@memoarchitect/ontology 0.6.3 → 0.6.5

package/README.md

@@ -1,5 +1,10 @@
 # @memoarchitect/ontology
 
+[Product website](https://memoarchitect.com/memo.html) ·
+[Documentation](https://memoarchitect.com/memo/) ·
+[GitHub repository](https://github.com/memoarchitect/memo) ·
+[npm package](https://www.npmjs.com/package/@memoarchitect/ontology)
+
 **MEMO — Medical Engineering Modelling Ontology** — the pure SysML v2 content layer.
 
 A standalone, tool-portable SysML v2 / KerML ontology for medical-device architecture
@@ -18,24 +23,41 @@ pin an exact release; the package has no repository or runtime dependency on Mem
 Tools or Memo Architect.
 
 ```bash
-pnpm add @memoarchitect/ontology@0.6.2
+pnpm add @memoarchitect/ontology@0.6.4
 ```
 
+> **Pre-1.0 notice:** ontology names, relationships, and package layout may
+> change before 1.0. Use the exact npm version above or a
+> [tagged release](https://github.com/memoarchitect/memo/releases) rather than
+> tracking `main` for reproducible project work.
+
 For coordinated development, the private `memo-meta` workspace checks out
 Ontology, Tools, and Architect as sibling repositories and links this package
 into its dependants with meta-only pnpm overrides.
 
+`VERSION` is the sole release-version source for this repository. Run
+`pnpm version:sync` after changing it; CI rejects unsynchronized manifests and
+automatically creates the matching `v<version>` tag when the change reaches
+`main`.
+
 ## Documentation
 
-Start with the [user guide](docs/index.md) to learn MEMO's layer model, choose
+Start with the [published documentation](https://memoarchitect.com/memo/) to learn
+MEMO's layer model, choose
 elements and relationships, and follow the GPCA pump example. The reference
-section describes packages, source layout, and maintenance. Build the site with:
+section describes packages, source layout, and maintenance. Its source starts at
+[`docs/index.md`](docs/index.md). Build the site with:
 
 ```bash
 python3 -m pip install "mkdocs>=1.6" "mkdocs-material>=9.5" "pymdown-extensions>=10.0"
 pnpm run docs:build
 ```
 
+Related products: [MEMO Tools documentation](https://memoarchitect.com/memo-tools/)
+and [repository](https://github.com/memoarchitect/memo-tools) ·
+[MEMO Architect documentation](https://memoarchitect.com/memo-architect/)
+and [repository](https://github.com/memoarchitect/memo-architect).
+
 ## Layout
 
 The package exposes four logical MEMO packages through `memo.manifest.yaml`.

package/examples/embedded-infusion-pump/model/catalog/embedded_infusion_pump.sysml

@@ -14,7 +14,7 @@ package memo_examples_embedded_infusion_pump {
 
     // Module view (IEC 62304).
     part swInfusionControl : SoftwareModule {
-        attribute :>> moduleKind = ModuleKind::item;
+        attribute :>> moduleKind = ModuleKind::'item';
         attribute :>> id = "EIP-SW-001"; attribute :>> name = "InfusionControlItem";
         attribute :>> iec62304Role = "software item, class C";
         attribute :>> safetyClass = SafetyClassKind::C;

package/examples/gpca-pump/analysis/Samples/01-model-overview.ipynb

@@ -0,0 +1,148 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "memo-1",
+   "metadata": {},
+   "source": [
+    "# Model overview\n",
+    "\n",
+    "Visual summary of model size, semantic content, and diagnostics.\n",
+    "\n",
+    "This sample uses only standard SysML v2 concepts and automatically discovers the project's `model/` or `src/` directory."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "memo-2",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2026-07-29T22:31:46.345732Z",
+     "iopub.status.busy": "2026-07-29T22:31:46.345598Z",
+     "iopub.status.idle": "2026-07-29T22:31:46.699014Z",
+     "shell.execute_reply": "2026-07-29T22:31:46.698564Z"
+    }
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Loaded 42 SysML files from /Users/poojakashyap/sandbox/memo-meta/memo/examples/gpca-pump/model\n"
+     ]
+    }
+   ],
+   "source": [
+    "from pathlib import Path\n",
+    "from collections import Counter, defaultdict\n",
+    "import syside\n",
+    "\n",
+    "def find_sysml_root(start=Path.cwd()):\n",
+    "    \"\"\"Find the nearest model/ or src/ folder containing textual SysML.\"\"\"\n",
+    "    for directory in (start, *start.parents):\n",
+    "        for folder_name in ('model', 'src'):\n",
+    "            candidate = directory / folder_name\n",
+    "            if candidate.is_dir() and next(candidate.rglob('*.sysml'), None):\n",
+    "                return candidate\n",
+    "    raise FileNotFoundError('No model/ or src/ directory containing .sysml files was found')\n",
+    "\n",
+    "SYSML_ROOT = find_sysml_root()\n",
+    "SYSML_FILES = sorted(SYSML_ROOT.rglob('*.sysml'))\n",
+    "model, diagnostics = syside.try_load_model([str(path) for path in SYSML_FILES])\n",
+    "print(f'Loaded {len(SYSML_FILES)} SysML files from {SYSML_ROOT}')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "memo-3",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2026-07-29T22:31:46.700004Z",
+     "iopub.status.busy": "2026-07-29T22:31:46.699937Z",
+     "iopub.status.idle": "2026-07-29T22:31:46.707568Z",
+     "shell.execute_reply": "2026-07-29T22:31:46.707310Z"
+    }
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<h3>Semantic inventory</h3><table><tr><th>Element type</th><th>Count</th><th>Relative size</th></tr><tr><td>AttributeUsage</td><td>5,056</td><td><div style=\"background:#2d8d70;height:12px;width:320px\"></div></td></tr><tr><td>ConnectionUsage</td><td>691</td><td><div style=\"background:#2d8d70;height:12px;width:44px\"></div></td></tr><tr><td>PartUsage</td><td>425</td><td><div style=\"background:#2d8d70;height:12px;width:27px\"></div></td></tr><tr><td>RequirementUsage</td><td>105</td><td><div style=\"background:#2d8d70;height:12px;width:7px\"></div></td></tr><tr><td>ActionUsage</td><td>44</td><td><div style=\"background:#2d8d70;height:12px;width:3px\"></div></td></tr><tr><td>Package</td><td>42</td><td><div style=\"background:#2d8d70;height:12px;width:3px\"></div></td></tr><tr><td>StateUsage</td><td>10</td><td><div style=\"background:#2d8d70;height:12px;width:2px\"></div></td></tr><tr><td>ActionDefinition</td><td>6</td><td><div style=\"background:#2d8d70;height:12px;width:2px\"></div></td></tr><tr><td>PortDefinition</td><td>1</td><td><div style=\"background:#2d8d70;height:12px;width:2px\"></div></td></tr><tr><td>PartDefinition</td><td>0</td><td><div style=\"background:#2d8d70;height:12px;width:2px\"></div></td></tr><tr><td>RequirementDefinition</td><td>0</td><td><div style=\"background:#2d8d70;height:12px;width:2px\"></div></td></tr><tr><td>PortUsage</td><td>0</td><td><div style=\"background:#2d8d70;height:12px;width:2px\"></div></td></tr><tr><td>ConnectionDefinition</td><td>0</td><td><div style=\"background:#2d8d70;height:12px;width:2px\"></div></td></tr><tr><td>StateDefinition</td><td>0</td><td><div style=\"background:#2d8d70;height:12px;width:2px\"></div></td></tr><tr><td>AttributeDefinition</td><td>0</td><td><div style=\"background:#2d8d70;height:12px;width:2px\"></div></td></tr></table>"
+      ],
+      "text/plain": [
+       "<IPython.core.display.HTML object>"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/plain": [
+       "{'SysML files': 42, 'Errors': 8009, 'Warnings': 0, 'Information': 0}"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "from IPython.display import HTML, display\n",
+    "\n",
+    "semantic_types = [\n",
+    "    'Package', 'PartDefinition', 'PartUsage', 'RequirementDefinition',\n",
+    "    'RequirementUsage', 'ActionDefinition', 'ActionUsage', 'PortDefinition',\n",
+    "    'PortUsage', 'ConnectionDefinition', 'ConnectionUsage', 'StateDefinition',\n",
+    "    'StateUsage', 'AttributeDefinition', 'AttributeUsage'\n",
+    "]\n",
+    "counts = {}\n",
+    "for type_name in semantic_types:\n",
+    "    node_type = getattr(syside, type_name, None)\n",
+    "    if node_type is not None:\n",
+    "        counts[type_name] = len(list(model.elements(node_type)))\n",
+    "\n",
+    "largest = max(counts.values(), default=1)\n",
+    "rows = ''.join(\n",
+    "    f'<tr><td>{name}</td><td>{count:,}</td><td><div style=\"background:#2d8d70;height:12px;width:{max(2, count * 320 / largest):.0f}px\"></div></td></tr>'\n",
+    "    for name, count in sorted(counts.items(), key=lambda item: item[1], reverse=True)\n",
+    ")\n",
+    "display(HTML(f'<h3>Semantic inventory</h3><table><tr><th>Element type</th><th>Count</th><th>Relative size</th></tr>{rows}</table>'))\n",
+    "\n",
+    "{\n",
+    "    'SysML files': len(SYSML_FILES),\n",
+    "    'Errors': len(list(diagnostics.errors)),\n",
+    "    'Warnings': len(list(diagnostics.warnings)),\n",
+    "    'Information': len(list(diagnostics.infos)),\n",
+    "}"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.13"
+  },
+  "memo": {
+   "description": "Visual summary of model size, semantic content, and diagnostics.",
+   "starter": true
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

package/examples/gpca-pump/analysis/Samples/02-architecture-hotspots.ipynb

@@ -0,0 +1,301 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "memo-1",
+   "metadata": {},
+   "source": [
+    "# Architecture hotspots\n",
+    "\n",
+    "Find busy containers, deep ownership paths, and dominant semantic types.\n",
+    "\n",
+    "This sample uses only standard SysML v2 concepts and automatically discovers the project's `model/` or `src/` directory."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "memo-2",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2026-07-29T22:31:48.480637Z",
+     "iopub.status.busy": "2026-07-29T22:31:48.480406Z",
+     "iopub.status.idle": "2026-07-29T22:31:48.765461Z",
+     "shell.execute_reply": "2026-07-29T22:31:48.765134Z"
+    }
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Loaded 42 SysML files from /Users/poojakashyap/sandbox/memo-meta/memo/examples/gpca-pump/model\n"
+     ]
+    }
+   ],
+   "source": [
+    "from pathlib import Path\n",
+    "from collections import Counter, defaultdict\n",
+    "import syside\n",
+    "\n",
+    "def find_sysml_root(start=Path.cwd()):\n",
+    "    \"\"\"Find the nearest model/ or src/ folder containing textual SysML.\"\"\"\n",
+    "    for directory in (start, *start.parents):\n",
+    "        for folder_name in ('model', 'src'):\n",
+    "            candidate = directory / folder_name\n",
+    "            if candidate.is_dir() and next(candidate.rglob('*.sysml'), None):\n",
+    "                return candidate\n",
+    "    raise FileNotFoundError('No model/ or src/ directory containing .sysml files was found')\n",
+    "\n",
+    "SYSML_ROOT = find_sysml_root()\n",
+    "SYSML_FILES = sorted(SYSML_ROOT.rglob('*.sysml'))\n",
+    "model, diagnostics = syside.try_load_model([str(path) for path in SYSML_FILES])\n",
+    "print(f'Loaded {len(SYSML_FILES)} SysML files from {SYSML_ROOT}')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "memo-3",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2026-07-29T22:31:48.768663Z",
+     "iopub.status.busy": "2026-07-29T22:31:48.768585Z",
+     "iopub.status.idle": "2026-07-29T22:31:48.814237Z",
+     "shell.execute_reply": "2026-07-29T22:31:48.813848Z"
+    }
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Top containers by directly owned semantic elements\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "[(19,\n",
+       "  'RequirementUsage',\n",
+       "  'memo_examples_gpca_pump_model_catalog_gpca_requirements::reqWatchdogSafeState'),\n",
+       " (19,\n",
+       "  'RequirementUsage',\n",
+       "  'memo_examples_gpca_pump_model_catalog_gpca_requirements::reqDoorOpen'),\n",
+       " (18,\n",
+       "  'RequirementUsage',\n",
+       "  'memo_examples_gpca_pump_model_catalog_gpca_requirements::reqPowerLossRetention'),\n",
+       " (18,\n",
+       "  'RequirementUsage',\n",
+       "  'memo_examples_gpca_pump_model_catalog_gpca_requirements::reqPost'),\n",
+       " (18,\n",
+       "  'RequirementUsage',\n",
+       "  'memo_examples_gpca_pump_model_catalog_gpca_requirements::reqDrugLibraryLimits'),\n",
+       " (18,\n",
+       "  'ActionUsage',\n",
+       "  'memo_examples_gpca_pump_model_catalog_gpca_behavior_actions::infusionDeliveryFlow'),\n",
+       " (17,\n",
+       "  'ViewUsage',\n",
+       "  'memo_examples_gpca_pump_model_views_logical_system_decomposition_view::gpcaSystemDecompositionView'),\n",
+       " (16,\n",
+       "  'ViewUsage',\n",
+       "  'memo_examples_gpca_pump_model_views_software_software_architecture_view::gpcaSoftwareArchitectureView'),\n",
+       " (16,\n",
+       "  'ViewUsage',\n",
+       "  'memo_examples_gpca_pump_model_views_risk_risk_chain_view::gpcaRiskChainView'),\n",
+       " (16,\n",
+       "  'ViewUsage',\n",
+       "  'memo_examples_gpca_pump_model_views_operational_use_case_view::gpcaUseCaseView'),\n",
+       " (16,\n",
+       "  'ViewUsage',\n",
+       "  'memo_examples_gpca_pump_model_views_logical_mode_state_view::gpcaModeStateView'),\n",
+       " (16,\n",
+       "  'ViewUsage',\n",
+       "  'memo_examples_gpca_pump_model_views_logical_logical_architecture_view::gpcaLogicalArchitectureView'),\n",
+       " (16,\n",
+       "  'ViewUsage',\n",
+       "  'memo_examples_gpca_pump_model_views_logical_device_interconnect_view::gpcaDeviceInterconnectView'),\n",
+       " (16,\n",
+       "  'ViewUsage',\n",
+       "  'memo_examples_gpca_pump_model_views_document_dhf_index_view::dhfIndexView'),\n",
+       " (16,\n",
+       "  'ViewUsage',\n",
+       "  'memo_examples_gpca_pump_model_views_document_architecture_description_view::architectureDescriptionView'),\n",
+       " (16,\n",
+       "  'ViewUsage',\n",
+       "  'memo_examples_gpca_pump_model_views_cybersecurity_cybersecurity_view::gpcaCybersecurityView'),\n",
+       " (16,\n",
+       "  'ViewUsage',\n",
+       "  'memo_examples_gpca_pump_model_views_context_system_context_view::gpcaSystemContextView'),\n",
+       " (16,\n",
+       "  'ViewUsage',\n",
+       "  'memo_examples_gpca_pump_model_views_behavior_action_flow_view::gpcaActionFlowView'),\n",
+       " (15,\n",
+       "  'ViewUsage',\n",
+       "  'memo_examples_gpca_pump_model_views_verification_verification_coverage_view::gpcaVerificationCoverageView'),\n",
+       " (15,\n",
+       "  'ViewUsage',\n",
+       "  'memo_examples_gpca_pump_model_views_risk_fmea_view::gpcaFmeaView'),\n",
+       " (15,\n",
+       "  'ViewUsage',\n",
+       "  'memo_examples_gpca_pump_model_views_requirements_requirements_trace_view::gpcaRequirementsTraceView'),\n",
+       " (15,\n",
+       "  'ViewUsage',\n",
+       "  'memo_examples_gpca_pump_model_views_physical_physical_bom_view::gpcaPhysicalBomView'),\n",
+       " (15,\n",
+       "  'ViewUsage',\n",
+       "  'memo_examples_gpca_pump_model_views_operational_scenario_sequence_view::gpcaScenarioSequenceView'),\n",
+       " (15,\n",
+       "  'ViewUsage',\n",
+       "  'memo_examples_gpca_pump_model_views_functional_function_browser_view::gpcaFunctionBrowserView'),\n",
+       " (15,\n",
+       "  'ViewUsage',\n",
+       "  'memo_examples_gpca_pump_model_views_functional_function_allocation_view::gpcaFunctionAllocationView')]"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Deepest ownership paths\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "[(5, 'ReferenceUsage', 'sensorStatus'),\n",
+       " (5, 'ReferenceUsage', 'sensorStatus'),\n",
+       " (5, 'ReferenceUsage', 'flowCommand'),\n",
+       " (5, 'ReferenceUsage', 'flowCommand'),\n",
+       " (5, 'ReferenceUsage', 'authorizedBolus'),\n",
+       " (5, 'ReferenceUsage', 'authorizedBolus'),\n",
+       " (5, 'ReferenceUsage', 'alarmSignal'),\n",
+       " (5, 'ReferenceUsage', 'alarmSignal'),\n",
+       " (5, 'ReferenceUsage', 'actuation'),\n",
+       " (5, 'ReferenceUsage', 'actuation'),\n",
+       " (4, 'AttributeUsage', '<unnamed>'),\n",
+       " (4, 'AttributeUsage', '<unnamed>'),\n",
+       " (4, 'AttributeUsage', '<unnamed>'),\n",
+       " (4, 'AttributeUsage', '<unnamed>'),\n",
+       " (4, 'AttributeUsage', '<unnamed>'),\n",
+       " (4, 'AttributeUsage', '<unnamed>'),\n",
+       " (4, 'AttributeUsage', '<unnamed>'),\n",
+       " (4, 'AttributeUsage', '<unnamed>'),\n",
+       " (4, 'AttributeUsage', '<unnamed>'),\n",
+       " (4, 'AttributeUsage', '<unnamed>'),\n",
+       " (4, 'AttributeUsage', '<unnamed>'),\n",
+       " (4, 'AttributeUsage', '<unnamed>'),\n",
+       " (4, 'AttributeUsage', '<unnamed>'),\n",
+       " (4, 'AttributeUsage', '<unnamed>'),\n",
+       " (4, 'AttributeUsage', '<unnamed>')]"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Most common semantic types\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "[('AttributeUsage', 5056),\n",
+       " ('ConnectionUsage', 691),\n",
+       " ('PartUsage', 425),\n",
+       " ('ReferenceUsage', 174),\n",
+       " ('RequirementUsage', 105),\n",
+       " ('ItemUsage', 49),\n",
+       " ('ActionUsage', 44),\n",
+       " ('SuccessionAsUsage', 29),\n",
+       " ('VerificationCaseUsage', 27),\n",
+       " ('ViewUsage', 26),\n",
+       " ('InterfaceUsage', 14),\n",
+       " ('StateUsage', 10),\n",
+       " ('AllocationUsage', 6),\n",
+       " ('ActionDefinition', 6),\n",
+       " ('FlowUsage', 5),\n",
+       " ('ItemDefinition', 5),\n",
+       " ('UseCaseUsage', 1),\n",
+       " ('PortDefinition', 1),\n",
+       " ('ConjugatedPortDefinition', 1),\n",
+       " ('InterfaceDefinition', 1)]"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "from IPython.display import display\n",
+    "\n",
+    "semantic_elements = (\n",
+    "    list(model.elements(syside.Usage, include_subtypes=True))\n",
+    "    + list(model.elements(syside.Definition, include_subtypes=True))\n",
+    ")\n",
+    "\n",
+    "def safe_name(element):\n",
+    "    value = element.qualified_name or element.name or element.declared_name\n",
+    "    return str(value) if value else '<unnamed>'\n",
+    "\n",
+    "def ownership_depth(element):\n",
+    "    depth, current, seen = 0, element.owner, set()\n",
+    "    while current is not None and id(current) not in seen:\n",
+    "        seen.add(id(current))\n",
+    "        depth += 1\n",
+    "        current = getattr(current, 'owner', None)\n",
+    "    return depth\n",
+    "\n",
+    "containers = []\n",
+    "for element in semantic_elements:\n",
+    "    children = [child for child in element.owned_elements if isinstance(child, (syside.Usage, syside.Definition))]\n",
+    "    if children:\n",
+    "        containers.append((len(children), type(element).__name__, safe_name(element)))\n",
+    "\n",
+    "print('Top containers by directly owned semantic elements')\n",
+    "display(sorted(containers, reverse=True)[:25])\n",
+    "\n",
+    "print('Deepest ownership paths')\n",
+    "display(sorted(\n",
+    "    ((ownership_depth(item), type(item).__name__, safe_name(item)) for item in semantic_elements),\n",
+    "    reverse=True,\n",
+    ")[:25])\n",
+    "\n",
+    "print('Most common semantic types')\n",
+    "Counter(type(item).__name__ for item in semantic_elements).most_common(30)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.13"
+  },
+  "memo": {
+   "description": "Find busy containers, deep ownership paths, and dominant semantic types.",
+   "starter": true
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}