tooluniverse 1.0.9.1__py3-none-any.whl → 1.0.11__py3-none-any.whl

tooluniverse/tools/ClinVar_search_variants.py

@@ -1,30 +1,36 @@
 """
-ClinVar_search_variants
+clinvar_search_variants
 
-Search ClinVar via NCBI E-utilities (esearch→esummary) and return concise variant records for a q...
+Search for variants in ClinVar database by gene name, condition, or variant ID. Returns variant i...
 """
 
 from typing import Any, Optional, Callable
 from ._shared_client import get_shared_client
 
 
-def ClinVar_search_variants(
-    query: str,
-    retmax: Optional[int] = 5,
+def clinvar_search_variants(
+    gene: Optional[str] = None,
+    condition: Optional[str] = None,
+    variant_id: Optional[str] = None,
+    max_results: Optional[int] = 20,
     *,
     stream_callback: Optional[Callable[[str], None]] = None,
     use_cache: bool = False,
     validate: bool = True,
-) -> list[Any]:
+) -> dict[str, Any]:
     """
-    Search ClinVar via NCBI E-utilities (esearch→esummary) and return concise variant records for a q...
+    Search for variants in ClinVar database by gene name, condition, or variant ID. Returns variant i...
 
     Parameters
     ----------
-    query : str
-        ClinVar search term (e.g., BRCA1).
-    retmax : int
-        Max records.
+    gene : str
+        Gene name or symbol (e.g., 'BRCA1', 'BRCA2')
+    condition : str
+        Disease or condition name (e.g., 'breast cancer', 'diabetes')
+    variant_id : str
+        ClinVar variant ID (e.g., '12345')
+    max_results : int
+        Maximum number of results to return
     stream_callback : Callable, optional
         Callback for streaming output
     use_cache : bool, default False
@@ -34,14 +40,19 @@ def ClinVar_search_variants(
 
     Returns
     -------
-    list[Any]
+    dict[str, Any]
     """
     # Handle mutable defaults to avoid B006 linting error
 
     return get_shared_client().run_one_function(
         {
-            "name": "ClinVar_search_variants",
-            "arguments": {"query": query, "retmax": retmax},
+            "name": "clinvar_search_variants",
+            "arguments": {
+                "gene": gene,
+                "condition": condition,
+                "variant_id": variant_id,
+                "max_results": max_results,
+            },
         },
         stream_callback=stream_callback,
         use_cache=use_cache,
@@ -49,4 +60,4 @@ def ClinVar_search_variants(
     )
 
 
-__all__ = ["ClinVar_search_variants"]
+__all__ = ["clinvar_search_variants"]

tooluniverse/tools/CodeQualityAnalyzer.py

@@ -14,12 +14,12 @@ def CodeQualityAnalyzer(
     tool_parameters: str,
     implementation_code: str,
     test_cases: str,
-    test_execution_results: Optional[str] = None,
+    test_execution_results: str,
     *,
     stream_callback: Optional[Callable[[str], None]] = None,
     use_cache: bool = False,
     validate: bool = True,
-) -> Any:
+) -> dict[str, Any]:
     """
     Analyzes code quality from multiple dimensions including algorithmic correctness, functional impl...
 
@@ -46,7 +46,7 @@ def CodeQualityAnalyzer(
 
     Returns
     -------
-    Any
+    dict[str, Any]
     """
     # Handle mutable defaults to avoid B006 linting error
 

tooluniverse/tools/EMDB_get_structure.py

@@ -0,0 +1,46 @@
+"""
+EMDB_get_structure
+
+Get electron microscopy structure data from EMDB
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def EMDB_get_structure(
+    emdb_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Get electron microscopy structure data from EMDB
+
+    Parameters
+    ----------
+    emdb_id : str
+        EMDB structure ID (e.g., EMD-1234)
+    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": "EMDB_get_structure", "arguments": {"emdb_id": emdb_id}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["EMDB_get_structure"]

tooluniverse/tools/GtoPdb_get_targets.py

@@ -0,0 +1,52 @@
+"""
+GtoPdb_get_targets
+
+Get pharmacological targets from Guide to Pharmacology database
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def GtoPdb_get_targets(
+    target_type: Optional[str] = "protein",
+    limit: Optional[int] = 20,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> list[Any]:
+    """
+    Get pharmacological targets from Guide to Pharmacology database
+
+    Parameters
+    ----------
+    target_type : str
+        Target type
+    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
+    -------
+    list[Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "GtoPdb_get_targets",
+            "arguments": {"target_type": target_type, "limit": limit},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["GtoPdb_get_targets"]

tooluniverse/tools/InterPro_get_domain_details.py

@@ -0,0 +1,46 @@
+"""
+InterPro_get_domain_details
+
+Get detailed information about a specific InterPro domain entry including description, hierarchy,...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def InterPro_get_domain_details(
+    accession: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Get detailed information about a specific InterPro domain entry including description, hierarchy,...
+
+    Parameters
+    ----------
+    accession : str
+        InterPro accession ID (e.g., IPR000719, IPR000719)
+    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": "InterPro_get_domain_details", "arguments": {"accession": accession}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["InterPro_get_domain_details"]

tooluniverse/tools/InterPro_get_protein_domains.py

@@ -0,0 +1,49 @@
+"""
+InterPro_get_protein_domains
+
+Get protein domain annotations from InterPro database using UniProt protein ID. Returns domain fa...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def InterPro_get_protein_domains(
+    protein_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> list[Any]:
+    """
+    Get protein domain annotations from InterPro database using UniProt protein ID. Returns domain fa...
+
+    Parameters
+    ----------
+    protein_id : str
+        UniProt protein ID (e.g., P05067, Q9Y6K9)
+    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_get_protein_domains",
+            "arguments": {"protein_id": protein_id},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["InterPro_get_protein_domains"]

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"]