Merge branch 'develop' into test_numpy2

.github/dependabot.yml

@@ -0,0 +1,10 @@
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    ignore:
+      - dependency-name: "*"
+        update-types: ["version-update:semver-patch", "version-update:semver-minor"]

python/sdist/amici/de_model.py

@@ -1561,16 +1561,18 @@ def _compute_equation(self, name: str) -> None:
             self._eqs[name] = smart_jacobian(self.eq("root"), time_symbol)
 
         elif name == "drootdt_total":
-            # backsubstitution of optimized right-hand side terms into RHS
-            # calling subs() is costly. Due to looping over events though, the
-            # following lines are only evaluated if a model has events
-            w_sorted = toposort_symbols(
-                dict(zip(self.sym("w"), self.eq("w"), strict=True))
-            )
-            tmp_xdot = smart_subs_dict(self.eq("xdot"), w_sorted)
             self._eqs[name] = self.eq("drootdt")
-            if self.num_states_solver():
-                self._eqs[name] += smart_multiply(self.eq("drootdx"), tmp_xdot)
+            # backsubstitution of optimized right-hand side terms into RHS
+            # calling subs() is costly. We can skip it if we don't have any
+            # state-dependent roots.
+            if self.num_states_solver() and not smart_is_zero_matrix(
+                drootdx := self.eq("drootdx")
+            ):
+                w_sorted = toposort_symbols(
+                    dict(zip(self.sym("w"), self.eq("w"), strict=True))
+                )
+                tmp_xdot = smart_subs_dict(self.eq("xdot"), w_sorted)
+                self._eqs[name] += smart_multiply(drootdx, tmp_xdot)
 
         elif name == "deltax":
             # fill boluses for Heaviside functions, as empty state updates

python/sdist/amici/logging.py

@@ -175,7 +175,8 @@ def get_logger(
     elif kwargs:
         warnings.warn(
             "AMICI logger already exists, ignoring keyword "
-            "arguments to setup_logger"
+            "arguments to setup_logger",
+            stacklevel=2,
         )
 
     logger = logging.getLogger(logger_name)

python/sdist/amici/parameter_mapping.py

@@ -27,6 +27,7 @@
 warnings.warn(
     "Importing amici.parameter_mapping is deprecated. Use `amici.petab.parameter_mapping` instead.",
     DeprecationWarning,
+    stacklevel=2,
 )
 
 __all__ = [

python/sdist/amici/petab/conditions.py

@@ -67,6 +67,7 @@ def fill_in_parameters(
             "The following problem parameters were not used: "
             + str(unused_parameters),
             RuntimeWarning,
+            stacklevel=2,
         )
 
     for edata, mapping_for_condition in zip(

python/sdist/amici/petab_import.py

@@ -13,6 +13,7 @@
 warnings.warn(
     "Importing amici.petab_import is deprecated. Use `amici.petab` instead.",
     DeprecationWarning,
+    stacklevel=2,
 )
 
 from .petab.import_helpers import (  # noqa # pylint: disable=unused-import

python/sdist/amici/petab_import_pysb.py

@@ -14,6 +14,7 @@
 warnings.warn(
     "Importing amici.petab_import_pysb is deprecated. Use `amici.petab.pysb_import` instead.",
     DeprecationWarning,
+    stacklevel=2,
 )
 
 __all__ = [

python/sdist/amici/petab_objective.py

@@ -12,6 +12,7 @@
 warnings.warn(
     f"Importing {__name__} is deprecated. Use `amici.petab.simulations` instead.",
     DeprecationWarning,
+    stacklevel=2,
 )
 
 from .petab.conditions import fill_in_parameters  # noqa: F401

python/sdist/amici/petab_simulate.py

@@ -11,6 +11,7 @@
 warnings.warn(
     f"Importing {__name__} is deprecated. Use `amici.petab.simulator` instead.",
     DeprecationWarning,
+    stacklevel=2,
 )
 
 from .petab.simulator import PetabSimulator  # noqa: F401

python/sdist/amici/petab_util.py

@@ -15,6 +15,7 @@
 warnings.warn(
     f"Importing {__name__} is deprecated. Use `amici.petab.util` instead.",
     DeprecationWarning,
+    stacklevel=2,
 )
 
 __all__ = [

python/sdist/amici/sbml_import.py

@@ -442,7 +442,8 @@ def sbml2amici(
             if not has_clibs:
                 warnings.warn(
                     "AMICI C++ extensions have not been built. "
-                    "Generated model code, but unable to compile."
+                    "Generated model code, but unable to compile.",
+                    stacklevel=2,
                 )
             exporter.compile_model()
 
@@ -1838,7 +1839,8 @@ def _process_event_observables(
                     f'Event observable {eo["name"]} uses `t` in '
                     "it's formula which is not the time variable. "
                     "For the time variable, please use `time` "
-                    "instead!"
+                    "instead!",
+                    stacklevel=1,
                 )
 
         # check for nesting of observables (unsupported)
@@ -2157,7 +2159,8 @@ def _get_conservation_laws_demartino(
                 "Conservation laws for non-constant species in "
                 "combination with parameterized stoichiometric "
                 "coefficients are not currently supported "
-                "and will be turned off."
+                "and will be turned off.",
+                stacklevel=1,
             )
             return []
 
@@ -2234,7 +2237,8 @@ def _get_conservation_laws_rref(
                 "Conservation laws for non-constant species in "
                 "combination with parameterized stoichiometric "
                 "coefficients are not currently supported "
-                "and will be turned off."
+                "and will be turned off.",
+                stacklevel=1,
             )
             return []
 
@@ -3048,7 +3052,8 @@ def _non_const_conservation_laws_supported(sbml_model: sbml.Model) -> bool:
         warnings.warn(
             "Conservation laws for non-constant species in "
             "models with RateRules are currently not supported "
-            "and will be turned off."
+            "and will be turned off.",
+            stacklevel=1,
         )
         return False
 
@@ -3060,7 +3065,8 @@ def _non_const_conservation_laws_supported(sbml_model: sbml.Model) -> bool:
         warnings.warn(
             "Conservation laws for non-constant species in "
             "models with Species-AssignmentRules are currently not "
-            "supported and will be turned off."
+            "supported and will be turned off.",
+            stacklevel=1,
         )
         return False
 

python/sdist/amici/swig_wrappers.py

@@ -78,7 +78,8 @@ def runAmiciSimulation(
         warnings.warn(
             "Adjoint sensitivity analysis for models with discontinuous right hand sides (events/piecewise functions) has not been thoroughly tested."
             "Sensitivities might be wrong. Tracked at https://github.com/AMICI-dev/AMICI/issues/18. "
-            "Adjoint sensitivity analysis may work if the location of the discontinuity is not parameter-dependent, but we still recommend testing accuracy of gradients."
+            "Adjoint sensitivity analysis may work if the location of the discontinuity is not parameter-dependent, but we still recommend testing accuracy of gradients.",
+            stacklevel=1,
         )
 
     with _capture_cstdout():
@@ -119,7 +120,8 @@ def runAmiciSimulations(
         warnings.warn(
             "Adjoint sensitivity analysis for models with discontinuous right hand sides (events/piecewise functions) has not been thoroughly tested. "
             "Sensitivities might be wrong. Tracked at https://github.com/AMICI-dev/AMICI/issues/18. "
-            "Adjoint sensitivity analysis may work if the location of the discontinuity is not parameter-dependent, but we still recommend testing accuracy of gradients."
+            "Adjoint sensitivity analysis may work if the location of the discontinuity is not parameter-dependent, but we still recommend testing accuracy of gradients.",
+            stacklevel=1,
         )
 
     with _capture_cstdout():

python/sdist/pyproject.toml

@@ -126,4 +126,5 @@ line-length = 79
 extend-include = ["*.ipynb"]
 
 [tool.ruff.lint]
+extend-select = ["B028"]
 ignore = ["E402", "F403", "F405", "E741"]

python/tests/splines_utils.py

@@ -6,6 +6,7 @@
 
 import math
 import os
+import platform
 import uuid
 from tempfile import mkdtemp
 from typing import Any
@@ -716,13 +717,7 @@ def param_by_name(id):
             if sllh_atol is None:
                 sllh_atol = np.finfo(float).eps
             sllh_err_abs = abs(sllh).max()
-            if (
-                sllh_err_abs > sllh_atol and debug is not True
-            ) or debug == "print":
-                print(f"sllh_atol={sllh_atol}")
-                print(f"sllh_err_abs = {sllh_err_abs}")
-            if not debug:
-                assert sllh_err_abs <= sllh_atol
+            assert sllh_err_abs <= sllh_atol, f"{sllh_err_abs=} {sllh_atol=}"
     else:
         assert sllh is None
 
@@ -917,11 +912,11 @@ def example_spline_1(
         extrapolate=extrapolate,
     )
 
-    if os.name == "nt":
+    if os.name == "nt" or platform.system() == "Darwin":
         tols = (
             dict(llh_rtol=1e-15, x_rtol=1e-8, x_atol=1e-7),
             dict(llh_rtol=1e-15, x_rtol=1e-8, x_atol=1e-7),
-            dict(llh_rtol=1e-15, sllh_atol=5e-8, x_rtol=1e-8, x_atol=1e-7),
+            dict(llh_rtol=1e-15, sllh_atol=5e-7, x_rtol=1e-8, x_atol=1e-7),
         )
     else:
         tols = (

python/tests/test_sbml_import.py

@@ -759,7 +759,7 @@ def test_constraints():
         #  in practice
         assert np.any(rdata.x < 0)
 
-        amici_solver.setRelativeTolerance(1e-14)
+        amici_solver.setRelativeTolerance(1e-13)
         amici_solver.setConstraints(
             [Constraint.non_negative, Constraint.non_negative]
         )

tests/cpp/steadystate/tests1.cpp

@@ -1,7 +1,6 @@
 #include "testfunctions.h"
 
 #include "wrapfunctions.h"
-#include <cstring>
 
 #include <gtest/gtest.h>
 
@@ -175,7 +174,8 @@ TEST(ExampleSteadystate, SensitivityForwardErrorNewt)
 
 TEST(ExampleSteadystate, SensitivityForwardDense)
 {
-    amici::simulateVerifyWrite("/model_steadystate/sensiforwarddense/");
+    amici::simulateVerifyWrite("/model_steadystate/sensiforwarddense/",
+                               1e-9, TEST_RTOL);
 }
 
 TEST(ExampleSteadystate, SensiFwdNewtonPreeq)