Windowns Installation of ete3-3.0.0b35 with Python 3.6.3?

[eric.g...@gmail.com]

Hello there,

I just discovered ETE3 yesterday and just tried quickly to run the following installation command using PIP on my win10 machine with a properly installed Python 3.6.3:

python -m pip install --upgrade ete3

However, I am getting the following error:

#######################################################################
Collecting ete3
Using cached ete3-3.0.0b35.tar.gz
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "c:\users\egourjon\appdata\local\temp\pip-build-m408eskt\ete3\ete3\clustering\clustvalidation.py", line 196, in <module>
from scipy import stats
ModuleNotFoundError: No module named 'scipy'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "<string>", line 1, in <module>
File "C:\Users\egourjon\AppData\Local\Temp\pip-build-m408eskt\ete3\setup.py", line 41, in <module>
import ete3
File "c:\users\egourjon\appdata\local\temp\pip-build-m408eskt\ete3\ete3\__init__.py", line 61, in <module>
from .clustering.clustertree import *
File "c:\users\egourjon\appdata\local\temp\pip-build-m408eskt\ete3\ete3\clustering\__init__.py", line 40, in <module>
from .clustertree import *
File "c:\users\egourjon\appdata\local\temp\pip-build-m408eskt\ete3\ete3\clustering\clustertree.py", line 43, in <module>
from . import clustvalidation
File "c:\users\egourjon\appdata\local\temp\pip-build-m408eskt\ete3\ete3\clustering\clustvalidation.py", line 199, in <module>
from . import stats
File "c:\users\egourjon\appdata\local\temp\pip-build-m408eskt\ete3\ete3\clustering\stats.py", line 1933, in <module>
geometricmean = Dispatch ( (lgeometricmean, (ListType, TupleType)), )
NameError: name 'ListType' is not defined

----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in C:\Users\egourjon\AppData\Local\Temp\pip-build-m408eskt\ete3\

#######################################################################

I have seen that the online website provides an installation guide for Linux and mac but none for windows.

Is there somewhere a proper documentation that describes the various steps to have ETE3 installed on Win?

Related question: I cannot locate on the website any details around ETE3 dependencies nor a confirmation somewhere against which Python version it is compliant with (especially v3 vs. v2 of Python). Is there also such a material available somewhere online?

Thanks
Cheers
Eric

[Jaime Huerta Cepas]

Hi Eric, 

Windows is not officially supported, but most of the functionality (except i.e. ete-build)  should work. This is the list of dependencies (you can get some insights from the website in Download->Linux->Native): 

	- six
	- lxml
	- numpy
	- scipy
	- pyqt4
	- qt4


Then, you can install  ete with pip install -U https://github.com/etetoolkit/ete/archive/qt5.zip




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[Jaime Huerta Cepas]

I forgot to mention that the ete3 branch I referred in my previous email should also work with pyqt5