matplotlib can't import docstring causes error in checkinputs

sanjaynagi / rna-seq-pop

Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data

https://sanjaynagi.github.io/rna-seq-pop/

MIT License

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matplotlib can't import docstring causes error in checkinputs #93

Closed azurillandfriend closed 6 months ago

azurillandfriend commented 7 months ago

Possibly due to some change in matplotlib? Last 3 lines of Checkinputs.log:

File "/usr/lib/python3/dist-packages/mpl_toolkits/mplot3d/axes3d.py", line 23, in from matplotlib import _api, cbook, docstring, _preprocess_data ImportError: cannot import name 'docstring' from 'matplotlib' (/home/dyern/lstm_scratch/rna-seq-pop/.snakemake/conda/bce977d41e12128f7e70506d022b4f3c/lib/python3.10/site-packages/matplotlib/init.py)

sanjaynagi commented 7 months ago

Hey Naomi, yeah, RNA-Seq-Pops conda env have been a bit messed up recently. Will try and fix tmw.

sanjaynagi commented 7 months ago

Have a go now, its working in CI and my computer, so should be OK

sanjaynagi commented 6 months ago

fixed by updating pythonGenomics.yaml - matplotlib==3.8.2, had a bug in 3.8.0