Fix DTD validation: Add required tbody elements to tables with thead

[Copilot]

Tables with <thead> were failing DTD validation due to missing required <tbody> elements. The error: expecting ((col* | colgroup*), ((thead?, tfoot?, tbody+) | tr+)), got (colgroup thead).

Root Cause

MasterPipeline._post_process_xml() explicitly skipped adding <tbody> for tables with multiple thead rows to avoid empty rows in HTML output, violating JATS DTD requirements.

Changes

• MasterPipeline.py (lines 980-1011)

  • Removed conditional that skipped tbody addition for multi-row thead tables
  • Always add <tbody> when <thead> exists but no <tbody> present
  • Calculate column count from colgroup or thead and apply colspan to empty tbody cell

• tests/test_table_and_article_type_fixes.py

  • Updated test_tables_with_thead_have_tbody to verify DTD compliance
  • Revised test_html_tables_no_empty_rows_at_end to accept minimal tbody as DTD-required

Example

Before:

<table>
  <colgroup><col width="50%"/><col width="50%"/></colgroup>
  <thead><tr><th>Header 1</th><th>Header 2</th></tr></thead>
</table>

After:

<table>
  <colgroup><col width="50%"/><col width="50%"/></colgroup>
  <thead><tr><th>Header 1</th><th>Header 2</th></tr></thead>
  <tbody><tr><td colspan="2"></td></tr></tbody>
</table>

Result

All 5 tables in generated XML now conform to DTD structure requirements with appropriate colspan attributes (2, 13, 12, 11, 3 columns respectively).

Warning

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Original prompt

The style checker recently reported a recurring DTD validation error due to incorrect table formatting in XML/HTML files. The error appears at multiple line numbers and is as follows:

error: Element table content does not follow the DTD, expecting ((col* | colgroup*) , ((thead? , tfoot? , tbody+) | tr+)), got (colgroup thead)

This indicates that the

elements contain and but are missing the required element or direct elements after the header row, as specified by the DTD. To fix this, each that currently has followed by must be updated to also include , ensuring it follows the structure required by the DTD:

.........

Please review all affected files across the main branch where this style checker error is reported and update them accordingly, by adding the necessary wrappers or rearranging content to satisfy the expected DTD structure.

This pull request was created from Copilot chat.

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