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

mxlpy/label_map.py

@@ -551,13 +551,13 @@ class LabelMapper:
 
         m = Model()
 
-        m.add_parameters(self.model.parameters)
+        m.add_parameters(self.model.get_parameter_values())
 
-        for name, dp in self.model.derived_parameters.items():
+        for name, dp in self.model.get_derived_parameters().items():
             m.add_derived(name, fn=dp.fn, args=dp.args)
 
         variables: dict[str, float | Derived] = {}
-        for k, v in self.model.variables.items():
+        for k, v in self.model.get_initial_conditions().items():
             if (isos := isotopomers.get(k)) is None:
                 variables[k] = v
             else:
@@ -585,14 +585,14 @@ class LabelMapper:
                 args=label_names,
             )
 
-        for name, dv in self.model.derived_variables.items():
+        for name, dv in self.model.get_derived_variables().items():
             m.add_derived(
                 name,
                 fn=dv.fn,
                 args=[f"{i}__total" if i in isotopomers else i for i in dv.args],
             )
 
-        for rxn_name, rxn in self.model.reactions.items():
+        for rxn_name, rxn in self.model.get_raw_reactions().items():
             if (label_map := self.label_maps.get(rxn_name)) is None:
                 m.add_reaction(
                     rxn_name,

mxlpy/linear_label_map.py

@@ -272,8 +272,10 @@ class LinearLabelMapper:
         m = Model()
         m.add_variables(variables)
         m.add_parameters(concs.to_dict() | fluxes.to_dict() | {"EXT": external_label})
+
+        rxns = self.model.get_raw_reactions()
         for rxn_name, label_map in self.label_maps.items():
-            rxn = self.model.reactions[rxn_name]
+            rxn = rxns[rxn_name]
             subs, prods = _unpack_stoichiometries(rxn.stoichiometry)
 
             subs = _stoichiometry_to_duplicate_list(subs)

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,
@@ -67,6 +66,7 @@ class ParameterScanWorker(Protocol):
         model: Model,
         *,
         parameters: pd.DataFrame,
+        y0: dict[str, float] | None,
         rel_norm: bool,
         integrator: IntegratorType,
     ) -> SteadyStates:
@@ -78,6 +78,7 @@ def _parameter_scan_worker(
     model: Model,
     *,
     parameters: pd.DataFrame,
+    y0: dict[str, float] | None,
     rel_norm: bool,
     integrator: IntegratorType,
 ) -> SteadyStates:
@@ -110,6 +111,7 @@ def _parameter_scan_worker(
         parallel=False,
         rel_norm=rel_norm,
         integrator=integrator,
+        y0=y0,
     )
 
 
@@ -122,7 +124,7 @@ 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.
 
@@ -153,6 +155,7 @@ def steady_state(
                 worker,
                 rel_norm=rel_norm,
                 integrator=integrator,
+                y0=None,
             ),
             model=model,
         ),
@@ -161,8 +164,8 @@ 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,
     )
 
@@ -176,7 +179,7 @@ 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.
 
@@ -207,6 +210,7 @@ def time_course(
                 worker,
                 time_points=time_points,
                 integrator=integrator,
+                y0=None,
             ),
             model=model,
         ),
@@ -217,8 +221,8 @@ 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,
     )
 
 
@@ -232,7 +236,7 @@ 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.
 
@@ -264,6 +268,7 @@ def time_course_over_protocol(
                 worker,
                 protocol=protocol,
                 integrator=integrator,
+                y0=None,
                 time_points_per_step=time_points_per_step,
             ),
             model=model,
@@ -272,8 +277,8 @@ 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,
@@ -292,7 +297,7 @@ 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.
 
@@ -339,6 +344,7 @@ def scan_steady_state(
                 parameters=to_scan,
                 rel_norm=rel_norm,
                 integrator=integrator,
+                y0=None,
             ),
             model=model,
         ),
@@ -346,8 +352,8 @@ 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,
@@ -422,7 +428,7 @@ 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(
@@ -486,7 +492,7 @@ 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(
@@ -501,7 +507,7 @@ 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.
 
@@ -558,9 +564,7 @@ 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

@@ -22,7 +22,6 @@ 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
@@ -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.
 
@@ -72,7 +71,7 @@ def _response_coefficient_worker(
             - Series of flux response coefficients
 
     """
-    old = model.parameters[parameter]
+    old = model.get_parameter_values()[parameter]
     if y0 is not None:
         model.update_variables(y0)
 
@@ -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
@@ -203,7 +205,7 @@ def parameter_elasticities(
 
     variables = model.get_initial_conditions() if variables is None else variables
     for par in to_scan:
-        old = model.parameters[par]
+        old = model.get_parameter_values()[par]
 
         model.update_parameters({par: old * (1 + displacement)})
         upper = model.get_fluxes(variables=variables, time=time)
@@ -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

@@ -2,12 +2,14 @@
 
 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
+from .codegen_latex import generate_latex_code, to_tex_export
+from .codegen_model import generate_model_code_py, generate_model_code_rs
+from .codegen_mxlpy import generate_mxlpy_code
 
 __all__ = [
     "generate_latex_code",
     "generate_model_code_py",
+    "generate_model_code_rs",
     "generate_mxlpy_code",
+    "to_tex_export",
 ]

mxlpy/meta/codegen_latex.py

@@ -7,7 +7,7 @@ from typing import TYPE_CHECKING
 
 import sympy
 
-from mxlpy.meta.source_tools import fn_to_sympy
+from mxlpy.meta.sympy_tools import fn_to_sympy, list_of_symbols
 from mxlpy.types import Derived, RateFn
 
 if TYPE_CHECKING:
@@ -21,6 +21,7 @@ __all__ = [
     "default_init",
     "generate_latex_code",
     "get_model_tex_diff",
+    "to_tex_export",
 ]
 
 cdot = r"\cdot"
@@ -31,10 +32,6 @@ newline = r"\\" + "\n"
 floatbarrier = r"\FloatBarrier"
 
 
-def _list_of_symbols(args: list[str]) -> list[sympy.Symbol | sympy.Expr]:
-    return [sympy.Symbol(arg) for arg in args]
-
-
 def default_init[T1, T2](d: dict[T1, T2] | None) -> dict[T1, T2]:
     """Return empty dict if d is None.
 
@@ -63,10 +60,6 @@ def _gls(s: str) -> str:
     return rf"\gls{{{s}}}"
 
 
-def _abbrev_and_full(s: str) -> str:
-    return rf"\acrfull{{{s}}}"
-
-
 def _gls_short(s: str) -> str:
     return rf"\acrshort{{{s}}}"
 
@@ -75,6 +68,10 @@ def _gls_full(s: str) -> str:
     return rf"\acrlong{{{s}}}"
 
 
+def _gls_short_and_full(s: str) -> str:
+    return rf"\acrfull{{{s}}}"
+
+
 def _rename_latex(s: str) -> str:
     if s[0].isdigit():
         s = s[1:]
@@ -109,6 +106,8 @@ def _sympy_to_latex(expr: sympy.Expr) -> str:
 
 def _fn_to_latex(
     fn: Callable,
+    *,
+    origin: str,
     arg_names: list[str],
     long_name_cutoff: int,
 ) -> tuple[str, dict[str, str]]:
@@ -121,10 +120,13 @@ def _fn_to_latex(
     replacements = {k: _name_to_latex(f"_x{i}") for i, k in enumerate(long_names)}
 
     expr = fn_to_sympy(
-        fn, _list_of_symbols([replacements.get(k, k) for k in tex_names])
+        fn,
+        origin=origin,
+        model_args=list_of_symbols([replacements.get(k, k) for k in tex_names]),
     )
-    fn_str = _sympy_to_latex(expr)
-    return fn_str, replacements
+    if expr is None:
+        return rf"\textcolor{{red}}{{{origin}}}", replacements
+    return _sympy_to_latex(expr), replacements
 
 
 def _table(
@@ -323,7 +325,8 @@ def _stoichs_to_latex(
             )
             sympy_fn = fn_to_sympy(
                 rxn_stoich.fn,
-                _list_of_symbols([replacements.get(k, k) for k in arg_names]),
+                origin=rxn_name,
+                model_args=list_of_symbols([replacements.get(k, k) for k in arg_names]),
             )
             expr = expr + sympy_fn * sympy.Symbol(rxn_name)  # type: ignore
         else:
@@ -480,7 +483,7 @@ class TexExport:
 
         def _add_gls_if_found(k: str) -> str:
             if (new := gls.get(k)) is not None:
-                return _abbrev_and_full(new)
+                return _gls_short_and_full(new)
             return k
 
         return TexExport(
@@ -564,7 +567,7 @@ class TexExport:
 
     def export_derived(
         self,
-        long_name_cutoff: int,
+        long_name_cutoff: int = 10,
     ) -> str:
         """Export derived quantities as LaTeX equations.
 
@@ -587,16 +590,20 @@ class TexExport:
         for k, v in sorted(self.derived.items()):
             fn_str, repls = _fn_to_latex(
                 v.fn,
+                origin=k,
                 arg_names=v.args,
                 long_name_cutoff=long_name_cutoff,
             )
-            rows.append(f"{_mathrm(_name_to_latex(k))} &= {fn_str} \\\\")
+            rows.append(f"    {_mathrm(_name_to_latex(k))} &= {fn_str} \\\\")
             if repls:
                 rows.append(_replacements_in_align(repls))
 
         return _latex_align(rows)
 
-    def export_reactions(self, long_name_cutoff: int) -> str:
+    def export_reactions(
+        self,
+        long_name_cutoff: int = 10,
+    ) -> str:
         """Export reactions as LaTeX equations.
 
         Returns
@@ -618,17 +625,18 @@ class TexExport:
         for k, v in sorted(self.reactions.items()):
             fn_str, repls = _fn_to_latex(
                 v.fn,
+                origin=k,
                 arg_names=v.args,
                 long_name_cutoff=long_name_cutoff,
             )
-            rows.append(f"{_mathrm(_name_to_latex(k))} &= {fn_str} \\\\")
+            rows.append(f"    {_mathrm(_name_to_latex(k))} &= {fn_str} \\\\")
             if repls:
                 rows.append(_replacements_in_align(repls))
         return _latex_align(rows)
 
     def export_diff_eqs(
         self,
-        long_name_cutoff: int,
+        long_name_cutoff: int = 10,
     ) -> str:
         """Export stoichiometries as LaTeX table.
 
@@ -654,12 +662,15 @@ class TexExport:
                 long_name_cutoff=long_name_cutoff,
             )
 
-            rows.append(f"{dxdt} &= {stoich_str} \\\\")
+            rows.append(f"    {dxdt} &= {stoich_str} \\\\")
             if repls:
                 rows.append(_replacements_in_align(repls))
         return _latex_align(rows)
 
-    def export_all(self, long_name_cutoff: int = 10) -> str:
+    def export_all(
+        self,
+        long_name_cutoff: int = 10,
+    ) -> str:
         """Export all model parts as a complete LaTeX document section.
 
         Returns
@@ -754,7 +765,7 @@ class TexExport:
 \usepackage[a4paper,top=2cm,bottom=2cm,left=2cm,right=2cm,marginparwidth=1.75cm]{{geometry}}
 \usepackage{{amsmath, amssymb, array, booktabs,
             breqn, caption, longtable, mathtools, placeins,
-            ragged2e, tabularx, titlesec, titling}}
+            ragged2e, tabularx, titlesec, titling, xcolor}}
 \newcommand{{\sectionbreak}}{{\clearpage}}
 \setlength{{\parindent}}{{0pt}}
 \allowdisplaybreaks
@@ -769,17 +780,20 @@ class TexExport:
 """
 
 
-def _to_tex_export(self: Model) -> TexExport:
+def to_tex_export(model: Model) -> TexExport:
+    """Create TexExport object from a model."""
     diff_eqs = {}
-    for rxn_name, rxn in self.reactions.items():
+    for rxn_name, rxn in model.get_raw_reactions().items():
         for var_name, factor in rxn.stoichiometry.items():
             diff_eqs.setdefault(var_name, {})[rxn_name] = factor
 
     return TexExport(
-        parameters=self.parameters,
-        variables=self.get_initial_conditions(),  # FIXME: think about this later
-        derived=self.derived,
-        reactions={k: TexReaction(v.fn, v.args) for k, v in self.reactions.items()},
+        parameters=model.get_parameter_values(),
+        variables=model.get_initial_conditions(),  # FIXME: think about this later
+        derived=model.get_raw_derived(),
+        reactions={
+            k: TexReaction(v.fn, v.args) for k, v in model.get_raw_reactions().items()
+        },
         diff_eqs=diff_eqs,
     )
 
@@ -820,7 +834,7 @@ def generate_latex_code(
     """
     gls = default_init(gls)
     return (
-        _to_tex_export(model)
+        to_tex_export(model)
         .rename_with_glossary(gls)
         .export_document(long_name_cutoff=long_name_cutoff)
     )
@@ -866,7 +880,7 @@ def get_model_tex_diff(
     return f"""{" start autogenerated ":%^60}
 {_clearpage()}
 {_subsubsection("Model changes")}{_label(section_label)}
-{((_to_tex_export(m1) - _to_tex_export(m2)).rename_with_glossary(gls).export_all(long_name_cutoff=long_name_cutoff))}
+{((to_tex_export(m1) - to_tex_export(m2)).rename_with_glossary(gls).export_all(long_name_cutoff=long_name_cutoff))}
 {_clearpage()}
 {" end autogenerated ":%^60}
 """