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Fix for pandas 3.0 - #561
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tompollard
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Jan 23, 2026
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thanks @larsoner, please could you remove the print statement?
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Jan 23, 2026
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Done @tompollard ! |
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Can we merge and release this PR @tompollard ? It is blocking braindecode and eegdash >.< |
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Thanks everyone! The fix is now available in the latest release on PyPI (v4.3.1): https://pypi.org/project/wfdb/ |
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Many thanks 🙏 @tompollard |
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…es (#575) Follow-up to #561 (v4.3.1). As analyzed in #574 (with a correction below), the module-level import crash is indeed fixed, but `get_contained_labels` still passes **string** columns' `.values` directly to `set_index`: - `label_map.set_index(label_map["symbol"].values, inplace=True)` - `label_map.set_index(label_map["description"].values, inplace=True)` Under pandas' new string dtype (pandas 3.0, or 2.x with `future.infer_string`), `Series.values` returns an `ArrowStringArrayNumpySemantics`, which `set_index` rejects with `TypeError`. Passing the column label is equivalent on every pandas version and immune to the dtype change. Correction to the analysis in #574 (verified by column dtype + a pandas sandbox): the other `.values` sites listed there (`label_store` columns at ~728/~1325/~1368/~1518/~3232) use **integer** columns, whose `.values` stays a numpy array and passes `set_index` today — they are not currently broken. This PR fixes the two sites that actually raise; the integer-column sites are left untouched to keep the diff minimal (they could be unified cosmetically later if preferred). Verified in a pandas sandbox (`future.infer_string = True`): - `df.set_index(df["str_col"].values)` → `TypeError` (both sites' pattern) - `df.set_index("str_col")` → OK - integer-column variants → OK (unchanged behavior) Fixes #574.
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A minimal fix to get
import wfdbworking again with pandas 3.0+. Not sure if others are required. Happy to iterate further with tests etc. as needed, or close if someone else is already working on a fix!Closes #560