process-bigraph 1.2.3__tar.gz → 1.3.1__tar.gz

{process_bigraph-1.2.3/process_bigraph.egg-info → process_bigraph-1.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: process-bigraph
-Version: 1.2.3
+Version: 1.3.1
 Summary: protocol and execution for compositional systems biology
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown

{process_bigraph-1.2.3 → process_bigraph-1.3.1}/process_bigraph/composite.py

@@ -1328,7 +1328,8 @@ class Composite(Process):
             initial_state['global_time'] = 0.0
 
         # Generate internal schema and state structures using the core engine.
-        self.schema, self.state = self.core.realize(
+        # Top-level realize: realize_root defaults to () so no merges escape.
+        self.schema, self.state, _ = self.core.realize(
             initial_schema,
             initial_state)
 
@@ -1442,7 +1443,7 @@ class Composite(Process):
         with open(path) as data:
             document = json.load(data)
             return cls(document, core=core)
-          
+
     def clean_front(self, state):
         self.find_instance_paths(state)
 
@@ -1497,8 +1498,18 @@ class Composite(Process):
                 continue
             if sub_schema is None:
                 continue
-            new_sub_schema, new_sub_state = self.core.realize(
+            # realize_root defaults to ``path`` so port_merges produced
+            # inside the subtree get applied locally with the prefix
+            # stripped. Merges that escape the subtree (via ``..``
+            # wires) come back as ``escape_merges`` and need to land
+            # in ``self.schema`` at their absolute paths.
+            new_sub_schema, new_sub_state, escape_merges = self.core.realize(
                 sub_schema, sub_state, path=tuple(path))
+            if escape_merges:
+                escape_merge_schema = self.core.resolve_merges(
+                    {}, escape_merges)
+                self.schema = self.core.resolve(
+                    self.schema, escape_merge_schema)
             if not path:
                 self.state = new_sub_state
                 continue
@@ -1546,8 +1557,19 @@ class Composite(Process):
                 continue
             if sub_schema is None:
                 continue
-            new_sub_schema, new_sub_state = self.core.realize(
+            # realize_root defaults to ``path`` so port_merges produced
+            # inside the new subtree are applied with the prefix
+            # stripped (correct for the local sub_schema). Merges that
+            # escape (e.g. ``..`` wires writing to global fields) come
+            # back as ``escape_merges`` and must land on ``self.schema``
+            # at their absolute paths.
+            new_sub_schema, new_sub_state, escape_merges = self.core.realize(
                 sub_schema, sub_state, path=tuple(path))
+            if escape_merges:
+                escape_merge_schema = self.core.resolve_merges(
+                    {}, escape_merges)
+                self.schema = self.core.resolve(
+                    self.schema, escape_merge_schema)
             # Splice the realized state back at its path. The parent
             # container is a mutable dict (Map keys are dict-keyed at
             # state level), so we rewrite the leaf entry. Schema dicts
@@ -2747,7 +2769,7 @@ class Composite(Process):
                 self._merge_paths_pending = []
             else:
                 # Fallback: no path info available — full realize.
-                self.schema, self.state = self.core.realize(
+                self.schema, self.state, _ = self.core.realize(
                     self.schema, self.state)
             self._build_view_project_cache()
 
@@ -2766,7 +2788,7 @@ class Composite(Process):
                 # detected an in-process update with no _add/_remove/
                 # _divide sentinel). Full realize + rescan is correct
                 # here — we don't know which subtrees changed.
-                self.schema, self.state = self.core.realize(
+                self.schema, self.state, _ = self.core.realize(
                     self.schema, self.state)
                 self.find_instance_paths(self.state)
             self._build_view_project_cache()

{process_bigraph-1.2.3 → process_bigraph-1.3.1}/process_bigraph/processes/parameter_scan.py

@@ -78,7 +78,7 @@ class RunProcess(Step):
             'inputs': {},
             'outputs': {}}
 
-        self.process_schema, self.process = self.core.realize(
+        self.process_schema, self.process, _ = self.core.realize(
             'process', process_state)
         self.process_instance = self.process['instance']
 

{process_bigraph-1.2.3 → process_bigraph-1.3.1}/process_bigraph/types/process.py

@@ -315,7 +315,7 @@ def realize(core, schema: SharedProcess, state, path=()):
     # fields (Quantity, Function, custom types) get reconstructed.
     config_schema = getattr(cls, 'config_schema', None)
     if config_schema:
-        _, config = core.realize(config_schema, config)
+        _, config, _ = core.realize(config_schema, config)
 
     instance = cls(config)
 
@@ -323,10 +323,14 @@ def realize(core, schema: SharedProcess, state, path=()):
     if not hasattr(instance, 'core') or instance.core is None:
         instance.core = core
 
-    # Restore process-internal RandomState if a checkpoint captured one.
+    # Restore process-internal RandomState if a checkpoint captured
+    # one. Cross-gen daughter loads should strip ``rng_state`` from
+    # the saved bundle before construction (so the daughter starts
+    # fresh from a freshly-seeded process); mid-tick checkpoints
+    # leave it in for bit-for-bit continuation.
     rng_state = state.get('rng_state')
-    if rng_state and hasattr(instance, 'random_state') and isinstance(
-            instance.random_state, np.random.RandomState):
+    if (rng_state and hasattr(instance, 'random_state')
+            and isinstance(instance.random_state, np.random.RandomState)):
         try:
             instance.random_state.set_state((
                 rng_state['alg'],

{process_bigraph-1.2.3 → process_bigraph-1.3.1/process_bigraph.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: process-bigraph
-Version: 1.2.3
+Version: 1.3.1
 Summary: protocol and execution for compositional systems biology
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown

{process_bigraph-1.2.3 → process_bigraph-1.3.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "process-bigraph"
-version = "1.2.3"
+version = "1.3.1"
 description = "protocol and execution for compositional systems biology"
 readme = "README.md"
 requires-python = ">=3.11"