Missing import TreeStyle #354

sebastianwindeck · 2018-05-10T18:13:20Z

Installed Packages

Requirement already satisfied: ete3 in /usr/local/lib/python3.6/dist-packages (3.0.0b35)
Requirement already satisfied: PyQt5 in /usr/local/lib/python3.6/dist-packages (5.10.1)
Requirement already satisfied: sip in /usr/local/lib/python3.6/dist-packages (4.19.8)
Requirement already satisfied: six in /usr/local/lib/python3.6/dist-packages (1.11.0)

Code to resproduce

Example Tree from Documentation: Documentation

from ete3 import Tree, TreeStyle t = Tree() t.populate(50, random_branches=True) t.convert_to_ultrametric() t.show()

Error message

ImportError: cannot import name 'TreeStyle'

Is there some change I missed in the package? Did the class 'TreeStyle' deprecated or did something else happen?

The text was updated successfully, but these errors were encountered:

jhcepas · 2018-05-11T06:51:48Z

this is the usual error you get when some graphic libraries are not correctly installed.
Could you try importing import PyQt5? could it be you are mixing python versions?

mapio · 2018-06-26T09:11:34Z

Really "this is the usual error you get when some graphic libraries are not correctly installed" @jhcepas?

This is an horrible way to signal the problem!

If TreeStyle requires PyQt5 this should be clearly reported in the requirements (your setup.py performs the test after the installation and just reports a warning), or at least should be imported in a try/catch that rises a more descriptive exception.

It's really bad for a new user to try the examples in the docs and have a completely uninformative ImportError: cannot import name 'TreeStyle' as a response.

jhcepas · 2018-06-26T10:53:32Z

I know! it is ugly! we need to fix this...

EricDeveaud · 2019-10-24T16:37:47Z

hello,

same problem here installed PyQt5 and ete3 in my ~/.local directory

module load Python/3.6.0
pip3 install --user PyQt5 ete3

and can't import TreeStyle

python3
Python 3.6.0 (default, Feb 20 2017, 18:52:46) 
[GCC 4.9.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import PyQt5
>>> from ete3 import TreeStyle
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: cannot import name 'TreeStyle'
>>>

NB

ete3 (3.1.1)
PyQt5 (5.13.1)

EricDeveaud · 2019-10-25T15:36:06Z

looking at pyqt libraries I found that (in my case) some system libraries were missing see:

 (py36) mob-suite:/opt/miniconda/envs/py36/lib/python3.6/site-packages/PyQt5> ldd *.so | grep 'not found'| sort | uniq
        libEGL.so.1 => not found
        libGL.so.1 => not found
        libXcomposite.so.1 => not found
        libXcursor.so.1 => not found
        libXdamage.so.1 => not found
        libXfixes.so.3 => not found
        libXi.so.6 => not found
        libXrandr.so.2 => not found
        libXss.so.1 => not found
        libXtst.so.6 => not found
        libasound.so.2 => not found

after installing missing libgGL.so.1

problem solved.

bigmess: ~ > python3.6 -c "from ete3 import TreeStyle"
bigmess: ~ > echo $?
0

jhcepas · 2020-03-28T18:08:38Z

related #444

biocyberman · 2020-04-07T20:17:12Z

Still got this error on Python 3.6, MacOS Catalina, Miniconda 4.6.12

axegard · 2020-04-09T04:57:51Z

I too have this error. Anyone have a temporary workaround? Importing PyQt5 v 5.14.2 does not resolve the issue.

Python 3.7, macOS Catalina 10.15.3 in a pipenv.

dengzq1234 · 2020-04-09T12:36:03Z

As my experience,

for conda user, I would suggest install it as
conda install pyqt

for pip user, I would suggess install with
pip install PyQt5

These work for me

exchhattu · 2020-05-06T00:00:51Z

Following step suggested by @dengzq1234, It worked.

Installed using pip
pip3 install PyQt5

Called TreeStyle as below

Python 3.7.5 (default, Nov  1 2019, 02:16:32)
[Clang 11.0.0 (clang-1100.0.33.8)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from ete3 import PhyloTree, TreeStyle
>>>

himanshub84 · 2020-05-12T20:16:02Z

pip3 install PyQt5==5.11.3
it will work for sure

hjfsg95 · 2020-06-17T21:22:04Z

tried PyQt5==5.14.0, PyQt5==5.11.3, not working
import PyQt5 works
just cannot import TreeStyle from ete3

neel404 · 2020-07-13T12:28:39Z

Any workaround for this issue?

krassowski · 2020-10-12T17:14:37Z

If you are getting this error after the following sequence:

Discovering you need to install PyQt5
Installing PyQt5

you also need to (3) restart your Python and then it should work

mapio · 2020-10-12T20:21:32Z

What do you exactly mean with "restart your Python"?

krassowski · 2020-10-12T20:48:01Z

if you are running Python as scripts - nothing,
if you use interactive Python session from command line - close it and open again,
if you use IPython kernel (e.g. in Jupyter) - restart the kernel.

mapio · 2020-10-13T06:40:24Z

Isn't this obvious given that you suggest to install a new package? I thought you meant something more exotic…

Cecilia-Sensalari · 2020-12-15T15:56:08Z

Hi, I had a TreeStyle import error as well and here is the story how I solved it:
I realized that I installed PyQt5 in /usr/lib/python3/dist-packages mostly likely by looking on the internet and using sudo apt-get. However, my program was using ete3 installed in /home/myname/.local/lib/python3.8/site-packages and it was looking for PyQt5 there too without success.
When I tried to install PyQt5 in that local folder with pip3, its installation was skipped because it found that it was already installed in the /usr/lib....
I solved by removing PyQt5 from /usr/lib... with sudo apt-get remove python3-pyqt5 and then by installing it again with pip3.
Hope this can help somebody else!

jsgounot · 2021-03-31T10:59:57Z

I've got the same problem. I installed ete3 (3.1.2) with conda, which installed pyqt (5.9.2) too. Now I've got the same error message but with nothing to help me.

dengzq1234 · 2021-03-31T11:19:06Z

hi, if you install pyqt successfully via conda, pyqt package should be installed in the python site package, for example `/miniconda3/envs/ete3.1.2/lib/python3.6/site-packages/PyQt5/`. if you couldn't find it try to locate yout pygt and create a link or reinstall it. If it still didn't work, please provide the errors and your installing command. best GOUNOT Jean-Sebastien ***@***.***> 于2021年3月31日周三下午1:00写道：

…

I've got the same problem. I installed ete3 (3.1.2) with conda, which installed pyqt (5.9.2) too. Now I've got the same error message but with nothing to help me. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#354 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGDS2VYUUIWIE7Z6HQ66FLDTGL6D7ANCNFSM4E7JIKXA> .

jsgounot · 2021-03-31T12:43:06Z

I don't know, am I missing something ?

dengzq1234 · 2021-03-31T13:28:57Z

Interesting, would you mind showing me the result of `import sys` `print(sys.path)` ? GOUNOT Jean-Sebastien ***@***.***> 于2021年3月31日周三下午2:43写道：

…

I don't know, am I missing something ? [image: image] <https://user-images.githubusercontent.com/13219245/113145883-92f5d700-9261-11eb-90b4-57da94797f46.png> — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#354 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGDS2V76CVTP3ID2KNDR2U3TGMKGXANCNFSM4E7JIKXA> .

jsgounot · 2021-03-31T13:37:24Z

['/home/jsgounot/anaconda3/envs/ete/bin', '/home/jsgounot/anaconda3/envs/ete/lib_pypy/__extensions__', '/home/jsgounot/anaconda3/envs/ete/lib_pypy', '/home/jsgounot/anaconda3/envs/ete/lib-python/3', '/home/jsgounot/anaconda3/envs/ete/lib-python/3/lib-tk', '/home/jsgounot/anaconda3/envs/ete/lib-python/3/plat-linux2', '', '/home/jsgounot/anaconda3/envs/ete/site-packages', '/home/jsgounot/anaconda3/envs/ete/site-packages/ete3-3.1.2-py3.7.egg', '/home/jsgounot/anaconda3/envs/ete/site-packages/IPython/extensions', '/home/jsgounot/.ipython']

Edit : Is there a place into ete3 code I can modify to have a better error message ?

dengzq1234 · 2021-03-31T13:53:50Z

it seems your PyQt5 is installed under the path "/home/jsgounot/anaconda3/ envs/ete/lib/python3.6/site-packages/", but your python built-in path doesn't include it. But I see you once successfully import PyQt5, do you mind also tracking the path of PyQt5 by "print(PyQt5.__file__)" GOUNOT Jean-Sebastien ***@***.***> 于2021年3月31日周三下午3:37写道：

…

['/home/jsgounot/anaconda3/envs/ete/bin', '/home/jsgounot/anaconda3/envs/ete/lib_pypy/__extensions__', '/home/jsgounot/anaconda3/envs/ete/lib_pypy', '/home/jsgounot/anaconda3/envs/ete/lib-python/3', '/home/jsgounot/anaconda3/envs/ete/lib-python/3/lib-tk', '/home/jsgounot/anaconda3/envs/ete/lib-python/3/plat-linux2', '', '/home/jsgounot/anaconda3/envs/ete/site-packages', '/home/jsgounot/anaconda3/envs/ete/site-packages/ete3-3.1.2-py3.7.egg', '/home/jsgounot/anaconda3/envs/ete/site-packages/IPython/extensions', '/home/jsgounot/.ipython'] — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#354 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGDS2V6ZA6OR7KT7OBB5XNTTGMQSJANCNFSM4E7JIKXA> .

jsgounot · 2021-03-31T14:35:43Z

/home/jsgounot/anaconda3/envs/ete/site-packages/PyQt5/__init__.py

jsgounot · 2021-04-07T10:24:49Z

I finally searched a bit and this is an issue I have with PyQt5. Nevertheless, if you encounter the same issue, try this import, should be more meaningful : from ete3.treeview.main import TreeStyle

dailing57 · 2021-06-10T11:48:52Z

I finally searched a bit and this is an issue I have with PyQt5. Nevertheless, if you encounter the same issue, try this import, should be more meaningful : from ete3.treeview.main import TreeStyle

It says I need QtPy4. But I've installed QtPy5. Should I install QtPy4 anyway?

jhcepas · 2021-06-10T15:51:43Z

no, it should work with Qt5. could you try if pyqt modules are importable regardless of ete3?

…

On Thu, 10 Jun 2021 at 13:49, dailing57 ***@***.***> wrote: I finally searched a bit and this is an issue I have with PyQt5. Nevertheless, if you encounter the same issue, try this import, should be more meaningful : from ete3.treeview.main import TreeStyle It says I need QtPy4. But I've installed QtPy5. Should I install QtPy4 anyway? — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub <#354 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABH6SS2DUE6VY3FS6OIXHDTSCRDHANCNFSM4E7JIKXA> .

dailing57 · 2021-06-10T16:34:11Z

no, it should work with Qt5. could you try if pyqt modules are importable regardless of ete3?
…
On Thu, 10 Jun 2021 at 13:49, dailing57 @.***> wrote: I finally searched a bit and this is an issue I have with PyQt5. Nevertheless, if you encounter the same issue, try this import, should be more meaningful : from ete3.treeview.main import TreeStyle It says I need QtPy4. But I've installed QtPy5. Should I install QtPy4 anyway? — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub <#354 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AABH6SS2DUE6VY3FS6OIXHDTSCRDHANCNFSM4E7JIKXA .

Yes, I can import PyQt5 successfully. But I can't overcome the TreeStyle problem.

stubbsrl · 2021-06-17T13:22:01Z

I have worked my way through this thread trying the solutions and I am now at this same issue. I can also successfully import PyQt5 but when typing from ete3.treeview.main import TreeStyle
I get:
from PyQt4.QtGui import *
ModuleNotFoundError: No module named 'PyQt4'

xguse · 2021-09-01T13:35:07Z

this is very frustrating. I know that that is not helpful. But I feel the need to express this.

theo-allnutt-bioinformatics · 2021-10-14T01:32:54Z

This is still not working.

I have invested a lot of time writing ete3 code and the module is now broken on every machine I install it.

As stubbsrl said, I have also tried every solution and got to the ModuleNotFoundError: No module named 'PyQt4' one.

Is there any dev trying to solve this?

As above, I am using a fresh conda environment python 3.8.

theo-allnutt-bioinformatics · 2021-10-14T01:44:13Z

Ok, because I am using CentOS, I had to do:

sudo yum install mesa-libGL

Then change import back to:

import PyQt5
from ete3 import Tree, PhyloTree,TreeStyle, NodeStyle, faces, AttrFace, CircleFace, TextFace

Now this seems to be working.

knightjdr · 2022-12-03T12:43:37Z

To get this from ete3 import TreeStyle to work on Ubuntu 20.04, I had to install one package:

sudo apt-get update
sudo apt-get install -y libgl1

My minimal requirements file looks like:

ete3==3.1.2
numpy==1.23.5
PyQt5==5.15.7
PyQt5-Qt5==5.15.2
PyQt5-sip==12.11.0
six==1.16.0

jeff-godwin · 2022-12-09T11:27:48Z

Installed everything through conda and it worked for me.

python==3.6.13
PyQt5==5.15.7
PyQt5-sip==12.11.0 (installs along with pyqt)
ete3==3-3.1.2
numpy==1.23.4

Imported TreeStyle through ete3-
import PyQt5
import ete3
from ete3 import Tree, PhyloTree,TreeStyle, NodeStyle, faces, AttrFace, CircleFace, TextFace

Took me a day but got it working for cafe_fig. Cheers for all the pointers above!

jungleblack007 · 2023-04-16T14:12:01Z

pip install PyQt5
works in my ubuntu in WSL

kuang-da · 2024-04-19T14:05:44Z

looking at pyqt libraries I found that (in my case) some system libraries were missing see:

 (py36) mob-suite:/opt/miniconda/envs/py36/lib/python3.6/site-packages/PyQt5> ldd *.so | grep 'not found'| sort | uniq
        libEGL.so.1 => not found
        libGL.so.1 => not found
        libXcomposite.so.1 => not found
        libXcursor.so.1 => not found
        libXdamage.so.1 => not found
        libXfixes.so.3 => not found
        libXi.so.6 => not found
        libXrandr.so.2 => not found
        libXss.so.1 => not found
        libXtst.so.6 => not found
        libasound.so.2 => not found

after installing missing libgGL.so.1

problem solved.

bigmess: ~ > python3.6 -c "from ete3 import TreeStyle"
bigmess: ~ > echo $?
0

I had the exact same error, and this is really helpful. Thank you!

For the missing libgGL.so.1, I did sudo apt install libgl1 as suggested here: https://stackoverflow.com/a/68666500/9936569

jhcepas added the improvement label Jun 26, 2018

taylorreiter mentioned this issue Apr 24, 2019

error in rule root_tree on blank AWS linux metagenome-atlas/atlas#202

Closed

LKremer mentioned this issue Sep 5, 2019

module 'ete3' has no attribute 'TreeStyle' LKremer/CAFE_fig#3

Closed

dengzq1234 mentioned this issue Feb 21, 2020

LnL error while running ete3 #427

Closed

jhcepas closed this as completed Mar 28, 2020

Neato-Nick mentioned this issue Feb 15, 2023

M1 MacBook Pro Installation Problem (osx-arm64?) #656

Open

Missing import TreeStyle #354

Missing import TreeStyle #354

Comments

sebastianwindeck commented May 10, 2018

jhcepas commented May 11, 2018

mapio commented Jun 26, 2018

jhcepas commented Jun 26, 2018

EricDeveaud commented Oct 24, 2019

EricDeveaud commented Oct 25, 2019

jhcepas commented Mar 28, 2020

biocyberman commented Apr 7, 2020

axegard commented Apr 9, 2020

dengzq1234 commented Apr 9, 2020 • edited Loading

exchhattu commented May 6, 2020

himanshub84 commented May 12, 2020

hjfsg95 commented Jun 17, 2020

neel404 commented Jul 13, 2020

krassowski commented Oct 12, 2020

mapio commented Oct 12, 2020

krassowski commented Oct 12, 2020

mapio commented Oct 13, 2020

Cecilia-Sensalari commented Dec 15, 2020 • edited Loading

jsgounot commented Mar 31, 2021

dengzq1234 commented Mar 31, 2021 via email

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dengzq1234 commented Mar 31, 2021 via email

jsgounot commented Mar 31, 2021

jsgounot commented Apr 7, 2021

dailing57 commented Jun 10, 2021

jhcepas commented Jun 10, 2021 via email

dailing57 commented Jun 10, 2021

stubbsrl commented Jun 17, 2021

xguse commented Sep 1, 2021

theo-allnutt-bioinformatics commented Oct 14, 2021

theo-allnutt-bioinformatics commented Oct 14, 2021

knightjdr commented Dec 3, 2022 • edited Loading

jeff-godwin commented Dec 9, 2022

jungleblack007 commented Apr 16, 2023

kuang-da commented Apr 19, 2024

dengzq1234 commented Apr 9, 2020 •

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