tooluniverse 1.0.6__py3-none-any.whl → 1.0.8__py3-none-any.whl

tooluniverse/tools/get_scrublet_info.py

@@ -0,0 +1,49 @@
+"""
+get_scrublet_info
+
+Get comprehensive information about Scrublet – single-cell doublet detection
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_scrublet_info(
+    include_examples: bool,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get comprehensive information about Scrublet – single-cell doublet detection
+
+    Parameters
+    ----------
+    include_examples : bool
+        Whether to include usage examples and quick start guide
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "get_scrublet_info",
+            "arguments": {"include_examples": include_examples},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_scrublet_info"]

tooluniverse/tools/get_scvelo_info.py

@@ -0,0 +1,49 @@
+"""
+get_scvelo_info
+
+Get comprehensive information about scVelo – RNA velocity analysis in single cells
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_scvelo_info(
+    include_examples: bool,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get comprehensive information about scVelo – RNA velocity analysis in single cells
+
+    Parameters
+    ----------
+    include_examples : bool
+        Whether to include usage examples and quick start guide
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "get_scvelo_info",
+            "arguments": {"include_examples": include_examples},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_scvelo_info"]

tooluniverse/tools/get_scvi_tools_info.py

@@ -0,0 +1,44 @@
+"""
+get_scvi_tools_info
+
+Get information about the scvi-tools package. Deep probabilistic analysis of single-cell omics data
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_scvi_tools_info(
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get information about the scvi-tools package. Deep probabilistic analysis of single-cell omics data
+
+    Parameters
+    ----------
+    No parameters
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {"name": "get_scvi_tools_info", "arguments": {}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_scvi_tools_info"]

tooluniverse/tools/get_seaborn_info.py

@@ -0,0 +1,49 @@
+"""
+get_seaborn_info
+
+Get comprehensive information about Seaborn – statistical data visualization
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_seaborn_info(
+    include_examples: bool,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get comprehensive information about Seaborn – statistical data visualization
+
+    Parameters
+    ----------
+    include_examples : bool
+        Whether to include usage examples and quick start guide
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "get_seaborn_info",
+            "arguments": {"include_examples": include_examples},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_seaborn_info"]

tooluniverse/tools/get_sequence_by_pdb_id.py

@@ -0,0 +1,46 @@
+"""
+get_sequence_by_pdb_id
+
+Retrieve amino acid or nucleotide sequence of polymer entities for a given PDB structure.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_sequence_by_pdb_id(
+    pdb_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Retrieve amino acid or nucleotide sequence of polymer entities for a given PDB structure.
+
+    Parameters
+    ----------
+    pdb_id : str
+        4-character RCSB PDB ID
+    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": "get_sequence_by_pdb_id", "arguments": {"pdb_id": pdb_id}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_sequence_by_pdb_id"]

tooluniverse/tools/get_sequence_lengths_by_pdb_id.py

@@ -0,0 +1,46 @@
+"""
+get_sequence_lengths_by_pdb_id
+
+Retrieve the sequence lengths of polymer entities for a given PDB structure.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_sequence_lengths_by_pdb_id(
+    pdb_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Retrieve the sequence lengths of polymer entities for a given PDB structure.
+
+    Parameters
+    ----------
+    pdb_id : str
+        4-character RCSB PDB ID
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {"name": "get_sequence_lengths_by_pdb_id", "arguments": {"pdb_id": pdb_id}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_sequence_lengths_by_pdb_id"]

tooluniverse/tools/get_sequence_positional_features_by_instance_id.py

@@ -0,0 +1,49 @@
+"""
+get_sequence_positional_features_by_instance_id
+
+Retrieve sequence positional features (e.g., binding sites, motifs) for a polymer entity instance.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_sequence_positional_features_by_instance_id(
+    instance_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Retrieve sequence positional features (e.g., binding sites, motifs) for a polymer entity instance.
+
+    Parameters
+    ----------
+    instance_id : str
+        Polymer entity instance ID like '1NDO.A'
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "get_sequence_positional_features_by_instance_id",
+            "arguments": {"instance_id": instance_id},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_sequence_positional_features_by_instance_id"]

tooluniverse/tools/get_skopt_info.py

@@ -0,0 +1,44 @@
+"""
+get_skopt_info
+
+Get information about the skopt package. Scikit-Optimize: sequential model-based optimization
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_skopt_info(
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get information about the skopt package. Scikit-Optimize: sequential model-based optimization
+
+    Parameters
+    ----------
+    No parameters
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {"name": "get_skopt_info", "arguments": {}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_skopt_info"]

tooluniverse/tools/get_souporcell_info.py

@@ -0,0 +1,46 @@
+"""
+get_souporcell_info
+
+Get comprehensive information about souporcell – scRNA-seq genotype clustering
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_souporcell_info(
+    info_type: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get comprehensive information about souporcell – scRNA-seq genotype clustering
+
+    Parameters
+    ----------
+    info_type : str
+        Type of information to retrieve about souporcell
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {"name": "get_souporcell_info", "arguments": {"info_type": info_type}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_souporcell_info"]

tooluniverse/tools/get_source_organism_by_pdb_id.py

@@ -0,0 +1,46 @@
+"""
+get_source_organism_by_pdb_id
+
+Retrieve the scientific name of the source organism for a given PDB structure.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_source_organism_by_pdb_id(
+    pdb_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Retrieve the scientific name of the source organism for a given PDB structure.
+
+    Parameters
+    ----------
+    pdb_id : str
+        4-character RCSB PDB ID of the structure
+    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": "get_source_organism_by_pdb_id", "arguments": {"pdb_id": pdb_id}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_source_organism_by_pdb_id"]

tooluniverse/tools/get_space_group_by_pdb_id.py

@@ -0,0 +1,46 @@
+"""
+get_space_group_by_pdb_id
+
+Get the crystallographic space group of the structure.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_space_group_by_pdb_id(
+    pdb_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get the crystallographic space group of the structure.
+
+    Parameters
+    ----------
+    pdb_id : str
+        4-character RCSB PDB ID
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {"name": "get_space_group_by_pdb_id", "arguments": {"pdb_id": pdb_id}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_space_group_by_pdb_id"]

tooluniverse/tools/get_statsmodels_info.py

@@ -0,0 +1,49 @@
+"""
+get_statsmodels_info
+
+Get comprehensive information about statsmodels – statistical modeling and econometrics
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_statsmodels_info(
+    include_examples: bool,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get comprehensive information about statsmodels – statistical modeling and econometrics
+
+    Parameters
+    ----------
+    include_examples : bool
+        Whether to include usage examples and quick start guide
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "get_statsmodels_info",
+            "arguments": {"include_examples": include_examples},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_statsmodels_info"]

tooluniverse/tools/get_structure_determination_software_by_pdb_id.py

@@ -0,0 +1,49 @@
+"""
+get_structure_determination_software_by_pdb_id
+
+Retrieve names of software used during structure determination.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_structure_determination_software_by_pdb_id(
+    pdb_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Retrieve names of software used during structure determination.
+
+    Parameters
+    ----------
+    pdb_id : str
+        RCSB PDB entry ID
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "get_structure_determination_software_by_pdb_id",
+            "arguments": {"pdb_id": pdb_id},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_structure_determination_software_by_pdb_id"]

tooluniverse/tools/get_structure_title_by_pdb_id.py

@@ -0,0 +1,46 @@
+"""
+get_structure_title_by_pdb_id
+
+Retrieve the structure title for a given PDB entry.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def get_structure_title_by_pdb_id(
+    pdb_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Retrieve the structure title for a given PDB entry.
+
+    Parameters
+    ----------
+    pdb_id : str
+        4-character PDB ID
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {"name": "get_structure_title_by_pdb_id", "arguments": {"pdb_id": pdb_id}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["get_structure_title_by_pdb_id"]