Fix repr() of single-monomer complexes w/ compartments (pysb#550)

* Fix repr() of single-monomer complexes w/ compartments

In BNG, a compartment applied to a complex is distinct from one
applied to a monomer, by use of prefix and postfix notation. In
PySB, one can use parentheses to add a compartment to a complex,
but this fails for a complex of length 1. One can use
`as_complex_pattern()` to explicitly upgrade to a complex from
a monomer, but the string representation and PySB flat exporter
currently fail to respect this.

    A() ** C  # Monomer compartment
    as_complex_pattern(A()) ** C  # Complex compartment

This PR adds `as_complex_pattern()` around complexes with a
single monomer pattern that also have a compartment, to make
sure their string representation and PySB flat export works
as expected.

Co-authored-by: Jeremy Muhlich <jmuhlich@bitflood.org>

pysb/core.py

@@ -1117,6 +1117,8 @@ def __repr__(self):
         if self.compartment:
             if len(self.monomer_patterns) > 1:
                 ret = '(%s)' % ret
+            else:
+                ret = 'as_complex_pattern(%s)' % ret
             ret += ' ** %s' % self.compartment.name
         if self.match_once:
             ret = 'MatchOnce(%s)' % ret

pysb/export/pysb_flat.py

@@ -82,7 +82,8 @@ def write_cset(cset):
         output.write("\n")
         output.write("from pysb import Model, Monomer, Parameter, Expression, "
                      "Compartment, Rule, Observable, Initial, MatchOnce, "
-                     "EnergyPattern, Annotation, MultiState, Tag, ANY, WILD\n")
+                     "EnergyPattern, Annotation, MultiState, Tag, ANY, WILD, "
+                     "as_complex_pattern\n")
         if sympy_functions:
             output.write(
                 "from sympy import " + ", ".join(sympy_functions) + "\n"

pysb/tests/test_core.py

@@ -359,6 +359,23 @@ def test_complex_pattern_equivalence_compartments():
     _check_pattern_equivalence((cp0, cp1))
 
 
+@with_model
+def test_complex_pattern_single_monomer_complex_compartment():
+    Monomer('A')
+    Compartment('C')
+    Parameter('A_0', 10)
+    cp_source = as_complex_pattern(A()) ** C
+
+    # Check executing the string representation of the above ComplexPattern
+    # leads to the correct application of compartment, i.e. compartment applies
+    # to complex, not to monomer
+    exec(f"Initial({str(cp_source)}, A_0)")
+
+    cp_in_model = model.initials[0].pattern
+    assert cp_in_model.compartment == C
+    assert cp_in_model.monomer_patterns[0].compartment is None
+
+
 @with_model
 def test_reaction_pattern_match_complex_pattern_ordering():
     """Ensure CP equivalence is insensitive to MP order."""
@@ -487,7 +504,7 @@ def test_tags():
 
     # Test tag with compartment
     Compartment('c')
-    assert repr((A().__matmul__(x)) ** c) == 'A() ** c @ x'
+    assert repr((A().__matmul__(x)) ** c) == 'as_complex_pattern(A()) ** c @ x'
     assert repr((A() ** c).__matmul__(x)) == 'A() ** c @ x'