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Two fixes: 1. _lazy_registry_static.py: update JLCSearchTool and DigiKeyTool mappings to their new location (tooluniverse.circuit.*) after the circuit tools were moved to the sub-package. 2. tool_registry.py: call _auto_import_subpackages() even when the static registry is loaded. Previously it returned early, so installed sub-packages (e.g. tooluniverse[circuit]) were never imported and their _list_config_registry entries were never populated.
Add _discover_entry_point_plugins() that finds installed packages in the tooluniverse.plugins entry point group, imports their .py tool files so @register_tool decorators fire, and loads their JSON configs into _list_config_registry. Call it in both code paths of build_lazy_registry() (static registry and AST discovery), so external plugins are always loaded at startup regardless of the lazy registry strategy used. Remove stale _lazy_registry_static.py entries for DigiKeyTool and JLCSearchTool (now auto-loaded via the circuit plugin entry point). This enables a simple, flat plugin package structure that mirrors the local ~/.tooluniverse/ workspace layout — making it trivial for users to create tool packages and share them on GitHub.
Add _discovered_plugin_names set and per-plugin guard so that calling _discover_entry_point_plugins() more than once (e.g. in tests or if build_lazy_registry() is invoked directly) does not append duplicate configs to _list_config_registry.
_discover_entry_point_plugins() was only called from build_lazy_registry() (the lazy path). The eager path in auto_discover_tools(lazy=False) never called it, so plugin tools were silently missing when: - TOOLUNIVERSE_LAZY_LOADING=false env var is set - force_full_discovery() is called explicitly - get_tool_class_lazy() fallback triggers pkgutil.iter_modules() only finds modules in the tooluniverse.* namespace, so entry-point plugin packages (tooluniverse_circuit, etc.) are invisible to it. Add an explicit _discover_entry_point_plugins() call at the end of the eager discovery loop, before setting _discovery_completed=True. The idempotency guard in _discover_entry_point_plugins() (added in previous commit) ensures this is safe: if plugins were already loaded via the lazy path first (e.g. frozen-env fallback), the second call is a no-op.
space.yaml is the standard "identity file" for any tool pack, whether it lives in ~/.tooluniverse/ or inside an installed plugin package. The system now reads it automatically in both places: - _read_space_yaml(): new helper that reads space.yaml from a directory, logs the pack name/description at INFO, and warns about missing required_env variables (e.g. DIGIKEY_CLIENT_ID not set). - _discover_entry_point_plugins(): calls _read_space_yaml() for each plugin directory before importing tool files. - _get_user_tool_files(): calls _read_space_yaml() for each workspace root directory before scanning for .py/.json files. tools.include_tool_types in space.yaml is intentionally NOT applied automatically — it remains a user-facing filter used only when explicitly loading a space via load_space() / --load.
- Default workspace is now ./.tooluniverse (local mode) instead of dual-scan - Add use_global=True to use ~/.tooluniverse as workspace default - Workspace space.yaml auto-applied at startup when no explicit space= given - When --load is used, workspace space.yaml acts as base config; loaded yaml deep-merges on top (override wins for same keys) - Add --global CLI flag to all 3 parsers (run_http_server, run_stdio_server, run_smcp_server); propagated through SMCP to ToolUniverse - Update test: _workspace_dir is no longer None by default - Fix test state pollution: add type field to registered test tool configs
- Remove circuit tools from main package (digikey_tool.py, jlcsearch_tool.py, data/digikey_tools.json, data/jlcsearch_tools.json) — moved to tooluniverse-circuit - Space system: SpaceLoader.resolve_to_local_dir(), get_tool_files_from_dir(), _deep_merge(), _resolve_extends(); validator schema additions (sources, workspace, package fields) - Plugin entry point discovery via tooluniverse.plugins group - Add BVBRC, CoL, EOL, FlyBase, HumanMine, LNCipedia, LOTUS, MSigDB, Pfam, PubChemTox, SASBDB, ZFIN, miRBase tools - Update tool metadata and space validator - Update tests for space loader, validator, and toolspace integration
# Conflicts: # src/tooluniverse/_lazy_registry_static.py # src/tooluniverse/default_config.py # src/tooluniverse/tools/.tool_metadata.json # src/tooluniverse/tools/BVBRC_search_taxonomy.py # src/tooluniverse/tools/BioTools_get_tool.py # src/tooluniverse/tools/IdentifiersOrg_resolve.py # src/tooluniverse/tools/SASBDB_get_scattering_profile.py # src/tooluniverse/tools/__init__.py
- Replace 11 example YAML files with single life-science.yaml covering all life science and general-purpose tool categories - Add default_space.yaml with sensible defaults - Consolidate workspace + space docs into toolspace.rst; update index.rst - Fix validator bug: run schema validation before fill_defaults() so missing required fields (name) are caught instead of silently injected - Remove version from required fields (optional, defaults to "1.0.0") - Fix _resolve_workspace(): raise clear ValueError when path is an existing file instead of crashing with bare FileExistsError - Add tests/test_robustness.py with 62 adversarial tests covering bad YAML, wrong workspace structure, bad API calls, and contradictory configs - Add tests/test_workspace_and_space.py for workspace and space loading - Update tool metadata, UniProt_get_proteome, OpenMeteo_get_air_quality
Revert .tool_metadata.json, OpenMeteo_get_air_quality.py, UniProt_get_proteome.py, and __init__.py to their origin/main content, undoing unintended changes introduced during the merge.
…ls() - _load_auto_discovered_configs(): skip configs already present in all_tools so repeated load_tools() calls don't accumulate duplicates - load_tools(): clear all_tools/all_tool_dict/tool_category_dicts at the start of a full reload (include_tools=None) so calling it multiple times is safe and efficient - refresh_tools(): implement as a clean reload (was a no-op TODO stub); picks up new JSON/Python tool files added to workspace since startup; add docstring noting that built-in package tools still need a restart
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