modelbase2 0.1.53__tar.gz → 0.1.55__tar.gz

{modelbase2-0.1.53 → modelbase2-0.1.55}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: modelbase2
-Version: 0.1.53
+Version: 0.1.55
 Summary: A package to build metabolic models
 Home-page: https://gitlab.com/qtb-hhu/modelbase-software
 License: GPL-3.0-or-later

{modelbase2-0.1.53 → modelbase2-0.1.55}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "modelbase2"
-version = "0.1.53"
+version = "0.1.55"
 description = "A package to build metabolic models"
 license = "GPL-3.0-or-later"
 authors = ["Marvin van Aalst <marvin.vanaalst@gmail.com>", "Oliver Ebenhöh <oliver.ebenhoeh@hhu.de>"]
@@ -60,6 +60,9 @@ build-backend = "poetry.core.masonry.api"
 line-length = 90
 target-version = ['py310']
 
+[tool.bandit]
+skips = ["B101", "B301", "B403", "B404", "B603", "B607"]
+
 [tool.isort]
 profile = "black"
 src_paths = ["src", "tests"]

{modelbase2-0.1.53 → modelbase2-0.1.55}/setup.py

@@ -25,7 +25,7 @@ install_requires = \
 
 setup_kwargs = {
     'name': 'modelbase2',
-    'version': '0.1.53',
+    'version': '0.1.55',
     'description': 'A package to build metabolic models',
     'long_description': 'None',
     'author': 'Marvin van Aalst',

{modelbase2-0.1.53 → modelbase2-0.1.55}/src/modelbase2/core/algebraic_module_container.py

@@ -1,12 +1,11 @@
 from __future__ import annotations
 
 import logging
-import numpy as np
+from ..types import Array
 from .data import AlgebraicModule, ModuleFunction
 from dataclasses import dataclass, field
 from queue import Empty, SimpleQueue
 from typing import Iterable, Iterator, Optional, cast
-from ..types import Array
 
 logger = logging.getLogger(__name__)
 
@@ -19,7 +18,9 @@ class AlgebraicModuleContainer:
     def __iter__(self) -> Iterator[AlgebraicModule]:
         return iter(self.modules.values())
 
-    def _sort_algebraic_modules(self, available_args: set[str], max_iterations: int = 10_000) -> None:
+    def _sort_algebraic_modules(
+        self, available_args: set[str], max_iterations: int = 10_000
+    ) -> None:
         module_order = []
         modules_to_sort: SimpleQueue[tuple[str, AlgebraicModule]] = SimpleQueue()
         for k, v in self.modules.items():
@@ -49,7 +50,11 @@ class AlgebraicModuleContainer:
         self.module_order = module_order
 
     def get_derived_variables(self) -> list[str]:
-        return [variable for module in self.modules.values() for variable in module.derived_variables]
+        return [
+            variable
+            for module in self.modules.values()
+            for variable in module.derived_variables
+        ]
 
     def add(
         self,
@@ -116,7 +121,9 @@ class AlgebraicModuleContainer:
             module = self.modules[name]
             # values = np.array(module.function(*(args[arg] for arg in module.args)), dtype=float)
             # values = values.reshape((len(module.derived_variables), -1))
-            _values = cast(Iterable[Array], module.function(*(args[arg] for arg in module.args)))
+            _values = cast(
+                Iterable[Array], module.function(*(args[arg] for arg in module.args))
+            )
             values = dict(zip(module.derived_variables, _values))
             derived_variables |= values
             args |= values

{modelbase2-0.1.53 → modelbase2-0.1.55}/src/modelbase2/core/constant_container.py

@@ -34,7 +34,9 @@ class ConstantContainer:
 
     def update_basic(self, name: str, value: float, update_derived: bool = True) -> None:
         if name not in self.constants:
-            raise KeyError(f"Constant {name} is not in the model. You have to add it first")
+            raise KeyError(
+                f"Constant {name} is not in the model. You have to add it first"
+            )
         self.constants[name].value = value
         self.values[name] = value
         if name in self._derived_from_constants and update_derived:
@@ -80,7 +82,9 @@ class ConstantContainer:
     def _update_derived_constant_values(self) -> None:
         for name in self._derived_constant_order:
             derived_constant = self.derived_constants[name]
-            value = derived_constant.function(*(self.values[i] for i in derived_constant.args))
+            value = derived_constant.function(
+                *(self.values[i] for i in derived_constant.args)
+            )
             self.values[name] = value
 
     def add_derived(self, constant: DerivedConstant, update_derived: bool = True) -> None:

{modelbase2-0.1.53 → modelbase2-0.1.55}/src/modelbase2/core/name_container.py

@@ -13,13 +13,14 @@ class NameContainer:
 
     def add(self, name: str, element_type: str) -> None:
         if (old_type := self.names.get(name)) is not None:
-            raise KeyError(f"Cannot add {element_type} {name}, as there already exists a {old_type} with that name.")
+            raise KeyError(
+                f"Cannot add {element_type} {name}, as there already exists a {old_type} with that name."
+            )
 
         logger.info(f"Adding name {name}")
         self.names[name] = element_type
 
     def remove(self, name: str) -> None:
-
         logger.info(f"Removing name {name}")
         del self.names[name]
 

{modelbase2-0.1.53 → modelbase2-0.1.55}/src/modelbase2/core/reaction_container.py

@@ -3,10 +3,10 @@ from __future__ import annotations
 import logging
 import numpy as np
 import pandas as pd
+from ..types import Array
 from .data import DerivedStoichiometry, RateFunction, Reaction, StoichiometryByVariable
 from dataclasses import dataclass, field
 from typing import Optional
-from ..types import Array
 
 logger = logging.getLogger()
 
@@ -14,7 +14,9 @@ logger = logging.getLogger()
 @dataclass
 class ReactionContainer:
     reactions: dict[str, Reaction] = field(default_factory=dict)
-    stoichiometries_by_variables: dict[str, StoichiometryByVariable] = field(default_factory=dict)
+    stoichiometries_by_variables: dict[str, StoichiometryByVariable] = field(
+        default_factory=dict
+    )
 
     def set_stoichiometry(self, variable: str, reaction: str, factor: float) -> None:
         self.stoichiometries_by_variables.setdefault(variable, {})[reaction] = factor
@@ -23,7 +25,9 @@ class ReactionContainer:
         for variable, factor in reaction.stoichiometry.items():
             self.set_stoichiometry(variable, name, factor)
 
-    def update_derived_stoichiometry(self, name: str, reaction: Reaction, constants: dict[str, float]) -> None:
+    def update_derived_stoichiometry(
+        self, name: str, reaction: Reaction, constants: dict[str, float]
+    ) -> None:
         for variable, derived_stoich in reaction.derived_stoichiometry.items():
             factor = derived_stoich.function(*(constants[i] for i in derived_stoich.args))
             self.set_stoichiometry(variable, name, factor)

{modelbase2-0.1.53 → modelbase2-0.1.55}/src/modelbase2/ode/integrator.py

@@ -1,13 +1,12 @@
 from __future__ import annotations
 
 import numpy as np
-import pandas as pd
+from ..types import Array
 from assimulo.problem import Explicit_Problem  # type: ignore
 from assimulo.solvers import CVode  # type: ignore
 from assimulo.solvers.sundials import CVodeError  # type: ignore
 from dataclasses import dataclass
 from typing import Callable, Optional, cast
-from ..types import Array
 
 
 @dataclass

{modelbase2-0.1.53 → modelbase2-0.1.55}/src/modelbase2/ode/mca.py

@@ -59,7 +59,9 @@ def get_variable_elasticities(
     Also called epsilon-elasticities. Not in steady state!
     """
     stoichiometries = m.get_stoichiometries().columns
-    elasticities = np.full(shape=(len(variables), len(stoichiometries)), fill_value=np.nan)
+    elasticities = np.full(
+        shape=(len(variables), len(stoichiometries)), fill_value=np.nan
+    )
     for i, variable in enumerate(variables):
         elasticities[i] = get_variable_elasticity(
             m=m,
@@ -105,7 +107,9 @@ def get_constant_elasticities(
     Also called pi-elasticities. Not in steady state!
     """
     stoichiometries = m.get_stoichiometries().columns
-    elasticities = np.full(shape=(len(constants), len(stoichiometries)), fill_value=np.nan)
+    elasticities = np.full(
+        shape=(len(constants), len(stoichiometries)), fill_value=np.nan
+    )
     for i, constant in enumerate(constants):
         elasticities[i] = get_constant_elasticity(
             m=m,
@@ -154,8 +158,12 @@ def _get_response_coefficients_single_constant(
     flux_resp_coef = (fluxes[0] - fluxes[1]) / (2 * displacement * old_value)
 
     return (
-        pd.Series(conc_resp_coef * y_ss_norm, index=list(y_full.keys())).replace([np.inf, -np.inf], np.nan),
-        pd.Series(flux_resp_coef * fluxes_norm, index=list(m.reactions)).replace([np.inf, -np.inf], np.nan),
+        pd.Series(conc_resp_coef * y_ss_norm, index=list(y_full.keys())).replace(
+            [np.inf, -np.inf], np.nan
+        ),
+        pd.Series(flux_resp_coef * fluxes_norm, index=list(m.reactions)).replace(
+            [np.inf, -np.inf], np.nan
+        ),
     )
 
 

{modelbase2-0.1.53 → modelbase2-0.1.55}/src/modelbase2/ode/model.py

@@ -62,13 +62,17 @@ def _sort_derived_compounds(m: Model, max_iterations: int = 10_000) -> list[str]
                 except Empty:
                     break
 
-            raise ValueError("Exceeded max iterations on sorting. Check if there are circular references.")
+            raise ValueError(
+                "Exceeded max iterations on sorting. Check if there are circular references."
+            )
     return order
 
 
 @dataclass
 class Model:
-    _algebraic_modules: AlgebraicModuleContainer = field(default_factory=AlgebraicModuleContainer)
+    _algebraic_modules: AlgebraicModuleContainer = field(
+        default_factory=AlgebraicModuleContainer
+    )
     _variables: VariableContainer = field(default_factory=VariableContainer)
     _constants: ConstantContainer = field(default_factory=ConstantContainer)
     _reactions: ReactionContainer = field(default_factory=ReactionContainer)
@@ -310,7 +314,9 @@ class Model:
             derived_variables = old_module.derived_variables
         if args is None:
             args = old_module.args
-        self.add_algebraic_module(AlgebraicModule(name, function, derived_variables, args))
+        self.add_algebraic_module(
+            AlgebraicModule(name, function, derived_variables, args)
+        )
 
         self._algebraic_modules.update(
             name,
@@ -378,7 +384,9 @@ class Model:
         args |= self._algebraic_modules.get_values_float(args)
         return args
 
-    def get_derived_variables(self, variables: dict[str, float], time: float = 0.0) -> dict[str, float]:
+    def get_derived_variables(
+        self, variables: dict[str, float], time: float = 0.0
+    ) -> dict[str, float]:
         args = variables | self.constant_values | {"time": time}
         return self._algebraic_modules.get_values_float(args)
 
@@ -435,7 +443,9 @@ class Model:
         else:
             raise NotImplementedError(f"Unknown return type {return_type}")
 
-    def get_right_hand_side(self, variables: dict[str, float], time: float = 0.0) -> dict[str, float]:
+    def get_right_hand_side(
+        self, variables: dict[str, float], time: float = 0.0
+    ) -> dict[str, float]:
         fluxes = self.get_fluxes(variables, time=time)
         return self._reactions.get_right_hand_side_float(fluxes)
 
@@ -451,7 +461,9 @@ class Model:
             old.add_derived_parameter(k, dc.function, dc.args)
 
         for k, am in self.algebraic_modules.items():
-            old.add_algebraic_module_from_args(k, am.function, am.derived_variables, am.args)
+            old.add_algebraic_module_from_args(
+                k, am.function, am.derived_variables, am.args
+            )
 
         for r in self.reactions.values():
             old.add_reaction_from_args(r.name, r.function, r.stoichiometry, r.args)

{modelbase2-0.1.53 → modelbase2-0.1.55}/src/modelbase2/ode/simulator.py

@@ -3,11 +3,11 @@ from __future__ import annotations
 import logging
 import numpy as np
 import pandas as pd
+from ..types import Array
 from .integrator import Assimulo
 from .model import Model
 from dataclasses import dataclass, field
 from typing import Any, Optional, Type
-from ..types import Array
 
 logger = logging.getLogger()
 
@@ -90,8 +90,12 @@ class Simulator:
         self.results.append(res)
         return res
 
-    def simulate_to_steady_state(self, tolerance: float = 1e-6) -> Optional[dict[str, float]]:
-        if (integration := self.integrator.integrate_to_steady_state(tolerance)) is not None:
+    def simulate_to_steady_state(
+        self, tolerance: float = 1e-6
+    ) -> Optional[dict[str, float]]:
+        if (
+            integration := self.integrator.integrate_to_steady_state(tolerance)
+        ) is not None:
             return dict(zip(self.model.stoichiometries, integration))
         else:
             logger.warning("Simulation failed")
@@ -109,7 +113,9 @@ class Simulator:
     ) -> dict[str, Array]:
         return self.model._algebraic_modules.get_values_array(args)
 
-    def _get_result_all_variables(self, result: SimulationResult, constants: dict[str, Array]) -> dict[str, Array]:
+    def _get_result_all_variables(
+        self, result: SimulationResult, constants: dict[str, Array]
+    ) -> dict[str, Array]:
         args = result.values | constants | {"time": result.time}
         return result.values | self._get_result_derived_variables(args)
 
@@ -124,7 +130,9 @@ class Simulator:
         for result in self.results:
             full_results.append(
                 SimulationResult(
-                    values=self._get_result_all_variables(result, self._get_result_constants(result)),
+                    values=self._get_result_all_variables(
+                        result, self._get_result_constants(result)
+                    ),
                     time=result.time,
                     constants=result.constants,
                 )

{modelbase2-0.1.53 → modelbase2-0.1.55}/src/modelbase2/utils/plotting.py

@@ -5,11 +5,11 @@ import math
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
+from ..types import Axes, Figure
 from matplotlib.collections import QuadMesh
 from matplotlib.colors import LogNorm, Normalize, SymLogNorm
 from matplotlib.colors import colorConverter as _colorConverter
 from typing import Any, Iterable, Optional, Sized, Union
-from ..types import Figure, Axes
 
 
 def _get_plot_kwargs(
@@ -191,7 +191,10 @@ def plot_grid(
     """Plot simulation results as a grid."""
     if ncols is None:
         _, ncols = min(
-            ((math.ceil(len(plot_groups) / i) * i - len(plot_groups), i) for i in range(2, 6)),
+            (
+                (math.ceil(len(plot_groups) / i) * i - len(plot_groups), i)
+                for i in range(2, 6)
+            ),
             key=lambda x: (x[0], -x[1]),
         )
     nrows = math.ceil(len(plot_groups) / ncols)
@@ -278,7 +281,6 @@ def relative_luminance(color: list[float]) -> float:
 
 
 def get_norm(vmin: float, vmax: float) -> plt.Normalize:
-
     if vmax < 1000 and vmin > -1000:
         norm = Normalize(vmin=vmin, vmax=vmax)
     elif vmin <= 0:
@@ -348,8 +350,12 @@ def heatmap_from_dataframe(
         text_kwargs = {"ha": "center", "va": "center"}
         hm.update_scalarmappable()  # So that get_facecolor is an array
         xpos, ypos = np.meshgrid(np.arange(len(columns)), np.arange(len(rows)))
-        for x, y, val, color in zip(xpos.flat, ypos.flat, hm.get_array(), hm.get_facecolor()):
-            text_kwargs["color"] = "black" if relative_luminance(color) > 0.45 else "white"
+        for x, y, val, color in zip(
+            xpos.flat, ypos.flat, hm.get_array(), hm.get_facecolor()
+        ):
+            text_kwargs["color"] = (
+                "black" if relative_luminance(color) > 0.45 else "white"
+            )
             if sci_annotation_bounds[0] < abs(val) <= sci_annotation_bounds[1]:
                 val_text = f"{val:.{annotation_style}}"
             else:

{modelbase2-0.1.53 → modelbase2-0.1.55}/src/modelbase2/ode/__init__.py

@@ -7,7 +7,7 @@ __all__ = [
     "mca",
 ]
 
+from . import mca
 from .integrator import Assimulo
 from .model import Model
 from .simulator import Simulator
-from . import mca