More ergonomic python API for the "patch" tool

.github/workflows/CI.yml

@@ -91,6 +91,7 @@ jobs:
         with:
           name: wheels-linux-${{ matrix.platform.target }}
           path: src/python/dist
+          retention-days: 1
 
   musllinux:
     runs-on: ${{ matrix.platform.runner }}
@@ -131,6 +132,7 @@ jobs:
         with:
           name: wheels-musllinux-${{ matrix.platform.target }}
           path: src/python/dist
+          retention-days: 1
 
   windows:
     runs-on: ${{ matrix.platform.runner }}
@@ -171,6 +173,7 @@ jobs:
         with:
           name: wheels-windows-${{ matrix.platform.target }}
           path: src/python/dist
+          retention-days: 1
 
   macos:
     runs-on: ${{ matrix.platform.runner }}
@@ -204,6 +207,7 @@ jobs:
         with:
           name: wheels-macos-${{ matrix.platform.target }}
           path: src/python/dist
+          retention-days: 1
 
   sdist:
     runs-on: ubuntu-latest
@@ -228,6 +232,7 @@ jobs:
         with:
           name: wheels-sdist
           path: src/python/dist
+          retention-days: 1
 
   release:
     name: Release

AGENTS.md

@@ -3,15 +3,15 @@
 ## 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.
 
 ## Build, Test, and Development Commands
 - Build workspace: `cargo build --workspace`
 - Run all tests: `cargo test --workspace`
-- Format (check): `cargo fmt --all -- --check` | Fix: `cargo fmt --all`
+- Format (check): `cargo +stable fmt --all -- --check` | Fix: `cargo +stable fmt --all`
 - Lint: `cargo clippy -p schemaview -p linkml_runtime -p linkml_tools -p linkml_runtime_python -p linkml_wasm --all-targets --all-features -- -D warnings --no-deps` (excludes autogenerated `linkml_meta`)
 - Run a CLI (example):
   - Validate: `cargo run -p linkml_tools --bin linkml-validate -- src/runtime/tests/data/schema.yaml Person src/runtime/tests/data/person_valid.yaml`
@@ -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