Release 0.4.4

* AMICI-related * Update to AMICI v0.11.2 (#295) * adjoint preequilibration * reduced memory requirements * Make proper use of amici::RDataReporting to avoid computing costly disregarded results (#296) * Add script / cmake target to update amici (Closes #288) * Handle AMICI failures more gracefully * Fix misc/rebuild_amici.sh in case of changed AMICI SWIG interface * Fix: HierarchicalOptimizationWrapper: Return full parameters and full gradient even if nothing computed analytically * Fix C++17 in CMakeLists template * Fix: Use absolute path in misc/setup_amici_model.sh * Fix PEtab import issues * Fix icpc option overriding warning (Closes #220) * Update example notebooks and run on github actions (#294) * Add CLI option to simulator to run simulations with nominal parameters (#293) * Various cleanup * #287, #285, #271, #270, #268, #267, and others * Remove obsolete parpeamici/steadystateSimulator.cpp * Remove outdated amiciHelper.py module for parsing AMICI source files * Remove all uses of std::tmpnam * Handle IpOpt reporting obj_value 0.0 in case of non-finite fval or gradient (#221) * Base image ubuntu:19.10 (EOL ubuntu:19.04) * adapt dataprovider and simulatio to df to third column in simulation condition table (#272) * Update gsllite (#269) * Fix petab import when online some measurements have preequilibrationCondition set * Add basic contribution guide * Fix race conditions in steadystate example (#265) * Cache sonar files on github actions * CI: No shallow clone for running sonarscanner * Remove obsolete and unreliabe functions parpe::launchedWithMpi and parpe::initMpiIfNeeded -- using MPI must be specified via CLI now
ICB-DCM · Oct 14, 2020 · 0750546 · 0750546
2 parents 142271c + 0324d38
commit 0750546
Show file tree

Hide file tree

Showing 1,100 changed files with 128,601 additions and 39,854 deletions.
diff --git a/.github/workflows/benchmark_models.yml b/.github/workflows/benchmark_models.yml
@@ -1,7 +1,7 @@
 # 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: Test benchmark collection models
-on: [push]
+on: [push, pull_request, workflow_dispatch]
 jobs:
   container:
     runs-on: ubuntu-latest
@@ -10,9 +10,9 @@ jobs:
     steps:
     - uses: actions/checkout@master
 
-    - run: echo "::set-env name=PARPE_BASE::$(pwd)"
-    - run: echo "::set-env name=PARPE_BUILD::${PARPE_BASE}/build"
-    - run: echo "::set-env name=AMICI_PATH::${PARPE_BASE}/deps/AMICI/"
+    - run: echo "PARPE_BASE=$(pwd)" >> $GITHUB_ENV
+    - run: echo "PARPE_BUILD=${PARPE_BASE}/build" >> $GITHUB_ENV
+    - run: echo "AMICI_PATH=${PARPE_BASE}/deps/AMICI/" >> $GITHUB_ENV
 
     # Build dependencies
 

diff --git a/.github/workflows/deploy_dockerhub.yml b/.github/workflows/deploy_dockerhub.yml
@@ -1,6 +1,6 @@
 # https://github.com/marketplace/actions/publish-docker
 name: Deploy to dockerhub
-on: [push]
+on: [push, workflow_dispatch]
 jobs:
   build:
     name: Deploy to dockerhub

diff --git a/.github/workflows/parpe_tests.yml b/.github/workflows/parpe_tests.yml
@@ -1,28 +1,32 @@
 # 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]
+on: [push, pull_request, workflow_dispatch]
 jobs:
   container:
     runs-on: ubuntu-latest
     container: dweindl/parpeci:1511078
     name: parPE tests
+    env:
+      # mpiexec prefix for running tests
+      # If we are running in docker, we generally don't have SYS_PTRACE
+      #  permissions  and thus, cannot use vader. Also disable Infiniband.
+      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
+
     steps:
     - uses: actions/checkout@master
-      with:
-        fetch-depth: 42
+    - run: git fetch --prune --unshallow
 
-
-    - run: echo "::set-env name=PARPE_BASE::$(pwd)"
-    - run: echo "::set-env name=PARPE_BUILD::${PARPE_BASE}/build"
-    - run: echo "::set-env name=AMICI_PATH::${PARPE_BASE}/deps/AMICI/"
+    - run: echo "PARPE_BASE=$(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 "::set-env name=SONAR_SCANNER_VERSION::4.2.0.1873"
-    - run: echo "::set-env name=SONAR_SCANNER_HOME::/root/.sonar/sonar-scanner-$SONAR_SCANNER_VERSION-linux"
-    - run: echo "::set-env name=SONAR_SCANNER_OPTS::-server"
-    - run: echo "::add-path::${SONAR_SCANNER_HOME}/bin"
-    - run: echo "::add-path::/root/.sonar/build-wrapper-linux-x86"
+    - run: echo "SONAR_SCANNER_VERSION=4.2.0.1873" >> $GITHUB_ENV
+    - run: echo "SONAR_SCANNER_HOME=/root/.sonar/sonar-scanner-$SONAR_SCANNER_VERSION-linux" >> $GITHUB_ENV
+    - run: echo "SONAR_SCANNER_OPTS=-server" >> $GITHUB_ENV
+    - run: echo "${SONAR_SCANNER_HOME}/bin" >> $GITHUB_PATH
+    - run: echo "/root/.sonar/build-wrapper-linux-x86" >> $GITHUB_PATH
 
     - name: Info
       run: lsb_release -a && printenv
@@ -83,7 +87,7 @@ jobs:
         && $PARPE_BASE/misc/run_in_venv.sh $PARPE_BASE/build/venv \
           pytest \
             --cov-report=xml:$PARPE_BUILD/coverage_py.xml \
-            --cov=./ \
+            --cov=parpe --cov-append \
             $PARPE_BASE/python/tests/
 
     # Redundant with parpe_coverage_cobertura
@@ -96,6 +100,13 @@ jobs:
           && CTEST_OUTPUT_ON_FAILURE=1 make parpe_coverage \
           && make ExperimentalCoverage
 
+    - name: Cache sonar files
+      id: cache-sonar
+      uses: actions/cache@v1
+      with:
+        path: sonar_cache
+        key: ${{ runner.os }}-sonar_cache
+
     - name: Run sonar-scanner
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -104,6 +115,10 @@ jobs:
          -Dsonar.cfamily.build-wrapper-output=bw-output \
          -Dsonar.projectVersion="$(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
+
     - name: Run valgrind
       run: |
         cd ${PARPE_BUILD} \

diff --git a/.github/workflows/petab_testsuite.yml b/.github/workflows/petab_testsuite.yml
@@ -2,7 +2,7 @@
 # https://help.github.com/en/actions/configuring-and-managing-workflows/using-environment-variables
 
 name: PEtab test suite
-on: [push]
+on: [push, pull_request, workflow_dispatch]
 jobs:
   container:
     runs-on: ubuntu-latest
@@ -11,9 +11,9 @@ jobs:
     steps:
     - uses: actions/checkout@master
 
-    - run: echo "::set-env name=PARPE_BASE::$(pwd)"
-    - run: echo "::set-env name=PARPE_BUILD::${PARPE_BASE}/build"
-    - run: echo "::set-env name=AMICI_PATH::${PARPE_BASE}/deps/AMICI/"
+    - run: echo "PARPE_BASE=$(pwd)" >> $GITHUB_ENV
+    - run: echo "PARPE_BUILD=${PARPE_BASE}/build" >> $GITHUB_ENV
+    - run: echo "AMICI_PATH=${PARPE_BASE}/deps/AMICI/" >> $GITHUB_ENV
 
     # Build dependencies
 

diff --git a/.gitignore b/.gitignore
@@ -44,4 +44,11 @@ python/test_*.png
 # breathe-generatd files
 doc/source/api/
 
+
+# test files
+tests/petab-test-suite/
 test_*.png
+
+# containers
+/container/charliecloud/parpe_base/parpe.tar.gz
+*.sif
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -10,7 +10,7 @@ project(parpe)
 
 set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/CMakeModules/")
 
-set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED True)
 
 include(BuildType) # Ensure CMAKE_BUILD_TYPE is always set
@@ -20,9 +20,9 @@ include(CTest)
 set(CMAKE_DEBUG_POSTFIX "-dbg")
 # -D_GNU_SOURCE for pthread recursive mutex
 set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} \
-    -std=c99 -Wall -Wno-unused-function -fopenmp -D_GNU_SOURCE")
+    -std=c99 -Wall -Wno-unused-function -D_GNU_SOURCE")
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} \
-    -std=c++11 -Wall -Wno-unused-function -fopenmp -D_GNU_SOURCE")
+   -Wall -Wno-unused-function -D_GNU_SOURCE")
 
 if(BUILD_PYTHON_MODULE)
     # Build PIC code to be used for swig/python module
@@ -57,9 +57,6 @@ set(IPOPT_INCLUDE_DIRS "${IPOPT_DIR}/include/coin/"
 set(IPOPT_LIBRARIES "${IPOPT_DIR}/lib/libipopt.a"
     "${IPOPT_DIR}/lib/libcoinhsl.a" "gfortran"
     CACHE STRING "IpOpt library")
-set(CERES_INCLUDE_DIRS "" "/usr/include/eigen3"
-    CACHE PATH "CERES include directories")
-set(CERES_LIBRARIES "" CACHE STRING "CERES libraries")
 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?")
@@ -68,6 +65,9 @@ set(PARPE_ENABLE_FSQP FALSE CACHE BOOL "Enable FSQP optimizer?")
 set(PARPE_EXPORT_PACKAGE FALSE CACHE BOOL
     "Export this build to CMake registry?")
 
+# OpenMP?
+find_package(OpenMP)
+
 # Enable MPI?
 if(${PARPE_ENABLE_MPI})
     find_package(MPI REQUIRED)
@@ -97,6 +97,9 @@ set(HDF5_LIBRARIES
 
 # Guidelines Support Library (GSL-lite) directory
 set(GSL_INCLUDE_DIRS "${CMAKE_SOURCE_DIR}/ThirdParty/gsl")
+# Throw on contract violation instead of terminate to get more meaningful
+#  message
+add_definitions(-Dgsl_CONFIG_CONTRACT_VIOLATION_THROWS)
 
 # Build tests?
 if(${BUILD_TESTING})

diff --git a/CMakeModules/BuildOptimized.cmake b/CMakeModules/BuildOptimized.cmake
@@ -6,8 +6,7 @@ if(CMAKE_BUILD_TYPE MATCHES Release OR CMAKE_BUILD_TYPE MATCHES RelWithDebInfo)
 
     if(COMPILER_SUPPORTS_XHOST)
         set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xHOST")
-    endif()
-    if(COMPILER_SUPPORTS_MARCHNATIVE)
+    elseif(COMPILER_SUPPORTS_MARCHNATIVE)
         set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native")
     endif()
 endif()
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -0,0 +1,47 @@
+# How to contribute
+
+We are happy about contributions to parPE in any form, be it new functionality,
+documentation, bug reports, or anything else.
+
+When planning to contribute to parPE, it may be best to first create an issue
+at [https://github.com/ICB-DCM/parPE/issues](https://github.com/ICB-DCM/parPE/issues)
+to outline plans to avoid any redundant work.
+
+For any contribution, please create a pull request. By creating a pull request,
+you agree on contributing your code/text/image/etc. under the license terms
+stated in [https://github.com/ICB-DCM/parPE/blob/master/LICENSE](https://github.com/ICB-DCM/parPE/blob/master/LICENSE). 
+
+
+## Style guide
+
+For any code contributions, please follow the guidelines below.
+
+
+### General
+
+* All files and functions should come with file-level and function-level
+  documentation.
+
+* All new functionality should be covered by unit or integration tests. Runtime
+  of those tests should be kept as short as possible. 
+
+
+### C++
+
+* We use C++14
+
+* New contributions should follow the
+  [Google C++ Style Guide](https://google.github.io/styleguide/cppguide.html).
+  Existing code does not yet, but will be adapted accordingly.
+
+
+### Python 
+
+* We want to be compatible with Python 3.7
+
+* For the Python code we want to follow 
+  [PEP8](https://www.python.org/dev/peps/pep-0008/). Although this is not the
+  case for all existing code, any new contributions should do so. 
+
+* We use Python [type hints](https://docs.python.org/3/library/typing.html)
+  for all functions.
diff --git a/README.md b/README.md
@@ -59,7 +59,7 @@ For full functionality, parPE requires the following libraries:
 * CBLAS compatible BLAS (libcblas, Intel MKL, ...)
 * [AMICI](https://github.com/ICB-DCM/AMICI) (included in this repository)
   (uses SuiteSparse, Sundials)
-* C++14 compiler
+* C++17 compiler
 * Python >= 3.6, including header files
 
 On Debian-based systems, dependencies can be installed via: