Merge pull request #2497 from dweindl/release_0.26.2

Release 0.26.2

.github/workflows/test_benchmark_collection_models.yml

@@ -61,6 +61,7 @@ jobs:
       run: |
         git clone --depth 1 https://github.com/benchmarking-initiative/Benchmark-Models-PEtab.git \
           && export BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \
+          && pip3 install -e $BENCHMARK_COLLECTION/../src/python \
           && AMICI_PARALLEL_COMPILE="" tests/benchmark-models/test_benchmark_collection.sh
 
     # run gradient checks

.github/workflows/test_python_cplusplus.yml

@@ -125,6 +125,13 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
+    - name: Cache
+      uses: actions/cache@v4
+      with:
+        path: |
+          ~/.cache/pooch
+        key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
+
     - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
 
@@ -201,6 +208,13 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
+    - name: Cache
+      uses: actions/cache@v4
+      with:
+        path: |
+          ~/.cache/pooch
+        key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
+
     - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
 
@@ -259,6 +273,17 @@ jobs:
     - name: C++ tests
       run: scripts/run-cpp-tests.sh
 
+    - name: Get Pooch Cache Directory
+      id: get-pooch-cache
+      run: |
+        echo "pooch-cache=$(source venv/bin/activate && python -c 'import pooch; print(pooch.os_cache("pooch"))')" >> $GITHUB_ENV
+
+    - name: Cache Pooch Directory
+      uses: actions/cache@v4
+      with:
+        path: ${{ env.pooch-cache }}
+        key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
+
     - name: Python tests
       run: |
         scripts/run-python-tests.sh \
@@ -301,6 +326,18 @@ jobs:
     - name: Get BioNetGen
       run: scripts/buildBNGL.sh
 
+
+    - name: Get Pooch Cache Directory
+      id: get-pooch-cache
+      run: |
+        echo "pooch-cache=$(source venv/bin/activate && python -c 'import pooch; print(pooch.os_cache("pooch"))')" >> $GITHUB_ENV
+
+    - name: Cache Pooch Directory
+      uses: actions/cache@v4
+      with:
+        path: ${{ env.pooch-cache }}
+        key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
+
     - name: Python tests
       run: |
         scripts/run-python-tests.sh \

.github/workflows/test_python_ver_matrix.yml

@@ -60,6 +60,17 @@ jobs:
     - run: source venv/bin/activate && pip3 install "sympy>=1.12.1"
       if: matrix.python-version != '3.12'
 
+    - name: Get Pooch Cache Directory
+      id: get-pooch-cache
+      run: |
+        echo "pooch-cache=$(source venv/bin/activate && python -c 'import pooch; print(pooch.os_cache("pooch"))')" >> $GITHUB_ENV
+
+    - name: Cache Pooch Directory
+      uses: actions/cache@v4
+      with:
+        path: ${{ env.pooch-cache }}
+        key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
+
     - name: Python tests
       run: |
         source venv/bin/activate \

.github/workflows/test_windows.yml

@@ -77,6 +77,18 @@ jobs:
 
     - run: python -m amici
 
+    - name: Get Pooch Cache Directory
+      id: get-pooch-cache
+      run: |
+        echo "pooch-cache=$(python -c 'import pooch; print(pooch.os_cache("pooch"))')" >> $GITHUB_ENV
+      shell: bash
+
+    - name: Cache Pooch Directory
+      uses: actions/cache@v4
+      with:
+        path: ${{ env.pooch-cache }}
+        key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
+
     - name: Run Python tests
       shell: bash
       run: |

.gitignore

@@ -182,6 +182,7 @@ ThirdParty/sundials/build/*
 ThirdParty/SuiteSparse/lib/*
 ThirdParty/SuiteSparse/include/
 ThirdParty/SuiteSparse/share/*
+ThirdParty/SuiteSparse/install/*
 ThirdParty/SuperLU_MT_3.1/
 ThirdParty/superlu_mt_3.1.tar.gz
 ThirdParty/swig-*

.pre-commit-config.yaml

@@ -12,7 +12,7 @@ repos:
   - id: trailing-whitespace
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.4.1
+  rev: v0.6.7
   hooks:
     # Run the linter.
     - id: ruff
@@ -28,7 +28,7 @@ repos:
         - python/sdist/pyproject.toml
 
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.2
+    rev: v3.17.0
     hooks:
     -   id: pyupgrade
         args: ["--py310-plus"]

CHANGELOG.md

@@ -4,6 +4,26 @@ See also our [versioning policy](https://amici.readthedocs.io/en/latest/versioni
 
 ## v0.X Series
 
+### v0.26.2 (2024-09-25)
+
+**Fixes**
+
+* Fixed a sympy float comparison issue in spline code that would cause
+  an `AssertionError`
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2499
+
+* Fixed some warnings from recent CMake versions
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2492
+
+* Fixed a potential issue when including AMICI in a CMake project
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2493
+
+**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.26.1...v0.26.2
+
+
 ### v0.26.1 (2024-07-11)
 
 **Fixes**

CMakeLists.txt

@@ -2,16 +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)
-# cmake >= 3.30
-if(POLICY CMP0167)
-  cmake_policy(SET CMP0167 NEW)
-endif(POLICY CMP0167)
+# When updating the policy version, please also update it in
+# src/CMakeLists.template.cmake
+cmake_policy(VERSION 3.15...3.30)
 
 project(amici)
 
@@ -377,7 +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)

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 ( )

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

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

ThirdParty/SuiteSparse/AMD/Doc/amd_version.tex

@@ -1,2 +1,2 @@
 % version of SuiteSparse/AMD
-\date{VERSION 3.3.1, Jan 10, 2024}
+\date{VERSION 3.3.3, June 20, 2024}

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

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 ( )

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

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

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

ThirdParty/SuiteSparse/CITATION.bib

@@ -474,17 +474,16 @@ @article{10.1145/3337792
 
 @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},
 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}
 }