mxlpy 0.21.0__py3-none-any.whl → 0.23.0__py3-none-any.whl

mxlpy/units.py

@@ -0,0 +1,133 @@
+"""Unit definitions for MxlPy."""
+
+from sympy.physics.units import (
+    ampere,
+    becquerel,
+    candela,
+    coulomb,
+    farad,
+    gram,
+    gray,
+    henry,
+    hertz,
+    hour,
+    joule,
+    katal,
+    kelvin,
+    kilogram,
+    liter,
+    lux,
+    meter,
+    micro,
+    milli,
+    minute,
+    mol,
+    nano,
+    newton,
+    ohm,
+    pascal,
+    pico,
+    radian,
+    second,
+    siemens,
+    steradian,
+    tesla,
+    volt,
+    watt,
+    weber,
+)
+from sympy.physics.units.quantities import Quantity
+
+__all__ = [
+    "ampere",
+    "becquerel",
+    "coulomb",
+    "dimensionless",
+    "farad",
+    "gram",
+    "gray",
+    "henry",
+    "hertz",
+    "hour",
+    "item",
+    "joule",
+    "katal",
+    "kelvin",
+    "liter",
+    "lumen",
+    "lux",
+    "micro",
+    "milli",
+    "minute",
+    "mmol",
+    "mmol_g",
+    "mmol_s",
+    "mol",
+    "nano",
+    "newton",
+    "nmol",
+    "ohm",
+    "pascal",
+    "ppfd",
+    "radian",
+    "second",
+    "siemens",
+    "sievert",
+    "sqm",
+    "tesla",
+    "volt",
+    "watt",
+    "weber",
+]
+
+# time unit
+per_second = 1 / second  # type: ignore
+per_minute = 1 / minute  # type: ignore
+per_hour = 1 / hour  # type: ignore
+
+
+sqm = meter**2
+cbm = meter**3
+
+mol_s = mol / second  # type: ignore
+mol_m = mol / minute  # type: ignore
+mol_h = mol / hour  # type: ignore
+mol_g = mol / gram  # type: ignore
+
+mmol = mol * milli
+mmol_s = mmol / second
+mmol_m = mmol / minute
+mmol_h = mmol / hour
+mmol_g = mmol / gram
+
+mumol = mol * micro
+mumol_s = mumol / second
+mumol_m = mumol / minute
+mumol_h = mumol / hour
+mumol_g = mumol / gram
+
+nmol = mol * nano
+nmol_s = nmol / second
+nmol_m = nmol / minute
+nmol_h = nmol / hour
+nmol_g = nmol / gram
+
+pmol = mol * pico
+pmol_s = pmol / second
+pmol_m = pmol / minute
+pmol_h = pmol / hour
+pmol_g = pmol / gram
+
+ppfd = mumol / sqm / second
+
+
+# SBML units
+avogadro = 6.02214076e23
+sievert = joule / kilogram  # type: ignore
+lumen = candela * steradian  # type: ignore
+dimensionless = None
+item = 1  # pseudounit for one thing
+
+# Plant units
+mol_chl = Quantity("mol_chl", abbrev="mol_chl")
+mmol_mol_chl = mmol / mol_chl

{mxlpy-0.21.0.dist-info → mxlpy-0.23.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mxlpy
-Version: 0.21.0
+Version: 0.23.0
 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>
@@ -22,6 +22,7 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Software Development
 Requires-Python: >=3.12
+Requires-Dist: diffrax>=0.7.0
 Requires-Dist: dill>=0.3.9
 Requires-Dist: latexify-py>=0.4.4
 Requires-Dist: lazy-import>=0.2.2
@@ -32,6 +33,7 @@ Requires-Dist: numpy>=2.1.2
 Requires-Dist: pandas>=2.2.3
 Requires-Dist: parameteriser>=0.1.0
 Requires-Dist: pebble>=5.0.7
+Requires-Dist: pysbml>=0.2.0
 Requires-Dist: python-libsbml>=5.20.4
 Requires-Dist: salib>=1.5.1
 Requires-Dist: scipy>=1.14.1
@@ -42,6 +44,7 @@ Requires-Dist: tabulate>=0.9.0
 Requires-Dist: toml>=0.10.2
 Requires-Dist: tqdm>=4.66.6
 Requires-Dist: typing-extensions>=4.12.2
+Requires-Dist: wadler-lindig>=0.1.7
 Provides-Extra: keras
 Requires-Dist: keras>=3.9.2; extra == 'keras'
 Provides-Extra: tensorflow

mxlpy-0.23.0.dist-info/RECORD

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mxlpy/meta/codegen_modebase.py

@@ -1,112 +0,0 @@
-"""Generate mxlpy code from a model."""
-
-from __future__ import annotations
-
-import warnings
-from typing import TYPE_CHECKING
-
-import sympy
-
-from mxlpy.meta.source_tools import fn_to_sympy, sympy_to_fn
-from mxlpy.types import Derived
-
-if TYPE_CHECKING:
-    from mxlpy.model import Model
-
-__all__ = [
-    "generate_mxlpy_code",
-]
-
-
-def _list_of_symbols(args: list[str]) -> list[sympy.Symbol | sympy.Expr]:
-    return [sympy.Symbol(arg) for arg in args]
-
-
-def generate_mxlpy_code(model: Model) -> str:
-    """Generate a mxlpy model from a model."""
-    functions = {}
-
-    # Variables and parameters
-    variables = model.variables
-    parameters = model.parameters
-
-    # Derived
-    derived_source = []
-    for k, der in model.derived.items():
-        fn = der.fn
-        fn_name = fn.__name__
-        functions[fn_name] = (
-            fn_to_sympy(fn, model_args=_list_of_symbols(der.args)),
-            der.args,
-        )
-
-        derived_source.append(
-            f"""        .add_derived(
-                "{k}",
-                fn={fn_name},
-                args={der.args},
-            )"""
-        )
-
-    # Reactions
-    reactions_source = []
-    for k, rxn in model.reactions.items():
-        fn = rxn.fn
-        fn_name = fn.__name__
-        functions[fn_name] = (
-            fn_to_sympy(fn, model_args=_list_of_symbols(rxn.args)),
-            rxn.args,
-        )
-        stoichiometry: list[str] = []
-        for var, stoich in rxn.stoichiometry.items():
-            if isinstance(stoich, Derived):
-                functions[fn_name] = (
-                    fn_to_sympy(fn, model_args=_list_of_symbols(stoich.args)),
-                    rxn.args,
-                )
-                args = ", ".join(f'"{k}"' for k in stoich.args)
-                stoich = (  # noqa: PLW2901
-                    f"""Derived(fn={fn.__name__}, args=[{args}])"""
-                )
-            stoichiometry.append(f""""{var}": {stoich}""")
-
-        reactions_source.append(
-            f"""        .add_reaction(
-                "{k}",
-                fn={fn_name},
-                args={rxn.args},
-                stoichiometry={{{",".join(stoichiometry)}}},
-            )"""
-        )
-
-    # Surrogates
-    if len(model._surrogates) > 0:  # noqa: SLF001
-        warnings.warn(
-            "Generating code for Surrogates not yet supported.",
-            stacklevel=1,
-        )
-
-    # Combine all the sources
-    functions_source = "\n\n".join(
-        sympy_to_fn(fn_name=name, args=args, expr=expr)
-        for name, (expr, args) in functions.items()
-    )
-    source = [
-        "from mxlpy import Model\n",
-        functions_source,
-        "def create_model() -> Model:",
-        "    return (",
-        "        Model()",
-    ]
-    if len(parameters) > 0:
-        source.append(f"        .add_parameters({parameters})")
-    if len(variables) > 0:
-        source.append(f"        .add_variables({variables})")
-    if len(derived_source) > 0:
-        source.append("\n".join(derived_source))
-    if len(reactions_source) > 0:
-        source.append("\n".join(reactions_source))
-
-    source.append("    )")
-
-    return "\n".join(source)

mxlpy/meta/codegen_py.py

@@ -1,115 +0,0 @@
-"""Module to export models as code."""
-
-from __future__ import annotations
-
-import warnings
-from typing import TYPE_CHECKING
-
-import sympy
-
-from mxlpy.meta.source_tools import fn_to_sympy, sympy_to_inline
-from mxlpy.types import Derived
-
-if TYPE_CHECKING:
-    from collections.abc import Callable, Generator, Iterable, Iterator
-
-    from mxlpy.model import Model
-
-__all__ = [
-    "generate_model_code_py",
-]
-
-
-def _conditional_join[T](
-    iterable: Iterable[T],
-    question: Callable[[T], bool],
-    true_pat: str,
-    false_pat: str,
-) -> str:
-    """Join an iterable, applying a pattern to each element based on a condition."""
-
-    def inner(it: Iterator[T]) -> Generator[str, None, None]:
-        yield str(next(it))
-        while True:
-            try:
-                el = next(it)
-                if question(el):
-                    yield f"{true_pat}{el}"
-                else:
-                    yield f"{false_pat}{el}"
-            except StopIteration:
-                break
-
-    return "".join(inner(iter(iterable)))
-
-
-def _list_of_symbols(args: list[str]) -> list[sympy.Symbol | sympy.Expr]:
-    return [sympy.Symbol(arg) for arg in args]
-
-
-# FIXME: generate from SymbolicModel, should be easier?
-def generate_model_code_py(model: Model) -> str:
-    """Transform the model into a single function, inlining the function calls."""
-    source = [
-        "from collections.abc import Iterable\n",
-        "from mxlpy.types import Float\n",
-        "def model(t: Float, variables: Float) -> Iterable[Float]:",
-    ]
-
-    # Variables
-    variables = model.variables
-    if len(variables) > 0:
-        source.append("    {} = variables".format(", ".join(variables)))
-
-    # Parameters
-    parameters = model.parameters
-    if len(parameters) > 0:
-        source.append("\n".join(f"    {k} = {v}" for k, v in model.parameters.items()))
-
-    # Derived
-    for name, derived in model.derived.items():
-        expr = fn_to_sympy(derived.fn, model_args=_list_of_symbols(derived.args))
-        source.append(f"    {name} = {sympy_to_inline(expr)}")
-
-    # Reactions
-    for name, rxn in model.reactions.items():
-        expr = fn_to_sympy(rxn.fn, model_args=_list_of_symbols(rxn.args))
-        source.append(f"    {name} = {sympy_to_inline(expr)}")
-
-    # Stoichiometries; FIXME: do this with sympy instead as well?
-    stoich_srcs = {}
-    for rxn_name, rxn in model.reactions.items():
-        for i, (cpd_name, factor) in enumerate(rxn.stoichiometry.items()):
-            if isinstance(factor, Derived):
-                expr = fn_to_sympy(factor.fn, model_args=_list_of_symbols(factor.args))
-                src = f"{sympy_to_inline(expr)} * {rxn_name}"
-            elif factor == 1:
-                src = rxn_name
-            elif factor == -1:
-                src = f"-{rxn_name}" if i == 0 else f"- {rxn_name}"
-            else:
-                src = f"{factor} * {rxn_name}"
-            stoich_srcs.setdefault(cpd_name, []).append(src)
-    for variable, stoich in stoich_srcs.items():
-        source.append(
-            f"    d{variable}dt = {_conditional_join(stoich, lambda x: x.startswith('-'), ' ', ' + ')}"
-        )
-
-    # Surrogates
-    if len(model._surrogates) > 0:  # noqa: SLF001
-        warnings.warn(
-            "Generating code for Surrogates not yet supported.",
-            stacklevel=1,
-        )
-
-    # Return
-    if len(variables) > 0:
-        source.append(
-            "    return {}".format(
-                ", ".join(f"d{i}dt" for i in variables),
-            ),
-        )
-    else:
-        source.append("    return ()")
-
-    return "\n".join(source)