-
Notifications
You must be signed in to change notification settings - Fork 36
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
py3: relative imports fail #26
Comments
If I am reading your Travis build log correctly, you only test on Pretend edit: tested |
Relative imports were removed in import os
import sys
import time
from metaseq import helpers
from metaseq.helpers import data_dir, example_filename
from metaseq._genomic_signal import genomic_signal
import metaseq.plotutils
import integration
import integration.chipseq
import metaseq.colormap_adjust
import metaseq.results_table
import metaseq.tableprinter
from metaseq.version import __version__
import metaseq.persistence but then I got this error:
which I do not have time to look up now, but I'd guess it has to do with the same import issue. |
Yep, due to the dependency on Whenever I need to use it within snakemake, I end up writing a separate script and run it in a py27 env. Awkward? Yes. I think the best solution here is to replace bx-python with the py3-compatible pybigwig. That will require a bit of work and lots more tests. It's already on my list though. That said, depending on what you need to do, deepTools might be a better option than metaseq. |
bx-python has actually been python3 compatible for a year or so, IIRC. Perhaps you should try installing it again? But do not put this high on your todo-list for my sake, I'll easily find a workaround. |
The error you reported is a common error in non-py3-compatible code and, judging from your paths, is coming from bx-python as installed under py35. I had also tried building it a few months ago for py3 in bioconda and didn't have any luck. Are you able to use the |
Sorry, probably not! I always think bx = intervaltree, clustertree because On Tue, May 24, 2016 at 3:46 PM, Ryan Dale notifications@github.com wrote:
|
When I learn more about bigwig, I'll try out https://bitbucket.org/mruffalo/bx-python3 and see if it works. Perhaps it can be bundled with metaseq? It probably will not get more updates, but might be good enough. |
I think it might be more beneficial to port the original bx-python (which I believe is bxlab/bx-python) to Python3 rather than switching to an unmaintained fork. @endrebak you could get Python3 behaviour in Python2 by importing
After this import the following
could be concisely written as
|
(Conda gives a conflicting requirements error, so I installed metaseq with pip.)
When trying to import metaseq, I get the following error:
The text was updated successfully, but these errors were encountered: