Release 0.11.19

Merge pull request #1568 from AMICI-dev/release_0.11.19

.github/workflows/test_install.yml

@@ -33,10 +33,6 @@ jobs:
       run: |
         scripts/buildSundials.sh
 
-    - name: Build cpputest
-      run: |
-        scripts/buildCpputest.sh
-
     - name: Build AMICI
       run: |
         scripts/buildAmici.sh

.github/workflows/test_petab_test_suite.yml

@@ -44,7 +44,7 @@ jobs:
       - run: |
           echo "${HOME}/.local/bin/" >> $GITHUB_PATH
           echo "${GITHUB_WORKSPACE}/tests/performance/" >> $GITHUB_PATH
-          echo "BNGPATH=${GITHUB_WORKSPACE}/ThirdParty/BioNetGen-2.5.2" >> $GITHUB_ENV
+          echo "BNGPATH=${GITHUB_WORKSPACE}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
 
       # install AMICI
       - name: Install python package

.github/workflows/test_python_cplusplus.yml

@@ -17,7 +17,7 @@ jobs:
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
-    - run: echo "BNGPATH=${GITHUB_WORKSPACE}/ThirdParty/BioNetGen-2.5.2" >> $GITHUB_ENV
+    - run: echo "BNGPATH=${GITHUB_WORKSPACE}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
 
     # sonar cloud
     - run: echo "SONAR_SCANNER_VERSION=4.5.0.2216" >> $GITHUB_ENV
@@ -69,7 +69,7 @@ jobs:
 
     - name: C++ tests
       run: |
-        scripts/run-cpputest.sh
+        scripts/run-cpp-tests.sh
 
     - name: Install python package
       run: |
@@ -85,7 +85,7 @@ jobs:
           --cov-report=xml:"${AMICI_DIR}/build/coverage_py.xml" \
           --cov-append \
           ${AMICI_DIR}/python/tests
-          
+
     - name: example notebooks
       run: |
         scripts/runNotebook.sh python/examples/example_*/
@@ -96,7 +96,7 @@ jobs:
 
     - name: Codecov Python
       uses: codecov/codecov-action@v1
-      with: 
+      with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./build/coverage_py.xml
         flags: python
@@ -138,7 +138,7 @@ jobs:
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
-    - run: echo "BNGPATH=${AMICI_DIR}/ThirdParty/BioNetGen-2.5.2" >> $GITHUB_ENV
+    - run: echo "BNGPATH=${AMICI_DIR}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
 
     # install amici dependencies
     - name: homebrew
@@ -163,4 +163,4 @@ jobs:
 
     - name: C++ tests
       run: |
-        scripts/run-cpputest.sh
+        scripts/run-cpp-tests.sh

.github/workflows/test_python_ver_matrix.yml

@@ -31,7 +31,7 @@ jobs:
 
     steps:
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
-    - run: echo "BNGPATH=${AMICI_DIR}/ThirdParty/BioNetGen-2.5.2" >> $GITHUB_ENV
+    - run: echo "BNGPATH=${AMICI_DIR}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
 
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2

.gitignore

@@ -4,9 +4,9 @@ build/*
 build-debug/*
 build_xcode/*
 swig/python/build/*
-tests/cpputest/build/*
-tests/cpputest/build_xcode/*
-tests/cpputest/Testing/*
+tests/cpp/build/*
+tests/cpp/build_xcode/*
+tests/cpp/Testing/*
 
 doc-venv/*
 doc/*
@@ -136,8 +136,8 @@ tests/test/*
 */tests/fricker_2010_apoptosis_amici/*
 */tests/explicit_amici/*
 */tests/fixed_initial_amici/*
-tests/cpputest/writeResults.h5
-tests/cpputest/writeResults.h5.bak
+tests/cpp/writeResults.h5
+tests/cpp/writeResults.h5.bak
 tests/sbml-test-suite/*
 tests/sbml-test-suite/
 tests/sedml-test-suite/
@@ -171,7 +171,6 @@ AMICI_guide.pdf
 
 ThirdParty/bionetgen.tar.gz
 ThirdParty/BioNetGen-*
-ThirdParty/cpputest-master*
 ThirdParty/doxygen/*
 ThirdParty/mtocpp-master*
 ThirdParty/sundials/build/*

CHANGELOG.md

@@ -2,6 +2,26 @@
 
 ## v0.X Series
 
+### v0.11.19 (2021-10-13)
+
+New:
+* Added support for observable transformations (lin/log/log10) (#1567). Thereby supporting additional noise distributions in combination with least squares solvers.
+
+Fixes:
+* Fixed a bug when Newton sensitivity computation was activated despite specifying newton_steps == 0. The error occurs when simulation converges to a steadystate but simulation sensitivities are not converged according to convergence criteria. In that case simulation returned failure, but the newton rootfinding "finds" a steadystate even before the iteration check, leading to the erroneous computation of sensitivities via Newton/IFT. For singular jacobians this means the overall simulation still fails, but a different, more informative error message is displayed. (#1541)
+* Fixed a bug where argument "outdir" in ODEExporter.__init__ would not be used (#1543)
+
+Other:
+* Improve checking support for SBML extensions (#1546)
+* SBML import: Use more descriptive IDs for flux expressions (#1551)
+* Optimized SUNMatrixWrapper functions (#1538)
+* C++: Changed test suite from CppUTest to gtest (#1532)
+* Add CITATION.cff (#1559)
+* Updated documentation (#1563, #1554, #1536)
+* Removed distutils dependency (#1557)
+* Require sympy<1.9
+
+
 ### v0.11.18 (2021-07-12)
 
 New:

CITATION.cff

@@ -0,0 +1,79 @@
+authors:
+   - 
+     family-names: "Fröhlich"
+     given-names: "Fabian"
+     orcid: "https://orcid.org/0000-0002-5360-4292"
+   - 
+     family-names: "Weindl"
+     given-names: "Daniel"
+     orcid: "https://orcid.org/0000-0001-9963-6057"
+   - 
+     family-names: "Schälte"
+     given-names: "Yannik"
+     orcid: "https://orcid.org/0000-0003-1293-820X"
+   - 
+     family-names: "Pathirana"
+     given-names: "Dilan"
+     orcid: "https://orcid.org/0000-0001-7000-2659"
+   - 
+     family-names: "Paszkowski"
+     given-names: "Lukasz"
+   - 
+     family-names: "Lines"
+     given-names: "Glenn Terje"
+     orcid: "https://orcid.org/0000-0002-6294-1805"
+   - 
+     family-names: "Stapor"
+     given-names: "Paul"
+     orcid: "https://orcid.org/0000-0002-7567-3985"
+   - 
+     family-names: "Hasenauer"
+     given-names: "Jan"
+     orcid: "https://orcid.org/0000-0002-4935-3312"
+title: "AMICI: High-Performance Sensitivity Analysis for Large Ordinary Differential Equation Models"
+
+preferred-citation:
+   type: article
+   title: "AMICI: High-Performance Sensitivity Analysis for Large Ordinary Differential Equation Models"
+   doi: 10.1093/bioinformatics/btab227
+   journal: "Bioinformatics"
+   year: 2021
+   month: 4
+   start: 1
+   end: 1
+   authors:
+      - 
+        family-names: "Fröhlich"
+        given-names: "Fabian"
+        orcid: "https://orcid.org/0000-0002-5360-4292"
+      - 
+        family-names: "Weindl"
+        given-names: "Daniel"
+        orcid: "https://orcid.org/0000-0001-9963-6057"
+      - 
+        family-names: "Schälte"
+        given-names: "Yannik"
+        orcid: "https://orcid.org/0000-0003-1293-820X"
+      - 
+        family-names: "Pathirana"
+        given-names: "Dilan"
+        orcid: "https://orcid.org/0000-0001-7000-2659"
+      - 
+        family-names: "Paszkowski"
+        given-names: "Lukasz"
+      - 
+        family-names: "Lines"
+        given-names: "Glenn Terje"
+        orcid: "https://orcid.org/0000-0002-6294-1805"
+      - 
+        family-names: "Stapor"
+        given-names: "Paul"
+        orcid: "https://orcid.org/0000-0002-7567-3985"
+      - 
+        family-names: "Hasenauer"
+        given-names: "Jan"
+        orcid: "https://orcid.org/0000-0002-4935-3312"
+cff-version: 1.2.0
+message: "If you use this software, please cite both the article from preferred-citation and the software itself."
+url: "https://github.com/AMICI-dev/AMICI"
+doi: 10.5281/zenodo.597928

CMakeLists.txt

@@ -268,7 +268,7 @@ if(BUILD_TESTS)
     if(ENABLE_HDF5)
         enable_testing()
 
-        add_subdirectory(tests/cpputest)
+        add_subdirectory(tests/cpp)
     else()
         message(WARNING "Cannot build tests with ENABLE_HDF5=OFF.")
     endif()