Update AMICI to develop@8ef53c88 (#347)

git subrepo clone --branch=develop --force [email protected]:AMICI-dev/AMICI.git deps/AMICI 

subrepo:
  subdir:   "deps/AMICI"
  merged:   "8ef53c88"
upstream:
  origin:   "[email protected]:AMICI-dev/AMICI.git"
  branch:   "develop"
  commit:   "8ef53c88"
git-subrepo:
  version:  "0.4.1"
  origin:   "https://github.com/ingydotnet/git-subrepo"
  commit:   "a04d8c2"

deps/AMICI/.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\"}}"

deps/AMICI/.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

deps/AMICI/.gitrepo

@@ -5,8 +5,8 @@
 ;
 [subrepo]
 	remote = [email protected]:ICB-DCM/AMICI.git
-	branch = v0.11.17
-	commit = c0377065207b68c881143d203de1f56fd52878b9
-	parent = d0bd8c19b9bb5426affdcd8386d893eee7940e80
+	branch = develop
+	commit = 8ef53c8808437cafc171d6ab9545a59d61bb83af
+	parent = eb33a10abde3faf2835ce846482817df06afcfe1
 	cmdver = 0.4.1
 	method = merge

deps/AMICI/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, ...);
+
 };
 
 

deps/AMICI/python/amici/__init__.py

@@ -28,7 +28,7 @@
 import re
 import sys
 from contextlib import suppress
-from types import ModuleType
+from types import ModuleType as ModelModule
 from typing import Optional, Union, Sequence, List
 
 
@@ -134,6 +134,17 @@ def _imported_from_setup() -> bool:
     from .sbml_import import SbmlImporter, assignmentRules2observables
     from .ode_export import ODEModel, ODEExporter
 
+    try:
+        # Requires Python>=3.8
+        from typing import Protocol
+
+        class ModelModule(Protocol):
+            """Enable Python static type checking for AMICI-generated model modules"""
+            def getModel(self) -> amici.Model:
+                pass
+    except ImportError:
+        pass
+
 hdf5_enabled = 'readSolverSettingsFromHDF5' in dir()
 
 
@@ -283,7 +294,7 @@ def __exit__(self, exc_type, exc_value, traceback):
 
 
 def import_model_module(module_name: str,
-                        module_path: Optional[str] = None) -> ModuleType:
+                        module_path: Optional[str] = None) -> ModelModule:
     """
     Import Python module of an AMICI model
 

deps/AMICI/python/amici/petab_import.py

@@ -378,7 +378,7 @@ def import_model_sbml(
         model_output_dir: Optional[str] = None,
         verbose: Optional[Union[bool, int]] = True,
         allow_reinit_fixpar_initcond: bool = True,
-        **kwargs) -> None:
+        **kwargs) -> amici.SbmlImporter:
     """
     Create AMICI model from PEtab problem
 
@@ -415,6 +415,9 @@ def import_model_sbml(
     :param kwargs:
         Additional keyword arguments to be passed to
         :meth:`amici.sbml_import.SbmlImporter.sbml2amici`.
+
+    :return:
+        The created :class:`amici.sbml_import.SbmlImporter` instance.
     """
 
     set_log_level(logger, verbose)
@@ -584,6 +587,8 @@ def import_model_sbml(
         verbose=verbose,
         **kwargs)
 
+    return sbml_importer
+
 
 # for backwards compatibility
 import_model = import_model_sbml

deps/AMICI/python/amici/petab_objective.py

@@ -17,6 +17,7 @@
 import numpy as np
 import pandas as pd
 import petab
+import sympy as sp
 from petab.C import *  # noqa: F403
 
 from . import AmiciModel, AmiciExpData
@@ -346,11 +347,21 @@ def _set_initial_concentration(condition_id, species_id, init_par_id,
             value = petab.to_float_if_float(
                 petab_problem.condition_df.loc[condition_id, species_id])
             if pd.isna(value):
-                value = float(
-                    get_species_initial(
-                        petab_problem.sbml_model.getSpecies(species_id)
-                    )
+                value = get_species_initial(
+                    petab_problem.sbml_model.getSpecies(species_id)
                 )
+                try:
+                    value = float(value)
+                except ValueError:
+                    if sp.nsimplify(value).is_Atom:
+                        # Get rid of multiplication with one
+                        value = sp.nsimplify(value)
+                    else:
+                        raise NotImplementedError(
+                            "Cannot handle non-trivial expressions for "
+                            f"species initial for {species_id}: {value}")
+                    # this should be a parameter ID
+                    value = str(value)
                 logger.debug(f'The species {species_id} has no initial value '
                              f'defined for the condition {condition_id} in '
                              'the PEtab conditions table. The initial value is '
@@ -728,4 +739,4 @@ def rdatas_to_simulation_df(
     df = rdatas_to_measurement_df(rdatas=rdatas, model=model,
                                   measurement_df=measurement_df)
 
-    return df.rename(columns={MEASUREMENT: SIMULATION})
+    return df.rename(columns={MEASUREMENT: SIMULATION})

deps/AMICI/src/CMakeLists.template.cmake

@@ -18,10 +18,13 @@ set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 
 include(CheckCXXCompilerFlag)
-set(MY_CXX_FLAGS -Wall -Wno-unused-function -Wno-unused-variable -Wno-unused-but-set-variable)
+set(MY_CXX_FLAGS -Wall -Wno-unused-function -Wno-unused-variable)
+if (CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
+    list(APPEND MY_CXX_FLAGS  -Wno-unused-but-set-variable)
+endif()
 foreach(FLAG ${MY_CXX_FLAGS})
     unset(CUR_FLAG_SUPPORTED CACHE)
-    CHECK_CXX_COMPILER_FLAG(${FLAG} CUR_FLAG_SUPPORTED)
+    CHECK_CXX_COMPILER_FLAG(-Werror ${FLAG} CUR_FLAG_SUPPORTED)
     if(${CUR_FLAG_SUPPORTED})
         set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${FLAG}")
     endif()

deps/AMICI/src/exception.cpp

@@ -8,12 +8,18 @@
 
 namespace amici {
 
-AmiException::AmiException(const char *fmt, ...) {
+AmiException::AmiException()
+{
+    storeBacktrace(12);
+}
+
+AmiException::AmiException(const char *fmt, ...)
+    : AmiException()
+{
     va_list ap;
     va_start(ap, fmt);
-    vsnprintf(msg_.data(), msg_.size(), fmt, ap);
+    storeMessage(fmt, ap);
     va_end(ap);
-    storeBacktrace(12);
 }
 
 const char *AmiException::what() const noexcept {
@@ -29,6 +35,11 @@ void AmiException::storeBacktrace(const int nMaxFrames) {
              backtraceString(nMaxFrames).c_str());
 }
 
+void AmiException::storeMessage(const char *fmt, va_list argptr)
+{
+    vsnprintf(msg_.data(), msg_.size(), fmt, argptr);
+}
+
 CvodeException::CvodeException(const int error_code, const char *function) :
     AmiException("Cvode routine %s failed with error code %i",function,error_code){}
 
@@ -48,4 +59,12 @@ NewtonFailure::NewtonFailure(int code, const char *function) :
     error_code = code;
 }
 
+SetupFailure::SetupFailure(const char *fmt, ...)
+{
+    va_list ap;
+    va_start(ap, fmt);
+    storeMessage(fmt, ap);
+    va_end(ap);
+}
+
 } // namespace amici