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Fix pandas 3.1 deprecation warnings in overview - #341

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dweindl merged 1 commit into
Benchmarking-Initiative:masterfrom
dweindl:fix-pandas-3.1-warnings
Oct 26, 2026
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dweindl merged 1 commit into
Benchmarking-Initiative:masterfrom
dweindl:fix-pandas-3.1-warnings

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@dweindl dweindl commented Oct 22, 2026

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Fixes the Pandas4Warnings emitted from this package with pandas 3.1:

  • Replace the deprecated inplace=True in set_index (PDEP-8) in overview.py and overview_v2.py.
  • In get_noise_distributions, convert columns to the string dtype before filling missing values with lin/normal. Columns without any values are read as float64, and filling those with strings will raise in future pandas versions.

Regenerated README and HTML overview tables are unchanged (checked with pandas 3.1.0). The remaining pandas warnings come from petab and bokeh.

🤖 Generated with Claude Code

Avoid the deprecated `inplace` keyword (PDEP-8), and avoid filling
all-empty (float) columns with strings, which will raise in future
pandas versions.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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dweindl marked this pull request as ready for review October 22, 2026 14:36

@dilpath dilpath left a comment

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Thanks!

@dweindl
dweindl merged commit c44d5ed into Benchmarking-Initiative:master Oct 26, 2026
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@dweindl
dweindl deleted the fix-pandas-3.1-warnings branch October 26, 2026 20:11
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2 participants