Release 0.4.3

Merge pull request #262 from ICB-DCM/develop Library * Update to current PEtab * Save more metadata in simulator result file (#259) * More informative output for hierarchical optimization (Closes #210) (#255) * Update to AMICI v0.10.21 and petab 0.1.7 (#261) * Fix: Handle paths with blanks in build scripts (Fixes #246) * Remove old example models lucarelli and raia (Closes #215) * Misc fixups * Cleanup build system, e.g. replace redundant CMake option BUILD_TESTS by auto-provided BUILD_TESTING Documentation * Update documentation, now created with sphinx/breeze/exhale and available at https://readthedocs.org/projects/parpe/ (#249) (#251) CI * Use Github actions instead of shippable (#256) * Set up sonarcloud for static code analysis (#254) * Various fixes (#258) (#236) * Better integration of google tests in ctest using gtest_discover_tests. Raise CMake requirement. (#253) * Run PEtab test suite (#244) * Run python package tests via CTest * Tests with steadystate example to pytest
ICB-DCM · Apr 4, 2020 · 142271c · 142271c
2 parents 40432be + 47799b5
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diff --git a/.github/workflows/benchmark_models.yml b/.github/workflows/benchmark_models.yml
@@ -0,0 +1,77 @@
+# 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]
+jobs:
+  container:
+    runs-on: ubuntu-latest
+    container: dweindl/parpeci:1511078
+    name: benchmark models
+    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/"
+
+    # Build dependencies
+
+    - name: Install AMICI deps
+      run: |
+        cd $AMICI_PATH \
+          && scripts/buildSuiteSparse.sh \
+          && scripts/buildSundials.sh
+
+    - name: Install AMICI
+      run: |
+        cmake \
+            -S ${AMICI_PATH} \
+            -B ${AMICI_PATH}/build \
+            -DCMAKE_BUILD_TYPE=Debug \
+            -DENABLE_PYTHON=ON \
+            -DBUILD_TESTS=OFF \
+          && cmake --build "${AMICI_PATH}/build" --parallel -- VERBOSE=1
+
+    - name: Install parPE Python deps
+      run: |
+        pip install -r ${PARPE_BASE}/python/requirements.txt
+
+    - name: Configure parpe
+      run: |
+        CC=mpicc CXX=mpiCC \
+          cmake \
+          -S"${PARPE_BASE}" \
+          -B"${PARPE_BUILD}" \
+          -DIPOPT_INCLUDE_DIRS=/usr/include/coin/ \
+          -DIPOPT_LIBRARIES=/usr/lib/libipopt.so \
+          -DCERES_LIBRARIES="/usr/lib/libceres.so;/usr/lib/x86_64-linux-gnu/libglog.so;/usr/lib/x86_64-linux-gnu/libgflags.so" \
+          -DCERES_INCLUDE_DIRS="/usr/include/;/usr/include/eigen3" \
+          -DMPI_INCLUDE_DIRS=/usr/include/openmpi-x86_64/ \
+          -DGCOVR_REPORT=TRUE \
+          -DBUILD_TESTING=FALSE
+
+    - name: Build parPE
+      run: |
+        cmake --build "${PARPE_BUILD}" --parallel -- VERBOSE=1
+
+    # Actual Benchmark model tests
+
+    - name: Benchmark models --- requirements
+      run: |
+        sudo apt install bc \
+          && $PARPE_BASE/misc/run_in_venv.sh $PARPE_BASE/build/venv \
+              pip3 install shyaml
+
+    - name: Benchmark models --- repository
+      env:
+        BM_REPO_URL: https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git
+      run: |
+        cd $PARPE_BASE/benchmark_collection \
+          && git clone --depth 1 $BM_REPO_URL
+
+    - name: Benchmark models --- tests
+      run: |
+        cd $PARPE_BASE/benchmark_collection \
+          && AMICI_PARALLEL_COMPILE=4 \
+             BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \
+             $PARPE_BASE/misc/run_in_venv.sh $PARPE_BASE/build/venv ./all.sh
diff --git a/.github/workflows/deploy_dockerhub.yml b/.github/workflows/deploy_dockerhub.yml
@@ -3,6 +3,7 @@ name: Deploy to dockerhub
 on: [push]
 jobs:
   build:
+    name: Deploy to dockerhub
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@master

diff --git a/.github/workflows/parpe_tests.yml b/.github/workflows/parpe_tests.yml
@@ -0,0 +1,112 @@
+# 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]
+jobs:
+  container:
+    runs-on: ubuntu-latest
+    container: dweindl/parpeci:1511078
+    name: parPE tests
+    steps:
+    - uses: actions/checkout@master
+      with:
+        fetch-depth: 42
+
+
+    - 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::${PARPE_BASE}/deps/AMICI/"
+
+    # sonar cloud
+    - run: echo "::set-env name=SONAR_SCANNER_VERSION::4.2.0.1873"
+    - run: echo "::set-env name=SONAR_SCANNER_HOME::/root/.sonar/sonar-scanner-$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"
+
+    - name: Info
+      run: lsb_release -a && printenv
+
+      # Build dependencies
+
+    - name: Install AMICI deps
+      run: |
+        cd $AMICI_PATH \
+          && scripts/buildSuiteSparse.sh \
+          && scripts/buildSundials.sh \
+          && scripts/buildCpputest.sh #&& scripts/buildAmici.sh
+
+    - name: Install AMICI
+      # with tests:
+      # CPPUTEST_BUILD_DIR=${AMICI_PATH}/ThirdParty/cpputest-master/build/
+      # -DCppUTest_DIR=${CPPUTEST_BUILD_DIR}
+      run: |
+        cmake \
+          -S ${AMICI_PATH} \
+          -B ${AMICI_PATH}/build \
+          -DCMAKE_BUILD_TYPE=Debug \
+          -DENABLE_PYTHON=ON \
+          -DBUILD_TESTS=OFF \
+          && cmake --build "${AMICI_PATH}/build" --parallel -- VERBOSE=1
+
+    - name: Install google test
+      run: ThirdParty/installGoogleTest.sh
+
+    - name: Install parPE Python deps
+      run: |
+        pip install -r ${PARPE_BASE}/python/requirements.txt
+
+    - name: Configure parPE
+      run: |
+        CC=mpicc CXX=mpiCC \
+          cmake \
+            -S"${PARPE_BASE}" \
+            -B"${PARPE_BUILD}" \
+            -DIPOPT_INCLUDE_DIRS=/usr/include/coin/ \
+            -DIPOPT_LIBRARIES=/usr/lib/libipopt.so \
+            -DCERES_LIBRARIES="/usr/lib/libceres.so;/usr/lib/x86_64-linux-gnu/libglog.so;/usr/lib/x86_64-linux-gnu/libgflags.so" \
+            -DCERES_INCLUDE_DIRS="/usr/include/;/usr/include/eigen3" \
+            -DMPI_INCLUDE_DIRS=/usr/include/openmpi-x86_64/ \
+            -DGCOV_REPORT=TRUE \
+            -DBUILD_TESTING=TRUE
+
+    - name: Build parPE
+      # with sonar build wrapper
+      run: |
+        build-wrapper-linux-x86-64 --out-dir bw-output \
+          cmake --build "${PARPE_BUILD}" --parallel -- VERBOSE=1
+
+    - name: Run parPE python unittests
+      run: |
+        $PARPE_BASE/misc/run_in_venv.sh $PARPE_BASE/build/venv \
+          pip install pytest-cov \
+        && $PARPE_BASE/misc/run_in_venv.sh $PARPE_BASE/build/venv \
+          pytest \
+            --cov-report=xml:$PARPE_BUILD/coverage_py.xml \
+            --cov=./ \
+            $PARPE_BASE/python/tests/
+
+    # Redundant with parpe_coverage_cobertura
+    #- name: Run CTEST
+    #  run: cd ${PARPE_BUILD} && CTEST_OUTPUT_ON_FAILURE=1 make test
+
+    - name: Create coverage report
+      run: |
+        cd ${PARPE_BUILD} \
+          && CTEST_OUTPUT_ON_FAILURE=1 make parpe_coverage \
+          && make ExperimentalCoverage
+
+    - name: Run sonar-scanner
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        sonar-scanner \
+         -Dsonar.cfamily.build-wrapper-output=bw-output \
+         -Dsonar.projectVersion="$(git describe --abbrev=4 --dirty=-dirty --always --tags | tr -d '\n')"
+
+    - name: Run valgrind
+      run: |
+        cd ${PARPE_BUILD} \
+          && if (CTEST_OUTPUT_ON_FAILURE=1 make ExperimentalMemCheck); \
+              then cat Testing/Temporary/MemoryChecker.*.log; \
+              else cat Testing/Temporary/MemoryChecker.*.log; exit 1; fi
diff --git a/.github/workflows/petab_testsuite.yml b/.github/workflows/petab_testsuite.yml
@@ -0,0 +1,77 @@
+# https://help.github.com/en/actions/reference/workflow-syntax-for-github-actions
+# https://help.github.com/en/actions/configuring-and-managing-workflows/using-environment-variables
+
+name: PEtab test suite
+on: [push]
+jobs:
+  container:
+    runs-on: ubuntu-latest
+    container: dweindl/parpeci:1511078
+    name: PEtab test suite
+    steps:
+    - uses: actions/checkout@master
+
+    - run: echo "::set-env name=PARPE_BASE::$(pwd)"
+    - run: echo "::set-env name=PARPE_BUILD::${PARPE_BASE}/build"
+    - run: echo "::set-env name=AMICI_PATH::${PARPE_BASE}/deps/AMICI/"
+
+    # Build dependencies
+
+    - name: Install AMICI deps
+      run: |
+        cd $AMICI_PATH \
+          && scripts/buildSuiteSparse.sh \
+          && scripts/buildSundials.sh
+
+    - name: Install AMICI
+      run: |
+        cmake \
+            -S ${AMICI_PATH} \
+            -B ${AMICI_PATH}/build \
+            -DCMAKE_BUILD_TYPE=Debug \
+            -DENABLE_PYTHON=ON \
+            -DBUILD_TESTS=OFF \
+          && cmake --build "${AMICI_PATH}/build" --parallel -- VERBOSE=1
+
+    - name: Install parPE Python deps
+      run: |
+        pip install -r ${PARPE_BASE}/python/requirements.txt
+
+    - name: Configure parpe
+      run: |
+        CC=mpicc CXX=mpiCC \
+          cmake \
+          -S"${PARPE_BASE}" \
+          -B"${PARPE_BUILD}" \
+          -DIPOPT_INCLUDE_DIRS=/usr/include/coin/ \
+          -DIPOPT_LIBRARIES=/usr/lib/libipopt.so \
+          -DCERES_LIBRARIES="/usr/lib/libceres.so;/usr/lib/x86_64-linux-gnu/libglog.so;/usr/lib/x86_64-linux-gnu/libgflags.so" \
+          -DCERES_INCLUDE_DIRS="/usr/include/;/usr/include/eigen3" \
+          -DMPI_INCLUDE_DIRS=/usr/include/openmpi-x86_64/ \
+          -DGCOVR_REPORT=TRUE \
+          -DBUILD_TESTING=FALSE
+
+    - name: Build parPE
+      run: |
+        cmake --build "${PARPE_BUILD}" --parallel -- VERBOSE=1
+
+    # Actual PEtab test suite
+
+    - name: PEtab test suite --- requirements
+      run: |
+        $PARPE_BASE/misc/run_in_venv.sh $PARPE_BASE/build/venv \
+          pip3 install pytest-xdist
+
+    - name: PEtab test suite --- repository
+      env:
+        PETAB_TEST_URL: https://github.com/PEtab-dev/petab_test_suite.git
+      run: |
+        cd $PARPE_BASE/ \
+          && git clone --depth 1 $PETAB_TEST_URL \
+          && $PARPE_BASE/misc/run_in_venv.sh $PARPE_BASE/build/venv \
+            pip3 install -e petab_test_suite
+
+    - name: PEtab test suite --- tests
+      run: |
+        $PARPE_BASE/misc/run_in_venv.sh $PARPE_BASE/build/venv \
+          pytest -v -n 2 $PARPE_BASE/tests/petab-test-suite
diff --git a/.gitignore b/.gitignore
@@ -5,6 +5,7 @@ CMakeLists.txt.user
 /ThirdParty/*
 /doc/Doxyfile
 /doc/doxy/*
+/doc/exhale_cpp_api/
 .project
 .pydevproject
 .idea/*
@@ -18,6 +19,7 @@ __pycache__/
 */swig/*_wrap.cpp
 /amici/examples/steadystate/model_steadystate_scaled
 /amici/examples/lucarelli/lucarelli_12/lucarelli_12/
+/activate
 
 # snakemake
 .snakemake/
@@ -38,3 +40,8 @@ python/test_*.png
 
 /benchmark_collection/*_*[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/
+
+test_*.png
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -0,0 +1,29 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  builder: html
+  configuration: doc/conf.py
+#  fail_on_warning: True
+
+# Build documentation with MkDocs
+#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
+  install:
+    - requirements: doc/requirements_doc.txt
+
+#build:
+#  image: latest