PyBioNetGen: Add PLA support to BNGsim backend bridge

Previously the BNGsim backend hook rejected PLA actions and routed them
to the BNG2.pl subprocess, where the bundled run_network binary fails
on the '-p pla' method. Now PLA is treated like ode/ssa/psa: the Perl
hook intercepts it and delegates to the backend helper, which passes it
through to BNGsim when available. The method alias map, routing checks,
and test patch hook are all updated accordingly.

Author: akutuva21

bionetgen/core/tools/bngsim_backend_helper.py

@@ -41,6 +41,7 @@
     "ode": "ode",
     "ssa": "ssa",
     "psa": "psa",
+    "pla": "pla",
     "rm": "rm",
 }
 

bionetgen/core/tools/bngsim_bridge.py

@@ -1199,7 +1199,7 @@ def _nfsim_session_kwargs(nf_params):
     FORMAT_ANTIMONY,
 }
 
-_BNGSIM_NETWORK_METHODS = frozenset({"ode", "ssa", "psa", "rm"})
+_BNGSIM_NETWORK_METHODS = frozenset({"ode", "ssa", "psa", "pla", "rm"})
 
 _BNGL_ROUTING_COMPLEX_ACTIONS = frozenset(
     {
@@ -1424,40 +1424,11 @@ def _classify_bngl_actions_for_bngsim(
     if len(sim_actions) > 1:
         has_backend_hook_workflow = True
 
-    if any(workflow_method == "pla" for workflow_method in workflow_methods):
-        return BngsimRouteDecision(
-            ROUTE_SUBPROCESS,
-            "BNGL PLA is not supported by BNGsim",
-            method="pla",
-        )
-
     if method is not None:
         method_name = _strip_quotes(str(method).strip()).lower()
         if sim_actions:
-            if any(
-                _bngl_action_method_for_routing(action) == "pla"
-                for action in sim_actions
-            ):
-                return BngsimRouteDecision(
-                    ROUTE_SUBPROCESS,
-                    "BNGL PLA is not supported by BNGsim",
-                    method="pla",
-                )
-            action_method = _bngl_action_method_for_routing(sim_actions[0])
-            if action_method == "pla":
-                return BngsimRouteDecision(
-                    ROUTE_SUBPROCESS,
-                    "BNGL PLA is not supported by BNGsim",
-                    method="pla",
-                )
             if method_name == "ssa" and "poplevel" in (sim_actions[0].args or {}):
                 method_name = "psa"
-        if method_name == "pla":
-            return BngsimRouteDecision(
-                ROUTE_SUBPROCESS,
-                "BNGL PLA is not supported by BNGsim",
-                method="pla",
-            )
         if _method_supported_by_bngsim_for_routing(method_name, bngsim_has_nfsim):
             return BngsimRouteDecision(
                 ROUTE_BNGL_BNGSIM,
@@ -1473,21 +1444,9 @@ def _classify_bngl_actions_for_bngsim(
     candidate_methods = []
     for action in sim_actions:
         method_name = _bngl_action_method_for_routing(action)
-        if method_name == "pla":
-            return BngsimRouteDecision(
-                ROUTE_SUBPROCESS,
-                "BNGL PLA is not supported by BNGsim",
-                method="pla",
-            )
         candidate_methods.append(method_name)
 
     for method_name in workflow_methods:
-        if method_name == "pla":
-            return BngsimRouteDecision(
-                ROUTE_SUBPROCESS,
-                "BNGL PLA is not supported by BNGsim",
-                method="pla",
-            )
         if method_name != "protocol":
             candidate_methods.append(method_name)
 
@@ -1602,18 +1561,6 @@ def classify_bngsim_route(
                 method=method_name,
             )
         method_name = _strip_quotes(str(method).strip()).lower() if method else None
-        if method_name == "pla":
-            if fmt in FALLBACK_FORMATS:
-                return BngsimRouteDecision(
-                    ROUTE_SUBPROCESS,
-                    "PLA is not supported by the direct BNGsim route",
-                    method=method_name,
-                )
-            return BngsimRouteDecision(
-                ROUTE_ERROR,
-                f"Format '{fmt}' requires BNGsim but method='pla' is not supported",
-                method=method_name,
-            )
         return BngsimRouteDecision(
             ROUTE_DIRECT_BNGSIM,
             f"Format '{fmt}' routes directly to BNGsim",

tests/test_bngsim_backend_hook.py

@@ -64,7 +64,7 @@ def _patch_real_bng_action(bng_root):
     hook = r"""
     # PyBioNetGen/BNGsim backend hook. BNG2.pl has already normalized the
     # model state, artifact path, method, options, and output prefix.
-    if ($ENV{'BIONETGEN_BNGSIM_BACKEND'} && $method =~ /^(cvode|ssa|psa)$/)
+    if ($ENV{'BIONETGEN_BNGSIM_BACKEND'} && $method =~ /^(cvode|ssa|psa|pla)$/)
     {
         my @helper_command;
         if ($ENV{'BIONETGEN_BNGSIM_BACKEND_HELPER'})
@@ -640,15 +640,17 @@ def test_fake_helper_receives_psa_as_psa(tmp_path, real_bng_backend_runtime):
     assert jobs[0]["simulation_options"]["poplevel"] == 100
 
 
-def test_pla_action_does_not_call_helper(tmp_path, real_bng_backend_runtime):
+def test_fake_helper_receives_pla_as_pla(tmp_path, real_bng_backend_runtime):
     _run_real_hook(
         tmp_path,
         real_bng_backend_runtime,
         "PLA",
         "generate_network({overwrite=>1})\nsimulate_pla({t_end=>1,n_steps=>1})",
     )
 
-    assert _captured_jobs(real_bng_backend_runtime["capture"]) == []
+    jobs = _captured_jobs(real_bng_backend_runtime["capture"])
+    assert len(jobs) == 1
+    assert jobs[0]["method"] == "pla"
 
 
 @pytest.mark.parametrize(