fix: correct formatting in docstrings and enhance checkbox rendering for installed items

EvoScientist/cli/_app.py

@@ -14,7 +14,7 @@ app.add_typer(config_app, name="config")
 
 # MCP subcommand group
 _MCP_HELP = """\
-Configure and manage MCP servers.
+Configure and manage MCP servers
 
 Examples:
   # Add a local MCP server (stdio auto-detected):

EvoScientist/cli/commands.py

@@ -36,7 +36,7 @@ def onboard(
         help="Skip API key validation during setup"
     ),
 ):
-    """Interactive setup wizard for EvoScientist.
+    """Interactive setup wizard for EvoScientist
 
     Guides you through configuring API keys, model selection,
     workspace settings, and agent parameters.
@@ -51,14 +51,14 @@ def onboard(
 
 @config_app.callback(invoke_without_command=True)
 def config_callback(ctx: typer.Context):
-    """Configuration management commands."""
+    """Configuration management commands"""
     if ctx.invoked_subcommand is None:
         config_list()
 
 
 @config_app.command("list")
 def config_list():
-    """List all configuration values."""
+    """List all configuration values"""
     from ..config import list_config, get_config_path
 
     config_data = list_config()
@@ -84,7 +84,7 @@ def config_list():
 
 @config_app.command("get")
 def config_get(key: str = typer.Argument(..., help="Configuration key to get")):
-    """Get a single configuration value."""
+    """Get a single configuration value"""
     from ..config import get_config_value
 
     value = get_config_value(key)
@@ -108,7 +108,7 @@ def config_set(
     key: str = typer.Argument(..., help="Configuration key to set"),
     value: str = typer.Argument(..., help="New value"),
 ):
-    """Set a single configuration value."""
+    """Set a single configuration value"""
     from ..config import set_config_value
 
     if set_config_value(key, value):
@@ -122,7 +122,7 @@ def config_set(
 def config_reset(
     yes: bool = typer.Option(False, "--yes", "-y", help="Skip confirmation prompt"),
 ):
-    """Reset configuration to defaults."""
+    """Reset configuration to defaults"""
     from ..config import reset_config, get_config_path
 
     config_path = get_config_path()
@@ -143,7 +143,7 @@ def config_reset(
 
 @config_app.command("path")
 def config_path():
-    """Show the configuration file path."""
+    """Show the configuration file path"""
     from ..config import get_config_path
 
     path = get_config_path()
@@ -158,14 +158,14 @@ def config_path():
 
 @mcp_app.callback(invoke_without_command=True)
 def mcp_callback(ctx: typer.Context):
-    """MCP server management commands."""
+    """MCP server management commands"""
     if ctx.invoked_subcommand is None:
         mcp_list()
 
 
 @mcp_app.command("list")
 def mcp_list():
-    """List configured MCP servers."""
+    """List configured MCP servers"""
     _mcp_list_servers()
 
 
@@ -173,7 +173,7 @@ def mcp_list():
 def mcp_config(
     name: Optional[str] = typer.Argument(None, help="Server name (omit to show all)"),
 ):
-    """Show detailed configuration for MCP servers.
+    """Show detailed configuration for MCP servers
 
     \b
     Examples:
@@ -200,7 +200,7 @@ def mcp_add(
     env: Optional[list[str]] = typer.Option(None, "--env", help="Env var as KEY=VALUE for stdio (repeatable)"),
     env_ref: Optional[list[str]] = typer.Option(None, "--env-ref", help="Env var name as ${NAME} runtime ref (repeatable)"),
 ):
-    """Add an MCP server to user config.
+    """Add an MCP server to user config
 
     \b
     Transport is auto-detected: URLs default to http, commands default to stdio.
@@ -249,7 +249,7 @@ def mcp_edit(
     header: Optional[list[str]] = typer.Option(None, "--header", "-H", help="HTTP header as Key:Value (repeatable)"),
     env: Optional[list[str]] = typer.Option(None, "--env", help="Env var as KEY=VALUE for stdio (repeatable)"),
 ):
-    """Edit an existing MCP server in user config.
+    """Edit an existing MCP server in user config
 
     \b
     Examples:
@@ -278,7 +278,7 @@ def mcp_edit(
 def mcp_remove(
     name: str = typer.Argument(..., help="Server name to remove"),
 ):
-    """Remove an MCP server from user config."""
+    """Remove an MCP server from user config"""
     if not _mcp_remove_server(name, show_reload_hint=False):
         raise typer.Exit(1)
 
@@ -308,7 +308,7 @@ def _main_callback(
     use_cwd: bool = typer.Option(False, "--use-cwd", help="Use current working directory as workspace"),
     no_thinking: bool = typer.Option(False, "--no-thinking", help="Disable thinking display"),
 ):
-    """EvoScientist Agent - AI-powered research & code execution CLI."""
+    """EvoScientist Agent - AI-powered research & code execution CLI"""
     # If a subcommand was invoked, don't run the default behavior
     if ctx.invoked_subcommand is not None:
         return

EvoScientist/onboard.py

@@ -9,6 +9,7 @@ from __future__ import annotations
 import os
 import subprocess
 import sys
+from pathlib import Path
 
 import questionary
 from prompt_toolkit.formatted_text import FormattedText
@@ -42,6 +43,7 @@ WIZARD_STYLE = Style.from_dict({
     "highlighted": "noreverse bold",      # No background, bold text
     "selected": "fg:#4caf50 bold",        # Green ● indicator
     "separator": "fg:#6c6c6c",            # Dim separator
+    "disabled": "fg:#858585",             # Dim disabled indicator (-)
     "instruction": "fg:#858585",          # Dim instructions
     "text": "fg:#858585",                 # Dim gray ○ and unselected text
 })
@@ -56,6 +58,38 @@ CONFIRM_STYLE = Style.from_dict({
 
 QMARK = "❯"
 
+# Installed-item indicator style for disabled checkbox choices.
+_INSTALLED_INDICATOR = ("fg:#4caf50", "✓ ")
+
+
+def _checkbox_ask(choices, message: str, **kwargs):
+    """``questionary.checkbox`` that renders disabled items with ✓ instead of ``-``.
+
+    Temporarily patches the rendering so the hard-coded ``"- "`` prefix for
+    disabled choices is replaced by a green ``"✓ "`` — keeping alignment with
+    the ``○`` indicator of normal choices.
+    """
+    from questionary.prompts.common import InquirerControl
+
+    original = InquirerControl._get_choice_tokens
+
+    def _patched(self):
+        tokens = original(self)
+        return [
+            _INSTALLED_INDICATOR
+            if cls == "class:disabled" and text == "- "
+            else (cls, text)
+            for cls, text in tokens
+        ]
+
+    InquirerControl._get_choice_tokens = _patched
+    try:
+        return questionary.checkbox(
+            message, choices=choices, style=WIZARD_STYLE, qmark=QMARK, **kwargs,
+        ).ask()
+    finally:
+        InquirerControl._get_choice_tokens = original
+
 STEPS = ["Provider", "API Key", "Model", "Tavily Key", "Workspace", "Parameters", "Skills", "MCP Servers", "Channels"]
 
 
@@ -757,24 +791,53 @@ def _ensure_npx(reason: str) -> bool:
 def _step_skills() -> list[str]:
     """Step 7: Optionally install recommended skills.
 
-    Shows checkbox first. If user selects nothing, checks npx as an
-    easter egg — confirms skill discovery is available, or offers to
-    install Node.js if missing.
+    Shows checkbox first. Already-installed skills are shown as disabled
+    so users don't accidentally reinstall them. If user selects nothing,
+    checks npx as an easter egg — confirms skill discovery is available,
+    or offers to install Node.js if missing.
 
     Returns:
         List of skill sources that were selected (empty if skipped).
     """
-    choices = [
-        Choice(title=skill["label"], value=skill["source"])
-        for skill in _RECOMMENDED_SKILLS
-    ]
+    from .paths import USER_SKILLS_DIR
 
-    selected = questionary.checkbox(
-        "Install predefined skills:",
-        choices=choices,
-        style=WIZARD_STYLE,
-        qmark=QMARK,
-    ).ask()
+    # Collect names of already-installed user skills
+    skills_dir = Path(USER_SKILLS_DIR)
+    installed_names: set[str] = set()
+    if skills_dir.exists():
+        installed_names = {e.name for e in skills_dir.iterdir() if e.is_dir()}
+
+    def _hint_name(source: str) -> str:
+        """Derive expected skill directory name from source URL."""
+        if "@" in source and "://" not in source:
+            return source.split("@", 1)[1].strip()
+        return source.rstrip("/").rsplit("/", 1)[-1]
+
+    choices = []
+    for skill in _RECOMMENDED_SKILLS:
+        if _hint_name(skill["source"]) in installed_names:
+            choices.append(
+                Choice(
+                    title=[
+                        ("", skill["label"]),
+                        ("class:instruction", "  (already installed)"),
+                    ],
+                    value=skill["source"],
+                    disabled=True,
+                )
+            )
+        else:
+            choices.append(Choice(title=skill["label"], value=skill["source"]))
+
+    all_installed = all(
+        _hint_name(skill["source"]) in installed_names
+        for skill in _RECOMMENDED_SKILLS
+    )
+    if all_installed:
+        console.print("  [green]✓ All recommended skills are already installed.[/green]")
+        return []
+
+    selected = _checkbox_ask(choices, "Install predefined skills:")
 
     if selected is None:
         raise KeyboardInterrupt()
@@ -896,9 +959,12 @@ def _step_mcp_servers() -> list[str]:
         if srv["name"] in existing_config:
             choices.append(
                 Choice(
-                    title=srv["label"],
+                    title=[
+                        ("", srv["label"]),
+                        ("class:instruction", "  (already configured)"),
+                    ],
                     value=srv["name"],
-                    disabled="already configured",
+                    disabled=True,
                 )
             )
         else:
@@ -909,12 +975,7 @@ def _step_mcp_servers() -> list[str]:
         console.print("  [green]✓ All recommended MCP servers are already configured.[/green]")
         return []
 
-    selected = questionary.checkbox(
-        "Install recommended MCP servers:",
-        choices=choices,
-        style=WIZARD_STYLE,
-        qmark=QMARK,
-    ).ask()
+    selected = _checkbox_ask(choices, "Install recommended MCP servers:")
 
     if selected is None:
         raise KeyboardInterrupt()