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methylprep not working with pandas version >2 due to API changes #125

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ghost opened this issue Jul 19, 2023 · 0 comments
Open

methylprep not working with pandas version >2 due to API changes #125

ghost opened this issue Jul 19, 2023 · 0 comments

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@ghost
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ghost commented Jul 19, 2023

Exception raised when running a pipeline:

Traceback (most recent call last):
File "", line 1, in
File "/home/paul/miniconda3/lib/python3.11/site-packages/methylprep/processing/pipeline.py", line 331, in run_pipeline
data_container = SampleDataContainer(
^^^^^^^^^^^^^^^^^^^^
File "/home/paul/miniconda3/lib/python3.11/site-packages/methylprep/processing/pipeline.py", line 590, in init
infer_type_I_probes(self, debug=self.debug)
File "/home/paul/miniconda3/lib/python3.11/site-packages/methylprep/processing/infer_channel_switch.py", line 19, in infer_type_I_probes
channels = get_infer_channel_probes(container.manifest, container.green_idat, container.red_idat, debug=debug)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/paul/miniconda3/lib/python3.11/site-packages/methylprep/processing/infer_channel_switch.py", line 171, in get_infer_channel_probes
oobG_IG = oobG.append(green_in_band).sort_index()
^^^^^^^^^^^
File "/home/paul/miniconda3/lib/python3.11/site-packages/pandas/core/generic.py", line 5989, in getattr
return object.getattribute(self, name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'DataFrame' object has no attribute 'append'. Did you mean: '_append'?

It seems this is the reason:
https://stackoverflow.com/questions/75956209/dataframe-object-has-no-attribute-append
Problem's solved if I downgrade to pandas 1.5.3

Suggested change:

  1. Bump the requirement to >2 and adapt the corresponding change
  2. Limit the requirement to <2
  3. Check pandas version and use different functions accordingly
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