update
This commit is contained in:
X-iZhang
@@ -87,6 +87,10 @@ def get_chat_model(
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if provider == "anthropic" and "thinking" not in kwargs:
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kwargs["thinking"] = {"type": "enabled", "budget_tokens": 2000}
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# Auto-enable thinking visibility for Google GenAI models
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if provider == "google-genai":
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kwargs.setdefault("include_thoughts", True)
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return init_chat_model(model=model_id, model_provider=provider, **kwargs)
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+120
-8
@@ -618,17 +618,50 @@ def _step_parameters(config: EvoScientistConfig) -> tuple[int, int, bool]:
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_RECOMMENDED_SKILLS = [
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# ── Ideation ──
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{
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"label": "ML Paper Writing",
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"source": "Orchestra-Research/AI-Research-SKILLs@20-ml-paper-writing",
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"label": "Scientific Brainstorming (generate & refine research ideas)",
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"source": "https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/scientific-brainstorming",
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},
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{
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"label": "Literature Review",
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"label": "Scientific Critical Thinking (evaluate claims & arguments rigorously)",
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"source": "https://github.com/K-Dense-AI/claude-scientific-writer/tree/main/skills/scientific-critical-thinking",
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},
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# ── Literature & Data ──
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{
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"label": "Literature Review (systematic survey of existing work)",
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"source": "https://github.com/K-Dense-AI/claude-scientific-writer/tree/main/skills/literature-review",
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},
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{
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"label": "Scientific Brainstorming",
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"source": "https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/scientific-brainstorming",
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"label": "BioRxiv Database (search & retrieve preprints)",
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"source": "https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/biorxiv-database",
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},
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{
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"label": "Citation Management (organize references & generate BibTeX)",
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"source": "https://github.com/K-Dense-AI/claude-scientific-writer/tree/main/skills/citation-management",
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},
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# ── Experimentation ──
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{
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"label": "HuggingFace Model Trainer (fine-tune & train models on HF)",
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"source": "https://github.com/huggingface/skills/tree/main/skills/hugging-face-model-trainer",
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},
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# ── Writing & Presentation ──
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{
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"label": "ML Paper Writing (draft publication-ready ML/AI papers)",
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"source": "Orchestra-Research/AI-Research-SKILLs@20-ml-paper-writing",
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},
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{
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"label": "Doc Co-authoring (structured collaborative writing workflow)",
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"source": "https://github.com/anthropics/skills/tree/main/skills/doc-coauthoring",
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},
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{
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"label": "Scientific Slides (create research presentations)",
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"source": "https://github.com/K-Dense-AI/claude-scientific-writer/tree/main/skills/scientific-slides",
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},
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# ── Review ──
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{
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"label": "Peer Review (critique & improve manuscripts)",
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"source": "https://github.com/K-Dense-AI/claude-scientific-writer/tree/main/skills/peer-review",
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},
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]
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@@ -782,26 +815,78 @@ def _step_skills() -> list[str]:
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_RECOMMENDED_MCP_SERVERS = [
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# ── Built-in ──
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{
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"label": "Sequential Thinking (structured reasoning for non-reasoning models)",
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"label": "Sequential Thinking (structured reasoning for non-reasoning models)",
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"name": "sequential-thinking",
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"command": "npx",
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"args": ["-y", "@modelcontextprotocol/server-sequential-thinking"],
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},
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{
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"label": "Docs by LangChain (documentation for building agents)",
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"label": "Docs by LangChain (documentation for building agents)",
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"name": "docs-langchain",
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"url": "https://docs.langchain.com/mcp",
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},
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# ── Search & Knowledge ──
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{
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"label": "Perplexity (AI-powered web search — requires PERPLEXITY_API_KEY)",
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"name": "perplexity",
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"command": "npx",
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"args": ["-y", "@perplexity-ai/mcp-server"],
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"env": {"PERPLEXITY_API_KEY": "${PERPLEXITY_API_KEY}"},
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"env_key": "PERPLEXITY_API_KEY",
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"env_hint": "export PERPLEXITY_API_KEY=pplx-... (get one at perplexity.ai/settings/api)",
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},
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{
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"label": "Context7 (fast documentation lookup — API key unlocks higher rate limits)",
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"name": "context7",
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"command": "npx",
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"args": ["-y", "@upstash/context7-mcp"],
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"env": {"CONTEXT7_API_KEY": "${CONTEXT7_API_KEY}"},
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"env_key": "CONTEXT7_API_KEY",
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"env_hint": "export CONTEXT7_API_KEY=... (optional — unlocks higher rate limits)",
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"env_optional": True,
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},
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# ── Research ──
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{
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"label": "DeepWiki (search & read GitHub repo documentation)",
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"name": "deepwiki",
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"url": "https://mcp.deepwiki.com/mcp",
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},
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{
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"label": "ArXiv (search & fetch academic papers from arXiv)",
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"name": "arxiv",
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"pip_package": "arxiv-mcp-server",
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"command": "arxiv-mcp-server",
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"args": [],
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},
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]
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def _install_pip_package(package: str) -> bool:
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"""Silently install a pip package.
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Returns:
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True if installation succeeded.
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"""
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try:
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result = subprocess.run(
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[sys.executable, "-m", "pip", "install", "-q", package],
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capture_output=True, text=True, timeout=120,
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)
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return result.returncode == 0
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except (FileNotFoundError, subprocess.TimeoutExpired):
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return False
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def _step_mcp_servers() -> list[str]:
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"""Step 8: Optionally install recommended MCP servers.
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Shows a checkbox list of recommended servers. Selected ones are added
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to the user MCP config via ``add_mcp_server()``.
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Handles env-key prompts, pip package installs, and URL-based servers.
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Returns:
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List of server names that were installed.
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"""
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@@ -830,10 +915,37 @@ def _step_mcp_servers() -> list[str]:
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for name in selected:
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srv = next(s for s in _RECOMMENDED_MCP_SERVERS if s["name"] == name)
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try:
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# Prompt for required API keys
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env_key = srv.get("env_key")
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if env_key:
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is_optional = srv.get("env_optional", False)
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hint = srv.get("env_hint", "")
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if is_optional:
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console.print(f" [dim]{hint}[/dim]")
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else:
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console.print(f" [yellow]⚠ Requires {env_key}[/yellow]")
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console.print(f" [dim]{hint}[/dim]")
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if not os.environ.get(env_key):
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console.print(f" [dim]Set it before running EvoScientist: export {env_key}=...[/dim]")
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# Install pip package if needed
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pip_pkg = srv.get("pip_package")
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if pip_pkg:
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console.print(f" [dim]Installing {pip_pkg}...[/dim]")
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if not _install_pip_package(pip_pkg):
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_print_step_result("MCP", f"{name} — pip install {pip_pkg} failed", success=False)
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continue
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# Add to MCP config
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if "url" in srv:
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add_mcp_server(name, "streamable_http", url=srv["url"])
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else:
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add_mcp_server(name, "stdio", command=srv["command"], args=srv["args"])
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add_mcp_server(
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name, "stdio",
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command=srv["command"],
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args=srv.get("args", []),
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env=srv.get("env"),
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)
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_print_step_result("MCP", f"{name}")
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installed.append(name)
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except Exception as e:
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+1
-3
@@ -33,12 +33,10 @@ dependencies = [
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"httpx>=0.27",
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"markdownify>=0.14",
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"nest-asyncio>=1.6",
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"langchain-mcp-adapters>=0.1",
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]
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[project.optional-dependencies]
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mcp = [
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"langchain-mcp-adapters>=0.1",
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]
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dev = [
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"pytest>=8.0",
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"pytest-cov>=5.0",
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