process-bigraph 1.8.4__tar.gz → 1.9.0__tar.gz

{process_bigraph-1.8.4/process_bigraph.egg-info → process_bigraph-1.9.0}/PKG-INFO

@@ -1,12 +1,13 @@
 Metadata-Version: 2.4
 Name: process-bigraph
-Version: 1.8.4
+Version: 1.9.0
 Summary: protocol and execution for compositional systems biology
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
 License-File: AUTHORS.md
-Requires-Dist: bigraph-schema>=1.6.0
+Requires-Dist: bigraph-schema>=1.8.1
+Requires-Dist: requests>=2.31
 Requires-Dist: matplotlib
 Requires-Dist: pint>=0.24.4
 Requires-Dist: scipy>=1.8
@@ -118,7 +119,8 @@ core.register_link('Grow', Grow)                      # register it in the local
 composite = Composite({'state': {
     'level': 1.0,                                     # a shared store
     'grow': {'_type': 'process', 'address': 'local:Grow', 'config': {'rate': 0.5},
-             'interval': 1.0, 'inputs': {'level': ['level']}, 'outputs': {'level': ['level']}},
+             'interval': 1.0,                         # seconds; a unit string like '1 min' also works
+             'inputs': {'level': ['level']}, 'outputs': {'level': ['level']}},
     'emitter': emitter_from_wires({'level': ['level'], 'time': ['global_time']}),
 }}, core=core)
 composite.run(5.0)
@@ -233,7 +235,8 @@ rendered to HTML and published automatically on GitHub Pages.
 
 - **Tutorial 3 — Declarative Math**  
   *Defining mathematical relationships, signal pipelines, and events using `MathExpressionStep`*  
-  https://vivarium-collective.github.io/process-bigraph/notebooks/tutorial_3.html
+  https://vivarium-collective.github.io/process-bigraph/notebooks/tutorial_3.html  
+  Requires the companion package [`viva-basic-processes`](https://github.com/vivarium-collective/viva-basic-processes), published to PyPI as `pbg-basic-processes` (`pip install "pbg-basic-processes[plotting]>=0.3.0"`), which provides `MathExpressionStep`, the `Tick` process, and the plotting helpers.
 
 - **Tutorial 4 — Composing a Biological Model**  
   *The central dogma from four small processes: composition over shared molecular state, biological units in the port types, and adding regulation by adding a wire*  

{process_bigraph-1.8.4 → process_bigraph-1.9.0}/README.md

@@ -92,7 +92,8 @@ core.register_link('Grow', Grow)                      # register it in the local
 composite = Composite({'state': {
     'level': 1.0,                                     # a shared store
     'grow': {'_type': 'process', 'address': 'local:Grow', 'config': {'rate': 0.5},
-             'interval': 1.0, 'inputs': {'level': ['level']}, 'outputs': {'level': ['level']}},
+             'interval': 1.0,                         # seconds; a unit string like '1 min' also works
+             'inputs': {'level': ['level']}, 'outputs': {'level': ['level']}},
     'emitter': emitter_from_wires({'level': ['level'], 'time': ['global_time']}),
 }}, core=core)
 composite.run(5.0)
@@ -207,7 +208,8 @@ rendered to HTML and published automatically on GitHub Pages.
 
 - **Tutorial 3 — Declarative Math**  
   *Defining mathematical relationships, signal pipelines, and events using `MathExpressionStep`*  
-  https://vivarium-collective.github.io/process-bigraph/notebooks/tutorial_3.html
+  https://vivarium-collective.github.io/process-bigraph/notebooks/tutorial_3.html  
+  Requires the companion package [`viva-basic-processes`](https://github.com/vivarium-collective/viva-basic-processes), published to PyPI as `pbg-basic-processes` (`pip install "pbg-basic-processes[plotting]>=0.3.0"`), which provides `MathExpressionStep`, the `Tick` process, and the plotting helpers.
 
 - **Tutorial 4 — Composing a Biological Model**  
   *The central dogma from four small processes: composition over shared molecular state, biological units in the port types, and adding regulation by adding a wire*  

{process_bigraph-1.8.4 → process_bigraph-1.9.0}/process_bigraph/__init__.py

@@ -1,4 +1,20 @@
-from bigraph_schema import allocate_core  # noqa: F401
+from bigraph_schema import allocate_core as _allocate_core
+
+
+def allocate_core(*args, strict=False, **kwargs):
+    """Allocate a core (see :func:`bigraph_schema.allocate_core`).
+
+    Adds process-bigraph's opt-in strict-config mode (issue #232): with
+    ``strict=True`` the returned core carries ``strict_config = True``, so
+    instantiating a Process/Step with a config key that is not declared in
+    its ``config_schema`` raises a clear error instead of silently ignoring
+    the key. The default (``strict=False``) preserves existing behavior
+    exactly. You can also toggle it on an existing core with
+    ``core.strict_config = True``.
+    """
+    core = _allocate_core(*args, **kwargs)
+    core.strict_config = bool(strict)
+    return core
 
 # The installed distribution's version, exposed so a run manifest can record
 # *which* engine produced an artifact. Read from installed metadata rather

process_bigraph-1.9.0/process_bigraph/audit_contracts.py

@@ -0,0 +1,128 @@
+"""CI audit gate for declared process contracts (spec section 5).
+
+Audits every registered process's DECLARED contract (static — no instantiation)
+and fails (exit 1) on any error-severity finding, or on a declared-coverage
+floor. Read the class `.contract` directly (contract_of drops amendments). In
+process-bigraph's own CI few processes declare contracts, so the error-gate is
+largely a regression guard; the real value is downstream workspaces running
+`python -m process_bigraph.audit_contracts` against their registries, and the
+--require-declared floor makes coverage visible.
+"""
+import argparse
+import json as _json
+import sys
+
+try:
+    from bigraph_schema.contract_audit import audit_contract, completeness
+    from bigraph_schema.assembly import contract_of
+    from bigraph_schema.contract import resolve_contract
+    AUDIT_AVAILABLE = True
+except Exception:  # noqa: BLE001
+    AUDIT_AVAILABLE = False
+
+from process_bigraph import allocate_core
+
+_INCOMPLETE_BELOW = 0.5
+
+
+def _class_key(cls):
+    return f'{getattr(cls, "__module__", "?")}.{getattr(cls, "__qualname__", getattr(cls, "__name__", "?"))}'
+
+
+def _contract_for(core, address, cls):
+    """Declared contract of a class, amendments preserved. Reads the class
+    `.contract` first (contract_of drops amendments), then falls back."""
+    declared = getattr(cls, 'contract', None)
+    if declared is not None:
+        try:
+            return resolve_contract(cls)   # normalizes ProcessContract/dict; never raises
+        except Exception:  # noqa: BLE001
+            pass
+    try:
+        return contract_of(core, address)
+    except Exception:  # noqa: BLE001
+        return None
+
+
+def audit_all(core, *, require_declared=0, strict_resolve=False):
+    from process_bigraph.core_introspection import list_processes
+    reports = {}
+    for address in list_processes(core):
+        try:
+            cls = core.link_registry.get(address)
+        except Exception:  # noqa: BLE001 - per-entry import failure
+            cls = None
+        if cls is None:
+            reports.setdefault(f'unresolvable:{address}',
+                               {'address': address, 'cls': address, 'status': 'unresolvable',
+                                'grade': None, 'findings': [], 'declared': False})
+            continue
+        key = _class_key(cls)
+        if key in reports:
+            continue   # alias dedup
+        contract = _contract_for(core, address, cls)
+        if contract is None:
+            reports[key] = {'address': address, 'cls': key, 'status': 'not-declared', 'grade': None, 'findings': [], 'declared': False}
+            continue
+        try:
+            report = audit_contract(core, contract)
+            grade = completeness(contract)
+            findings = [{'severity': f.severity, 'code': f.code, 'where': f.where, 'message': f.message}
+                        for f in report.findings]
+        except Exception as error:  # noqa: BLE001
+            reports[key] = {'address': address, 'cls': key, 'status': 'unresolvable', 'grade': None,
+                            'findings': [{'severity': 'error', 'code': 'audit_raised', 'where': key, 'message': str(error)}], 'declared': False}
+            continue
+        has_contract_attr = getattr(cls, 'contract', None) is not None
+        is_declared = has_contract_attr or bool(contract.conditions())
+        if any(f['severity'] == 'error' for f in findings):
+            status = 'fail'
+        elif not is_declared:
+            status = 'not-declared'
+        elif grade < _INCOMPLETE_BELOW:
+            status = 'incomplete'
+        else:
+            status = 'pass'
+        reports[key] = {'address': address, 'cls': key, 'status': status, 'grade': round(grade, 3), 'findings': findings, 'declared': is_declared}
+
+    rows = list(reports.values())
+    errors = sum(1 for r in rows for f in r['findings'] if f['severity'] == 'error')
+    if strict_resolve:
+        errors += sum(1 for r in rows if r['status'] == 'unresolvable')
+    declared_count = sum(1 for r in rows if r.get('declared'))
+    exit_code = 1 if (errors > 0 or (require_declared > 0 and declared_count < require_declared)) else 0
+    return {'reports': rows, 'declared': declared_count, 'errors': errors, 'exit_code': exit_code}
+
+
+def _build_parser():
+    p = argparse.ArgumentParser(prog='python -m process_bigraph.audit_contracts',
+                                description='Audit registered process contracts; exit 1 on any error finding.')
+    p.add_argument('--require-declared', type=int, default=0, metavar='N',
+                   help='fail if fewer than N processes declare a real contract (default 0 = off).')
+    p.add_argument('--strict-resolve', action='store_true', help='treat unresolvable processes as failures.')
+    p.add_argument('--json', action='store_true', help='emit the full report as JSON.')
+    return p
+
+
+def main(argv=None):
+    args = _build_parser().parse_args(argv)
+    if not AUDIT_AVAILABLE:
+        print('contract audit unavailable: bigraph-schema >= 1.7.0 required', file=sys.stderr)
+        return 2
+    core = allocate_core()
+    result = audit_all(core, require_declared=args.require_declared, strict_resolve=args.strict_resolve)
+    if args.json:
+        print(_json.dumps(result, indent=2))
+        return result['exit_code']
+    for r in sorted(result['reports'], key=lambda x: (x['status'] != 'fail', x['cls'])):
+        grade = '' if r['grade'] is None else f" {int(r['grade'] * 100)}%"
+        print(f"{r['status']:13} {r['cls']}{grade}")
+        for f in r['findings']:
+            print(f"    {f['severity']} {f['code']} {f['where']}: {f['message']}")
+    print(f"\n{result['declared']} declared, {result['errors']} error finding(s) "
+          f"-> {'FAIL' if result['exit_code'] else 'OK'}")
+    return result['exit_code']
+
+
+if __name__ == '__main__':
+    sys.exit(main())