Jupyter Notebook vs Python/PyCharm

[hansen7]

Hi, there.

I am following the tutorial here, it works perfectly with Jupyter Notebook, but I do encounter the following errors when running the code in command line or PyCharm.

• [x] I have checked that this issue has not already been reported.
• [x] I have confirmed this bug exists on the latest version of scanpy.
• [ ] (optional) I have confirmed this bug exists on the master branch of scanpy.

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Minimal code sample (that we can copy&paste without having any data)

from https://scanpy-tutorials.readthedocs.io/en/latest/pbmc3k.html

adata.var['mt'] = adata.var_names.str.startswith('MT-')
sc.pp.calculate_qc_metrics(adata, qc_vars=['mt'], percent_top=None, log1p=False, inplace=True)

TypeError: calculate_qc_metrics() got an unexpected keyword argument 'log1p'

Versions

[Paste the output of scanpy.logging.print_versions() leaving a blank line after the details tag]

[Zethson]

Hi,

As requested in the issue template, what scanpy versions are you running? Thanks.

[hansen7]

Thanks, I am running the version of 1.4.5.1

[Zethson]

Thanks, I am running the version of 1.4.5.1

Assuming that it is one of 1.4.1 or 1.5.1 I would suggest that you upgrade to the latest scanpy version. What you are using is quite old. If the problem still occurs we can discuss it further.