mxlpy 0.20.0__py3-none-any.whl → 0.22.0__py3-none-any.whl

mxlpy/symbolic/symbolic_model.py

@@ -4,15 +4,13 @@
 from __future__ import annotations
 
 from dataclasses import dataclass
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, cast
 
 import sympy
 
-from mxlpy.meta.source_tools import fn_to_sympy
+from mxlpy.meta.sympy_tools import fn_to_sympy, list_of_symbols
 
 if TYPE_CHECKING:
-    from collections.abc import Iterable
-
     from mxlpy.model import Model
 
 __all__ = [
@@ -36,30 +34,44 @@ class SymbolicModel:
         )
 
 
-def _list_of_symbols(args: Iterable[str]) -> list[sympy.Symbol]:
-    return [sympy.Symbol(arg) for arg in args]
-
-
 def to_symbolic_model(model: Model) -> SymbolicModel:
     cache = model._create_cache()  # noqa: SLF001
+    initial_conditions = model.get_initial_conditions()
 
     variables: dict[str, sympy.Symbol] = dict(
-        zip(model.variables, _list_of_symbols(model.variables), strict=True)
+        zip(
+            initial_conditions,
+            cast(list[sympy.Symbol], list_of_symbols(initial_conditions)),
+            strict=True,
+        )
     )
     parameters: dict[str, sympy.Symbol] = dict(
-        zip(model.parameters, _list_of_symbols(model.parameters), strict=True)
+        zip(
+            model.get_parameter_values(),
+            cast(list[sympy.Symbol], list_of_symbols(model.get_parameter_values())),
+            strict=True,
+        )
     )
     symbols: dict[str, sympy.Symbol | sympy.Expr] = variables | parameters  # type: ignore
 
     # Insert derived into symbols
-    for k, v in model.derived.items():
-        symbols[k] = fn_to_sympy(v.fn, [symbols[i] for i in v.args])
+    for k, v in model.get_raw_derived().items():
+        if (
+            expr := fn_to_sympy(v.fn, origin=k, model_args=[symbols[i] for i in v.args])
+        ) is None:
+            msg = f"Unable to parse derived value '{k}'"
+            raise ValueError(msg)
+        symbols[k] = expr
 
     # Insert derived into reaction via args
-    rxns = {
-        k: fn_to_sympy(v.fn, [symbols[i] for i in v.args])
-        for k, v in model.reactions.items()
-    }
+    rxns: dict[str, sympy.Expr] = {}
+    for k, v in model.get_raw_reactions().items():
+        if (
+            expr := fn_to_sympy(v.fn, origin=k, model_args=[symbols[i] for i in v.args])
+        ) is None:
+            msg = f"Unable to parse reaction '{k}'"
+            raise ValueError(msg)
+        rxns[k] = expr
 
     eqs: dict[str, sympy.Expr] = {}
     for cpd, stoich in cache.stoich_by_cpds.items():
@@ -80,5 +92,5 @@ def to_symbolic_model(model: Model) -> SymbolicModel:
         parameters=parameters,
         eqs=[eqs[i] for i in cache.var_names],
         initial_conditions=model.get_initial_conditions(),
-        parameter_values=model.parameters,
+        parameter_values=model.get_parameter_values(),
     )

mxlpy/types.py

@@ -36,6 +36,7 @@ __all__ = [
     "McSteadyStates",
     "MockSurrogate",
     "Param",
+    "Parameter",
     "ProtocolByPars",
     "RateFn",
     "Reaction",
@@ -45,13 +46,14 @@ __all__ = [
     "RetType",
     "SteadyStates",
     "TimeCourseByPars",
+    "Variable",
     "unwrap",
     "unwrap2",
 ]
 
 type RateFn = Callable[..., float]
 type Array = NDArray[np.floating[Any]]
-type ArrayLike = NDArray[np.floating[Any]] | list[float]
+type ArrayLike = NDArray[np.floating[Any]] | pd.Index | list[float]
 
 
 Param = ParamSpec("Param")
@@ -59,6 +61,8 @@ RetType = TypeVar("RetType")
 
 
 if TYPE_CHECKING:
+    import sympy
+
     from mxlpy.model import Model
 
 
@@ -147,34 +151,53 @@ type IntegratorType = Callable[
 ]
 
 
+@dataclass
+class Parameter:
+    """Container for parameter meta information."""
+
+    value: float
+    unit: sympy.Expr | None = None
+    source: str | None = None
+
+
+@dataclass
+class Variable:
+    """Container for variable meta information."""
+
+    initial_value: float | Derived
+    unit: sympy.Expr | None = None
+    source: str | None = None
+
+
 @dataclass(kw_only=True, slots=True)
 class Derived:
     """Container for a derived value."""
 
     fn: RateFn
     args: list[str]
+    unit: sympy.Expr | None = None
 
-    def calculate(self, dependent: dict[str, Any]) -> float:
+    def calculate(self, args: dict[str, Any]) -> float:
         """Calculate the derived value.
 
         Args:
-            dependent: Dictionary of dependent variables.
+            args: Dictionary of args variables.
 
         Returns:
             The calculated derived value.
 
         """
-        return cast(float, self.fn(*(dependent[arg] for arg in self.args)))
+        return cast(float, self.fn(*(args[arg] for arg in self.args)))
 
-    def calculate_inpl(self, name: str, dependent: dict[str, Any]) -> None:
+    def calculate_inpl(self, name: str, args: dict[str, Any]) -> None:
         """Calculate the derived value in place.
 
         Args:
             name: Name of the derived variable.
-            dependent: Dictionary of dependent variables.
+            args: Dictionary of args variables.
 
         """
-        dependent[name] = cast(float, self.fn(*(dependent[arg] for arg in self.args)))
+        args[name] = cast(float, self.fn(*(args[arg] for arg in self.args)))
 
 
 @dataclass(kw_only=True, slots=True)
@@ -183,28 +206,29 @@ class Readout:
 
     fn: RateFn
     args: list[str]
+    unit: sympy.Expr | None = None
 
-    def calculate(self, dependent: dict[str, Any]) -> float:
+    def calculate(self, args: dict[str, Any]) -> float:
         """Calculate the derived value.
 
         Args:
-            dependent: Dictionary of dependent variables.
+            args: Dictionary of args variables.
 
         Returns:
             The calculated derived value.
 
         """
-        return cast(float, self.fn(*(dependent[arg] for arg in self.args)))
+        return cast(float, self.fn(*(args[arg] for arg in self.args)))
 
-    def calculate_inpl(self, name: str, dependent: dict[str, Any]) -> None:
+    def calculate_inpl(self, name: str, args: dict[str, Any]) -> None:
         """Calculate the reaction in place.
 
         Args:
             name: Name of the derived variable.
-            dependent: Dictionary of dependent variables.
+            args: Dictionary of args variables.
 
         """
-        dependent[name] = cast(float, self.fn(*(dependent[arg] for arg in self.args)))
+        args[name] = cast(float, self.fn(*(args[arg] for arg in self.args)))
 
 
 @dataclass(kw_only=True, slots=True)
@@ -214,35 +238,36 @@ class Reaction:
     fn: RateFn
     stoichiometry: Mapping[str, float | Derived]
     args: list[str]
+    unit: sympy.Expr | None = None
 
     def get_modifiers(self, model: Model) -> list[str]:
         """Get the modifiers of the reaction."""
-        include = set(model.variables)
+        include = set(model.get_variable_names())
         exclude = set(self.stoichiometry)
 
         return [k for k in self.args if k in include and k not in exclude]
 
-    def calculate(self, dependent: dict[str, Any]) -> float:
+    def calculate(self, args: dict[str, Any]) -> float:
         """Calculate the derived value.
 
         Args:
-            dependent: Dictionary of dependent variables.
+            args: Dictionary of args variables.
 
         Returns:
             The calculated derived value.
 
         """
-        return cast(float, self.fn(*(dependent[arg] for arg in self.args)))
+        return cast(float, self.fn(*(args[arg] for arg in self.args)))
 
-    def calculate_inpl(self, name: str, dependent: dict[str, Any]) -> None:
+    def calculate_inpl(self, name: str, args: dict[str, Any]) -> None:
         """Calculate the reaction in place.
 
         Args:
             name: Name of the derived variable.
-            dependent: Dictionary of dependent variables.
+            args: Dictionary of args variables.
 
         """
-        dependent[name] = cast(float, self.fn(*(dependent[arg] for arg in self.args)))
+        args[name] = cast(float, self.fn(*(args[arg] for arg in self.args)))
 
 
 @dataclass(kw_only=True)

mxlpy/units.py

@@ -0,0 +1,128 @@
+"""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,
+)
+
+__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

{mxlpy-0.20.0.dist-info → mxlpy-0.22.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mxlpy
-Version: 0.20.0
+Version: 0.22.0
 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>
@@ -69,6 +69,8 @@ Description-Content-Type: text/markdown
 [docs-badge]: https://img.shields.io/badge/docs-main-green.svg?style=flat-square
 [docs]: https://computational-biology-aachen.github.io/mxlpy/
 
+MxlPy (pronounced "em axe el pie") is a Python package for mechanistic learning (Mxl) - the combination of mechanistic modeling and machine learning to deliver explainable, data-informed solutions.
+
 ## Installation
 
 You can install mxlpy using pip: `pip install mxlpy`.

mxlpy-0.22.0.dist-info/RECORD

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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)

mxlpy-0.20.0.dist-info/RECORD

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