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saketkc / pysradb

Package for fetching metadata and downloading data from SRA/ENA/GEO
https://saketkc.github.io/pysradb
BSD 3-Clause "New" or "Revised" License
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[BUG] #71

Closed mflynn-lanl closed 3 years ago

mflynn-lanl commented 3 years ago

Describe the bug ModuleNotFoundError when importing SRAweb

To Reproduce conda create -c bioconda -n pysradb PYTHON=3 pysradb conda activate pysradb python

from pysradb import SRAweb Traceback (most recent call last): File "", line 1, in ModuleNotFoundError: No module named 'pysradb.sraweb'

Desktop (please complete the following information):

saketkc commented 3 years ago

Thanks for the bug report @mflynn-lanl! I suspect this is coming from a pip+conda mixup. Note that the latest stable version of pysradb is 0.11.1. I think you have 0.9.0 installed through pip? bioconda also has the latest pysradb.

Here's a Google colab notebook for demonstration: https://colab.research.google.com/drive/15DIzoN04KeQosXSe1JRlDyKqIoKb9V-o?usp=sharing

I would suggest deleting the pysradb environment and redoing the steps:

conda env remove -n pysradb
conda create -c bioconda -n pysradb PYTHON=3 pysradb
conda activate pysradb

Newer versions of conda also support deleting automatically if you create an environment with a name that already exists. Please feel free to reopen if you are still facing issues.

mflynn-lanl commented 3 years ago

I used the exact steps you suggested

mflynn-lanl commented 3 years ago

I was able to install the latest version using pip

saketkc commented 3 years ago

Thanks for the update @mflynn-lanl! I am unable to reproduce this either using pip or conda, so I will go ahead and (re)close this.