celltype-cli 0.1.3__tar.gz → 0.2.1__tar.gz

celltype_cli-0.2.1/.git

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

{celltype_cli-0.1.3 → celltype_cli-0.2.1}/.gitignore

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

{celltype_cli-0.1.3 → celltype_cli-0.2.1}/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.4
 Name: celltype-cli
-Version: 0.1.3
+Version: 0.2.1
 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>=0.74.0
@@ -16,7 +16,9 @@ Requires-Dist: numpy>=1.24
 Requires-Dist: openai>=1.0
 Requires-Dist: pandas>=2.0
 Requires-Dist: prompt-toolkit>=3.0
+Requires-Dist: pydantic>=2.0
 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
@@ -33,6 +35,12 @@ 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'
@@ -44,6 +52,9 @@ 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'
@@ -64,6 +75,11 @@ 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
+> curl -fsSL https://raw.githubusercontent.com/celltype/celltype-agent/main/install.sh | bash
+> ```
+
 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.
@@ -99,10 +115,10 @@ CellType CLI achieves **90% accuracy** on [BixBench-Verified-50](https://hugging
 ### Quick install
 
 ```bash
-curl -fsSL https://raw.githubusercontent.com/celltype/cli/main/install.sh | bash
+curl -fsSL https://raw.githubusercontent.com/celltype/celltype-agent/main/install.sh | bash
 ```
 
-Detects Python 3.10+, installs via `pipx` or `pip`, and launches an interactive setup wizard.
+Detects Python 3.10+, installs the latest `celltype-cli` release from PyPI via `uv`, `pipx`, or `pip`, and launches the interactive setup wizard.
 
 ### Manual install
 

{celltype_cli-0.1.3 → celltype_cli-0.2.1}/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
+> curl -fsSL https://raw.githubusercontent.com/celltype/celltype-agent/main/install.sh | bash
+> ```
+
 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.
@@ -35,10 +40,10 @@ CellType CLI achieves **90% accuracy** on [BixBench-Verified-50](https://hugging
 ### Quick install
 
 ```bash
-curl -fsSL https://raw.githubusercontent.com/celltype/cli/main/install.sh | bash
+curl -fsSL https://raw.githubusercontent.com/celltype/celltype-agent/main/install.sh | bash
 ```
 
-Detects Python 3.10+, installs via `pipx` or `pip`, and launches an interactive setup wizard.
+Detects Python 3.10+, installs the latest `celltype-cli` release from PyPI via `uv`, `pipx`, or `pip`, and launches the interactive setup wizard.
 
 ### Manual install
 

{celltype_cli-0.1.3 → celltype_cli-0.2.1}/install.sh

@@ -1,10 +1,9 @@
 #!/usr/bin/env bash
 # celltype-cli — One-liner installer
-# Usage: curl -fsSL https://raw.githubusercontent.com/celltype/cli/main/install.sh | bash
+# Usage: curl -fsSL https://raw.githubusercontent.com/celltype/celltype-agent/main/install.sh | bash
 set -euo pipefail
 
 PACKAGE="celltype-cli"
-REPO_URL="git+https://github.com/celltype/cli.git"
 MIN_PYTHON="3.10"
 
 # ── Helpers ────────────────────────────────────────────────────
@@ -46,15 +45,15 @@ esac
 
 # ── Install package ────────────────────────────────────────────
 
-INSTALL_SPEC="${PACKAGE} @ ${REPO_URL}"
+INSTALL_SPEC="${PACKAGE}"
 
 if command -v uv >/dev/null 2>&1; then
-    info "Installing ${PACKAGE} via uv..."
-    uv tool install "$INSTALL_SPEC" || uv tool install --force "$INSTALL_SPEC"
+    info "Installing latest ${PACKAGE} from PyPI via uv..."
+    uv tool install "$INSTALL_SPEC" || uv tool install --upgrade "$INSTALL_SPEC" || uv tool install --force "$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"
+    info "Installing latest ${PACKAGE} from PyPI via pipx..."
+    pipx install "$INSTALL_SPEC" || pipx upgrade "$PACKAGE" || pipx install --force "$INSTALL_SPEC"
     ok "Installed with pipx"
 else
     warn "uv/pipx not found — falling back to pip install --user"
@@ -83,7 +82,16 @@ ok "ct $(ct --version 2>/dev/null || echo '(installed)')"
 
 # ── Run setup wizard ───────────────────────────────────────────
 
-info ""
-info "Running setup wizard..."
-info ""
-ct setup
+if "$PYTHON" -c 'import os; fd = os.open("/dev/tty", os.O_RDONLY); os.close(fd)' 2>/dev/null; then
+    info ""
+    info "Running setup wizard..."
+    info ""
+    # When installed via `curl ... | bash`, stdin is the download pipe rather
+    # than the user's keyboard. Reattach setup to the controlling terminal so
+    # interactive prompts and masked input work normally.
+    ct setup < /dev/tty
+else
+    warn ""
+    warn "Skipping interactive setup because no terminal is available."
+    warn "Run: ct setup"
+fi

{celltype_cli-0.1.3 → celltype_cli-0.2.1}/pyproject.toml

@@ -4,10 +4,10 @@ build-backend = "hatchling.build"
 
 [project]
 name = "celltype-cli"
-version = "0.1.3"
+version = "0.2.1"
 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." },
@@ -28,6 +28,8 @@ dependencies = [
     "python-dotenv>=1.0",
     "markdown>=3.5",
     "nbformat>=5.7",
+    "pyyaml>=6.0",
+    "pydantic>=2.0",
 ]
 
 [project.optional-dependencies]
@@ -61,6 +63,17 @@ 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-0.1.3 → celltype_cli-0.2.1}/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-0.1.3 → celltype_cli-0.2.1}/src/ct/agent/config.py

@@ -29,11 +29,10 @@ 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,
-
     "data.base": str(CONFIG_DIR / "data"),
     "data.depmap": None,
     "data.prism": None,
@@ -67,6 +66,14 @@ 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"),

{celltype_cli-0.1.3 → celltype_cli-0.2.1}/src/ct/agent/doctor.py

@@ -340,6 +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-0.1.3 → celltype_cli-0.2.1}/src/ct/agent/mcp_server.py

@@ -71,6 +71,14 @@ _PY_TYPE_MAP = {
 }
 
 
+def _is_json_schema(parameters: dict) -> bool:
+    return (
+        isinstance(parameters, dict)
+        and parameters.get("type") == "object"
+        and isinstance(parameters.get("properties"), dict)
+    )
+
+
 def _params_to_json_schema(parameters: dict) -> dict:
     """Convert a ct tool parameters dict to a JSON Schema object.
 
@@ -81,6 +89,9 @@ def _params_to_json_schema(parameters: dict) -> dict:
     if not parameters:
         return {"type": "object", "properties": {}}
 
+    if _is_json_schema(parameters):
+        return parameters
+
     properties = {}
     for name, desc in parameters.items():
         # Extract type hint from description if present (e.g., "gene name (str)")
@@ -110,29 +121,43 @@ def _make_tool_handler(tool_obj, session):
         call_args["_session"] = session
         call_args["_prior_results"] = {}
 
-        # Coerce string values to numeric types when they look like numbers.
-        # MCP sends all parameters as strings, but tools often expect int/float.
-        for key, val in list(call_args.items()):
-            if key.startswith("_"):
-                continue
-            if isinstance(val, str):
-                # Try int first, then float
-                try:
-                    call_args[key] = int(val)
+        # Legacy flat ct manifests describe every parameter as a string, so keep
+        # backwards-compatible coercion there. Structured JSON Schema tools should
+        # preserve the exact payload emitted by the SDK.
+        if not _is_json_schema(getattr(tool_obj, "parameters", {})):
+            for key, val in list(call_args.items()):
+                if key.startswith("_"):
                     continue
-                except ValueError:
-                    pass
-                try:
-                    call_args[key] = float(val)
-                    continue
-                except ValueError:
-                    pass
-                # Boolean coercion
-                if val.lower() in ("true", "false"):
-                    call_args[key] = val.lower() == "true"
+                if isinstance(val, str):
+                    try:
+                        call_args[key] = int(val)
+                        continue
+                    except ValueError:
+                        pass
+                    try:
+                        call_args[key] = float(val)
+                        continue
+                    except ValueError:
+                        pass
+                    if val.lower() in ("true", "false"):
+                        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) or getattr(tool_obj, "cpu_only", 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 +172,66 @@ 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-0.1.3 → celltype_cli-0.2.1}/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]

{celltype_cli-0.1.3 → celltype_cli-0.2.1}/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-0.1.3 → celltype_cli-0.2.1}/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")