Merge PR #40: Fix MCP integration tests and linting errors

integrations/beads-mcp/src/beads_mcp/bd_client.py

@@ -101,12 +101,8 @@ class BdClient:
         self.bd_path = bd_path if bd_path is not None else config.beads_path
         self.beads_db = beads_db if beads_db is not None else config.beads_db
         self.actor = actor if actor is not None else config.beads_actor
-        self.no_auto_flush = (
+        self.no_auto_flush = no_auto_flush if no_auto_flush is not None else config.beads_no_auto_flush
-            no_auto_flush if no_auto_flush is not None else config.beads_no_auto_flush
+        self.no_auto_import = no_auto_import if no_auto_import is not None else config.beads_no_auto_import
-        )
-        self.no_auto_import = (
-            no_auto_import if no_auto_import is not None else config.beads_no_auto_import
-        )
         self.working_dir = working_dir if working_dir is not None else config.beads_working_dir
 
     def _get_working_dir(self) -> str:
@@ -161,9 +157,7 @@ class BdClient:
             )
             stdout, stderr = await process.communicate()
         except FileNotFoundError as e:
-            raise BdNotFoundError(
+            raise BdNotFoundError(BdNotFoundError.installation_message(self.bd_path)) from e
-                BdNotFoundError.installation_message(self.bd_path)
-            ) from e
 
         if process.returncode != 0:
             raise BdCommandError(
@@ -205,9 +199,7 @@ class BdClient:
             )
             stdout, stderr = await process.communicate()
         except FileNotFoundError as e:
-            raise BdNotFoundError(
+            raise BdNotFoundError(BdNotFoundError.installation_message(self.bd_path)) from e
-                BdNotFoundError.installation_message(self.bd_path)
-            ) from e
 
         if process.returncode != 0:
             raise BdCommandError(
@@ -220,9 +212,7 @@ class BdClient:
         version_output = stdout.decode().strip()
         match = re.search(r"(\d+)\.(\d+)\.(\d+)", version_output)
         if not match:
-            raise BdVersionError(
+            raise BdVersionError(f"Could not parse bd version from: {version_output}")
-                f"Could not parse bd version from: {version_output}"
-            )
 
         version = tuple(int(x) for x in match.groups())
 
@@ -418,9 +408,7 @@ class BdClient:
             )
             _stdout, stderr = await process.communicate()
         except FileNotFoundError as e:
-            raise BdNotFoundError(
+            raise BdNotFoundError(BdNotFoundError.installation_message(self.bd_path)) from e
-                BdNotFoundError.installation_message(self.bd_path)
-            ) from e
 
         if process.returncode != 0:
             raise BdCommandError(
@@ -446,9 +434,7 @@ class BdClient:
             )
             stdout, stderr = await process.communicate()
         except FileNotFoundError as e:
-            raise BdNotFoundError(
+            raise BdNotFoundError(BdNotFoundError.installation_message(self.bd_path)) from e
-                BdNotFoundError.installation_message(self.bd_path)
-            ) from e
 
         if process.returncode != 0:
             raise BdCommandError(
@@ -513,9 +499,7 @@ class BdClient:
             )
             stdout, stderr = await process.communicate()
         except FileNotFoundError as e:
-            raise BdNotFoundError(
+            raise BdNotFoundError(BdNotFoundError.installation_message(self.bd_path)) from e
-                BdNotFoundError.installation_message(self.bd_path)
-            ) from e
 
         if process.returncode != 0:
             raise BdCommandError(

integrations/beads-mcp/src/beads_mcp/config.py

@@ -5,7 +5,7 @@ import shutil
 import sys
 from pathlib import Path
 
-from pydantic import field_validator
+from pydantic import Field, field_validator
 from pydantic_settings import BaseSettings, SettingsConfigDict
 
 
@@ -31,7 +31,7 @@ class Config(BaseSettings):
 
     model_config = SettingsConfigDict(env_prefix="")
 
-    beads_path: str = _default_beads_path()
+    beads_path: str = Field(default_factory=_default_beads_path)
     beads_db: str | None = None
     beads_actor: str | None = None
     beads_no_auto_flush: bool = False
@@ -71,9 +71,7 @@ class Config(BaseSettings):
                 )
 
         if not os.access(v, os.X_OK):
-            raise ValueError(
+            raise ValueError(f"bd executable at {v} is not executable.\nPlease check file permissions.")
-                f"bd executable at {v} is not executable.\nPlease check file permissions."
-            )
 
         return v
 
@@ -97,8 +95,7 @@ class Config(BaseSettings):
         path = Path(v)
         if not path.exists():
             raise ValueError(
-                f"BEADS_DB points to non-existent file: {v}\n"
+                f"BEADS_DB points to non-existent file: {v}\n" + "Please verify the database path is correct."
-                + "Please verify the database path is correct."
             )
 
         return v
@@ -124,7 +121,7 @@ def load_config() -> Config:
     except Exception as e:
         default_path = _default_beads_path()
         error_msg = (
-            f"Beads MCP Server Configuration Error\n\n"
+            "Beads MCP Server Configuration Error\n\n"
             + f"{e}\n\n"
             + "Common fix: Install the bd CLI first:\n"
             + "  curl -fsSL https://raw.githubusercontent.com/steveyegge/beads/main/install.sh | bash\n\n"

integrations/beads-mcp/src/beads_mcp/server.py

@@ -216,7 +216,7 @@ async def debug_env() -> str:
     info.append(f"USER: {os.environ.get('USER', 'NOT SET')}\n")
     info.append("\n=== All Environment Variables ===\n")
     for key, value in sorted(os.environ.items()):
-        if not key.startswith('_'):  # Skip internal vars
+        if not key.startswith("_"):  # Skip internal vars
             info.append(f"{key}={value}\n")
     return "".join(info)
 

integrations/beads-mcp/src/beads_mcp/tools.py

@@ -68,13 +68,9 @@ async def beads_ready_work(
 
 
 async def beads_list_issues(
-    status: Annotated[
+    status: Annotated[IssueStatus | None, "Filter by status (open, in_progress, blocked, closed)"] = None,
-        IssueStatus | None, "Filter by status (open, in_progress, blocked, closed)"
-    ] = None,
     priority: Annotated[int | None, "Filter by priority (0-4, 0=highest)"] = None,
-    issue_type: Annotated[
+    issue_type: Annotated[IssueType | None, "Filter by type (bug, feature, task, epic, chore)"] = None,
-        IssueType | None, "Filter by type (bug, feature, task, epic, chore)"
-    ] = None,
     assignee: Annotated[str | None, "Filter by assignee"] = None,
     limit: Annotated[int, "Maximum number of issues to return (1-1000)"] = 50,
 ) -> list[Issue]:
@@ -110,9 +106,7 @@ async def beads_create_issue(
     acceptance: Annotated[str | None, "Acceptance criteria"] = None,
     external_ref: Annotated[str | None, "External reference (e.g., gh-9, jira-ABC)"] = None,
     priority: Annotated[int, "Priority (0-4, 0=highest)"] = 2,
-    issue_type: Annotated[
+    issue_type: Annotated[IssueType, "Type: bug, feature, task, epic, or chore"] = DEFAULT_ISSUE_TYPE,
-        IssueType, "Type: bug, feature, task, epic, or chore"
-    ] = DEFAULT_ISSUE_TYPE,
     assignee: Annotated[str | None, "Assignee username"] = None,
     labels: Annotated[list[str] | None, "List of labels"] = None,
     id: Annotated[str | None, "Explicit issue ID (e.g., bd-42)"] = None,
@@ -243,9 +237,7 @@ async def beads_blocked() -> list[BlockedIssue]:
 
 
 async def beads_init(
-    prefix: Annotated[
+    prefix: Annotated[str | None, "Issue prefix (e.g., 'myproject' for myproject-1, myproject-2)"] = None,
-        str | None, "Issue prefix (e.g., 'myproject' for myproject-1, myproject-2)"
-    ] = None,
 ) -> str:
     """Initialize bd in current directory.
 

integrations/beads-mcp/tests/test_bd_client.py

@@ -1,18 +1,15 @@
 """Unit tests for BdClient."""
 
-import asyncio
 import json
 from unittest.mock import AsyncMock, MagicMock, patch
 
 import pytest
+
 from beads_mcp.bd_client import BdClient, BdCommandError, BdNotFoundError
 from beads_mcp.models import (
     AddDependencyParams,
     CloseIssueParams,
     CreateIssueParams,
-    DependencyType,
-    IssueStatus,
-    IssueType,
     ListIssuesParams,
     ReadyWorkParams,
     ShowIssueParams,

integrations/beads-mcp/tests/test_bd_client_integration.py

@@ -7,14 +7,11 @@ from pathlib import Path
 
 import pytest
 
-from beads_mcp.bd_client import BdClient, BdCommandError, BdNotFoundError
+from beads_mcp.bd_client import BdClient, BdCommandError
 from beads_mcp.models import (
     AddDependencyParams,
     CloseIssueParams,
     CreateIssueParams,
-    DependencyType,
-    IssueStatus,
-    IssueType,
     ListIssuesParams,
     ReadyWorkParams,
     ShowIssueParams,
@@ -358,7 +355,6 @@ async def test_init_creates_beads_directory(bd_executable):
     This is a critical test for the bug where init was using --db flag
     and creating the database in the wrong location.
     """
-    import asyncio
     from beads_mcp.bd_client import BdClient
     from beads_mcp.models import InitParams
 
@@ -370,30 +366,22 @@ async def test_init_creates_beads_directory(bd_executable):
         # Ensure .beads doesn't exist yet
         assert not beads_dir.exists()
 
-        # Create client WITHOUT beads_db set (this was the bug!)
+        # Create client WITHOUT beads_db set and WITH working_dir set to temp_dir
-        client = BdClient(bd_path=bd_executable, beads_db=None)
+        client = BdClient(bd_path=bd_executable, beads_db=None, working_dir=temp_dir)
 
-        # Change to temp directory and run init
+        # Initialize with custom prefix (no need to chdir!)
-        original_cwd = os.getcwd()
+        params = InitParams(prefix="test")
-        try:
+        result = await client.init(params)
-            os.chdir(temp_dir)
 
-            # Initialize with custom prefix
+        # Verify .beads directory was created in temp directory
-            params = InitParams(prefix="test")
+        assert beads_dir.exists(), f".beads directory not created in {temp_dir}"
-            result = await client.init(params)
+        assert beads_dir.is_dir(), ".beads exists but is not a directory"
 
-            # Verify .beads directory was created in current directory
+        # Verify database file was created with correct prefix
-            assert beads_dir.exists(), f".beads directory not created in {temp_dir}"
+        db_files = list(beads_dir.glob("*.db"))
-            assert beads_dir.is_dir(), f".beads exists but is not a directory"
+        assert len(db_files) > 0, "No database file created in .beads/"
+        assert any("test" in str(db.name) for db in db_files), \
+            f"Database file doesn't contain prefix 'test': {[db.name for db in db_files]}"
 
-            # Verify database file was created with correct prefix
+        # Verify success message
-            db_files = list(beads_dir.glob("*.db"))
+        assert "initialized" in result.lower() or "created" in result.lower()
-            assert len(db_files) > 0, "No database file created in .beads/"
-            assert any("test" in str(db.name) for db in db_files), \
-                f"Database file doesn't contain prefix 'test': {[db.name for db in db_files]}"
-
-            # Verify success message
-            assert "initialized" in result.lower() or "created" in result.lower()
-
-        finally:
-            os.chdir(original_cwd)

integrations/beads-mcp/tests/test_config.py

@@ -1,7 +1,5 @@
 """Tests for beads_mcp.config module."""
 
-import os
-import shutil
 from pathlib import Path
 from unittest.mock import patch
 
@@ -19,7 +17,7 @@ class TestConfig:
         monkeypatch.delenv("BEADS_PATH", raising=False)
 
         # Mock shutil.which to return a test path
-        with patch("shutil.which", return_value="/usr/local/bin/bd"):
+        with patch("shutil.which", return_value="/usr/local/bin/bd"), patch("os.access", return_value=True):
             config = Config()
             assert config.beads_path == "/usr/local/bin/bd"
 
@@ -39,11 +37,9 @@ class TestConfig:
         monkeypatch.setenv("BEADS_PATH", "bd")
 
         # Mock shutil.which to simulate finding bd in PATH
-        with patch("shutil.which", return_value="/usr/local/bin/bd"):
+        with patch("shutil.which", return_value="/usr/local/bin/bd"), patch("os.access", return_value=True):
-            # Mock os.access to say the file is executable
+            config = Config()
-            with patch("os.access", return_value=True):
+            assert config.beads_path == "/usr/local/bin/bd"
-                config = Config()
-                assert config.beads_path == "/usr/local/bin/bd"
 
     def test_beads_path_not_found(self, monkeypatch: pytest.MonkeyPatch) -> None:
         """Test that invalid BEADS_PATH raises ValueError."""

integrations/beads-mcp/tests/test_tools.py

@@ -4,8 +4,7 @@ from unittest.mock import AsyncMock, patch
 
 import pytest
 
-from beads_mcp.bd_client import BdClient
+from beads_mcp.models import BlockedIssue, Issue, Stats
-from beads_mcp.models import BlockedIssue, Issue, IssueStatus, IssueType, Stats
 from beads_mcp.tools import (
     beads_add_dependency,
     beads_blocked,

integrations/beads-mcp/uv.lock

@@ -48,7 +48,7 @@ wheels = [
 
 [[package]]
 name = "beads-mcp"
-version = "0.9.4"
+version = "0.9.6"
 source = { editable = "." }
 dependencies = [
     { name = "fastmcp" },