Release 0.4.10

Merge pull request #382 from ICB-DCM/develop

.github/workflows/benchmark_models.yml

@@ -9,6 +9,9 @@ jobs:
     name: benchmark models
     steps:
     - uses: actions/checkout@master
+    - name: chown checkout directory
+      # https://github.com/actions/runner/issues/2033
+      run: chown -R $(id -u):$(id -g) $PWD
 
     - run: echo "PARPE_BASE=$(pwd)" >> $GITHUB_ENV
     - run: echo "PARPE_BUILD=${PARPE_BASE}/build" >> $GITHUB_ENV
@@ -68,6 +71,6 @@ jobs:
     - name: Benchmark models --- tests
       run: |
         cd $PARPE_BASE/benchmark_collection \
-          && AMICI_PARALLEL_COMPILE=4 \
+          && AMICI_PARALLEL_COMPILE="" \
              BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \
              $PARPE_BASE/misc/run_in_venv.sh $PARPE_BASE/build/venv ./all.sh

.github/workflows/deploy_dockerhub.yml

@@ -9,7 +9,7 @@ jobs:
     - uses: actions/checkout@master
     - run: git archive -v -o container/charliecloud/parpe_base/parpe.tar.gz --format=tar.gz HEAD
     - name: Publish to Registry
-      uses: elgohr/Publish-Docker-Github-Action@2.8
+      uses: elgohr/Publish-Docker-Github-Action@v5
       with:
         name: dweindl/parpe
         username: ${{ secrets.DOCKER_USERNAME }}

.github/workflows/parpe_tests.yml

@@ -1,7 +1,13 @@
 # https://help.github.com/en/actions/reference/workflow-syntax-for-github-actions
 # https://help.github.com/en/actions/configuring-and-managing-workflows/using-environment-variables
 name: parPE tests
-on: [push, pull_request, workflow_dispatch]
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+  schedule:
+    - cron:  '48 4 * * *'
+
 jobs:
   container:
     runs-on: ubuntu-latest
@@ -15,14 +21,17 @@ jobs:
 
     steps:
     - uses: actions/checkout@master
+    - name: chown checkout directory
+      # https://github.com/actions/runner/issues/2033
+      run: chown -R $(id -u):$(id -g) $PWD
     - run: git fetch --prune --unshallow
 
     - run: echo "PARPE_BASE=$(pwd)" >> $GITHUB_ENV
     - run: echo "PARPE_BUILD=${PARPE_BASE}/build" >> $GITHUB_ENV
     - run: echo "AMICI_PATH=${PARPE_BASE}/deps/AMICI/" >> $GITHUB_ENV
 
     # sonar cloud
-    - run: echo "SONAR_SCANNER_VERSION=4.6.1.2450" >> $GITHUB_ENV
+    - run: echo "SONAR_SCANNER_VERSION=5.0.1.3006" >> $GITHUB_ENV
     - run: echo "SONAR_SCANNER_HOME=/root/.sonar/sonar-scanner-$SONAR_SCANNER_VERSION-linux" >> $GITHUB_ENV
     - run: echo "SONAR_SCANNER_OPTS=-server" >> $GITHUB_ENV
     - run: echo "${SONAR_SCANNER_HOME}/bin" >> $GITHUB_PATH
@@ -51,7 +60,8 @@ jobs:
 
     - name: Install parPE Python deps
       run: |
-        pip install -r ${PARPE_BASE}/python/requirements.txt
+        pip install -r ${PARPE_BASE}/python/requirements.txt \
+          && sudo apt install lcov
 
     - name: "Install parPE deps: fides"
       run: |
@@ -97,22 +107,26 @@ jobs:
 
     - name: Cache sonar files
       id: cache-sonar
-      uses: actions/cache@v1
+      uses: actions/cache@v3
       with:
         path: sonar_cache
         key: ${{ runner.os }}-sonar_cache
 
     - name: Run sonar-scanner
+      if: ${{ env.SONAR_TOKEN != '' }}
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
       run: |
         sonar-scanner \
          -Dsonar.cfamily.build-wrapper-output=bw-output \
          -Dsonar.projectVersion="$(git describe --abbrev=4 --dirty=-dirty --always --tags | tr -d '\n')"
 
     - name: Run example notebooks
       run: |
-        misc/run_notebook.sh examples/parpeamici/steadystate/parpeExampleSteadystateBasic.ipynb examples/parpeamici/steadystate/parpeExampleSteadystateHierarchical.ipynb
+        misc/run_notebook.sh \
+          examples/parpeamici/steadystate/parpeExampleSteadystateBasic.ipynb \
+          examples/parpeamici/steadystate/parpeExampleSteadystateHierarchical.ipynb
 
     - name: Run valgrind
       run: |

.github/workflows/petab_testsuite.yml

@@ -10,6 +10,9 @@ jobs:
     name: PEtab test suite
     steps:
     - uses: actions/checkout@master
+    - name: chown checkout directory
+      # https://github.com/actions/runner/issues/2033
+      run: chown -R $(id -u):$(id -g) $PWD
 
     - run: echo "PARPE_BASE=$(pwd)" >> $GITHUB_ENV
     - run: echo "PARPE_BUILD=${PARPE_BASE}/build" >> $GITHUB_ENV
@@ -63,7 +66,7 @@ jobs:
         PETAB_TEST_URL: https://github.com/PEtab-dev/petab_test_suite.git
       run: |
         cd $PARPE_BASE/ \
-          && git clone --depth 1 --branch develop $PETAB_TEST_URL \
+          && git clone --depth 1 --branch main $PETAB_TEST_URL \
           && $PARPE_BASE/misc/run_in_venv.sh $PARPE_BASE/build/venv \
             pip3 install -e petab_test_suite
 

.readthedocs.yml

@@ -19,9 +19,12 @@ sphinx:
 #  - pdf
 
 python:
-  version: 3.8
   install:
     - requirements: doc/requirements_doc.txt
-
 build:
-  image: latest
+  os: "ubuntu-22.04"
+#  apt_packages:
+#    - libatlas-base-dev
+#    - swig
+  tools:
+    python: "3.11"

CITATION.cff

@@ -0,0 +1,58 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: parPE
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Daniel
+    family-names: Weindl
+    email: sci@danielweindl.de
+    orcid: 'https://orcid.org/0000-0001-9963-6057'
+  -
+    family-names: "Stapor"
+    given-names: "Paul"
+    orcid: "https://orcid.org/0000-0002-7567-3985"
+  -
+    family-names: "Schmiester"
+    given-names: "Leonard"
+    orcid: "https://orcid.org/0000-0001-7946-3232"
+
+repository-code: 'https://github.com/ICB-DCM/parPE/'
+license: MIT
+doi: 10.5281/zenodo.3478612
+preferred-citation:
+   type: article
+   title: "Efficient parameterization of large-scale dynamic models based on relative measurements"
+   doi: 10.1093/bioinformatics/btz581
+   journal: "Bioinformatics"
+   year: 2020
+   month: 1
+   start: 594
+   end: 602
+   issue: 2
+   volume: 36
+   authors:
+      -
+        family-names: "Schmiester"
+        given-names: "Leonard"
+        orcid: "https://orcid.org/0000-0001-7946-3232"
+      -
+        family-names: "Schälte"
+        given-names: "Yannik"
+        orcid: "https://orcid.org/0000-0003-1293-820X"
+      -
+        family-names: "Fröhlich"
+        given-names: "Fabian"
+        orcid: "https://orcid.org/0000-0002-5360-4292"
+      -
+        family-names: "Hasenauer"
+        given-names: "Jan"
+        orcid: "https://orcid.org/0000-0002-4935-3312"
+      -
+        family-names: "Weindl"
+        given-names: "Daniel"
+        orcid: "https://orcid.org/0000-0001-9963-6057"

CMakeLists.txt

@@ -1,5 +1,5 @@
-cmake_minimum_required(VERSION 3.13) # pkg_search_module GLOBAL
-cmake_policy(VERSION 3.13)
+cmake_minimum_required(VERSION 3.15) # pkg_search_module GLOBAL
+cmake_policy(VERSION 3.15...3.28)
 
 if(POLICY CMP0074)
   # Use package_ROOT environment variables
@@ -17,11 +17,8 @@ include(BuildType) # Ensure CMAKE_BUILD_TYPE is always set
 include(CTest)
 
 set(CMAKE_DEBUG_POSTFIX "-dbg")
-# -D_GNU_SOURCE for pthread recursive mutex
-set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} \
-    -std=c99 -Wall -Wno-unused-function -D_GNU_SOURCE")
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} \
-   -Wall -Wno-unused-function -D_GNU_SOURCE")
+set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -std=c99 -Wall -Wno-unused-function")
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wno-unused-function")
 
 if(BUILD_PYTHON_MODULE)
     # Build PIC code to be used for swig/python module
@@ -86,11 +83,6 @@ if(${PARPE_ENABLE_DLIB})
         CACHE PATH "DLIB base directory")
 endif(${PARPE_ENABLE_DLIB})
 
-# PThreads
-set(THREADS_PREFER_PTHREAD_FLAG ON)
-find_package(Threads REQUIRED)
-
-
 # HDF5
 #set(HDF5_PREFER_PARALLEL TRUE)
 find_package(HDF5 COMPONENTS CXX C HL REQUIRED)
@@ -207,7 +199,7 @@ endif()
 if(BUILD_PYTHON_MODULE AND CMAKE_BUILD_TYPE MATCHES Debug)
     # Only build swig/python module when we are in debug mode
     # This requires PIC, but we don't want PIC for release build at the moment
-    add_subdirectory(python/swig)
+    add_subdirectory(swig)
 endif()
 
 

README.md

@@ -48,10 +48,9 @@ described in [doc/petab_model_import.md](doc/petab_model_import.md).
 
 For full functionality, parPE requires the following libraries:
 
-* CMAKE (>=3.10)
+* CMAKE (>=3.15)
 * MPI ([OpenMPI](https://www.open-mpi.org/),
   [MPICH](https://www.mpich.org/), ...)
-* PTHREADS
 * IPOPT (>= 1.2.7) (requires coinhsl)
 * CERES (>=1.13)
   ([requires Eigen](http://ceres-solver.org/installation.html#dependencies))
@@ -61,7 +60,7 @@ For full functionality, parPE requires the following libraries:
 * [AMICI](https://github.com/AMICI-dev/AMICI) (included in this repository)
   (uses SuiteSparse, Sundials)
 * C++17 compiler
-* Python >= 3.7, including header files
+* Python >= 3.9, including header files
 
 On Debian-based systems, dependencies can be installed via:
 ```shell
@@ -73,6 +72,7 @@ sudo apt-get install \
   curl \
   gfortran \
   libblas-dev \
+  libboost-chrono-dev \
   libboost-serialization-dev \
   libboost-thread-dev \
   libceres-dev \
@@ -121,7 +121,7 @@ can be found on [dockerhub](https://hub.docker.com/r/dweindl/parpe/).
 
 Some high-level documentation is available at
 [https://parpe.readthedocs.io/en/latest/](https://parpe.readthedocs.io/en/latest/)
-and among [Github issues](https://github.com/ICB-DCM/parPE/issues). No extensive
+and among [GitHub issues](https://github.com/ICB-DCM/parPE/issues). No extensive
 full-text documentation is available for the C++ interface yet. For usage of
 the C++ interface see [`examples/`](examples/) and `*/tests`.
 
@@ -141,6 +141,11 @@ parPE is being used or has been used in the following projects:
   (2022). [doi:10.1038/s41467-021-27374-6](https://doi.org/10.1038/s41467-021-27374-6)
   (preprint: [doi:10.1101/859884](https://doi.org/10.1101/859884)).
 
+- Paul F. Lang, David R. Penas, Julio R. Banga, Daniel Weindl, Bela Novak.
+  *Reusable rule-based cell cycle model explains compartment-resolved dynamics*
+  *of 16 observables in RPE-1 cells*. bioRxiv (2023).
+  [doi:10.1101/2023.05.04.539349](https://doi.org/10.1101/2023.05.04.539349)
+
 - [CanPathPro](http://canpathpro.eu/)
 
 

container/charliecloud/parpe_base/Dockerfile

@@ -1,12 +1,16 @@
-FROM ubuntu:20.04
+FROM ubuntu:22.04
 
-COPY . /u18
+COPY . /container-files
 
-RUN /u18/install.sh && rm -rf /tmp && mkdir /tmp
+RUN /container-files/install.sh && rm -rf /tmp && mkdir /tmp
 
 ENV BASH_ENV "/etc/drydock/.env"
+ENV CC clang
+ENV CXX clang++
+ENV OMPI_CC clang
+ENV OMPI_CXX clang++
 
-RUN /u18/install_parpe.sh
+RUN /container-files/install_parpe.sh
 
 ENV PARPE_DIR "/parPE"
 

container/charliecloud/parpe_base/install.sh

@@ -13,11 +13,11 @@ locale-gen en_US en_US.UTF-8
 dpkg-reconfigure locales
 
 echo "HOME=$HOME"
-cd /u18
 
 echo "================= parPE requirements ============"
 # using openmpi coming with libboost-all-dev instead of libmpich-dev
 apt-get install -q -y \
+  clang \
   cmake \
   curl \
   coinor-libipopt-dev \
@@ -28,16 +28,18 @@ apt-get install -q -y \
   libboost-all-dev \
   libceres-dev \
   libhdf5-dev \
+  libomp-dev \
+  nano \
   python3-dev \
+  python3-numpy \
   python3-pip \
   python3-venv \
   libspdlog-dev \
-  swig3.0 \
+  swig \
   unzip \
   wget
 
 # for setuptools to find:
-ln -s /usr/bin/swig3.0 /usr/bin/swig
 python3 -m pip install --upgrade pip
 pip3 install -U setuptools pkgconfig wheel
 

container/charliecloud/parpe_base/install_parpe.sh

@@ -7,7 +7,7 @@ export PARPE_BASE="${PARPE_DIR:-/parPE}"
 
 # unpack git archive
 mkdir "$PARPE_BASE" && cd "$PARPE_BASE"
-tar -xzf /u18/parpe.tar.gz
+tar -xzf /container-files/parpe.tar.gz
 
 # Build dependencies
 
@@ -18,10 +18,10 @@ cd "${AMICI_PATH}" \
   && scripts/buildSundials.sh
 mkdir -p "${AMICI_PATH}/build" && cd "${AMICI_PATH}/build"
 cmake \
-  -DCMAKE_BUILD_TYPE=Debug \
+  -DCMAKE_BUILD_TYPE=RelWithDebInfo \
   -DENABLE_PYTHON=ON \
   -DBUILD_TESTS=OFF \
-  .. && make -j12
+  .. && make -j
 
 # install fides optimizer
 cd "$PARPE_BASE/ThirdParty" && ./installFides.sh
@@ -55,7 +55,7 @@ CC=mpicc CXX=mpiCC cmake \
       -DTESTS_MPIEXEC_COMMAND="$mpi_cmd" \
       ..
 
-make -j12 VERBOSE=1
+make -j VERBOSE=1
 
 # MPI settings for python tests
 export PARPE_TESTS_MPIEXEC="mpiexec -n 5 --oversubscribe --allow-run-as-root --mca btl_vader_single_copy_mechanism none --mca btl ^openib --mca oob_tcp_if_include lo --mca btl_tcp_if_include lo --mca orte_base_help_aggregate 0"