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Fix spurious index column in v2 table round-trips - #542
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`from_df` of the v2 parameter, measurement, observable and mapping tables unconditionally called `reset_index()`, which turned an unnamed index into an extra `index` column that was kept and written out. Now only named index levels are moved to columns. Also: * accept empty `observableParameters` / `noiseParameters` strings, so `MeasurementTable.from_df(table.to_df())` works * don't modify the input DataFrame in `ObservableTable.from_df` Fixes PEtab-dev#541. Relates to PEtab-dev#523. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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dweindl
marked this pull request as ready for review
October 14, 2026 18:12
This was referenced Oct 14, 2026
dilpath
approved these changes
Oct 14, 2026
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| df.index = [5, 7] | ||
| df_orig = df.copy() | ||
| table = table_cls.from_df(df) | ||
| assert_frame_equal(df, df_orig) |
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What does this assert do? It looks like this must be equal because one is a copy of the other?
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This is related to the df = get_observable_df(df.copy()) line in petab/v2/core.py. Previously, from_df would mutated the input via get_observable_df.
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from_dfof the v2 parameter, measurement, observable and mapping tables unconditionally calledreset_index(), which turned an unnamed index (e.g. the defaultRangeIndexfromfrom_tsv) into an extraindexcolumn. That column was kept due toextra="allow"and written out again, adding another column on each load/save cycle. Now only named index levels are moved to columns.Also:
observableParameters/noiseParametersstrings, so thatMeasurementTable.from_df(table.to_df())worksObservableTable.from_df(get_observable_dfoperates in place)Fixes #541. Relates to #523.
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