mxlpy 0.19.0__py3-none-any.whl → 0.21.0__py3-none-any.whl

mxlpy/integrators/__init__.py

@@ -6,9 +6,6 @@ It includes support for both Assimulo and Scipy integrators, with Assimulo being
 
 from __future__ import annotations
 
-__all__ = ["DefaultIntegrator"]
-
-
 from .int_scipy import Scipy
 
 try:
@@ -17,3 +14,7 @@ try:
     DefaultIntegrator = Assimulo
 except ImportError:
     DefaultIntegrator = Scipy
+
+__all__ = [
+    "DefaultIntegrator",
+]

mxlpy/integrators/int_assimulo.py

@@ -2,14 +2,9 @@
 
 from __future__ import annotations
 
-from dataclasses import dataclass
-
-__all__ = [
-    "Assimulo",
-]
-
 import contextlib
 import os
+from dataclasses import dataclass
 from typing import TYPE_CHECKING, Literal
 
 import numpy as np
@@ -25,6 +20,11 @@ if TYPE_CHECKING:
     from mxlpy.types import Array, ArrayLike
 
 
+__all__ = [
+    "Assimulo",
+]
+
+
 @dataclass
 class Assimulo:
     """Assimulo integrator for solving ODEs.

mxlpy/integrators/int_scipy.py

@@ -2,13 +2,8 @@
 
 from __future__ import annotations
 
-from dataclasses import dataclass, field
-
-__all__ = [
-    "Scipy",
-]
-
 import copy
+from dataclasses import dataclass, field
 from typing import TYPE_CHECKING, cast
 
 import numpy as np
@@ -20,6 +15,11 @@ if TYPE_CHECKING:
     from collections.abc import Callable
 
 
+__all__ = [
+    "Scipy",
+]
+
+
 @dataclass
 class Scipy:
     """Scipy integrator for solving ODEs.

mxlpy/label_map.py

@@ -24,13 +24,15 @@ import numpy as np
 
 from mxlpy.model import Model
 
-__all__ = ["LabelMapper"]
-
 if TYPE_CHECKING:
     from collections.abc import Callable, Mapping
 
     from mxlpy.types import Derived
 
+__all__ = [
+    "LabelMapper",
+]
+
 
 def _total_concentration(*args: float) -> float:
     """Calculate sum of isotopomer concentrations.

mxlpy/linear_label_map.py

@@ -16,13 +16,15 @@ from typing import TYPE_CHECKING
 
 from mxlpy.model import Derived, Model
 
-__all__ = ["LinearLabelMapper"]
-
 if TYPE_CHECKING:
     from collections.abc import Mapping
 
     import pandas as pd
 
+__all__ = [
+    "LinearLabelMapper",
+]
+
 
 def _generate_isotope_labels(base_name: str, num_labels: int) -> list[str]:
     """Generate list of isotopomer names for a compound.

mxlpy/mc.py

@@ -22,7 +22,6 @@ from typing import TYPE_CHECKING, Protocol, cast
 import pandas as pd
 
 from mxlpy import mca, scan
-from mxlpy.integrators import DefaultIntegrator
 from mxlpy.parallel import Cache, parallelise
 from mxlpy.scan import (
     ProtocolWorker,
@@ -42,6 +41,11 @@ from mxlpy.types import (
     TimeCourseByPars,
 )
 
+if TYPE_CHECKING:
+    from mxlpy.model import Model
+    from mxlpy.types import Array
+
+
 __all__ = [
     "ParameterScanWorker",
     "parameter_elasticities",
@@ -53,20 +57,6 @@ __all__ = [
     "variable_elasticities",
 ]
 
-if TYPE_CHECKING:
-    from mxlpy.model import Model
-    from mxlpy.types import Array
-
-__ALL__ = [
-    "steady_state",
-    "time_course",
-    "time_course_over_protocol",
-    "parameter_scan_ss",
-    "compound_elasticities",
-    "parameter_elasticities",
-    "response_coefficients",
-]
-
 
 class ParameterScanWorker(Protocol):
     """Protocol for the parameter scan worker function."""
@@ -131,7 +121,7 @@ def steady_state(
     cache: Cache | None = None,
     rel_norm: bool = False,
     worker: SteadyStateWorker = _steady_state_worker,
-    integrator: IntegratorType = DefaultIntegrator,
+    integrator: IntegratorType | None = None,
 ) -> SteadyStates:
     """Monte-carlo scan of steady states.
 
@@ -162,6 +152,7 @@ def steady_state(
                 worker,
                 rel_norm=rel_norm,
                 integrator=integrator,
+                y0=None,
             ),
             model=model,
         ),
@@ -170,8 +161,8 @@ def steady_state(
         cache=cache,
     )
     return SteadyStates(
-        variables=pd.concat({k: v.variables for k, v in res.items()}, axis=1).T,
-        fluxes=pd.concat({k: v.fluxes for k, v in res.items()}, axis=1).T,
+        variables=pd.concat({k: v.variables for k, v in res}, axis=1).T,
+        fluxes=pd.concat({k: v.fluxes for k, v in res}, axis=1).T,
         parameters=mc_to_scan,
     )
 
@@ -185,7 +176,7 @@ def time_course(
     max_workers: int | None = None,
     cache: Cache | None = None,
     worker: TimeCourseWorker = _time_course_worker,
-    integrator: IntegratorType = DefaultIntegrator,
+    integrator: IntegratorType | None = None,
 ) -> TimeCourseByPars:
     """MC time course.
 
@@ -216,6 +207,7 @@ def time_course(
                 worker,
                 time_points=time_points,
                 integrator=integrator,
+                y0=None,
             ),
             model=model,
         ),
@@ -226,8 +218,8 @@ def time_course(
 
     return TimeCourseByPars(
         parameters=mc_to_scan,
-        variables=pd.concat({k: v.variables.T for k, v in res.items()}, axis=1).T,
-        fluxes=pd.concat({k: v.fluxes.T for k, v in res.items()}, axis=1).T,
+        variables=pd.concat({k: v.variables.T for k, v in res}, axis=1).T,
+        fluxes=pd.concat({k: v.fluxes.T for k, v in res}, axis=1).T,
     )
 
 
@@ -241,7 +233,7 @@ def time_course_over_protocol(
     max_workers: int | None = None,
     cache: Cache | None = None,
     worker: ProtocolWorker = _protocol_worker,
-    integrator: IntegratorType = DefaultIntegrator,
+    integrator: IntegratorType | None = None,
 ) -> ProtocolByPars:
     """MC time course.
 
@@ -273,6 +265,7 @@ def time_course_over_protocol(
                 worker,
                 protocol=protocol,
                 integrator=integrator,
+                y0=None,
                 time_points_per_step=time_points_per_step,
             ),
             model=model,
@@ -281,8 +274,8 @@ def time_course_over_protocol(
         max_workers=max_workers,
         cache=cache,
     )
-    concs = {k: v.variables.T for k, v in res.items()}
-    fluxes = {k: v.fluxes.T for k, v in res.items()}
+    concs = {k: v.variables.T for k, v in res}
+    fluxes = {k: v.fluxes.T for k, v in res}
     return ProtocolByPars(
         variables=pd.concat(concs, axis=1).T,
         fluxes=pd.concat(fluxes, axis=1).T,
@@ -301,7 +294,7 @@ def scan_steady_state(
     cache: Cache | None = None,
     rel_norm: bool = False,
     worker: ParameterScanWorker = _parameter_scan_worker,
-    integrator: IntegratorType = DefaultIntegrator,
+    integrator: IntegratorType | None = None,
 ) -> McSteadyStates:
     """Parameter scan of mc distributed steady states.
 
@@ -348,6 +341,7 @@ def scan_steady_state(
                 parameters=to_scan,
                 rel_norm=rel_norm,
                 integrator=integrator,
+                y0=None,
             ),
             model=model,
         ),
@@ -355,8 +349,8 @@ def scan_steady_state(
         cache=cache,
         max_workers=max_workers,
     )
-    concs = {k: v.variables.T for k, v in res.items()}
-    fluxes = {k: v.fluxes.T for k, v in res.items()}
+    concs = {k: v.variables.T for k, v in res}
+    fluxes = {k: v.fluxes.T for k, v in res}
     return McSteadyStates(
         variables=pd.concat(concs, axis=1).T,
         fluxes=pd.concat(fluxes, axis=1).T,
@@ -431,7 +425,7 @@ def variable_elasticities(
         cache=cache,
         max_workers=max_workers,
     )
-    return cast(pd.DataFrame, pd.concat(res))
+    return cast(pd.DataFrame, pd.concat(dict(res)))
 
 
 def parameter_elasticities(
@@ -495,7 +489,7 @@ def parameter_elasticities(
         cache=cache,
         max_workers=max_workers,
     )
-    return cast(pd.DataFrame, pd.concat(res))
+    return cast(pd.DataFrame, pd.concat(dict(res)))
 
 
 def response_coefficients(
@@ -510,7 +504,7 @@ def response_coefficients(
     disable_tqdm: bool = False,
     max_workers: int | None = None,
     rel_norm: bool = False,
-    integrator: IntegratorType = DefaultIntegrator,
+    integrator: IntegratorType | None = None,
 ) -> ResponseCoefficientsByPars:
     """Calculate response coefficients using Monte Carlo analysis.
 
@@ -567,9 +561,7 @@ def response_coefficients(
     )
 
     return ResponseCoefficientsByPars(
-        variables=cast(
-            pd.DataFrame, pd.concat({k: v.variables for k, v in res.items()})
-        ),
-        fluxes=cast(pd.DataFrame, pd.concat({k: v.fluxes for k, v in res.items()})),
+        variables=cast(pd.DataFrame, pd.concat({k: v.variables for k, v in res})),
+        fluxes=cast(pd.DataFrame, pd.concat({k: v.fluxes for k, v in res})),
         parameters=mc_to_scan,
     )

mxlpy/mca.py

@@ -22,21 +22,20 @@ from typing import TYPE_CHECKING
 
 import pandas as pd
 
-from mxlpy.integrators import DefaultIntegrator
 from mxlpy.parallel import parallelise
 from mxlpy.scan import _steady_state_worker
 from mxlpy.types import ResponseCoefficients
 
+if TYPE_CHECKING:
+    from mxlpy.model import Model
+    from mxlpy.types import IntegratorType
+
 __all__ = [
     "parameter_elasticities",
     "response_coefficients",
     "variable_elasticities",
 ]
 
-if TYPE_CHECKING:
-    from mxlpy.model import Model
-    from mxlpy.types import IntegratorType
-
 
 def _response_coefficient_worker(
     parameter: str,
@@ -46,7 +45,7 @@ def _response_coefficient_worker(
     normalized: bool,
     rel_norm: bool,
     displacement: float = 1e-4,
-    integrator: IntegratorType,
+    integrator: IntegratorType | None,
 ) -> tuple[pd.Series, pd.Series]:
     """Calculate response coefficients for a single parameter.
 
@@ -81,6 +80,7 @@ def _response_coefficient_worker(
         model,
         rel_norm=rel_norm,
         integrator=integrator,
+        y0=None,
     )
 
     model.update_parameters({parameter: old * (1 - displacement)})
@@ -88,6 +88,7 @@ def _response_coefficient_worker(
         model,
         rel_norm=rel_norm,
         integrator=integrator,
+        y0=None,
     )
 
     conc_resp = (upper.variables - lower.variables) / (2 * displacement * old)
@@ -99,6 +100,7 @@ def _response_coefficient_worker(
             model,
             rel_norm=rel_norm,
             integrator=integrator,
+            y0=None,
         )
         conc_resp *= old / norm.variables
         flux_resp *= old / norm.fluxes
@@ -237,7 +239,7 @@ def response_coefficients(
     parallel: bool = True,
     max_workers: int | None = None,
     rel_norm: bool = False,
-    integrator: IntegratorType = DefaultIntegrator,
+    integrator: IntegratorType | None = None,
 ) -> ResponseCoefficients:
     """Calculate response coefficients.
 
@@ -284,6 +286,6 @@ def response_coefficients(
         max_workers=max_workers,
     )
     return ResponseCoefficients(
-        variables=pd.DataFrame({k: v[0] for k, v in res.items()}),
-        fluxes=pd.DataFrame({k: v[1] for k, v in res.items()}),
+        variables=pd.DataFrame({k: v[0] for k, v in res}),
+        fluxes=pd.DataFrame({k: v[1] for k, v in res}),
     )

mxlpy/meta/__init__.py

@@ -1,11 +1,13 @@
 """Metaprogramming facilities."""
 
+from __future__ import annotations
+
+from .codegen_latex import generate_latex_code
+from .codegen_modebase import generate_mxlpy_code
+from .codegen_py import generate_model_code_py
+
 __all__ = [
     "generate_latex_code",
     "generate_model_code_py",
     "generate_mxlpy_code",
 ]
-
-from .codegen_latex import generate_latex_code
-from .codegen_modebase import generate_mxlpy_code
-from .codegen_py import generate_model_code_py