Merge pull request #1273 from AMICI-dev/release_0_11_7

Release 0.11.7
AMICI-dev · Sep 22, 2020 · d16078e · d16078e
2 parents 7a1dc5e + 3052de7
commit d16078e
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diff --git a/.github/workflows/deploy_branch.yml b/.github/workflows/deploy_branch.yml
@@ -1,11 +1,11 @@
 name: Deploy Branch
 on: [push, pull_request]
-        
+
 jobs:
   sdist:
     name: Deploy Python Source Distribution
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
 
     steps:
     - uses: actions/checkout@v1

diff --git a/.github/workflows/deploy_protected.yml b/.github/workflows/deploy_protected.yml
@@ -13,7 +13,7 @@ jobs:
     # https://github.com/marketplace/actions/publish-docker
     name: Deploy Dockerhub
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
 
     steps:
     - uses: actions/checkout@master

diff --git a/.github/workflows/deploy_release.yml b/.github/workflows/deploy_release.yml
@@ -8,7 +8,7 @@ jobs:
   pages:
     name: Deploy GH-Pages
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
 
     steps:
     - uses: actions/checkout@master
@@ -43,7 +43,7 @@ jobs:
   pypi:
     name: Deploy PyPI
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
 
     steps:
     - uses: actions/checkout@v1

diff --git a/.github/workflows/test_benchmark_collection_models.yml b/.github/workflows/test_benchmark_collection_models.yml
@@ -14,7 +14,7 @@ jobs:
   build:
     name: Benchmark Collection
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
 
     steps:
     - uses: actions/checkout@v1
@@ -26,7 +26,7 @@ jobs:
       run: |
         sudo apt-get update \
           && sudo apt-get install -y swig libatlas-base-dev
-          
+
     - name: pip
       run: |
         pip3 install --upgrade --user wheel \

diff --git a/.github/workflows/test_doc.yml b/.github/workflows/test_doc.yml
@@ -13,7 +13,7 @@ jobs:
   doxygen:
     name: Test Doxygen
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
 
     steps:
     - uses: actions/checkout@master
@@ -35,25 +35,29 @@ jobs:
     - name: Run doxygen
       run: |
         scripts/run-doxygen.sh
-        
+
   sphinx:
     name: Test Sphinx
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
 
     steps:
       - uses: actions/checkout@master
       - run: git fetch --prune --unshallow
-      
+
       - run: echo "::set-env name=AMICI_DIR::$(pwd)"
       - run: echo "::set-env name=SWIG::${AMICI_DIR}/ThirdParty/swig-4.0.1/install/bin/swig"
-
+
+      - name: Build doxygen
+        run: |
+          sudo scripts/downloadAndBuildDoxygen.sh
+
       - name: Set up Python 3.8
         uses: actions/setup-python@v2
         with:
           # Semantic version range syntax or exact version of a Python version
           python-version: '3.8'
-      
+
       # install amici dependencies
       - name: apt
         run: |
@@ -62,16 +66,17 @@ jobs:
               g++ \
               libatlas-base-dev \
               libboost-serialization-dev \
+              pandoc \
               python3-venv \
 
       - name: Build swig
         run: |
           sudo scripts/downloadAndBuildSwig.sh
-              
+
       - name: pip
         run: |
           pip3 install setuptools
-      
+
       - name: sphinx
         run: |
           scripts/run-sphinx.sh
diff --git a/.github/workflows/test_install.yml b/.github/workflows/test_install.yml
@@ -5,7 +5,7 @@ jobs:
   archive:
     name: Archive Install
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
 
     steps:
     - uses: actions/checkout@master
@@ -28,7 +28,7 @@ jobs:
     - name: Build suitesparse
       run: |
         scripts/buildSuiteSparse.sh
-     
+
     - name: Build sundials
       run: |
         scripts/buildSundials.sh
@@ -52,7 +52,7 @@ jobs:
   sdist:
     name: sdist Install
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
 
     steps:
     - uses: actions/checkout@master
@@ -74,9 +74,9 @@ jobs:
     - name: Create AMICI sdist
       run: |
         scripts/buildSdist.sh
-    
+
     - name: Install python sdist
       run: |
         pip3 install -v --user $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)
-                
-        
+
+
diff --git a/.github/workflows/test_large_model.yml → .github/workflows/test_performance.yml b/.github/workflows/test_large_model.yml → .github/workflows/test_performance.yml
@@ -4,16 +4,19 @@ on:
     branches:
       - develop
       - master
+      - speedup
 
   pull_request:
     branches:
       - master
 
+  workflow_dispatch:
+
 jobs:
   build:
     name: Performance Test
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
 
     steps:
     - uses: actions/checkout@v1
@@ -85,3 +88,9 @@ jobs:
     - name: adjoint_sensitivities_non_optimal_parameters
       run: |
         check_time.sh adjoint_sensitivities_non_optimal_parameters tests/performance/test.py adjoint_sensitivities_non_optimal_parameters
+    - name: forward_steadystate_sensitivities_non_optimal_parameters
+      run: |
+        check_time.sh forward_steadystate_sensitivities_non_optimal_parameters tests/performance/test.py forward_steadystate_sensitivities_non_optimal_parameters
+    - name: adjoint_steadystate_sensitivities_non_optimal_parameters
+      run: |
+        check_time.sh adjoint_steadystate_sensitivities_non_optimal_parameters tests/performance/test.py adjoint_steadystate_sensitivities_non_optimal_parameters
diff --git a/.github/workflows/test_petab_test_suite.yml b/.github/workflows/test_petab_test_suite.yml
@@ -14,7 +14,7 @@ jobs:
   build:
     name: PEtab Testsuite
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
 
     env:
       ENABLE_GCOV_COVERAGE: TRUE

diff --git a/.github/workflows/test_python_cplusplus.yml b/.github/workflows/test_python_cplusplus.yml
@@ -6,7 +6,7 @@ jobs:
     name: Tests Ubuntu
 
     # TODO: prepare image with more deps preinstalled
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
 
     env:
       ENABLE_GCOV_COVERAGE: "TRUE"
@@ -49,7 +49,8 @@ jobs:
             libhdf5-serial-dev \
             python3-venv \
             swig \
-            lcov
+            lcov \
+            libboost-math-dev
 
     - name: Build AMICI dependencies
       run: |
@@ -92,17 +93,17 @@ jobs:
         file: ./build/coverage_py.xml
         flags: python
         fail_ci_if_error: true
-      
+
     - name: lcov
       run: |
         lcov --compat-libtool --no-external \
         -d ${AMICI_DIR}/build/CMakeFiles/amici.dir/src \
         -b ${AMICI_DIR} -c -o coverage_cpp.info \
         && lcov --compat-libtool --no-external \
-        -d ${AMICI_DIR}/python/sdist/build/temp.linux-x86_64-3.6/amici/src \
+        -d ${AMICI_DIR}/python/sdist/build/temp.linux-x86_64-$(python3 --version | sed -E 's/.*([0-9]+\.[0-9]+)\..*/\1/')/amici/src \
         -b ${AMICI_DIR}/python/sdist -c -o coverage_py.info \
         && lcov -a coverage_cpp.info -a coverage_py.info -o coverage.info
-      
+
     - name: Codecov CPP
       uses: codecov/codecov-action@v1
       with:
@@ -134,20 +135,20 @@ jobs:
     # install amici dependencies
     - name: homebrew
       run: |
-        brew install hdf5 swig gcc cppcheck libomp
+        brew install hdf5 swig gcc cppcheck libomp boost
 
     - name: Build AMICI
       run: |
         scripts/buildAll.sh
-        
+
     - name: Install python package
       run: |
         scripts/installAmiciSource.sh
-        
+
     - name: cppcheck
       run: |
         scripts/run-cppcheck.sh
-        
+
     - name: Python tests
       run: |
         scripts/run-python-tests.sh

diff --git a/.github/workflows/test_python_ver_matrix.yml b/.github/workflows/test_python_ver_matrix.yml
@@ -13,24 +13,24 @@ jobs:
   build:
     name: Python Version Matrix
 
-    runs-on: ubuntu-latest
-    
+    runs-on: ubuntu-20.04
+
     env:
       AMICI_SKIP_CMAKE_TESTS: "TRUE"
-    
+
     strategy:
       matrix:
         python-version: [3.6, 3.7, 3.8]
 
     steps:
     - run: echo "::set-env name=AMICI_DIR::$(pwd)"
     - run: echo "::set-env name=BNGPATH::${AMICI_DIR}/ThirdParty/BioNetGen-2.3.2"
-    
+
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
-    
+
     - uses: actions/checkout@v1
       with:
         fetch-depth: 20
@@ -42,12 +42,13 @@ jobs:
           && sudo apt-get install -y \
           swig \
           libatlas-base-dev \
-          libhdf5-serial-dev
+          libhdf5-serial-dev \
+          libboost-math-dev
     - name: pip
       run: |
         pip3 install --upgrade --user wheel \
           && pip3 install --upgrade --user setuptools
-          
+
 
     # install AMICI
     - name: Build BNGL
@@ -56,7 +57,7 @@ jobs:
     - name: Install python package
       run: |
         scripts/installAmiciSource.sh
-        
+
     - name: Python tests
       run: |
         source build/venv/bin/activate \

diff --git a/.github/workflows/test_sbml_semantic_test_suite.yml b/.github/workflows/test_sbml_semantic_test_suite.yml
@@ -18,7 +18,7 @@ jobs:
   build:
     name: SBML Semantic Test Suite
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
 
     steps:
     - uses: actions/checkout@v1
@@ -36,7 +36,7 @@ jobs:
       with:
         name: amici-semantic-results
         path: tests/amici-semantic-results
-        
+
     - name: Codecov SBMLSuite
       uses: codecov/codecov-action@v1
       with:

diff --git a/.github/workflows/test_valgrind.yml b/.github/workflows/test_valgrind.yml
@@ -3,6 +3,7 @@ on:
   push:
     branches:
       - master
+      - feature_cpp_hierarchical_derivatives
   pull_request:
     branches:
       - master
@@ -12,7 +13,7 @@ jobs:
     name: Tests Valgrind
 
     # TODO: prepare image with more deps preinstalled
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
 
     steps:
     - uses: actions/checkout@master
@@ -37,4 +38,12 @@ jobs:
 
     - name: C++ tests / Valgrind
       run: |
-        scripts/run-valgrind.sh
+        scripts/run-valgrind-cpp.sh
+        
+    - name: Install python package
+      run: |
+        scripts/installAmiciSource.sh
+    
+    - name: Python tests / Valgrind
+      run: |
+        scripts/run-valgrind-py.sh