Merge pull request #948 from IanCa/develop

Add 8.3.0 to built in schemas

hed/schema/schema_compare.py

@@ -312,25 +312,29 @@ def _add_suggested_tag_changes(change_dict, entry1, entry2, attribute, label):
              'tag': entry1.short_tag_name})
 
 
-def pretty_print_change_dict(change_dict, title="Schema changes"):
+def pretty_print_change_dict(change_dict, title="Schema changes", use_markdown=True):
     """Formats the change_dict into a string.
 
     Parameters:
         change_dict(dict): The result from calling gather_schema_changes
         title(str): Optional header to add, a default on will be added otherwise.
-
+        use_markdown(bool): If True, adds Markdown formatting characters to output.
     Returns:
         changelog(str): the changes listed out by section
     """
     final_strings = []
+    line_prefix = " - " if use_markdown else "\t"
     if change_dict:
         final_strings.append(title)
+        final_strings.append("") # add blank line
         for section_key, section_dict in change_dict.items():
             name = SectionEntryNamesPlural.get(section_key, section_key)
-            final_strings.append(f"{name}:")
+            line_endings = "**" if use_markdown else ""
+            final_strings.append(f"{line_endings}{name}:{line_endings}")
             for item in section_dict:
                 change, tag, change_type = item['change'], item['tag'], item['change_type']
-                final_strings.append(f"\t{tag} ({change_type}): {change}")
+                final_strings.append(f"{line_prefix}{tag} ({change_type}): {change}")
+            final_strings.append("")
     return "\n".join(final_strings)
 
 

tests/errors/test_error_reporter.py

@@ -10,7 +10,7 @@ class Test(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
         cls.error_handler = ErrorHandler()
-        cls._schema = load_schema_version("8.2.0")
+        cls._schema = load_schema_version("8.3.0")
         pass
 
     def test_push_error_context(self):

tests/models/test_base_input.py

@@ -102,7 +102,7 @@ def test_needs_sort(self):
         opened_file = TabularInput(df)
         self.assertFalse(opened_file.needs_sorting)
 
-        issues = opened_file.validate(load_schema_version("8.2.0"))
+        issues = opened_file.validate(load_schema_version("8.3.0"))
         self.assertEqual(issues[1][ErrorContext.ROW], 5)
         df.at[3, "onset"] = 1.5
         opened_file = TabularInput(df)
@@ -111,7 +111,7 @@ def test_needs_sort(self):
         df.at[3, "onset"] = 1.0
         opened_file = TabularInput(df)
         self.assertTrue(opened_file.needs_sorting)
-        issues = opened_file.validate(load_schema_version("8.2.0"))
+        issues = opened_file.validate(load_schema_version("8.3.0"))
         # Should still report the same issue row despite needing sorting for validation
         self.assertEqual(issues[1]['code'], ValidationErrors.ONSETS_OUT_OF_ORDER)
         self.assertEqual(issues[2][ErrorContext.ROW], 5)

tests/models/test_basic_search.py

@@ -19,7 +19,7 @@ def setUpClass(cls):
         cls.events_path = os.path.realpath(
             os.path.join(bids_root_path, 'sub-002/eeg/sub-002_task-FacePerception_run-1_events.tsv'))
         cls.base_input = TabularInput(cls.events_path, sidecar1_path)
-        cls.schema = load_schema_version("8.2.0")
+        cls.schema = load_schema_version("8.3.0")
         cls.df = cls.base_input.series_filtered
 
     def test_find_matching_results(self):

tests/models/test_definition_dict.py

@@ -10,7 +10,7 @@
 class TestDefBase(TestHedBase):
     @classmethod
     def setUpClass(cls):
-        cls.hed_schema = load_schema_version("8.2.0")
+        cls.hed_schema = load_schema_version("8.3.0")
 
     def check_def_base(self, test_strings, expected_issues):
         for test_key in test_strings:

tests/models/test_df_util.py

@@ -10,7 +10,7 @@
 
 class TestShrinkDefs(unittest.TestCase):
     def setUp(self):
-        self.schema = load_schema_version("8.2.0")
+        self.schema = load_schema_version("8.3.0")
 
     def test_shrink_defs_normal(self):
         df = pd.DataFrame({"column1": ["(Def-expand/TestDefNormal,(Acceleration/2471,Action/TestDef2)),Event/SomeEvent"]})
@@ -67,7 +67,7 @@ def test_shrink_defs_series_placeholder(self):
 
 class TestExpandDefs(unittest.TestCase):
     def setUp(self):
-        self.schema = load_schema_version("8.2.0")
+        self.schema = load_schema_version("8.3.0")
         self.def_dict = DefinitionDict(["(Definition/TestDefNormal,(Acceleration/2471,Action/TestDef2))",
                                        "(Definition/TestDefPlaceholder/#,(Acceleration/#,Action/TestDef2))"],
                                        hed_schema=self.schema)
@@ -527,7 +527,7 @@ def test_complex_scenarios_df(self):
 
 
 class TestSplitDelayTags(unittest.TestCase):
-    schema = load_schema_version("8.2.0")
+    schema = load_schema_version("8.3.0")
     def test_empty_series_and_onsets(self):
         empty_series = pd.Series([], dtype="object")
         empty_onsets = pd.Series([], dtype="float")

tests/models/test_hed_string.py

@@ -7,7 +7,7 @@
 class TestHedStrings(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
-        cls.schema = load_schema_version("8.2.0")
+        cls.schema = load_schema_version("8.3.0")
 
     def validator_scalar(self, test_strings, expected_results, test_function):
         for test_key in test_strings:

tests/models/test_hed_tag.py

@@ -10,7 +10,7 @@ class TestValidatorUtilityFunctions(TestHedBase):
 
     @classmethod
     def setUpClass(cls):
-        cls.hed_schema = load_schema_version("8.2.0")
+        cls.hed_schema = load_schema_version("8.3.0")
 
     def test_if_tag_exists(self):
         valid_tag1 = HedTag('Left-handed', hed_schema=self.hed_schema)
@@ -45,7 +45,7 @@ def test_if_tag_exists(self):
 class TestSchemaUtilityFunctions(TestHedBase):
     @classmethod
     def setUpClass(cls):
-        cls.hed_schema = load_schema_version("8.2.0")
+        cls.hed_schema = load_schema_version("8.3.0")
 
     def test_correctly_determine_tag_takes_value(self):
         value_tag1 = HedTag('Distance/35 px', hed_schema=self.hed_schema)

tests/models/test_string_util.py

@@ -7,7 +7,7 @@
 class TestHedStringSplit(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
-        cls.schema = load_schema_version("8.2.0")
+        cls.schema = load_schema_version("8.3.0")
 
     def check_split_base_tags(self, hed_string, base_tags, expected_string, expected_string2):
         # Test case 1: remove_group=False
@@ -70,7 +70,7 @@ def test_case_5(self):
 class TestHedStringSplitDef(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
-        cls.schema = load_schema_version("8.2.0")
+        cls.schema = load_schema_version("8.3.0")
 
     def check_split_def_tags(self, hed_string, def_names, expected_string, expected_string2):
         # Test case 1: remove_group=False
@@ -133,7 +133,7 @@ def test_case_5(self):
 
 class TestGatherDescriptions(unittest.TestCase):
     def setUp(self):
-        self.schema = load_schema_version("8.2.0")
+        self.schema = load_schema_version("8.3.0")
 
     def test_gather_single_description(self):
         input_str = "Sensory-event, Description/This is a test."

tests/schema/test_hed_schema.py

@@ -115,7 +115,7 @@ def test_schema_compliance(self):
         self.assertEqual(len(warnings), 18)
 
     def test_bad_prefixes(self):
-        schema = load_schema_version(xml_version="8.2.0")
+        schema = load_schema_version(xml_version="8.3.0")
 
         self.assertTrue(schema.get_tag_entry("Event"))
         self.assertFalse(schema.get_tag_entry("sc:Event"))
@@ -126,7 +126,7 @@ def test_bad_prefixes(self):
         self.assertFalse(schema.get_tag_entry("Event", schema_namespace='unknown'))
 
     def test_bad_prefixes_library(self):
-        schema = load_schema_version(xml_version="tl:8.2.0")
+        schema = load_schema_version(xml_version="tl:8.3.0")
 
         self.assertTrue(schema.get_tag_entry("tl:Event", schema_namespace="tl:"))
         self.assertFalse(schema.get_tag_entry("sc:Event", schema_namespace="tl:"))

tests/schema/test_hed_schema_io.py

@@ -591,7 +591,7 @@ def test_triple_prefixes(self):
 # class TestOwlBase(unittest.TestCase):
 #     @classmethod
 #     def setUpClass(cls):
-#         cls.base_schema = schema.load_schema_version("8.2.0")
+#         cls.base_schema = schema.load_schema_version("8.3.0")
 #
 #     @with_temp_file(".owl")
 #     def test_schema2xml(self, filename):

tests/schema/test_ontology_util.py

@@ -14,7 +14,7 @@ def setUp(self):
 
     def test_get_library_name_and_id_default(self):
         # Test default case where no library name is provided
-        schema = load_schema_version("8.2.0")
+        schema = load_schema_version("8.3.0")
         name, first_id = get_library_name_and_id(schema)
         self.assertEqual(name, "Standard")
         self.assertEqual(first_id, 10000)
@@ -145,7 +145,7 @@ def test_update_dataframes_from_schema(self):
         for key, df in updated_dataframes.items():
             self.assertTrue((df['test_column'] == fixed_value).all())
         # this is expected to bomb horribly, since schema lacks many of the spreadsheet entries.
-        schema = load_schema_version("8.2.0")
+        schema = load_schema_version("8.3.0")
         schema_dataframes_new = load_schema_version("8.3.0").get_as_dataframes()
         try:
             updated_dataframes = update_dataframes_from_schema(schema_dataframes_new, schema)

tests/schema/test_schema_validation_util.py

@@ -75,9 +75,9 @@ def test_schema_version_for_library(self):
         self.assertEqual(util.schema_version_for_library(schema1, ""), "8.0.0")
         self.assertEqual(util.schema_version_for_library(schema1, None), "8.0.0")
 
-        schema2 = load_schema_version("8.2.0")
-        self.assertEqual(util.schema_version_for_library(schema2, ""), "8.2.0")
-        self.assertEqual(util.schema_version_for_library(schema2, None), "8.2.0")
+        schema2 = load_schema_version("8.3.0")
+        self.assertEqual(util.schema_version_for_library(schema2, ""), "8.3.0")
+        self.assertEqual(util.schema_version_for_library(schema2, None), "8.3.0")
 
         schema3 = load_schema_version(["testlib_2.0.0", "score_1.1.0"])
         self.assertEqual(util.schema_version_for_library(schema3, ""), "8.2.0")

tests/schema/util_create_schemas.py

@@ -1,7 +1,7 @@
 from hed.schema import HedKey, HedSectionKey, from_string
 
 
-library_schema_start = """HED library="testcomparison" version="1.1.0" withStandard="8.2.0" unmerged="true"
+library_schema_start = """HED library="testcomparison" version="1.1.0" withStandard="8.3.0" unmerged="true"
 
 '''Prologue'''
 

tests/scripts/test_convert_and_update_schema.py

@@ -37,7 +37,7 @@ def test_schema_conversion_and_update(self):
         self.assertEqual(schema, schema_reload2)
 
         # Now verify after doing this again with a new schema, they're still the same.
-        schema = load_schema_version("8.2.0")
+        schema = load_schema_version("8.3.0")
         schema.save_as_dataframes(tsv_filename)
 
         filenames = [os.path.join(tsv_filename, "test_schema_Tag.tsv")]

tests/validator/test_spreadsheet_validator.py

@@ -13,7 +13,7 @@
 class TestSpreadsheetValidation(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
-        cls.schema = load_schema_version("8.2.0")
+        cls.schema = load_schema_version("8.3.0")
         cls.validator = SpreadsheetValidator(cls.schema)
         base = os.path.join(os.path.dirname(os.path.realpath(__file__)), '../data/')
         cls.base_data_dir = base