stat-agent 2.0.0__tar.gz → 2.0.1__tar.gz

{stat_agent-2.0.0/src/stat_agent.egg-info → stat_agent-2.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stat-agent
-Version: 2.0.0
+Version: 2.0.1
 Summary: STAT: Spatial Transcriptomics Analytical agenT - AI-powered, provenance-aware spatial omics analysis
 Author-email: Yihang Chen <ychenlp@connect.ust.hk>
 License-Expression: BSD-3-Clause
@@ -11,7 +11,6 @@ Classifier: Development Status :: 3 - Alpha
 Classifier: Intended Audience :: Science/Research
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
@@ -21,6 +20,8 @@ Requires-Dist: pandas>=2.0
 Requires-Dist: anndata>=0.10
 Requires-Dist: scipy>=1.10
 Requires-Dist: scanpy>=1.10
+Requires-Dist: igraph<1.0,>=0.10
+Requires-Dist: leidenalg<0.12,>=0.10
 Requires-Dist: geopandas>=0.14
 Requires-Dist: shapely>=2.0
 Requires-Dist: pillow>=9.0
@@ -66,6 +67,7 @@ Requires-Dist: harmonypy>=0.0.9; extra == "skills"
 Requires-Dist: bbknn>=1.5.0; extra == "skills"
 Requires-Dist: scanorama>=1.7.0; extra == "skills"
 Requires-Dist: scvi-tools<2.0,>=1.0; extra == "skills"
+Requires-Dist: pyro-ppl<1.9.2,>=1.8; extra == "skills"
 Requires-Dist: tangram-sc>=1.0.0; extra == "skills"
 Requires-Dist: qpsolvers[osqp]>=4.0; extra == "skills"
 Requires-Dist: ray>=2.0; extra == "skills"
@@ -75,7 +77,6 @@ Requires-Dist: palantir>=1.0.0; extra == "skills"
 Requires-Dist: NaiveDE>=0.1; extra == "skills"
 Requires-Dist: SpatialDE>=1.1; extra == "skills"
 Requires-Dist: scikit-misc>=0.5; extra == "skills"
-Requires-Dist: igraph<1.0,>=0.9; extra == "skills"
 Requires-Dist: torch>=2.0; extra == "skills"
 Requires-Dist: SpaGCN>=1.2.5; extra == "skills"
 Requires-Dist: GraphST>=1.1.0; extra == "skills"
@@ -115,9 +116,10 @@ interactive tissue viewer.
 
 ## Installation
 
-Python 3.11 or newer.
+Python 3.11, for example in a conda environment:
 
 ```bash
+conda create -n stat python=3.11 && conda activate stat
 pip install stat-agent
 pip install "git+https://github.com/chenyhvvvv/STAT-agent.git"   # or the latest main from GitHub
 ```

{stat_agent-2.0.0 → stat_agent-2.0.1}/README.md

@@ -28,9 +28,10 @@ interactive tissue viewer.
 
 ## Installation
 
-Python 3.11 or newer.
+Python 3.11, for example in a conda environment:
 
 ```bash
+conda create -n stat python=3.11 && conda activate stat
 pip install stat-agent
 pip install "git+https://github.com/chenyhvvvv/STAT-agent.git"   # or the latest main from GitHub
 ```

{stat_agent-2.0.0 → stat_agent-2.0.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "stat-agent"
-version = "2.0.0"
+version = "2.0.1"
 description = "STAT: Spatial Transcriptomics Analytical agenT - AI-powered, provenance-aware spatial omics analysis"
 readme = "README.md"
 requires-python = ">=3.11"
@@ -16,7 +16,6 @@ classifiers = [
   "Intended Audience :: Science/Research",
   "Programming Language :: Python :: 3",
   "Programming Language :: Python :: 3.11",
-  "Programming Language :: Python :: 3.12",
   "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
 
@@ -27,6 +26,8 @@ dependencies = [
   "anndata>=0.10",
   "scipy>=1.10",
   "scanpy>=1.10",
+  "igraph>=0.10,<1.0",  # scanpy's Leiden clustering (leidenalg 0.12 needs igraph 1.x)
+  "leidenalg>=0.10,<0.12",
   "geopandas>=0.14",
   "shapely>=2.0",
   "pillow>=9.0",
@@ -75,6 +76,7 @@ skills = [
   "bbknn>=1.5.0",
   "scanorama>=1.7.0",
   "scvi-tools>=1.0,<2.0",
+  "pyro-ppl>=1.8,<1.9.2",  # 1.9.2 removed deep_getattr, which cell2location imports
   "tangram-sc>=1.0.0",
   "qpsolvers[osqp]>=4.0",
   "ray>=2.0",
@@ -84,7 +86,6 @@ skills = [
   "NaiveDE>=0.1",
   "SpatialDE>=1.1",
   "scikit-misc>=0.5",
-  "igraph>=0.9,<1.0",
   "torch>=2.0",
   "SpaGCN>=1.2.5",
   "GraphST>=1.1.0",

{stat_agent-2.0.0 → stat_agent-2.0.1}/src/stat_agent/__init__.py

@@ -2,5 +2,5 @@
 
 from stat_agent import _compat  # noqa: F401  (third-party compatibility patches)
 
-__version__ = "2.0.0"
+__version__ = "2.0.1"
 __all__ = ["__version__"]

{stat_agent-2.0.0 → stat_agent-2.0.1}/src/stat_agent/agent/nodes/selection.py

@@ -2,6 +2,8 @@
 
 from __future__ import annotations
 
+import importlib.metadata
+import importlib.util
 import re
 from typing import Any
 
@@ -193,6 +195,23 @@ async def synthesize_card_node(state: TurnState, runtime: LGRuntime[Context]):
     return Command(update={"current": current}, goto="verify")
 
 
+def _missing_packages(contract: SkillFrontmatter) -> list[str]:
+    """The skill's declared python packages that are installed neither as a module nor as a distribution."""
+    importlib.invalidate_caches()  # a package installed while STAT runs counts on the next request
+    missing = []
+    for name in contract.dependencies.python:
+        try:
+            if importlib.util.find_spec(name) is not None:
+                continue
+        except (ImportError, ValueError):
+            pass
+        try:
+            importlib.metadata.distribution(name)
+        except importlib.metadata.PackageNotFoundError:
+            missing.append(name)
+    return missing
+
+
 def _file_free_alternative(ctx: Context, current: dict, contract: SkillFrontmatter) -> str | None:
     """A compatible, enabled skill that produces everything the declined skill would, without needing a file."""
     wanted = {a.id for a in contract.produces}
@@ -218,6 +237,16 @@ async def verify_node(state: TurnState, runtime: LGRuntime[Context]):
         step = step.model_copy(update={"refined_query": step.refined_query + current["switch_note"]})
     contract = _contract(ctx, current)
     slug = current.get("skill") or (contract.slug if contract else None)
+    missing = _missing_packages(contract) if current.get("skill") else []
+    if missing:
+        # the code would only fail on the import: say what to install instead of running it
+        advice = (
+            f"{ctx.registry.get(slug).name} needs {', '.join(missing)}, which {'is' if len(missing) == 1 else 'are'} not installed in STAT's Python environment. "
+            'Install the analysis packages with `pip install "stat-agent[skills]"` (the skill\'s SKILL.md lists any it does not cover), then ask again.'
+        )
+        ctx.emit(AdviceEvent(message=advice, skill=slug, step_id=current["step_id"], unmet=missing))
+        current.update(status="blocked", mode="advice", advice=advice, unmet=missing)
+        return Command(update={"current": current}, goto="block_step")
     if contract is None or not ctx.ablation.verifier:
         current["complete_query"] = step.refined_query
         ctx.emit(VerifyComplete(step_id=current["step_id"], skill=slug, verdicts=[], decided_by="bypass", complete_query=step.refined_query))

{stat_agent-2.0.0 → stat_agent-2.0.1/src/stat_agent.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stat-agent
-Version: 2.0.0
+Version: 2.0.1
 Summary: STAT: Spatial Transcriptomics Analytical agenT - AI-powered, provenance-aware spatial omics analysis
 Author-email: Yihang Chen <ychenlp@connect.ust.hk>
 License-Expression: BSD-3-Clause
@@ -11,7 +11,6 @@ Classifier: Development Status :: 3 - Alpha
 Classifier: Intended Audience :: Science/Research
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
@@ -21,6 +20,8 @@ Requires-Dist: pandas>=2.0
 Requires-Dist: anndata>=0.10
 Requires-Dist: scipy>=1.10
 Requires-Dist: scanpy>=1.10
+Requires-Dist: igraph<1.0,>=0.10
+Requires-Dist: leidenalg<0.12,>=0.10
 Requires-Dist: geopandas>=0.14
 Requires-Dist: shapely>=2.0
 Requires-Dist: pillow>=9.0
@@ -66,6 +67,7 @@ Requires-Dist: harmonypy>=0.0.9; extra == "skills"
 Requires-Dist: bbknn>=1.5.0; extra == "skills"
 Requires-Dist: scanorama>=1.7.0; extra == "skills"
 Requires-Dist: scvi-tools<2.0,>=1.0; extra == "skills"
+Requires-Dist: pyro-ppl<1.9.2,>=1.8; extra == "skills"
 Requires-Dist: tangram-sc>=1.0.0; extra == "skills"
 Requires-Dist: qpsolvers[osqp]>=4.0; extra == "skills"
 Requires-Dist: ray>=2.0; extra == "skills"
@@ -75,7 +77,6 @@ Requires-Dist: palantir>=1.0.0; extra == "skills"
 Requires-Dist: NaiveDE>=0.1; extra == "skills"
 Requires-Dist: SpatialDE>=1.1; extra == "skills"
 Requires-Dist: scikit-misc>=0.5; extra == "skills"
-Requires-Dist: igraph<1.0,>=0.9; extra == "skills"
 Requires-Dist: torch>=2.0; extra == "skills"
 Requires-Dist: SpaGCN>=1.2.5; extra == "skills"
 Requires-Dist: GraphST>=1.1.0; extra == "skills"
@@ -115,9 +116,10 @@ interactive tissue viewer.
 
 ## Installation
 
-Python 3.11 or newer.
+Python 3.11, for example in a conda environment:
 
 ```bash
+conda create -n stat python=3.11 && conda activate stat
 pip install stat-agent
 pip install "git+https://github.com/chenyhvvvv/STAT-agent.git"   # or the latest main from GitHub
 ```

{stat_agent-2.0.0 → stat_agent-2.0.1}/src/stat_agent.egg-info/requires.txt

@@ -3,6 +3,8 @@ pandas>=2.0
 anndata>=0.10
 scipy>=1.10
 scanpy>=1.10
+igraph<1.0,>=0.10
+leidenalg<0.12,>=0.10
 geopandas>=0.14
 shapely>=2.0
 pillow>=9.0
@@ -53,6 +55,7 @@ harmonypy>=0.0.9
 bbknn>=1.5.0
 scanorama>=1.7.0
 scvi-tools<2.0,>=1.0
+pyro-ppl<1.9.2,>=1.8
 tangram-sc>=1.0.0
 qpsolvers[osqp]>=4.0
 ray>=2.0
@@ -62,7 +65,6 @@ palantir>=1.0.0
 NaiveDE>=0.1
 SpatialDE>=1.1
 scikit-misc>=0.5
-igraph<1.0,>=0.9
 torch>=2.0
 SpaGCN>=1.2.5
 GraphST>=1.1.0