Release 0.11.27

Merge pull request #1759 from AMICI-dev/release_0.11.27
AMICI-dev · Apr 7, 2022 · 82abf37 · 82abf37
2 parents f02dde9 + d8f8ad6
commit 82abf37
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diff --git a/.github/workflows/test_performance.yml b/.github/workflows/test_performance.yml
@@ -4,7 +4,7 @@ on:
     branches:
       - develop
       - master
-      - compile_without_optimization
+      - sparsify_jacobian
 
   pull_request:
     branches:
@@ -63,7 +63,7 @@ jobs:
     # import test model
     - name: Import test model
       run: |
-        check_time.sh petab_import python tests/performance/test.py import
+        AMICI_IMPORT_NPROCS=2 check_time.sh petab_import python tests/performance/test.py import
 
     - name: "Upload artifact: CS_Signalling_ERBB_RAS_AKT_petab"
       uses: actions/upload-artifact@v1

diff --git a/.github/workflows/test_petab_test_suite.yml b/.github/workflows/test_petab_test_suite.yml
@@ -81,7 +81,7 @@ jobs:
             --cov-report=xml --cov-append --cov=amici tests/petab_test_suite/
 
       - name: Codecov
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v2
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml

diff --git a/.github/workflows/test_pypi.yml b/.github/workflows/test_pypi.yml
@@ -31,11 +31,8 @@ jobs:
       - name: homebrew
         run: |
           if [[ ${{ matrix.os }} == macos* ]] ; then \
-            brew install hdf5@1.10 swig gcc libomp \
-               && echo "/usr/local/opt/hdf5@1.10/bin" >> $GITHUB_PATH \
-               && echo LDFLAGS="-L/usr/local/lib/ -L/usr/local/opt/hdf5@1.10/lib" >> $GITHUB_ENV \
-               && echo CPPFLAGS="-I/usr/local/opt/hdf5@1.10/include" >> $GITHUB_ENV \
-               && echo HDF5_BASE="/usr/local/opt/hdf5@1.10/" >> $GITHUB_ENV
+            brew install hdf5 swig gcc libomp \
+               && echo LDFLAGS="-L/usr/local/lib/" >> $GITHUB_ENV
           fi
 
       - name: Set up Python ${{ matrix.python-version }}

diff --git a/.github/workflows/test_python_cplusplus.yml b/.github/workflows/test_python_cplusplus.yml
@@ -104,7 +104,7 @@ jobs:
         scripts/runNotebook.sh documentation/GettingStarted.ipynb
 
     - name: Codecov Python
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v2
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./build/coverage_py.xml
@@ -122,7 +122,7 @@ jobs:
         && lcov -a coverage_cpp.info -a coverage_py.info -o coverage.info
 
     - name: Codecov CPP
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v2
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.info
@@ -152,13 +152,11 @@ jobs:
     # install amici dependencies
     - name: homebrew
       run: |
-        brew install hdf5@1.10 swig gcc cppcheck libomp boost \
+        brew install hdf5 swig gcc cppcheck libomp boost \
           && brew ls -v boost \
           && brew ls -v libomp \
-          && echo "/usr/local/opt/hdf5@1.10/bin" >> $GITHUB_PATH \
-          && echo LDFLAGS="-L/usr/local/lib/ -L/usr/local/opt/hdf5@1.10/lib -L/usr/local/Cellar/boost/1.78.0_1/lib/" >> $GITHUB_ENV \
-          && echo CPPFLAGS="-I/usr/local/opt/hdf5@1.10/include -I/usr/local/Cellar/boost/1.78.0_1/include/" >> $GITHUB_ENV \
-          && echo HDF5_BASE="/usr/local/opt/hdf5@1.10/" >> $GITHUB_ENV
+          && echo LDFLAGS="-L/usr/local/lib/ -L/usr/local/Cellar/boost/1.78.0_1/lib/" >> $GITHUB_ENV \
+          && echo CPPFLAGS="-I/usr/local/Cellar/boost/1.78.0_1/include/" >> $GITHUB_ENV
 
     - name: Build AMICI
       run: |

diff --git a/.github/workflows/test_sbml_semantic_test_suite.yml b/.github/workflows/test_sbml_semantic_test_suite.yml
@@ -52,7 +52,7 @@ jobs:
         path: tests/amici-semantic-results
 
     - name: Codecov SBMLSuite
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v2
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage_SBMLSuite.xml

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,63 @@
 
 ## v0.X Series
 
+### v0.11.27 (2022-04-04)
+
+New features:
+* Checking condition number when computing sensitivities via Newton
+  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1730
+* Removed SPBCG solver by @FFroehlich in
+  https://github.com/AMICI-dev/AMICI/pull/1729
+* Added Newton step convergence checks to steadystate solver by @FFroehlich in
+  https://github.com/AMICI-dev/AMICI/pull/1737
+* Removed legacy options/members `amioption.newton_preeq` and `Solver::r… by
+  @dweindl in https://github.com/AMICI-dev/AMICI/pull/1744
+* Added `ReturnData::cpu_time_total` to track total time spent in
+  `runAmiciSimulation` by @dweindl in
+  https://github.com/AMICI-dev/AMICI/pull/1743
+* SBML import: Alternative algorithm for identifying conservation laws by
+  @dweindl in https://github.com/AMICI-dev/AMICI/pull/1748
+* Use `amici.AmiciVersionError` to indicate version mismatch by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1764
+
+Performance:
+* Optional parallel computation of derivatives during model import by @dweindl
+  in https://github.com/AMICI-dev/AMICI/pull/1740
+* Sparsify jacobian by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1766
+* Speedup for models with conservation laws by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1765
+* Speedup conservation law computation by @FFroehlich in
+  https://github.com/AMICI-dev/AMICI/pull/1754
+* Exploit stoichiometric matrix in pysb import by @FFroehlich in
+  https://github.com/AMICI-dev/AMICI/pull/1761
+* Speedup edata construction from petab problems by @FFroehlich in
+  https://github.com/AMICI-dev/AMICI/pull/1746
+
+Fixes:
+* Fixed `get_model_settings` that would to setting incorrect initial states and
+  initial state sensitivities for models with parameter-dependent initial
+  states by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1751
+* Use correct tolerances for convergence check in Newton solver by @FFroehlich
+  in https://github.com/AMICI-dev/AMICI/pull/1728
+* Harmonized convergence checks by @FFroehlich in
+  https://github.com/AMICI-dev/AMICI/pull/1731
+* Made sundials' KLU_INDEXTYPE match actual klu index type by @dweindl in
+  https://github.com/AMICI-dev/AMICI/pull/1733
+* Fixed `Model::setStateIsNonNegative` logic that would raise exceptions in
+  cases where it shouldn't by @dweindl in
+  https://github.com/AMICI-dev/AMICI/pull/1736
+* Fixed undefined reference to dladdr by @kristianmeyerr in
+  https://github.com/AMICI-dev/AMICI/pull/1738
+* Fixed HDF5 OSX intermediate group creation errors by @dweindl in
+  https://github.com/AMICI-dev/AMICI/pull/1741
+* Fixed recent cmake-based build issues due to changed sundials library
+  directory by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1756
+* Updated Windows installation instructions by @paulflang in
+  https://github.com/AMICI-dev/AMICI/pull/1763
+
+... and other contributions by @FFroehlich, @dweindl
+
+**Full Changelog**:
+https://github.com/AMICI-dev/AMICI/compare/v0.11.26...v0.11.27
+
 ### v0.11.26 (2022-03-14)
 
 New features:

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -54,34 +54,7 @@ set(SUITESPARSE_LIBRARIES
     ${SUITESPARSE_DIR}/SuiteSparse_config/libsuitesparseconfig${CMAKE_STATIC_LIBRARY_SUFFIX}
     )
 
-set(SUNDIALS_LIB_DIR "${CMAKE_SOURCE_DIR}/ThirdParty/sundials/build/${CMAKE_INSTALL_LIBDIR}")
-set(SUNDIALS_LIBRARIES
-    ${SUNDIALS_LIB_DIR}/libsundials_nvecserial${CMAKE_STATIC_LIBRARY_SUFFIX}
-    ${SUNDIALS_LIB_DIR}/libsundials_sunlinsolband${CMAKE_STATIC_LIBRARY_SUFFIX}
-    ${SUNDIALS_LIB_DIR}/libsundials_sunlinsolklu${CMAKE_STATIC_LIBRARY_SUFFIX}
-    ${SUNDIALS_LIB_DIR}/libsundials_sunlinsolpcg${CMAKE_STATIC_LIBRARY_SUFFIX}
-    ${SUNDIALS_LIB_DIR}/libsundials_sunlinsolspbcgs${CMAKE_STATIC_LIBRARY_SUFFIX}
-    ${SUNDIALS_LIB_DIR}/libsundials_sunlinsolspfgmr${CMAKE_STATIC_LIBRARY_SUFFIX}
-    ${SUNDIALS_LIB_DIR}/libsundials_sunmatrixband${CMAKE_STATIC_LIBRARY_SUFFIX}
-    ${SUNDIALS_LIB_DIR}/libsundials_sunmatrixdense${CMAKE_STATIC_LIBRARY_SUFFIX}
-    ${SUNDIALS_LIB_DIR}/libsundials_sunmatrixsparse${CMAKE_STATIC_LIBRARY_SUFFIX}
-    ${SUNDIALS_LIB_DIR}/libsundials_sunnonlinsolfixedpoint${CMAKE_STATIC_LIBRARY_SUFFIX}
-    ${SUNDIALS_LIB_DIR}/libsundials_sunnonlinsolnewton${CMAKE_STATIC_LIBRARY_SUFFIX}
-    ${SUNDIALS_LIB_DIR}/libsundials_cvodes${CMAKE_STATIC_LIBRARY_SUFFIX}
-    ${SUNDIALS_LIB_DIR}/libsundials_idas${CMAKE_STATIC_LIBRARY_SUFFIX}
-    )
-set(SUNDIALS_INCLUDE_DIRS "${CMAKE_SOURCE_DIR}/ThirdParty/sundials/build/include")
-
-option(SUNDIALS_SUPERLUMT_ENABLE "Enable sundials SuperLUMT?" OFF)
-if(SUNDIALS_SUPERLUMT_ENABLE)
-    set(SUNDIALS_LIBRARIES ${SUNDIALS_LIBRARIES}
-        ${SUNDIALS_LIB_DIR}/libsundials_sunlinsolsuperlumt${CMAKE_STATIC_LIBRARY_SUFFIX}
-        ${CMAKE_SOURCE_DIR}/ThirdParty/SuperLU_MT_3.1/lib/libsuperlu_mt_PTHREAD${CMAKE_STATIC_LIBRARY_SUFFIX}
-        -lblas
-        )
-    set(SUNDIALS_INCLUDE_DIRS ${SUNDIALS_INCLUDE_DIRS}
-        "${CMAKE_SOURCE_DIR}/ThirdParty/SuperLU_MT_3.1/SRC/")
-endif()
+find_package(SUNDIALS REQUIRED PATHS "${CMAKE_SOURCE_DIR}/ThirdParty/sundials/build/lib/cmake/sundials/")
 
 set(GSL_LITE_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/ThirdParty/gsl")
 
@@ -187,7 +160,6 @@ target_include_directories(${PROJECT_NAME}
     PUBLIC $<BUILD_INTERFACE:${CMAKE_BINARY_DIR}/include>
     PUBLIC swig
     PUBLIC ${GSL_LITE_INCLUDE_DIR}
-    PUBLIC ${SUNDIALS_INCLUDE_DIRS}
     PUBLIC ${SUITESPARSE_INCLUDE_DIRS}
     PUBLIC ${HDF5_INCLUDE_DIRS}
     )
@@ -197,12 +169,40 @@ if(NOT "${BLAS_INCLUDE_DIRS}" STREQUAL "")
 endif()
 
 target_link_libraries(${PROJECT_NAME}
-    PUBLIC ${SUNDIALS_LIBRARIES}
+    PUBLIC SUNDIALS::generic_static
+    PUBLIC SUNDIALS::nvecserial_static
+    PUBLIC SUNDIALS::sunmatrixband_static
+    PUBLIC SUNDIALS::sunmatrixdense_static
+    PUBLIC SUNDIALS::sunmatrixsparse_static
+    PUBLIC SUNDIALS::sunlinsolband_static
+    PUBLIC SUNDIALS::sunlinsoldense_static
+    PUBLIC SUNDIALS::sunlinsolpcg_static
+    PUBLIC SUNDIALS::sunlinsolspbcgs_static
+    PUBLIC SUNDIALS::sunlinsolspfgmr_static
+    PUBLIC SUNDIALS::sunlinsolspgmr_static
+    PUBLIC SUNDIALS::sunlinsolsptfqmr_static
+    PUBLIC SUNDIALS::sunlinsolklu_static
+    PUBLIC SUNDIALS::sunnonlinsolnewton_static
+    PUBLIC SUNDIALS::sunnonlinsolfixedpoint_static
+    PUBLIC SUNDIALS::cvodes_static
+    PUBLIC SUNDIALS::idas_static
     PUBLIC ${SUITESPARSE_LIBRARIES}
     PUBLIC ${HDF5_LIBRARIES}
     PUBLIC ${BLAS_LIBRARIES}
+    PUBLIC ${CMAKE_DL_LIBS}
     )
 
+option(SUNDIALS_SUPERLUMT_ENABLE "Enable sundials SuperLUMT?" OFF)
+if(SUNDIALS_SUPERLUMT_ENABLE)
+    set(SUNDIALS_LIBRARIES ${SUNDIALS_LIBRARIES}
+        ${SUNDIALS_LIB_DIR}/libsundials_sunlinsolsuperlumt${CMAKE_STATIC_LIBRARY_SUFFIX}
+        ${CMAKE_SOURCE_DIR}/ThirdParty/SuperLU_MT_3.1/lib/libsuperlu_mt_PTHREAD${CMAKE_STATIC_LIBRARY_SUFFIX}
+        -lblas
+        )
+    target_include_directories(${PROJECT_NAME}
+        PUBLIC "${CMAKE_SOURCE_DIR}/ThirdParty/SuperLU_MT_3.1/SRC/")
+endif()
+
 # Create targets to make the sources show up in IDEs for convenience
 
 # For matlab interface

diff --git a/ThirdParty/SuiteSparse/AMD/Include/amd_internal.h b/ThirdParty/SuiteSparse/AMD/Include/amd_internal.h
@@ -159,6 +159,8 @@
 #define ID  SuiteSparse_long_id
 #define Int_MAX SuiteSparse_long_max
 
+#define UnsignedInt SuiteSparse_unsigned_long
+
 #define AMD_order amd_l_order
 #define AMD_defaults amd_l_defaults
 #define AMD_control amd_l_control
@@ -180,6 +182,8 @@
 #define ID "%d"
 #define Int_MAX INT_MAX
 
+#define UnsignedInt unsigned int
+
 #define AMD_order amd_order
 #define AMD_defaults amd_defaults
 #define AMD_control amd_control

diff --git a/ThirdParty/SuiteSparse/AMD/Source/amd_2.c b/ThirdParty/SuiteSparse/AMD/Source/amd_2.c
@@ -462,7 +462,7 @@ GLOBAL void AMD_2
 	nvi, nvj, nvpiv, slenme, wbig, we, wflg, wnvi, ok, ndense, ncmpa,
 	dense, aggressive ;
 
-    unsigned Int hash ;	    /* unsigned, so that hash % n is well defined.*/
+    UnsignedInt hash ;	    /* unsigned, so that hash % n is well defined.*/
 
 /*
  * deg:		the degree of a variable or element

diff --git a/ThirdParty/SuiteSparse/CAMD/Include/camd_internal.h b/ThirdParty/SuiteSparse/CAMD/Include/camd_internal.h
@@ -160,6 +160,8 @@
 #define ID  SuiteSparse_long_id
 #define Int_MAX SuiteSparse_long_max
 
+#define UnsignedInt SuiteSparse_unsigned_long
+
 #define CAMD_order camd_l_order
 #define CAMD_defaults camd_l_defaults
 #define CAMD_control camd_l_control
@@ -182,6 +184,8 @@
 #define ID "%d"
 #define Int_MAX INT_MAX
 
+#define UnsignedInt unsigned int
+
 #define CAMD_order camd_order
 #define CAMD_defaults camd_defaults
 #define CAMD_control camd_control

diff --git a/ThirdParty/SuiteSparse/CAMD/Source/camd_2.c b/ThirdParty/SuiteSparse/CAMD/Source/camd_2.c
@@ -504,7 +504,7 @@ GLOBAL void CAMD_2
 	nvi, nvj, nvpiv, slenme, wbig, we, wflg, wnvi, ok, ndense, ncmpa, nnull,
 	dense, aggressive ;
 
-    unsigned Int hash ;	    /* unsigned, so that hash % n is well defined.*/
+    UnsignedInt hash ;	    /* unsigned, so that hash % n is well defined.*/
 
 /*
  * deg:		the degree of a variable or element

diff --git a/ThirdParty/SuiteSparse/COLAMD/Source/colamd.c b/ThirdParty/SuiteSparse/COLAMD/Source/colamd.c
@@ -663,6 +663,8 @@
 #define ID  SuiteSparse_long_id
 #define Int_MAX SuiteSparse_long_max
 
+#define UnsignedInt SuiteSparse_unsigned_long
+
 #define COLAMD_recommended colamd_l_recommended
 #define COLAMD_set_defaults colamd_l_set_defaults
 #define COLAMD_MAIN colamd_l
@@ -676,6 +678,8 @@
 #define ID "%d"
 #define Int_MAX INT_MAX
 
+#define UnsignedInt unsigned int
+
 #define COLAMD_recommended colamd_recommended
 #define COLAMD_set_defaults colamd_set_defaults
 #define COLAMD_MAIN colamd
@@ -2193,7 +2197,7 @@ PRIVATE Int find_ordering	/* return the number of garbage collections */
     Int col ;			/* a column index */
     Int max_score ;		/* maximum possible score */
     Int cur_score ;		/* score of current column */
-    unsigned Int hash ;		/* hash value for supernode detection */
+    UnsignedInt hash ;		/* hash value for supernode detection */
     Int head_column ;		/* head of hash bucket */
     Int first_col ;		/* first column in hash bucket */
     Int tag_mark ;		/* marker value for mark array */

diff --git a/ThirdParty/SuiteSparse/SuiteSparse_config/SuiteSparse_config.h b/ThirdParty/SuiteSparse/SuiteSparse_config/SuiteSparse_config.h
@@ -44,6 +44,7 @@ extern "C" {
 
 #include <limits.h>
 #include <stdlib.h>
+#include <inttypes.h>
 
 /* ========================================================================== */
 /* === SuiteSparse_long ===================================================== */
@@ -59,12 +60,13 @@ extern "C" {
 
 #else
 
-#define SuiteSparse_long long
-#define SuiteSparse_long_max LONG_MAX
-#define SuiteSparse_long_idd "ld"
+#define SuiteSparse_long int64_t
+#define SuiteSparse_long_max INT64_MAX
+#define SuiteSparse_long_idd PRId64
 
 #endif
 #define SuiteSparse_long_id "%" SuiteSparse_long_idd
+#define SuiteSparse_unsigned_long uint64_t
 #endif
 
 /* ========================================================================== */

diff --git a/ThirdParty/SuiteSparse/include/SuiteSparse_config.h b/ThirdParty/SuiteSparse/include/SuiteSparse_config.h
@@ -44,6 +44,7 @@ extern "C" {
 
 #include <limits.h>
 #include <stdlib.h>
+#include <inttypes.h>
 
 /* ========================================================================== */
 /* === SuiteSparse_long ===================================================== */
@@ -59,12 +60,13 @@ extern "C" {
 
 #else
 
-#define SuiteSparse_long long
-#define SuiteSparse_long_max LONG_MAX
-#define SuiteSparse_long_idd "ld"
+#define SuiteSparse_long int64_t
+#define SuiteSparse_long_max INT64_MAX
+#define SuiteSparse_long_idd PRId64
 
 #endif
 #define SuiteSparse_long_id "%" SuiteSparse_long_idd
+#define SuiteSparse_unsigned_long uint64_t
 #endif
 
 /* ========================================================================== */