celltype-cli 0.1.2__tar.gz → 0.1.3__tar.gz

{celltype_cli-0.1.2 → celltype_cli-0.1.3}/PKG-INFO

@@ -1,15 +1,16 @@
 Metadata-Version: 2.4
 Name: celltype-cli
-Version: 0.1.2
+Version: 0.1.3
 Summary: CellType CLI — An autonomous agent for drug discovery research
 Author: CellType Inc.
 License-Expression: 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
@@ -71,7 +72,7 @@ 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-0.1.3}/README.md

@@ -8,7 +8,7 @@ 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-0.1.3}/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-0.1.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "celltype-cli"
-version = "0.1.2"
+version = "0.1.3"
 description = "CellType CLI — An autonomous agent for drug discovery research"
 readme = "README.md"
 license = "MIT"
@@ -17,13 +17,14 @@ 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",

{celltype_cli-0.1.2 → celltype_cli-0.1.3}/src/ct/agent/config.py

@@ -456,6 +456,13 @@ 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 +471,9 @@ 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-0.1.3}/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

{celltype_cli-0.1.2 → celltype_cli-0.1.3}/src/ct/agent/runner.py

@@ -357,6 +357,24 @@ 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-0.1.3}/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-0.1.3}/src/ct/cli.py

@@ -128,6 +128,13 @@ def setup_cmd(
 
     cfg = Config.load()
 
+    # Azure AI Foundry: skip interactive key prompt when Foundry is configured
+    if os.environ.get("ANTHROPIC_FOUNDRY_API_KEY") or os.environ.get("ANTHROPIC_FOUNDRY_RESOURCE"):
+        console.print("\n  [green]Azure AI Foundry detected. No API key needed.[/green]")
+        cfg.set("llm.provider", "anthropic")
+        cfg.save()
+        return
+
     console.print()
     console.print(
         Panel(

{celltype_cli-0.1.2 → celltype_cli-0.1.3}/src/ct/models/llm.py

@@ -120,9 +120,12 @@ class LLMClient:
 
         if self.provider == "anthropic":
             import anthropic
-            self._client = anthropic.Anthropic(
-                api_key=self.api_key or os.environ.get("ANTHROPIC_API_KEY")
-            )
+            if os.environ.get("ANTHROPIC_FOUNDRY_API_KEY") or os.environ.get("ANTHROPIC_FOUNDRY_RESOURCE"):
+                self._client = anthropic.AnthropicFoundry()
+            else:
+                self._client = anthropic.Anthropic(
+                    api_key=self.api_key or os.environ.get("ANTHROPIC_API_KEY")
+                )
 
         elif self.provider == "openai":
             import openai

{celltype_cli-0.1.2 → celltype_cli-0.1.3}/tests/test_config.py

@@ -21,13 +21,33 @@ def test_load_invalid_json_does_not_crash(monkeypatch, tmp_path):
     assert cfg.get("llm.provider") == "anthropic"
 
 
-def test_llm_preflight_requires_anthropic_key():
+def test_llm_preflight_requires_anthropic_key(monkeypatch):
+    monkeypatch.delenv("ANTHROPIC_API_KEY", raising=False)
+    monkeypatch.delenv("ANTHROPIC_FOUNDRY_API_KEY", raising=False)
+    monkeypatch.delenv("ANTHROPIC_FOUNDRY_RESOURCE", raising=False)
     cfg = Config(data={"llm.provider": "anthropic"})
     issue = cfg.llm_preflight_issue()
     assert issue is not None
     assert "Anthropic API key" in issue
 
 
+def test_llm_preflight_accepts_foundry_env_vars(monkeypatch):
+    monkeypatch.delenv("ANTHROPIC_API_KEY", raising=False)
+    monkeypatch.setenv("ANTHROPIC_FOUNDRY_API_KEY", "test-key")
+    monkeypatch.setenv("ANTHROPIC_FOUNDRY_RESOURCE", "test-resource")
+    cfg = Config(data={"llm.provider": "anthropic"})
+    assert cfg.llm_preflight_issue() is None
+
+
+def test_llm_preflight_error_mentions_foundry(monkeypatch):
+    monkeypatch.delenv("ANTHROPIC_API_KEY", raising=False)
+    monkeypatch.delenv("ANTHROPIC_FOUNDRY_API_KEY", raising=False)
+    monkeypatch.delenv("ANTHROPIC_FOUNDRY_RESOURCE", raising=False)
+    cfg = Config(data={"llm.provider": "anthropic"})
+    issue = cfg.llm_preflight_issue()
+    assert "Foundry" in issue
+
+
 def test_llm_preflight_requires_openai_key():
     cfg = Config(data={"llm.provider": "openai"})
     issue = cfg.llm_preflight_issue()