git subrepo clone (merge) --branch=v0.11.18 --force [email protected]:AM…

…ICI-dev/AMICI.git deps/AMICI (#350) subrepo: subdir: "deps/AMICI" merged: "bd3b89d3" upstream: origin: "[email protected]:AMICI-dev/AMICI.git" branch: "v0.11.18" commit: "bd3b89d3" git-subrepo: version: "0.4.3" origin: "https://github.com/ingydotnet/git-subrepo" commit: "be9f02a"
ICB-DCM · Jul 13, 2021 · c25dd97 · c25dd97
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diff --git a/deps/AMICI/.gitrepo b/deps/AMICI/.gitrepo
@@ -5,8 +5,8 @@
 ;
 [subrepo]
 	remote = [email protected]:ICB-DCM/AMICI.git
-	branch = develop
-	commit = 8ef53c8808437cafc171d6ab9545a59d61bb83af
-	parent = eb33a10abde3faf2835ce846482817df06afcfe1
-	cmdver = 0.4.1
+	branch = v0.11.18
+	commit = bd3b89d3839e6518532d547e54e7fe66ef3cfec3
+	parent = 98a0746a708be9e43c7daeb54ec38bcb6709f7d9
+	cmdver = 0.4.3
 	method = merge
diff --git a/deps/AMICI/CHANGELOG.md b/deps/AMICI/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:

diff --git a/deps/AMICI/include/amici/defines.h b/deps/AMICI/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;

diff --git a/deps/AMICI/include/amici/model_dimensions.h b/deps/AMICI/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;
 

diff --git a/deps/AMICI/include/amici/serialization.h b/deps/AMICI/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;
+    }
 }
 
 /**

diff --git a/deps/AMICI/include/amici/solver.h b/deps/AMICI/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_;
 

diff --git a/deps/AMICI/include/amici/solver_cvodes.h b/deps/AMICI/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;
 

diff --git a/deps/AMICI/include/amici/solver_idas.h b/deps/AMICI/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;
 

diff --git a/deps/AMICI/python/amici/__init__.py b/deps/AMICI/python/amici/__init__.py
@@ -18,16 +18,13 @@
 :var has_clibs:
     boolean indicating if this is the full package with swig interface or
     the raw package without
-:var capture_cstdout:
-    context to redirect C/C++ stdout to python stdout if python stdout was
-    redirected (doing nothing if not redirected).
 """
 
 import importlib
 import os
 import re
 import sys
-from contextlib import suppress
+from contextlib import suppress, contextmanager
 from types import ModuleType as ModelModule
 from typing import Optional, Union, Sequence, List
 
@@ -84,14 +81,22 @@ def _imported_from_setup() -> bool:
     return False
 
 
-# redirect C/C++ stdout to python stdout if python stdout is redirected,
-# e.g. in ipython notebook
-capture_cstdout = suppress
-if sys.stdout != sys.__stdout__:
-    try:
-        from wurlitzer import sys_pipes as capture_cstdout
-    except ModuleNotFoundError:
-        pass
+try:
+    from wurlitzer import sys_pipes
+except ModuleNotFoundError:
+    sys_pipes = suppress
+
+
+@contextmanager
+def _capture_cstdout():
+    """Redirect C/C++ stdout to python stdout if python stdout is redirected,
+    e.g. in ipython notebook"""
+    if sys.stdout == sys.__stdout__:
+        yield
+    else:
+        with sys_pipes():
+            yield
+
 
 # Initialize AMICI paths
 amici_path = _get_amici_path()
@@ -188,8 +193,7 @@ def runAmiciSimulation(
     :returns:
         ReturnData object with simulation results
     """
-
-    with capture_cstdout():
+    with _capture_cstdout():
         rdata = amici.runAmiciSimulation(_get_ptr(solver), _get_ptr(edata),
                                          _get_ptr(model))
     return numpy.ReturnDataView(rdata)
@@ -235,7 +239,7 @@ def runAmiciSimulations(
 
     :returns: list of simulation results
     """
-    with capture_cstdout():
+    with _capture_cstdout():
         edata_ptr_vector = amici.ExpDataPtrVector(edata_list)
         rdata_ptr_list = amici.runAmiciSimulations(_get_ptr(solver),
                                                    edata_ptr_vector,

diff --git a/deps/AMICI/python/amici/custom_commands.py b/deps/AMICI/python/amici/custom_commands.py
@@ -1,13 +1,13 @@
 """Custom setuptools commands for AMICI installation"""
 
-import contextlib
 import glob
 import os
 import subprocess
 import sys
 from shutil import copyfile
 from typing import Dict, List, Tuple
 
+from amici.swig import fix_typehints
 from amici.setuptools import generate_swig_interface_files
 from setuptools.command.build_clib import build_clib
 from setuptools.command.build_ext import build_ext
@@ -142,9 +142,6 @@ def run(self):
         log.debug("running AmiciDevelop")
 
         if not self.no_clibs:
-            generate_swig_interface_files(
-                swig_outdir=os.path.join(os.path.abspath(os.getcwd()),
-                                         "amici"))
             self.get_finalized_command('build_clib').run()
 
         develop.run(self)
@@ -226,8 +223,11 @@ def run(self):
                 log.info(f"copying {src} -> {dest}")
                 copyfile(src, dest)
 
-            generate_swig_interface_files(
-                swig_outdir=os.path.join(build_dir, 'amici'))
+            swig_outdir = os.path.join(os.path.abspath(build_dir), "amici")
+            generate_swig_interface_files(swig_outdir=swig_outdir)
+            swig_py_module_path = os.path.join(swig_outdir, 'amici.py')
+            log.debug("updating typehints")
+            fix_typehints(swig_py_module_path, swig_py_module_path)
 
         # Always force recompilation. The way setuptools/distutils check for
         # whether sources require recompilation is not reliable and may lead
@@ -326,3 +326,4 @@ def set_compiler_specific_extension_options(
         except AttributeError:
             # No compiler-specific options set
             pass
+
diff --git a/deps/AMICI/python/amici/parameter_mapping.py b/deps/AMICI/python/amici/parameter_mapping.py
@@ -93,9 +93,9 @@ def __init__(
 
 
 class ParameterMapping(Sequence):
-    """Parameter mapping for multiple conditions.
+    r"""Parameter mapping for multiple conditions.
 
-    This can be used like a list of :class:`ParameterMappingForCondition`\\ s.
+    This can be used like a list of :class:`ParameterMappingForCondition`\ s.
 
     :param parameter_mappings:
         List of parameter mappings for specific conditions.

diff --git a/deps/AMICI/python/amici/petab_objective.py b/deps/AMICI/python/amici/petab_objective.py
@@ -49,7 +49,9 @@ def simulate_petab(
         edatas: List[AmiciExpData] = None,
         parameter_mapping: ParameterMapping = None,
         scaled_parameters: Optional[bool] = False,
-        log_level: int = logging.WARNING
+        log_level: int = logging.WARNING,
+        num_threads: int = 1,
+        failfast: bool = True,
 ) -> Dict[str, Any]:
     """Simulate PEtab model.
 
@@ -78,6 +80,12 @@ def simulate_petab(
         are assumed to be in linear scale.
     :param log_level:
         Log level, see :mod:`amici.logging` module.
+    :param num_threads:
+        Number of threads to use for simulating multiple conditions
+        (only used if compiled with OpenMP).
+    :param failfast:
+        Returns as soon as an integration failure is encountered, skipping
+        any remaining simulations.
 
     :return:
         Dictionary of
@@ -136,7 +144,9 @@ def simulate_petab(
         amici_model=amici_model)
 
     # Simulate
-    rdatas = amici.runAmiciSimulations(amici_model, solver, edata_list=edatas)
+    rdatas = amici.runAmiciSimulations(
+        amici_model, solver, edata_list=edatas,
+        num_threads=num_threads, failfast=failfast)
 
     # Compute total llh
     llh = sum(rdata['llh'] for rdata in rdatas)