This PR addresses SQLAlchemy 2.0 compatibility issues to prepare for upgrading Invenio packages that require SQLAlchemy>=2.0.0. The changes ensure the codebase works with both SQLAlchemy 1.4 and 2.0 by following the official migration guide.

Key Changes

String SQL Query Execution

SQLAlchemy 2.0 requires string-based SQL queries to be wrapped with the text() function. Updated:

• CLI execute function (hepdata/cli.py): Wrapped SQL query parameter with text()
• Data cleanup operations (hepdata/modules/records/utils/data_files.py): Wrapped complex multi-line SQL with text() and added necessary import

Syntax Warning Fix

Fixed invalid escape sequence in regex pattern (hepdata/ext/opensearch/query_builder.py) by using raw string literal to eliminate Python deprecation warnings.

Compatibility

These changes maintain full backwards compatibility with SQLAlchemy 1.4 while ensuring forward compatibility with 2.0. The existing db.select() patterns and result iteration methods are already 2.0-compatible and require no changes.

Testing

Validated that:

• All modified files pass syntax validation
• Imports work correctly with SQLALCHEMY_WARN_20=1 enabled
• No SQLAlchemy 2.0 deprecation warnings are triggered by HEPData code
• Functionality remains unchanged

With these minimal surgical changes, the repository is ready for the Invenio package upgrades that require SQLAlchemy 2.0.

Fixes #848.

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