process-bigraph 1.9.1__tar.gz → 1.10.1__tar.gz

{process_bigraph-1.9.1/process_bigraph.egg-info → process_bigraph-1.10.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: process-bigraph
-Version: 1.9.1
+Version: 1.10.1
 Summary: protocol and execution for compositional systems biology
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
@@ -128,28 +128,44 @@ print(gather_emitter_results(composite))
 # {('emitter',): [{'level': 1.0, 'time': 0.0}, {'level': 1.5, ...}, ... {'level': 7.59, 'time': 5.0}]}
 ```
 
-**2. A draft process — a present-but-inert placeholder node.** It declares a contract
-(ports + description) but has no `update`, so a composite containing it still runs; the
-draft just no-ops. Complementary to a *site* (step 3): a draft is a node that is *there
-but inert*, a site is an empty *hole*.
+**2. A draft — an open hole whose sort is a contract.** A not-yet-implemented
+process-slot is a *hole*: an open **site** (step 3) whose `_sort` names a
+`ProcessContract` (its typed face + conditions). You design and review the topology
+with the hole in place, then fill it with any process the contract *admits*.
+`Composite` refuses to build while a required hole is open, and reports **which** hole,
+**what** contract it requires, and **which** registered processes would fill it.
 
 ```python
-from process_bigraph import DraftProcess, draft_process
-
-@draft_process(name="PTH secretion",
-    inputs={'ca_sense': 'float'}, outputs={'pth_out': 'float'},
-    contract={'summary': 'senses serum Ca, secretes PTH', 'senses': 'calcium', 'makes': 'PTH'})
-class PTHSecretion(DraftProcess):
-    pass
-
-core.register_link('PTHSecretion', PTHSecretion)
-print(PTHSecretion({}, core=core).describe())
-# DRAFT — senses serum Ca, secretes PTH  ·  makes: PTH  ·  senses: calcium  ·  status: draft - no update dynamics yet
+from bigraph_schema.contract import ProcessContract
+from process_bigraph import find_candidates, UnfilledHoleError
+
+# register the intended interface as a named contract …
+core.register_contract('PTHSecretion', ProcessContract(
+    summary='senses serum Ca, secretes PTH',
+    face={'inputs': {'ca_sense': 'float'}, 'outputs': {'pth_out': 'float'}}))
+
+# … and leave the slot as a hole sorted by it
+template = core.access({'parathyroid': {'ca': 2.5, 'pth': 0.0,
+    'secretion': {'_type': 'site', '_sort': 'PTHSecretion'}}})
+
+# Composite(..., unfilled) → UnfilledHoleError, not an opaque KeyError:
+#   not ground — required site(s) left unfilled: 'parathyroid/secretion'
+#     • parathyroid/secretion
+#         requires:
+#           inputs: ca_sense: float
+#           outputs: pth_out: float
+#         candidates:
+#           ✓ <any registered process whose contract admits the hole>
 ```
 
-A module-scope draft auto-registers, so it appears in the vivarium-workbench dashboard
-(Modules → Processes) marked **DRAFT** with its ports and contract — no code change
-needed. Replace it with a real `Process` once the mechanism is committed.
+Fill it (step 3) with a process `find_candidates(core, site)` reports as admissible,
+and build. The full design → inspect → fill → build lifecycle — and the rejection
+report in full — is in
+[docs/concepts/designing-with-holes.md](docs/concepts/designing-with-holes.md).
+
+> **Deprecated:** `@draft_process` / `DraftProcess` (an inert placeholder *node*) still
+> work but now emit `DraftProcessDeprecationWarning` — model a draft as a hole instead.
+> `draft_to_contract(cls)` bridges an existing draft's interface to a `ProcessContract`.
 
 **3. A template — a composite with an open site (hole).** A template is a document that
 isn't *ground*: it has open **sites** (`{"_type": "site"}`). `Composite` refuses to run
@@ -184,7 +200,7 @@ def model(rate):                                      # any conforming composite
 sim = Composite({'state': template_document(core, template, {'study/model': model(0.5)})}, core=core)
 sim.run(4.0)
 print(sim.state['study']['verdict'])                  # pass  (a slower model → fail)
-# template_document(core, template, {}) → ValueError: not ground — required site 'study/model'
+# template_document(core, template, {}) → UnfilledHoleError: not ground — required site 'study/model'
 ```
 
 **4. An investigation — one site per member study; gating is *filling*.** Fill a

{process_bigraph-1.9.1 → process_bigraph-1.10.1}/README.md

@@ -101,28 +101,44 @@ print(gather_emitter_results(composite))
 # {('emitter',): [{'level': 1.0, 'time': 0.0}, {'level': 1.5, ...}, ... {'level': 7.59, 'time': 5.0}]}
 ```
 
-**2. A draft process — a present-but-inert placeholder node.** It declares a contract
-(ports + description) but has no `update`, so a composite containing it still runs; the
-draft just no-ops. Complementary to a *site* (step 3): a draft is a node that is *there
-but inert*, a site is an empty *hole*.
+**2. A draft — an open hole whose sort is a contract.** A not-yet-implemented
+process-slot is a *hole*: an open **site** (step 3) whose `_sort` names a
+`ProcessContract` (its typed face + conditions). You design and review the topology
+with the hole in place, then fill it with any process the contract *admits*.
+`Composite` refuses to build while a required hole is open, and reports **which** hole,
+**what** contract it requires, and **which** registered processes would fill it.
 
 ```python
-from process_bigraph import DraftProcess, draft_process
-
-@draft_process(name="PTH secretion",
-    inputs={'ca_sense': 'float'}, outputs={'pth_out': 'float'},
-    contract={'summary': 'senses serum Ca, secretes PTH', 'senses': 'calcium', 'makes': 'PTH'})
-class PTHSecretion(DraftProcess):
-    pass
-
-core.register_link('PTHSecretion', PTHSecretion)
-print(PTHSecretion({}, core=core).describe())
-# DRAFT — senses serum Ca, secretes PTH  ·  makes: PTH  ·  senses: calcium  ·  status: draft - no update dynamics yet
+from bigraph_schema.contract import ProcessContract
+from process_bigraph import find_candidates, UnfilledHoleError
+
+# register the intended interface as a named contract …
+core.register_contract('PTHSecretion', ProcessContract(
+    summary='senses serum Ca, secretes PTH',
+    face={'inputs': {'ca_sense': 'float'}, 'outputs': {'pth_out': 'float'}}))
+
+# … and leave the slot as a hole sorted by it
+template = core.access({'parathyroid': {'ca': 2.5, 'pth': 0.0,
+    'secretion': {'_type': 'site', '_sort': 'PTHSecretion'}}})
+
+# Composite(..., unfilled) → UnfilledHoleError, not an opaque KeyError:
+#   not ground — required site(s) left unfilled: 'parathyroid/secretion'
+#     • parathyroid/secretion
+#         requires:
+#           inputs: ca_sense: float
+#           outputs: pth_out: float
+#         candidates:
+#           ✓ <any registered process whose contract admits the hole>
 ```
 
-A module-scope draft auto-registers, so it appears in the vivarium-workbench dashboard
-(Modules → Processes) marked **DRAFT** with its ports and contract — no code change
-needed. Replace it with a real `Process` once the mechanism is committed.
+Fill it (step 3) with a process `find_candidates(core, site)` reports as admissible,
+and build. The full design → inspect → fill → build lifecycle — and the rejection
+report in full — is in
+[docs/concepts/designing-with-holes.md](docs/concepts/designing-with-holes.md).
+
+> **Deprecated:** `@draft_process` / `DraftProcess` (an inert placeholder *node*) still
+> work but now emit `DraftProcessDeprecationWarning` — model a draft as a hole instead.
+> `draft_to_contract(cls)` bridges an existing draft's interface to a `ProcessContract`.
 
 **3. A template — a composite with an open site (hole).** A template is a document that
 isn't *ground*: it has open **sites** (`{"_type": "site"}`). `Composite` refuses to run
@@ -157,7 +173,7 @@ def model(rate):                                      # any conforming composite
 sim = Composite({'state': template_document(core, template, {'study/model': model(0.5)})}, core=core)
 sim.run(4.0)
 print(sim.state['study']['verdict'])                  # pass  (a slower model → fail)
-# template_document(core, template, {}) → ValueError: not ground — required site 'study/model'
+# template_document(core, template, {}) → UnfilledHoleError: not ground — required site 'study/model'
 ```
 
 **4. An investigation — one site per member study; gating is *filling*.** Fill a

{process_bigraph-1.9.1 → process_bigraph-1.10.1}/process_bigraph/__init__.py

@@ -14,6 +14,35 @@ def allocate_core(*args, strict=False, **kwargs):
     """
     core = _allocate_core(*args, **kwargs)
     core.strict_config = bool(strict)
+    _register_builtin_emitters(core)
+    return core
+
+
+def _register_builtin_emitters(core):
+    """Ensure process-bigraph's built-in emitters are registered under their
+    SHORT names (``RAMEmitter`` etc.), not only their fully-qualified names.
+
+    Discovery normally registers both, but when several emitter packages
+    co-register in an unlucky import order the short alias is silently dropped
+    (see ``process_bigraph.emitter._VIVA_REEXPORTS``) — leaving only the FQN
+    ``process_bigraph.emitter.RAMEmitter`` and breaking the framework's own
+    default sink ``local:RAMEmitter``. Registering the built-ins explicitly here
+    is order-independent and idempotent (we only fill a missing short alias).
+    """
+    try:
+        from process_bigraph.emitter import (
+            Emitter, ConsoleEmitter, RAMEmitter, JSONEmitter)
+    except Exception:
+        return
+    registry = getattr(core, 'link_registry', None)
+    for cls in (Emitter, ConsoleEmitter, RAMEmitter, JSONEmitter):
+        name = cls.__name__
+        if registry is not None and name in registry:
+            continue
+        try:
+            core.register_link(name, cls)
+        except Exception:
+            pass
     return core
 
 # The installed distribution's version, exposed so a run manifest can record
@@ -41,7 +70,16 @@ from process_bigraph.composite_spec import (  # noqa: F401
     normalize_type, CANONICAL_TYPES,
 )
 from process_bigraph.bundle import load_bundle  # noqa: F401
-from process_bigraph.draft_process import DraftProcess, draft_process  # noqa: F401
+from process_bigraph.draft_process import (  # noqa: F401
+    DraftProcess, draft_process, draft_to_contract, DraftProcessDeprecationWarning,
+)
+# Holes-in-place: the public lifecycle for a process-slot left as a hole whose
+# sort is a ProcessContract — design, inspect, see what fits, fill, build.
+from process_bigraph.holes import UnfilledHoleError  # noqa: F401
+from process_bigraph.templates import (  # noqa: F401
+    open_sites, required_open_sites, is_ground_document, fill_template, template_document,
+)
+from bigraph_schema.matching import find_candidates  # noqa: F401
 from process_bigraph.emitter import Emitter, gather_emitter_results, generate_emitter_state  # noqa: F401
 from process_bigraph.types import StepLink, ProcessLink, CompositeLink  # noqa: F401
 from process_bigraph import core_introspection  # noqa: F401