1    *
+        AMD 3.3.3
+        BTF 2.3.2
+        CAMD 3.3.3
+        CCOLAMD 3.3.4
+        CHOLMOD 5.3.0
+        COLAMD 3.3.4
+        CSparse 4.3.2
+        CXSparse 4.4.1
+        Example 1.8.1               *
+        GraphBLAS 9.3.1             *
+        KLU 2.3.4
+        LDL 3.3.2
+        LAGraph 1.1.3
+        SuiteSparse_Mongoose 3.3.4
+        ParU 0.2.0
+        RBio 4.3.3
+        SPEX 3.2.0
+        SPQR 4.3.4
+        UMFPACK 6.3.4
+
+Aug 2, 2024: version 7.8.0
+
+    * ParU 0.2.0: many changes; nearing a stable release.
+    * CHOLMOD 5.3.0: added cholmod_query, and #define's in cholmod.h,
+        to query which Modules and features have been configured.
+    * GraphBLAS 9.3.0: simpler MATLAB install; sanitize environment variables;
+        code restructuring.
+    * SPQR 4.3.4: changes to reflect updates to CHOLMOD
+    * SPEX 3.2.0: control Python interface, fix build issues on Mac,
+        split SPEX Cholesky into LDL and Cholesky.
+    * SuiteSparse_config: changes to SuiteSparse timer, BLA_VENDOR.  Added
+        SUITESPARSE_USE_PYTHON option.  Split BLAS prototypes and macros.
+    * .github: new CI runner for riscv64, and other changes in CI workflows.
+    * AMD, CAMD, COLAMD, CCOLAMD, CXSparse, KLU, SuiteSparse_Mongoose,
+        RBio, UMFPACK: minor changes for MATLAB in Windows
+    * no changes to: BTF, CSparse, LDL, and LAGraph
+    * Package versions in this release: (* denotes a new version)
+        SuiteSparse_config 7.8.0    *
+        AMD 3.3.3                   *
+        BTF 2.3.2                   same as SuiteSparse 7.7.0
+        CAMD 3.3.3                  *
+        CCOLAMD 3.3.4               *
+        CHOLMOD 5.3.0               *
+        COLAMD 3.3.4                *
+        CSparse 4.3.2               same as SuiteSparse 7.7.0
+        CXSparse 4.4.1              *
+        Example 1.8.0               *
+        GraphBLAS 9.3.0             *
+        KLU 2.3.4                   *
+        LDL 3.3.2                   same as SuiteSparse 7.7.0
+        LAGraph 1.1.3               same as SuiteSparse 7.7.0
+        SuiteSparse_Mongoose 3.3.4  *
+        ParU 0.2.0                  *
+        RBio 4.3.3                  *
+        SPEX 3.2.0                  *
+        SPQR 4.3.4                  *
+        UMFPACK 6.3.4               *
+
+Mar 22, 2024: version 7.7.0
+
+    * SPEX 3.1.0: major revision to API, new methods.  Added SPEX_Cholesky,
+        SPEX_Backslash, and python interface.  MATLAB interface revised.
+    * Example 1.7.0: revised for change in SPEX API
+    * GraphBLAS 9.1.0: revised defn of C11 or MSVC complex type, bug fix
+    * CXSparse 4.4.0: revise malloc/calloc/realloc/free wrappers
+    * All others: minor changes to build system
+    * Package versions in this release:
+        SuiteSparse_config 7.7.0
+        AMD 3.3.2
+        BTF 2.3.2
+        CAMD 3.3.2
+        CCOLAMD 3.3.3
+        CHOLMOD 5.2.1
+        COLAMD 3.3.3
+        CSparse 4.3.2
+        CXSparse 4.4.0
+        Example 1.7.0
+        GraphBLAS 9.1.0
+        KLU 2.3.3
+        LDL 3.3.2
+        LAGraph 1.1.3
+        SuiteSparse_Mongoose 3.3.3
+        ParU 0.1.3
+        RBio 4.3.2
+        SPEX 3.1.0
+        SPQR 4.3.3
+        UMFPACK 6.3.3
+
+Mar 2, 2024: version 7.6.1
+
+    * GraphBLAS 9.0.3: performance bug fix (JIT kernels were not compiled with
+        OpenMP, since v8.3.1), and fix to Makefile ("make static")
+    * SuiteSparse_config 7.6.1: version number, added link to math.js in README
+    * Package versions in this release:
+        SuiteSparse_config 7.6.1
+        AMD 3.3.1
+        BTF 2.3.1
+        CAMD 3.3.1
+        CCOLAMD 3.3.2
+        CHOLMOD 5.2.0
+        COLAMD 3.3.2
+        CSparse 4.3.1
+        CXSparse 4.3.1
+        Example 1.6.2
+        GraphBLAS 9.0.3
+        KLU 2.3.2
+        LDL 3.3.1
+        LAGraph 1.1.2
+        SuiteSparse_Mongoose 3.3.2
+        ParU 0.1.2
+        RBio 4.3.1
+        SPEX 2.3.2
+        SPQR 4.3.2
+        UMFPACK 6.3.2
+
 Jan 20, 2024: version 7.6.0
 
     * CHOLMOD 5.2.0: bug fix (restore ABI compatibility with 5.0.x, i.e., 5.2.0