@memoarchitect/ontology 0.6.4 → 0.7.0

package/README.md

@@ -23,7 +23,7 @@ pin an exact release; the package has no repository or runtime dependency on Mem
 Tools or Memo Architect.
 
 ```bash
-pnpm add @memoarchitect/ontology@0.6.4
+pnpm add @memoarchitect/ontology@0.7.0
 ```
 
 > **Pre-1.0 notice:** ontology names, relationships, and package layout may

package/examples/connected-patient-monitor/model/catalog/project.sysml

@@ -0,0 +1,24 @@
+// Connected Patient Monitor — project identity and method binding.
+//
+// The native entrypoint. The imports name what this project contains and the
+// binding names the methodology it is governed by. No YAML file participates.
+package memo_examples_connected_patient_monitor_project {
+    private import ScalarValues::*;
+
+    private import memo_core_enumerations::*;
+    private import memo_methodology_core::*;
+    private import memo_methodology_profiles::*;
+
+    // The project's own content, imported so the catalog is one reachable
+    // closure from a single entrypoint.
+    private import memo_examples_connected_patient_monitor_viewpoints_unassigned::*;
+    private import memo_examples_connected_patient_monitor_viewpoints_unassigned_views_connected_patient_monitor_overview::*;
+
+    part projectBinding : ProjectMethodBinding {
+        attribute :>> id = "PMB-PATIENT-MONITOR-001";
+        attribute :>> name = "ConnectedPatientMonitorProjectMethodBinding";
+        attribute :>> projectName = "Connected Patient Monitor";
+        ref :>> selectedMethodology = mdDefaultDefinition;
+        attribute :>> scopeMode = ScopeModeKind::explicit;
+    }
+}

package/examples/connected-patient-monitor/model/catalog/viewpoints/unassigned/viewpoint.sysml

@@ -0,0 +1,9 @@
+// unassigned viewpoint.
+//
+// This project does not define its own viewpoint here; it binds the reusable
+// MEMO viewpoint that frames these concerns. The views it governs sit beneath
+// `views/`.
+package memo_examples_connected_patient_monitor_viewpoints_unassigned {
+    // The reusable package declaring unassigned could not be resolved during
+    // conversion. Import it here so the views beneath this viewpoint resolve.
+}

package/examples/connected-patient-monitor/model/{viewpoints → catalog/viewpoints/unassigned/views}/connected_patient_monitor_overview.sysml

@@ -1,4 +1,4 @@
-package memo_examples_connected_patient_monitor_viewpoints {
+package memo_examples_connected_patient_monitor_viewpoints_unassigned_views_connected_patient_monitor_overview {
     private import memo_examples_connected_patient_monitor::*;
     private import memo_viewpoints_definitions::*;
     private import memo_core_enumerations::*;

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

@@ -0,0 +1,24 @@
+// Embedded Infusion Pump — project identity and method binding.
+//
+// The native entrypoint. The imports name what this project contains and the
+// binding names the methodology it is governed by. No YAML file participates.
+package memo_examples_embedded_infusion_pump_project {
+    private import ScalarValues::*;
+
+    private import memo_core_enumerations::*;
+    private import memo_methodology_core::*;
+    private import memo_methodology_profiles::*;
+
+    // The project's own content, imported so the catalog is one reachable
+    // closure from a single entrypoint.
+    private import memo_examples_embedded_infusion_pump_viewpoints_unassigned::*;
+    private import memo_examples_embedded_infusion_pump_viewpoints_unassigned_views_embedded_infusion_pump_overview::*;
+
+    part projectBinding : ProjectMethodBinding {
+        attribute :>> id = "PMB-INFUSION-PUMP-001";
+        attribute :>> name = "EmbeddedInfusionPumpProjectMethodBinding";
+        attribute :>> projectName = "Embedded Infusion Pump";
+        ref :>> selectedMethodology = mdDefaultDefinition;
+        attribute :>> scopeMode = ScopeModeKind::explicit;
+    }
+}

package/examples/embedded-infusion-pump/model/catalog/viewpoints/unassigned/viewpoint.sysml

@@ -0,0 +1,9 @@
+// unassigned viewpoint.
+//
+// This project does not define its own viewpoint here; it binds the reusable
+// MEMO viewpoint that frames these concerns. The views it governs sit beneath
+// `views/`.
+package memo_examples_embedded_infusion_pump_viewpoints_unassigned {
+    // The reusable package declaring unassigned could not be resolved during
+    // conversion. Import it here so the views beneath this viewpoint resolve.
+}

package/examples/embedded-infusion-pump/model/{viewpoints → catalog/viewpoints/unassigned/views}/embedded_infusion_pump_overview.sysml

@@ -1,4 +1,4 @@
-package memo_examples_embedded_infusion_pump_viewpoints {
+package memo_examples_embedded_infusion_pump_viewpoints_unassigned_views_embedded_infusion_pump_overview {
     private import memo_examples_embedded_infusion_pump::*;
     private import memo_viewpoints_definitions::*;
     private import memo_core_enumerations::*;

package/examples/extensions/clinical/memo.package.yaml

@@ -1,9 +1,18 @@
-name: "@memoarchitect/example-extension-clinical"
-version: "0.6.1"
-type: methodology
-extends: "@memoarchitect/methodology-default"
-sysmlDir: "./src"
-description: "Example methodology extension for clinical-procedure vocabulary"
-license: "MIT"
-tags: ["memo", "methodology", "extension", "clinical"]
-usage: ["extension", "clinical-procedures"]
+# Application/distribution descriptor for this MEMO package.
+#
+# Identity and location only. It records what this package is called, what
+# version it is, and where its SysML source sits so a resolver can find it.
+# It does not select model content: the project's native SysML imports and its
+# ProjectMethodBinding decide what is in the model. Semantic fields
+# (`type`, `extends`, `usage`, `ontologies`, `methodology`, `modules`) were
+# removed at the native semantic flip and are now rejected if present.
+name: '@memoarchitect/example-extension-clinical'
+version: 0.6.1
+description: Example methodology extension for clinical-procedure vocabulary
+license: MIT
+tags:
+- memo
+- methodology
+- extension
+- clinical
+sysmlDir: ./src

package/examples/extensions/clinical/src/methodology/clinical_methodology.sysml

@@ -1,14 +1,22 @@
 package memo_extension_clinical_methodology {
     private import ScalarValues::*;
     private import memo_methodology_core::*;
+    private import memo_methodology_profiles::*;
+    private import memo_core_enumerations::*;
 
     part clinicalExtensionMethod : MethodologyDefinition {
         attribute :>> id = "EXT-CLINICAL-001";
         attribute :>> name = "ClinicalProcedureExtension";
-        attribute :>> version = "0.6.1";
+        attribute :>> version = "0.6.5";
         attribute :>> domain = "clinical procedures";
         attribute :>> description = "Adds optional clinical-procedure vocabulary to a MEMO project.";
-        attribute :>> baseMethodName = "MedicalDeviceLightDefault";
+        // The base is a typed SysML reference, not a name to keep in sync with
+        // another file. `baseMethodName` was the pre-flip spelling and no
+        // longer resolves.
+        ref :>> baseMethodology = mdDefaultDefinition;
+        // An extension adds its own module to whatever its base selected;
+        // saying so explicitly is required now that an empty list means empty.
+        attribute :>> scopeMode = ScopeModeKind::explicit;
         attribute :>> includedModule = "memo_extension_clinical";
     }
 }

package/examples/extensions/template/memo.package.yaml

@@ -1,9 +1,17 @@
-name: "{{name}}"
-version: "0.1.0"
-type: methodology
-extends: "@memoarchitect/methodology-default"
-sysmlDir: "./src"
-description: "MEMO methodology extension"
-license: "MIT"
-tags: ["memo", "methodology", "extension"]
-usage: ["extension"]
+# Application/distribution descriptor for this MEMO package.
+#
+# Identity and location only. It records what this package is called, what
+# version it is, and where its SysML source sits so a resolver can find it.
+# It does not select model content: the project's native SysML imports and its
+# ProjectMethodBinding decide what is in the model. Semantic fields
+# (`type`, `extends`, `usage`, `ontologies`, `methodology`, `modules`) were
+# removed at the native semantic flip and are now rejected if present.
+name: '{{name}}'
+version: 0.1.0
+description: MEMO methodology extension
+license: MIT
+tags:
+- memo
+- methodology
+- extension
+sysmlDir: ./src

package/examples/functional-logical-physical/model/catalog/project.sysml

@@ -0,0 +1,24 @@
+// Functional Logical Physical — project identity and method binding.
+//
+// The native entrypoint. The imports name what this project contains and the
+// binding names the methodology it is governed by. No YAML file participates.
+package memo_examples_functional_logical_physical_project {
+    private import ScalarValues::*;
+
+    private import memo_core_enumerations::*;
+    private import memo_methodology_core::*;
+    private import memo_methodology_profiles::*;
+
+    // The project's own content, imported so the catalog is one reachable
+    // closure from a single entrypoint.
+    private import memo_examples_functional_logical_physical_viewpoints_unassigned::*;
+    private import memo_examples_functional_logical_physical_viewpoints_unassigned_views_functional_logical_physical_overview::*;
+
+    part projectBinding : ProjectMethodBinding {
+        attribute :>> id = "PMB-LOGICAL-PHYSICAL-001";
+        attribute :>> name = "FunctionalLogicalPhysicalProjectMethodBinding";
+        attribute :>> projectName = "Functional Logical Physical";
+        ref :>> selectedMethodology = mdDefaultDefinition;
+        attribute :>> scopeMode = ScopeModeKind::explicit;
+    }
+}

package/examples/functional-logical-physical/model/catalog/viewpoints/unassigned/viewpoint.sysml

@@ -0,0 +1,9 @@
+// unassigned viewpoint.
+//
+// This project does not define its own viewpoint here; it binds the reusable
+// MEMO viewpoint that frames these concerns. The views it governs sit beneath
+// `views/`.
+package memo_examples_functional_logical_physical_viewpoints_unassigned {
+    // The reusable package declaring unassigned could not be resolved during
+    // conversion. Import it here so the views beneath this viewpoint resolve.
+}

package/examples/functional-logical-physical/model/{viewpoints → catalog/viewpoints/unassigned/views}/functional_logical_physical_overview.sysml

@@ -1,4 +1,4 @@
-package memo_examples_functional_logical_physical_viewpoints {
+package memo_examples_functional_logical_physical_viewpoints_unassigned_views_functional_logical_physical_overview {
     private import memo_examples_functional_logical_physical::*;
     private import memo_viewpoints_definitions::*;
     private import memo_core_enumerations::*;

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
+}