tooluniverse 1.0.8__py3-none-any.whl → 1.0.9__py3-none-any.whl

tooluniverse/smcp_server.py

@@ -7,6 +7,7 @@ It creates a minimal SMCP server that exposes all ToolUniverse tools as MCP tool
 """
 
 import argparse
+import os
 import sys
 from .smcp import SMCP
 
@@ -134,6 +135,22 @@ def run_stdio_server():
     This function provides compatibility with the original MCP server's run_claude_desktop function.
     It accepts the same arguments as run_smcp_server but forces transport='stdio'.
     """
+    # Set environment variable and reconfigure logging for stdio mode
+    os.environ["TOOLUNIVERSE_STDIO_MODE"] = "1"
+
+    # Import and reconfigure logging to stderr
+    from .logging_config import reconfigure_for_stdio
+
+    reconfigure_for_stdio()
+    # Ensure stdout is line-buffered for immediate JSON-RPC flushing in stdio mode
+    try:
+        import sys as _sys
+
+        if hasattr(_sys.stdout, "reconfigure"):
+            _sys.stdout.reconfigure(line_buffering=True)
+    except Exception:
+        pass
+
     parser = argparse.ArgumentParser(
         description="Start SMCP (Scientific Model Context Protocol) Server with stdio transport",
         formatter_class=argparse.RawDescriptionHelpFormatter,
@@ -297,107 +314,35 @@ Examples:
             from .execute_function import ToolUniverse
 
             tu = ToolUniverse()
-            tool_types = tu.get_tool_types()
+            # Use ToolUniverse API to list categories consistently
+            stats = tu.list_built_in_tools(mode="config", scan_all=False)
 
             print("Available tool categories:", file=sys.stderr)
             print("=" * 50, file=sys.stderr)
 
-            # Group categories for better readability
-            scientific_db = []
-            literature = []
-            software = []
-            special = []
-            clinical = []
-            other = []
-
-            for category in sorted(tool_types):
-                if category in [
-                    "uniprot",
-                    "ChEMBL",
-                    "opentarget",
-                    "pubchem",
-                    "hpa",
-                    "rcsb_pdb",
-                    "reactome",
-                    "go",
-                ]:
-                    scientific_db.append(category)
-                elif category in [
-                    "EuropePMC",
-                    "semantic_scholar",
-                    "pubtator",
-                    "OpenAlex",
-                ]:
-                    literature.append(category)
-                elif category.startswith("software_"):
-                    software.append(category)
-                elif category in [
-                    "special_tools",
-                    "tool_finder",
-                    "tool_composition",
-                    "agents",
-                ]:
-                    special.append(category)
-                elif category in [
-                    "clinical_trials",
-                    "fda_drug_label",
-                    "fda_drug_adverse_event",
-                    "dailymed",
-                    "medlineplus",
-                ]:
-                    clinical.append(category)
-                else:
-                    other.append(category)
-
-            if scientific_db:
-                print("\n🔬 Scientific Databases:", file=sys.stderr)
-                for cat in scientific_db:
-                    print(f"  {cat}", file=sys.stderr)
-
-            if literature:
-                print("\n📚 Literature & Knowledge:", file=sys.stderr)
-                for cat in literature:
-                    print(f"  {cat}", file=sys.stderr)
-
-            if clinical:
-                print("\n🏥 Clinical & Drug Information:", file=sys.stderr)
-                for cat in clinical:
-                    print(f"  {cat}", file=sys.stderr)
-
-            if software:
-                print("\n💻 Software Tools:", file=sys.stderr)
-                for cat in software[:5]:  # Show first 5
-                    print(f"  {cat}", file=sys.stderr)
-                if len(software) > 5:
-                    print(
-                        f"  ... and {len(software, file=sys.stderr) - 5} more software categories"
-                    )
-
-            if special:
-                print("\n🛠 Special & Meta Tools:", file=sys.stderr)
-                for cat in special:
-                    print(f"  {cat}", file=sys.stderr)
-
-            if other:
-                print("\n📂 Other Categories:", file=sys.stderr)
-                for cat in other:
-                    print(f"  {cat}", file=sys.stderr)
+            categories = stats.get("categories", {})
+            # Sort by count desc, then name asc
+            sorted_items = sorted(
+                categories.items(), key=lambda kv: (-kv[1].get("count", 0), kv[0])
+            )
+            for key, info in sorted_items:
+                display = key.replace("_", " ").title()
+                count = info.get("count", 0)
+                print(f"  {display}: {count}", file=sys.stderr)
 
-            print(f"\nTotal: {len(tool_types, file=sys.stderr)} categories available")
-            print("\nCommon combinations:", file=sys.stderr)
             print(
-                "  Scientific research: uniprot ChEMBL opentarget pubchem hpa",
+                f"\nTotal categories: {stats.get('total_categories', 0)}",
                 file=sys.stderr,
             )
             print(
-                "  Drug discovery: ChEMBL fda_drug_label clinical_trials pubchem",
+                f"Total unique tools: {stats.get('total_tools', 0)}",
                 file=sys.stderr,
             )
+
             print(
-                "  Literature analysis: EuropePMC semantic_scholar pubtator",
+                "\nTip: Use --exclude-categories or --include-tools to customize loading",
                 file=sys.stderr,
             )
-            print("  Minimal setup: special_tools tool_finder", file=sys.stderr)
 
         except Exception as e:
             print(f"❌ Error listing categories: {e}", file=sys.stderr)
@@ -415,13 +360,20 @@ Examples:
             print("Available tools:", file=sys.stderr)
             print("=" * 50, file=sys.stderr)
 
-            # Group tools by category
+            # Group tools by category (use ToolUniverse's canonical 'type' field)
             tools_by_category = {}
             for tool in tu.all_tools:
-                tool_type = getattr(tool, "tool_type", "unknown")
+                # Handle both dict and object tool formats
+                if isinstance(tool, dict):
+                    tool_type = tool.get("type", "unknown")
+                    tool_name = tool.get("name", "unknown")
+                else:
+                    tool_type = getattr(tool, "type", "unknown")
+                    tool_name = getattr(tool, "name", "unknown")
+
                 if tool_type not in tools_by_category:
                     tools_by_category[tool_type] = []
-                tools_by_category[tool_type].append(tool.name)
+                tools_by_category[tool_type].append(tool_name)
 
             total_tools = 0
             for category in sorted(tools_by_category.keys()):
@@ -554,7 +506,7 @@ Examples:
             print("🔗 Hooks disabled", file=sys.stderr)
 
         print(f"⚡ Max workers: {args.max_workers}", file=sys.stderr)
-        print()
+        print(file=sys.stderr)
 
         # Create SMCP server with hook support
         server = SMCP(
@@ -769,96 +721,27 @@ Examples:
             from .execute_function import ToolUniverse
 
             tu = ToolUniverse()
-            tool_types = tu.get_tool_types()
+            # Use ToolUniverse API to list categories consistently
+            stats = tu.list_built_in_tools(mode="config", scan_all=False)
 
             print("Available tool categories:")
             print("=" * 50)
 
-            # Group categories for better readability
-            scientific_db = []
-            literature = []
-            software = []
-            special = []
-            clinical = []
-            other = []
-
-            for category in sorted(tool_types):
-                if category in [
-                    "uniprot",
-                    "ChEMBL",
-                    "opentarget",
-                    "pubchem",
-                    "hpa",
-                    "rcsb_pdb",
-                    "reactome",
-                    "go",
-                ]:
-                    scientific_db.append(category)
-                elif category in [
-                    "EuropePMC",
-                    "semantic_scholar",
-                    "pubtator",
-                    "OpenAlex",
-                ]:
-                    literature.append(category)
-                elif category.startswith("software_"):
-                    software.append(category)
-                elif category in [
-                    "special_tools",
-                    "tool_finder",
-                    "tool_composition",
-                    "agents",
-                ]:
-                    special.append(category)
-                elif category in [
-                    "clinical_trials",
-                    "fda_drug_label",
-                    "fda_drug_adverse_event",
-                    "dailymed",
-                    "medlineplus",
-                ]:
-                    clinical.append(category)
-                else:
-                    other.append(category)
-
-            if scientific_db:
-                print("\n🔬 Scientific Databases:")
-                for cat in scientific_db:
-                    print(f"  {cat}")
-
-            if literature:
-                print("\n📚 Literature & Knowledge:")
-                for cat in literature:
-                    print(f"  {cat}")
-
-            if clinical:
-                print("\n🏥 Clinical & Drug Information:")
-                for cat in clinical:
-                    print(f"  {cat}")
-
-            if software:
-                print("\n💻 Software Tools:")
-                for cat in software[:5]:  # Show first 5
-                    print(f"  {cat}")
-                if len(software) > 5:
-                    print(f"  ... and {len(software) - 5} more software categories")
-
-            if special:
-                print("\n🛠 Special & Meta Tools:")
-                for cat in special:
-                    print(f"  {cat}")
-
-            if other:
-                print("\n📂 Other Categories:")
-                for cat in other:
-                    print(f"  {cat}")
-
-            print(f"\nTotal: {len(tool_types)} categories available")
-            print("\nCommon combinations:")
-            print("  Scientific research: uniprot ChEMBL opentarget pubchem hpa")
-            print("  Drug discovery: ChEMBL fda_drug_label clinical_trials pubchem")
-            print("  Literature analysis: EuropePMC semantic_scholar pubtator")
-            print("  Minimal setup: special_tools tool_finder")
+            categories = stats.get("categories", {})
+            # Sort by count desc, then name asc
+            sorted_items = sorted(
+                categories.items(), key=lambda kv: (-kv[1].get("count", 0), kv[0])
+            )
+            for key, info in sorted_items:
+                display = key.replace("_", " ").title()
+                count = info.get("count", 0)
+                print(f"  {display}: {count}")
+
+            print(f"\nTotal categories: {stats.get('total_categories', 0)}")
+            print(f"Total unique tools: {stats.get('total_tools', 0)}")
+            print(
+                "\nTip: Use --exclude-categories or --include-tools to customize loading"
+            )
 
         except Exception as e:
             print(f"❌ Error listing categories: {e}")
@@ -871,30 +754,37 @@ Examples:
             from .execute_function import ToolUniverse
 
             tu = ToolUniverse()
-            tu.load_tools()  # Load all tools to list them
-
-            print("Available tools:")
-            print("=" * 50)
-
-            # Group tools by category
-            tools_by_category = {}
-            for tool in tu.all_tools:
-                tool_type = getattr(tool, "tool_type", "unknown")
-                if tool_type not in tools_by_category:
-                    tools_by_category[tool_type] = []
-                tools_by_category[tool_type].append(tool.name)
+            # Reuse ToolUniverse selection logic directly (applies API key skipping internally)
+            tool_config_files = {}
+            if args.tool_config_files:
+                for config_spec in args.tool_config_files:
+                    if ":" in config_spec:
+                        category, path = config_spec.split(":", 1)
+                        tool_config_files[category] = path
+
+            tu.load_tools(
+                tool_type=(
+                    args.categories
+                    if args.categories and len(args.categories) > 0
+                    else None
+                ),
+                exclude_tools=args.exclude_tools,
+                exclude_categories=args.exclude_categories,
+                include_tools=args.include_tools,
+                tool_config_files=(tool_config_files or None),
+                tools_file=args.tools_file,
+                include_tool_types=args.include_tool_types,
+                exclude_tool_types=args.exclude_tool_types,
+            )
 
-            total_tools = 0
-            for category in sorted(tools_by_category.keys()):
-                tools = sorted(tools_by_category[category])
-                print(f"\n📁 {category} ({len(tools)} tools):")
-                for tool in tools[:10]:  # Show first 10 tools per category
-                    print(f"  {tool}")
-                if len(tools) > 10:
-                    print(f"  ... and {len(tools) - 10} more tools")
-                total_tools += len(tools)
+            # Names of tools that are actually available under current configuration
+            tool_names = tu.get_available_tools(name_only=True)
 
-            print(f"\nTotal: {total_tools} tools available")
+            print("Available tools (for this server configuration):")
+            print("=" * 50)
+            for name in sorted(tool_names)[:200]:  # cap output for readability
+                print(f"  {name}")
+            print(f"\nTotal: {len(tool_names)} tools available")
             print("\nNote: Use --exclude-tools to exclude specific tools by name")
             print("      Use --exclude-categories to exclude entire categories")
 

tooluniverse/tools/__init__.py

@@ -1,7 +1,7 @@
 """
 ToolUniverse Tools
 
-Type-safe Python interface to 670 scientific tools.
+Type-safe Python interface to 669 scientific tools.
 Each tool is in its own module for minimal import overhead.
 
 Usage:
@@ -497,7 +497,6 @@ from .MedlinePlus_get_genetics_gene_by_name import MedlinePlus_get_genetics_gene
 from .MedlinePlus_get_genetics_index import MedlinePlus_get_genetics_index
 from .MedlinePlus_search_topics_by_keyword import MedlinePlus_search_topics_by_keyword
 from .MethodologyRigorReviewer import MethodologyRigorReviewer
-from .MultiAgentLiteratureSearch import MultiAgentLiteratureSearch
 from .NICE_Clinical_Guidelines_Search import NICE_Clinical_Guidelines_Search
 from .NICE_Guideline_Full_Text import NICE_Guideline_Full_Text
 from .NoveltySignificanceReviewer import NoveltySignificanceReviewer
@@ -1351,7 +1350,6 @@ __all__ = [
     "MedlinePlus_get_genetics_index",
     "MedlinePlus_search_topics_by_keyword",
     "MethodologyRigorReviewer",
-    "MultiAgentLiteratureSearch",
     "NICE_Clinical_Guidelines_Search",
     "NICE_Guideline_Full_Text",
     "NoveltySignificanceReviewer",

{tooluniverse-1.0.8.dist-info → tooluniverse-1.0.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tooluniverse
-Version: 1.0.8
+Version: 1.0.9
 Summary: A comprehensive collection of scientific tools for Agentic AI, offering integration with the ToolUniverse SDK and MCP Server to support advanced scientific workflows.
 Author-email: Shanghua Gao <shanghuagao@gmail.com>
 Project-URL: Homepage, https://github.com/mims-harvard/ToolUniverse
@@ -29,6 +29,7 @@ Requires-Dist: sentence-transformers>=5.1.0
 Requires-Dist: fitz>=0.0.1.dev2
 Requires-Dist: pandas>=2.2.3
 Requires-Dist: admet-ai>=1.2.0
+Requires-Dist: setuptools>=70.0.0
 Requires-Dist: pdfplumber>=0.11.0
 Requires-Dist: playwright>=1.55.0
 Requires-Dist: faiss-cpu>=1.12.0

{tooluniverse-1.0.8.dist-info → tooluniverse-1.0.9.dist-info}/RECORD

@@ -1,5 +1,5 @@
-tooluniverse/__init__.py,sha256=JlK1_ZXAVh6blkJ2VRWSaedO3usOD9XwC1bvTOGZhFs,17138
-tooluniverse/admetai_tool.py,sha256=pZJ8ictFDE0GMFI2i-jMGVWfbO6bTUYnDDLDMfMotnA,3175
+tooluniverse/__init__.py,sha256=PvYhaTdU4pSC8V3DMzbybfkLSad2OkpQWgf74P-lfH8,17507
+tooluniverse/admetai_tool.py,sha256=xeYCpROq7oGjYrzKtDCHSN94sB5jVLuLSu3E_eT5Ko8,3470
 tooluniverse/agentic_tool.py,sha256=i0TEs6WhF21B4gs5k7DM67qTND4qDMPD2lUzLyEWnnM,25627
 tooluniverse/alphafold_tool.py,sha256=NkKQttC0MfuetCTTcWTFEG2MdhyKwy3jb5TR4odiqAw,4658
 tooluniverse/arxiv_tool.py,sha256=60e5moGt3XnwZeKx_nrvRZrwAavE11ok0j78AI5F6Xs,3610
@@ -11,7 +11,7 @@ tooluniverse/build_optimizer.py,sha256=UReMfhTGhGJqcEWdH6d5xfI-y3zJlaNfsei7qXxeC
 tooluniverse/cellosaurus_tool.py,sha256=W_npl3ga45-Hpsdq7YyGsD5_DnR2AmyaQVYNjiZoNOs,47902
 tooluniverse/chem_tool.py,sha256=tJusjamWNp0x8Ke-cvVgKB7-clvD6LXTaXA0Q0fqQv4,8336
 tooluniverse/clinvar_tool.py,sha256=2NKPKC3b3eBzuwK0yc65bzPuRF4I-Jv_KjsVnBdiE6M,2945
-tooluniverse/compose_tool.py,sha256=f_3X_fbdrzogBdKJXoXXpxVvdb1OWt7KMxhpPUtEu24,17109
+tooluniverse/compose_tool.py,sha256=Q0KwVPgbac17VDnkP3pV-st0rNbG__CX0AMux-Os5lg,17117
 tooluniverse/core_tool.py,sha256=hHD8nVSIy6lK2vF3ygKz73gsDEPYEL-otXZXeR7M2SY,5083
 tooluniverse/crossref_tool.py,sha256=oba0kkWI9m9dugf_th1nEXPWPF4onJkFUyhp5h5H4pM,5736
 tooluniverse/ctg_tool.py,sha256=3nR_F-YGpxVmTa6u5xi-mrTmLSH7OBehP4EJo-CQS0Y,46053
@@ -30,7 +30,7 @@ tooluniverse/enrichr_tool.py,sha256=YXuHwoG_Hi-kUWK7cY_X21b5pbqoREdG7fJxKq050Jg,
 tooluniverse/ensembl_tool.py,sha256=i-kYliN5juitLTJqGiWcm7RXFV8k29XlfNBUC1Y1Z-M,2195
 tooluniverse/europe_pmc_tool.py,sha256=-3CAq5tDhS5NoeHifevadBgP_MHDZJdwNmM5SvjbAa8,6080
 tooluniverse/exceptions.py,sha256=3svVCG7H_G_8E1mco74KWi44u1M7V1JojVycSEWdi_o,5386
-tooluniverse/execute_function.py,sha256=M2tjcwhYzIoLwyFrTY5JcZ6lcweWdqJCkYH6Dxhfuu8,106091
+tooluniverse/execute_function.py,sha256=hJxcHbewIfXXjPvV7HBZ0PrECMOKTQVhMOFRI5K6fbQ,107533
 tooluniverse/extended_hooks.py,sha256=1Cg0rETh6_D21YFVqD-FhL7y4inZAGyQ6vMtHyugueg,15376
 tooluniverse/fatcat_tool.py,sha256=-QEOYbv6KEcrOiOa27Ms1xm0sySB-vW4rWEinsS6EDw,2051
 tooluniverse/gene_ontology_tool.py,sha256=l89XYdBEBm3eN3dG0lR4oV01H16_9IUB6a2c7W_c7Lg,7180
@@ -44,7 +44,7 @@ tooluniverse/hal_tool.py,sha256=HrU27B6TK_gMtk8tjafpVkpD1ABDlCOo1bsLmBNhaQU,2485
 tooluniverse/hpa_tool.py,sha256=siRA0usQ0Rggloy3VL1b56QlytabndXS8Xzc9H3uWs8,64998
 tooluniverse/humanbase_tool.py,sha256=xojNboYvFrW_LAzOzKaexp6tvyGSbUazpMfOvX5ETXY,15006
 tooluniverse/llm_clients.py,sha256=6EAhxUmEpdKYjWMG6S0Q57mdp1JuCPxPehIudofCPzA,30484
-tooluniverse/logging_config.py,sha256=SWM8TCrv0RZJZbC8NNwy8h04V9BvqSVyzwJFcW43eFI,7212
+tooluniverse/logging_config.py,sha256=rMjpGw5jkJGsIN2AakLOCQ-jVEYf8UhET7sJGdrfCNQ,9107
 tooluniverse/markitdown_tool.py,sha256=bnUA0Sw8KjVygqf8F6k3ATY7K23NWFqycnnfs9mm5qQ,5492
 tooluniverse/mcp_client_tool.py,sha256=1AxczGYkW6kMynLwz1WLzH3KoIKM2cDQ9WMUTOsejTo,29053
 tooluniverse/mcp_integration.py,sha256=9VtFDFbcVIuKO_sd1gFrOd-R0r6uxlYRjdsOKiqV1zs,13912
@@ -52,15 +52,15 @@ tooluniverse/mcp_tool_registry.py,sha256=GsTXbGbMGo3oXtoHSFXq_4p6XieZhzm4mHP82fN
 tooluniverse/medlineplus_tool.py,sha256=__D7W2Khl05WllMnoV4Owv3pyl5EXS1lzEJmAE7PbD0,13214
 tooluniverse/medrxiv_tool.py,sha256=QCJ0BdgI47IfSwvKw90LdZLRq_4sbV4ok5HdGzv5w5c,4140
 tooluniverse/memory_manager.py,sha256=hAUvWen6xG5DMO28GokSfGPCTz0zrzMK-QO8EzRFnPM,6130
-tooluniverse/molecule_2d_tool.py,sha256=p08EgesUytxxsbva66aVxctO3BMSsqbteCHnTtgyv4I,10278
-tooluniverse/molecule_3d_tool.py,sha256=XbruNN2Tg_pgXf199KE7xCmReo6_mHcrT0q2W5vpevg,18437
+tooluniverse/molecule_2d_tool.py,sha256=SPXqi_KTN76ksG1DO0QP9ZKzcRbdQpXjfOau11hgC0w,10568
+tooluniverse/molecule_3d_tool.py,sha256=uq3Q58q0LlB4y7xRaOUzoyQQp8GLjbWSSFdHin4tOsg,18727
 tooluniverse/odphp_tool.py,sha256=5MUPcXBSi6wGGTN56vhNOyAZvIRLiTraxKpxKiQy1pU,9627
 tooluniverse/openaire_tool.py,sha256=LPic0ErGhHV6ceGsUPlS2zTzQdwWvNPZDrnDAtou3I4,4578
 tooluniverse/openalex_tool.py,sha256=ou_INKT8nct_NKjWTan7bdKzZ_i8ZwkxeHCwU9mN7dw,9439
 tooluniverse/openfda_adv_tool.py,sha256=t5kffba0iNDVtFHYPtfLW8ql4dKLaWwdcFnE9cNmNWE,10168
 tooluniverse/openfda_tool.py,sha256=AetafmFr1IygGAL8p1-URsNahVdN52tN0FvToTlkcMw,27425
 tooluniverse/osf_preprints_tool.py,sha256=uO0VmCWdROXoq1U4w1YIfTxZkDpgYWBXh7MJ-fe_Jak,2193
-tooluniverse/output_hook.py,sha256=2f95WFXA9DC6-HV4uJb8ZJAF-VmlmM2DPVvG2up_4EE,46279
+tooluniverse/output_hook.py,sha256=6alRemNqe367xKX1USyXB-FEzDmmPVF9me_DPtopDCc,49433
 tooluniverse/package_tool.py,sha256=Ri-TPc_jTY3olHjPsMkEe2z45vknM7yynjtMXkh3Le8,8294
 tooluniverse/pmc_tool.py,sha256=2K8ux4jv38XbEY6FPBiW5KZDflHo8WA7nRmLJ3HOHYk,6268
 tooluniverse/protein_structure_3d_tool.py,sha256=byvtvW-B6aPUmW_OpcYKHFdbL-g3IWZk1RSN0cNYjcg,12318
@@ -72,8 +72,8 @@ tooluniverse/reactome_tool.py,sha256=ngmJXCcQfsu5d8XcX258ZHW4DIBi45sSjYNwUBk8nxo
 tooluniverse/remote_tool.py,sha256=ywb5xaJBqOT38_r5FBVoF3QFQDcLvfOH5AQrT-g7Fcs,3368
 tooluniverse/restful_tool.py,sha256=H7alq_vO3G4iVgZIZrrWh9vq2ForJN52Fl7_QOq7yaM,4409
 tooluniverse/semantic_scholar_tool.py,sha256=gaDDL5Xy4Ij3qNqipZvwRfOBSyzGyIN8AANT-pYKHvI,3227
-tooluniverse/smcp.py,sha256=HO6ACPQzqBqLYEni5ZGI6W3V5lL3BHBuRRhh6r9hKVQ,103751
-tooluniverse/smcp_server.py,sha256=SAItoFvUsVwGktRZBqMvHRZrHAdVGOmgxetgA0IwyAQ,35960
+tooluniverse/smcp.py,sha256=8wUqsfU23hokFheTec3arbezLTWhyC-j-AQ4gbTSA0Y,104045
+tooluniverse/smcp_server.py,sha256=7_e7Pwd5nMenKz1B9Y0HDkRcPaDbWy-RdFqKbXWKI_0,32428
 tooluniverse/string_tool.py,sha256=3rio0Lt97FuU6fbpykq3ETqD9pA4h_gPR0uXKRb7Zu4,3936
 tooluniverse/tool_finder_embedding.py,sha256=O0WMCT6z7a_pDDew04QtpyPk_qzfGCX_647rsrBs0ug,11239
 tooluniverse/tool_finder_keyword.py,sha256=_Nt4-C1RranoywTk8vi6MePWPoNqFwOhafMDiTYl_SU,23480
@@ -102,7 +102,7 @@ tooluniverse/compose_scripts/drug_safety_analyzer.py,sha256=4lmGYY8a4T4WbeHIUG1a
 tooluniverse/compose_scripts/enhanced_multi_agent_literature_search.py,sha256=GbdI4uYY8Y1OOXub5fOoMnLOOZ-7hD4kl3CA6b3jqG8,9948
 tooluniverse/compose_scripts/literature_tool.py,sha256=8-NITTQHj6vdn-vo_d0W8l6Ed8bvDTkDOJ7yvhaE-lI,976
 tooluniverse/compose_scripts/multi_agent_literature_search.py,sha256=O320QpaIjEbo0n2lxo5VZNbfvZjmZO4hsYALtEhR5j0,30416
-tooluniverse/compose_scripts/output_summarizer.py,sha256=dCT9GAcplaaIWuOjF9uJTVer7z-xbclb2V9tqR1BPAY,10331
+tooluniverse/compose_scripts/output_summarizer.py,sha256=jcUA-6kIIMjOzS78QvobIWPDiAzl7M70KU9qBAb0ZXo,12225
 tooluniverse/compose_scripts/tool_description_optimizer.py,sha256=L6Kd8e6Af8pD6dy8jrFzJq5jq-QNbg72gkQktn8IDBE,32175
 tooluniverse/compose_scripts/tool_discover.py,sha256=RKzCmhDWzDCsAl2KCcEQRNH96mOf_2bTQOH2EVGvpC8,24976
 tooluniverse/compose_scripts/tool_graph_composer.py,sha256=lmGeN94Mc9SZCeYo8ez55tKYLS1-dI3JDm-onKB5DZA,15566
@@ -110,8 +110,8 @@ tooluniverse/compose_scripts/tool_graph_generation.py,sha256=rbkvAZFnGu1frsafHt_
 tooluniverse/compose_scripts/tool_metadata_generator.py,sha256=73_JBPS-yAZEbViBwEFxcLzpbAt-arfMpahzrdhsxMc,20846
 tooluniverse/data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tooluniverse/data/admetai_tools.json,sha256=08LCNSCZJxL6ZuPF1mVfbdlh9f2X5tnEwIYU7RcLLSM,6497
-tooluniverse/data/adverse_event_tools.json,sha256=EDU_X8r4YtMnVt7SJpyimdo3FlcSNFSdvckWLShDODA,12752
-tooluniverse/data/agentic_tools.json,sha256=GlY5yi7NX16iUfPElPyfLLVJMO4vipkr0Nb8g_On4Wc,95981
+tooluniverse/data/adverse_event_tools.json,sha256=gmO2euqIvLqc9lfmf9h9W0_TR33AYpMg_M1tzBNKm7w,12084
+tooluniverse/data/agentic_tools.json,sha256=Z5BSUxwC9uTJuP0SK5k_WnFs6qq4ow8Ib7m0mY-NlLo,93696
 tooluniverse/data/alphafold_tools.json,sha256=bNFUKlidqkAF9euRJxX2XXXZ9YfnHg1laDekumH3RTU,14167
 tooluniverse/data/arxiv_tools.json,sha256=v4FNgFMhNX2WBNajje1xpa5250kvifm_RXY1WzPGgFw,2591
 tooluniverse/data/biorxiv_tools.json,sha256=i7iNyLJDRCPlNd6QjQ9Ml0rUwkcBPjXLG3QOa6cT2sI,2007
@@ -119,7 +119,7 @@ tooluniverse/data/boltz_tools.json,sha256=_pMSRBkO3uj4vjYnQ7H6qbZFa4rzc9Looj6zHR
 tooluniverse/data/cellosaurus_tools.json,sha256=JLn0d5BAj9U5bA2Soy9PRsfO4EeSLOK0nlYT_HCJnio,7388
 tooluniverse/data/chembl_tools.json,sha256=e7l7Z2r6EM6QL_DL6UEdtJ5BTJysebxgSZBixeKEL3o,850
 tooluniverse/data/clinicaltrials_gov_tools.json,sha256=2trH2fs6iKrJrazSiNp-nxbTjdjpSohlOpdM4uy8BMQ,14321
-tooluniverse/data/compose_tools.json,sha256=SYwoNb03pP0Yn2BatqdLpbVR0ghRKs-rmwKCgu11-sA,13417
+tooluniverse/data/compose_tools.json,sha256=3CiMpiFdGNkJDw07CH4M-SU0Kl_xVGAQC376IxmlUtg,11721
 tooluniverse/data/core_tools.json,sha256=UB8aFpPZ5MVIju0OrfjQcJQedTPwCcVNqYNhPs0FmLU,3461
 tooluniverse/data/crossref_tools.json,sha256=oUXs3xHmNBq2ugsjpmQsY1JTRctD_NF6Qx6Yg3I82sk,3975
 tooluniverse/data/dailymed_tools.json,sha256=rWi5pV8EmITq0UJ-MzRQDVzKA2XVmR7v2ItFHCqqdSY,2288
@@ -127,7 +127,7 @@ tooluniverse/data/dataset_tools.json,sha256=BKf0HAQC9r499fL3S5s0aH0FyDC0V2vawo5u
 tooluniverse/data/dblp_tools.json,sha256=_D5zz8ChRJK7XE_YQ2TOrYRz5kFTiuSIkdtKswk7NUQ,4202
 tooluniverse/data/disease_target_score_tools.json,sha256=Z0-Uc_tZG83ToTIQvxe3cV5I2P6xh7eTq0aUpmGmxmo,23399
 tooluniverse/data/doaj_tools.json,sha256=P2A_UM7TdJyEO3gM-TH1dK1ehWKigoTWvxTD1pUTyCY,3915
-tooluniverse/data/drug_discovery_agents.json,sha256=QVktmkrTvSEZn8CifczXtiGRYNxZ6yITf5M253uJ6VE,18672
+tooluniverse/data/drug_discovery_agents.json,sha256=MXtIzEGAtx7LXmSXE55nwtF8uyjMK56Yyz5CNuhFwCQ,18392
 tooluniverse/data/efo_tools.json,sha256=qsEElKp1Z4EX09OD4r1ETcw6jT2t_w32SlDz-v8RyDc,564
 tooluniverse/data/embedding_tools.json,sha256=PKIinGNbM7O2sH_7qFoT1TWkksDtQlk-8sNZL3-_ajM,11393
 tooluniverse/data/enrichr_tools.json,sha256=zUUMFMphgyzX_0xJYK8KDjnFTp4_eoaUN5ZCSyh_7as,1162
@@ -146,7 +146,7 @@ tooluniverse/data/hal_tools.json,sha256=6-Zk7KKZQDY6w08ixZmNKba6U3Ky1aE1rfsEwuBm
 tooluniverse/data/hpa_tools.json,sha256=q96siPOkcEgKjO3VUvdJ3FF5wRr9WR_6rlZeIpHCwVk,17997
 tooluniverse/data/humanbase_tools.json,sha256=bhe5qVwkbFgq5aGlAGgYc4FiLX46YIAjJcqLXQZvhC4,2239
 tooluniverse/data/idmap_tools.json,sha256=ApTXD6RaR7ljIBtHYwHxnvvjuDL8Gz3E1vj6TxNV74s,2830
-tooluniverse/data/literature_search_tools.json,sha256=uOeAAcufsp77wDYqPoPVjYvlxGYYPYohL3eYry4-10I,11229
+tooluniverse/data/literature_search_tools.json,sha256=nguJ7BTHvkexJUb82lHsDRvPNJVAoBleCyG5CdMe68I,10664
 tooluniverse/data/markitdown_tools.json,sha256=RPYWiJnvnYgIzwuZh649F9ky1VxdHvQ3pQHb8cdN4Oc,1483
 tooluniverse/data/mcp_client_tools_example.json,sha256=5Ug57s25IjvMg29_vOpe4TsVsr0JQdtbwa0nhmj6Mh8,3435
 tooluniverse/data/mcpautoloadertool_defaults.json,sha256=I1Z6Xnno6BRX7u9Ec4LlXlz-384GWpaBafPVHsqTr_c,998
@@ -154,13 +154,13 @@ tooluniverse/data/medlineplus_tools.json,sha256=J1pE-5nH6LGuZP4lRmiOiec_pgr8Vtg1
 tooluniverse/data/medrxiv_tools.json,sha256=Ku4hts720cx9zR7E3oWzlP6nICOocERW174KfV4W5fM,2005
 tooluniverse/data/molecule_2d_tools.json,sha256=EvU07cSVLjl9pEareMvPyeuI9RtFn0dDxsnh8EbsFNI,3919
 tooluniverse/data/molecule_3d_tools.json,sha256=IVmxcynWJdMNDcRIWpS1YrlOQ3iHDSn1_dGZn3OAg-w,4614
-tooluniverse/data/monarch_tools.json,sha256=7u_Mx_kUZ7NckAIssG7ek96jyWH5vTCXVgRuCWfRggg,2750
+tooluniverse/data/monarch_tools.json,sha256=t-dfYKPmsbJr9_hUPlBYdmCtrI34fmxeYFMn6zQEwZ0,2720
 tooluniverse/data/odphp_tools.json,sha256=9EeqOA2eu54BoDMVqGZkBNcRiTSCFYrNNfW3BhopCsI,19570
 tooluniverse/data/openaire_tools.json,sha256=-epEkMGactUo3BNYQg7ZA4P4mrCQYyOjszkOsxeYPTA,2771
 tooluniverse/data/openalex_tools.json,sha256=v6vMCsg8QOIkssS0dHmiQQhyKf1PFUY-oC60Ss36dEo,3287
-tooluniverse/data/opentarget_tools.json,sha256=ZoUvHZzs9lTmZVuCgSR87AkiQaZUczOWsMBD84ReBwo,59067
+tooluniverse/data/opentarget_tools.json,sha256=VNegtPOncIRM-bEeKr6T7nSqXKMSY3d8hI3L_n6cw-E,58807
 tooluniverse/data/osf_preprints_tools.json,sha256=KO03NqtCSF3e5ttk0ioTzdSSltTwb6lFVHmWwqY0ewg,2341
-tooluniverse/data/output_summarization_tools.json,sha256=9BxZAkzexsDp8jGMKUHW3LIRThZjleRjYRvk0y-bxEs,3944
+tooluniverse/data/output_summarization_tools.json,sha256=_224cQuxV_PFAO8Jp1nBPAGc2G_2bO7_02iXQ2Kyi-U,3731
 tooluniverse/data/pmc_tools.json,sha256=01RsH8y6wF8CdX3hQO4qqTgyGDA7uoJ4bD8H4Ss5MIs,3645
 tooluniverse/data/ppi_tools.json,sha256=tWpPiPbBkvrPFXpn-W1DEXjtuMQrZIcwXrjER37vO0E,4541
 tooluniverse/data/protein_structure_3d_tools.json,sha256=J_BOw3lS8_mAkFxvFSQ7hsxRhtQwMwBdXYk_QNs2LOM,3924
@@ -171,7 +171,7 @@ tooluniverse/data/rcsb_pdb_tools.json,sha256=rhMg9GztmbBfJUYcvs4_9-BZIMsNZYljSYf
 tooluniverse/data/reactome_tools.json,sha256=h8Ubkllr4LMFc8UPUFQ8SZf_-wdWdh_NaHAKhx31Db0,557
 tooluniverse/data/semantic_scholar_tools.json,sha256=1X6zFX38Io7y2bCGUJiveN18Xi328exRCy6qdS2rpO8,1792
 tooluniverse/data/special_tools.json,sha256=nlhyXeqAnzH90GaWxnTptktAcPkZDj5wczzlsgy5bUo,1025
-tooluniverse/data/tool_composition_tools.json,sha256=HyDz7wxmOnu7VnpRqAA6S9BLUkKbxlFMkwwjc72EJz4,6118
+tooluniverse/data/tool_composition_tools.json,sha256=8zFAgAN_vUQ1H-7m0_1RaN_hrPI8Eh0OYptEOduYYco,6062
 tooluniverse/data/toolfinderkeyword_defaults.json,sha256=bydTVd0IUSDiilNQ6kZU-cn4lPqOfInfUAxhh8yMXqY,1050
 tooluniverse/data/txagent_client_tools.json,sha256=GdQk5H6uP_Uj9Ejz3nMdzNhZJV42t75aiRW8oWtkzRw,409
 tooluniverse/data/unified_guideline_tools.json,sha256=SzBhv6MCojmdtV6tGyZ5sUqskrr5zS_SQC5TXowVUAo,30688
@@ -183,19 +183,19 @@ tooluniverse/data/uspto_tools.json,sha256=yPIMBbwGNaAj0XbHBEGmcRDC8yeE-1OtyNceil
 tooluniverse/data/wikidata_sparql_tools.json,sha256=HPHrVszbqZdSGxxdq249N6gFSFe8XW-_pXIXdapfqAE,1830
 tooluniverse/data/xml_tools.json,sha256=C950u2om1lIOeUu2c5MnVWJccVGzjwDdjmelXqfcmz8,111763
 tooluniverse/data/zenodo_tools.json,sha256=iVjjuSHDlbDUCxROPqzbNASkvSGCVj1hXhq56Qd1aC0,2563
-tooluniverse/data/packages/bioinformatics_core_tools.json,sha256=D4RHSmDpcsfkwyjEsKMCIbR_YOa8HYZE_ll0v4h6umY,165313
+tooluniverse/data/packages/bioinformatics_core_tools.json,sha256=LA_zS-7Le41jsBkh7_sFpNEFwSOknQOKYhqoC8v2umk,165309
 tooluniverse/data/packages/categorized_tools.txt,sha256=NweDa6MbgS_4480RuNk-sw9LaxyA05VkzSgIRfvYkLI,4823
-tooluniverse/data/packages/cheminformatics_tools.json,sha256=FSE7aM-Infrc47YjlebEfwsFLQuT0f4rhBfVhPCxI9E,31125
+tooluniverse/data/packages/cheminformatics_tools.json,sha256=qZiJ4mYSQPe1oFMh_4zIbrwnqd7hs6nMULtRC-FIwOs,31117
 tooluniverse/data/packages/earth_sciences_tools.json,sha256=qqzphH4QLfX5wEszxI33AfRmo1HjVKmpFJ3P5nXKFsc,1927
-tooluniverse/data/packages/genomics_tools.json,sha256=xhf3HhTogqqoEnKQoAk4rsh9LgOYPBvuhmxvDTuZhrY,48822
+tooluniverse/data/packages/genomics_tools.json,sha256=K3H0WdXne2fm1zMBqE7Y_2eB98j0rN4oMJTZxODUT8Q,48817
 tooluniverse/data/packages/image_processing_tools.json,sha256=Kjpjwy2fAaTMM6mKEgRbtgE2-HUKCvJiqviIxgcTD5g,965
 tooluniverse/data/packages/machine_learning_tools.json,sha256=MAfLNwZy6xvBquiSrYAvUlAIAampkELd75WfjwqzTNw,42149
 tooluniverse/data/packages/neuroscience_tools.json,sha256=SzXmakL7GIldONBlV_kGMG_ov68lkVSY00Ux7Ggo4a0,1538
 tooluniverse/data/packages/original_tools.txt,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tooluniverse/data/packages/physics_astronomy_tools.json,sha256=n0ovkqOXhUcDBUPDGNKrCs3NbYJOcnOEADXCafgI4SE,1527
 tooluniverse/data/packages/scientific_computing_tools.json,sha256=7hwzeFkn_MYjfxat1spfaxryRplVDh1lfE3jj-jMiyU,28580
-tooluniverse/data/packages/single_cell_tools.json,sha256=tP-7wguF8zFXfJLUpSJtTgct10hrXVdpJCqEeYv0PtI,36349
-tooluniverse/data/packages/structural_biology_tools.json,sha256=EHwzSDKTphiRyEMD7MtuUhEQ2OEfsn3vn9UphALJ_1E,31979
+tooluniverse/data/packages/single_cell_tools.json,sha256=MaZXish9-5Zsbhzbj4sMTtUzLlogi-E1nAt_447SE_k,36347
+tooluniverse/data/packages/structural_biology_tools.json,sha256=z71yIPMKVoE1WUFtZxzH2pg6iHCyszPZmEsXQDM3iUQ,31978
 tooluniverse/data/packages/visualization_tools.json,sha256=SxRkpeqQj5gpouOkNirjG73cFom1_cICkwLc-jH7lV8,25457
 tooluniverse/remote/boltz/boltz_mcp_server.py,sha256=GKqtQp5CkI7RQKHIGBW3z81O8zSl3dG6vD4xmH3lz8w,2102
 tooluniverse/remote/depmap_24q2/depmap_24q2_mcp_tool.py,sha256=6G_8MZuohXrt-jMmt8jVEsHHIPgL1IP5vcJHp4Coeb4,18994
@@ -465,7 +465,6 @@ tooluniverse/tools/MedlinePlus_get_genetics_gene_by_name.py,sha256=6o4HPtrHF7cqc
 tooluniverse/tools/MedlinePlus_get_genetics_index.py,sha256=RSpDgVA7lQxIZaKvH0wY3INkOe79nX3sgKXv8XBcflw,1125
 tooluniverse/tools/MedlinePlus_search_topics_by_keyword.py,sha256=Oh7Gl-mSHw4-3EbvJ1LT2Nu3jWrCT2bViroSZuWQSjw,1568
 tooluniverse/tools/MethodologyRigorReviewer.py,sha256=VxW-uelP96-z-j_qFD6G7So1U02_gG25vlR3Ih758eI,1182
-tooluniverse/tools/MultiAgentLiteratureSearch.py,sha256=t-51jgdIcBOcOKUZd_iG6xwOlB5KryUSMYQCP--EveM,1574
 tooluniverse/tools/NICE_Clinical_Guidelines_Search.py,sha256=k7x-aYOJsSI3SUekSXs-Zg7IUQpvqceziN4dtSI2GPk,1419
 tooluniverse/tools/NICE_Guideline_Full_Text.py,sha256=C6OyHfJEurqSgvSAG4ReBSVMq76xzDwHmnPC_XHgap8,1240
 tooluniverse/tools/NoveltySignificanceReviewer.py,sha256=zN7RMKXRM2cnfOwMyo3BbeHKV-PScSOVPJufmqaOK9o,1463
@@ -589,7 +588,7 @@ tooluniverse/tools/WHO_Guidelines_Search.py,sha256=skaP8MvndBmB8bg9HM3mQjWpFTJFL
 tooluniverse/tools/Wikidata_SPARQL_query.py,sha256=7KoUwdza5R9uVOT6TzyU3oshRzUYDO91qqpwJA8PB_8,1426
 tooluniverse/tools/WritingPresentationReviewer.py,sha256=7OiJnRcSWjZSp1lJsM9wxBupdMAeHXNymYev-AWU-iI,1171
 tooluniverse/tools/Zenodo_search_records.py,sha256=PfoUaXvGUCifJqFvlkFei6t8CeiT5BHuiEO7d5WApUE,1638
-tooluniverse/tools/__init__.py,sha256=6LuLnVBWoQgr_nnNxxuFzXlA75YlQFALjE0DhPhmeN4,78677
+tooluniverse/tools/__init__.py,sha256=TjCVrrE0xDFTZGmXR_FL7_6KpXNLdjB9y9aI8cOd0Ng,78576
 tooluniverse/tools/_shared_client.py,sha256=USiz6n6TD5T42TRasjOvYqUvl8GnDIxzubfiv_U5obE,4839
 tooluniverse/tools/alphafold_get_annotations.py,sha256=QqykC55liO1JyPebtS_fnnAGaJ9niTgex6IL14JplIo,1401
 tooluniverse/tools/alphafold_get_prediction.py,sha256=7W9r_U6ZoZAnMKUBWWZwnaY4WVpMORJxkIdnCiXmBTo,1489
@@ -883,9 +882,9 @@ tooluniverse/tools/search_clinical_trials.py,sha256=skW3aPZ1gXfjKJz8WkxGpt93XlHp
 tooluniverse/tools/visualize_molecule_2d.py,sha256=yaaGErioVPG5qMi8nR6DbZbojJVCUc2mDiO7icBG60U,2462
 tooluniverse/tools/visualize_molecule_3d.py,sha256=0fFkjGz0hrNyRBiXRV_FY8yWXR47jZQXatXLxXwbrXw,2693
 tooluniverse/tools/visualize_protein_structure_3d.py,sha256=ifTkgPvtNtvJ9q8d7zmSqSnd32oFmRcKkoO8p1SdVUU,2358
-tooluniverse-1.0.8.dist-info/licenses/LICENSE,sha256=0P0qDClpVzrnQUe3QAu7V-alszSBa-6hVHXyn9Xe60k,11351
-tooluniverse-1.0.8.dist-info/METADATA,sha256=EhJLw1EG2362RivOT1wF66xR8tKSFV_6nudTz8paTNY,21125
-tooluniverse-1.0.8.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-tooluniverse-1.0.8.dist-info/entry_points.txt,sha256=IL3WSOgt9bAT8IWPMQSUYJmV_mma7a60E77oO0u3Jik,928
-tooluniverse-1.0.8.dist-info/top_level.txt,sha256=zZ8YeCJ5FAkEwdd_mxsFtSCQMBDgBdxrrmHo3RNBiWs,13
-tooluniverse-1.0.8.dist-info/RECORD,,
+tooluniverse-1.0.9.dist-info/licenses/LICENSE,sha256=0P0qDClpVzrnQUe3QAu7V-alszSBa-6hVHXyn9Xe60k,11351
+tooluniverse-1.0.9.dist-info/METADATA,sha256=O-jvVL_cYpObdnviT8DoBx4ciJ384Ry31TRPgRhoGA8,21159
+tooluniverse-1.0.9.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+tooluniverse-1.0.9.dist-info/entry_points.txt,sha256=SAdqP4tU4mMOtp1YWaOHTwnIHhnoiD1wmfKGlSfNSy0,647
+tooluniverse-1.0.9.dist-info/top_level.txt,sha256=zZ8YeCJ5FAkEwdd_mxsFtSCQMBDgBdxrrmHo3RNBiWs,13
+tooluniverse-1.0.9.dist-info/RECORD,,

{tooluniverse-1.0.8.dist-info → tooluniverse-1.0.9.dist-info}/entry_points.txt

@@ -1,13 +1,10 @@
 [console_scripts]
 generate-mcp-tools = tooluniverse.generate_mcp_tools:run_generate
-tooluniverse-agent-search = tooluniverse.web_tools.literature_search_ui.agent_search_app:main
 tooluniverse-doctor = tooluniverse.doctor:main
 tooluniverse-expert-feedback = tooluniverse.remote.expert_feedback.human_expert_mcp_tools:main
 tooluniverse-expert-feedback-web = tooluniverse.remote.expert_feedback.start_web_interface:main
 tooluniverse-mcp = tooluniverse.smcp_server:run_http_server
 tooluniverse-mcp-claude = tooluniverse.smcp_server:run_stdio_server
-tooluniverse-regular-search = tooluniverse.web_tools.literature_search_ui.regular_search_app:main
 tooluniverse-smcp = tooluniverse.smcp_server:run_smcp_server
 tooluniverse-smcp-server = tooluniverse.smcp_server:run_http_server
 tooluniverse-smcp-stdio = tooluniverse.smcp_server:run_stdio_server
-tooluniverse-wide-research = tooluniverse.web_tools.literature_search_ui.simple_app:main