Release 0.4.5

Merge pull request #327 from ICB-DCM/develop

.github/workflows/benchmark_models.yml

@@ -5,7 +5,7 @@ on: [push, pull_request, workflow_dispatch]
 jobs:
   container:
     runs-on: ubuntu-latest
-    container: dweindl/parpeci:1511078
+    container: dweindl/parpeci:1902967
     name: benchmark models
     steps:
     - uses: actions/checkout@master
@@ -38,15 +38,11 @@ jobs:
 
     - name: Configure parpe
       run: |
-        CC=mpicc CXX=mpiCC \
-          cmake \
+        cmake \
           -S"${PARPE_BASE}" \
           -B"${PARPE_BUILD}" \
           -DIPOPT_INCLUDE_DIRS=/usr/include/coin/ \
           -DIPOPT_LIBRARIES=/usr/lib/libipopt.so \
-          -DCERES_LIBRARIES="/usr/lib/libceres.so;/usr/lib/x86_64-linux-gnu/libglog.so;/usr/lib/x86_64-linux-gnu/libgflags.so" \
-          -DCERES_INCLUDE_DIRS="/usr/include/;/usr/include/eigen3" \
-          -DMPI_INCLUDE_DIRS=/usr/include/openmpi-x86_64/ \
           -DGCOVR_REPORT=TRUE \
           -DBUILD_TESTING=FALSE
 

.github/workflows/parpe_tests.yml

@@ -5,7 +5,7 @@ on: [push, pull_request, workflow_dispatch]
 jobs:
   container:
     runs-on: ubuntu-latest
-    container: dweindl/parpeci:1511078
+    container: dweindl/parpeci:1902967
     name: parPE tests
     env:
       # mpiexec prefix for running tests
@@ -22,7 +22,7 @@ jobs:
     - run: echo "AMICI_PATH=${PARPE_BASE}/deps/AMICI/" >> $GITHUB_ENV
 
     # sonar cloud
-    - run: echo "SONAR_SCANNER_VERSION=4.2.0.1873" >> $GITHUB_ENV
+    - run: echo "SONAR_SCANNER_VERSION=4.6.0.2311" >> $GITHUB_ENV
     - run: echo "SONAR_SCANNER_HOME=/root/.sonar/sonar-scanner-$SONAR_SCANNER_VERSION-linux" >> $GITHUB_ENV
     - run: echo "SONAR_SCANNER_OPTS=-server" >> $GITHUB_ENV
     - run: echo "${SONAR_SCANNER_HOME}/bin" >> $GITHUB_PATH
@@ -62,17 +62,14 @@ jobs:
 
     - name: Configure parPE
       run: |
-        CC=mpicc CXX=mpiCC \
-          cmake \
-            -S"${PARPE_BASE}" \
-            -B"${PARPE_BUILD}" \
-            -DIPOPT_INCLUDE_DIRS=/usr/include/coin/ \
-            -DIPOPT_LIBRARIES=/usr/lib/libipopt.so \
-            -DCERES_LIBRARIES="/usr/lib/libceres.so;/usr/lib/x86_64-linux-gnu/libglog.so;/usr/lib/x86_64-linux-gnu/libgflags.so" \
-            -DCERES_INCLUDE_DIRS="/usr/include/;/usr/include/eigen3" \
-            -DMPI_INCLUDE_DIRS=/usr/include/openmpi-x86_64/ \
-            -DGCOV_REPORT=TRUE \
-            -DBUILD_TESTING=TRUE
+        cmake \
+          -S"${PARPE_BASE}" \
+          -B"${PARPE_BUILD}" \
+          -DCMAKE_CXX_FLAGS="-Wall -Wextra -Werror -Wno-deprecated-copy" \
+          -DIPOPT_INCLUDE_DIRS=/usr/include/coin/ \
+          -DIPOPT_LIBRARIES=/usr/lib/libipopt.so \
+          -DGCOV_REPORT=TRUE \
+          -DBUILD_TESTING=TRUE
 
     - name: Build parPE
       # with sonar build wrapper

.github/workflows/petab_testsuite.yml

@@ -6,7 +6,7 @@ on: [push, pull_request, workflow_dispatch]
 jobs:
   container:
     runs-on: ubuntu-latest
-    container: dweindl/parpeci:1511078
+    container: dweindl/parpeci:1902967
     name: PEtab test suite
     steps:
     - uses: actions/checkout@master
@@ -39,15 +39,11 @@ jobs:
 
     - name: Configure parpe
       run: |
-        CC=mpicc CXX=mpiCC \
-          cmake \
+        cmake \
           -S"${PARPE_BASE}" \
           -B"${PARPE_BUILD}" \
           -DIPOPT_INCLUDE_DIRS=/usr/include/coin/ \
           -DIPOPT_LIBRARIES=/usr/lib/libipopt.so \
-          -DCERES_LIBRARIES="/usr/lib/libceres.so;/usr/lib/x86_64-linux-gnu/libglog.so;/usr/lib/x86_64-linux-gnu/libgflags.so" \
-          -DCERES_INCLUDE_DIRS="/usr/include/;/usr/include/eigen3" \
-          -DMPI_INCLUDE_DIRS=/usr/include/openmpi-x86_64/ \
           -DGCOVR_REPORT=TRUE \
           -DBUILD_TESTING=FALSE
 
@@ -67,7 +63,7 @@ jobs:
         PETAB_TEST_URL: https://github.com/PEtab-dev/petab_test_suite.git
       run: |
         cd $PARPE_BASE/ \
-          && git clone --depth 1 $PETAB_TEST_URL \
+          && git clone --depth 1 --branch develop $PETAB_TEST_URL \
           && $PARPE_BASE/misc/run_in_venv.sh $PARPE_BASE/build/venv \
             pip3 install -e petab_test_suite
 

.gitignore

@@ -4,8 +4,9 @@ CMakeLists.txt.user
 /data/*
 /ThirdParty/*
 /doc/Doxyfile
-/doc/doxy/*
-/doc/exhale_cpp_api/
+/doc/_exhale_doxygen_output/
+/doc/cpp_api/
+/doc/_autosummary/
 .project
 .pydevproject
 .idea/*
@@ -18,12 +19,11 @@ __pycache__/
 .directory
 */swig/*_wrap.cpp
 /amici/examples/steadystate/model_steadystate_scaled
-/amici/examples/lucarelli/lucarelli_12/lucarelli_12/
 /activate
 
 # snakemake
 .snakemake/
-
+/snakemake/results
 # amici
 deps/AMICI/python/sdist/amici.egg-info/
 deps/AMICI/python/sdist/amici/amici.py
@@ -39,7 +39,7 @@ python/test_*.png
 *.log
 
 /benchmark_collection/*_*[0-9][0-9][0-9][0-9]/
-/benchmark_collection/parpe_*_*[0-9][0-9][0-9][0-9]/
+/benchmark_collection/parpe_*_*[0-9][0-9][0-9][0-9]*/
 
 # breathe-generatd files
 doc/source/api/
@@ -48,7 +48,7 @@ doc/source/api/
 # test files
 tests/petab-test-suite/
 test_*.png
-
+examples/parpeamici/steadystate/*.h5
 # containers
 /container/charliecloud/parpe_base/parpe.tar.gz
 *.sif

.readthedocs.yml

@@ -15,15 +15,13 @@ sphinx:
 #mkdocs:
 #  configuration: mkdocs.yml
 
-# Optionally build your docs in additional formats such as PDF and ePub
 #formats:
 #  - pdf
 
-# Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.7
+  version: 3.8
   install:
     - requirements: doc/requirements_doc.txt
 
-#build:
-#  image: latest
+build:
+  image: latest

CMakeLists.txt

@@ -51,12 +51,6 @@ set(BUILD_PYTHON_MODULE FALSE CACHE BOOL "Build Python module?")
 set(BLAS "CBLAS" CACHE STRING "BLAS library to use")
 set_property(CACHE BLAS PROPERTY STRINGS "CBLAS" "MKL")
 set(PARPE_ENABLE_MPI TRUE CACHE BOOL "Use MPI?")
-set(IPOPT_DIR "" CACHE PATH "IpOpt root directory")
-set(IPOPT_INCLUDE_DIRS "${IPOPT_DIR}/include/coin/"
-    CACHE PATH "IpOpt include directory")
-set(IPOPT_LIBRARIES "${IPOPT_DIR}/lib/libipopt.a"
-    "${IPOPT_DIR}/lib/libcoinhsl.a" "gfortran"
-    CACHE STRING "IpOpt library")
 set(PARPE_ENABLE_IPOPT TRUE CACHE BOOL "Enable ipopt optimizer?")
 set(PARPE_ENABLE_CERES TRUE CACHE BOOL "Enable ceres optimizer?")
 set(PARPE_ENABLE_DLIB FALSE CACHE BOOL "Enable dlib optimizers?")
@@ -71,14 +65,12 @@ find_package(OpenMP)
 # Enable MPI?
 if(${PARPE_ENABLE_MPI})
     find_package(MPI REQUIRED)
-    if(IS_DIRECTORY ${MPI_INCLUDE_DIRS})
-        # may be undefined. will be provided by MPI compiler wrapped.
-        # this is only added for convenient IDE integration
-        include_directories(${MPI_INCLUDE_DIRS})
-    endif()
 endif(${PARPE_ENABLE_MPI})
 # </Build options>
 
+find_package(PkgConfig)
+pkg_search_module(IPOPT REQUIRED IMPORTED_TARGET GLOBAL ipopt>=3.11.0 )
+
 if(${ENABLE_DLIB})
     set(DLIB_DIR "${CMAKE_CURRENT_LIST_DIR}/ThirdParty/dlib-19.7"
         CACHE FILEPATH "DLIB base directory")
@@ -233,7 +225,6 @@ add_library(${PROJECT_NAME} /dev/null)
 target_link_libraries(${PROJECT_NAME}
     PUBLIC parpecommon parpeloadbalancer parpeoptimization parpeamici)
 
-
 # <Export cmake configuration>
 install(TARGETS ${PROJECT_NAME} EXPORT ParPETargets
     LIBRARY DESTINATION lib
@@ -267,9 +258,6 @@ install(
     "${CMAKE_CURRENT_BINARY_DIR}/ParPEConfigVersion.cmake"
     DESTINATION "${LIB_INSTALL_DIR}/cmake/")
 
-configure_file("CMakeModules/ParPEConfig.cmake.in"
-    "${CMAKE_CURRENT_BINARY_DIR}/ParPEConfig.cmake"
-    @ONLY)
 
 # Register package
 if(${PARPE_EXPORT_PACKAGE})

CMakeModules/ParPEConfig.cmake.in

@@ -1,8 +1,30 @@
+@PACKAGE_INIT@
+
+include(CMakeFindDependencyMacro)
+
+set(PARPE_ENABLE_MPI @PARPE_ENABLE_MPI@)
+set(PARPE_ENABLE_IPOPT @PARPE_ENABLE_IPOPT@)
+set(PARPE_ENABLE_CERES @PARPE_ENABLE_CERES@)
+
+if(${PARPE_ENABLE_MPI})
+find_dependency(MPI REQUIRED)
+endif()
+
+if(${PARPE_ENABLE_IPOPT})
+find_dependency(PkgConfig REQUIRED)
+pkg_search_module(IPOPT REQUIRED IMPORTED_TARGET GLOBAL ipopt>=3.11.0)
+endif()
+
+if(${PARPE_ENABLE_CERES})
+find_dependency(Ceres COMPONENTS
+    HINTS "${CMAKE_SOURCE_DIR}/ThirdParty/ceres-solver-2.0.0/build/install")
+find_dependency(Eigen3 REQUIRED)
+endif()
+
+find_dependency(Amici REQUIRED)
+find_dependency(OpenMP)
+find_dependency(HDF5 COMPONENTS C CXX HL REQUIRED)
+
 include("${CMAKE_CURRENT_LIST_DIR}/ParPETargets.cmake")
-set_property(TARGET Upstream::parpe PROPERTY INCLUDE_DIRECTORIES @ParPEConfigIncludes@ @ParPEConfigIncludesCommon@ @ParPEConfigIncludesLoadbalancer@ @ParPEConfigIncludesOptimization@ @ParPEConfigIncludesAmici@)
-set_property(TARGET Upstream::parpecommon PROPERTY INCLUDE_DIRECTORIES @ParPEConfigIncludesCommon@)
-set_property(TARGET Upstream::parpeloadbalancer PROPERTY INCLUDE_DIRECTORIES @ParPEConfigIncludesLoadbalancer@)
-set_property(TARGET Upstream::parpeoptimization PROPERTY INCLUDE_DIRECTORIES @ParPEConfigIncludesOptimization@)
-set_property(TARGET Upstream::parpeamici PROPERTY INCLUDE_DIRECTORIES @ParPEConfigIncludesAmici@)
-get_property(ParPE_INCLUDE_DIRS TARGET Upstream::parpe PROPERTY INCLUDE_DIRECTORIES)
-set(ParPE_LIBRARIES Upstream::parpe)
+
+check_required_components(ParPE)

README.md

@@ -48,7 +48,7 @@ described in [doc/petab_model_import.md](doc/petab_model_import.md).
 
 For full functionality, parPE requires the following libraries:
 
-* CMAKE (>=3.6)
+* CMAKE (>=3.10)
 * MPI ([OpenMPI](https://www.open-mpi.org/),
   [MPICH](https://www.mpich.org/), ...)
 * PTHREADS
@@ -60,7 +60,7 @@ For full functionality, parPE requires the following libraries:
 * [AMICI](https://github.com/ICB-DCM/AMICI) (included in this repository)
   (uses SuiteSparse, Sundials)
 * C++17 compiler
-* Python >= 3.6, including header files
+* Python >= 3.7, including header files
 
 On Debian-based systems, dependencies can be installed via:
 ```shell
@@ -77,10 +77,12 @@ Scripts to fetch and build the remaining dependencies are provided in
 ThirdParty/installDeps.sh
 ```
 
-NOTE: When using `ThirdParty/installIpopt.sh` to build Ipopt, follow the
-instructions in `ThirdParty/Ipopt-3.12.12/ThirdParty/HSL/INSTALL.HSL` for
-obtaining the hsl library before continuing, otherwise IpOpt will not be
-usable. Afterwards, (re)run `ThirdParty/installIpopt.sh`.
+NOTE: When using `ThirdParty/installIpopt.sh` to build Ipopt, you may have to
+download the HSL library separately as described at
+https://coin-or.github.io/Ipopt/INSTALL.html#DOWNLOAD_HSL. Place the HSL
+archive into `ThirdParty` before running `ThirdParty/installIpopt.sh`. If asked
+type in your coinhsl version (e.g. `2019.05.21` if you
+have `coinhsl-2019.05.21.tar.gz`).
 
 
 ## Building
@@ -95,7 +97,7 @@ Other sample build scripts are provided as `/build*.sh`.
 
 ## Recently tested compilers
 
-* GCC 8.3.0
+* GCC 10.2.0
 * Intel icpc (ICC) 17.0.6
 
 ## Docker