First stage in fixing inLibrary attribute for schema extras

[VisLab]

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[Copilot]

Pull request overview

This PR is the first step toward correctly tracking the inLibrary / in_library origin for schema “extras” (Sources/Prefixes/External annotations) when working with partnered library schemas, and updates the test fixtures to reflect merged library schemas.

Changes:

• Add in_library tagging/merge behavior when loading extras from XML/MediaWiki/JSON/DataFrame inputs, and adjust serializers to use a merged-extras accessor.
• Update merged-schema serialization paths to better control whether base-standard extras are included, and ensure in_library metadata is not serialized.
• Refresh schema test fixtures (TSV/XML/MediaWiki) and a few tests to reflect merged library schema state and newly required extras sections.

Reviewed changes

Copilot reviewed 32 out of 36 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
tests/schema/test_schema_extras_comprehensive.py	Adjusts expectation for merged test schemas (schema.merged).
tests/schema/test_schema_compliance.py	Modifies dc:source compliance test (currently includes debug I/O and removed assertion).
tests/schema/test_hed_schema_io.py	Updates prerelease library fixture name/library (testliba).
tests/data/schema_tests/test_merge/HED_testlib_4.0.0/HED_testlib_4.0.0_ValueClass.tsv	Expands value class fixtures for merged test library schema.
tests/data/schema_tests/test_merge/HED_testlib_4.0.0/HED_testlib_4.0.0_UnitModifier.tsv	Adds SI unit modifier fixtures.
tests/data/schema_tests/test_merge/HED_testlib_4.0.0/HED_testlib_4.0.0_UnitClass.tsv	Adds unit class fixtures.
tests/data/schema_tests/test_merge/HED_testlib_4.0.0/HED_testlib_4.0.0_Unit.tsv	Adds unit fixtures and relationships to unit classes.
tests/data/schema_tests/test_merge/HED_testlib_4.0.0/HED_testlib_4.0.0_Tag.tsv	Rebuilds merged tag TSV (including inLibrary=testlib markings for library-origin tags).
tests/data/schema_tests/test_merge/HED_testlib_4.0.0/HED_testlib_4.0.0_Structure.tsv	Updates header structure (removes unmerged="True" in fixture).
tests/data/schema_tests/test_merge/HED_testlib_4.0.0/HED_testlib_4.0.0_ObjectProperty.tsv	Adds object-property fixtures.
tests/data/schema_tests/test_merge/HED_testlib_4.0.0/HED_testlib_4.0.0_DataProperty.tsv	Adds data-property fixtures (including inLibrary definition).
tests/data/schema_tests/test_merge/HED_testlib_4.0.0/HED_testlib_4.0.0_AttributeProperty.tsv	Adds attribute-property fixtures.
tests/data/schema_tests/test_merge/HED_testlib_4.0.0/HED_testlib_4.0.0_AnnotationProperty.tsv	Expands annotation-property fixtures.
tests/data/schema_tests/prerelease/HED9.9.9.mediawiki	Adds extras section headers required for parsing (Sources/External annotations).
tests/data/schema_tests/prerelease/HED_testpre_1.0.0.mediawiki	Adds Prefixes section header required for parsing.
tests/data/schema_tests/prerelease/HED_testliba_2.1.0.xml	Renames prerelease library fixture and updates withStandard.
tests/data/schema_tests/HED_testlib_2.1.0.xml	Adds a non-prerelease XML library schema fixture including extras sections.
hed/scripts/check_schema_loading.py	Adds support for testing additional flat schema directories + CLI flag to exclude them.
hed/schema/schema_io/xml2schema.py	Adds in_library column tagging for extras when loading library schemas (XML).
hed/schema/schema_io/wiki2schema.py	Adds in_library column tagging for extras when loading library schemas (MediaWiki).
hed/schema/schema_io/schema2xml.py	Switches extras output to use merged-extras accessor.
hed/schema/schema_io/schema2wiki.py	Switches extras output to use merged-extras accessor and skips in_library when serializing.
hed/schema/schema_io/schema2json.py	Switches extras output to use merged-extras accessor.
hed/schema/schema_io/schema2df.py	Updates DataFrame serializer extras output; ensures in_library is stripped from serialized extras.
hed/schema/schema_io/schema2base.py	Adds base-schema loading + merged-extras helper to support merged output behavior.
hed/schema/schema_io/json2schema.py	Adds in_library column tagging for extras when loading library schemas (JSON).
hed/schema/schema_io/df2schema.py	Adds in_library column tagging for extras when loading from DataFrames.
hed/schema/schema_io/df_util.py	Updates extras merge logic to prefer library rows for duplicates (and keeps in_library for comparison semantics).
hed/schema/schema_io/base2schema.py	Strips in_library column during normalization to avoid serializing internal metadata.
hed/schema/hed_schema.py	Adjusts save_as_dataframes behavior to preserve serializer-merged extras when saving merged output and strip in_library when appropriate.
.github/copilot-instructions.md	Updates contributor guidance on placing temporary files in .status/.

[Copilot]

Pull request overview

Copilot reviewed 34 out of 38 changed files in this pull request and generated 2 comments.

[Copilot]

Pull request overview

Copilot reviewed 34 out of 38 changed files in this pull request and generated 2 comments.