work on odefactory

src/sbmlutils/converters/odefac.py

@@ -54,20 +54,35 @@ def __init__(self, doc: libsbml.SBMLDocument):
         """
         self.doc: libsbml.SBMLDocument = doc
 
+        self.names: Dict[str, str] = {}
         self.units: Dict[str, Optional[str]] = {}  # model units
+
+        # --- fixed model entities ---
+        # p: constants (parameters, compartments, species)
+        # x: initial values (state variables)
+
+        # assignments
+        # p=: assignment rules (species, parameters, compartments)
+        # x0=: initial values
+
+        # kinetics dx/dt
+        # x: state variables (species, parameters, compartments)
+
         self.x0: Dict = {}  # initial amounts/concentrations
         self.a_ast: Dict = {}  # initial assignments
         self.dx: Dict = {}
         self.dx_ast: Dict = {}  # state variables x (odes)
         self.x_units: Dict = {}  # state variables x units
         self.x_compartments: Dict = {}  # compartments of species
         self.x_: Set = set()  # species state variables as concentrations
+
         self.p: Dict = {}  # parameters p (constants)
         self.p_units: Dict = {}  # parameter units
+
         self.y_ast: Dict = {}  # assigned variables
         self.yids_ordered: List[str]  # yids in order of math dependencies
         self.y_units: Dict = {}  # y units
-        self.names: Dict[str, str] = {}
+
 
         # create name dictionary
         sbase: libsbml.SBase
@@ -417,56 +432,71 @@ def create_ordered_variables(
         yids = create_ordered_variables(g)
         return yids
 
-    def to_python(self, py_file: Path) -> None:
+    def to_python(self, py_file: Optional[Path]=None) -> str:
         """Write ODEs to python."""
         content = self._render_template(
             template_file="odefac_template.pytemp",
             index_offset=0,
             replace_symbols=True,
         )
-        with open(py_file, "w") as f:
-            f.write(content)
+        if py_file:
+            with open(py_file, "w") as f:
+                f.write(content)
 
-    def to_tex(self, tex_file: Path) -> None:
+        return content
+
+    def to_tex(self, tex_file: Optional[Path]=None) -> str:
         """Write ODEs to tex/latex."""
         content = self._render_template(
             template_file="odefac_template.tex",
             index_offset=0,
             replace_symbols=False,
         )
-        with open(tex_file, "w") as f:
-            f.write(content)
+        if tex_file:
+            with open(tex_file, "w") as f:
+                f.write(content)
+
+        return content
 
-    def to_R(self, r_file: Path) -> None:
+    def to_R(self, r_file: Optional[Path]=None) -> str:
         """Write ODEs to R."""
         content = self._render_template(
             template_file="odefac_template.R",
             index_offset=1,
             replace_symbols=True,
         )
-        with open(r_file, "w") as f:
-            f.write(content)
+        if r_file:
+            with open(r_file, "w") as f:
+                f.write(content)
 
-    def to_markdown(self, md_file: Path) -> None:
+        return content
+
+    def to_markdown(self, md_file: Optional[Path]=None) -> str:
         """Write ODEs to markdown."""
         content = self._render_template(
             template_file="odefac_template.md",
             index_offset=0,
             replace_symbols=False,
         )
-        with open(md_file, "w") as f:
-            f.write(content)
+        if md_file:
+            with open(md_file, "w") as f:
+                f.write(content)
+
+        return content
 
-    def to_custom_template(self, output_file: Path, template_file: Path) -> None:
+    def to_custom_template(self, template_file: Path, output_file: Optional[Path]=None) -> str:
         """Write ODEs to custom template."""
         content = self._render_template(
             template_file=template_file.name,
             index_offset=0,
             replace_symbols=False,
             template_dir=template_file.parent,
         )
-        with open(output_file, "w") as f:
-            f.write(content)
+        if output_file:
+            with open(output_file, "w") as f:
+                f.write(content)
+
+        return content
 
     def _render_template(
         self,

src/sbmlutils/examples/assignment.py

@@ -1,4 +1,6 @@
 """AssignmentRule and InitialAssignment example."""
+from sbmlutils.console import console
+from sbmlutils.converters import odefac
 from sbmlutils.examples import templates
 from sbmlutils.factory import *
 
@@ -90,7 +92,7 @@ class U(Units):
         "Cve",
         "A/Vblood",
         U.mg_per_l,
-        name="rule to calulate concentration",
+        name="rule to calculate concentration",
         notes="""
         Assignment rule to calculate the concentration `Cve` in [mg/l] from the
         species `A` and the volume `Vblood`.
@@ -106,4 +108,9 @@ class U(Units):
 if __name__ == "__main__":
     from sbmlutils.resources import EXAMPLES_DIR
 
-    create_model(model=model, filepath=EXAMPLES_DIR / f"{model.sid}.xml")
+    results: FactoryResult = create_model(model=model, filepath=EXAMPLES_DIR / f"{model.sid}.xml")
+    factory = odefac.SBML2ODE.from_file(sbml_file=results.sbml_path)
+    md_str = factory.to_markdown()
+    from rich.markdown import Markdown
+    console.print(Markdown(md_str))
+

src/sbmlutils/factory.py

@@ -400,7 +400,7 @@ def __init__(
     def __str__(self) -> str:
         """Get string."""
         field_str = ", ".join(
-            [str(getattr(self, f)) for f in self.fields if getattr(self, f)]
+            [str(getattr(self, f)) for f in self.fields if getattr(self, f) if f not in {"notes", "annotations"}]
         )
         return f"{self.__class__.__name__}({field_str})"
 

src/sbmlutils/resources/converters/odefac_template.R

@@ -1,8 +1,8 @@
-# -----------------------------------------------------------
-# Autogenerated ODE definition from SBML file with sbmlutils.
+# ---------------------------------------------------------------------------------------------------------
+# Autogenerated ODE definition from SBML file with sbmlutils (https://github.com/matthiaskoenig/sbmlutils).
 #
 #    model: {{ model.getId() }}
-# -----------------------------------------------------------
+# ---------------------------------------------------------------------------------------------------------
 
 # -------------------
 # ids
@@ -95,4 +95,4 @@ f_z <- function(times, X, p){
     }
     colnames(Z) <- c ("time", xids, yids)
     Z
-}
+}

src/sbmlutils/resources/converters/odefac_template.md

@@ -1,5 +1,5 @@
 # model: {{ model.getId() }}
-Autogenerated ODE System from SBML with [sbmlutils](https://github.com/matthiaskoenig/sbmlutils.git).
+Autogenerated ODE System from SBML with [sbmlutils](https://github.com/matthiaskoenig/sbmlutils).
 ```
 time: [{{units["time"]}}]
 substance: [{{units["substance"]}}]

src/sbmlutils/resources/converters/odefac_template.pytemp

@@ -1,5 +1,5 @@
 """
-Autogenerated ODE definition SBML file with sbmlutils (https://github.com/matthiaskoenig/sbmlutils.git).
+Autogenerated ODE definition SBML file with sbmlutils (https://github.com/matthiaskoenig/sbmlutils).
 
     model: {{ model.getId() }}
 

src/sbmlutils/resources/converters/odefac_template.tex

@@ -1,5 +1,5 @@
 % model: {{ model.getId() }}
-% Autogenerated ODE System from SBML with sbmlutils (https://github.com/matthiaskoenig/sbmlutils.git).
+% Autogenerated ODE System from SBML with sbmlutils (https://github.com/matthiaskoenig/sbmlutils).
 %
 % add the following packages:
 % \usepackage{amsmath}

src/sbmlutils/resources/examples/assignment.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" level="3" version="1" comp:required="true">
   <notes>
     <body xmlns="http://www.w3.org/1999/xhtml">
       <p>Created with <a href="https://github.com/matthiaskoenig/sbmlutils">https://github.com/matthiaskoenig/sbmlutils</a>.
@@ -17,7 +17,7 @@ AssignmentRules are evaluated at every time point.</p>
         <p>The content of this model has been carefully created in a manual research effort.
 This file has been created by <a href="https://livermetabolism.com">Matthias König</a>
 using <a href="https://github.com/matthiaskoenig/sbmlutils">sbmlutils</a>.
-For questions contact <a href="mailto:koenigmx@hu-berlin.de">koenigmx@hu-berlin.de</a>. Copyright © 2022 Matthias König.</p>
+For questions contact <a href="mailto:koenigmx@hu-berlin.de">koenigmx@hu-berlin.de</a>. Copyright © 2024 Matthias König.</p>
         <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">
           <img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png"/>
         </a>
@@ -123,7 +123,7 @@ An InitialAssignment is used to set the parameter.</p>
       <parameter id="BW" name="body weight" value="70" units="kg" constant="true"/>
       <parameter id="FVblood" name="fractional volume of the blood" value="0.05" units="l_per_kg" constant="true"/>
       <parameter id="Vblood" name="blood volume" value="NaN" units="litre" constant="true"/>
-      <parameter id="Cve" name="rule to calulate concentration" value="NaN" units="mg_per_l" constant="false"/>
+      <parameter id="Cve" name="rule to calculate concentration" value="NaN" units="mg_per_l" constant="false"/>
     </listOfParameters>
     <listOfInitialAssignments>
       <initialAssignment symbol="D">