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rmarkello / abagen

A toolbox for working with Allen Human Brain Atlas microarray expression data
https://abagen.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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DataFrame.set_axis() got an unexpected keyword argument 'inplace' with pandas 2.1.2 #225

Closed JohannesWiesner closed 9 months ago

JohannesWiesner commented 10 months ago

With the latest version of pandas I get this error:


  File ~/micromamba/envs/csp_wiesner_johannes/lib/python3.11/site-packages/abagen/allen.py:444 in get_expression_data
    microarray = probes_.collapse_probes(flatten_dict(files, 'microarray'),

  File ~/micromamba/envs/csp_wiesner_johannes/lib/python3.11/site-packages/abagen/probes_.py:757 in collapse_probes
    micro = micro.set_axis(symbols, axis=1, inplace=False)

TypeError: DataFrame.set_axis() got an unexpected keyword argument 'inplace'

Seem like the latest version of pandas does not have this argument anymore.

One should either update the requirements file and specify a maximum pandas version or rewrite the code so it works with pandas 2.1.2

dadabende commented 10 months ago

happened the same to me. A PR has been made to update the code; try git clone installation instead of pip install to get the most up-to-date probes_.py (worked for me)

liuzhenqi77 commented 9 months ago

Fixed for the main branch. Please reopen if this issue still persists.

JohannesWiesner commented 7 months ago

Issue still persists. Created a new environment using

micromamba create -n abagen -c conda-forge nilearn numpy pandas spyder

(this will result in pandas == 2.2.0)

Activated this environment and pip-installed abagen:

micromamba activate abagen pip install abagen

Ran abagen.get_expression_data and got 

 expression, counts, report = abagen.get_expression_data(atlas_img,

  File ~/micromamba/envs/abagen/lib/python3.12/site-packages/abagen/allen.py:444 in get_expression_data
    microarray = probes_.collapse_probes(flatten_dict(files, 'microarray'),

  File ~/micromamba/envs/abagen/lib/python3.12/site-packages/abagen/probes_.py:757 in collapse_probes
    micro = micro.set_axis(symbols, axis=1, inplace=False)

TypeError: DataFrame.set_axis() got an unexpected keyword argument 'inplace'
liuzhenqi77 commented 7 months ago

Hi @JohannesWiesner, please install from GitHub (pip install git+https://github.com/rmarkello/abagen.git) as we have not released a new version on PyPI yet.

elosse commented 6 months ago

Hi @JohannesWiesner, please install from GitHub (pip install git+https://github.com/rmarkello/abagen.git) as we have not released a new version on PyPI yet.

Hi @liuzhenqi77 , I have encountered the same issue and tried following your suggestion to download directly from GitHub. This unfortunately yielded the following error: 

 File ~/anaconda3/lib/python3.11/site-packages/abagen/allen.py:461 in get_expression_data
    labels = atlas[subj].label_samples(annotation[subj], tolerance)

  File ~/anaconda3/lib/python3.11/site-packages/abagen/matching.py:255 in label_samples
    labels = self._match_volume(samples, abs(tolerance))

  File ~/anaconda3/lib/python3.11/site-packages/abagen/matching.py:334 in _match_volume
    matches = self.tree.query_ball_point(subsamp[cols], tol)

  File _ckdtree.pyx:947 in scipy.spatial._ckdtree.cKDTree.query_ball_point

  File ~/anaconda3/lib/python3.11/site-packages/pandas/core/generic.py:1526 in __nonzero__
    raise ValueError(

ValueError: The truth value of a Series is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().
liuzhenqi77 commented 6 months ago

Hi @elosse, this might have been cause by scipy scipy/scipy/issues/18800 and appears to have been fixed. Could you please update your scipy to latest version if possible, and let us know if it works? Thanks!

elosse commented 6 months ago

Hi @liuzhenqi77 , updating scipy did fix the issue, while using pandas 2.2.1 . Thank you!

Feliciayww commented 5 months ago

I had the same problem.

expression = abagen.get_expression_data(atlas['image'])
C:\Users\12772\AppData\Roaming\Python\Python311\site-packages\abagen\probes_.py:147: FutureWarning: DataFrame.groupby with axis=1 is deprecated. Do `frame.T.groupby(...)` without axis instead.
  return io.read_microarray(microarray).groupby(sid, axis=1).mean()
C:\Users\12772\AppData\Roaming\Python\Python311\site-packages\abagen\probes_.py:147: FutureWarning: DataFrame.groupby with axis=1 is deprecated. Do `frame.T.groupby(...)` without axis instead.
  return io.read_microarray(microarray).groupby(sid, axis=1).mean()
C:\Users\12772\AppData\Roaming\Python\Python311\site-packages\abagen\probes_.py:147: FutureWarning: DataFrame.groupby with axis=1 is deprecated. Do `frame.T.groupby(...)` without axis instead.
  return io.read_microarray(microarray).groupby(sid, axis=1).mean()
C:\Users\12772\AppData\Roaming\Python\Python311\site-packages\abagen\probes_.py:147: FutureWarning: DataFrame.groupby with axis=1 is deprecated. Do `frame.T.groupby(...)` without axis instead.
  return io.read_microarray(microarray).groupby(sid, axis=1).mean()
C:\Users\12772\AppData\Roaming\Python\Python311\site-packages\abagen\probes_.py:147: FutureWarning: DataFrame.groupby with axis=1 is deprecated. Do `frame.T.groupby(...)` without axis instead.
  return io.read_microarray(microarray).groupby(sid, axis=1).mean()
C:\Users\12772\AppData\Roaming\Python\Python311\site-packages\abagen\probes_.py:147: FutureWarning: DataFrame.groupby with axis=1 is deprecated. Do `frame.T.groupby(...)` without axis instead.
  return io.read_microarray(microarray).groupby(sid, axis=1).mean()
Traceback (most recent call last):
  File "F:\ProgramData\anaconda3\Lib\site-packages\IPython\core\interactiveshell.py", line 3553, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-13-3a6b7b093269>", line 1, in <module>
    expression = abagen.get_expression_data(atlas['image'])
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\12772\AppData\Roaming\Python\Python311\site-packages\abagen\allen.py", line 444, in get_expression_data
    microarray = probes_.collapse_probes(flatten_dict(files, 'microarray'),
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\12772\AppData\Roaming\Python\Python311\site-packages\abagen\probes_.py", line 757, in collapse_probes
    micro = micro.set_axis(symbols, axis=1, inplace=False)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: DataFrame.set_axis() got an unexpected keyword argument 'inplace'

I installed abagen version 0.1.4, python3.11, pandas 2.2.1, and scipy is also the latest version.

HelloWorldLTY commented 5 months ago

Same problem here.

HelloWorldLTY commented 5 months ago

Downgrade pandas to 1.5.3 works for me, with a warning:

FutureWarning: DataFrame.set_axis 'inplace' keyword is deprecated and will be removed in a future version. Use obj = obj.set_axis(..., copy=False) instead tar_collect.set_axis(selected_targets, axis=1, inplace=True)

liuzhenqi77 commented 5 months ago

Please try installing from GitHub (pip install git+https://github.com/rmarkello/abagen.git) as we have not released a new version on PyPI yet.

Feliciayww commented 5 months ago

pip install git+https://github.com/rmarkello/abagen.git

Thank you. My problem was solved after downloading the latest version of abagen.