Redid the imports to make MATLAB happier and avoid circular references

hed/__init__.py

@@ -8,12 +8,33 @@
 from hed.models.tabular_input import TabularInput
 from hed.models.sidecar import Sidecar
 from hed.models.definition_dict import DefinitionDict
-
+from hed.models.query_handler import QueryHandler
+from hed.models.query_service import get_query_handlers, search_strings
 
 from hed.schema.hed_schema import HedSchema
 from hed.schema.hed_schema_group import HedSchemaGroup
 from hed.schema.hed_schema_io import load_schema, load_schema_version
 
+from hed.tools.bids.bids_dataset import BidsDataset
+from hed.tools.analysis.event_manager import EventManager
+from hed.tools.analysis.file_dictionary import FileDictionary
+from hed.tools.analysis.hed_tag_manager import HedTagManager
+from hed.tools.analysis.hed_type_defs import HedTypeDefs
+from hed.tools.analysis.hed_type_factors import HedTypeFactors
+from hed.tools.analysis.hed_type import HedType
+from hed.tools.analysis.hed_type_manager import HedTypeManager
+from hed.tools.analysis.hed_type_counts import HedTypeCount
+from hed.tools.analysis.key_map import KeyMap
+from hed.tools.analysis.tabular_summary import TabularSummary
+from hed.tools.analysis.temporal_event import TemporalEvent
+from hed.tools.analysis.hed_tag_manager import HedTagManager
+from hed.tools.analysis.annotation_util import (check_df_columns, extract_tags, generate_sidecar_entry, 
+    get_bids_dataset, hed_to_df, df_to_hed, merge_hed_dict, str_to_tabular, strs_to_sidecar, to_strlist)
+
+from hed.tools.util.hed_logger import HedLogger
+from hed.tools.util.data_util import get_new_dataframe, get_value_dict, replace_values, reorder_columns
+from hed.tools.util.io_util import check_filename, clean_filename, extract_suffix_path, get_file_list, make_path
+from hed.tools.util.io_util import get_dir_dictionary, get_file_list, get_path_components, parse_bids_filename
 
 from . import _version
 __version__ = _version.get_versions()['version']

hed/models/__init__.py

@@ -6,6 +6,7 @@
 from .definition_dict import DefinitionDict
 from .definition_entry import DefinitionEntry
 from .query_handler import QueryHandler
+from .query_service import get_query_handlers, search_strings
 from .hed_group import HedGroup
 from .spreadsheet_input import SpreadsheetInput
 from .hed_string import HedString

hed/schema/schema_compare.py

@@ -1,3 +1,6 @@
+""" Functions supporting comparison of schemas. """
+
+
 from hed.schema.hed_schema import HedKey
 from hed.schema.hed_schema_constants import HedSectionKey
 from collections import defaultdict

hed/schema/schema_data/HED_testlib_2.0.0.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" ?>
 <HED version="2.0.0" library="testlib" withStandard="8.2.0">
-   <prologue>This schema tests the ordering effects of various combinations of rooted and extension allowed for rooted schemas.</prologue>
+   <prologue>This schema tests the ordering effects of various combinations of rooted and extension allowed for rooted schemas. It is compatible with testlib version 3.0.0 but not testlib 2.0.0.</prologue>
    <schema>
       <node>
          <name>Event</name>
@@ -139,35 +139,6 @@
             </attribute>
          </node>
       </node>
-      <node>
-         <name>C-nonextension</name>
-         <description>These should not be sorted.  C should be last</description>
-         <attribute>
-            <name>inLibrary</name>
-            <value>testlib</value>
-         </attribute>
-         <node>
-            <name>SubnodeC3</name>
-            <attribute>
-               <name>inLibrary</name>
-               <value>testlib</value>
-            </attribute>
-         </node>
-         <node>
-            <name>SubnodeC1</name>
-            <attribute>
-               <name>inLibrary</name>
-               <value>testlib</value>
-            </attribute>
-         </node>
-         <node>
-            <name>SubnodeC2</name>
-            <attribute>
-               <name>inLibrary</name>
-               <value>testlib</value>
-            </attribute>
-         </node>
-      </node>
       <node>
          <name>Action</name>
          <description>Do something.</description>
@@ -874,7 +845,7 @@
          </node>
       </node>
       <node>
-         <name>A-extensionallowed</name>
+         <name>D-extensionallowed</name>
          <description>These should be sorted.  This section should be first.</description>
          <attribute>
             <name>extensionAllowed</name>
@@ -905,38 +876,6 @@
             </attribute>
          </node>
       </node>
-      <node>
-         <name>B-extensionallowed</name>
-         <description>These should be sorted.  This section should be second.</description>
-         <attribute>
-            <name>extensionAllowed</name>
-         </attribute>
-         <attribute>
-            <name>inLibrary</name>
-            <value>testlib</value>
-         </attribute>
-         <node>
-            <name>SubnodeE1</name>
-            <attribute>
-               <name>inLibrary</name>
-               <value>testlib</value>
-            </attribute>
-         </node>
-         <node>
-            <name>SubnodeE2</name>
-            <attribute>
-               <name>inLibrary</name>
-               <value>testlib</value>
-            </attribute>
-         </node>
-         <node>
-            <name>SubnodeE3</name>
-            <attribute>
-               <name>inLibrary</name>
-               <value>testlib</value>
-            </attribute>
-         </node>
-      </node>
       <node>
          <name>Item</name>
          <description>An independently existing thing (living or nonliving).</description>
@@ -7516,4 +7455,5 @@
          <description>Indicates that the schema attribute is meant to be applied to value classes.</description>
       </propertyDefinition>
    </propertyDefinitions>
+   <epilogue>A final section.</epilogue>
 </HED>