Feat/rename linkmlvalue to linkmlinstance

AGENTS.md

@@ -3,7 +3,7 @@
 ## Project Structure & Module Organization
 - `src/metamodel` (`linkml_meta`): Autogenerated metamodel types; optional Serde/PyO3.
 - `src/schemaview` (`schemaview`/`linkml_schemaview`): Schema loading/resolution and views (SchemaView, ClassView, SlotView, EnumView).
-- `src/runtime` (`linkml_runtime`): Core runtime (LinkMLValue parse/validate, diff/patch, turtle). Pure Rust lib.
+- `src/runtime` (`linkml_runtime`): Core runtime (LinkMLInstance parse/validate, diff/patch, turtle). Pure Rust lib.
 - `src/tools` (`linkml_tools`): CLI binaries: `linkml-validate`, `linkml-convert`, `linkml-diff`, `linkml-patch`, `linkml-schema-validate`.
 - `src/python` (`linkml_runtime_python`): PyO3 bindings and Python package `linkml_runtime_rust._native` plus helpers.
 - `src/wasm` (`linkml_wasm`): WASM build target.
@@ -25,12 +25,14 @@
 - Python (bindings helpers): follow PEP 8; prefer type hints where feasible.
 
 ## Testing Guidelines
+- When testing locally, always provide network access. never try to run the tests offline
 - Add integration tests under `src/runtime/tests/` when changing CLI/runtime behavior.
 - Prefer `assert_cmd` for CLI and `predicates` for output checks. Keep fixtures in `src/runtime/tests/data/`.
 - Run `cargo test --workspace` locally; ensure tests don’t rely on network input.
+ - Prefer modifying existing tests over adding new ones for new code paths. Extend current scenarios with extra assertions/fixtures to avoid redundant tests proliferating. For example, if adding null-handling in diff/patch, enhance the existing diff tests rather than introducing separate "basic diff works" tests that become redundant.
 
 ## Commit & Pull Request Guidelines
-- Commits: short, imperative summary (e.g., “Add __repr__ for LinkMLValue”); group related changes.
+- Commits: short, imperative summary (e.g., “Add __repr__ for LinkMLInstance”); group related changes.
 - PRs: include clear description, rationale, and usage examples; link issues; update docs/tests; ensure CI passes: fmt, clippy (no warnings), and tests.
 
 ### Pre-commit checklist

README.md

@@ -1,15 +1,15 @@
 # linkml-core
 
-core linkml schema operations written in rust :)
+core linkml schema operations written in rust
 
 ## Crates
 
 - linkml_meta (`src/metamodel`): Autogenerated LinkML metamodel types and helpers. Optional Serde/PyO3 features for serialization and Python interop.
 - schemaview (`src/schemaview`): Schema loading, CURIE/URI conversion, resolution (feature-gated), and view utilities: `SchemaView`, `ClassView`, `SlotView`, `EnumView`.
-- linkml_runtime (`src/runtime`): Core runtime: `LinkMLValue` parsing (YAML/JSON), basic validation, diff/patch, and Turtle serialization. Pure Rust library.
+- linkml_runtime (`src/runtime`): Core runtime: `LinkMLInstance` parsing (YAML/JSON), basic validation, diff/patch, and Turtle serialization. Pure Rust library.
 - linkml_tools (`src/tools`): CLI tools wrapping the runtime and schemaview:
   - `linkml-validate`, `linkml-convert`, `linkml-diff`, `linkml-patch`, `linkml-schema-validate`.
-- linkml_runtime_python (`src/python`): PyO3 bindings and Python package (`linkml_runtime_rust._native`) exposing SchemaView and LinkMLValue to Python; includes small Python helpers.
+- linkml_runtime_python (`src/python`): PyO3 bindings and Python package (`linkml_runtime_rust._native`) exposing SchemaView and LinkMLInstance to Python; includes small Python helpers.
 - linkml_wasm (`src/wasm`): WASM build target (experimental).
 
 ## Regenerating the metamodel

src/python/python/linkml_runtime_rust/__init__.py

@@ -3,6 +3,5 @@
 from ._native import *  # noqa: F401,F403
 from ._resolver import resolve_schemas
 from .schemaview import SchemaView
-from .debug_utils import pretty_linkml_value
+from .debug_utils import pretty_linkml_instance
 __all__ = [name for name in globals() if not name.startswith("_")]
-

src/python/python/linkml_runtime_rust/debug_utils.py

@@ -1,6 +1,6 @@
-"""Utilities for pretty-printing LinkMLValue trees.
+"""Utilities for pretty-printing LinkMLInstance trees.
 
-This module provides a pure Python helper to render a :class:`LinkMLValue`
+This module provides a pure Python helper to render a :class:`LinkMLInstance`
 as a human readable tree. It is intended for debugging and diagnostic use.
 """
 
@@ -9,19 +9,19 @@
 from typing import Any, List
 
 try:  # pragma: no cover - runtime optional during type checking
-    from . import LinkMLValue
+    from . import LinkMLInstance
 except Exception:  # pragma: no cover - fallback when extension missing
-    LinkMLValue = Any  # type: ignore[misc]
+    LinkMLInstance = Any  # type: ignore[misc]
 
-__all__ = ["pretty_linkml_value"]
+__all__ = ["pretty_linkml_instance"]
 
 
-def pretty_linkml_value(value: "LinkMLValue", prefix: str = '', nofirstline: bool = False) -> str:
+def pretty_linkml_instance(value: "LinkMLInstance", prefix: str = '', nofirstline: bool = False) -> str:
     """Return a tree-style string representation of ``value``.
 
     Parameters
     ----------
-    value: LinkMLValue
+    value: LinkMLInstance
         The value to render.
     indent: int, optional
         Starting indentation (number of spaces).
@@ -35,18 +35,18 @@ def pretty_linkml_value(value: "LinkMLValue", prefix: str = '', nofirstline: boo
             if rval.kind == "scalar":
                 txt += f"{prefix}  | {key}={rval.as_python()}\n"
             elif rval.kind == "list":
-                txt += f"{prefix}  | {key}:\n{pretty_linkml_value(rval, prefix + '  | ')}"
+                txt += f"{prefix}  | {key}:\n{pretty_linkml_instance(rval, prefix + '  | ')}"
             else:
                 pfx =  f"{prefix}  | " + ' ' * len(key)
-                txt += f"{prefix}  | {key}: {pretty_linkml_value(rval, pfx, nofirstline=True)}"
+                txt += f"{prefix}  | {key}: {pretty_linkml_instance(rval, pfx, nofirstline=True)}"
                 txt += f"{prefix}  |\n"
     elif value.kind == "list":
         for idx in range(len(value)):
             rval = value[idx]
             if rval.kind == "scalar":
                 txt = f"{prefix} - {rval.as_python()}\n"
             else:
-                txt = f"{prefix} - {pretty_linkml_value(rval, prefix + ' ', nofirstline=True)}"
+                txt = f"{prefix} - {pretty_linkml_instance(rval, prefix + ' ', nofirstline=True)}"
     elif value.kind == "scalar":
         txt = f"{prefix}{value.as_python()}\n"
     else: