Merge branch 'develop' into check_grad_sbml_test_suite

Author: dweindl

.github/workflows/test_python_cplusplus.yml

@@ -36,7 +36,7 @@ jobs:
     - run: echo "BNGPATH=${GITHUB_WORKSPACE}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
 
     # sonar cloud
-    - run: echo "SONAR_SCANNER_VERSION=4.7.0.2747" >> $GITHUB_ENV
+    - run: echo "SONAR_SCANNER_VERSION=5.0.1.3006" >> $GITHUB_ENV
     - run: echo "SONAR_SCANNER_HOME=${HOME}/.sonar/sonar-scanner-$SONAR_SCANNER_VERSION-linux" >> $GITHUB_ENV
     - run: echo "SONAR_SCANNER_OPTS=-server" >> $GITHUB_ENV
     - run: echo "${SONAR_SCANNER_HOME}/bin" >> $GITHUB_PATH
@@ -77,13 +77,6 @@ jobs:
       run: |
         CI_SONARCLOUD=TRUE scripts/buildAmici.sh
 
-    - name: Cache sonar files
-      id: cache-sonar
-      uses: actions/cache@v3
-      with:
-        path: sonar_cache
-        key: ${{ runner.os }}-sonar_cache
-
     - name: C++ tests
       run: |
         scripts/run-cpp-tests.sh
@@ -157,6 +150,7 @@ jobs:
     - name: Run sonar-scanner
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
       run: |
         sonar-scanner \
          -Dsonar.cfamily.build-wrapper-output=bw-output \

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ repos:
   hooks:
     - id: isort
       name: isort (python)
-      args: ["--profile", "black", "--filter-files"]
+      args: ["--profile", "black", "--filter-files", "--line-length", "79"]
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.4.0
   hooks:
@@ -17,12 +17,14 @@ repos:
   - id: end-of-file-fixer
   - id: trailing-whitespace
 - repo: https://github.com/psf/black
-  rev: 23.3.0
+  rev: 23.7.0
   hooks:
-    - id: black
+    - id: black-jupyter
       # It is recommended to specify the latest version of Python
       # supported by your project here, or alternatively use
       # pre-commit's default_language_version, see
       # https://pre-commit.com/#top_level-default_language_version
       language_version: python3.11
+      args: ["--line-length", "79"]
+
 exclude: '^(ThirdParty|models)/'

CHANGELOG.md

@@ -2,15 +2,84 @@
 
 ## v0.X Series
 
+### v0.19.0 (2023-08-26)
+
+**Features**
+* SBML import now supports `rateOf`
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2120
+* Added `Model.{get,set}SteadyStateComputationMode` (analogous to `SteadyStateSensitivityMode`)
+  which allows to choose how steady state is computed.
+  by @plakrisenko in https://github.com/AMICI-dev/AMICI/pull/2074
+
+  **Note: The default `SteadyStateSensitivityMode` changed from `newtonOnly` to `integrateIfNewtonFails`.**
+
+* SBML import: Allow hardcoding of numerical values
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2134
+* Added `antimony2amici` for more convenient antimony import
+  (simplifies working with raw ODEs, see documentation)
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2142
+* Added `AMICI_TRY_ENABLE_HDF5` environment variable to control whether to search for HDF5 or not
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2148
+
+**Fixes**
+
+* Fixed SBML import for events with trigger functions depending on parameters that are initial
+  assignment targets
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2145
+* Fixed SBML import for event-assigned parameters with non-float initial assignments
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2156
+* Fixed `unistd.h` dependency of `hdf5.cpp` that led to compilation
+  failures on Windows
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2154
+* Set CMake policies for cmake 3.27 by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2162
+* Fixed a `lib/` vs `lib64/` issue, leading to `SUNDIALSConfig.cmake`-not-found issues
+  on some systems
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2165
+* CMake: fixed scope of `-DHAS_BOOST_CHRONO` which may have lead to a mix of
+  `boost::chrono::thread_clock` and `std::clock` being used in programs using amici,
+  and potentially segmentation faults
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2163
+
+Performance:
+* Combined code for sparse model functions and their index files for slightly faster
+  compilation of small models
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2159
+
+* Removed complex / complex long KLU functions for slightly faster amici package installation
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2160
+
+**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.18.1...v0.19.0
+
+
+### v0.18.1 (2023-06-26)
+
+Fixes:
+* Fixed pysb pattern matching during PEtab import
+  by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/2118
+* Fixed `sp.Matrix` errors with `numpy==1.25`
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2124
+* Readme: added info containers
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2125
+* Fixed deprecation warnings
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2122
+  https://github.com/AMICI-dev/AMICI/pull/2131
+* Fixed logging typo in SBML import
+  by @dilpath in https://github.com/AMICI-dev/AMICI/pull/2126
+* Added minimum version for `pandas`
+  by @dilpath in https://github.com/AMICI-dev/AMICI/pull/2129
+
+**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.18.0...v0.18.1
+
 ### v0.18.0 (2023-05-26)
+
 Features:
 * More efficient handling of splines in SBML models
   by @paulstapor, @lcontento, @dweindl
   in https://github.com/AMICI-dev/AMICI/pull/1515
 * Partial support of current PEtab2.0 draft, including support for PySB models
   by @dweindl, @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1800
 
-Fixes
+Fixes:
 * **Fixed incorrect forward sensitivities for models with events with**
   **state-dependent trigger functions**
   by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2084

CMakeLists.txt

@@ -2,12 +2,18 @@
 # Build AMICI library
 #
 cmake_minimum_required(VERSION 3.15)
+cmake_policy(VERSION 3.15...3.27)
 
 project(amici)
 
 # misc options
+if(DEFINED ENV{AMICI_TRY_ENABLE_HDF5})
+  option(AMICI_TRY_ENABLE_HDF5 "Build with HDF5 support if available?"
+         $ENV{AMICI_TRY_ENABLE_HDF5})
+else()
+  option(AMICI_TRY_ENABLE_HDF5 "Build with HDF5 support if available?" ON)
+endif()
 option(AMICI_PYTHON_BUILD_EXT_ONLY "Build only the Python extension?" OFF)
-option(AMICI_TRY_ENABLE_HDF5 "Build with HDF5 support if available?" ON)
 option(ENABLE_HDF5 "Build with HDF5 support?" OFF)
 option(SUNDIALS_SUPERLUMT_ENABLE "Enable sundials SuperLUMT?" OFF)
 option(EXPORT_PACKAGE "Export AMICI library to CMake package registry?" ON)
@@ -120,7 +126,7 @@ set(VENDORED_SUNDIALS_BUILD_DIR ${VENDORED_SUNDIALS_DIR}/build)
 set(VENDORED_SUNDIALS_INSTALL_DIR ${VENDORED_SUNDIALS_BUILD_DIR})
 set(SUNDIALS_PRIVATE_INCLUDE_DIRS "${VENDORED_SUNDIALS_DIR}/src")
 find_package(SUNDIALS REQUIRED PATHS
-             "${VENDORED_SUNDIALS_INSTALL_DIR}/lib/cmake/sundials/")
+             "${VENDORED_SUNDIALS_INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/cmake/sundials/")
 message(STATUS "Found SUNDIALS: ${SUNDIALS_DIR}")
 
 set(GSL_LITE_INCLUDE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/ThirdParty/gsl")
@@ -290,7 +296,7 @@ if("$ENV{ENABLE_AMICI_DEBUGGING}"
 endif()
 
 target_compile_definitions(
-  ${PROJECT_NAME} PRIVATE $<$<BOOL:${Boost_CHRONO_FOUND}>:HAS_BOOST_CHRONO>)
+  ${PROJECT_NAME} PUBLIC $<$<BOOL:${Boost_CHRONO_FOUND}>:HAS_BOOST_CHRONO>)
 
 target_link_libraries(
   ${PROJECT_NAME}
@@ -324,7 +330,10 @@ if(HDF5_FOUND)
   target_link_libraries(${PROJECT_NAME} PUBLIC hdf5::hdf5_hl_cpp hdf5::hdf5_hl
                                                hdf5::hdf5_cpp hdf5::hdf5)
 else()
-  message(STATUS "HDF5 library NOT found. Building AMICI WITHOUT HDF5 support.")
+  message(
+    STATUS
+      "HDF5 support disabled or HDF5 library not found. Building AMICI WITHOUT HDF5 support."
+  )
 endif()
 
 if(AMICI_PYTHON_BUILD_EXT_ONLY)