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[FIX/MAINT] tests in pubget - #64
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The article set used by the tests gained a table with 10 coordinate rows and 24 columns, and its <body> was re-indented, which left three tests asserting on the previous fixture: - the whole corpus now has 20 coordinate rows instead of 12; - `test_extract_data_to_csv_with_tables` read `text.csv` row 0, but the rows are in the order in which the article directories are visited, so row 0 is not necessarily an article with an "X Y Z" table (this test failed from the commit that introduced it). Look articles up by pmcid instead, and also check that the wide table is inserted in full; - the re-indented body makes the labelbuddy document start the body with a newline, so match the whitespace after the "Body" heading loosely. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_019toBA75BjG7HiUmmMChBzd
`DataFrame.fillna("")` raises in pandas 3.0 when a column is empty for
every article in the chunk: pandas gives it the float dtype and refuses
to store empty strings in it. Read the text fields as strings and
missing values as empty strings instead, which also stops a purely
numeric title or abstract from being parsed as a number.
The pinned CI environments still use pandas 2.x, but the whole test
suite fails on a plain `pip install .[dev]` without this.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_019toBA75BjG7HiUmmMChBzd
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