Merge pull request #1159 from ICB-DCM/release_0_11_12

Release 0.11.2

.github/workflows/deploy_sdist.yml

@@ -26,7 +26,7 @@ jobs:
       run: |
         cd python/sdist && /usr/bin/python3 setup.py sdist
 
-    - name: Archive sdist
+    - name: "Upload artifact: sdist"
       uses: actions/upload-artifact@v1
       with:
         name: sdist

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

@@ -6,8 +6,9 @@ on:
       - master
   pull_request:
     paths:
-      - python/amici/sbml_import.py
+      - .github/workflows/sbml-semantic-test-suite.yml
       - python/amici/ode_export.py
+      - python/amici/sbml_import.py
       - scripts/run-SBMLTestsuite.sh
       - tests/testSBMLSuite.py
   check_suite:
@@ -30,3 +31,9 @@ jobs:
           && sudo ln -s /usr/bin/swig3.0 /usr/bin/swig
     - run: AMICI_PARALLEL_COMPILE=2 ./scripts/installAmiciSource.sh
     - run: AMICI_PARALLEL_COMPILE=2 ./scripts/run-SBMLTestsuite.sh
+
+    - name: "Upload artifact: SBML semantic test suite results"
+      uses: actions/upload-artifact@v1
+      with:
+        name: amici-semantic-results
+        path: tests/amici-semantic-results

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

@@ -4,7 +4,6 @@ on:
     branches:
       - develop
       - master
-      - fix_sx0_zeros
 
   pull_request:
     branches:
@@ -59,6 +58,12 @@ jobs:
             -y 'FroehlichKes2018/PEtab/FroehlichKes2018.yaml' \
             --no-compile
 
+    - name: "Upload artifact: CS_Signalling_ERBB_RAS_AKT_petab"
+      uses: actions/upload-artifact@v1
+      with:
+        name: CS_Signalling_ERBB_RAS_AKT
+        path: CS_Signalling_ERBB_RAS_AKT/CS_Signalling_ERBB_RAS_AKT_petab
+
     # install model package
     - name: Install test model
       run: |

.github/workflows/test_cplusplus_osx.yml

@@ -0,0 +1,72 @@
+name: C++ testsuite / OSX
+on: [push]
+
+jobs:
+  build:
+    name: tests_osx
+
+    runs-on: macos-latest
+
+    env:
+      ENABLE_GCOV_COVERAGE: FALSE
+      CI_SONARCLOUD: FALSE
+
+    steps:
+    - uses: actions/checkout@master
+    - run: git fetch --prune --unshallow
+
+    - run: echo "::set-env name=AMICI_DIR::$(pwd)"
+    - run: echo "::set-env name=BNGPATH::${AMICI_DIR}/ThirdParty/BioNetGen-2.3.2"
+
+    # install amici dependencies
+    - name: homebrew
+      run: |
+        brew install hdf5 swig gcc cppcheck libomp
+
+    - name: Build suitesparse
+      run: |
+        scripts/buildSuiteSparse.sh
+
+    - name: Build sundials
+      run: |
+        scripts/buildSundials.sh
+
+    - name: Build cpputest
+      run: |
+        scripts/buildCpputest.sh
+
+    - name: Build cpputest
+      run: |
+        scripts/buildBNGL.sh
+
+    - name: Build AMICI
+      run: |
+        scripts/buildAmici.sh
+    
+    - name: Install python archive
+      run: |
+        scripts/installAmiciArchive.sh
+        
+    - name: Install python package
+      run: |
+        scripts/installAmiciSource.sh
+        
+    - name: cppcheck
+      run: |
+        scripts/run-cppcheck.sh
+        
+    - name: notebooks
+      run: |
+        scripts/runNotebook.sh python/examples/example_*/
+        
+    - name: Python tests
+      run: |
+        scripts/run-python-tests.sh
+
+    - name: C++ tests
+      run: |
+        scripts/run-cpputest.sh
+        
+    - name: sphinx
+      run: |
+        scripts/run-sphinx.sh

.github/workflows/test_cplusplus_valgrind.yml

@@ -4,8 +4,6 @@ on:
     branches:
       - develop
       - master
-      - feature_1053_sonarcloud
-
 
 jobs:
   build:

.gitignore

@@ -144,6 +144,8 @@ petab_test_suite
 python/examples/example_steadystate/model_steadystate_scaled/*
 python/examples/example_presimulation/model_presimulation/*
 python/examples/example_presimulation/model_presimulation_re/*
+python/examples/example_constant_species/model_constant_species_reduced/*
+python/examples/example_constant_species/model_constant_species/*
 
 python/sdist/amici.egg-info/*
 python/sdist/amici/version.txt

.travis.yml

@@ -69,32 +69,6 @@ matrix:
         - CI_PYTHON=TRUE
         - CI_NOTEBOOK=TRUE
 
-    - os: osx
-      osx_image: xcode11
-      language: minimal
-      compiler: clang
-      env:
-        - CI_BUILD=TRUE
-        - CI_CPPUTEST=TRUE
-        - CI_ARCHIVE=TRUE
-        - CI_CPPCHECK=TRUE
-        - CI_PYTHON=TRUE
-        - CI_NOTEBOOK=TRUE
-      addons:
-        homebrew:
-          packages:
-            - hdf5
-            - swig
-            - gcc
-            - cppcheck
-          update: true
-      before_install:
-        - travis_wait brew link --overwrite gcc # fix linker warning regarding /usr/local/include/c++
-        - brew link --overwrite python # https://github.com/ICB-DCM/AMICI/issues/894
-        - export -f travis_fold travis_nanoseconds travis_time_start travis_time_finish
-      after_success:
-        - cd $BASE_DIR # cd to base dir for correct relative path in deploy
-
     - os: osx
       osx_image: xcode11
       language: minimal

include/amici/abstract_model.h

@@ -68,6 +68,39 @@ class AbstractModel {
                         const AmiVector &dx, int ip, const AmiVector &sx,
                         const AmiVector &sdx, AmiVector &sxdot) = 0;
 
+    /**
+     * @brief Residual function backward when running in steady state mode
+     * @param t time
+     * @param xB adjoint state
+     * @param dxB time derivative of state (DAE only)
+     * @param xBdot array to which values of the residual function will be
+     * written
+     */
+    virtual void fxBdot_ss(const realtype t, const AmiVector &xB,
+                           const AmiVector &dxB, AmiVector &xBdot) = 0;
+
+    /**
+     * @brief Sparse Jacobian function backward, steady state case
+     * @param JB sparse matrix to which values of the Jacobian will be written
+     */
+    virtual void fJSparseB_ss(SUNMatrix JB) = 0;
+
+    /**
+     * @brief Computes the sparse backward Jacobian for steadystate integration
+     * and writes it to the model member
+     * @param t timepoint
+     * @param cj scalar in Jacobian
+     * @param x Vector with the states
+     * @param dx Vector with the derivative states
+     * @param xB Vector with the adjoint states
+     * @param dxB Vector with the adjoint derivative states
+     * @param xBdot Vector with the adjoint state right hand side
+     */
+    virtual void writeSteadystateJB(const realtype t, realtype cj,
+                                    const AmiVector &x, const AmiVector &dx,
+                                    const AmiVector &xB, const AmiVector &dxB,
+                                    const AmiVector &xBdot) = 0;
+
     /**
      * @brief Dense Jacobian function
      * @param t time
@@ -81,6 +114,22 @@ class AbstractModel {
                     const AmiVector &dx, const AmiVector &xdot,
                     SUNMatrix J) = 0;
 
+    /**
+     * @brief Dense Jacobian function
+     * @param t time
+     * @param cj scaling factor (inverse of timestep, DAE only)
+     * @param x state
+     * @param dx time derivative of state (DAE only)
+     * @param xB Vector with the adjoint states
+     * @param dxB Vector with the adjoint derivative states
+     * @param xBdot Vector with the adjoint right hand side (unused)
+     * @param JB dense matrix to which values of the jacobian will be written
+     */
+    virtual void fJB(const realtype t, realtype cj, const AmiVector &x,
+                     const AmiVector &dx, const AmiVector &xB,
+                     const AmiVector &dxB, const AmiVector &xBdot,
+                     SUNMatrix JB) = 0;
+
     /**
      * @brief Sparse Jacobian function
      * @param t time
@@ -94,6 +143,22 @@ class AbstractModel {
                           const AmiVector &dx, const AmiVector &xdot,
                           SUNMatrix J) = 0;
 
+    /**
+     * @brief Sparse Jacobian function
+     * @param t time
+     * @param cj scaling factor (inverse of timestep, DAE only)
+     * @param x state
+     * @param dx time derivative of state (DAE only)
+     * @param xB Vector with the adjoint states
+     * @param dxB Vector with the adjoint derivative states
+     * @param xBdot Vector with the adjoint right hand side (unused)
+     * @param JB dense matrix to which values of the jacobian will be written
+     */
+    virtual void fJSparseB(const realtype t, realtype cj, const AmiVector &x,
+                           const AmiVector &dx, const AmiVector &xB,
+                           const AmiVector &dxB, const AmiVector &xBdot,
+                           SUNMatrix JB) = 0;
+
     /**
      * @brief Diagonal Jacobian function
      * @param t time

include/amici/amici.h

@@ -87,15 +87,15 @@ class AmiciApplication {
      * @param format string with warning message printf-style format
      * @param ... arguments to be formatted
      */
-    void warningF(const char *identifier, const char *format, ...);
+    void warningF(const char *identifier, const char *format, ...) const;
 
     /**
      * @brief printf interface to error()
      * @param identifier warning identifier
      * @param format string with error message printf-style format
      * @param ... arguments to be formatted
      */
-    void errorF(const char *identifier, const char *format, ...);
+    void errorF(const char *identifier, const char *format, ...) const;
 
     /**
      * @brief Checks the values in an array for NaNs and Infs

include/amici/defines.h

@@ -29,6 +29,8 @@ constexpr int AMICI_ERR_FAILURE=              -3;
 constexpr int AMICI_CONV_FAILURE=             -4;
 constexpr int AMICI_ILL_INPUT=               -22;
 constexpr int AMICI_ERROR=                   -99;
+constexpr int AMICI_NO_STEADY_STATE=         -81;
+constexpr int AMICI_DAMPING_FACTOR_ERROR=    -86;
 constexpr int AMICI_SINGULAR_JACOBIAN=      -807;
 constexpr int AMICI_NOT_IMPLEMENTED=        -999;
 constexpr int AMICI_SUCCESS=                   0;
@@ -136,11 +138,21 @@ enum class SteadyStateSensitivityMode {
 };
 
 /** State in which the steady state computation finished */
-enum class NewtonStatus {
-    failed=-1,
-    newt=1,
-    newt_sim=2,
-    newt_sim_newt=3,
+enum class SteadyStateStatus {
+    failed_too_long_simulation = -5,
+    failed_damping = -4,
+    failed_factorization = -3,
+    failed_convergence = -2,
+    failed = -1,
+    not_run = 0,
+    success = 1
+};
+
+/** Context for which the sensitivity flag should be computed */
+enum class SteadyStateContext {
+    newtonSensi = 0,
+    sensiStorage = 1,
+    solverCreation = 2
 };
 
 /** Damping factor flag for the Newton method */

include/amici/exception.h

@@ -4,6 +4,7 @@
 #include "amici/defines.h" // necessary for realtype
 
 #include <exception>
+#include <array>
 
 namespace amici {
 
@@ -19,13 +20,13 @@ class AmiException : public std::exception {
      * @param fmt error message with printf format
      * @param ... printf formating variables
      */
-    AmiException(char const* fmt, ...);
+    explicit AmiException(char const* fmt, ...);
 
     /**
-     * @brief Copy constructor
-     * @param old object to copy from
+     * @brief Move constructor
+     * @param old object to move from
      */
-    AmiException(const AmiException& old);
+    AmiException(AmiException&& old) noexcept;
 
     /**
      * @brief Override of default error message function
@@ -46,8 +47,8 @@ class AmiException : public std::exception {
     void storeBacktrace(int nMaxFrames);
 
 private:
-    char msg[500]{};
-    char trace[500]{};
+    std::array<char, 500> msg;
+    std::array<char, 500> trace;
 };