process-bigraph 1.2.2__tar.gz → 1.2.3__tar.gz

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Files changed (35) hide show
  1. {process_bigraph-1.2.2/process_bigraph.egg-info → process_bigraph-1.2.3}/PKG-INFO +1 -1
  2. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/process_bigraph/composite.py +16 -11
  3. {process_bigraph-1.2.2 → process_bigraph-1.2.3/process_bigraph.egg-info}/PKG-INFO +1 -1
  4. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/pyproject.toml +1 -1
  5. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/AUTHORS.md +0 -0
  6. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/LICENSE +0 -0
  7. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/README.md +0 -0
  8. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/process_bigraph/__init__.py +0 -0
  9. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/process_bigraph/bundle.py +0 -0
  10. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/process_bigraph/emitter.py +0 -0
  11. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/process_bigraph/experiments/__init__.py +0 -0
  12. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/process_bigraph/experiments/minimal_gillespie.py +0 -0
  13. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/process_bigraph/nextflow.py +0 -0
  14. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/process_bigraph/plumbing.py +0 -0
  15. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/process_bigraph/processes/__init__.py +0 -0
  16. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/process_bigraph/processes/dynamic_structure.py +0 -0
  17. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/process_bigraph/processes/examples.py +0 -0
  18. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/process_bigraph/processes/growth_division.py +0 -0
  19. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/process_bigraph/processes/math_expression.py +0 -0
  20. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/process_bigraph/processes/parameter_scan.py +0 -0
  21. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/process_bigraph/processes/reaction.py +0 -0
  22. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/process_bigraph/protocols/__init__.py +0 -0
  23. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/process_bigraph/protocols/parallel.py +0 -0
  24. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/process_bigraph/protocols/rest.py +0 -0
  25. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/process_bigraph/protocols/socket.py +0 -0
  26. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/process_bigraph/run.py +0 -0
  27. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/process_bigraph/run_step.py +0 -0
  28. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/process_bigraph/types/__init__.py +0 -0
  29. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/process_bigraph/types/process.py +0 -0
  30. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/process_bigraph/units.py +0 -0
  31. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/process_bigraph.egg-info/SOURCES.txt +0 -0
  32. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/process_bigraph.egg-info/dependency_links.txt +0 -0
  33. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/process_bigraph.egg-info/requires.txt +0 -0
  34. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/process_bigraph.egg-info/top_level.txt +0 -0
  35. {process_bigraph-1.2.2 → process_bigraph-1.2.3}/setup.cfg +0 -0
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: process-bigraph
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- Version: 1.2.2
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+ Version: 1.2.3
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  Summary: protocol and execution for compositional systems biology
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  Requires-Python: >=3.11
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  Description-Content-Type: text/markdown
@@ -1454,11 +1454,11 @@ class Composite(Process):
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  - self.process_paths
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  - self.step_paths
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  """
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- # Structural change incoming — drop the compiled-apply cache:
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+ # Structural change incoming — drop schema-derived caches:
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  # ``apply(dict)`` mutates schemas in place for ``_divide``
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- # sentinels, so cached compiled functions may now reference
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- # stale schema layouts.
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- self.core.invalidate_compiled_apply()
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+ # sentinels, so the promote() memo may now key off stale
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+ # schema layouts.
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+ self.core.invalidate_caches()
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  self.process_paths = find_instance_paths(state, 'process_bigraph.composite.Process')
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  if hasattr(self, 'step_paths'):
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  previous_step_paths = self.step_paths.keys()
@@ -1581,14 +1581,14 @@ class Composite(Process):
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  - ``Divided``: drop the mother's entries, scan each daughter
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  subtree.
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- The compiled-apply cache is invalidated unconditionally because
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+ Schema-derived caches are invalidated unconditionally because
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  ``apply(dict)``'s ``_divide`` branch mutates schemas in place.
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  Step network rebuild is conditional on step_paths actually
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  changing — value-only structural events that don't add/remove
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  any Step instances skip the rebuild.
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  """
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- self.core.invalidate_compiled_apply()
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+ self.core.invalidate_caches()
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  previous_step_paths = (set(self.step_paths.keys())
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  if hasattr(self, 'step_paths') else set())
@@ -2695,12 +2695,17 @@ class Composite(Process):
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  combined_update,
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  update_has_structural=had_structural_sentinels,
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  events=structural_events)
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- # For structural sentinels, apply may have mutated
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- # apply_schema in place (e.g. _divide pops/inserts
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- # keys in a dict schema). Propagate back to self.schema
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- # so downstream realize sees the split.
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+ # For structural sentinels, apply mutates the
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+ # access-normalized form of ``apply_schema`` in place
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+ # (e.g. ``_divide`` pops the mother key and inserts
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+ # daughter keys in a dict subschema). ``apply_schema``
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+ # itself is the un-normalized input — it does NOT see
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+ # those mutations. Pull the cached normalized form
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+ # via ``access`` (cache hit since ``core.apply`` just
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+ # populated it) so ``self.schema`` reflects the post-
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+ # divide structure for downstream consumers.
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  if had_structural_sentinels:
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- self.schema = apply_schema
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+ self.schema = self.core.access(apply_schema)
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  if merges:
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  had_structural_changes = True
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: process-bigraph
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- Version: 1.2.2
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+ Version: 1.2.3
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  Summary: protocol and execution for compositional systems biology
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  Requires-Python: >=3.11
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  Description-Content-Type: text/markdown
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
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  [project]
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  name = "process-bigraph"
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- version = "1.2.2"
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+ version = "1.2.3"
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  description = "protocol and execution for compositional systems biology"
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  readme = "README.md"
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  requires-python = ">=3.11"
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