Update docstrings

py4cytoscape/annotations.py

@@ -137,7 +137,7 @@ def add_annotation_bounded_text(text=None, x_pos=None, y_pos=None, font_size=Non
         border_color (str): hexadecimal color; default is #000000 (black)
         border_opacity (int): Integer between 0 and 100; default is 100
         height (int): Height of bounding shape; default is based on text height
-        width (int) Width of bounding shape; default is based on text length
+        width (int): Width of bounding shape; default is based on text length
         name (str): Name of annotation object; default is "Text"
         canvas (str): Canvas to display annotation, i.e., foreground (default) or background
         z_order (int): Arrangement order specified by number (larger values are in front of smaller values); default is 0
@@ -221,7 +221,7 @@ def add_annotation_image(url=None, x_pos=None, y_pos=None, angle=None, opacity=N
         border_color (str): hexadecimal color; default is #000000 (black)
         border_opacity (int): Integer between 0 and 100; default is 100
         height (int): Height of bounding shape; default is based on text height
-        width (int) Width of bounding shape; default is based on text length
+        width (int): Width of bounding shape; default is based on text length
         name (str): Name of annotation object; default is "Text"
         canvas (str): Canvas to display annotation, i.e., foreground (default) or background
         z_order (int): Arrangement order specified by number (larger values are in front of smaller values); default is 0
@@ -311,7 +311,7 @@ def add_annotation_shape(type=None, custom_shape=None, x_pos=None, y_pos=None, a
         border_color (str): hexadecimal color; default is #000000 (black)
         border_opacity (int): Integer between 0 and 100; default is 100
         height (int): Height of bounding shape; default is based on text height
-        width (int) Width of bounding shape; default is based on text length
+        width (int): Width of bounding shape; default is based on text length
         name (str): Name of annotation object; default is "Text"
         canvas (str): Canvas to display annotation, i.e., foreground (default) or background
         z_order (int): Arrangement order specified by number (larger values are in front of smaller values); default is 0
@@ -612,7 +612,7 @@ def update_annotation_bounded_text(text=None, annotation_name=None, x_pos=None,
         border_color (str): hexadecimal color; default is #000000 (black)
         border_opacity (int): Integer between 0 and 100; default is 100
         height (int): Height of bounding shape; default is based on text height
-        width (int) Width of bounding shape; default is based on text length
+        width (int): Width of bounding shape; default is based on text length
         name (str): Name of annotation object; default is "Text"
         canvas (str): Canvas to display annotation, i.e., foreground (default) or background
         z_order (int): Arrangement order specified by number (larger values are in front of smaller values); default is 0
@@ -702,7 +702,7 @@ def update_annotation_shape(type=None, custom_shape=None, annotation_name=None,
         border_color (str): hexadecimal color; default is #000000 (black)
         border_opacity (int): Integer between 0 and 100; default is 100
         height (int): Height of bounding shape; default is based on text height
-        width (int) Width of bounding shape; default is based on text length
+        width (int): Width of bounding shape; default is based on text length
         name (str): Name of annotation object; default is "Text"
         canvas (str): Canvas to display annotation, i.e., foreground (default) or background
         z_order (int): Arrangement order specified by number (larger values are in front of smaller values); default is 0
@@ -783,7 +783,7 @@ def update_annotation_image(url=None, annotation_name=None, x_pos=None, y_pos=No
         border_color (str): hexadecimal color; default is #000000 (black)
         border_opacity (int): Integer between 0 and 100; default is 100
         height (int): Height of bounding shape; default is based on text height
-        width (int) Width of bounding shape; default is based on text length
+        width (int): Width of bounding shape; default is based on text length
         name (str): Name of annotation object; default is "Text"
         canvas (str): Canvas to display annotation, i.e., foreground (default) or background
         z_order (int): Arrangement order specified by number (larger values are in front of smaller values); default is 0

py4cytoscape/commands.py

@@ -375,7 +375,7 @@ def commands_post(cmd, base_url=DEFAULT_BASE_URL):
     query URL, executes a POST request, and parses the result content into a dict object.
 
     Args:
-        cmd_string (str): command
+        cmd (str): Command to be executed in Cytoscape.
         base_url (str): Ignore unless you need to specify a custom domain,
             port or version to connect to the CyREST API. Default is http://127.0.0.1:1234
             and the latest version of the CyREST API supported by this version of py4cytoscape.
@@ -556,6 +556,8 @@ def command_run_file(file, args=None, base_url=DEFAULT_BASE_URL):
     Cytoscape commands, one per line. Arguments to the script are provided by the args argument
 
     Args:
+        file (str): Path to the file containing Cytoscape commands, one per line.
+        args (list or None): Provide arguments to the script. Default is None.
         base_url (str): Ignore unless you need to specify a custom domain,
             port or version to connect to the CyREST API. Default is http://127.0.0.1:1234
             and the latest version of the CyREST API supported by this version of py4cytoscape.

py4cytoscape/cy_ndex.py

@@ -183,7 +183,6 @@ def get_network_ndex_id(network=None, base_url=DEFAULT_BASE_URL):
     Args:
         network (SUID or str or None): Name or SUID of a network. Default is the
             "current" network active in Cytoscape.
-        metadata (dict): A list of structured information describing the network
         base_url (str): Ignore unless you need to specify a custom domain,
             port or version to connect to the CyREST API. Default is http://localhost:1234
             and the latest version of the CyREST API supported by this version of py4cytoscape.

py4cytoscape/filters.py

@@ -95,7 +95,7 @@ def create_column_filter(filter_name, column, criterion, predicate, caseSensitiv
     Args:
         filter_name (str): Name for new filter.
         column (str): Table column to base filter upon.
-        criterion (list, bool, str, int or float): For boolean columns: True or False. For string columns: a
+        criterion (list or bool or str or int or float): For boolean columns: True or False. For string columns: a
             string value, e.g., "hello". If the predicate is REGEX then this can be a regular expression as
             accepted by the Java Pattern class (https://docs.oracle.com/javase/7/docs/api/java/util/regex/Pattern.html).
             For numeric columns: If the predicate is BETWEEN or IS_NOT_BETWEEN then this is a two-element list of
@@ -199,7 +199,7 @@ def create_degree_filter(filter_name, criterion, predicate='BETWEEN', edge_type=
         filter_name (str): Name for new filter.
         criterion (list): A two-element vector of numbers, example: [1,5].
         predicate (str):  BETWEEN (default) or IS_NOT_BETWEEN
-        edgeType (str): Type of edges to consider in degree count: ANY (default), UNDIRECTED, INCOMING, OUTGOING, DIRECTED
+        edge_type (str): Type of edges to consider in degree count: ANY (default), UNDIRECTED, INCOMING, OUTGOING, DIRECTED
         hide (bool): Whether to hide filtered out nodes and edges. Default is FALSE.
             Ignored if all nodes or edges are filtered out. This is an alternative to filtering for node and edge selection.
         network (SUID or str or None): Name or SUID of the network. Default is the "current" network active in Cytoscape.

py4cytoscape/groups.py

@@ -266,7 +266,7 @@ def get_group_info(group, network=None, base_url=DEFAULT_BASE_URL):
     """Retrieve information about a group by name or identifier.
 
     Args:
-        group_name (str or SUID): Group name or SUID.
+        group (str or SUID): Group name or SUID.
         network (SUID or str or None): Name or SUID of a network. Default is the
             "current" network active in Cytoscape.
         base_url (str): Ignore unless you need to specify a custom domain,
@@ -406,7 +406,7 @@ def delete_group(groups=None, groups_by_col='SUID', network=None, base_url=DEFAU
     """Delete one or more groups, while leaving member nodes intact.
 
     Args:
-        groups (list or str or None) List of group SUIDs, names, other column values or keywords: all, selected,
+        groups (list or str or None): List of group SUIDs, names, other column values or keywords: all, selected,
             unselected. Default is the currently selected group.
         groups_by_col (str): name of node table column corresponding to provided groups list. Default is 'SUID'.
         network (SUID or str or None): Name or SUID of a network. Default is the

py4cytoscape/network_views.py

@@ -277,7 +277,7 @@ def export_image(filename=None, type='PNG', resolution=None, units=None, height=
         type (str): Type of image to export, e.g., PNG (default), JPEG, PDF, SVG, PS (PostScript).
         resolution (int): The resolution of the exported image, in DPI. Valid only for bitmap formats, when the selected
             width and height 'units' is inches. The possible values are: 72 (default), 100, 150, 300, 600. [DEPRECATED as of Cytoscape v3.10]
-        units (str) The units for the 'width' and 'height' values. Valid only for bitmap formats, such as PNG and JPEG.
+        units (str): The units for the 'width' and 'height' values. Valid only for bitmap formats, such as PNG and JPEG.
             The possible values are: pixels (default), inches. [DEPRECATED as of Cytoscape v3.10]
         height (float): The height of the exported image. Valid only for bitmap formats, such as PNG and JPEG. [DEPRECATED as of Cytoscape v3.10]
         width (float): The width of the exported image. Valid only for bitmap formats, such as PNG and JPEG. [DEPRECATED as of Cytoscape v3.10]
@@ -448,8 +448,6 @@ def toggle_graphics_details(base_url=DEFAULT_BASE_URL):
     See :meth:`cytoscape_memory_status`.
 
     Args:
-        network (str or SUID or None): Name or SUID of the network or view. Default is the "current" network active in Cytoscape.
-            If a network view SUID is provided, then it is validated and returned.
         base_url (str): Ignore unless you need to specify a custom domain,
             port or version to connect to the CyREST API. Default is http://127.0.0.1:1234
             and the latest version of the CyREST API supported by this version of py4cytoscape.

py4cytoscape/networks.py

@@ -215,7 +215,7 @@ def get_network_suid(title=None, base_url=DEFAULT_BASE_URL):
     """Get the SUID of a network.
 
     Args:
-        suid (SUID or str or None): Name of the network; default is "current" network. If an SUID is
+        title (SUID or str or None): Name of the network; default is "current" network. If an SUID is
             provided, then it is validated and returned.
         base_url (str): Ignore unless you need to specify a custom domain,
             port or version to connect to the CyREST API. Default is http://127.0.0.1:1234
@@ -608,7 +608,7 @@ def add_cy_edges(source_target_list, edge_type='interacts with', directed=False,
 
     Args:
         source_target_list (list or list of lists): Source and target node pairs
-        edgeType (str): The type of interaction. Default is 'interacts with'.
+        edge_type (str): The type of interaction. Default is 'interacts with'.
         directed (bool): Indicates whether interactions are directed. Default is ``FALSE``.
         network (SUID or str or None): Name or SUID of a network or view. Default is the
             "current" network active in Cytoscape.
@@ -991,7 +991,7 @@ def create_network_from_networkx(netx, title='From networkx', collection='My Net
     """Create a Cytoscape network from a NetworkX graph.
 
     Args:
-        netx (Graph, DiGraph, MultiGraph or MultiDiGraph): networkx object
+        netx (Graph or DiGraph or MultiGraph or MultiDiGraph): networkx object
         title (str): network name
         collection (str): network collection name
         base_url (str): Ignore unless you need to specify a custom domain,

py4cytoscape/notebook.py

@@ -45,7 +45,7 @@ def notebook_export_show_image(filename='image', type='PNG', resolution=None, un
         type (str): Type of image to export, e.g., PNG (default), JPEG, PDF, SVG, PS (PostScript).
         resolution (int): The resolution of the exported image, in DPI. Valid only for bitmap formats, when the selected
             width and height 'units' is inches. The possible values are: 72 (default), 100, 150, 300, 600.
-        units (str) The units for the 'width' and 'height' values. Valid only for bitmap formats, such as PNG and JPEG.
+        units (str): The units for the 'width' and 'height' values. Valid only for bitmap formats, such as PNG and JPEG.
             The possible values are: pixels (default), inches.
         height (float): The height of the exported image. Valid only for bitmap formats, such as PNG and JPEG.
         width (float): The width of the exported image. Valid only for bitmap formats, such as PNG and JPEG.

py4cytoscape/sandbox.py

@@ -366,6 +366,7 @@ def sandbox_get_from(source_file, dest_file=None, overwrite=True, sandbox_name =
     Args:
         source_file (str): Name of file to read (as absolute path or sandbox-relative path)
         dest_file (str): Name of file in the Python workflow's file system ... if None, use file name in source_file
+        overwrite (bool): False causes error if dest_file already exists; True replaces it if it exists
         sandbox_name (str): Name of sandbox containing file. None means "the current sandbox".
         base_url (str): Ignore unless you need to specify a custom domain,
             port or version to connect to the CyREST API. Default is http://localhost:1234

py4cytoscape/style_auto_mappings.py

@@ -652,6 +652,12 @@ def palette_color_brewer_d_RdYlGn(reverse=False):
 def scheme_d_shapes(base_url=DEFAULT_BASE_URL):
     """Generate list of node shapes of a given size
 
+    Args:
+        base_url (str): Ignore unless you need to specify a custom domain, port or 
+        version to connect to the CyREST API. Default is http://localhost:1234 
+        and the latest version of the CyREST API supported by this version of 
+        py4cytoscape.
+
     Returns:
         lambda: generates a list of shapes
 
@@ -667,6 +673,12 @@ def scheme_d_shapes(base_url=DEFAULT_BASE_URL):
 def scheme_d_line_styles(base_url=DEFAULT_BASE_URL):
     """Generate list of line styles of a given size
 
+    Args:
+        base_url (str): Ignore unless you need to specify a custom domain, port or 
+        version to connect to the CyREST API. Default is http://localhost:1234 
+        and the latest version of the CyREST API supported by this version of 
+        py4cytoscape.
+
     Returns:
         lambda: generates a list of line styles
 
@@ -682,6 +694,12 @@ def scheme_d_line_styles(base_url=DEFAULT_BASE_URL):
 def scheme_d_arrow_shapes(base_url=DEFAULT_BASE_URL):
     """Generate list of arrow shapes of a given size
 
+    Args:
+        base_url (str): Ignore unless you need to specify a custom domain, port or 
+        version to connect to the CyREST API. Default is http://localhost:1234 
+        and the latest version of the CyREST API supported by this version of 
+        py4cytoscape.
+
     Returns:
         lambda: generates a list of arrow shapes
 
@@ -942,6 +960,7 @@ def gen_edge_opacity_map(table_column,
     Args:
         table_column (str): Name of Cytoscape edge table column to map values from
         number_scheme (dict or func): Descriptor for functions that return an opacity list of a given length
+        mapping_type (str): continuous or discrete (c, d) mapping; default is continuous
         default_number (int): Opacity value to set as default for all unmapped values
         style_name (str): name for style
         network (SUID or str or None): Name or SUID of a network or view. Default is the
@@ -1000,6 +1019,7 @@ def gen_node_width_map(table_column,
     Args:
         table_column (str): Name of Cytoscape node table column to map values from
         number_scheme (dict or func): Descriptor for functions that return a width list of a given length
+        mapping_type (str): continuous or discrete (c, d); default is continuous
         default_number (int): width value to set as default for all unmapped values
         style_name (str): name for style
         network (SUID or str or None): Name or SUID of a network or view. Default is the
@@ -1227,6 +1247,7 @@ def gen_edge_size_map(table_column,
     Args:
         table_column (str): Name of Cytoscape node table column to map values from
         number_scheme (dict or func): Descriptor for functions that return a size list of a given length
+        mapping_type (str): continuous or discrete (c, d); default is continuous
         default_number (int): size value to set as default for all unmapped values
         style_name (str): name for style
         network (SUID or str or None): Name or SUID of a network or view. Default is the

py4cytoscape/style_bypasses.py

@@ -181,7 +181,6 @@ def clear_node_property_bypass(node_names, visual_property, network=None, base_u
             comma-separated string of node names or SUIDs, or scalar node name
             or SUID. Node names should be found in the ``name`` column of the ``nodes table``.
         visual_property (str): Name of a visual property. See ``get_visual_property_names``.
-        bypass (bool): Whether to set permanent bypass value. Default is True
         network (SUID or str or None): Name or SUID of a network. Default is the
             "current" network active in Cytoscape.
         base_url (str): Ignore unless you need to specify a custom domain,
@@ -371,7 +370,6 @@ def clear_edge_property_bypass(edge_names, visual_property, network=None, base_u
             comma-separated string of edge names or SUIDs, or scalar edge name
             or SUID. Edge names should be found in the ``name`` column of the ``edges table``.
         visual_property (str): Name of a visual property. See ``get_visual_property_names``.
-        bypass (bool): Whether to set permanent bypass value. Default is True
         network (SUID or str or None): Name or SUID of a network. Default is the
             "current" network active in Cytoscape.
         base_url (str): Ignore unless you need to specify a custom domain,
@@ -485,7 +483,6 @@ def clear_network_property_bypass(visual_property, network=None, base_url=DEFAUL
 
     Args:
         visual_property (str): Name of a visual property. See ``get_visual_property_names``.
-        bypass (bool): Whether to set permanent bypass value. Default is True
         network (SUID or str or None): Name or SUID of a network. Default is the
             "current" network active in Cytoscape.
         base_url (str): Ignore unless you need to specify a custom domain,
@@ -693,8 +690,8 @@ def set_node_position_bypass(node_names, new_x_locations=None, new_y_locations=N
         node_names (str or list or int): List of nodes as ``list`` of node names or SUIDs,
             comma-separated string of node names or SUIDs, or scalar node name
             or SUID. Node names should be found in the ``name`` column of the ``nodes table``.
-        new_x_locations (list, int or float): List of x position values, or single value, default is current x position
-        new_y_locations (list, int or float): List of y position values, or single value, default is current y position
+        new_x_locations (list or int or float): List of x position values, or single value, default is current x position
+        new_y_locations (list or int or float): List of y position values, or single value, default is current y position
         network (SUID or str or None): Name or SUID of a network. Default is the
             "current" network active in Cytoscape.
         base_url (str): Ignore unless you need to specify a custom domain,