hed-standard · VisLab · Jul 10, 2023 · Jul 7, 2023 · Jul 8, 2023 · Jul 9, 2023
diff --git a/README.md b/README.md
@@ -2,7 +2,7 @@
 [![Maintainability](https://api.codeclimate.com/v1/badges/11bf2329590e7b0164ba/maintainability)](https://codeclimate.com/github/hed-standard/hed-python/maintainability)
 [![Test Coverage](https://api.codeclimate.com/v1/badges/11bf2329590e7b0164ba/test_coverage)](https://codeclimate.com/github/hed-standard/hed-python/test_coverage)
 ![PyPI - Status](https://img.shields.io/pypi/v/hedtools)
-
+[![Documentation Status](https://readthedocs.org/projects/hed-python/badge/?version=latest)](https://hed-python.readthedocs.io/en/latest/?badge=latest)
 
 # HEDTools - Python
 HED (Hierarchical Event Descriptors) is a framework for systematically describing

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -5,6 +5,7 @@ openpyxl>=3.1.0
 pandas>=1.3.5
 portalocker>=2.7.0
 semantic_version>=2.10.0
+myst-parser>=1.0.0
 Sphinx>=5.2.2
 sphinx_rtd_theme>=1.0.0
 wordcloud==1.9.2
diff --git a/docs/source/_static/images/croppedWideLogo.png b/docs/source/_static/images/croppedWideLogo.png
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -24,8 +24,8 @@
 author = 'HED Working Group'
 
 # The full version, including alpha/beta/rc tags
-version = '0.0.1'
-release = '0.0.1'
+version = '0.3.1'
+release = '0.3.1'
 
 currentdir = os.path.realpath(os.path.dirname(__file__))
 

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -1,6 +1,10 @@
 Hierarchical Event Descriptor (HED) Python Tools
 ================================================
 
+.. image:: _static/images/croppedWideLogo.png
+  :width: 220
+  :alt: HedLogo
+
 .. sidebar:: **Links**
 
    * `PDF docs <https://hed-python.readthedocs.io/_/downloads/en/latest/pdf/>`_

diff --git a/docs/source/introduction.rst b/docs/source/introduction.rst
@@ -29,12 +29,19 @@ you can install directly from the
 `GitHub repository <https://github.com/hed-standard/hed-python>`_
 using the following command:
 
+```code
 >>> pip install git+https://github.com/hed-standard/hed-python.git
-
+```
 
 Finding help
 ============
 
+:Documentation:
+
+    See `HED resources <https://www.hed-resources.org>`_ for user documentation and tutorials.
+
+    The `HED online tools <https://hedtools.org>`_ provide an easy-to-use interface that requires no programming. 
+
 :Mailing lists and forums:
 
     * Don't hesitate to ask questions about the python hedtools on `NeuroStars

diff --git a/hed/errors/error_reporter.py b/hed/errors/error_reporter.py
@@ -22,7 +22,6 @@
     ErrorContext.ROW,
     ErrorContext.COLUMN,
     ErrorContext.LINE,
-    # ErrorContext.HED_STRING, # temporarily disable hed string sort(maybe perm, not sure it's needed)
     ErrorContext.SCHEMA_SECTION,
     ErrorContext.SCHEMA_TAG,
     ErrorContext.SCHEMA_ATTRIBUTE,
@@ -33,10 +32,6 @@
     ErrorContext.ROW
 ]
 
-hed_string_sort_list = [
-    ErrorContext.HED_STRING
-]
-
 def _register_error_function(error_type, wrapper_func):
     if error_type in error_functions:
         raise KeyError(f"{error_type} defined more than once.")
@@ -191,11 +186,8 @@ def push_error_context(self, context_type, context):
 
         """
         if context is None:
-            from hed import HedString
             if context_type in int_sort_list:
                 context = 0
-            elif context_type in hed_string_sort_list:
-                context = HedString("")
             else:
                 context = ""
         self.error_context.append((context_type, context))
@@ -430,8 +422,6 @@ def _get_keys(d):
         for key in default_sort_list:
             if key in int_sort_list:
                 result.append(d.get(key, -1))
-            elif key in hed_string_sort_list:
-                result.append(d.get(key, HedString("")))
             else:
                 result.append(d.get(key, ""))
         return tuple(result)

diff --git a/hed/models/__init__.py b/hed/models/__init__.py
@@ -9,7 +9,6 @@
 from .hed_group import HedGroup
 from .spreadsheet_input import SpreadsheetInput
 from .hed_string import HedString
-from .hed_string_group import HedStringGroup
 from .hed_tag import HedTag
 from .sidecar import Sidecar
 from .tabular_input import TabularInput

diff --git a/hed/models/base_input.py b/hed/models/base_input.py
@@ -70,14 +70,14 @@ def __init__(self, file, file_type=None, worksheet_name=None, has_column_names=T
         self._dataframe = None
 
         if isinstance(file, pandas.DataFrame):
-            self._dataframe = file
+            self._dataframe = file.astype(str)
             self._has_column_names = self._dataframe_has_names(self._dataframe)
         elif not file:
             raise HedFileError(HedExceptions.FILE_NOT_FOUND, "Empty file passed to BaseInput.", file)
         elif input_type in self.TEXT_EXTENSION:
             try:
                 self._dataframe = pandas.read_csv(file, delimiter='\t', header=pandas_header,
-                                                  dtype=str, keep_default_na=True, na_values=None)
+                                                  dtype=str, keep_default_na=True, na_values=["", "null"])
             except Exception as e:
                 raise HedFileError(HedExceptions.INVALID_FILE_FORMAT, str(e), self.name) from e
             # Convert nan values to a known value
@@ -493,7 +493,7 @@ def combine_dataframe(dataframe):
         )
         return dataframe
 
-    def get_def_dict(self, hed_schema=None, extra_def_dicts=None):
+    def get_def_dict(self, hed_schema, extra_def_dicts=None):
         """ Returns the definition dict for this file
 
         Note: Baseclass implementation returns just extra_def_dicts.

diff --git a/hed/models/column_mapper.py b/hed/models/column_mapper.py
@@ -378,11 +378,11 @@ def _finalize_mapping(self):
     def _remove_from_list(list_to_alter, to_remove):
         return [item for item in list_to_alter if item not in to_remove]
 
-    def get_def_dict(self, hed_schema=None, extra_def_dicts=None):
+    def get_def_dict(self, hed_schema, extra_def_dicts=None):
         """ Return def dicts from every column description.
 
         Parameters:
-            hed_schema (Schema or None): A HED schema object to use for extracting definitions.
+            hed_schema (Schema): A HED schema object to use for extracting definitions.
             extra_def_dicts (list, DefinitionDict, or None): Extra dicts to add to the list.
 
         Returns:

diff --git a/hed/models/def_expand_gather.py b/hed/models/def_expand_gather.py
@@ -201,7 +201,4 @@ def get_ambiguous_group(ambiguous_def):
         Returns:
             HedGroup: the ambiguous definition with known placeholders filled in
         """
-        if not ambiguous_def:
-            # mostly to not crash, this shouldn't happen.
-            return HedString("")
         return ambiguous_def.get_group()
diff --git a/hed/models/definition_dict.py b/hed/models/definition_dict.py
@@ -50,7 +50,7 @@ def add_definitions(self, def_dicts, hed_schema=None):
                 for definition in def_dict:
                     self.check_for_definitions(HedString(definition, hed_schema))
             else:
-                raise TypeError("Invalid type '{type(def_dict)}' passed to DefinitionDict")
+                raise TypeError(f"Invalid type '{type(def_dict)}' passed to DefinitionDict")
 
     def _add_definition(self, def_tag, def_value):
         if def_tag in self.defs:

diff --git a/hed/models/definition_entry.py b/hed/models/definition_entry.py
@@ -18,7 +18,8 @@ def __init__(self, name, contents, takes_value, source_context):
         """
         self.name = name
         if contents:
-            contents = contents.copy().sort()
+            contents = contents.copy()
+            contents.sort()
         self.contents = contents
         self.takes_value = takes_value
         self.source_context = source_context

diff --git a/hed/models/hed_group.py b/hed/models/hed_group.py
@@ -126,13 +126,8 @@ def copy(self):
         return return_copy
 
     def sort(self):
-        """ Sort the tags and groups in this HedString in a consistent order.
-
-        Returns:
-            self
-        """
+        """ Sort the tags and groups in this HedString in a consistent order."""
         self.sorted(update_self=True)
-        return self
 
     def sorted(self, update_self=False):
         """ Returns a sorted copy of this hed group as a list of it's children