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Fix: Error handling and robustness improvements in gmd()#7

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Yicheng-Zhao1999 wants to merge 10 commits into
KMueller-Lab:mainfrom
Yicheng-Zhao1999:20260616/#414-double-check-errors-in-python
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Fix: Error handling and robustness improvements in gmd()#7
Yicheng-Zhao1999 wants to merge 10 commits into
KMueller-Lab:mainfrom
Yicheng-Zhao1999:20260616/#414-double-check-errors-in-python

docs: document whole-file download bottleneck and parquet recommendation

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