tooluniverse 1.0.10__py3-none-any.whl → 1.0.11.1__py3-none-any.whl

tooluniverse/tools/InterPro_search_domains.py

@@ -0,0 +1,52 @@
+"""
+InterPro_search_domains
+
+Search InterPro database for protein domains and families by name or accession. Returns matching ...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def InterPro_search_domains(
+    query: str,
+    size: Optional[int] = 20,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> list[Any]:
+    """
+    Search InterPro database for protein domains and families by name or accession. Returns matching ...
+
+    Parameters
+    ----------
+    query : str
+        Domain name, accession, or search term (e.g., 'kinase', 'IPR000719')
+    size : int
+        Number of results to return (default: 20, max: 100)
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    list[Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "InterPro_search_domains",
+            "arguments": {"query": query, "size": size},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["InterPro_search_domains"]

tooluniverse/tools/JASPAR_get_transcription_factors.py

@@ -0,0 +1,52 @@
+"""
+JASPAR_get_transcription_factors
+
+Get transcription factor binding site matrices from JASPAR
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def JASPAR_get_transcription_factors(
+    collection: Optional[str] = "CORE",
+    limit: Optional[int] = 20,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Get transcription factor binding site matrices from JASPAR
+
+    Parameters
+    ----------
+    collection : str
+        JASPAR collection
+    limit : int
+        Number of results
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "JASPAR_get_transcription_factors",
+            "arguments": {"collection": collection, "limit": limit},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["JASPAR_get_transcription_factors"]

tooluniverse/tools/MPD_get_phenotype_data.py

@@ -0,0 +1,59 @@
+"""
+MPD_get_phenotype_data
+
+Get mouse phenotype data from Mouse Phenome Database for specific strains and phenotypes
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def MPD_get_phenotype_data(
+    strain: str,
+    phenotype_category: Optional[str] = "behavior",
+    limit: Optional[int] = 10,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Get mouse phenotype data from Mouse Phenome Database for specific strains and phenotypes
+
+    Parameters
+    ----------
+    strain : str
+        Mouse strain (e.g., C57BL/6J, BALB/c, DBA/2J)
+    phenotype_category : str
+        Phenotype category (behavior, physiology, morphology)
+    limit : int
+        Number of results to return
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "MPD_get_phenotype_data",
+            "arguments": {
+                "strain": strain,
+                "phenotype_category": phenotype_category,
+                "limit": limit,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["MPD_get_phenotype_data"]

tooluniverse/tools/PRIDE_search_proteomics.py

@@ -0,0 +1,52 @@
+"""
+PRIDE_search_proteomics
+
+Search PRIDE proteomics database for experiments
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def PRIDE_search_proteomics(
+    query: str,
+    page_size: Optional[int] = 20,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Search PRIDE proteomics database for experiments
+
+    Parameters
+    ----------
+    query : str
+        Search query
+    page_size : int
+        Results per page
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "PRIDE_search_proteomics",
+            "arguments": {"query": query, "page_size": page_size},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["PRIDE_search_proteomics"]

tooluniverse/tools/PackageAnalyzer.py

@@ -0,0 +1,55 @@
+"""
+PackageAnalyzer
+
+Analyzes package candidates and recommends the best options based on quality metrics and suitability
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def PackageAnalyzer(
+    tool_description: str,
+    package_candidates: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Analyzes package candidates and recommends the best options based on quality metrics and suitability
+
+    Parameters
+    ----------
+    tool_description : str
+        Description of the tool being generated
+    package_candidates : str
+        JSON string containing package candidates with their metadata (from PyPI, sea...
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "PackageAnalyzer",
+            "arguments": {
+                "tool_description": tool_description,
+                "package_candidates": package_candidates,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["PackageAnalyzer"]

tooluniverse/tools/Paleobiology_get_fossils.py

@@ -0,0 +1,52 @@
+"""
+Paleobiology_get_fossils
+
+Get fossil records from Paleobiology Database
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def Paleobiology_get_fossils(
+    taxon: str,
+    limit: Optional[int] = 20,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Get fossil records from Paleobiology Database
+
+    Parameters
+    ----------
+    taxon : str
+        Taxon name
+    limit : int
+        Number of results
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "Paleobiology_get_fossils",
+            "arguments": {"taxon": taxon, "limit": limit},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["Paleobiology_get_fossils"]

tooluniverse/tools/PyPIPackageInspector.py

@@ -0,0 +1,59 @@
+"""
+PyPIPackageInspector
+
+Extracts comprehensive package information from PyPI and GitHub for quality evaluation. Provides ...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def PyPIPackageInspector(
+    package_name: str,
+    include_github: Optional[bool] = True,
+    include_downloads: Optional[bool] = True,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Extracts comprehensive package information from PyPI and GitHub for quality evaluation. Provides ...
+
+    Parameters
+    ----------
+    package_name : str
+        Name of the Python package to inspect on PyPI (e.g., 'requests', 'numpy', 'pa...
+    include_github : bool
+        Whether to fetch GitHub repository statistics (stars, forks, issues, last pus...
+    include_downloads : bool
+        Whether to fetch download statistics from pypistats.org (downloads per day/we...
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "PyPIPackageInspector",
+            "arguments": {
+                "package_name": package_name,
+                "include_github": include_github,
+                "include_downloads": include_downloads,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["PyPIPackageInspector"]

tooluniverse/tools/ReMap_get_transcription_factor_binding.py

@@ -0,0 +1,59 @@
+"""
+ReMap_get_transcription_factor_binding
+
+Get transcription factor binding sites from ReMap database for specific genes and cell types
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ReMap_get_transcription_factor_binding(
+    gene_name: str,
+    cell_type: Optional[str] = "HepG2",
+    limit: Optional[int] = 10,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Get transcription factor binding sites from ReMap database for specific genes and cell types
+
+    Parameters
+    ----------
+    gene_name : str
+        Gene symbol (e.g., BRCA1, TP53, MYC)
+    cell_type : str
+        Cell type (e.g., HepG2, K562, MCF-7)
+    limit : int
+        Number of results to return
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "ReMap_get_transcription_factor_binding",
+            "arguments": {
+                "gene_name": gene_name,
+                "cell_type": cell_type,
+                "limit": limit,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ReMap_get_transcription_factor_binding"]

tooluniverse/tools/ReferenceInfoAnalyzer.py

@@ -0,0 +1,55 @@
+"""
+ReferenceInfoAnalyzer
+
+Analyzes and curates reference information to provide high-quality context for tool generation
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ReferenceInfoAnalyzer(
+    tool_description: str,
+    raw_reference_info: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Analyzes and curates reference information to provide high-quality context for tool generation
+
+    Parameters
+    ----------
+    tool_description : str
+        Description of the tool being generated
+    raw_reference_info : str
+        JSON string containing raw reference information from web search and package ...
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "ReferenceInfoAnalyzer",
+            "arguments": {
+                "tool_description": tool_description,
+                "raw_reference_info": raw_reference_info,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ReferenceInfoAnalyzer"]

tooluniverse/tools/RegulomeDB_query_variant.py

@@ -0,0 +1,46 @@
+"""
+RegulomeDB_query_variant
+
+Query RegulomeDB for regulatory variant annotations using rsID
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def RegulomeDB_query_variant(
+    rsid: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Query RegulomeDB for regulatory variant annotations using rsID
+
+    Parameters
+    ----------
+    rsid : str
+        dbSNP rsID (e.g., rs123456)
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {"name": "RegulomeDB_query_variant", "arguments": {"rsid": rsid}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["RegulomeDB_query_variant"]

tooluniverse/tools/SCREEN_get_regulatory_elements.py

@@ -0,0 +1,59 @@
+"""
+SCREEN_get_regulatory_elements
+
+Get candidate cis-regulatory elements (cCREs) from SCREEN database for specific genomic regions
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def SCREEN_get_regulatory_elements(
+    gene_name: str,
+    element_type: Optional[str] = "enhancer",
+    limit: Optional[int] = 10,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Get candidate cis-regulatory elements (cCREs) from SCREEN database for specific genomic regions
+
+    Parameters
+    ----------
+    gene_name : str
+        Gene symbol to search for regulatory elements (e.g., BRCA1, TP53)
+    element_type : str
+        Type of regulatory element (promoter, enhancer, insulator)
+    limit : int
+        Number of results to return
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "SCREEN_get_regulatory_elements",
+            "arguments": {
+                "gene_name": gene_name,
+                "element_type": element_type,
+                "limit": limit,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["SCREEN_get_regulatory_elements"]

tooluniverse/tools/{ArgumentDescriptionOptimizer.py → TestResultsAnalyzer.py}

@@ -1,30 +1,30 @@
 """
-ArgumentDescriptionOptimizer
+TestResultsAnalyzer
 
-Optimizes the descriptions of tool arguments/parameters based on test case results and actual usa...
+Analyzes test execution results and extracts key issues for targeted optimization
 """
 
 from typing import Any, Optional, Callable
 from ._shared_client import get_shared_client
 
 
-def ArgumentDescriptionOptimizer(
-    parameter_schema: str,
+def TestResultsAnalyzer(
     test_results: str,
+    tool_implementation: str,
     *,
     stream_callback: Optional[Callable[[str], None]] = None,
     use_cache: bool = False,
     validate: bool = True,
-) -> Any:
+) -> dict[str, Any]:
     """
-    Optimizes the descriptions of tool arguments/parameters based on test case results and actual usa...
+    Analyzes test execution results and extracts key issues for targeted optimization
 
     Parameters
     ----------
-    parameter_schema : str
-        JSON string of the original parameter schema with properties and descriptions.
     test_results : str
-        A JSON string containing test case input/output pairs showing parameter usage.
+        JSON string containing test execution results with pass/fail status, error me...
+    tool_implementation : str
+        Current tool implementation code for context
     stream_callback : Callable, optional
         Callback for streaming output
     use_cache : bool, default False
@@ -34,16 +34,16 @@ def ArgumentDescriptionOptimizer(
 
     Returns
     -------
-    Any
+    dict[str, Any]
     """
     # Handle mutable defaults to avoid B006 linting error
 
     return get_shared_client().run_one_function(
         {
-            "name": "ArgumentDescriptionOptimizer",
+            "name": "TestResultsAnalyzer",
             "arguments": {
-                "parameter_schema": parameter_schema,
                 "test_results": test_results,
+                "tool_implementation": tool_implementation,
             },
         },
         stream_callback=stream_callback,
@@ -52,4 +52,4 @@ def ArgumentDescriptionOptimizer(
     )
 
 
-__all__ = ["ArgumentDescriptionOptimizer"]
+__all__ = ["TestResultsAnalyzer"]