Fix stale docs: tool counts, versions, server.py refs, CHANGELOG

AGENTS.md

@@ -31,11 +31,11 @@ The tool surface is built by `uxarray_mcp.registry.build_registry()`:
   No deferred tools, no BM25 discovery.  This is what clients see by
   default when running `uxarray-mcp serve`.
 
-- **`deferred-full` (~58 loaded, ~28 visible)** — core set stays visible.
-  30 raw implementation tools are loaded with `defer=True` so they don't
-  appear in the initial tool list.  Agents discover them via
-  `discover_tools` (BM25 search), and operators promote them from the
-  admin panel.
+- **`deferred-full` (~64 loaded, ~32 visible)** — core set stays visible.
+  32 raw implementation tools are loaded with `defer=True` so they don't
+  appear in the initial tool list, plus `discover_tools`.  Agents discover
+  the deferred tools via `discover_tools` (BM25 search), and operators
+  promote them from the admin panel.
 
 ### Core tools
 
@@ -68,7 +68,7 @@ Documentation: `docs/` (Sphinx, built to ReadTheDocs).
 ## Key design decisions
 
 - **Domain/tool separation** — pure computation lives in `domain/`, server
-  wiring lives in `registry.py` + `server.py`.  The same domain functions
+  wiring lives in `registry.py` + `app.py`.  The same domain functions
   run locally or get serialized and sent to an HPC worker via Globus
   Compute.  Never put MCP, provenance, or I/O logic in `domain/`.
 
@@ -120,7 +120,7 @@ Documentation: `docs/` (Sphinx, built to ReadTheDocs).
 ```
 src/uxarray_mcp/
   registry.py             # build_registry() — namespace plan, tags, prompt-as-tool
-  server.py               # make_registry(), make_mcp_server(), run() — multi-transport
+  app.py                  # UXarrayApp, make_registry(), make_mcp_server() — multi-transport
   cli.py                  # uxarray-mcp serve/setup/doctor/endpoints/install-claude
   provenance.py           # attach_provenance() used by all tools
   domain/                 # Pure computation — no MCP, no I/O
@@ -173,8 +173,8 @@ config.yaml.example       # Template — private config is normally written by t
 
 - **Python** ≥ 3.12, < 3.13 (pinned for Globus Compute pickle compat)
 - **toolregistry** ≥ 0.11.0 — tool registration, schema generation, policy tags
-- **toolregistry-server** ≥ 0.3.3 — MCP + OpenAPI adapters
-- **UXarray** ≥ 2025.12.0 — unstructured mesh analysis
+- **toolregistry-server** ≥ 0.4.0 — MCP + OpenAPI adapters
+- **UXarray** ≥ 2026.6.0 — unstructured mesh analysis
 - **Matplotlib** ≥ 3.9.0 + **Holoviews** ≥ 1.19.0 — visualization
 - **PyYAML** ≥ 6.0 — config file parsing
 - **uv** — package management and script runner (not conda, not pip directly)

CHANGELOG.md

@@ -5,6 +5,8 @@ uses Semantic Versioning for public releases.
 
 ## Unreleased
 
+## 0.1.2 — 2026-07-05
+
 ### Added
 - Guided science workflows as `prompt/` tools, each composing existing
   operations around a scientific question: `cyclone_structure` (storm radial
@@ -23,16 +25,12 @@ uses Semantic Versioning for public releases.
 ### Changed
 - Bumped the `uxarray` floor to `>=2026.6.0` for the new zonal-anomaly,
   rectilinear-remap, and radius-scaled gradient/curl APIs.
-
-## 0.2.0 — 2026-06-19
-
-### Changed
 - **Server engine**: replaced FastMCP with
   [toolregistry](https://github.com/Oaklight/ToolRegistry) +
   [toolregistry-server](https://github.com/Oaklight/toolregistry-server).
   `fastmcp` is no longer a dependency.
-- **Two-profile tool surface**: `core` (~27 tools, conservative default) and
-  `deferred-full` (all tools loaded, 30 deferred behind BM25 discovery).
+- **Two-profile tool surface**: `core` (~31 tools, conservative default) and
+  `deferred-full` (all tools loaded, 32 deferred behind BM25 discovery).
 - **Namespace grouping**: control tools under `session/` and `hpc/`, IO under
   `io/`, prompts under `prompt/`.
 - **Policy tags**: every tool carries `ToolTag` metadata (`READ_ONLY`,

CONTRIBUTING.md

@@ -33,8 +33,8 @@ Full coding conventions and architecture notes are in [AGENTS.md](AGENTS.md).
 
 - Work on a feature branch (`git checkout -b your-name/short-description`).
 - Keep changes focused — one logical change per PR.
-- All new tools must call `attach_provenance()` and be registered in
-  `server.py` and exported from `tools/__init__.py`.
+- All new tools must call `attach_provenance()`, be assigned to a bucket in
+  `registry.py`, and be exported from `tools/__init__.py`.
 - All new tool functions need tests (see `tests/` for patterns).
 - Run the full check suite before pushing:
 

GETTING_STARTED.md

@@ -37,9 +37,11 @@ If you want HPC support too:
 uv sync --extra hpc
 ```
 
-## Claude Desktop Example
+## MCP Client Example
 
-Use absolute paths in your Claude Desktop MCP config:
+The server speaks standard MCP over stdio, so it works with any MCP-compatible
+client (Claude Desktop, Claude Code, Cursor, Continue, or your own). Most
+clients accept an `mcpServers` block like the one below — use absolute paths:
 
 ```json
 {
@@ -52,14 +54,14 @@ Use absolute paths in your Claude Desktop MCP config:
         "run",
         "python",
         "-m",
-        "uxarray_mcp.server"
+        "uxarray_mcp"
       ]
     }
   }
 }
 ```
 
-Then fully quit and reopen Claude Desktop.
+Then restart your MCP client so it picks up the new server.
 
 ## If You Want HPC
 

README.md

@@ -114,8 +114,9 @@ client's MCP docs.
 uxarray-mcp doctor
 ```
 
-Should print `local execution: ok` and (if no endpoints configured) skip the
-remote checks.
+Prints a JSON diagnostic report. With no endpoints configured it reports a
+passing local setup and skips the remote checks; the process exits `0` when
+`passed` is true.
 
 ### Step 5 — Ask the AI to do something
 

SETUP.sh

@@ -2,8 +2,8 @@
 set -e
 
 echo "[SETUP] Checking prerequisites..."
-if ! python3 -c "import sys; assert sys.version_info >= (3, 11)" &> /dev/null; then
-  echo "[ERROR] Python 3.11+ is required."
+if ! python3 -c "import sys; assert (3, 12) <= sys.version_info < (3, 13)" &> /dev/null; then
+  echo "[ERROR] Python 3.12 is required (>=3.12,<3.13, pinned for Globus Compute compatibility)."
   exit 1
 fi
 

conda/recipe/meta.yaml

@@ -27,11 +27,11 @@ requirements:
     # a second output/variant after globus-compute-sdk and academy-py solver
     # behavior is validated on conda-forge.
     - python >={{ python_min }}
-    - toolregistry-server >=0.3.3
+    - toolregistry-server >=0.4.0
     - holoviews >=1.19.0
     - matplotlib-base >=3.9.0
     - pyyaml >=6.0
-    - uxarray >=2025.12.0
+    - uxarray >=2026.6.0
 
 test:
   requires:

docs/getting-started.md

@@ -8,7 +8,7 @@ This guide uses Claude Desktop as the MCP client. Other MCP-compatible clients s
 
 ## Prerequisites
 
-- **Python 3.11+** — Check with: `python3 --version`
+- **Python 3.12** — required (`>=3.12,<3.13`, pinned for Globus Compute compatibility). Check with: `python3 --version`
 - **uv** — Install with: `pip install uv`
 - **MCP Client** — Claude Desktop or any MCP-compatible client
 - **Git** (optional) — For cloning the repository

docs/provenance.md

@@ -26,8 +26,8 @@ Every tool result includes a `_provenance` block that records what ran, when, wh
     "inputs": { "file_path": "healpix:4", "data_path": null, "variable_name": null },
     "execution_venue": "local",
     "timestamp_utc": "2026-03-18T...",
-    "uxarray_version": "2025.12.0",
-    "python_version": "3.13.0",
+    "uxarray_version": "2026.6.0",
+    "python_version": "3.12.0",
     "warnings": [],
     "artifacts": [
       { "type": "mesh_topology", "n_face": 3072, "n_node": 3074, "format": "HEALPix" },

docs/remote-hpc.md

@@ -84,8 +84,8 @@ This adds the `globus-compute-sdk` to your local install. Verify:
 uxarray-mcp doctor
 ```
 
-You should see the SDK listed. (No endpoint health checks yet — that's
-Step 4.)
+The JSON report should show the Globus Compute SDK as available. (No endpoint
+health checks yet — that's Step 4.)
 
 ---
 
@@ -202,7 +202,7 @@ back. Reasons appear in the response's `warnings` and in
 | Symptom | Likely cause | Fix |
 |---|---|---|
 | `globus_compute_sdk not installed` | Missing HPC extras | `uv tool upgrade --extra hpc uxarray-mcp` |
-| Browser doesn't open on first auth | Headless laptop / SSH session | Run `uxarray-mcp doctor` with `--no-browser`, paste the URL into a local browser |
+| Browser doesn't open on first auth | Headless laptop / SSH session | The Globus login prints an auth URL to the terminal — copy it into a local browser and paste the code back. |
 | `endpoint status: registered, probe timed out` | Worker isn't responding | Operator's problem. Ask them. May be scheduler backlog. |
 | `endpoint status: not found` | Wrong UUID or you've been removed | Re-check UUID with operator. Globus Auth identity must match endpoint's allow-list. |
 | Tool returns `execution_venue: local` when you asked for remote | Auto-fallback fired | Check `warnings` in response. Common: path didn't match `path_prefix`, or endpoint unhealthy. |

src/uxarray_mcp/cli.py

@@ -308,16 +308,16 @@ def build_parser() -> argparse.ArgumentParser:
         choices=("core", "deferred-full"),
         default="core",
         help=(
-            "core: gateway + control + list_datasets + prompts (~27 tools). "
-            "deferred-full: also load 30 raw tools as deferred, gated "
+            "core: gateway + control + list_datasets + prompts (~31 tools). "
+            "deferred-full: also load 32 raw tools as deferred, gated "
             "behind discover_tools / admin promotion."
         ),
     )
     serve.add_argument(
         "--transport",
         choices=("stdio", "sse", "http"),
         default="stdio",
-        help="MCP transport. stdio for Claude Desktop subprocess use.",
+        help="MCP transport. stdio for subprocess use by MCP clients.",
     )
     serve.add_argument("--host", default="127.0.0.1", help="Bind host for SSE/HTTP.")
     serve.add_argument("--port", type=int, default=8001, help="Port for SSE/HTTP.")
@@ -330,8 +330,8 @@ def build_parser() -> argparse.ArgumentParser:
         choices=("core", "deferred-full"),
         default="core",
         help=(
-            "core: gateway + control + list_datasets + prompts (~27 tools). "
-            "deferred-full: also load 30 raw tools as deferred, gated "
+            "core: gateway + control + list_datasets + prompts (~31 tools). "
+            "deferred-full: also load 32 raw tools as deferred, gated "
             "behind discover_tools / admin promotion."
         ),
     )

src/uxarray_mcp/registry.py

@@ -5,9 +5,9 @@
 * ``"core"`` (default) — small, predictable surface visible to LLMs.
   Mirrors the original MCP server's 11 front-door tools, adds 12
   control/status tools, the ``list_datasets`` discovery helper, and
-  three prompt-as-tool helpers (former ``@mcp.prompt()`` decorators).
+  seven prompt-as-tool helpers (former ``@mcp.prompt()`` decorators).
 * ``"deferred-full"`` — loads every public function with the core set
-  enabled and 30 raw implementation tools marked ``defer=True``.
+  enabled and 32 raw implementation tools marked ``defer=True``.
   Includes ``discover_tools`` (BM25 search) so LLMs find deferred
   tools by intent.
 
@@ -592,9 +592,9 @@ def build_registry(
     """Build a ``ToolRegistry`` for the chosen profile.
 
     Args:
-        profile: ``"core"`` for the small default surface (~27 tools),
+        profile: ``"core"`` for the small default surface (~31 tools),
             ``"deferred-full"`` for the complete pool (core visible,
-            30 raw tools deferred, ``discover_tools`` added).
+            32 raw tools deferred, ``discover_tools`` added).
         registry_name: Identifier for server titles and labels.
 
     Returns: