[BUG]

[kavousisiavash]

Describe the bug Hi i get this error TypeError: DeseqDataSet.init() got an unexpected keyword argument 'design'

when run this part of documentation :

https://pydeseq2.readthedocs.io/en/latest/auto_examples/plot_step_by_step.html#sphx-glr-auto-examples-plot-step-by-step-py

If I remove the design, the code will run, but this has consequences that you know better. How should I solve this problem?

[BorisMuzellec]

Hi @kavousisiavash, indeed, this is because this feature is only available in the 0.5.0-rc1 pre-release that was published yesterday.

You can either:

• install the latest version using the --pre flag (pip install --pre pydeseq2)
• or use the version you have currently installed and refer to the "stable" version of the docs: https://pydeseq2.readthedocs.io/en/stable/auto_examples/plot_minimal_pydeseq2_pipeline.html

You should be able to see (and choose) which version of the docs you are reading from the bottom-right corner of the read-the-docs page:

[kavousisiavash]

Hello Thanks for your help I first ran the code you introduced Then I checked the version via the command prompt But the problem was not solved.

[BorisMuzellec]

@kavousisiavash you still have v 0.4.12 installed. If you want to use the same environment, you need to use the --upgrade flag. (pip install --upgrade --pre pydeseq2)

Also, remember to restart the jupyter kernel once the installation is done.