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tariks / peakachu

Genome-wide contact analysis using sklearn
MIT License
57 stars 9 forks source link

No module named 'straw' #24

Open SSHH007 opened 8 months ago

SSHH007 commented 8 months ago

Hello Tariks,

I run into the problem "No module named 'straw'", although I have installed hicstraw. What package do I miss? Many thanks.

sshh

jgoodson commented 8 months ago

It appears that straw refers to https://github.com/aidenlab/straw although the current versions of the hic-straw PyPI package installs as hicstraw and not straw. I was able to work around this by installing hic-straw from PyPI and manually changing all instances of import straw in this package to import hicstraw as straw. This appeared to successfully complete a full training run on the training dataset in the readme.

I expect this has something to do with refactoring of some package(s) which this program depends on. This package should probably specify the specific straw package version it has a dependency on in the package setup, although there may be more appropriate solutions. It appears from a quick inspection that version 1.0.0 of hic-straw changed the module name, meaning installing version 0.0.6 (the prior version on PyPI) might be what is expected here, although I am not sure how this dependency would have previously been brought in with the install procedure described in the readme. Installing hic-straw==0.0.6 also allowed the program to run, without any further modification.

SSHH007 commented 8 months ago

Thanks. the problem was solved.

SSHH007 commented 8 months ago

thank you very much.

On Wed, Jan 3, 2024 at 8:30 AM Jonathan Goodson @.***> wrote:

It appears that straw refers to https://github.com/aidenlab/straw although the current versions of the hic-straw PyPI package https://pypi.org/project/hic-straw/ installs as hicstraw and not straw. I was able to work around this by installing hic-straw from PyPI and manually changing all instances of import straw in this package to import hicstraw as straw. This appeared to successfully complete a full training run on the training dataset in the readme.

I expect this has something to do with refactoring of some package(s) which this program depends on. This package should probably specify the specific straw package version it has a dependency on in the package setup, although there may be more appropriate solutions. It appears from a quick inspection that version 1.0.0 of hic-straw changed the module name, meaning installing version 0.0.6 (the prior version on PyPI) might be what is expected here, although I am not sure how this dependency would have previously been brought in with the install procedure described in the readme.

— Reply to this email directly, view it on GitHub https://github.com/tariks/peakachu/issues/24#issuecomment-1875375274, or unsubscribe https://github.com/notifications/unsubscribe-auth/AH6AF6Q7WHHTJF6MB3UABDLYMVMPLAVCNFSM6AAAAABBKZJEZSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNZVGM3TKMRXGQ . You are receiving this because you authored the thread.Message ID: @.***>