Release 0.11.29

Merge pull request #1793 from AMICI-dev/release_0.11.29

.github/workflows/test_petab_test_suite.yml

@@ -71,20 +71,24 @@ jobs:
       - name: Run PEtab-related unit tests
         run: |
           source ./build/venv/bin/activate \
-            && pytest --cov-report=xml --cov=./ python/tests/test_*petab*.py
+            && pytest --cov-report=xml:coverage.xml \
+              --cov=./ python/tests/test_*petab*.py
 
       # run test models
       - name: Run PEtab test suite
         # git clone --depth 1 https://github.com/petab-dev/petab_test_suite
         run: |
           source ./build/venv/bin/activate \
           && AMICI_PARALLEL_COMPILE=2 pytest -v \
-            --cov-report=xml --cov-append --cov=amici tests/petab_test_suite/
+            --cov-report=xml:coverage.xml \
+            --cov-append \
+            --cov=amici \
+            tests/petab_test_suite/
 
       - name: Codecov
-        uses: codecov/codecov-action@v2
+        uses: codecov/codecov-action@v3.1.0
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
-          file: ./coverage.xml
+          file: coverage.xml
           flags: petab
           fail_ci_if_error: true

.github/workflows/test_python_cplusplus.yml

@@ -104,28 +104,29 @@ jobs:
         scripts/runNotebook.sh documentation/GettingStarted.ipynb
 
     - name: Codecov Python
-      uses: codecov/codecov-action@v2
+      uses: codecov/codecov-action@v3.1.0
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
-        file: ./build/coverage_py.xml
+        file: build/coverage_py.xml
         flags: python
         fail_ci_if_error: true
+        verbose: 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 ${AMICI_DIR}/python/sdist/build/temp.linux-x86_64-$(python3 --version | sed -E 's/.*([0-9]+\.[0-9]+)\..*/\1/')/amici/src \
+        -d ${AMICI_DIR}/python/sdist/build/temp.linux-x86_64-$(python -c "import sys; print(sys.implementation.cache_tag)")/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@v2
+      uses: codecov/codecov-action@v3.1.0
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
-        file: ./coverage.info
+        file: coverage.info
         flags: cpp
         fail_ci_if_error: true
 

.github/workflows/test_sbml_semantic_test_suite.yml

@@ -53,9 +53,9 @@ jobs:
         path: tests/amici-semantic-results
 
     - name: Codecov SBMLSuite
-      uses: codecov/codecov-action@v2
+      uses: codecov/codecov-action@v3.1.0
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
-        file: ./coverage_SBMLSuite.xml
+        file: coverage_SBMLSuite.xml
         flags: sbmlsuite
         fail_ci_if_error: true

CHANGELOG.md

@@ -2,6 +2,30 @@
 
 ## v0.X Series
 
+### v0.11.29 (2022-05-06)
+
+## What's Changed
+
+Features:
+* Performance: Limit newton step convergence check by @FFroehlich in
+  https://github.com/AMICI-dev/AMICI/pull/1780
+* More informative NaN/Inf warnings by @dweindl in
+  https://github.com/AMICI-dev/AMICI/pull/1640
+* SBML import can now handle initial events by @FFroehlich in
+  https://github.com/AMICI-dev/AMICI/pull/1789
+
+Fixes:
+* Avoid error if no measurements in PEtab problem; fixed type handling in
+  PEtab parameter mapping by @dilpath in
+  https://github.com/AMICI-dev/AMICI/pull/1783
+* Fixed substitution of expressions in root and stau by @dilpath in
+  https://github.com/AMICI-dev/AMICI/pull/1784
+* Workaround for PEtab problems with state-dependent noise models by @dweindl
+  in https://github.com/AMICI-dev/AMICI/pull/1791
+
+**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.11.28...v0.11.29
+
+
 ### v0.11.28 (2022-04-08)
 
 New features:

documentation/python_interface.rst

@@ -26,7 +26,7 @@ AMICI can import :term:`SBML` models via the
 Status of SBML support in Python-AMICI
 ++++++++++++++++++++++++++++++++++++++
 
-Python-AMICI currently **passes 1014 out of the 1821 (~56%) test cases** from
+Python-AMICI currently **passes 1030 out of the 1821 (~57%) test cases** from
 the semantic
 `SBML Test Suite <https://github.com/sbmlteam/sbml-test-suite/>`_
 (`current status <https://github.com/AMICI-dev/AMICI/actions>`_).

include/amici/forwardproblem.h

@@ -290,9 +290,11 @@ class ForwardProblem {
      *
      * @param tlastroot pointer to the timepoint of the last event
      * @param seflag Secondary event flag
+     * @param initial_event initial event flag
      */
 
-    void handleEvent(realtype *tlastroot,bool seflag);
+    void handleEvent(realtype *tlastroot, bool seflag,
+                     bool initial_event);
 
     /**
      * @brief Extract output information for events

include/amici/misc.h

@@ -187,6 +187,17 @@ class ContextManager{
     ContextManager(ContextManager &&other) = delete;
 };
 
+
+/**
+ * @brief Convert a flat index to a pair of row/column indices,
+ * assuming row-major order.
+ * @param flat_idx flat index
+ * @param num_cols number of columns of referred to matrix
+ * @return row index, column index
+ */
+auto unravel_index(size_t flat_idx, size_t num_cols)
+    -> std::pair<size_t, size_t>;
+
 } // namespace amici
 
 #endif // AMICI_MISC_H

include/amici/model.h

@@ -34,6 +34,42 @@ void serialize(Archive &ar, amici::Model &m, unsigned int version);
 
 namespace amici {
 
+/**
+ * @brief Describes the various model quantities
+ */
+enum class ModelQuantity {
+    J,
+    JB,
+    Jv,
+    JvB,
+    JDiag,
+    sx,
+    sy,
+    ssigmay,
+    xdot,
+    sxdot,
+    xBdot,
+    x0_rdata,
+    x0,
+    x_rdata,
+    x,
+    dwdw,
+    dwdx,
+    dwdp,
+    y,
+    dydp,
+    dydx,
+    w,
+    root,
+    qBdot,
+    qBdot_ss,
+    xBdot_ss,
+    JSparseB_ss,
+};
+
+extern const std::map<ModelQuantity, std::string> model_quantity_to_str;
+
+
 /**
  * @brief The Model class represents an AMICI ODE/DAE model.
  *
@@ -61,7 +97,8 @@ class Model : public AbstractModel, public ModelDimensions {
           SimulationParameters simulation_parameters,
           amici::SecondOrderMode o2mode,
           std::vector<amici::realtype> idlist,
-          std::vector<int> z2event, bool pythonGenerated = false,
+          std::vector<int> z2event,
+          bool pythonGenerated = false,
           int ndxdotdp_explicit = 0, int ndxdotdx_explicit = 0,
           int w_recursion_depth = 0);
 
@@ -166,9 +203,11 @@ class Model : public AbstractModel, public ModelDimensions {
      * @param sdx Reference to time derivative of state sensitivities (DAE only)
      * @param computeSensitivities Flag indicating whether sensitivities are to
      * be computed
+     * @param roots_found boolean indicators indicating whether roots were found at t0 by this fun
      */
     void initialize(AmiVector &x, AmiVector &dx, AmiVectorArray &sx,
-                    AmiVectorArray &sdx, bool computeSensitivities);
+                    AmiVectorArray &sdx, bool computeSensitivities,
+                    std::vector<int> &roots_found);
 
     /**
      * @brief Initialize model properties.
@@ -200,8 +239,10 @@ class Model : public AbstractModel, public ModelDimensions {
      *
      * @param x Reference to state variables
      * @param dx Reference to time derivative of states (DAE only)
+     * @param roots_found boolean indicators indicating whether roots were found at t0 by this fun
      */
-    void initHeaviside(const AmiVector &x, const AmiVector &dx);
+    void initEvents(const AmiVector &x, const AmiVector &dx,
+                    std::vector<int> &roots_found);
 
     /**
      * @brief Get number of parameters wrt to which sensitivities are computed.
@@ -1201,18 +1242,43 @@ class Model : public AbstractModel, public ModelDimensions {
      */
     void updateHeavisideB(const int *rootsfound);
 
+
+    /**
+     * @brief Check if the given array has only finite elements.
+     *
+     * For (1D) spans.
+     *
+     * @param array
+     * @param model_quantity The model quantity `array` corresponds to
+     * @return
+     */
+    int checkFinite(gsl::span<const realtype> array,
+                           ModelQuantity model_quantity) const;
+    /**
+     * @brief Check if the given array has only finite elements.
+     *
+     * For flattened 2D arrays.
+     *
+     * @param array Flattened matrix
+     * @param model_quantity The model quantity `array` corresponds to
+     * @param num_cols Number of columns of the non-flattened matrix
+     * @return
+     */
+    int checkFinite(gsl::span<const realtype> array,
+                    ModelQuantity model_quantity,
+                    size_t num_cols) const;
+
     /**
      * @brief Check if the given array has only finite elements.
      *
-     * If not, try to give hints by which other fields this could be caused.
+     * For SUNMatrix.
      *
-     * @param array Array to check
-     * @param fun Name of the function that generated the values (for more
-     * informative messages).
-     * @return `amici::AMICI_RECOVERABLE_ERROR` if a NaN/Inf value was found,
-     * `amici::AMICI_SUCCESS` otherwise
+     * @param m Matrix to check
+     * @param model_quantity The model quantity `m` corresponds to
+     * @param t current timepoint
+     * @return
      */
-    int checkFinite(gsl::span<const realtype> array, const char *fun) const;
+    int checkFinite(SUNMatrix m, ModelQuantity model_quantity, realtype t) const;
 
     /**
      * @brief Set whether the result of every call to `Model::f*` should be
@@ -1803,6 +1869,11 @@ class Model : public AbstractModel, public ModelDimensions {
     /** vector of bools indicating whether state variables are to be assumed to
      * be positive */
     std::vector<bool> state_is_non_negative_;
+
+    /** Vector of booleans indicating the initial boolean value for every event trigger function. Events at t0
+     * can only trigger if the initial value is set to `false`. Must be specified during model compilation by
+     * setting the `initialValue` attribute of an event trigger. */
+    std::vector<bool> root_initial_values_;
 
     /** boolean indicating whether any entry in stateIsNonNegative is `true` */
     bool any_state_non_negative_ {false};

include/amici/sundials_matrix_wrapper.h

@@ -532,6 +532,16 @@ class SUNMatrixWrapper {
     bool ownmat = true;
 };
 
+
+/**
+ * @brief Convert a flat index to a pair of row/column indices.
+ * @param i flat index
+ * @param m referred to matrix
+ * @return row index, column index
+ */
+auto unravel_index(sunindextype i, SUNMatrix m)
+    -> std::pair<sunindextype, sunindextype>;
+
 } // namespace amici
 
 namespace gsl {