coala-cli 0.2.4__tar.gz → 0.2.6__tar.gz

coala_cli-0.2.6/.gitignore

@@ -0,0 +1,6 @@
+__pycache__/
+dist/
+docs
+Pipfile.lock
+*archieve*
+.pypirc

{coala_cli-0.2.4 → coala_cli-0.2.6}/PKG-INFO

@@ -1,21 +1,21 @@
-Metadata-Version: 2.4
+Metadata-Version: 2.5
 Name: coala-cli
-Version: 0.2.4
+Version: 0.2.6
 Summary: Command-line LLM-agent Adapter
-License: MIT
 Author: Qiang
-Requires-Python: >=3.12,<3.15
+License-Expression: MIT
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: 3.14
-Requires-Dist: cwltool (>=3.2.20260413085819,<4.0.0)
-Requires-Dist: fastapi (>=0.115.0)
-Requires-Dist: mcp (>=1.12.0,<2.0.0)
-Requires-Dist: pydantic (>=2.10.0,<3.0.0)
-Requires-Dist: requests (>=2.33.0,<3.0.0)
-Requires-Dist: uvicorn (>=0.32.0,<0.33.0)
+Requires-Python: <3.15,>=3.12
+Requires-Dist: cwltool<4.0.0,>=3.2.20260413085819
+Requires-Dist: fastapi>=0.115.0
+Requires-Dist: mcp<3,>=2.2
+Requires-Dist: pydantic<3.0.0,>=2.10.0
+Requires-Dist: requests<3.0.0,>=2.33.0
+Requires-Dist: uvicorn<0.33.0,>=0.32.0
 Description-Content-Type: text/markdown
 
 # Coala: Command-line LLM-agent Adapter
@@ -29,4 +29,3 @@ Coala integrates the [Common Workflow Language (CWL)](https://www.commonwl.org/s
 
 Please find Coala documuentations through [Coala website](https://coala.info/), including [overview](https://coala.info/guide/), [installation](https://coala.info/guide/installation.html), [quick start](https://coala.info/guide/quick-start.html), and [use cases](https://coala.info/use-cases/). 
 
-

{coala_cli-0.2.4 → coala_cli-0.2.6}/coala/mcp_api.py

@@ -15,7 +15,7 @@ from cwltool.context import RuntimeContext
 from threading import Thread
 import time
 from typing import Optional, List, Annotated
-from mcp.server.fastmcp import FastMCP
+from mcp.server.mcpserver import MCPServer
 from coala.tool_logic import run_tool, configure_container_runner  # <-- import shared logic
 import threading
 import sys
@@ -57,7 +57,8 @@ class mcp_api():
         self.container_runner = container_runner
         self.server = None
         self.url = None
-        self.mcp = FastMCP(host=host, port=port)
+        # mcp 2: host and port are run() options, no longer constructor arguments.
+        self.mcp = MCPServer()
         self.tools = {}  # tool_name -> tool info
         self.system_prompt = """
 At the end of your response, append a summary listing the tool name and version from the tool's description using this exact format:
@@ -521,7 +522,10 @@ tool_version: <TOOL_VERSION>
             # For stdio transport, don't print startup messages to stdout
             logger.info("Starting MCP server with stdio transport")
         
-        self.mcp.run(transport=transport)
+        if transport == 'streamable-http':
+            self.mcp.run(transport=transport, host=self.host, port=self.port)
+        else:
+            self.mcp.run(transport=transport)
         # thread = threading.Thread(target=self.mcp.run, kwargs={'transport': 'sse'}, daemon=True)
         # thread.start()
         # self.server_thread = thread

{coala_cli-0.2.4 → coala_cli-0.2.6}/coala/tool_logic.py

@@ -6,6 +6,7 @@ from pathlib import Path
 from urllib.parse import urlparse, unquote
 from urllib.request import url2pathname
 from cwltool.context import RuntimeContext
+from cwltool.factory import WorkflowStatus
 
 
 def _canonical_file_uri(uri: str) -> str:
@@ -57,6 +58,66 @@ def configure_container_runner(runtime_context: RuntimeContext, container_runner
             or shutil.which('xcrunner') or 'xcrunner'
         )
 
+class ToolRunFailed(RuntimeError):
+    """A CWL run that exited non-zero, carrying what the tool itself printed."""
+
+
+# Enough to hold a tool's closing error and the lines that lead to it, without flooding the
+# caller with a long progress log.
+_FAILED_OUTPUT_LINES = 40
+_FAILED_OUTPUT_CHARS = 6000
+
+
+def _captured_stream_outputs(tool) -> dict:
+    """``{output id: "stdout" | "stderr"}`` for outputs that capture the tool's own streams.
+
+    cwltool rewrites ``type: stdout`` into a ``File`` whose glob is the tool's ``stdout`` value,
+    so the glob, not the type, identifies it — and still does when that value is an expression.
+    """
+    spec = getattr(getattr(tool, "t", None), "tool", None) or {}
+    streams = {spec.get(s): s for s in ("stdout", "stderr") if spec.get(s)}
+    found = {}
+    for out in spec.get("outputs") or []:
+        glob = (out.get("outputBinding") or {}).get("glob")
+        if isinstance(glob, str) and glob in streams:
+            found[str(out.get("id", "")).rsplit("#", 1)[-1]] = streams[glob]
+    return found
+
+
+def _tail(path: str) -> str:
+    try:
+        with open(path, "r", encoding="utf-8", errors="replace") as fh:
+            lines = fh.read().splitlines()
+    except OSError:
+        return ""
+    text = "\n".join(lines[-_FAILED_OUTPUT_LINES:]).strip()
+    return text[-_FAILED_OUTPUT_CHARS:]
+
+
+def _failed_run_output(tool, partial) -> str:
+    """The tail of the tool's own stdout/stderr capture files from a failed run, or ``""``.
+
+    A tool that prints its error to standard output, into a file the CWL declares with
+    ``stdout:``, leaves cwltool's log with nothing but "exited with status: 1": cellranger-arc
+    ``mkref`` reported an unknown GTF contig that way, and the caller retried blind for three
+    hours. cwltool still collects that file when the run fails and passes it in the exception,
+    so read it back.
+    """
+    if not isinstance(partial, dict):
+        return ""
+    parts = []
+    for out_id, stream in _captured_stream_outputs(tool).items():
+        entry = partial.get(out_id)
+        location = entry.get("location") if isinstance(entry, dict) else None
+        if not isinstance(location, str) or not location.startswith("file://"):
+            continue
+        text = _tail(url2pathname(urlparse(location).path))
+        if text:
+            name = entry.get("basename") or out_id
+            parts.append(f"The tool's {stream} ({name}), last lines:\n{text}")
+    return "\n\n".join(parts)
+
+
 def _read_file_content(filepath):
     """Read file content, handling gzipped files."""
     try:
@@ -198,7 +259,13 @@ def run_tool(tool, params, outputs, read_outs=False, container_runner=None):
             configure_container_runner(original_runtime_context, container_runner)
     
     # Execute tool (no need to pass runtime_context if we modified it in place)
-    res = tool(**params)
+    try:
+        res = tool(**params)
+    except WorkflowStatus as exc:
+        detail = _failed_run_output(tool, exc.out)
+        if not detail:
+            raise
+        raise ToolRunFailed(f"Completed {exc.status}.\n\n{detail}") from exc
     outs = {}
     for ot in outputs:
         out_content = res[ot['name']]

coala_cli-0.2.6/pyproject.toml

@@ -0,0 +1,42 @@
+[project]
+name = "coala-cli"
+version = "0.2.6"
+description = "Command-line LLM-agent Adapter"
+authors = [{ name = "Qiang" }]
+license = "MIT"
+readme = "README.md"
+requires-python = ">=3.12,<3.15"
+classifiers = [
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+]
+dependencies = [
+    "fastapi>=0.115.0",
+    "requests>=2.33.0,<3.0.0",
+    "pydantic>=2.10.0,<3.0.0",
+    "uvicorn>=0.32.0,<0.33.0",
+    "cwltool>=3.2.20260413085819,<4.0.0",
+    "mcp>=2.2,<3",
+]
+
+[dependency-groups]
+dev = ["pytest>=8.0.0", "pytest-asyncio>=0.24.0"]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+# The sdist carries what the Poetry build did: the package and the README.
+[tool.hatch.build.targets.sdist]
+include = ["coala", "README.md"]
+
+[tool.hatch.build.targets.wheel]
+packages = ["coala"]
+
+[tool.pytest.ini_options]
+filterwarnings = [
+    "ignore::pydantic.warnings.UnsupportedFieldAttributeWarning",
+]

coala_cli-0.2.4/pyproject.toml

@@ -1,27 +0,0 @@
-[tool.poetry]
-name = "coala-cli"
-version = "0.2.4"
-description = "Command-line LLM-agent Adapter"
-authors = ["Qiang"]
-license = "MIT"
-readme = "README.md"
-packages = [{ include = "coala" }]
-
-[tool.poetry.dependencies]
-python = ">=3.12,<3.15"
-fastapi = ">=0.115.0"
-requests = "^2.33.0"
-pydantic = "^2.10.0"
-uvicorn = "^0.32.0"
-cwltool = "^3.2.20260413085819"
-mcp = "^1.12.0"
-
-
-[build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
-
-[tool.pytest.ini_options]
-filterwarnings = [
-    "ignore::pydantic.warnings.UnsupportedFieldAttributeWarning",
-]