Added the raises directive

hed/models/base_input.py

@@ -198,8 +198,10 @@ def to_excel(self, file):
 
         Parameters:
             file (str or file-like):      Location to save this base input.
-        Raises:
-            ValueError: if empty file object or file cannot be opened.
+
+        :raises ValueError:
+            - if empty file object or file cannot be opened.
+
         """
         if not file:
             raise ValueError("Empty file name or object passed in to BaseInput.save.")

hed/models/definition_entry.py

@@ -36,8 +36,8 @@ def get_definition(self, replace_tag, placeholder_value=None, return_copy_of_tag
             str:          The expanded def tag name
             HedGroup:     The contents of this definition(including the def tag itself)
 
-        Raises:
-            ValueError:  If a placeholder_value is passed, but this definition doesn't have a placeholder.
+        :raises ValueError:
+            - If a placeholder_value is passed, but this definition doesn't have a placeholder.
 
         """
         if self.takes_value == (placeholder_value is None):

hed/models/hed_group.py

@@ -37,8 +37,8 @@ def append(self, tag_or_group):
         Parameters:
             tag_or_group (HedTag or HedGroup): The new object to add to this group.
 
-        Raises:
-            ValueError: If a HedGroupFrozen.
+        :raises ValueError:
+            If a HedGroupFrozen.
 
         """
         tag_or_group._parent = self

hed/models/hed_string.py

@@ -179,8 +179,8 @@ def split_into_groups(hed_string, hed_schema=None, def_dict=None):
         Returns:
             list:  A list of HedTag and/or HedGroup.
 
-        Raises:
-            ValueError: If the string is significantly malformed, such as mismatched parentheses.
+        :raises ValueError:
+            - If the string is significantly malformed, such as mismatched parentheses.
 
         Notes:
             - The parse tree consists of tag groups, tags, and delimiters.

hed/models/hed_tag.py

@@ -130,8 +130,8 @@ def short_base_tag(self, new_tag_val):
         Parameters:
             new_tag_val (str): The new short_base_tag for this tag.
 
-        Raises:
-            ValueError: If tags cannot unidentified.
+        :raises ValueError:
+            - If tags cannot unidentified.
 
         Note:
             - Generally this is used to swap def to def-expand.

hed/models/sidecar.py

@@ -120,8 +120,9 @@ def load_sidecar_file(self, file):
         Parameters:
             file (str or FileLike): If a string, this is a filename. Otherwise, it will be parsed as a file-like.
 
-        Raises:
-            HedFileError: If the file was not found or could not be parsed into JSON.
+        :raises HedFileError:
+            - If the file was not found or could not be parsed into JSON.
+
         """
         if not file:
             return {}
@@ -143,8 +144,10 @@ def load_sidecar_files(self, files):
 
         Parameters:
             files (str or FileLike or list): A string or file-like object representing a JSON file, or a list of such.
-        Raises:
-            HedFileError: If the file was not found or could not be parsed into JSON.
+
+        :raises HedFileError:
+            - If the file was not found or could not be parsed into JSON.
+
         """
         if not files:
             return {}
@@ -184,8 +187,9 @@ def _load_json_file(self, fp):
         Parameters:
             fp (File-like): The JSON source stream.
 
-        Raises:
-            HedFileError:  If the file cannot be parsed.
+        :raises HedFileError:
+            - If the file cannot be parsed.
+
         """
         try:
             return json.load(fp)

hed/schema/hed_schema_group.py

@@ -26,8 +26,8 @@ def __init__(self, schema_list):
         Returns:
             HedSchemaGroup: the container created.
 
-        Raises:
-            HedFileError:  If multiple schemas have the same library prefixes.
+        :raises HedFileError:
+            - If multiple schemas have the same library prefixes.
 
         """
         if len(schema_list) == 0:

hed/schema/hed_schema_io.py

@@ -22,8 +22,8 @@ def from_string(schema_string, file_type=".xml", schema_namespace=None):
     Returns:
         (HedSchema):  The loaded schema.
 
-    Raises:
-        HedFileError:  If empty string or invalid extension is passed.
+    :raises HedFileError:
+        - If empty string or invalid extension is passed.
 
     Notes:
         - The loading is determined by file type.
@@ -78,8 +78,8 @@ def load_schema(hed_path=None, schema_namespace=None):
     Returns:
         HedSchema: The loaded schema.
 
-    Raises:
-         HedFileError: If there are any fatal issues when loading the schema.
+    :raises HedFileError:
+        - If there are any fatal issues when loading the schema.
 
     """
     if not hed_path:
@@ -129,8 +129,8 @@ def _load_schema_version(xml_version=None, xml_folder=None):
     Returns:
         HedSchema or HedSchemaGroup: The requested HedSchema object.
 
-    Raises:
-        HedFileError: If the xml_version is not valid.
+    :raises HedFileError:
+        - If the xml_version is not valid.
 
     Notes:
         - The library schema files have names of the form HED_(LIBRARY_NAME)_(version).xml.
@@ -178,8 +178,8 @@ def load_schema_version(xml_version=None, xml_folder=None):
     Returns:
         HedSchema or HedSchemaGroup: The schema or schema group extracted.
 
-    Raises:
-        HedFileError: If the xml_version is not valid.
+    :raises HedFileError:
+        - If the xml_version is not valid.
 
     Notes:
         - Loads the latest schema value if an empty version is given (string or list).

hed/schema/schema_validation_util.py

@@ -80,8 +80,8 @@ def validate_attributes(attrib_dict, filename):
     Returns:
         list: List of issues. Each issue is a dictionary.
 
-    Raises:
-        HedFileError: if invalid or version not found in the dictionary.
+    :raises  HedFileError:
+        - If invalid or version not found in the dictionary.
 
     """
     validate_present_attributes(attrib_dict, filename)
@@ -111,8 +111,8 @@ def find_rooted_entry(tag_entry, schema, loading_merged):
         rooted_tag(HedTagEntry or None): The base tag entry from the standard schema
             Returns None if this tag isn't rooted
 
-    Raises:
-        HedValueError: Raises if the tag doesn't exist or similar
+    :raises HedValueError:
+        - If the tag doesn't exist or similar
 
     """
     rooted_tag = tag_entry.has_attribute(constants.HedKey.Rooted, return_value=True)

hed/tools/analysis/analysis_util.py

@@ -55,8 +55,8 @@ def get_expression_parsers(queries, query_names=None):
         Returns:
             DataFrame - containing the search strings
 
-        Raises:   
-            ValueError - if query names are invalid or duplicated.
+        :raises ValueError:
+            - If query names are invalid or duplicated.
 
         """
     expression_parsers = []
@@ -93,8 +93,8 @@ def search_strings(hed_strings, queries, query_names=None):
     Returns:
         DataFrame - containing the factor vectors with results of the queries
 
-    Raises:   
-        ValueError - if query names are invalid or duplicated.
+    :raises ValueError:
+        - If query names are invalid or duplicated.
 
     """
 

hed/tools/analysis/event_manager.py

@@ -15,8 +15,8 @@ def __init__(self, data, schema):
             data (TabularInput): A tabular input file.
             schema (HedSchema): A HED schema
 
-        Raises:
-            HedFileError: if there are any unmatched offsets.
+        :raises HedFileError:
+            - if there are any unmatched offsets.
 
         """
 
@@ -46,8 +46,8 @@ def iter_context(self):
     def _create_event_list(self):
         """ Create a list of events of extended duration.
 
-        Raises:
-            HedFileError: If the hed_strings contain unmatched offsets.
+        :raises HedFileError:
+            - If the hed_strings contain unmatched offsets.
 
         """
 
@@ -107,8 +107,8 @@ def _update_onset_list(self, group, onset_dict, event_index):
             onset_dict (dict): A dictionary of OnsetGroup objects that keep track of span of an event.
             event_index (int): The event number in the list.
 
-        Raises:
-            HedFileError if an unmatched offset is encountered.
+        :raises HedFileError:
+            - if an unmatched offset is encountered.
 
         Notes:
             - Modifies onset_dict and onset_list.

hed/tools/analysis/hed_context_manager.py

@@ -27,8 +27,8 @@ def __init__(self, hed_strings, hed_schema):
             hed_strings (list): A list of HedString objects to be managed.
             hed_schema (HedSchema):  A HedSchema
 
-        Raises:
-            HedFileError: if there are any unmatched offsets.
+        :raises HedFileError:
+            - If there are any unmatched offsets.
 
         Notes:
             The constructor has the side-effect of splitting each element of the hed_strings list into two
@@ -69,8 +69,8 @@ def iter_context(self):
     def _create_onset_list(self):
         """ Create a list of events of extended duration.
 
-        Raises:
-            HedFileError: If the hed_strings contain unmatched offsets.
+        :raises HedFileError:
+            - If the hed_strings contain unmatched offsets.
 
         """
 
@@ -122,8 +122,8 @@ def _update_onset_list(self, group, onset_dict, event_index, is_offset=False):
             event_index (int): The event number in the list.
             is_offset (bool):  True if processing an offset.
 
-        Raises:
-            HedFileError if an unmatched offset is encountered.
+        :raises HedFileError:
+            - If an unmatched offset is encountered.
 
         Notes:
             - Modifies onset_dict and onset_list.

hed/tools/analysis/hed_type_manager.py

@@ -16,8 +16,9 @@ def __init__(self, hed_strings, hed_schema, definitions):
             hed_schema (HedSchema or HedSchemaGroup): The HED schema to use for processing.
             definitions (dict): A dictionary of DefinitionEntry objects.
 
-        Raises:
-            HedFileError:  On errors such as unmatched onsets or missing definitions.
+        :raises HedFileError:
+            - On errors such as unmatched onsets or missing definitions.
+
         """
 
         self.definitions = definitions

hed/tools/analysis/hed_type_values.py

@@ -19,8 +19,8 @@ def __init__(self, context_manager, definitions, name, type_tag="condition-varia
             name (str): Name of the tabular file as a unique identifier.
             type_tag (str): Lowercase short form of the tag to be managed.
 
-        Raises:
-            HedFileError:  On errors such as unmatched onsets or missing definitions.
+        :raises HedFileError:
+            - On errors such as unmatched onsets or missing definitions.
 
         """
         self.name = name

hed/tools/analysis/key_map.py

@@ -63,8 +63,8 @@ def make_template(self, additional_cols=None):
         Returns:
             DataFrame:  A dataframe containing the template.
 
-        Raises:
-            HedFileError: If additional columns are not disjoint from the key columns.
+        :raises HedFileError:
+            - If additional columns are not disjoint from the key columns.
 
         Notes:
             -  The template consists of the unique key columns in this map plus additional columns.
@@ -90,8 +90,8 @@ def remap(self, data):
                 - DataFrame: New dataframe with columns remapped.
                 - list:  List of row numbers that had no correspondence in the mapping.
 
-        Raises:
-            HedFileError:  If data is missing some of the key columns.
+        :raises HedFileError:
+            - If data is missing some of the key columns.
 
         """
 
@@ -145,8 +145,8 @@ def update(self, data, allow_missing=True, keep_counts=True):
         Returns:
             list: The indices of duplicates.
 
-        Raises:
-            HedFileError:  If there are missing keys and allow_missing is False.
+        :raises HedFileError:
+            - If there are missing keys and allow_missing is False.
 
         """
         df = get_new_dataframe(data)

hed/tools/bids/bids_file_dictionary.py

@@ -20,8 +20,8 @@ def __init__(self, collection_name, files, entities=('sub', 'ses', 'task', 'run'
             files (list or dict):   Full paths of files to include.
             entities (tuple):  Entity names to use in creating the keys.
 
-        Raises:
-            HedFileError: If files has inappropriate values.
+        :raises HedFileError:
+            - If files has inappropriate values.
 
         Notes:
             - This function is used for cross listing BIDS style files for different studies.
@@ -117,8 +117,8 @@ def make_dict(self, files, entities):
         Returns:
             dict:  A dictionary whose keys are entity keys and values are BidsFile objects.
 
-        Raises:
-            HedFileError: If incorrect format is passed or something not recognizable as a Bids file.
+        :raises HedFileError:
+            - If incorrect format is passed or something not recognizable as a Bids file.
 
         """
         file_dict = {}
@@ -244,8 +244,8 @@ def _correct_file(cls, the_file):
         Returns:
             BidsFile:  Either the original file or a newly created BidsTabularFile.
 
-        Raises:
-            HedFileError: If the_file isn't str or BidsFile.
+        :raises HedFileError:
+            - If the_file isn't str or BidsFile.
 
         """
         if isinstance(the_file, str):

hed/tools/bids/bids_tabular_dictionary.py

@@ -190,8 +190,8 @@ def _correct_file(cls, the_file):
         Returns:
             BidsTabularFile:  Either the original file or a newly created BidsTabularFile.
 
-        Raises:
-            HedFileError: If the_file isn't str or BidsTabularFile.
+        :raises HedFileError:
+            - If the_file isn't str or BidsTabularFile.
 
         """
         if isinstance(the_file, str):