Release 0.11.18

Merge pull request #1531 from AMICI-dev/release_0.11.18

.github/workflows/deploy_release.yml

@@ -33,3 +33,28 @@ jobs:
         password: ${{ secrets.pypi_password }}
         packages_dir: python/sdist/dist
 
+  bioSimulatorsUpdateCliAndDockerImage:
+    name: Release to BioSimulators
+    needs: pypi
+    runs-on: ubuntu-latest
+    env:
+      # Owner/repository-id for the GitHub repository for the downstream command-line interface and Docker image
+      DOWNSTREAM_REPOSITORY: biosimulators/Biosimulators_AMICI
+
+      # Username/token to use the GitHub API to trigger an action on the GitHub repository for the downstream
+      # command-line interface and Docker image. Tokens can be generated at https://github.com/settings/tokens.
+      # The token should have the scope `repo`
+      GH_ISSUE_USERNAME: ${{ secrets.BIOSIMULATORS_USERNAME }}
+      GH_ISSUE_TOKEN: ${{ secrets.BIOSIMULATORS_TOKEN }}
+    steps:
+      - name: Trigger GitHub action that will build and release the downstream command-line interface and Docker image
+        run: |
+          PACKAGE_VERSION="${GITHUB_REF/refs\/tags\/v/}"
+          WORKFLOW_FILE=ci.yml
+
+          curl \
+            -X POST \
+            -u ${GH_ISSUE_USERNAME}:${GH_ISSUE_TOKEN} \
+            -H "Accept: application/vnd.github.v3+json" \
+              https://api.github.com/repos/${DOWNSTREAM_REPOSITORY}/actions/workflows/${WORKFLOW_FILE}/dispatches \
+            -d "{\"ref\": \"dev\", \"inputs\": {\"simulatorVersion\": \"${PACKAGE_VERSION}\", \"simulatorVersionLatest\": \"true\"}}"

.github/workflows/test_windows.yml

@@ -33,7 +33,7 @@ jobs:
         python -m pip install --upgrade pip \
           && pip install pytest petab \
           && choco install -y ninja \
-          && choco install -y swig --version=4.0.1
+          && choco install -y swig
 
     - name: Install OpenBLAS
       shell: powershell

CHANGELOG.md

@@ -2,6 +2,30 @@
 
 ## v0.X Series
 
+### v0.11.18 (2021-07-12)
+
+New:
+* Allow specifying maximum integration time via
+  `amici::Solver::setMaxTime()` (#1530)
+* Py: Add `failfast` and `num_threads` argument to `simulate_petab`
+  (#1528, #1524)
+* Enable typehints / static type checking for AMICI-generated model modules
+  (#1514) (`amici.ModelModule`, available with Python>=3.8)
+
+Fixes:
+* Python: Fix unused argument `generate_sensitivity_code` in `pysb2amici`
+  (#1526)
+* Python: Fix C(++) stdout redirection which could have let to deadlocks in
+  exotic situations (#1529)
+* Py: Fixed deprecation warning (#1525)
+* Py: Proper typehints for SWIG interface (#1523), enabling better static type
+  checking and IDE integration (available with Python>=3.9)
+* C++: Fixed clang compiler warning (#1521)
+* C++: Fix inherited variadic ctor in exception class (#1520)
+* PEtab: More informative output for unhandled species overrides (#1519)
+* Return SbmlImporter from PEtab model import (#1517)
+
+
 ### v0.11.17 (2021-05-30)
 
 Fixes:

include/amici/defines.h

@@ -68,12 +68,14 @@ constexpr int AMICI_TOO_MUCH_WORK=            -1;
 constexpr int AMICI_TOO_MUCH_ACC=             -2;
 constexpr int AMICI_ERR_FAILURE=              -3;
 constexpr int AMICI_CONV_FAILURE=             -4;
+constexpr int AMICI_RHSFUNC_FAIL=             -8;
 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=      -809;
 constexpr int AMICI_NOT_IMPLEMENTED=        -999;
+constexpr int AMICI_MAX_TIME_EXCEEDED  =   -1000;
 constexpr int AMICI_SUCCESS=                   0;
 constexpr int AMICI_DATA_RETURN=               1;
 constexpr int AMICI_ROOT_RETURN=               2;

include/amici/exception.h

@@ -15,6 +15,13 @@ namespace amici {
  */
 class AmiException : public std::exception {
 public:
+    /**
+     * @brief Constructor with printf style interface
+     * @param fmt error message with printf format
+     * @param ... printf formatting variables
+     */
+    AmiException();
+
     /**
      * @brief Constructor with printf style interface
      * @param fmt error message with printf format
@@ -40,6 +47,14 @@ class AmiException : public std::exception {
      */
     void storeBacktrace(int nMaxFrames);
 
+  protected:
+    /**
+     * @brief Store the provided message
+     * @param fmt error message with printf format
+     * @param argptr pointer to variadic argument list
+     */
+    void storeMessage(const char *fmt, va_list argptr);
+
 private:
     std::array<char, 500> msg_;
     std::array<char, 500> trace_;
@@ -131,7 +146,13 @@ class IntegrationFailureB : public AmiException  {
  */
 class SetupFailure : public AmiException {
   public:
-    using AmiException::AmiException;
+    /**
+     * @brief Constructor with printf style interface
+     * @param fmt error message with printf format
+     * @param ... printf formatting variables
+     */
+    explicit SetupFailure(char const* fmt, ...);
+
 };
 
 

include/amici/model_dimensions.h

@@ -148,12 +148,12 @@ struct ModelDimensions {
      */
     int ndwdw {0};
 
-    /** Number of nonzero elements in the \f$w\f$ derivative of \f$xdot\f$ */
+    /** Number of nonzero elements in the \f$ w \f$ derivative of \f$ xdot \f$ */
     int ndxdotdw {0};
 
     /**
-     * Number of nonzero elements in the \f$y\f$ derivative of
-     * \f$dJy\f$ (dimension `nytrue`)
+     * Number of nonzero elements in the \f$ y \f$ derivative of
+     * \f$ dJy \f$ (dimension `nytrue`)
      */
     std::vector<int> ndJydy;
 

include/amici/serialization.h

@@ -9,6 +9,7 @@
 #include <cassert>
 #include <fstream>
 #include <iostream>
+#include <chrono>
 
 #include <boost/serialization/array.hpp>
 #include <boost/serialization/vector.hpp>
@@ -83,6 +84,24 @@ void serialize(Archive &ar, amici::Solver &s, const unsigned int /*version*/) {
     ar &s.cpu_time_;
     ar &s.cpu_timeB_;
     ar &s.rdata_mode_;
+    ar &s.maxtime_;
+}
+
+/**
+ * @brief Serialize std::chrono::duration to boost archive
+ * @param ar Archive
+ * @param d Duration
+ */
+template <class Archive, class Period, class Rep>
+void serialize(Archive &ar, std::chrono::duration<Period, Rep> &d, const unsigned int /*version*/) {
+    Period tmp_period;
+    if (Archive::is_loading::value) {
+        ar &tmp_period;
+        d = std::chrono::duration<Period, Rep>(tmp_period);
+    } else {
+        tmp_period = d.count();
+        ar &tmp_period;
+    }
 }
 
 /**

include/amici/solver.h

@@ -10,6 +10,7 @@
 #include <cmath>
 #include <functional>
 #include <memory>
+#include <chrono>
 
 namespace amici {
 
@@ -47,6 +48,9 @@ namespace amici {
  */
 class Solver {
   public:
+    /** Type of what is passed to Sundials solvers as user_data */
+    using user_data_type = std::pair<Model *, Solver const*>;
+
     Solver() = default;
 
     /**
@@ -468,6 +472,30 @@ class Solver {
      */
     void setMaxSteps(long int maxsteps);
 
+    /**
+     * @brief Returns the maximum time allowed for integration
+     * @return Time in seconds
+     */
+    double getMaxTime() const;
+
+    /**
+     * @brief Set the maximum time allowed for integration
+     * @param maxtime Time in seconds
+     */
+    void setMaxTime(double maxtime);
+
+    /**
+     * @brief Start timer for tracking integration time
+     */
+    void startTimer() const;
+
+    /**
+     * @brief Check whether maximum integration time was exceeded
+     * @return True if the maximum integration time was exceeded,
+     * false otherwise.
+     */
+    bool timeExceeded() const;
+
     /**
      * @brief returns the maximum number of solver steps for the backward
      * problem
@@ -1113,21 +1141,16 @@ class Solver {
     virtual void setErrHandlerFn() const = 0;
 
     /**
-     * @brief Attaches the user data instance (here this is a Model) to the
-     * forward problem
-     *
-     * @param model Model instance
+     * @brief Attaches the user data to the forward problem
      */
-    virtual void setUserData(Model *model) const = 0;
+    virtual void setUserData() const = 0;
 
     /**
-     * @brief attaches the user data instance (here this is a Model) to the
-     * backward problem
+     * @brief attaches the user data to the backward problem
      *
      * @param which identifier of the backwards problem
-     * @param model Model instance
      */
-    virtual void setUserDataB(int which, Model *model) const = 0;
+    virtual void setUserDataB(int which) const = 0;
 
     /**
      * @brief specifies the maximum number of steps for the forward
@@ -1519,6 +1542,9 @@ class Solver {
     mutable std::vector<std::unique_ptr<void, std::function<void(void *)>>>
         solver_memory_B_;
 
+    /** Sundials user_data */
+    mutable user_data_type user_data;
+
     /** internal sensitivity method flag used to select the sensitivity solution
      * method. Only applies for Forward Sensitivities. */
     InternalSensitivityMethod ism_ {InternalSensitivityMethod::simultaneous};
@@ -1540,6 +1566,12 @@ class Solver {
     /** maximum number of allowed integration steps */
     long int maxsteps_ {10000};
 
+    /** Maximum wall-time for integration in seconds */
+    std::chrono::duration<double, std::ratio<1>> maxtime_ {std::chrono::duration<double>::max()};
+
+    /** Time at which solver timer was started */
+    mutable std::chrono::time_point<std::chrono::system_clock> starttime_;
+
     /** linear solver for the forward problem */
     mutable std::unique_ptr<SUNLinSolWrapper> linear_solver_;
 

include/amici/solver_cvodes.h

@@ -137,9 +137,9 @@ class CVodeSolver : public Solver {
 
     void setErrHandlerFn() const override;
 
-    void setUserData(Model *model) const override;
+    void setUserData() const override;
 
-    void setUserDataB(int which, Model *model) const override;
+    void setUserDataB(int which) const override;
 
     void setMaxNumSteps(long int mxsteps) const override;
 

include/amici/solver_idas.h

@@ -134,9 +134,9 @@ class IDASolver : public Solver {
 
     void setErrHandlerFn() const override;
 
-    void setUserData(Model *model) const override;
+    void setUserData() const override;
 
-    void setUserDataB(int which, Model *model) const override;
+    void setUserDataB(int which) const override;
 
     void setMaxNumSteps(long int mxsteps) const override;