Merge pull request #181 from jmuhlich/export_pysb

Add pysb_flat exporter

pysb/core.py

@@ -1654,8 +1654,10 @@ def __init__(self):
 # implements an alternate __str__ method which just returns the base name.
 
 class KeywordMeta(type):
-    def __str__(cls):
+    def __repr__(cls):
         return cls.__name__
+    def __str__(cls):
+        return repr(cls)
 
 class Keyword(object): __metaclass__ = KeywordMeta
 

pysb/export/__init__.py

@@ -21,6 +21,7 @@
 - ``potterswheel``
 - ``sbml``
 - ``python``
+- ``pysb_flat``
 - ``mathematica``
 - ``matlab``
 
@@ -68,6 +69,7 @@
    bng_net
    kappa
    python
+   pysb_flat
 """
 
 import re
@@ -124,6 +126,7 @@ def export(self):
         'potterswheel': 'PottersWheelExporter',
         'sbml': 'SbmlExporter',
         'python': 'PythonExporter',
+        'pysb_flat': 'PysbFlatExporter',
         'mathematica': 'MathematicaExporter',
         'matlab': 'MatlabExporter',
         }

pysb/export/pysb_flat.py

@@ -0,0 +1,79 @@
+"""
+A module containing a class that exports a PySB model to a single Python source
+file that, when imported, will recreate the same model. This is intended for
+saving a dynamically generated model so that it can be reused without re-running
+the dynamic generation process. Note that any macro calls and other program
+structure in the original model are "flattened" in the process.
+
+For information on how to use the model exporters, see the documentation
+for :py:mod:`pysb.export`.
+
+Structure of the Python code
+============================
+
+The standalone Python code calls ``Model()``, then defines Monomers, Parameters,
+Expressions (constant), Compartments, Observables, Expressions (dynamic), Rules
+and initial conditions in that order. This can be considered a sort of "repr()"
+for a full model.
+
+If the output is saved as ``foo.py`` then one may load the model with the
+following line::
+
+    from foo import model
+
+"""
+
+import pysb
+from pysb.export import Exporter
+try:
+    from cStringIO import StringIO
+except ImportError:
+    from io import StringIO
+
+class PysbFlatExporter(Exporter):
+    """A class for generating PySB "flat" model source code from a model.
+
+    Inherits from :py:class:`pysb.export.Exporter`, which implements
+    basic functionality for all exporters.
+    """
+    def export(self):
+        """Export PySB source code from a model.
+
+        Returns
+        -------
+        string
+            String containing the Python code.
+        """
+
+        output = StringIO()
+
+        # Convenience function for writing out a componentset.
+        def write_cset(cset):
+            for c in cset:
+                output.write(repr(c))
+                output.write("\n")
+            output.write("\n")
+
+        if self.docstring:
+            output.write('"""')
+            output.write(self.docstring)
+            output.write('"""\n\n')
+        output.write("# exported from PySB model '%s'\n" % self.model.name)
+        output.write("\n")
+        output.write("from pysb import Model, Monomer, Parameter, Expression, "
+                     "Compartment, Rule, Observable, Initial, ANY, WILD\n")
+        output.write("\n")
+        output.write("Model()\n")
+        output.write("\n")
+        write_cset(self.model.monomers)
+        write_cset(self.model.parameters)
+        write_cset(self.model.expressions_constant())
+        write_cset(self.model.compartments)
+        write_cset(self.model.observables)
+        write_cset(self.model.expressions_dynamic())
+        write_cset(self.model.rules)
+        for pattern, value in self.model.initial_conditions:
+            output.write("Initial(%s, %s)\n" % (repr(pattern), value.name))
+        output.write("\n")
+
+        return output.getvalue()

pysb/export/python.py

@@ -107,9 +107,10 @@ def export(self):
         for i, p in enumerate(self.model.parameters):
             code_eqs = re.sub(r'\b(%s)\b' % p.name, 'p[%d]' % i, code_eqs)
 
-        output.write('"""')
-        output.write(self.docstring)
-        output.write('"""\n\n')
+        if self.docstring:
+            output.write('"""')
+            output.write(self.docstring)
+            output.write('"""\n\n')
         output.write("# exported from PySB model '%s'\n" % self.model.name)
         output.write(pad(r"""
             import numpy

pysb/macros.py

@@ -2173,7 +2173,7 @@ def chain_species_base(base, basesite, subunit, site1, site2, size, comp=1):
         >>> Monomer('Complex2', ['s1', 's2'])
         Monomer('Complex2', ['s1', 's2'])
         >>> chain_species_base(Base(b2=ANY), 'b1', Unit, 'p1', 'p2', 4, Complex1(s1=ANY) % Complex2(s1=ANY, s2=ANY))
-        MatchOnce(Complex1(s1=<class 'pysb.core.ANY'>) % Complex2(s1=<class 'pysb.core.ANY'>, s2=<class 'pysb.core.ANY'>) % Base(b1=1, b2=<class 'pysb.core.ANY'>) % Unit(p1=1, p2=2) % Unit(p1=2, p2=3) % Unit(p1=3, p2=4) % Unit(p1=4, p2=None))
+        MatchOnce(Complex1(s1=ANY) % Complex2(s1=ANY, s2=ANY) % Base(b1=1, b2=ANY) % Unit(p1=1, p2=2) % Unit(p1=2, p2=3) % Unit(p1=3, p2=4) % Unit(p1=4, p2=None))
     """
     _verify_sites(base, basesite)
     _verify_sites(subunit, site1, site2)
@@ -2262,10 +2262,10 @@ def assemble_chain_sequential_base(base, basesite, subunit, site1, site2, max_si
         Monomer('Complex2', ['s1', 's2'])
         >>> assemble_chain_sequential_base(Base(b2=ANY), 'b1', Unit, 'p1', 'p2', 3, [[1e-4, 1e-1]] * 2, Complex1(s1=ANY) % Complex2(s1=ANY, s2=ANY)) # doctest:+NORMALIZE_WHITESPACE
         ComponentSet([
-         Rule('assemble_chain_sequential_base_Unit_2', Unit(p1=None, p2=None) + Complex1(s1=<class 'pysb.core.ANY'>) % Complex2(s1=<class 'pysb.core.ANY'>, s2=<class 'pysb.core.ANY'>) % Base(b1=1, b2=<class 'pysb.core.ANY'>) % Unit(p1=1, p2=None) <> Complex1(s1=<class 'pysb.core.ANY'>) % Complex2(s1=<class 'pysb.core.ANY'>, s2=<class 'pysb.core.ANY'>) % Base(b1=1, b2=<class 'pysb.core.ANY'>) % Unit(p1=1, p2=2) % Unit(p1=2, p2=None), assemble_chain_sequential_base_Unit_2_kf, assemble_chain_sequential_base_Unit_2_kr),
+         Rule('assemble_chain_sequential_base_Unit_2', Unit(p1=None, p2=None) + Complex1(s1=ANY) % Complex2(s1=ANY, s2=ANY) % Base(b1=1, b2=ANY) % Unit(p1=1, p2=None) <> Complex1(s1=ANY) % Complex2(s1=ANY, s2=ANY) % Base(b1=1, b2=ANY) % Unit(p1=1, p2=2) % Unit(p1=2, p2=None), assemble_chain_sequential_base_Unit_2_kf, assemble_chain_sequential_base_Unit_2_kr),
          Parameter('assemble_chain_sequential_base_Unit_2_kf', 0.0001),
          Parameter('assemble_chain_sequential_base_Unit_2_kr', 0.1),
-         Rule('assemble_chain_sequential_base_Unit_3', Unit(p1=None, p2=None) + Complex1(s1=<class 'pysb.core.ANY'>) % Complex2(s1=<class 'pysb.core.ANY'>, s2=<class 'pysb.core.ANY'>) % Base(b1=1, b2=<class 'pysb.core.ANY'>) % Unit(p1=1, p2=2) % Unit(p1=2, p2=None) <> MatchOnce(Complex1(s1=<class 'pysb.core.ANY'>) % Complex2(s1=<class 'pysb.core.ANY'>, s2=<class 'pysb.core.ANY'>) % Base(b1=1, b2=<class 'pysb.core.ANY'>) % Unit(p1=1, p2=2) % Unit(p1=2, p2=3) % Unit(p1=3, p2=None)), assemble_chain_sequential_base_Unit_3_kf, assemble_chain_sequential_base_Unit_3_kr),
+         Rule('assemble_chain_sequential_base_Unit_3', Unit(p1=None, p2=None) + Complex1(s1=ANY) % Complex2(s1=ANY, s2=ANY) % Base(b1=1, b2=ANY) % Unit(p1=1, p2=2) % Unit(p1=2, p2=None) <> MatchOnce(Complex1(s1=ANY) % Complex2(s1=ANY, s2=ANY) % Base(b1=1, b2=ANY) % Unit(p1=1, p2=2) % Unit(p1=2, p2=3) % Unit(p1=3, p2=None)), assemble_chain_sequential_base_Unit_3_kf, assemble_chain_sequential_base_Unit_3_kr),
          Parameter('assemble_chain_sequential_base_Unit_3_kf', 0.0001),
          Parameter('assemble_chain_sequential_base_Unit_3_kr', 0.1),
          ])