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Merge pull request #1159 from ICB-DCM/release_0_11_12
Release 0.11.2
2 parents ffb5f33 + 40575bc commit d220128

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‎.github/workflows/deploy_sdist.yml‎

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run: |
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cd python/sdist && /usr/bin/python3 setup.py sdist
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- name: Archive sdist
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- name: "Upload artifact: sdist"
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uses: actions/upload-artifact@v1
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with:
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name: sdist

‎.github/workflows/sbml-semantic-test-suite.yml‎

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- master
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pull_request:
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paths:
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- python/amici/sbml_import.py
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- .github/workflows/sbml-semantic-test-suite.yml
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- python/amici/ode_export.py
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- python/amici/sbml_import.py
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- scripts/run-SBMLTestsuite.sh
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- tests/testSBMLSuite.py
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check_suite:
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&& sudo ln -s /usr/bin/swig3.0 /usr/bin/swig
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- run: AMICI_PARALLEL_COMPILE=2 ./scripts/installAmiciSource.sh
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- run: AMICI_PARALLEL_COMPILE=2 ./scripts/run-SBMLTestsuite.sh
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- name: "Upload artifact: SBML semantic test suite results"
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uses: actions/upload-artifact@v1
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with:
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name: amici-semantic-results
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path: tests/amici-semantic-results

‎.github/workflows/test-large-model.yml‎

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branches:
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- develop
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- master
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- fix_sx0_zeros
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pull_request:
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branches:
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-y 'FroehlichKes2018/PEtab/FroehlichKes2018.yaml' \
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--no-compile
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- name: "Upload artifact: CS_Signalling_ERBB_RAS_AKT_petab"
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uses: actions/upload-artifact@v1
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with:
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name: CS_Signalling_ERBB_RAS_AKT
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path: CS_Signalling_ERBB_RAS_AKT/CS_Signalling_ERBB_RAS_AKT_petab
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# install model package
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- name: Install test model
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run: |

‎.github/workflows/test_cplusplus_osx.yml‎

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name: C++ testsuite / OSX
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on: [push]
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jobs:
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build:
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name: tests_osx
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runs-on: macos-latest
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env:
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ENABLE_GCOV_COVERAGE: FALSE
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CI_SONARCLOUD: FALSE
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steps:
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- uses: actions/checkout@master
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- run: git fetch --prune --unshallow
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- run: echo "::set-env name=AMICI_DIR::$(pwd)"
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- run: echo "::set-env name=BNGPATH::${AMICI_DIR}/ThirdParty/BioNetGen-2.3.2"
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# install amici dependencies
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- name: homebrew
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run: |
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brew install hdf5 swig gcc cppcheck libomp
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- name: Build suitesparse
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run: |
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scripts/buildSuiteSparse.sh
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- name: Build sundials
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run: |
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scripts/buildSundials.sh
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- name: Build cpputest
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run: |
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scripts/buildCpputest.sh
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- name: Build cpputest
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run: |
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scripts/buildBNGL.sh
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- name: Build AMICI
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run: |
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scripts/buildAmici.sh
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- name: Install python archive
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run: |
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scripts/installAmiciArchive.sh
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- name: Install python package
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run: |
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scripts/installAmiciSource.sh
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- name: cppcheck
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run: |
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scripts/run-cppcheck.sh
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- name: notebooks
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run: |
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scripts/runNotebook.sh python/examples/example_*/
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- name: Python tests
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run: |
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scripts/run-python-tests.sh
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- name: C++ tests
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run: |
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scripts/run-cpputest.sh
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- name: sphinx
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run: |
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scripts/run-sphinx.sh

‎.github/workflows/test_cplusplus_valgrind.yml‎

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branches:
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- develop
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- master
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- feature_1053_sonarcloud
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jobs:
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build:

‎.gitignore‎

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python/examples/example_steadystate/model_steadystate_scaled/*
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python/examples/example_presimulation/model_presimulation/*
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python/examples/example_presimulation/model_presimulation_re/*
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python/examples/example_constant_species/model_constant_species_reduced/*
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python/examples/example_constant_species/model_constant_species/*
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python/sdist/amici.egg-info/*
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python/sdist/amici/version.txt

‎.travis.yml‎

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- CI_PYTHON=TRUE
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- CI_NOTEBOOK=TRUE
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- os: osx
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osx_image: xcode11
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language: minimal
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compiler: clang
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env:
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- CI_BUILD=TRUE
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- CI_CPPUTEST=TRUE
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- CI_ARCHIVE=TRUE
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- CI_CPPCHECK=TRUE
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- CI_PYTHON=TRUE
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- CI_NOTEBOOK=TRUE
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addons:
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homebrew:
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packages:
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- hdf5
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- swig
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- gcc
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- cppcheck
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update: true
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before_install:
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- travis_wait brew link --overwrite gcc # fix linker warning regarding /usr/local/include/c++
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- brew link --overwrite python # https://github.com/ICB-DCM/AMICI/issues/894
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- export -f travis_fold travis_nanoseconds travis_time_start travis_time_finish
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after_success:
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- cd $BASE_DIR # cd to base dir for correct relative path in deploy
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- os: osx
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osx_image: xcode11
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language: minimal

‎documentation/gfx/steadystate_solver_workflow.png‎

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‎include/amici/abstract_model.h‎

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const AmiVector &dx, int ip, const AmiVector &sx,
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const AmiVector &sdx, AmiVector &sxdot) = 0;
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/**
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* @brief Residual function backward when running in steady state mode
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* @param t time
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* @param xB adjoint state
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* @param dxB time derivative of state (DAE only)
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* @param xBdot array to which values of the residual function will be
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* written
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*/
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virtual void fxBdot_ss(const realtype t, const AmiVector &xB,
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const AmiVector &dxB, AmiVector &xBdot) = 0;
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/**
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* @brief Sparse Jacobian function backward, steady state case
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* @param JB sparse matrix to which values of the Jacobian will be written
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*/
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virtual void fJSparseB_ss(SUNMatrix JB) = 0;
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/**
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* @brief Computes the sparse backward Jacobian for steadystate integration
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* and writes it to the model member
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* @param t timepoint
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* @param cj scalar in Jacobian
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* @param x Vector with the states
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* @param dx Vector with the derivative states
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* @param xB Vector with the adjoint states
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* @param dxB Vector with the adjoint derivative states
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* @param xBdot Vector with the adjoint state right hand side
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*/
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virtual void writeSteadystateJB(const realtype t, realtype cj,
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const AmiVector &x, const AmiVector &dx,
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const AmiVector &xB, const AmiVector &dxB,
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const AmiVector &xBdot) = 0;
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/**
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* @brief Dense Jacobian function
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* @param t time
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const AmiVector &dx, const AmiVector &xdot,
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SUNMatrix J) = 0;
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/**
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* @brief Dense Jacobian function
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* @param t time
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* @param cj scaling factor (inverse of timestep, DAE only)
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* @param x state
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* @param dx time derivative of state (DAE only)
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* @param xB Vector with the adjoint states
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* @param dxB Vector with the adjoint derivative states
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* @param xBdot Vector with the adjoint right hand side (unused)
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* @param JB dense matrix to which values of the jacobian will be written
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*/
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virtual void fJB(const realtype t, realtype cj, const AmiVector &x,
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const AmiVector &dx, const AmiVector &xB,
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const AmiVector &dxB, const AmiVector &xBdot,
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SUNMatrix JB) = 0;
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/**
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* @brief Sparse Jacobian function
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* @param t time
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const AmiVector &dx, const AmiVector &xdot,
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SUNMatrix J) = 0;
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/**
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* @brief Sparse Jacobian function
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* @param t time
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* @param cj scaling factor (inverse of timestep, DAE only)
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* @param x state
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* @param dx time derivative of state (DAE only)
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* @param xB Vector with the adjoint states
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* @param dxB Vector with the adjoint derivative states
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* @param xBdot Vector with the adjoint right hand side (unused)
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* @param JB dense matrix to which values of the jacobian will be written
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*/
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virtual void fJSparseB(const realtype t, realtype cj, const AmiVector &x,
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const AmiVector &dx, const AmiVector &xB,
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const AmiVector &dxB, const AmiVector &xBdot,
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SUNMatrix JB) = 0;
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/**
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* @brief Diagonal Jacobian function
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* @param t time

‎include/amici/amici.h‎

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* @param format string with warning message printf-style format
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* @param ... arguments to be formatted
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*/
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void warningF(const char *identifier, const char *format, ...);
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void warningF(const char *identifier, const char *format, ...) const;
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/**
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* @brief printf interface to error()
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* @param identifier warning identifier
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* @param format string with error message printf-style format
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* @param ... arguments to be formatted
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*/
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void errorF(const char *identifier, const char *format, ...);
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void errorF(const char *identifier, const char *format, ...) const;
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/**
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* @brief Checks the values in an array for NaNs and Infs

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