Merge pull request #1034 from ICB-DCM/release_v0.10.21

Release v0.10.21

Author: dweindl

.coveragerc

@@ -0,0 +1,18 @@
+[run]
+
+source = amici
+omit =
+    */amici.py
+    */amici_without_hdf5.py
+    */ThirdParty/*
+    *.template.*
+parallel = true
+
+[report]
+
+exclude_lines =
+    pragma: no cover
+    raise
+    except:
+    import
+

.github/workflows/test-petab-test-suite.yml

@@ -47,18 +47,19 @@ jobs:
       run: |
         AMICI_PARALLEL_COMPILE=2 check_time.sh \
             install_sdist pip3 install -v --user \
-            $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)[petab]
+            $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)[petab,pysb]
 
     - name: Run PEtab-related unit tests
       run: |
-        pytest --cov-report=xml --cov=./ tests/testMisc.py
+        pytest --cov-report=xml --cov=./ python/tests/test_*petab*.py
 
     # retrieve test models
     - name: Download and run petab test suite
       run: |
         git clone --depth 1 https://github.com/petab-dev/petab_test_suite \
           && cd petab_test_suite; pip3 install -e .; cd .. \
-          && AMICI_PARALLEL_COMPILE=2 pytest -v --cov-report=xml --cov-append --cov=./ tests/petab_test_suite/
+          && AMICI_PARALLEL_COMPILE=2 pytest -v \
+            --cov-report=xml --cov-append --cov=amici tests/petab_test_suite/
 
     - name: Codecov
       uses: codecov/codecov-action@v1.0.6

.gitignore

@@ -104,29 +104,29 @@ python/testSpeedy.py
 python/test.txt
 
 tests/test/*
-tests/test_model_steadystate_scaled/*
-tests/test_model_presimulation/*
-tests/test_model_presimulation_pysb/*
-tests/test_model_presimulation_sbml/*
-tests/test_likelihoods/*
-tests/bax_pore_sequential_amici/*
-tests/bax_pore_amici/*
-tests/bngwiki_egfr_simple_amici/*
-tests/bngwiki_egfr_simple_deletemolecules_amici/*
-tests/earm_1_3_amici/*
-tests/earm_1_0_amici/*
-tests/expression_observables_amici/*
-tests/robertson_amici/*
-tests/tyson_oscillator_amici/*
-tests/bngwiki_simple_amici/*
-tests/bngwiki_enzymatic_cycle_mm_amici/*
-tests/move_connected_amici/*
-tests/michment_amici/*
-tests/kinase_cascade_amici/*
-tests/hello_pysb_amici/*
-tests/fricker_2010_apoptosis_amici/*
-tests/explicit_amici/*
-tests/fixed_initial_amici/*
+*/tests/test_model_steadystate_scaled/*
+*/tests/test_model_presimulation/*
+*/tests/test_model_presimulation_pysb/*
+*/tests/test_model_presimulation_sbml/*
+*/tests/test_likelihoods/*
+*/tests/bax_pore_sequential_amici/*
+*/tests/bax_pore_amici/*
+*/tests/bngwiki_egfr_simple_amici/*
+*/tests/bngwiki_egfr_simple_deletemolecules_amici/*
+*/tests/earm_1_3_amici/*
+*/tests/earm_1_0_amici/*
+*/tests/expression_observables_amici/*
+*/tests/robertson_amici/*
+*/tests/tyson_oscillator_amici/*
+*/tests/bngwiki_simple_amici/*
+*/tests/bngwiki_enzymatic_cycle_mm_amici/*
+*/tests/move_connected_amici/*
+*/tests/michment_amici/*
+*/tests/kinase_cascade_amici/*
+*/tests/hello_pysb_amici/*
+*/tests/fricker_2010_apoptosis_amici/*
+*/tests/explicit_amici/*
+*/tests/fixed_initial_amici/*
 tests/cpputest/writeResults.h5
 tests/cpputest/writeResults.h5.bak
 tests/sbml-test-suite/*

.travis.yml

@@ -78,7 +78,6 @@ matrix:
       env:
         - CI_BUILD=TRUE
         - CI_CPPUTEST=TRUE
-        - CI_CMAKE=TRUE
         - CI_ARCHIVE=TRUE
         - CI_CPPCHECK=TRUE
         - CI_PYTHON=TRUE
@@ -185,7 +184,6 @@ script:
     - if [[ "$CI_PYTHON" == "TRUE" ]] && [[ "$ENABLE_GCOV_COVERAGE" == "TRUE" ]]; then $FOLD codecov ./scripts/run-codecov.sh; fi
     - if [[ "$CI_PYTHON" == "TRUE" ]] && [[ "$ENABLE_GCOV_COVERAGE" != "TRUE" ]]; then $FOLD python-tests ./scripts/run-python-tests.sh; fi
     # needs to be run after python tests
-    - if [[ "$CI_CMAKE" == "TRUE" ]]; then $FOLD cmake ./tests/testCMakeCompilation.sh; fi
     - if [[ "$CI_CPPUTEST" == "TRUE" ]] && [[ "$TRAVIS_OS_NAME" == "linux" ]]; then $FOLD valgrind ./scripts/run-valgrind.sh; fi
     - if [[ "$CI_CPPUTEST" == "TRUE" ]] && [[ "$TRAVIS_OS_NAME" != "linux" ]]; then $FOLD cpputest ./scripts/run-cpputest.sh; fi
     - if [[ "$CI_DOC" == "TRUE" ]]; then $FOLD doxygen ./scripts/run-doxygen.sh; fi

documentation/_templates/autosummary/class.rst

@@ -5,7 +5,9 @@
 .. autoclass:: {{ objname }}
 
    {% block methods %}
+   {% if '__init__' in methods %}
    .. automethod:: __init__
+   {% endif %}
    {% if methods %}
    .. rubric:: Methods Summary
    .. autosummary::

documentation/conf.py

@@ -344,6 +344,7 @@ def fix_typehints(sig: str) -> str:
     sig = sig.replace('char const *', 'str')
     sig = sig.replace('amici::', '')
     sig = sig.replace('sunindextype', 'int')
+    sig = sig.replace('H5::H5File', 'object')
 
     # enum classes
     for ec in ['SteadyStateSensitivityMode', 'InternalSensitivityMethod',
@@ -418,9 +419,7 @@ def skip_member(app, what, name, obj, skip, options):
                'Model_DAE', 'ConditionContext', 'checkSigmaPositivity',
                'createGroup', 'createGroup', 'equals', 'printErrMsgIdAndTxt',
                'wrapErrHandlerFn', 'printWarnMsgIdAndTxt',
-               'AmiciApplication', 'writeSimulationExpData', 'writeReturnData',
-               'readSimulationExpData', 'readSolverSettingsFromHDF5',
-               'readModelDataFromHDF5', 'createOrOpenForWriting',
+               'AmiciApplication', 'writeReturnData',
                'writeReturnDataDiagnosis', 'attributeExists', 'locationExists',
                'createAndWriteDouble1DDataset',
                'createAndWriteDouble2DDataset',

documentation/rtd_requirements.txt

@@ -7,5 +7,5 @@ pkgconfig>=1.5.1
 nbsphinx>=0.5.1
 recommonmark>=0.6.0
 sphinx_rtd_theme>=0.4.3
-petab>=0.1.3
+petab>=0.1.5
 sphinx-autodoc-typehints>=1.10.3

include/amici/hdf5.h

@@ -42,13 +42,33 @@ H5::H5File createOrOpenForWriting(std::string const &hdf5filename);
 
 /**
  * @brief Read solver options from HDF5 file
- * @param fileId hdf5 file handle to read from
+ * @param file hdf5 file handle to read from
  * @param solver solver to set options on
  * @param datasetPath Path inside the HDF5 file
  */
 void readSolverSettingsFromHDF5(const H5::H5File &file, Solver &solver,
                                 std::string const &datasetPath);
 
+/**
+ * @brief Write solver options from HDF5 file
+ * @param hdf5Filenamehdf5 Name of HDF5 file
+ * @param solver solver to write options from
+ * @param hdf5Location Path inside the HDF5 file
+ */
+void writeSolverSettingsToHDF5(Solver const& solver,
+                              std::string const& hdf5Filename,
+                              std::string const& hdf5Location);
+
+/**
+ * @brief Write solver options from HDF5 file
+ * @param file file handle to read from
+ * @param solver solver to write options from
+ * @param hdf5Location Path inside the HDF5 file
+ */
+void writeSolverSettingsToHDF5(Solver const& solver,
+                              H5::H5File const& file,
+                              std::string const& hdf5Location);
+
 /**
  * @brief Read solver options from HDF5 file
  * @param hdffile Name of HDF5 file

matlab/mtoc/config/Doxyfile.template

@@ -697,7 +697,8 @@ EXCLUDE_PATTERNS       = "_SourceDir_/models/*" \
                          "_SourceDir_/matlab/mtoc/*" \
                          "_SourceDir_/matlab/auxiliary/*" \
                          "_SourceDir_/matlab/SBMLImporter/*" \
-                         "_SourceDir_/python/test/*" \
+                         "_SourceDir_/matlab/tests/*" \
+                         "_SourceDir_/python/tests/*" \
                          "_SourceDir_/python/sdist/*" \
                          "_SourceDir_/python/examples/example_*/model_*" \
                          "_SourceDir_/build/*" \