Reverting to BCSL Original Syntax: Implementing "::"

Testing/models/model_cmplx_in_abstr_seq1.txt

@@ -1,5 +1,5 @@
 #! rules
-S{i}:A():A2::cell  => A()::cell
+S{i}::A()::A2::cell  => A()::cell
 
 #! complexes
 A2 = A().A()

Testing/models/model_cmplx_in_abstr_seq2.txt

@@ -1,2 +1,2 @@
 #! rules
-S{i}:A():A().A()::cell => A()::cell
+S{i}::A()::A().A()::cell => A()::cell

Testing/models/model_miyoshi.txt

@@ -1,8 +1,8 @@
 #! rules
-S{u}:KaiC():KaiC6::cyt => S{p}:KaiC():KaiC6::cyt @ (kcat1*[KaiA2()::cyt]*[KaiC6::cyt])/(Km + [KaiC6::cyt])
-S{p}:KaiC():KaiC6::cyt => S{u}:KaiC():KaiC6::cyt @ (kcat2*[KaiB4{a}.KaiA2()::cyt]*[KaiC6::cyt])/(Km + [KaiC6::cyt])
-T{u}:KaiC():KaiC6::cyt => T{p}:KaiC():KaiC6::cyt @ (kcat3*[KaiA2()::cyt]*[KaiC6::cyt])/(Km + [KaiC6::cyt])
-T{p}:KaiC():KaiC6::cyt => T{u}:KaiC():KaiC6::cyt @ (kcat4*[KaiB4{a}.KaiA2()::cyt]*[KaiC6::cyt])/(Km + [KaiC6::cyt])
+S{u}::KaiC()::KaiC6::cyt => S{p}::KaiC()::KaiC6::cyt @ (kcat1*[KaiA2()::cyt]*[KaiC6::cyt])/(Km + [KaiC6::cyt])
+S{p}::KaiC()::KaiC6::cyt => S{u}::KaiC()::KaiC6::cyt @ (kcat2*[KaiB4{a}.KaiA2()::cyt]*[KaiC6::cyt])/(Km + [KaiC6::cyt])
+T{u}::KaiC()::KaiC6::cyt => T{p}::KaiC()::KaiC6::cyt @ (kcat3*[KaiA2()::cyt]*[KaiC6::cyt])/(Km + [KaiC6::cyt])
+T{p}::KaiC()::KaiC6::cyt => T{u}::KaiC()::KaiC6::cyt @ (kcat4*[KaiB4{a}.KaiA2()::cyt]*[KaiC6::cyt])/(Km + [KaiC6::cyt])
 KaiB4{i}::cyt => KaiB4{a}::cyt @ (kcatb2*[KaiB4{i}::cyt])/(Kmb2 + [KaiB4{i}::cyt])
 KaiB4{a}::cyt => KaiB4{i}::cyt @ (kcatb1*[KaiB4{a}::cyt])/(Kmb1 + [KaiB4{a}::cyt])
 KaiB4{a}.KaiA2()::cyt => KaiB4{a}::cyt + KaiA2()::cyt @ k12*[KaiB4{a}.KaiA2()::cyt]

Testing/models/model_with_complexes.txt

@@ -1,8 +1,8 @@
- #! rules
+#! rules
 // commenting
-X(T{a}):XX::rep => X(T{o}):XX::rep @ k2*[X().X()::rep]
-K{i}:X():XYZ::rep => K{p}:X():XYZ::rep @ k1*[X().Y().Z()::rep] // also here
-=> P{f}:XP::rep @ 1/(1+([X().P{_}::rep])**4) // ** means power (^)
+X(T{a})::XX::rep => X(T{o})::XX::rep @ k2*[X().X()::rep]
+K{i}::X()::XYZ::rep => K{p}::X()::XYZ::rep @ k1*[X().Y().Z()::rep] // also here
+=> P{f}::XP::rep @ 1/(1+([X().P{_}::rep])**4) // ** means power (^)
 
 #! inits
 // here

Testing/models/model_with_variable.txt

@@ -1,7 +1,7 @@
 #! rules
 // commenting
-T{a}:X():?::rep => T{o}:X():?::rep @ k2*[X().X()::rep] ; ? = { XX, XY }
-K{i}:X():XY::rep => K{p}:X():XY::rep @ k1*[X().Y().Z().X()::rep] // also here
+T{a}::X()::?::rep => T{o}::X()::?::rep @ k2*[X().X()::rep] ; ? = { XX, XY }
+K{i}::X()::XY::rep => K{p}::X()::XY::rep @ k1*[X().Y().Z().X()::rep] // also here
 
 #! inits
 // here

eBCSgen/Parsing/ParseBCSL.py

@@ -4,7 +4,7 @@
 from numpy import inf
 from copy import deepcopy
 from lark import Lark, Transformer, Tree
-from lark import UnexpectedCharacters, UnexpectedToken
+from lark import UnexpectedCharacters, UnexpectedToken, UnexpectedEOF
 from lark.load_grammar import _TERMINAL_NAMES
 import regex
 from sortedcontainers import SortedList
@@ -106,16 +106,16 @@ def to_side(self):
     model: (sections)* rules (sections | rules)*
     sections: inits | definitions | complexes | regulation
 
-    rules: RULES_START _NL+ ((rule|COMMENT) _NL+)* rule _NL*
-    inits: INITS_START _NL+ ((init|COMMENT) _NL+)* init _NL*
-    definitions: DEFNS_START _NL+ ((definition|COMMENT) _NL+)* definition _NL*
-    complexes: COMPLEXES_START _NL+ ((cmplx_dfn|COMMENT) _NL+)* cmplx_dfn _NL*
+    rules: RULES_START _NL+ (rule _NL+)* rule _NL*
+    inits: INITS_START _NL+ (init _NL+)* init _NL*
+    definitions: DEFNS_START _NL+ (definition _NL+)* definition _NL*
+    complexes: COMPLEXES_START _NL+ (cmplx_dfn _NL+)* cmplx_dfn _NL*
     regulation: REGULATION_START _NL+ regulation_def _NL*
 
-    init: const? rate_complex (COMMENT)?
-    definition: def_param "=" number (COMMENT)?
-    rule: ((label)? side ARROW side ("@" rate)? (";" variable)? (COMMENT)?) | ((label)? side BI_ARROW side ("@" rate "|" rate)? (";" variable)? (COMMENT)?)
-    cmplx_dfn: cmplx_name "=" value (COMMENT)?
+    init: const? rate_complex 
+    definition: def_param "=" number
+    rule: ((label)? side ARROW side ("@" rate)? (";" variable)?) | ((label)? side BI_ARROW side ("@" rate "|" rate )? (";" variable)?)
+    cmplx_dfn: cmplx_name "=" value
 
     side: (const? complex "+")* (const? complex)?
     complex: (abstract_sequence|value|cmplx_name) DOUBLE_COLON compartment
@@ -157,9 +157,9 @@ def to_side(self):
 
 EXTENDED_GRAMMAR = """
     abstract_sequence: atomic_complex | atomic_structure_complex | structure_complex
-    atomic_complex: atomic ":" (VAR | value)
-    atomic_structure_complex: atomic ":" structure ":" (VAR | value)
-    structure_complex: structure ":" (VAR | value)
+    atomic_complex: atomic "::" (VAR | value)
+    atomic_structure_complex: atomic "::" structure "::" (VAR | value)
+    structure_complex: structure "::" (VAR | value)
 
     variable: VAR "=" "{" cmplx_name ("," cmplx_name)+ "}"
     VAR: "?"
@@ -695,7 +695,7 @@ def __init__(self, start):
             + REGULATIONS_GRAMMAR
         )
         self.parser = Lark(
-            grammar, parser="lalr", propagate_positions=False, maybe_placeholders=False
+            grammar, parser="earley", propagate_positions=False, maybe_placeholders=False
         )
 
         self.terminals = dict((v, k) for k, v in _TERMINAL_NAMES.items())
@@ -796,4 +796,14 @@ def syntax_check(self, expression: str) -> Result:
                     "column": u.column,
                 },
             )
+        except UnexpectedEOF as u:
+            return Result(
+                False,
+                {
+                    "unexpected": str(u.token), 
+                    "expected": self.replace(u.expected),
+                    "line": u.line,
+                    "column": u.column,
+                },
+            )
         return Result(True, tree)