Merge pull request #2019 from AMICI-dev/release_0.16.1

Release 0.16.1

Author: dweindl

.github/CODEOWNERS

@@ -0,0 +1,5 @@
+# see https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-code-owners
+
+# default owners
+* @AMICI-dev/amici-maintainers
+

.github/workflows/deploy_protected.yml

@@ -7,7 +7,7 @@ on:
       - release**
   pull_request:
     paths:
-      - docker/Dockerfile
+      - container/Dockerfile
   workflow_dispatch:
 
 jobs:
@@ -27,7 +27,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - uses: actions/checkout@v3
-    - run: git archive -o docker/amici.tar.gz --format=tar.gz HEAD
+    - run: git archive -o container/amici.tar.gz --format=tar.gz HEAD
     - name: Set up QEMU
       uses: docker/setup-qemu-action@v2
     - name: Set up Docker Buildx
@@ -38,7 +38,7 @@ jobs:
         name: dweindl/amici
         username: ${{ secrets.DOCKER_USERNAME }}
         password: ${{ secrets.DOCKER_PASSWORD }}
-        workdir: docker/
+        workdir: container/
         dockerfile: Dockerfile
         tag_names: true
         platforms: linux/amd64,linux/arm64

.github/workflows/test_python_cplusplus.yml

@@ -162,8 +162,8 @@ jobs:
         brew install hdf5 swig gcc cppcheck libomp boost \
           && brew ls -v boost \
           && brew ls -v libomp \
-          && echo LDFLAGS="-L/usr/local/lib/ -L/usr/local/Cellar/boost/1.80.0/lib/" >> $GITHUB_ENV \
-          && echo CPPFLAGS="-I/usr/local/Cellar/boost/1.80.0/include/" >> $GITHUB_ENV
+          && echo LDFLAGS="-L/usr/local/lib/ -L/usr/local/Cellar/boost/1.81.0_1/lib/" >> $GITHUB_ENV \
+          && echo CPPFLAGS="-I /usr/local/Cellar/boost/1.81.0_1/include/" >> $GITHUB_ENV
 
     - name: Build AMICI
       run: |

.github/workflows/test_windows.yml

@@ -15,7 +15,11 @@ jobs:
     env:
       AMICI_SKIP_CMAKE_TESTS: "TRUE"
       openBLAS_version: "0.3.19"
-      AMICI_DLL_DIRS: "C:\\BLAS\\bin"
+      AMICI_DLL_DIRS: "C:\\BLAS\\OpenBLAS\\bin"
+      LIB: "C:/BLAS/OpenBLAS/lib"
+      CFLAGS: "-nologo"
+      CXXFLAGS: "-nologo"
+      LDFLAGS: "-nologo"
 
     strategy:
       matrix:
@@ -33,11 +37,11 @@ jobs:
     - shell: bash
       run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
     - shell: bash
-      run: echo "C:\\BLAS\\bin" >> $GITHUB_PATH
+      run: echo "C:\\BLAS\\OpenBLAS\\bin" >> $GITHUB_PATH
     - shell: bash
-      run: echo "BLAS_LIBS=/LIBPATH:C:/BLAS/lib openblas.lib" >> $GITHUB_ENV
+      run: echo "BLAS_LIBS=-LIBPATH:C:/BLAS/OpenBLAS/lib openblas.lib" >> $GITHUB_ENV
     - shell: bash
-      run: echo "BLAS_CFLAGS=-IC:/BLAS/OpenBLAS-${openBLAS_version}/OpenBLAS-${openBLAS_version}" >> $GITHUB_ENV
+      run: echo "BLAS_CFLAGS=-IC:/BLAS/OpenBLAS/include/openblas/" >> $GITHUB_ENV
 
     # Developer Command Prompt for Microsoft Visual C++
     - uses: ilammy/msvc-dev-cmd@v1
@@ -53,6 +57,11 @@ jobs:
       shell: powershell
       run: scripts/installOpenBLAS
 
+    - uses: actions/upload-artifact@v3
+      with:
+        name: OpenBLAS
+        path: C:\BLAS\OpenBLAS
+
     - name: Create sdist
       working-directory: python/sdist
       run: pip install build && python -m build --sdist

CHANGELOG.md

@@ -2,6 +2,86 @@
 
 ## v0.X Series
 
+### v0.16.1 (2023-02-24)
+
+Fixes:
+* Additional package names for finding blas via pkg-config
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1959
+* Changed default interpolation type from hermite to polynomial
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1960
+* PySB import: Change default simplify to work with multiprocessing
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1961
+* Add --no-validate to amici_import_petab
+  @dweindl in https://github.com/AMICI-dev/AMICI/pull/1963
+* Fix get_model for direct import of swig interface
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1969
+* Fix PytestReturnNotNoneWarning in test_conserved_quantities_demartino.py
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1968
+* Fix MSVC builds / remove -W* flags
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1972
+* Add option to use IDs when plotting trajectories
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1974
+* Fix assignmentRules2observables - skip non-assignment-rule targets
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1973
+* Use std::clock for measuring solver time
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1982
+  (*Note that this uses cpu-time consumed by all threads*)
+* Fix narrowing-conversion-warning
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1983
+* PEtab import: allow specifying default values for output parameters
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1987
+* Print stacktraces only with debug logging level
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1985
+* Change default ReturnData::status to AMICI_NOT_RUN
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1984
+* Reduce time-tracking overhead
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1988
+* Fix equilibraton status discrepancy
+  by @plakrisenko in https://github.com/AMICI-dev/AMICI/pull/1991
+* Pass model_name to _create_model_output_dir_name
+  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1994
+* CMake: Build with OpenMP support if available
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2000
+* Fix SuiteSparse Makefiles for compiler-paths
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2003
+* CMake: Build with HDF5 support if available
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1999
+* CMake: Fix reading version file on Windows
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2001
+* CMake: raise minimum required version to 3.15
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2002
+* Fix/extend runtime logging
+  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2005
+* Fix error logging in steadystate solver
+  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2008
+* Don't pass `-py3` to swig after 4.1.0
+  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2010
+* SWIG __repr__s for different templated vector classes
+  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2009
+* Matlab: If mex fails, print mex arguments
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2013
+* Simplify OpenBLAS installation on Windows
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2016
+* Remove model name prefix in generated model files
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2015
+* ...
+
+Documentation:
+* Restructure sphinx doc
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1978
+* Instructions for AMICI with singularity
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1964
+* Illustrate options for potentially speeding up model import/simulation
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1965
+* ...
+
+Dependencies:
+* Updated SuiteSparse to v7.0.1
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2018
+
+**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.16.0...v0.16.1
+
+
 ### v0.16.0 (2023-01-25)
 
 Features
@@ -453,7 +533,7 @@ https://github.com/AMICI-dev/AMICI/compare/v0.11.22...v0.11.23
 
 ### v0.11.22 (2021-12-02)
 
-* **Require sympy>=1.9,pysb>=1.13.1** by @FFroehlich, @dweindl
+* **Require sympy>=1.9,pysb>=1.13.1*  by @FFroehlich, @dweindl
   in https://github.com/AMICI-dev/AMICI/pull/1599
 * Fixed sympy deprecation warning by @dweindl in
   https://github.com/AMICI-dev/AMICI/pull/1600

CMakeLists.txt

@@ -1,15 +1,7 @@
 #
 # Build AMICI library
 #
-cmake_minimum_required(VERSION 3.3)
-
-if(POLICY CMP0077)
-  cmake_policy(SET CMP0077 NEW)
-endif(POLICY CMP0077)
-if(POLICY CMP0074)
-  # Use package_ROOT environment variables
-  cmake_policy(SET CMP0074 NEW)
-endif(POLICY CMP0074)
+cmake_minimum_required(VERSION 3.15)
 
 project(amici)
 
@@ -38,12 +30,21 @@ endforeach(FLAG)
 # find dependencies
 include(GNUInstallDirs)
 
-option(ENABLE_HDF5 "Build with HDF5 support?" ON)
+find_package(OpenMP)
+
+option(AMICI_TRY_ENABLE_HDF5 "Build with HDF5 support if available?" ON)
+option(ENABLE_HDF5 "Build with HDF5 support?" OFF)
+
 if(ENABLE_HDF5)
   find_package(
     HDF5
     COMPONENTS C HL CXX
     REQUIRED)
+elseif(AMICI_TRY_ENABLE_HDF5)
+    find_package(HDF5 COMPONENTS C HL CXX)
+endif()
+
+if(HDF5_FOUND)
   set(HDF5_LIBRARIES ${HDF5_HL_LIBRARIES} ${HDF5_C_LIBRARIES}
                      ${HDF5_CXX_LIBRARIES})
 endif()
@@ -52,11 +53,11 @@ set(SUITESPARSE_DIR "${CMAKE_SOURCE_DIR}/ThirdParty/SuiteSparse/")
 set(SUITESPARSE_INCLUDE_DIRS "${SUITESPARSE_DIR}/include"
                              "${CMAKE_SOURCE_DIR}/ThirdParty/sundials/src")
 set(SUITESPARSE_LIBRARIES
-    ${SUITESPARSE_DIR}/KLU/Lib/libklu${CMAKE_STATIC_LIBRARY_SUFFIX}
-    ${SUITESPARSE_DIR}/COLAMD/Lib/libcolamd${CMAKE_STATIC_LIBRARY_SUFFIX}
-    ${SUITESPARSE_DIR}/BTF/Lib/libbtf${CMAKE_STATIC_LIBRARY_SUFFIX}
-    ${SUITESPARSE_DIR}/AMD/Lib/libamd${CMAKE_STATIC_LIBRARY_SUFFIX}
-    ${SUITESPARSE_DIR}/SuiteSparse_config/libsuitesparseconfig${CMAKE_STATIC_LIBRARY_SUFFIX}
+    ${SUITESPARSE_DIR}/lib/libklu${CMAKE_STATIC_LIBRARY_SUFFIX}
+    ${SUITESPARSE_DIR}/lib/libcolamd${CMAKE_STATIC_LIBRARY_SUFFIX}
+    ${SUITESPARSE_DIR}/lib/libbtf${CMAKE_STATIC_LIBRARY_SUFFIX}
+    ${SUITESPARSE_DIR}/lib/libamd${CMAKE_STATIC_LIBRARY_SUFFIX}
+    ${SUITESPARSE_DIR}/lib/libsuitesparseconfig${CMAKE_STATIC_LIBRARY_SUFFIX}
 )
 
 find_package(
@@ -169,7 +170,7 @@ set(AMICI_SRC_LIST
     ${CMAKE_SOURCE_DIR}/include/amici/sundials_matrix_wrapper.h
     ${CMAKE_SOURCE_DIR}/include/amici/symbolic_functions.h
     ${CMAKE_SOURCE_DIR}/include/amici/vector.h)
-if(ENABLE_HDF5)
+if(HDF5_FOUND)
   list(APPEND AMICI_SRC_LIST ${CMAKE_SOURCE_DIR}/src/hdf5.cpp)
 endif()
 
@@ -216,10 +217,18 @@ target_link_libraries(
   PUBLIC SUNDIALS::cvodes_static
   PUBLIC SUNDIALS::idas_static
   PUBLIC ${SUITESPARSE_LIBRARIES}
-  PUBLIC ${HDF5_LIBRARIES}
   PUBLIC ${BLAS_LIBRARIES}
   PUBLIC ${CMAKE_DL_LIBS})
 
+if(HDF5_FOUND)
+  target_include_directories(${PROJECT_NAME} PUBLIC ${HDF5_INCLUDE_DIRS})
+  target_link_libraries(${PROJECT_NAME} PUBLIC ${HDF5_LIBRARIES})
+endif()
+
+if(OpenMP_FOUND)
+  target_link_libraries(${PROJECT_NAME} PUBLIC OpenMP::OpenMP_CXX)
+endif()
+
 option(SUNDIALS_SUPERLUMT_ENABLE "Enable sundials SuperLUMT?" OFF)
 if(SUNDIALS_SUPERLUMT_ENABLE)
   set(SUNDIALS_LIBRARIES
@@ -328,12 +337,12 @@ endif()
 
 option(BUILD_TESTS "Build integration tests?" ON)
 if(BUILD_TESTS)
-  if(ENABLE_HDF5)
+  if(HDF5_FOUND)
     enable_testing()
 
     add_subdirectory(tests/cpp)
   else()
-    message(WARNING "Cannot build tests with ENABLE_HDF5=OFF.")
+    message(WARNING "Cannot build tests without HDF5 support.")
   endif()
 
 endif()

README.md

@@ -25,7 +25,7 @@ forward sensitivity analysis, steady state sensitivity analysis and
 adjoint sensitivity analysis for likelihood-based output functions.
 
 The interface was designed to provide routines for efficient gradient
-computation in parameter estimation of biochemical reaction models but
+computation in parameter estimation of biochemical reaction models, but
 it is also applicable to a wider range of differential equation
 constrained optimization problems.
 
@@ -62,7 +62,6 @@ constrained optimization problems.
 * Pre-equilibration and pre-simulation conditions
 * Support for
   [discrete events and logical operations](https://academic.oup.com/bioinformatics/article/33/7/1049/2769435)
-  (Matlab-only)
 
 ## Interfaces & workflow
 
@@ -125,7 +124,7 @@ with AMICI:
 
 There is a list of [publications using AMICI](https://amici.readthedocs.io/en/latest/references.html).
 If you used AMICI in your work, we are happy to include
-your project, please let us know via a Github issue.
+your project, please let us know via a GitHub issue.
 
 When using AMICI in your project, please cite
 * Fröhlich, F., Weindl, D., Schälte, Y., Pathirana, D., Paszkowski, Ł., Lines, G.T., Stapor, P. and Hasenauer, J., 2021.

ThirdParty/SuiteSparse/.gitattributes

@@ -0,0 +1,2 @@
+# line endings in repository match line endings on disc
+* -text