mxlpy 0.8.0__tar.gz → 0.9.0__tar.gz

{mxlpy-0.8.0 → mxlpy-0.9.0}/.github/workflows/docs.yml

@@ -3,6 +3,7 @@ name: documentation
 on:
   release:
     types: [published]
+  workflow_dispatch: {}
 
 permissions:
   contents: write
@@ -12,6 +13,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # fetch all commits/branches
 
       - name: Configure Git Credentials
         run: |
@@ -32,5 +35,5 @@ jobs:
           restore-keys: |
             mkdocs-material-
       - run: uv sync --extra dev --extra torch
-      - run: uv run python -c "import toml;print('VERSION={}'.format(toml.load(open('pyproject.toml'))['project']['version']))" >> $GITHUB_ENV"
-      - run: mike deploy --push $(VERSION)
+      - run: uv run python -c "import toml;print('VERSION={}'.format(toml.load(open('pyproject.toml'))['project']['version']))" >> $GITHUB_ENV
+      - run: uv run mike deploy --push ${{ env.VERSION }}

{mxlpy-0.8.0 → mxlpy-0.9.0}/.github/workflows/python-publish.yml

@@ -3,6 +3,7 @@ name: Upload Python Package
 on:
   release:
     types: [published]
+  workflow_dispatch: {}
 
 permissions:
   contents: read

{mxlpy-0.8.0 → mxlpy-0.9.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mxlpy
-Version: 0.8.0
+Version: 0.9.0
 Summary: A package to build metabolic models
 Author-email: Marvin van Aalst <marvin.vanaalst@gmail.com>
 Maintainer-email: Marvin van Aalst <marvin.vanaalst@gmail.com>

{mxlpy-0.8.0 → mxlpy-0.9.0}/pyproject.toml

@@ -29,7 +29,7 @@ maintainers = [
 ]
 name = "mxlpy"
 readme = "README.md"
-version = "0.8.0"
+version = "0.9.0"
 dependencies = [
   "dill>=0.3.9",
   "latexify-py>=0.4.4",

{mxlpy-0.8.0 → mxlpy-0.9.0}/src/mxlpy/mc.py

@@ -22,6 +22,7 @@ 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,
@@ -33,6 +34,8 @@ from mxlpy.scan import (
     _update_parameters_and,
 )
 from mxlpy.types import (
+    ArrayLike,
+    IntegratorProtocol,
     McSteadyStates,
     ProtocolByPars,
     ResponseCoefficientsByPars,
@@ -52,6 +55,8 @@ __all__ = [
 ]
 
 if TYPE_CHECKING:
+    from collections.abc import Callable
+
     from mxlpy.model import Model
     from mxlpy.types import Array
 
@@ -76,6 +81,7 @@ class ParameterScanWorker(Protocol):
         *,
         parameters: pd.DataFrame,
         rel_norm: bool,
+        integrator: Callable[[Callable, ArrayLike], IntegratorProtocol],
     ) -> SteadyStates:
         """Call the worker function."""
         ...
@@ -87,6 +93,7 @@ def _parameter_scan_worker(
     *,
     parameters: pd.DataFrame,
     rel_norm: bool,
+    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol],
 ) -> SteadyStates:
     """Worker function for parallel steady state scanning across parameter sets.
 
@@ -117,6 +124,7 @@ def _parameter_scan_worker(
         y0=y0,
         parallel=False,
         rel_norm=rel_norm,
+        integrator=integrator,
     )
 
 
@@ -129,6 +137,7 @@ def steady_state(
     cache: Cache | None = None,
     rel_norm: bool = False,
     worker: SteadyStateWorker = _steady_state_worker,
+    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol] = DefaultIntegrator,
 ) -> SteadyStates:
     """Monte-carlo scan of steady states.
 
@@ -156,6 +165,7 @@ def steady_state(
                 worker,
                 y0=y0,
                 rel_norm=rel_norm,
+                integrator=integrator,
             ),
             model=model,
         ),
@@ -163,11 +173,9 @@ def steady_state(
         max_workers=max_workers,
         cache=cache,
     )
-    concs = {k: v.variables for k, v in res.items()}
-    fluxes = {k: v.fluxes for k, v in res.items()}
     return SteadyStates(
-        variables=pd.concat(concs, axis=1).T,
-        fluxes=pd.concat(fluxes, axis=1).T,
+        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,
         parameters=mc_parameters,
     )
 
@@ -180,6 +188,7 @@ def time_course(
     max_workers: int | None = None,
     cache: Cache | None = None,
     worker: TimeCourseWorker = _time_course_worker,
+    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol] = DefaultIntegrator,
 ) -> TimeCourseByPars:
     """MC time course.
 
@@ -207,6 +216,7 @@ def time_course(
                 worker,
                 time_points=time_points,
                 y0=y0,
+                integrator=integrator,
             ),
             model=model,
         ),
@@ -214,12 +224,11 @@ def time_course(
         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()}
+
     return TimeCourseByPars(
         parameters=mc_parameters,
-        variables=pd.concat(concs, axis=1).T,
-        fluxes=pd.concat(fluxes, axis=1).T,
+        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,
     )
 
 
@@ -232,6 +241,7 @@ def time_course_over_protocol(
     max_workers: int | None = None,
     cache: Cache | None = None,
     worker: ProtocolWorker = _protocol_worker,
+    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol] = DefaultIntegrator,
 ) -> ProtocolByPars:
     """MC time course.
 
@@ -260,6 +270,7 @@ def time_course_over_protocol(
                 worker,
                 protocol=protocol,
                 y0=y0,
+                integrator=integrator,
                 time_points_per_step=time_points_per_step,
             ),
             model=model,
@@ -288,6 +299,7 @@ def scan_steady_state(
     cache: Cache | None = None,
     rel_norm: bool = False,
     worker: ParameterScanWorker = _parameter_scan_worker,
+    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol] = DefaultIntegrator,
 ) -> McSteadyStates:
     """Parameter scan of mc distributed steady states.
 
@@ -317,6 +329,7 @@ def scan_steady_state(
         cache: Cache object for storing results
         rel_norm: Whether to use relative normalization in the steady state calculations
         worker: Worker function for parallel steady state scanning across parameter sets
+        integrator: Function producing an integrator for the simulation.
 
     Returns:
         McSteadyStates: Object containing the steady state solutions for the given parameter
@@ -330,6 +343,7 @@ def scan_steady_state(
                 parameters=parameters,
                 y0=y0,
                 rel_norm=rel_norm,
+                integrator=integrator,
             ),
             model=model,
         ),
@@ -487,6 +501,7 @@ def response_coefficients(
     disable_tqdm: bool = False,
     max_workers: int | None = None,
     rel_norm: bool = False,
+    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol] = DefaultIntegrator,
 ) -> ResponseCoefficientsByPars:
     """Calculate response coefficients using Monte Carlo analysis.
 
@@ -513,6 +528,7 @@ def response_coefficients(
         disable_tqdm: Whether to disable the tqdm progress bar
         max_workers: Maximum number of workers for parallel processing
         rel_norm: Whether to use relative normalization in the steady state calculations
+        integrator: Function producing an integrator for the simulation.
 
     Returns:
         ResponseCoefficientsByPars: Object containing the response coefficients for the given parameters
@@ -530,6 +546,7 @@ def response_coefficients(
                 rel_norm=rel_norm,
                 disable_tqdm=disable_tqdm,
                 parallel=False,
+                integrator=integrator,
             ),
             model=model,
         ),
@@ -538,11 +555,10 @@ def response_coefficients(
         max_workers=max_workers,
     )
 
-    crcs = {k: v.variables for k, v in res.items()}
-    frcs = {k: v.fluxes for k, v in res.items()}
-
     return ResponseCoefficientsByPars(
-        variables=cast(pd.DataFrame, pd.concat(crcs)),
-        fluxes=cast(pd.DataFrame, pd.concat(frcs)),
+        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()})),
         parameters=mc_parameters,
     )

{mxlpy-0.8.0 → mxlpy-0.9.0}/src/mxlpy/mca.py

@@ -22,9 +22,10 @@ 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
+from mxlpy.types import ArrayLike, ResponseCoefficients
 
 __all__ = [
     "parameter_elasticities",
@@ -33,6 +34,9 @@ __all__ = [
 ]
 
 if TYPE_CHECKING:
+    from collections.abc import Callable
+
+    from mxlpy import IntegratorProtocol
     from mxlpy.model import Model
 
 
@@ -165,6 +169,7 @@ def _response_coefficient_worker(
     normalized: bool,
     rel_norm: bool,
     displacement: float = 1e-4,
+    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol],
 ) -> tuple[pd.Series, pd.Series]:
     """Calculate response coefficients for a single parameter.
 
@@ -182,6 +187,7 @@ def _response_coefficient_worker(
         normalized: Whether to normalize the coefficients
         rel_norm: Whether to use relative normalization
         displacement: Relative perturbation size (default: 1e-4)
+        integrator: Integrator function to use for steady state calculation
 
     Returns:
         tuple[pd.Series, pd.Series]: Tuple containing:
@@ -196,6 +202,7 @@ def _response_coefficient_worker(
         model,
         y0=y0,
         rel_norm=rel_norm,
+        integrator=integrator,
     )
 
     model.update_parameters({parameter: old * (1 - displacement)})
@@ -203,6 +210,7 @@ def _response_coefficient_worker(
         model,
         y0=y0,
         rel_norm=rel_norm,
+        integrator=integrator,
     )
 
     conc_resp = (upper.variables - lower.variables) / (2 * displacement * old)
@@ -214,6 +222,7 @@ def _response_coefficient_worker(
             model,
             y0=y0,
             rel_norm=rel_norm,
+            integrator=integrator,
         )
         conc_resp *= old / norm.variables
         flux_resp *= old / norm.fluxes
@@ -231,6 +240,7 @@ def response_coefficients(
     parallel: bool = True,
     max_workers: int | None = None,
     rel_norm: bool = False,
+    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol] = DefaultIntegrator,
 ) -> ResponseCoefficients:
     """Calculate response coefficients.
 
@@ -250,6 +260,7 @@ def response_coefficients(
         parallel: Whether to parallelize the computation
         max_workers: Maximum number of workers
         rel_norm: Whether to use relative normalization
+        integrator: Integrator function to use for steady state calculation
 
     Returns:
         ResponseCoefficients object containing:
@@ -267,6 +278,7 @@ def response_coefficients(
             normalized=normalized,
             displacement=displacement,
             rel_norm=rel_norm,
+            integrator=integrator,
         ),
         inputs=list(zip(parameters, parameters, strict=True)),
         cache=None,

{mxlpy-0.8.0 → mxlpy-0.9.0}/src/mxlpy/scan.py

@@ -15,6 +15,8 @@ Functions:
 
 from __future__ import annotations
 
+from mxlpy.integrators import DefaultIntegrator
+
 __all__ = [
     "ProtocolWorker",
     "SteadyStateWorker",
@@ -35,7 +37,13 @@ import pandas as pd
 
 from mxlpy.parallel import Cache, parallelise
 from mxlpy.simulator import Result, Simulator
-from mxlpy.types import ProtocolByPars, SteadyStates, TimeCourseByPars
+from mxlpy.types import (
+    ArrayLike,
+    IntegratorProtocol,
+    ProtocolByPars,
+    SteadyStates,
+    TimeCourseByPars,
+)
 
 if TYPE_CHECKING:
     from collections.abc import Callable
@@ -278,6 +286,7 @@ class SteadyStateWorker(Protocol):
         y0: dict[str, float] | None,
         *,
         rel_norm: bool,
+        integrator: Callable[[Callable, ArrayLike], IntegratorProtocol],
     ) -> TimePoint:
         """Call the worker function."""
         ...
@@ -291,6 +300,8 @@ class TimeCourseWorker(Protocol):
         model: Model,
         y0: dict[str, float] | None,
         time_points: Array,
+        *,
+        integrator: Callable[[Callable, ArrayLike], IntegratorProtocol],
     ) -> TimeCourse:
         """Call the worker function."""
         ...
@@ -304,6 +315,8 @@ class ProtocolWorker(Protocol):
         model: Model,
         y0: dict[str, float] | None,
         protocol: pd.DataFrame,
+        *,
+        integrator: Callable[[Callable, ArrayLike], IntegratorProtocol],
         time_points_per_step: int = 10,
     ) -> TimeCourse:
         """Call the worker function."""
@@ -315,6 +328,7 @@ def _steady_state_worker(
     y0: dict[str, float] | None,
     *,
     rel_norm: bool,
+    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol],
 ) -> TimePoint:
     """Simulate the model to steady state and return concentrations and fluxes.
 
@@ -322,6 +336,7 @@ def _steady_state_worker(
         model: Model instance to simulate.
         y0: Initial conditions as a dictionary {species: value}.
         rel_norm: Whether to use relative normalization.
+        integrator: Function producing an integrator for the simulation.
 
     Returns:
         TimePoint: Object containing steady-state concentrations and fluxes.
@@ -329,7 +344,7 @@ def _steady_state_worker(
     """
     try:
         res = (
-            Simulator(model, y0=y0)
+            Simulator(model, y0=y0, integrator=integrator)
             .simulate_to_steady_state(rel_norm=rel_norm)
             .get_result()
         )
@@ -342,6 +357,7 @@ def _time_course_worker(
     model: Model,
     y0: dict[str, float] | None,
     time_points: Array,
+    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol],
 ) -> TimeCourse:
     """Simulate the model to steady state and return concentrations and fluxes.
 
@@ -349,6 +365,7 @@ def _time_course_worker(
         model: Model instance to simulate.
         y0: Initial conditions as a dictionary {species: value}.
         time_points: Array of time points for the simulation.
+        integrator: Integrator function to use for steady state calculation
 
     Returns:
         TimePoint: Object containing steady-state concentrations and fluxes.
@@ -356,7 +373,7 @@ def _time_course_worker(
     """
     try:
         res = (
-            Simulator(model, y0=y0)
+            Simulator(model, y0=y0, integrator=integrator)
             .simulate_time_course(time_points=time_points)
             .get_result()
         )
@@ -373,6 +390,8 @@ def _protocol_worker(
     model: Model,
     y0: dict[str, float] | None,
     protocol: pd.DataFrame,
+    *,
+    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol] = DefaultIntegrator,
     time_points_per_step: int = 10,
 ) -> TimeCourse:
     """Simulate the model over a protocol and return concentrations and fluxes.
@@ -381,7 +400,8 @@ def _protocol_worker(
         model: Model instance to simulate.
         y0: Initial conditions as a dictionary {species: value}.
         protocol: DataFrame containing the protocol steps.
-        time_points_per_step: Number of time points per protocol step (default: 10).
+        integrator: Integrator function to use for steady state calculation
+        time_points_per_step: Number of time points per protocol step.
 
     Returns:
         TimeCourse: Object containing protocol series concentrations and fluxes.
@@ -389,7 +409,7 @@ def _protocol_worker(
     """
     try:
         res = (
-            Simulator(model, y0=y0)
+            Simulator(model, y0=y0, integrator=integrator)
             .simulate_over_protocol(
                 protocol=protocol,
                 time_points_per_step=time_points_per_step,
@@ -420,6 +440,7 @@ def steady_state(
     rel_norm: bool = False,
     cache: Cache | None = None,
     worker: SteadyStateWorker = _steady_state_worker,
+    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol] = DefaultIntegrator,
 ) -> SteadyStates:
     """Get steady-state results over supplied parameters.
 
@@ -431,6 +452,7 @@ def steady_state(
         rel_norm: Whether to use relative normalization (default: False).
         cache: Optional cache to store and retrieve results.
         worker: Worker function to use for the simulation.
+        integrator: Integrator function to use for steady state calculation
 
     Returns:
         SteadyStates: Steady-state results for each parameter set.
@@ -464,6 +486,7 @@ def steady_state(
                 worker,
                 y0=y0,
                 rel_norm=rel_norm,
+                integrator=integrator,
             ),
             model=model,
         ),
@@ -492,6 +515,7 @@ def time_course(
     parallel: bool = True,
     cache: Cache | None = None,
     worker: TimeCourseWorker = _time_course_worker,
+    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol] = DefaultIntegrator,
 ) -> TimeCourseByPars:
     """Get time course for each supplied parameter.
 
@@ -536,6 +560,7 @@ def time_course(
         cache: Optional cache to store and retrieve results.
         parallel: Whether to execute in parallel (default: True).
         worker: Worker function to use for the simulation.
+        integrator: Integrator function to use for steady state calculation
 
     Returns:
         TimeCourseByPars: Time series results for each parameter set.
@@ -549,6 +574,7 @@ def time_course(
                 worker,
                 time_points=time_points,
                 y0=y0,
+                integrator=integrator,
             ),
             model=model,
         ),
@@ -575,6 +601,7 @@ def time_course_over_protocol(
     parallel: bool = True,
     cache: Cache | None = None,
     worker: ProtocolWorker = _protocol_worker,
+    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol] = DefaultIntegrator,
 ) -> ProtocolByPars:
     """Get protocol series for each supplied parameter.
 
@@ -599,6 +626,7 @@ def time_course_over_protocol(
         parallel: Whether to execute in parallel (default: True).
         cache: Optional cache to store and retrieve results.
         worker: Worker function to use for the simulation.
+        integrator: Integrator function to use for steady state calculation
 
     Returns:
         TimeCourseByPars: Protocol series results for each parameter set.
@@ -612,6 +640,7 @@ def time_course_over_protocol(
                 protocol=protocol,
                 y0=y0,
                 time_points_per_step=time_points_per_step,
+                integrator=integrator,
             ),
             model=model,
         ),

{mxlpy-0.8.0 → mxlpy-0.9.0}/tests/test_scan.py

@@ -5,6 +5,7 @@ import pandas as pd
 import pytest
 
 from mxlpy import Model, fns
+from mxlpy.integrators import DefaultIntegrator
 from mxlpy.scan import (
     TimeCourse,
     TimePoint,
@@ -239,7 +240,12 @@ def test_timecourse_results(simple_model: Model) -> None:
 
 
 def test_steady_state_worker(simple_model: Model) -> None:
-    result = _steady_state_worker(simple_model, y0=None, rel_norm=False)
+    result = _steady_state_worker(
+        simple_model,
+        y0=None,
+        rel_norm=False,
+        integrator=DefaultIntegrator,
+    )
     assert isinstance(result, TimePoint)
 
     # The model should reach steady state with S=0, P=0
@@ -251,7 +257,12 @@ def test_steady_state_worker(simple_model: Model) -> None:
 
 def test_time_course_worker(simple_model: Model) -> None:
     time_points = np.linspace(0, 1, 3)
-    result = _time_course_worker(simple_model, y0=None, time_points=time_points)
+    result = _time_course_worker(
+        simple_model,
+        y0=None,
+        time_points=time_points,
+        integrator=DefaultIntegrator,
+    )
 
     assert isinstance(result, TimeCourse)
     assert result.variables.shape == (3, 2)

{mxlpy-0.8.0 → mxlpy-0.9.0}/tests/test_scans.py

@@ -12,7 +12,9 @@ from mxlpy.scan import (
 )
 
 if TYPE_CHECKING:
-    from mxlpy.types import Array
+    from collections.abc import Callable
+
+    from mxlpy.types import Array, ArrayLike, IntegratorProtocol
 
 
 def mock_ss_worker(
@@ -20,6 +22,7 @@ def mock_ss_worker(
     y0: dict[str, float] | None,  # noqa: ARG001
     *,
     rel_norm: bool,  # noqa: ARG001
+    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol],  # noqa: ARG001
 ) -> TimePoint:
     return TimePoint(
         variables=pd.Series({"x1": 1.0, "x2": 2.0}),
@@ -31,6 +34,7 @@ def mock_tc_worker(
     model: Model,  # noqa: ARG001
     y0: dict[str, float] | None,  # noqa: ARG001
     time_points: Array,
+    integrator: Callable[[Callable, ArrayLike], IntegratorProtocol],  # noqa: ARG001
 ) -> TimeCourse:
     return TimeCourse(
         variables=pd.DataFrame({i: {"x1": 1.0, "x2": 2.0} for i in time_points}).T,