feat: Add Anthropic API key management for Claude Code

software/control/_def.py

@@ -1275,6 +1275,7 @@ def get_wellplate_settings(wellplate_format):
 ENABLE_MCP_SERVER_SUPPORT = True  # Set to False to hide all MCP-related menu items
 CONTROL_SERVER_HOST = "127.0.0.1"
 CONTROL_SERVER_PORT = 5050
+ANTHROPIC_API_KEY = None  # Set via GUI (Settings > Set Anthropic API Key...)
 
 
 # Slack Notifications - send real-time notifications during acquisition

software/control/widgets_claude.py

@@ -0,0 +1,176 @@
+"""Anthropic API key dialog for Claude Code integration.
+
+Provides a dialog for entering the Anthropic API key used when launching
+Claude Code from the GUI. The key is cached locally in cache/claude_api_key.yaml.
+"""
+
+import os
+
+import yaml
+
+from qtpy.QtCore import Qt
+from qtpy.QtWidgets import (
+    QDialog,
+    QVBoxLayout,
+    QHBoxLayout,
+    QLabel,
+    QPlainTextEdit,
+    QPushButton,
+)
+
+import control._def
+import squid.logging
+
+log = squid.logging.get_logger(__name__)
+
+CACHE_FILE = "cache/claude_api_key.yaml"
+
+_MASK_CHAR = "\u2022"  # bullet character for masking
+
+
+def load_claude_api_key_from_cache():
+    """Load Anthropic API key from cache file into runtime config.
+
+    This should be called during application startup to restore
+    the API key from the cache file.
+    """
+    if not os.path.exists(CACHE_FILE):
+        return
+    try:
+        with open(CACHE_FILE, "r") as f:
+            data = yaml.safe_load(f)
+        if data is None:
+            return
+        if not isinstance(data, dict):
+            log.error("Anthropic API key cache file has unexpected format (expected YAML dict)")
+            return
+        key = data.get("api_key")
+        if key:
+            if not isinstance(key, str):
+                log.error("Anthropic API key cache has invalid type " f"(expected str, got {type(key).__name__})")
+                return
+            control._def.ANTHROPIC_API_KEY = key
+            log.info("Loaded Anthropic API key from cache")
+    except (yaml.YAMLError, OSError) as e:
+        log.error(f"Failed to load Anthropic API key from cache: {e}")
+
+
+class ClaudeApiKeyDialog(QDialog):
+    """Dialog for entering the Anthropic API key used by Claude Code."""
+
+    def __init__(self, parent=None):
+        super().__init__(parent)
+        self.setWindowTitle("Set Anthropic API Key")
+        self.setWindowFlags(self.windowFlags() | Qt.WindowStaysOnTopHint)
+        self.setModal(True)
+        self.setMinimumWidth(500)
+
+        self._stored_key = ""
+        self._is_visible = False
+
+        self._setup_ui()
+        self._load_key()
+        self._connect_signals()
+
+    def _setup_ui(self):
+        layout = QVBoxLayout(self)
+
+        # API key input — multi-line for long keys
+        layout.addWidget(QLabel("API Key:"))
+        self.textedit_api_key = QPlainTextEdit()
+        self.textedit_api_key.setPlaceholderText("sk-ant-...")
+        self.textedit_api_key.setMaximumHeight(60)
+        self.textedit_api_key.setTabChangesFocus(True)
+        layout.addWidget(self.textedit_api_key)
+
+        # Show/hide toggle
+        toggle_layout = QHBoxLayout()
+        self.btn_show = QPushButton("Show")
+        self.btn_show.setCheckable(True)
+        self.btn_show.setMaximumWidth(60)
+        toggle_layout.addWidget(self.btn_show)
+        toggle_layout.addStretch()
+        layout.addLayout(toggle_layout)
+
+        # Help text
+        help_label = QLabel(
+            "<small>Get your API key from "
+            '<a href="https://console.anthropic.com/settings/keys">console.anthropic.com</a>.<br>'
+            "The key is stored locally and passed to Claude Code on launch.</small>"
+        )
+        help_label.setWordWrap(True)
+        help_label.setOpenExternalLinks(True)
+        help_label.setStyleSheet("color: gray;")
+        layout.addWidget(help_label)
+
+        # Status label
+        self.label_status = QLabel("")
+        self.label_status.setStyleSheet("color: gray;")
+        layout.addWidget(self.label_status)
+
+        # Buttons
+        button_layout = QHBoxLayout()
+        self.btn_clear = QPushButton("Clear")
+        self.btn_save = QPushButton("Save")
+        self.btn_close = QPushButton("Close")
+        button_layout.addWidget(self.btn_clear)
+        button_layout.addStretch()
+        button_layout.addWidget(self.btn_save)
+        button_layout.addWidget(self.btn_close)
+        layout.addLayout(button_layout)
+
+    def _connect_signals(self):
+        self.btn_show.toggled.connect(self._toggle_visibility)
+        self.btn_clear.clicked.connect(self._clear_key)
+        self.btn_save.clicked.connect(self._save_key)
+        self.btn_close.clicked.connect(self.close)
+        self.textedit_api_key.textChanged.connect(self._on_text_changed)
+
+    def _on_text_changed(self):
+        if self._is_visible:
+            self._stored_key = self.textedit_api_key.toPlainText().replace("\n", "").strip()
+
+    def _toggle_visibility(self, show: bool):
+        self._is_visible = show
+        if show:
+            self.textedit_api_key.setReadOnly(False)
+            self.textedit_api_key.setPlainText(self._stored_key)
+            self.btn_show.setText("Hide")
+        else:
+            self._stored_key = self.textedit_api_key.toPlainText().replace("\n", "").strip()
+            self.textedit_api_key.setPlainText(_MASK_CHAR * len(self._stored_key))
+            self.textedit_api_key.setReadOnly(True)
+            self.btn_show.setText("Show")
+
+    def _load_key(self):
+        key = control._def.ANTHROPIC_API_KEY or ""
+        self._stored_key = key
+        # Start masked and read-only
+        self.textedit_api_key.setPlainText(_MASK_CHAR * len(key))
+        self.textedit_api_key.setReadOnly(True)
+
+    def _save_key(self):
+        """Save the API key to runtime config and cache file."""
+        if self._is_visible:
+            self._stored_key = self.textedit_api_key.toPlainText().replace("\n", "").strip()
+        key = self._stored_key or None
+
+        data = {"api_key": key}
+        try:
+            os.makedirs(os.path.dirname(CACHE_FILE), exist_ok=True)
+            fd = os.open(CACHE_FILE, os.O_WRONLY | os.O_CREAT | os.O_TRUNC, 0o600)
+            with os.fdopen(fd, "w") as f:
+                yaml.dump(data, f, default_flow_style=False)
+            control._def.ANTHROPIC_API_KEY = key
+            self.label_status.setText("Saved" if key else "Cleared")
+            self.label_status.setStyleSheet("color: green;")
+            log.info("Anthropic API key %s in cache", "saved" if key else "cleared")
+        except (OSError, yaml.YAMLError) as e:
+            self.label_status.setText(f"Failed to save: {e}")
+            self.label_status.setStyleSheet("color: red;")
+            log.error(f"Failed to save Anthropic API key: {e}")
+
+    def _clear_key(self):
+        self._stored_key = ""
+        self.textedit_api_key.clear()
+        self._save_key()

software/docs/mcp_integration.md

@@ -27,15 +27,21 @@ This document describes how to use the Model Context Protocol (MCP) integration
 ### Option A: Launch from GUI (Recommended)
 
 1. Start the Squid GUI
-2. Go to **Settings → Launch Claude Code**
-3. If Claude Code is not installed, you'll be prompted to install it automatically
-4. A terminal will open with Claude Code running in the correct directory
+2. *(Optional)* Go to **Settings → Set Anthropic API Key...** and enter your API key (get one from [console.anthropic.com](https://console.anthropic.com/settings/keys)). If you are already logged into claude.ai, you can skip this step.
+3. Go to **Settings → Launch Claude Code**
+4. If Claude Code is not installed, you'll be prompted to install it automatically
+5. A terminal will open with Claude Code running in the correct directory
 
 This automatically:
 - Starts the MCP control server (on-demand)
+- Passes the API key if one is set (via a temporary launcher script that keeps it out of command-line arguments; the key is set as an environment variable for the Claude Code process)
 - Configures the MCP connection
 - Pre-approves all microscope commands
 
+**Authentication:** Claude Code supports two authentication methods:
+- **claude.ai login** (OAuth) — If you are already logged in via `claude login`, no API key is needed
+- **API key** — Set via **Settings → Set Anthropic API Key...**; cached locally in `cache/claude_api_key.yaml` and persists across restarts
+
 ### On-Demand Control Server
 
 The MCP control server does **not** start automatically when the GUI launches. It starts when:
@@ -266,6 +272,15 @@ The TCP protocol uses newline-delimited JSON:
 
 ## Troubleshooting
 
+### "API Key Not Set" when launching Claude Code
+- Go to **Settings → Set Anthropic API Key...** to enter your key
+- Get a key from [console.anthropic.com](https://console.anthropic.com/settings/keys)
+- The key is cached locally and persists across restarts
+
+### "Auth conflict" warning in Claude Code
+- This occurs when you have both an API key and an existing claude.ai login
+- Claude Code will use the API key; the warning is informational and can be ignored
+
 ### "Cannot connect to microscope"
 - Ensure the Squid GUI is running
 - Enable the control server via **Settings → Enable MCP Control Server** (or use **Launch Claude Code** which auto-starts it)