grapetree and Python 3.6

achtman-lab / GrapeTree

GrapeTree is a fully interactive, tree visualization program, which supports facile manipulations of both tree layout and metadata. Click the first link to launch: https://achtman-lab.github.io/GrapeTree/MSTree_holder.html

https://genome.cshlp.org/content/28/9/1395

GNU General Public License v3.0

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grapetree and Python 3.6 #80

Closed crarlus closed 5 years ago

crarlus commented 5 years ago

Hi, I am trying to run grapetree with python 3.6.

I created a conda environment with python 3.6.7 and pip
I installed grapetree via pip install grapetree

Successfully installed DendroPy-4.4.0 Flask-1.0.2 Jinja2-2.10 MarkupSafe-1.1.1 Werkzeug-0.14.1 click-7.0 decorator-4.3.2 grapetree-1.5 itsdangerous-1.1.0 llvmlite-0.27.1 networkx-2.2 numba-0.42.1 numpy-1.16.2 psutil-5.5.1

I get the following error message

$ grapetree -h
Traceback (most recent call last):
File "/home/user/anaconda3/envs/grapetree3/bin/grapetree", line 6, in <module>
from grapetree.grapetree import main
File "/home/user/anaconda3/envs/grapetree3/lib/python3.6/site-packages/grapetree/grapetree.py", line 29, in <module>
from module import app
ModuleNotFoundError: No module named 'module'

The same works however when I install a conda environment with python 2.7

Do you have any hints? Thanks!

zheminzhou commented 5 years ago

It has now been fully tested and updated to work in python 3.6.

martinbaste commented 5 years ago

I'm still seeing this issue. I created a clean environment using conda for python3.6. I tried installing from pypi repository and also from this gh repository by using pip install git+<url>. Getting the same message in both cases.

ModuleNotFoundError: No module named 'module'

luolyaduo commented 5 years ago

python /home/user/anaconda3/envs/grapetree3/lib/python3.6/site-packages/grapetree/grapetree.py -h will work. But I meet with another problem of numba.

dutchscientist commented 5 years ago

I have the same problem as https://github.com/achtman-lab/GrapeTree/issues/80#issuecomment-504987898. Separate Conda environments for python 3.6 does not make a difference. I can run it in a separate environment for 2.7 (lots of warnings though).

Ubuntu 16.04.

mabouelk commented 4 years ago

I have the same problem, is there any help ?

File "/Users/moh/anaconda2/bin/grapetree", line 5, in from grapetree.grapetree import main File "/Users/moh/anaconda2/lib/python2.7/site-packages/grapetree/grapetree.py", line 33, in from module import app ImportError: No module named module