[dweindl]

Fixes the deprecation warnings raised with pandas 3.1.0 and raises the minimum pandas version.

• Don't pass float_precision to read_csv for pandas>=3.1, where round-trip float parsing is the default (kept for older pandas).
• Replace deprecated inplace=True by reassignment. As a consequence, get_{condition,observable,parameter,mapping}_df no longer modify DataFrames passed by the caller.
• Avoid fillna with incompatible fill values.
• Use a full-length key when adding the sum row to a MultiIndex DataFrame in get_data_per_observable.
• Turn all warnings, including DeprecationWarnings, into errors in tests. The pandas deprecation warnings derive from DeprecationWarning, which was ignored so far, which is why these went unnoticed. The SWIG-related DeprecationWarning from python-libcombine on Python 3.14 remains ignored, since raising it during module initialization segfaults.
• Require pandas>=2.3 in accordance with NEP 29 (2.3, 3.0, 3.1 released within the past 24 months).

Tests pass with pandas 3.1.0 and 2.3.3.

Closes #570

🤖 Generated with Claude Code

[codecov-commenter]

Codecov Report

❌ Patch coverage is 96.77419% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 78.87%. Comparing base (68be6d1) to head (0b22e8c).

Files with missing lines	Patch %	Lines
petab/v1/mapping.py	66.66%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #571      +/-   ##
==========================================
+ Coverage   78.85%   78.87%   +0.02%     
==========================================
  Files          69       69              
  Lines        8043     8051       +8     
  Branches     1445     1445              
==========================================
+ Hits         6342     6350       +8     
  Misses       1214     1214              
  Partials      487      487              

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