Merge branch 'fix_install_mac' into extend_dataframes

.github/workflows/test_petab_test_suite.yml

@@ -57,27 +57,27 @@ jobs:
 
       - name: Install petab
         run: |
-          source ./build/venv/bin/activate \
+          source ./venv/bin/activate \
             && pip3 install wheel pytest shyaml pytest-cov pysb
 
       # retrieve test models
       - name: Download and install PEtab test suite
         run: |
           git clone --depth 1 --branch main \
             https://github.com/PEtab-dev/petab_test_suite \
-            && source ./build/venv/bin/activate \
+            && source ./venv/bin/activate \
             && cd petab_test_suite && pip3 install -e .
 
       - name: Run PEtab-related unit tests
         run: |
-          source ./build/venv/bin/activate \
+          source ./venv/bin/activate \
             && pytest --cov-report=xml:coverage.xml \
               --cov=./ python/tests/test_*petab*.py python/tests/petab/
 
       # run test models
       - name: Run PEtab test suite
         run: |
-          source ./build/venv/bin/activate \
+          source ./venv/bin/activate \
           && AMICI_PARALLEL_COMPILE="" pytest -v \
             --cov-report=xml:coverage.xml \
             --cov-append \

.github/workflows/test_python_cplusplus.yml

@@ -45,11 +45,11 @@ jobs:
       run: scripts/installAmiciSource.sh
 
     - name: Check OpenMP support
-      run: source build/venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiledWithOpenMP())"
+      run: source venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiledWithOpenMP())"
 
     - name: Python tests (part 1)
       run: |
-        source build/venv/bin/activate \
+        source venv/bin/activate \
         && pytest \
           --ignore-glob=*petab* \
           --ignore-glob=*test_splines.py \
@@ -64,7 +64,7 @@ jobs:
     - name: Python tests splines
       if: ${{ github.base_ref == 'master' || github.event.merge_group.base_ref == 'master'}}
       run: |
-        source build/venv/bin/activate \
+        source venv/bin/activate \
         && pytest \
           --cov=amici \
           --cov-report=xml:"${AMICI_DIR}/build/coverage_py.xml" \
@@ -138,7 +138,7 @@ jobs:
 
     - name: Python tests
       run: |
-        source build/venv/bin/activate \
+        source venv/bin/activate \
         && pytest \
           --cov=amici \
           --cov-report=xml:"${AMICI_DIR}/build/coverage_py.xml" \
@@ -214,7 +214,7 @@ jobs:
 
     - name: Install notebook dependencies
       run: |
-        source build/venv/bin/activate \
+        source venv/bin/activate \
         && pip install jax[cpu]
 
     - name: example notebooks
@@ -251,7 +251,7 @@ jobs:
       run: scripts/installAmiciSource.sh
 
     - name: Check OpenMP support
-      run: source build/venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiledWithOpenMP())"
+      run: source venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiledWithOpenMP())"
 
     - name: cppcheck
       run: scripts/run-cppcheck.sh
@@ -296,7 +296,7 @@ jobs:
         scripts/installAmiciSource.sh
 
     - name: Check OpenMP support
-      run: source build/venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiledWithOpenMP())"
+      run: source venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiledWithOpenMP())"
 
     - name: Get BioNetGen
       run: scripts/buildBNGL.sh

.github/workflows/test_python_ver_matrix.yml

@@ -51,15 +51,15 @@ jobs:
       run: scripts/installAmiciSource.sh
 
     # 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
+    - run: source venv/bin/activate && pip3 install git+https://github.com/pysb/pysb
 
     # until sympy>1.12 is released
-    - run: source build/venv/bin/activate && pip3 install git+https://github.com/sympy/sympy.git@master
+    - run: source venv/bin/activate && pip3 install git+https://github.com/sympy/sympy.git@master
       if: matrix.python-version == '3.12'
 
     - name: Python tests
       run: |
-        source build/venv/bin/activate \
+        source venv/bin/activate \
           && python3 -m pytest \
             --durations=10 \
             --ignore-glob=*petab* \

.gitignore

@@ -202,3 +202,4 @@ CS_Signalling_ERBB_RAS_AKT/
 cache_fiddy/*
 debug/*
 tests/benchmark-models/cache_fiddy/*
+venv/*

CMakeLists.txt

@@ -354,12 +354,12 @@ target_link_libraries(
          SUNDIALS::sunnonlinsolfixedpoint_static
          SUNDIALS::cvodes_static
          SUNDIALS::idas_static
-         ${BLAS_LIBRARIES}
          $<$<BOOL:${Boost_CHRONO_FOUND}>:Boost::chrono>
          $<$<BOOL:${OpenMP_FOUND}>:OpenMP::OpenMP_CXX>
          ${CMAKE_DL_LIBS}
   PRIVATE
     $<$<BOOL:${SUNDIALS_SUPERLUMT_ENABLE}>:SUNDIALS::sundials_sunlinsolsuperlumt>
+    BLAS::BLAS
 )
 
 if(HDF5_FOUND)

cmake/AmiciConfig.cmake

@@ -62,6 +62,8 @@ if(@HDF5_FOUND@)
     REQUIRED)
 endif()
 
+find_package(BLAS)
+
 include("${CMAKE_CURRENT_LIST_DIR}/AmiciTargets.cmake")
 
 check_required_components(Amici)

include/amici/defines.h

@@ -68,6 +68,7 @@ constexpr int AMICI_TOO_MUCH_WORK=            -1;
 constexpr int AMICI_TOO_MUCH_ACC=             -2;
 constexpr int AMICI_ERR_FAILURE=              -3;
 constexpr int AMICI_CONV_FAILURE=             -4;
+constexpr int AMICI_LSETUP_FAIL=              -6;
 constexpr int AMICI_RHSFUNC_FAIL=             -8;
 constexpr int AMICI_FIRST_RHSFUNC_ERR=        -9;
 constexpr int AMICI_ILL_INPUT=               -22;

include/amici/model.h

@@ -1334,10 +1334,12 @@ class Model : public AbstractModel, public ModelDimensions {
      *
      * @param array
      * @param model_quantity The model quantity `array` corresponds to
+     * @param t Current timepoint
      * @return
      */
     int checkFinite(
-        gsl::span<realtype const> array, ModelQuantity model_quantity
+        gsl::span<realtype const> array, ModelQuantity model_quantity,
+        realtype t
     ) const;
     /**
      * @brief Check if the given array has only finite elements.
@@ -1347,11 +1349,12 @@ class Model : public AbstractModel, public ModelDimensions {
      * @param array Flattened matrix
      * @param model_quantity The model quantity `array` corresponds to
      * @param num_cols Number of columns of the non-flattened matrix
+     * @param t Current timepoint
      * @return
      */
     int checkFinite(
         gsl::span<realtype const> array, ModelQuantity model_quantity,
-        size_t num_cols
+        size_t num_cols, realtype t
     ) const;
 
     /**

python/sdist/amici/MANIFEST.template.in

@@ -1 +1,3 @@
 include *.cpp *.h
+include CMakeLists.txt
+recursive-include swig/ *

python/sdist/amici/cxxcodeprinter.py

@@ -339,7 +339,7 @@ def csc_matrix(
     for col in range(ncols):
         symbol_col_ptrs.append(idx)
         for row in range(nrows):
-            if matrix[row, col] == 0:
+            if matrix[row, col].is_zero:
                 continue
 
             symbol_row_vals.append(row)

python/sdist/amici/de_model.py

@@ -2115,7 +2115,7 @@ def state_is_constant(self, ix: int) -> bool:
         if isinstance(state, AlgebraicState):
             return False
 
-        return state.get_dt() == 0.0
+        return state.get_dt().is_zero
 
     def conservation_law_has_multispecies(self, tcl: ConservationLaw) -> bool:
         """
@@ -2179,7 +2179,7 @@ def _get_unique_root(
             return None
 
         for root in roots:
-            if sp.simplify(root_found - root.get_val()) == 0:
+            if sp.simplify(root_found - root.get_val()).is_zero:
                 return root.get_id()
 
         # create an event for a new root function

scripts/buildAmici.sh

@@ -25,7 +25,10 @@ else
 fi
 
 # required for build swig interface
-pip show numpy > /dev/null || python3 -m pip install numpy
+python3 -m venv "${amici_path}/venv"
+source "${amici_path}/venv/bin/activate"
+export PYTHON_EXECUTABLE="${amici_path}/venv/bin/python"
+pip3 show numpy > /dev/null || python3 -m pip install numpy
 
 ${cmake} \
   -Wdev -DAMICI_CXX_OPTIONS="-Wall;-Wextra${extra_cxx_flags}" \

scripts/installAmiciArchive.sh

@@ -18,18 +18,18 @@ rm -f ${AMICI_PATH}/python/sdist/amici/amici_without_hdf5.py
 
 # test install from archive
 set +e
-python3 -m venv ${AMICI_PATH}/build/venvArchive --clear
+python3 -m venv ${AMICI_PATH}/venvArchive --clear
 # in case this fails (usually due to missing ensurepip, try getting pip
 # manually
 if [[ $? ]]; then
     set -e
-    python3 -m venv ${AMICI_PATH}/build/venvArchive --clear --without-pip
-    source ${AMICI_PATH}/build/venvArchive/bin/activate
+    python3 -m venv ${AMICI_PATH}/venvArchive --clear --without-pip
+    source ${AMICI_PATH}/venvArchive/bin/activate
     curl https://bootstrap.pypa.io/get-pip.py -o ${AMICI_PATH}/build/get-pip.py
-    python ${AMICI_PATH}/build/get-pip.py
+    python ${AMICI_PATH}/get-pip.py
 else
     set -e
-    source ${AMICI_PATH}/build/venvArchive/bin/activate
+    source ${AMICI_PATH}/venvArchive/bin/activate
 fi
 
 pip install $(ls -t ${AMICI_PATH}/build/python/amici-*.tar.gz | head -1)

scripts/installAmiciSource.sh

@@ -5,7 +5,7 @@ set -e
 SCRIPT_PATH=$(dirname $BASH_SOURCE)
 AMICI_PATH=$(cd "$SCRIPT_PATH/.." && pwd)
 
-venv_dir="${AMICI_PATH}/build/venv"
+venv_dir="${AMICI_PATH}/venv"
 # Disabled until cmake package is made compatible with updated setup.py
 #make python-wheel
 #pip3 install --user --prefix= `ls -t ${AMICI_PATH}/build/python/amici-*.whl | head -1`

scripts/run-SBMLTestsuite.sh

@@ -9,7 +9,7 @@ if [[ ! -d "tests/sbml-test-suite" ]]; then
     mv -f ./sbml-test-suite ./tests/sbml-test-suite
 fi
 
-source build/venv/bin/activate
+source venv/bin/activate
 pip show pytest-xdist > /dev/null 2>&1 || pip install pytest-xdist
 pip install coverage pytest-cov
 

scripts/run-codecov.sh

@@ -4,7 +4,7 @@
 script_path=$(dirname $BASH_SOURCE)
 amici_path=$(cd "$script_path"/.. && pwd)
 
-source "${amici_path}"/build/venv/bin/activate
+source "${amici_path}"/venv/bin/activate
 pip install coverage pytest pytest-cov
 
 if [[ -z "${BNGPATH}" ]]; then

scripts/run-python-tests.sh

@@ -12,7 +12,7 @@ if [[ -z "${BNGPATH}" ]]; then
 fi
 
 cd "${amici_path}"/python/tests
-source "${amici_path}"/build/venv/bin/activate
+source "${amici_path}"/venv/bin/activate
 
 # PEtab tests are run separately
 pytest \

scripts/run-valgrind-py.sh

@@ -15,7 +15,7 @@ if [ $# -eq 0 ]
   then
     # No arguments supplied, run all tests
     cd "${amici_path}"/python/tests
-    source "${amici_path}"/build/venv/bin/activate
+    source "${amici_path}"/venv/bin/activate
     command=(python -m pytest -vv --ignore-glob=*petab* -W 'ignore:Signature ')
     #                                                    ^ ignores the following warning that occurs only under valgrind,
     # e.g. `valgrind python -c "import h5py"`:

src/amici.cpp

@@ -69,6 +69,7 @@ std::map<int, std::string> simulation_status_to_str_map = {
     {AMICI_MAX_TIME_EXCEEDED, "AMICI_MAX_TIME_EXCEEDED"},
     {AMICI_SUCCESS, "AMICI_SUCCESS"},
     {AMICI_NOT_RUN, "AMICI_NOT_RUN"},
+    {AMICI_LSETUP_FAIL, "AMICI_LSETUP_FAIL"},
 };
 
 std::unique_ptr<ReturnData> runAmiciSimulation(
@@ -222,8 +223,8 @@ std::unique_ptr<ReturnData> runAmiciSimulation(
 
     try {
         rdata->processSimulationObjects(
-            preeq.get(), fwd.get(), bwd_success ? bwd.get() : nullptr, posteq.get(),
-            model, solver, edata
+            preeq.get(), fwd.get(), bwd_success ? bwd.get() : nullptr,
+            posteq.get(), model, solver, edata
         );
     } catch (std::exception const& ex) {
         rdata->status = AMICI_ERROR;