Feature 2327 constraints

.github/actions/setup-amici-cpp/action.yml

@@ -18,6 +18,9 @@ runs:
     - run: echo "ENABLE_GCOV_COVERAGE=TRUE" >> $GITHUB_ENV
       shell: bash
 
+    - run: echo "PYTHONFAULTHANDLER=1" >> $GITHUB_ENV
+      shell: bash
+
     - name: Set up Sonar tools
       uses: ./.github/actions/setup-sonar-tools
 

.github/workflows/deploy_protected.yml

@@ -13,9 +13,25 @@ on:
   workflow_dispatch:
 
 jobs:
+  check-secret:
+    runs-on: ubuntu-latest
+    outputs:
+      secrets-defined: ${{ steps.secret-check.outputs.defined }}
+    steps:
+      - name: Check for Secret availability
+        id: secret-check
+        shell: bash
+        run: |
+          if [ "${{ secrets.DOCKER_USERNAME }}" != '' ]; then
+            echo "defined=true" >> $GITHUB_OUTPUT;
+          else
+            echo "defined=false" >> $GITHUB_OUTPUT;
+          fi
+
   dockerhub:
     name: Deploy Dockerhub
-    if: github.event.pull_request.head.repo.fork == false
+    needs: [check-secret]
+    if: needs.check-secret.outputs.secrets-defined == 'true'
     runs-on: ubuntu-22.04
 
     strategy:

.github/workflows/test_python_cplusplus.yml

@@ -18,6 +18,13 @@ jobs:
         python-version: [ "3.9" ]
 
     steps:
+    - name: Cache
+      uses: actions/cache@v3
+      with:
+        path: |
+          ~/.cache/pooch
+        key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
+
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:
@@ -265,6 +272,13 @@ jobs:
     runs-on: macos-latest
 
     steps:
+    - name: Cache
+      uses: actions/cache@v3
+      with:
+        path: |
+          ~/Library/Caches/pooch
+        key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
+
     - name: Set up Python
       uses: actions/setup-python@v5
       with:

.github/workflows/test_python_ver_matrix.yml

@@ -50,10 +50,6 @@ jobs:
     - name: Install python package
       run: scripts/installAmiciSource.sh
 
-    # until https://github.com/dateutil/dateutil >2.8.2 is released https://github.com/dateutil/dateutil/issues/1314
-    - run: source build/venv/bin/activate && pip3 install git+https://github.com/dateutil/dateutil.git@296d419fe6bf3b22897f8f210735ac9c4e1cb796
-      if: matrix.python-version == '3.12'
-
     # install pysb before sympy to allow for sympy>=1.12 (https://github.com/pysb/pysb/commit/e83937cb8c74afc9b2fa96595b68464946745f33)
     - run: source build/venv/bin/activate && pip3 install git+https://github.com/pysb/pysb
 

.github/workflows/test_sbml_semantic_test_suite.yml

@@ -9,7 +9,7 @@ on:
     paths:
       - .github/workflows/test_sbml_semantic_test_suite.yml
       - python/sdist/amici/de_export.py
-      - python/sdist/amici/de_model.py
+      - python/sdist/amici/de_model_components.py
       - python/sdist/amici/sbml_import.py
       - python/sdist/amici/import_utils.py
       - scripts/run-SBMLTestsuite.sh

CMakeLists.txt

@@ -169,9 +169,35 @@ if(${BLAS} STREQUAL "MKL" OR DEFINED ENV{MKLROOT})
         -lmkl
         CACHE STRING "")
   endif()
-elseif(NOT DEFINED ENV{BLAS_LIBS} AND NOT DEFINED ENV{BLAS_CFLAGS})
+elseif(
+  NOT DEFINED ENV{BLAS_LIBS}
+  AND NOT DEFINED ENV{BLAS_CFLAGS}
+  AND NOT BLAS_FOUND)
   # if nothing is specified via environment variables, let's try FindBLAS
-  find_package(BLAS)
+  if($(CMAKE_VERSION) VERSION_GREATER_EQUAL 3.22)
+    set(BLA_SIZEOF_INTEGER 8)
+  endif()
+
+  if(APPLE AND (NOT DEFINED BLA_VENDOR OR BLA_VENDOR STREQUAL "All"))
+    set(BLA_VENDOR Apple)
+    find_package(BLAS)
+    if(BLAS_FOUND)
+      set_property(
+        TARGET BLAS::BLAS
+        APPEND
+        PROPERTY INTERFACE_COMPILE_DEFINITIONS ACCELERATE_NEW_LAPACK)
+      set_property(
+        TARGET BLAS::BLAS
+        APPEND
+        PROPERTY INTERFACE_COMPILE_DEFINITIONS ACCELERATE_LAPACK_ILP64)
+    else()
+      set(BLA_VENDOR "All")
+    endif()
+
+  endif()
+  if(NOT BLAS_FOUND)
+    find_package(BLAS)
+  endif()
   if(NOT BLAS_FOUND)
     # Nothing specified by the user and FindBLAS didn't find anything; let's try
     # if cblas is available on the system paths.

ThirdParty/SuiteSparse/.gitignore

@@ -127,6 +127,7 @@ CSparse/Tcov/cov.sort
 CSparse/Tcov/cover.out
 CSparse/Tcov/covs.out
 CSparse/Tcov/cs_*.c
+CSparse/Tcov/csparse_version.c
 CSparse/Tcov/cstcov_test
 CSparse/Tcov/*.out
 CSparse/Tcov/cs_demo1
@@ -138,6 +139,7 @@ CXSparse/Tcov/cov.sort
 CXSparse/Tcov/cover.out
 CXSparse/Tcov/covs.out
 CXSparse/Tcov/cs_*.c
+CXSparse/Tcov/cxsparse_version.c
 CXSparse/Tcov/*.out
 CXSparse/Tcov/cs_demo1_ci
 CXSparse/Tcov/cs_demo1_cl
@@ -168,7 +170,9 @@ SPQR/Tcov/gpu_results.txt
 SPQR/Tcov/gpuqrengine_demo
 SPQR/Tcov/qrdemo_gpu
 SPQR/Tcov/qrtest
+SPQR/Tcov/qrtest32
 SPQR/Tcov/qrtest_out.txt
+SPQR/Tcov/qrtest_out32.txt
 SPQR/Tcov/troll.m
 SPQR/Tcov/cov.out