Fix event loop warning filter and example configs

examples/everything/colin.toml

@@ -1,10 +1,7 @@
 [project]
 name = "everything"
-version = "0.1.0"
-
-[paths]
-models = "models"
-target = "target"
+model-path = "models"
+output-path = "output"
 
 [[providers.llm]]
 model = "anthropic:claude-haiku-4-5"

examples/everything/models/analysis.md

@@ -7,13 +7,17 @@ description: Extracted insights from product data
 {{ colin.mcp.demo.resource('demo://greeting/Analyst') }}
 
 ## Key Pain Points
-{{ ref('data') | llm_extract('List the top 3 user pain points mentioned in the feedback, as bullet points') }}
+
+{{ ref('data.md') | llm_extract('List the top 3 user pain points mentioned in the feedback, as bullet points') }}
 
 ## Performance Summary
-{{ ref('data') | llm_extract('Summarize the technical performance in one sentence') }}
+
+{{ ref('data.md') | llm_extract('Summarize the technical performance in one sentence') }}
 
 ## Strengths
-{{ ref('data') | llm_extract('What are users happy about? List as bullet points') }}
+
+{{ ref('data.md') | llm_extract('What are users happy about? List as bullet points') }}
 
 ## Analysis Guidance
+
 {{ colin.mcp.demo.prompt('summarize', style='detailed') }}

examples/everything/models/executive_brief.md

@@ -5,19 +5,19 @@ description: High-level summary for leadership
 # Executive Brief: Q1 2025 Planning
 
 ## TL;DR
-{{ ref('recommendations') | llm_extract('Summarize the top 3 priorities in one sentence each') }}
+{{ ref('recommendations.md') | llm_extract('Summarize the top 3 priorities in one sentence each') }}
 
 ## Current State
-{{ ref('goal_status') | llm_extract('Give a one-paragraph executive summary of goal progress') }}
+{{ ref('goal_status.md') | llm_extract('Give a one-paragraph executive summary of goal progress') }}
 
 ## Detailed Recommendations
-{{ ref('recommendations').content }}
+{{ ref('recommendations.md').content }}
 
 ---
 
 ## Appendix: Raw Data
 <details>
 <summary>Click to expand source data</summary>
 
-{{ ref('data').content }}
+{{ ref('data.md').content }}
 </details>

examples/everything/models/goal_status.md

@@ -7,10 +7,10 @@ description: Assessment of progress toward goals
 Based on current metrics and stated objectives:
 
 **Current Data:**
-{{ ref('data').content }}
+{{ ref('data.md').content }}
 
 **Goals:**
-{{ ref('goals').content }}
+{{ ref('goals.md').content }}
 
 {% llm %}
 Compare the current metrics from the data above against the stated goals.

examples/everything/models/metrics_api.md

@@ -2,7 +2,8 @@
 name: Metrics API
 description: Structured JSON output for API consumption
 colin:
-  output: json
+  output:
+    format: json
 ---
 
 ## product

examples/everything/models/recommendations.md

@@ -5,10 +5,10 @@ description: Prioritized action items based on analysis
 # Strategic Recommendations
 
 ## Analysis Summary
-{{ ref('analysis').content }}
+{{ ref('analysis.md').content }}
 
 ## Goal Status
-{{ ref('goal_status') | llm_extract('Which goals are at risk or behind?') }}
+{{ ref('goal_status.md') | llm_extract('Which goals are at risk or behind?') }}
 
 ## Recommended Actions
 

examples/hello_world/models/summary.md

@@ -7,19 +7,19 @@ description: Demonstrates LLM blocks and extract filter
 
 Here's some content to work with:
 
-{{ ref('greeting').content }}
+{{ ref('greeting.md').content }}
 
 
 
 ## Extracted Info
 
-{{ ref('greeting') | llm_extract('the main message in one sentence') }}
+{{ ref('greeting.md') | llm_extract('the main message in one sentence') }}
 
 ## LLM-Generated Content
 
 {% llm %}
 Given this greeting:
-{{ ref('greeting').content }}
+{{ ref('greeting.md').content }}
 
 Write a haiku about being welcomed.
 {% endllm %}

examples/hello_world/models/welcome.md

@@ -5,7 +5,7 @@ description: Demonstrates ref() and LLM blocks
 
 # Welcome
 
-{{ ref('greeting').content }}
+{{ ref('greeting.md').content }}
 
 ---
 
@@ -17,7 +17,7 @@ Colin automatically compiles documents in the right order based on their depende
 {% llm %}
 Translate this greeting message for French users of the Colin library:
 
-{{ ref('greeting').content }}
+{{ ref('greeting.md').content }}
 
 The translation should feel welcoming and appropriate for a technical audience.
 {% endllm %}

examples/mcp/.colin/compiled/greeting.md

@@ -0,0 +1,9 @@
+# MCP Demo
+
+## Resource Example
+
+Hello, World! Welcome to the demo.
+
+## Prompt Example
+
+Summarize the following in a detailed style.

examples/mcp/.colin/manifest.json

@@ -0,0 +1,55 @@
+{
+  "version": "1",
+  "project_name": "mcp",
+  "config_hash": "f6a9b770bee3be5d",
+  "compiled_at": "2026-01-07T21:57:28.998543Z",
+  "documents": {
+    "project://greeting.md": {
+      "uri": "project://greeting.md",
+      "source_path": null,
+      "source_hash": "44d23c70d58c7e85",
+      "output_hash": "326780bff734af74",
+      "output_path": "greeting.md",
+      "is_published": true,
+      "compiled_at": "2026-01-07T21:53:49.341310Z",
+      "refs": [
+        {
+          "provider": "mcp",
+          "connection": "demo",
+          "method": "config",
+          "args": {}
+        },
+        {
+          "provider": "mcp",
+          "connection": "demo",
+          "method": "resource",
+          "args": {
+            "uri": "demo://greeting/World"
+          }
+        },
+        {
+          "provider": "mcp",
+          "connection": "demo",
+          "method": "prompt",
+          "args": {
+            "name": "summarize",
+            "arguments": {
+              "style": "detailed"
+            }
+          }
+        }
+      ],
+      "ref_versions": {
+        "{\"args\": {}, \"connection\": \"demo\", \"method\": \"config\", \"provider\": \"mcp\"}": "e0569178996485f6",
+        "{\"args\": {\"uri\": \"demo://greeting/World\"}, \"connection\": \"demo\", \"method\": \"resource\", \"provider\": \"mcp\"}": "6236c65af4fdeed5",
+        "{\"args\": {\"arguments\": {\"style\": \"detailed\"}, \"name\": \"summarize\"}, \"connection\": \"demo\", \"method\": \"prompt\", \"provider\": \"mcp\"}": "e31eb0daa2d308b8"
+      },
+      "llm_calls": {},
+      "total_cost_usd": 0.0,
+      "artifacts": [],
+      "sections": {},
+      "config_hash": "f6a9b770bee3be5d"
+    }
+  },
+  "cache": {}
+}

examples/mcp/colin.toml

@@ -0,0 +1,18 @@
+[project]
+name = "mcp"
+model-path = "models"
+output-path = "output"
+
+[[providers.mcp]]
+name = "demo"
+command = "uvx"
+args = [
+    "--with",
+    "fastmcp",
+    "fastmcp",
+    "run",
+    "--no-banner",
+    "--log-level",
+    "ERROR",
+    "examples/mcp/mcp_server.py",
+]

examples/mcp/mcp_server.py

@@ -0,0 +1,21 @@
+"""Simple MCP server for the mcp example."""
+
+from fastmcp import FastMCP
+
+mcp = FastMCP("demo")
+
+
+@mcp.resource(uri="demo://greeting/{name}")
+def greeting(name: str) -> str:
+    """Get a personalized greeting."""
+    return f"Hello, {name}! Welcome to the demo."
+
+
+@mcp.prompt()
+def summarize(style: str = "brief") -> str:
+    """Summarization guidance."""
+    return f"Summarize the following in a {style} style."
+
+
+if __name__ == "__main__":
+    mcp.run()

examples/mcp/models/greeting.md

@@ -0,0 +1,13 @@
+---
+name: MCP Greeting
+description: Demonstrates MCP resource and prompt usage
+---
+# MCP Demo
+
+## Resource Example
+
+{{ colin.mcp.demo.resource('demo://greeting/World') }}
+
+## Prompt Example
+
+{{ colin.mcp.demo.prompt('summarize', style='detailed') }}

examples/mcp/output/greeting.md

@@ -0,0 +1,9 @@
+# MCP Demo
+
+## Resource Example
+
+Hello, World! Welcome to the demo.
+
+## Prompt Example
+
+Summarize the following in a detailed style.

pyproject.toml

@@ -13,7 +13,7 @@ dependencies = [
     "rich>=14.2.0",
     "tomli>=2.3.0",
     "tomli-w>=1.2.0",
-    "fastmcp>=2.14.1",
+    "fastmcp @ git+https://github.com/jlowin/fastmcp@main",
     "pydantic-ai>=1.39.0",
     "httpx>=0.27.0",
 ]
@@ -42,7 +42,7 @@ env = [
     "COLIN_DEFAULT_LLM_MODEL=test",
 ]
 filterwarnings = [
-    "ignore::pytest.PytestUnraisableExceptionWarning:.*Event loop is closed.*",
+    "ignore:.*BaseSubprocessTransport.*:pytest.PytestUnraisableExceptionWarning",
 ]
 
 [tool.ty.terminal]
@@ -59,6 +59,9 @@ select = ["E", "F", "I", "UP"]
 requires = ["hatchling", "uv-dynamic-versioning"]
 build-backend = "hatchling.build"
 
+[tool.hatch.metadata]
+allow-direct-references = true
+
 [tool.hatch.version]
 source = "uv-dynamic-versioning"
 

src/colin/compiler/engine.py

@@ -485,17 +485,20 @@ def _load_document(self, path: Path) -> ColinDocument:
         content = path.read_text(encoding="utf-8")
         post = fm_parser.loads(content)
 
+        # Build relative path for URIs and error messages
+        relative = path.relative_to(self.config.model_path)
+
         # Extract colin config
         raw_colin = post.metadata.pop("colin", {})
         colin_data = cast(dict[str, Any], raw_colin) if isinstance(raw_colin, dict) else {}
-        colin_config = ColinConfig.model_validate(colin_data)
+        try:
+            colin_config = ColinConfig.model_validate(colin_data)
+        except Exception as e:
+            raise ValueError(f"Invalid frontmatter in {relative}:\n{e}") from e
 
         # Rest is document metadata
         metadata = cast(dict[str, Any], post.metadata)
         frontmatter = Frontmatter(colin=colin_config, metadata=metadata)
-
-        # Build URI from path
-        relative = path.relative_to(self.config.model_path)
         uri = f"project://{relative}"
 
         # Hash the FULL content (including frontmatter) for change detection

src/colin/providers/base.py

@@ -1,5 +1,7 @@
 """Provider base class."""
 
+import hashlib
+import json
 from collections.abc import AsyncIterator, Awaitable, Callable
 from contextlib import asynccontextmanager
 from typing import TYPE_CHECKING, Any, ClassVar
@@ -94,8 +96,6 @@ def from_config(cls, name: str | None, config: dict[str, Any]) -> Self:
         Returns:
             Configured provider instance.
         """
-        import hashlib
-        import json
 
         instance = cls(**config)
         instance._connection = name or ""

src/colin/providers/mcp.py

@@ -112,6 +112,10 @@ def from_config(cls, name: str | None, config: dict[str, Any]) -> Self:
         """
         if not name:
             raise ValueError("MCP provider requires an instance name")
+        # Set keep_alive=False for stdio servers to ensure proper subprocess cleanup
+        # and avoid "Event loop is closed" warnings during shutdown.
+        if "command" in config and "keep_alive" not in config:
+            config = {**config, "keep_alive": False}
         server = MCPServerAdapter.validate_python(config)
         return cls(name, server)