chore: stabilization merge — CLI fix, pytest warnings, claudeignore

.claudeignore

@@ -0,0 +1,39 @@
+# Python-specific ignores
+__pycache__/
+*.pyc
+*.pyo
+*.pyd
+.Python
+*.so
+*.egg
+*.egg-info/
+dist/
+build/
+.eggs/
+
+# Virtual environments
+.venv/
+venv/
+ENV/
+env/
+
+# Testing & coverage
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+htmlcov/
+.coverage
+.coverage.*
+.tox/
+noxfile.py
+.nox/
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+
+# Git
+.git/

pyproject.toml

@@ -42,6 +42,7 @@ dev = [
     "pytest>=8.0",
     "pytest-asyncio>=0.23",
     "pytest-cov>=5.0",
+    "pytest-timeout>=2.0",
 ]
 
 [project.scripts]
@@ -76,6 +77,10 @@ markers = [
     "network: tests that require network access (deselect with -m 'not network')",
     "skipif: conditional skip",
 ]
+filterwarnings = [
+    # nmrglue uses deprecated NumPy 2.0 dtype aliases (fixed in their repo, pending release)
+    "ignore::DeprecationWarning:nmrglue.*",
+]
 
 [tool.coverage.run]
 source = ["device_use"]

src/device_use/cli.py

@@ -255,6 +255,8 @@ def _scaffold(device_name: str, output_dir: str):
     class_name = "".join(
         w.capitalize() for w in device_name.replace("-", " ").replace("_", " ").split()
     )
+    # Extract vendor from device name (first part before dash/underscore)
+    vendor = device_name.split("-")[0].split("_")[0].capitalize()
     root = os.path.join(output_dir, pkg_name)
 
     if os.path.exists(root):
@@ -337,7 +339,7 @@ def __init__(self, mode: ControlMode = ControlMode.OFFLINE):
     def info(self) -> InstrumentInfo:
         return InstrumentInfo(
             name="{class_name}",
-            vendor="TODO",
+            vendor="{vendor}",
             instrument_type="{slug}",
             supported_modes=[ControlMode.OFFLINE, ControlMode.API, ControlMode.GUI],
             version="0.1.0",

tests/test_cli.py

@@ -257,6 +257,27 @@ def test_scaffold_existing_dir(self, tmp_path, capsys):
         out = capsys.readouterr().out
         assert "already exists" in out
 
+    def test_scaffold_vendor_extraction(self, tmp_path):
+        """Vendor should be extracted from device name (first part before dash)."""
+        cli._scaffold("biotek-gen5", str(tmp_path))
+        adapter_file = (
+            tmp_path / "device_use_biotek_gen5" / "src" / "device_use_biotek_gen5" / "adapter.py"
+        )
+        content = adapter_file.read_text()
+        assert 'vendor="Biotek"' in content
+        # Ensure vendor field doesn't have the placeholder
+        assert 'vendor="TODO"' not in content
+
+    def test_scaffold_vendor_single_word(self, tmp_path):
+        """Vendor should be capitalized for single-word device names."""
+        cli._scaffold("mydevice", str(tmp_path))
+        adapter_file = (
+            tmp_path / "device_use_mydevice" / "src" / "device_use_mydevice" / "adapter.py"
+        )
+        content = adapter_file.read_text()
+        assert 'vendor="Mydevice"' in content
+        assert 'vendor="TODO"' not in content
+
 
 # ---------------------------------------------------------------------------
 # _write

tests/test_converter_coverage.py

@@ -28,7 +28,7 @@
 
 
 class TestResolveRedirect:
-    def test_url_without_enUS_pattern_returns_none(self, tmp_path):
+    def test_url_without_en_us_pattern_returns_none(self, tmp_path):
         """Line 182: redirect URL that doesn't match the en-US regex."""
         stub = tmp_path / "stub.html"
         stub.write_text('<meta http-equiv="refresh" content="0;url=/some/other/path/page.html">')
@@ -247,7 +247,7 @@ def test_description_fallback_summary(self, tmp_path):
         assert result["summary"] == "This is a detailed description for the command page."
         assert result["commands"] == []
 
-    def test_convert_missing_enUS_dir(self, tmp_path):
+    def test_convert_missing_en_us_dir(self, tmp_path):
         """convert_topspin_command returns None when en-US dir is missing."""
         stub = tmp_path / "missing.html"
         stub.write_text(
@@ -291,7 +291,6 @@ def test_exception_in_convert_is_caught(self, tmp_path, capsys):
             pass
 
         # More direct approach: patch convert_topspin_command itself
-        original = convert_topspin_command
         with patch(
             "device_use.knowledge.converter.convert_topspin_command",
             side_effect=RuntimeError("boom"),
@@ -589,7 +588,7 @@ def test_single_word_no_dash(self):
 
 
 class TestRedirectParserEdgeCases:
-    def test_uppercase_REFRESH(self):
+    def test_uppercase_refresh(self):
         """http-equiv='REFRESH' (uppercase) is matched case-insensitively."""
         html = (
             '<meta http-equiv="REFRESH"'
@@ -774,7 +773,7 @@ def test_main_with_index_output_flag(self, tmp_path, capsys):
         ):
             main()
 
-        captured = capsys.readouterr()
+        capsys.readouterr()
         assert custom_index.exists()
 
     def test_main_no_entries_no_index(self, tmp_path, capsys):

tests/test_openai_compat.py

@@ -15,9 +15,9 @@
 @pytest.fixture
 def mock_async_openai():
     """Fixture to mock AsyncOpenAI client."""
-    with patch("device_use.backends.openai_compat.AsyncOpenAI") as MockAsyncOpenAI:
-        mock_client = MockAsyncOpenAI.return_value
-        yield MockAsyncOpenAI, mock_client
+    with patch("device_use.backends.openai_compat.AsyncOpenAI") as mock_openai_cls:
+        mock_client = mock_openai_cls.return_value
+        yield mock_openai_cls, mock_client
 
 
 class TestSupportsComputerUse:
@@ -55,8 +55,8 @@ class TestOpenAICompatBackendInitialization:
         ],
     )
     def test_initialization(self, mock_async_openai, model, expected_native_cu):
-        MockAsyncOpenAI_class, mock_async_openai_instance = mock_async_openai
-        MockAsyncOpenAI_class.reset_mock()
+        mock_openai_cls, mock_async_openai_instance = mock_async_openai
+        mock_openai_cls.reset_mock()
         backend = OpenAICompatBackend(model=model, api_key="test_key", base_url="http://test.url")
 
         assert backend._model == model
@@ -66,19 +66,17 @@ def test_initialization(self, mock_async_openai, model, expected_native_cu):
         assert backend.system_prompt == ""
         assert backend._previous_response_id is None
 
-        MockAsyncOpenAI_class.assert_called_once_with(
-            api_key="test_key", base_url="http://test.url"
-        )
+        mock_openai_cls.assert_called_once_with(api_key="test_key", base_url="http://test.url")
 
     def test_default_values(self, mock_async_openai):
-        MockAsyncOpenAI_class, mock_async_openai_instance = mock_async_openai
+        mock_openai_cls, mock_async_openai_instance = mock_async_openai
         backend = OpenAICompatBackend(api_key="test_key")  # Add api_key here
         assert backend._model == "gpt-5.4"
         assert backend._max_tokens == 4096
         assert backend._native_cu is True  # gpt-5.4 is default
 
     def test_supports_grounding_property(self, mock_async_openai):
-        MockAsyncOpenAI_class, mock_async_openai_instance = mock_async_openai
+        mock_openai_cls, mock_async_openai_instance = mock_async_openai
         cu_backend = OpenAICompatBackend(model="gpt-5.4", api_key="test_key")
         assert cu_backend.supports_grounding is True
 
@@ -87,7 +85,7 @@ def test_supports_grounding_property(self, mock_async_openai):
 
     @pytest.fixture(autouse=True)
     def setup(self, mock_async_openai):
-        MockAsyncOpenAI_class, self.mock_client = mock_async_openai
+        mock_openai_cls, self.mock_client = mock_async_openai
         self.cu_backend = OpenAICompatBackend(model="gpt-5.4", api_key="test_key")
         self.mock_responses_create = AsyncMock()
         self.mock_client.responses.create = self.mock_responses_create
@@ -272,7 +270,7 @@ class TestMapCUAction:
 
     @pytest.fixture(autouse=True)
     def setup(self, mock_async_openai):
-        MockAsyncOpenAI_class, mock_client = (
+        mock_openai_cls, mock_client = (
             mock_async_openai  # unpack here, not used directly in this fixture, but good practice
         )
         self.backend = OpenAICompatBackend(model="gpt-5.4", api_key="test_key")
@@ -633,7 +631,7 @@ class TestPlanObserveLocate:
 
     @pytest.fixture(autouse=True)
     def setup(self, mock_async_openai):
-        MockAsyncOpenAI_class, self.mock_client = mock_async_openai
+        mock_openai_cls, self.mock_client = mock_async_openai
         self.cu_backend = OpenAICompatBackend(model="gpt-5.4", api_key="test_key")
         self.legacy_backend = OpenAICompatBackend(model="gpt-4o", api_key="test_key")
         self.mock_responses_create = AsyncMock()
@@ -813,9 +811,10 @@ async def test_plan_native_remaining_actions(self):
 
     async def test_plan_legacy(self):
         mock_choice = MagicMock()
-        mock_choice.message.content = """
-{"action": {"action_type": "type", "text": "hello"}, "reasoning": "type text", "done": false, "confidence": 0.8}
-"""
+        mock_choice.message.content = (
+            '{"action": {"action_type": "type", "text": "hello"},'
+            ' "reasoning": "type text", "done": false, "confidence": 0.8}'
+        )
         self.mock_chat_completions_create.return_value = MagicMock(choices=[mock_choice])
 
         result = await self.legacy_backend.plan(self.screenshot_bytes, "task", history=[])
@@ -865,7 +864,7 @@ class TestLegacyChatCompletions:
 
     @pytest.fixture(autouse=True)
     def setup(self, mock_async_openai):
-        MockAsyncOpenAI_class, self.mock_client = mock_async_openai
+        mock_openai_cls, self.mock_client = mock_async_openai
         self.legacy_backend = OpenAICompatBackend(model="gpt-4o", api_key="test_key")
         self.mock_chat_completions_create = AsyncMock()
         self.mock_client.chat.completions.create = self.mock_chat_completions_create

tests/test_spectral_library.py

@@ -527,7 +527,7 @@ def test_from_examdata_skips_no_fid(self, tmp_path):
         expno_dir.mkdir()
         # No fid file
 
-        mock_processor = MagicMock()
+        MagicMock()  # processor not directly needed
         lib = SpectralLibrary(tolerance_ppm=0.05)
         for sample_dir_child in sorted(examdata.iterdir()):
             if not sample_dir_child.is_dir() or sample_dir_child.name.startswith("."):

tests/test_web.py

@@ -356,8 +356,8 @@ def test_analyze_stream_sse_with_formula(self, mock_get_adapter, client):
 
 class TestPubChemEndpoint:
     def test_pubchem_lookup_success(self, client):
-        with patch("device_use.tools.pubchem.PubChemTool") as MockTool:
-            mock_tool = MockTool.return_value
+        with patch("device_use.tools.pubchem.PubChemTool") as mock_tool_cls:
+            mock_tool = mock_tool_cls.return_value
             mock_tool.lookup_by_name.return_value = {
                 "CID": 1234,
                 "IUPACName": "test-name",
@@ -373,8 +373,8 @@ def test_pubchem_lookup_success(self, client):
     def test_pubchem_lookup_not_found(self, client):
         from device_use.tools.pubchem import PubChemError
 
-        with patch("device_use.tools.pubchem.PubChemTool") as MockTool:
-            mock_tool = MockTool.return_value
+        with patch("device_use.tools.pubchem.PubChemTool") as mock_tool_cls:
+            mock_tool = mock_tool_cls.return_value
             mock_tool.lookup_by_name.side_effect = PubChemError("Not found")
             res = client.get("/api/pubchem/nonexistent_xyz")
         assert res.status_code == 404