celltype-cli 0.1.2__tar.gz → 0.2.0__tar.gz

celltype_cli-0.2.0/.git

@@ -0,0 +1 @@
+gitdir: ../.git/modules/cli

{celltype_cli-0.1.2 → celltype_cli-0.2.0}/.gitignore

@@ -52,3 +52,4 @@ busco_downloads/
 
 
 
+.vercel

{celltype_cli-0.1.2 → celltype_cli-0.2.0}/PKG-INFO

@@ -1,21 +1,23 @@
 Metadata-Version: 2.4
 Name: celltype-cli
-Version: 0.1.2
+Version: 0.2.0
 Summary: CellType CLI — An autonomous agent for drug discovery research
 Author: CellType Inc.
-License-Expression: MIT
+License: MIT
 License-File: LICENSE
 Requires-Python: >=3.10
-Requires-Dist: anthropic>=0.40
+Requires-Dist: anthropic>=0.74.0
 Requires-Dist: claude-agent-sdk>=0.1
 Requires-Dist: httpx>=0.27
 Requires-Dist: markdown>=3.5
+Requires-Dist: matplotlib>=3.7
 Requires-Dist: nbformat>=5.7
 Requires-Dist: numpy>=1.24
 Requires-Dist: openai>=1.0
 Requires-Dist: pandas>=2.0
 Requires-Dist: prompt-toolkit>=3.0
 Requires-Dist: python-dotenv>=1.0
+Requires-Dist: pyyaml>=6.0
 Requires-Dist: rich>=13.0
 Requires-Dist: scipy>=1.10
 Requires-Dist: typer>=0.12
@@ -32,6 +34,12 @@ Requires-Dist: seaborn>=0.13; extra == 'all'
 Requires-Dist: tiledbsoma>=1.0; extra == 'all'
 Requires-Dist: torch>=2.0; extra == 'all'
 Requires-Dist: transformers>=4.40; extra == 'all'
+Provides-Extra: alpha
+Requires-Dist: duckdb>=1.0; extra == 'alpha'
+Requires-Dist: fastapi>=0.100; extra == 'alpha'
+Requires-Dist: jinja2>=3.1; extra == 'alpha'
+Requires-Dist: pydantic>=2.0; extra == 'alpha'
+Requires-Dist: uvicorn[standard]>=0.20; extra == 'alpha'
 Provides-Extra: analysis
 Requires-Dist: scikit-learn>=1.3; extra == 'analysis'
 Requires-Dist: seaborn>=0.13; extra == 'analysis'
@@ -43,6 +51,9 @@ Provides-Extra: biology
 Requires-Dist: biopython>=1.81; extra == 'biology'
 Provides-Extra: chemistry
 Requires-Dist: rdkit>=2023.03; extra == 'chemistry'
+Provides-Extra: cloud
+Requires-Dist: modal>=1.0; extra == 'cloud'
+Requires-Dist: pyjwt>=2.0; extra == 'cloud'
 Provides-Extra: dev
 Requires-Dist: pytest-cov>=5.0; extra == 'dev'
 Requires-Dist: pytest>=8.0; extra == 'dev'
@@ -63,6 +74,11 @@ Description-Content-Type: text/markdown
 
 # celltype-cli
 
+> **v0.2.0 is out** — Offload GPU-accelerated tools to CellType Cloud with no additional setup. ESMFold, Boltz-2, RFdiffusion, ProteinMPNN, and more. Update now:
+> ```bash
+> pip install --upgrade celltype-cli
+> ```
+
 An autonomous agent for drug discovery research. Like Claude Code, but for biology.
 
 Ask questions in natural language. celltype-cli plans the analysis, selects the right tools, executes them, validates results, and returns data-backed conclusions.
@@ -71,7 +87,7 @@ Ask questions in natural language. celltype-cli plans the analysis, selects the
 
 ## Benchmark
 
-CellType CLI achieves **90% accuracy** on [BixBench-Verified-50](https://github.com/bixbench/bixbench), outperforming all existing agentic systems for computational biology.
+CellType CLI achieves **90% accuracy** on [BixBench-Verified-50](https://huggingface.co/datasets/phylobio/BixBench-Verified-50), outperforming all existing agentic systems for computational biology.
 
 ![BixBench Benchmark Results](assets/bixbench_benchmark.png)
 

{celltype_cli-0.1.2 → celltype_cli-0.2.0}/README.md

@@ -1,5 +1,10 @@
 # celltype-cli
 
+> **v0.2.0 is out** — Offload GPU-accelerated tools to CellType Cloud with no additional setup. ESMFold, Boltz-2, RFdiffusion, ProteinMPNN, and more. Update now:
+> ```bash
+> pip install --upgrade celltype-cli
+> ```
+
 An autonomous agent for drug discovery research. Like Claude Code, but for biology.
 
 Ask questions in natural language. celltype-cli plans the analysis, selects the right tools, executes them, validates results, and returns data-backed conclusions.
@@ -8,7 +13,7 @@ Ask questions in natural language. celltype-cli plans the analysis, selects the
 
 ## Benchmark
 
-CellType CLI achieves **90% accuracy** on [BixBench-Verified-50](https://github.com/bixbench/bixbench), outperforming all existing agentic systems for computational biology.
+CellType CLI achieves **90% accuracy** on [BixBench-Verified-50](https://huggingface.co/datasets/phylobio/BixBench-Verified-50), outperforming all existing agentic systems for computational biology.
 
 ![BixBench Benchmark Results](assets/bixbench_benchmark.png)
 

{celltype_cli-0.1.2 → celltype_cli-0.2.0}/install.sh

@@ -4,6 +4,7 @@
 set -euo pipefail
 
 PACKAGE="celltype-cli"
+REPO_URL="git+https://github.com/celltype/cli.git"
 MIN_PYTHON="3.10"
 
 # ── Helpers ────────────────────────────────────────────────────
@@ -45,17 +46,19 @@ esac
 
 # ── Install package ────────────────────────────────────────────
 
-if command -v pipx >/dev/null 2>&1; then
-    info "Installing ${PACKAGE} via pipx..."
-    pipx install "$PACKAGE" || pipx upgrade "$PACKAGE"
-    ok "Installed with pipx"
-elif command -v uv >/dev/null 2>&1; then
+INSTALL_SPEC="${PACKAGE} @ ${REPO_URL}"
+
+if command -v uv >/dev/null 2>&1; then
     info "Installing ${PACKAGE} via uv..."
-    uv tool install "$PACKAGE" || uv tool upgrade "$PACKAGE"
+    uv tool install "$INSTALL_SPEC" || uv tool install --force "$INSTALL_SPEC"
     ok "Installed with uv"
+elif command -v pipx >/dev/null 2>&1; then
+    info "Installing ${PACKAGE} via pipx..."
+    pipx install "$REPO_URL" || pipx install --force "$REPO_URL"
+    ok "Installed with pipx"
 else
-    warn "pipx/uv not found — falling back to pip install --user"
-    "$PYTHON" -m pip install --user --upgrade "$PACKAGE"
+    warn "uv/pipx not found — falling back to pip install --user"
+    "$PYTHON" -m pip install --user --upgrade "$INSTALL_SPEC"
     ok "Installed with pip"
 
     # Check if user bin is on PATH

{celltype_cli-0.1.2 → celltype_cli-0.2.0}/pyproject.toml

@@ -4,10 +4,10 @@ build-backend = "hatchling.build"
 
 [project]
 name = "celltype-cli"
-version = "0.1.2"
+version = "0.2.0"
 description = "CellType CLI — An autonomous agent for drug discovery research"
 readme = "README.md"
-license = "MIT"
+license = {text = "MIT"}
 requires-python = ">=3.10"
 authors = [
     { name = "CellType Inc." },
@@ -17,16 +17,18 @@ dependencies = [
     "typer>=0.12",
     "rich>=13.0",
     "prompt-toolkit>=3.0",
-    "anthropic>=0.40",
+    "anthropic>=0.74.0",
     "openai>=1.0",
     "claude-agent-sdk>=0.1",
     "httpx>=0.27",
     "pandas>=2.0",
     "numpy>=1.24",
     "scipy>=1.10",
+    "matplotlib>=3.7",
     "python-dotenv>=1.0",
     "markdown>=3.5",
     "nbformat>=5.7",
+    "pyyaml>=6.0",
 ]
 
 [project.optional-dependencies]
@@ -60,6 +62,17 @@ api = [
     "uvicorn[standard]>=0.20",
     "duckdb>=1.0",
 ]
+alpha = [
+    "fastapi>=0.100",
+    "uvicorn[standard]>=0.20",
+    "duckdb>=1.0",
+    "jinja2>=3.1",
+    "pydantic>=2.0",
+]
+cloud = [
+    "modal>=1.0",
+    "pyjwt>=2.0",
+]
 all = [
     "rdkit>=2023.03",
     "biopython>=1.81",

{celltype_cli-0.1.2 → celltype_cli-0.2.0}/src/ct/__init__.py

@@ -1,3 +1,3 @@
 """celltype-cli: An autonomous agent for drug discovery research."""
 
-__version__ = "0.1.0"
+__version__ = "0.2.0"

{celltype_cli-0.1.2 → celltype_cli-0.2.0}/src/ct/agent/config.py

@@ -29,7 +29,7 @@ logger = logging.getLogger("ct.config")
 
 DEFAULTS = {
     "llm.provider": "anthropic",
-    "llm.model": "claude-sonnet-4-5-20250929",
+    "llm.model": "claude-opus-4-6",
     "llm.api_key": None,
     "llm.openai_api_key": None,
     "llm.temperature": 0.1,
@@ -67,6 +67,14 @@ DEFAULTS = {
     "compute.lambda_api_key": None,
     "compute.runpod_api_key": None,
     "compute.default_provider": "lambda",
+    "compute.mode": "cloud",
+
+    "cloud.endpoint": "https://api.celltype.com",
+    "cloud.dashboard_url": "https://cloud.celltype.com",
+
+    "gpu.name": None,
+    "gpu.vram_mb": None,
+    "gpu.setup_completed": False,
 
     "sandbox.timeout": 30,
     "sandbox.output_dir": str(Path.cwd() / "outputs"),
@@ -456,6 +464,13 @@ class Config:
         if self.llm_api_key(provider):
             return None
 
+        # Azure AI Foundry: Foundry-specific env vars are valid Anthropic auth
+        if provider == "anthropic" and (
+            os.environ.get("ANTHROPIC_FOUNDRY_API_KEY")
+            or os.environ.get("ANTHROPIC_FOUNDRY_RESOURCE")
+        ):
+            return None
+
         if provider == "openai":
             return (
                 "OpenAI API key not configured. Set OPENAI_API_KEY or run:\n"
@@ -464,7 +479,9 @@ class Config:
 
         return (
             "Anthropic API key not configured. Set ANTHROPIC_API_KEY or run:\n"
-            "  ct config set llm.api_key <key>"
+            "  ct config set llm.api_key <key>\n"
+            "For Azure AI Foundry: set ANTHROPIC_FOUNDRY_API_KEY and "
+            "ANTHROPIC_FOUNDRY_RESOURCE"
         )
 
     def keys_table(self) -> Table:

{celltype_cli-0.1.2 → celltype_cli-0.2.0}/src/ct/agent/doctor.py

@@ -6,6 +6,7 @@ Used by `ct doctor` and interactive `/doctor` to surface actionable setup issues
 
 from dataclasses import dataclass
 import logging
+import os
 from pathlib import Path
 
 from rich.table import Table
@@ -67,12 +68,12 @@ def run_checks(config: Config | None = None, session=None) -> list[DoctorCheck]:
     if llm_issue:
         checks.append(DoctorCheck(name="llm", status="error", detail=llm_issue))
     else:
+        if os.environ.get("ANTHROPIC_FOUNDRY_API_KEY") or os.environ.get("ANTHROPIC_FOUNDRY_RESOURCE"):
+            detail = f"provider=anthropic (Azure Foundry), model={model}"
+        else:
+            detail = f"provider={provider}, model={model}"
         checks.append(
-            DoctorCheck(
-                name="llm",
-                status="ok",
-                detail=f"provider={provider}, model={model}",
-            )
+            DoctorCheck(name="llm", status="ok", detail=detail)
         )
 
     # 3) Output directory availability
@@ -339,6 +340,59 @@ def run_checks(config: Config | None = None, session=None) -> list[DoctorCheck]:
             )
         )
 
+    # GPU compute readiness
+    compute_mode = str(cfg.get("compute.mode", "cloud")).lower()
+    if compute_mode == "cloud":
+        try:
+            from ct.cloud.auth import is_logged_in
+            if is_logged_in():
+                checks.append(DoctorCheck(
+                    name="gpu_compute",
+                    status="ok",
+                    detail="compute.mode=cloud, logged in to CellType Cloud",
+                ))
+            else:
+                checks.append(DoctorCheck(
+                    name="gpu_compute",
+                    status="warn",
+                    detail="compute.mode=cloud but not logged in. Run `ct login`.",
+                ))
+        except Exception:
+            checks.append(DoctorCheck(
+                name="gpu_compute",
+                status="warn",
+                detail="compute.mode=cloud, could not check login status",
+            ))
+    elif compute_mode == "local":
+        try:
+            from ct.cloud.router import _detect_local_gpu_info
+            gpus = _detect_local_gpu_info()
+            if gpus:
+                best = max(gpus, key=lambda g: g.vram_mb)
+                checks.append(DoctorCheck(
+                    name="gpu_compute",
+                    status="ok",
+                    detail=f"compute.mode=local, GPU: {best.name} ({best.vram_gb}GB)",
+                ))
+            else:
+                checks.append(DoctorCheck(
+                    name="gpu_compute",
+                    status="error",
+                    detail="compute.mode=local but no GPU detected. Run `ct setup-gpu`.",
+                ))
+        except Exception:
+            checks.append(DoctorCheck(
+                name="gpu_compute",
+                status="warn",
+                detail="compute.mode=local, could not detect GPU",
+            ))
+    else:
+        checks.append(DoctorCheck(
+            name="gpu_compute",
+            status="ok",
+            detail="compute.mode=auto (will detect at runtime)",
+        ))
+
     return checks
 
 

{celltype_cli-0.1.2 → celltype_cli-0.2.0}/src/ct/agent/mcp_server.py

@@ -132,7 +132,21 @@ def _make_tool_handler(tool_obj, session):
                     call_args[key] = val.lower() == "true"
 
         try:
-            result = await asyncio.to_thread(tool_obj.run, **call_args)
+            # Route GPU tools through compute router
+            if getattr(tool_obj, "requires_gpu", False):
+                from ct.cloud.router import ComputeRouter
+                router = ComputeRouter(config=getattr(session, "config", None))
+                result = await asyncio.to_thread(router.route, tool_obj, **call_args)
+
+                # Handle "needs_user_prompt" — the router couldn't run locally
+                # and needs the user to decide about cloud fallback.
+                # We prompt here on the main thread where input() works.
+                if isinstance(result, dict) and result.get("needs_user_prompt"):
+                    result = await _prompt_cloud_fallback(
+                        router, tool_obj, result, call_args, session,
+                    )
+            else:
+                result = await asyncio.to_thread(tool_obj.run, **call_args)
             text = _format_tool_result(result)
         except Exception as e:
             logger.warning("Tool %s raised: %s", tool_obj.name, e)
@@ -147,6 +161,66 @@ def _make_tool_handler(tool_obj, session):
     return handler
 
 
+async def _prompt_cloud_fallback(router, tool_obj, prompt_result, call_args, session):
+    """Prompt the user on the main thread about switching to CellType Cloud.
+
+    Called when compute.mode=local but the tool can't run locally.
+    Runs on the event loop (main thread) so input() works correctly.
+
+    Options:
+      y   — run this tool on CellType Cloud (one-time)
+      n   — skip this tool
+      n!  — skip and don't ask again for this session
+    """
+    from rich.console import Console
+    console = getattr(session, "console", None) or Console()
+
+    # Stop the spinner so it doesn't interfere with the prompt
+    spinner = getattr(session, "_active_spinner", None)
+    if spinner is not None:
+        spinner.stop()
+        session._active_spinner = None
+
+    msg = prompt_result.get("prompt_message", "GPU tool cannot run locally.")
+
+    console.print(f"\n  [yellow]{msg}[/yellow]")
+
+    try:
+        answer = input(
+            "  Use CellType Cloud for this tool call?\n"
+            "  [y] yes  [y!] yes for all (switch to cloud mode)  [n] no (skip this tool call): "
+        ).strip().lower()
+    except (EOFError, KeyboardInterrupt):
+        answer = "n"
+
+    if answer in ("y", "yes"):
+        # One-time cloud dispatch for this tool call
+        result = await asyncio.to_thread(router.route_cloud_for_tool, tool_obj, **call_args)
+        return result
+    elif answer in ("y!", "yes!"):
+        # Switch to cloud mode permanently — no more prompts
+        try:
+            from ct.agent.config import Config
+            cfg = Config.load()
+            cfg.set("compute.mode", "cloud")
+            cfg.save()
+            console.print("  [green]compute.mode switched to cloud[/green]")
+        except Exception:
+            pass
+        result = await asyncio.to_thread(router.route_cloud_for_tool, tool_obj, **call_args)
+        return result
+    else:
+        # n / anything else — skip this tool call
+        return {
+            "summary": (
+                f"[Skipped] {tool_obj.name} — {msg} "
+                "User chose to skip this tool call."
+            ),
+            "skipped": True,
+            "reason": "user_skipped",
+        }
+
+
 # ---------------------------------------------------------------------------
 # run_python sandbox tool
 # ---------------------------------------------------------------------------

{celltype_cli-0.1.2 → celltype_cli-0.2.0}/src/ct/agent/runner.py

@@ -101,6 +101,8 @@ async def process_messages(
                         thinking_status = None
                         if runner is not None:
                             runner._active_spinner = None
+                            if hasattr(runner, "session"):
+                                runner.session._active_spinner = None
                         
                     text = block.text or ""
                     full_text.append(text)
@@ -130,6 +132,9 @@ async def process_messages(
                             thinking_status.start_async_refresh()
                             if runner is not None:
                                 runner._active_spinner = thinking_status
+                            # Also store on session so MCP prompt can stop it
+                            if runner is not None and hasattr(runner, "session"):
+                                runner.session._active_spinner = thinking_status
                         except ImportError:
                             pass
                         
@@ -337,7 +342,7 @@ class AgentRunner:
         )
 
         # ----- Configure Agent SDK -----
-        model = config.get("llm.model") or "claude-sonnet-4-5-20250929"
+        model = config.get("llm.model") or "claude-opus-4-6"
         max_turns = int(config.get("agent.max_sdk_turns", 30))
 
         allowed_tools = [f"mcp__ct-tools__{name}" for name in tool_names]
@@ -357,6 +362,24 @@ class AgentRunner:
         # Suppress warnings in SDK subprocess (matplotlib, pydeseq2, numpy, etc.)
         clean_env["PYTHONWARNINGS"] = "ignore"
 
+        # Enable Foundry mode for Agent SDK subprocess if Foundry env vars present
+        if any(clean_env.get(v) for v in (
+            "ANTHROPIC_FOUNDRY_API_KEY",
+            "ANTHROPIC_FOUNDRY_RESOURCE",
+            "ANTHROPIC_FOUNDRY_BASE_URL",
+        )):
+            clean_env["CLAUDE_CODE_USE_FOUNDRY"] = "1"
+            # Pin model names for Foundry deployments
+            clean_env.setdefault(
+                "ANTHROPIC_DEFAULT_SONNET_MODEL", model
+            )
+            clean_env.setdefault(
+                "ANTHROPIC_DEFAULT_OPUS_MODEL", model
+            )
+            clean_env.setdefault(
+                "ANTHROPIC_DEFAULT_HAIKU_MODEL", model
+            )
+
         # Plan mode: use SDK's built-in plan permission mode.
         # In plan mode, Claude outputs a plan then calls ExitPlanMode.
         # We intercept that to show the plan and ask for approval.

{celltype_cli-0.1.2 → celltype_cli-0.2.0}/src/ct/agent/sandbox.py

@@ -20,8 +20,11 @@ warnings.filterwarnings("ignore", message="Unable to import Axes3D")
 warnings.filterwarnings("ignore", category=UserWarning, module="matplotlib")
 
 # Force non-interactive matplotlib backend before any import
-import matplotlib
-matplotlib.use("Agg")
+try:
+    import matplotlib
+    matplotlib.use("Agg")
+except ImportError:
+    pass  # matplotlib is a required dep; deferred error in _setup_namespace()
 
 
 # Modules blocked from import inside the sandbox

{celltype_cli-0.1.2 → celltype_cli-0.2.0}/src/ct/agent/session.py

@@ -54,7 +54,7 @@ class Session:
         """Return the current model name."""
         if self._llm:
             return self._llm.model
-        return self.config.get("llm.model") or "claude-sonnet-4-5-20250929"
+        return self.config.get("llm.model") or "claude-opus-4-6"
 
     def log(self, message: str):
         """Log to scratchpad (for debugging/transparency)."""

{celltype_cli-0.1.2 → celltype_cli-0.2.0}/src/ct/agent/system_prompt.py

@@ -69,6 +69,20 @@ BANNED PHRASES — never write these:
 If tools failed, pivot to answering from your knowledge instead.
 """
 
+_STRUCTURE_INPUT_GUIDANCE = """\
+
+## Structure File Inputs
+
+For tools that accept `target_pdb`, `backbone_pdb`, or `protein_pdb`, you may
+provide either:
+- inline PDB/mmCIF text, or
+- a local filesystem path to a `.pdb`, `.cif`, `.mmcif`, or `.ent` file.
+
+If the structure is already saved locally, prefer passing the file path instead
+of pasting the full structure text. The local runner and CellType Cloud client
+will inline the file contents automatically before dispatch.
+"""
+
 
 # ---------------------------------------------------------------------------
 # Builder
@@ -167,6 +181,9 @@ def build_system_prompt(
     # 8. Synthesis instructions
     parts.append(_SYNTHESIS_INSTRUCTIONS)
 
+    # 8b. Structure input guidance
+    parts.append(_STRUCTURE_INPUT_GUIDANCE)
+
     # 9. Dynamic data context
     if data_context:
         parts.append("\n## Data Context\n")