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pysurfer on python3.6 status

See original GitHub issue

I wanted to keep track of the status of pysurfer on python 3.6, which currently seems to work, but not as straightforwardly as one would like.

This could also be a wiki page, but I always forget those exist, and ideally this will be “closed” one day. And hopefully we can link to relevant issues in upstream packages.

Here’s how I had success getting a conda environment with pysurfer dependencies and a few other tools that are useful for doing science.

conda create -n mayavi pip 
. activate mayavi
conda install -c conda-forge mayavi
conda install -c conda-forge mayavi matplotlib pandas scipy seaborn ipython jupyter
pip install pysurfer

Then I was able to start IPython and use pysurfer with the following environment variable settings:

QT_API=pyqt
ETS_TOOLKIT=qt4

As I understand it, the current blocker is that Mayavi’s dependencies require PyQT4, whereas the main anaconda matplotlib only works with PyQT5. However, there are now conda-forge packages with sufficient dependency chains.

Does this look right? Does anyone know what issues to track to see when Mayavi will work with PyQT5?

Issue Analytics

State:
Created 6 years ago
Comments:25 (23 by maintainers)

Top GitHub Comments

2reactions

mwaskomcommented, Oct 24, 2017

Seems to!

[kianilab-cs1 ~]$ conda create -n pysurfer -c conda-forge python=3.6 pysurfer
Fetching package metadata .............
Solving package specifications: .

Package plan for installation in environment /home/mwaskom/anaconda/envs/pysurfer:

The following NEW packages will be INSTALLED:

    apptools:        4.4.0-py36_0          conda-forge
    ca-certificates: 2017.7.27.1-0         conda-forge
    cairo:           1.14.6-4              conda-forge
    certifi:         2017.7.27.1-py36_0    conda-forge
    configobj:       5.0.6-py36_0                     
    cycler:          0.10.0-py36_0         conda-forge
    envisage:        4.5.1-py36_0          conda-forge
    expat:           2.2.1-0               conda-forge
    fontconfig:      2.12.1-4              conda-forge
    freetype:        2.7-1                 conda-forge
    future:          0.16.0-py36_0         conda-forge
    gettext:         0.19.7-1              conda-forge
    glib:            2.51.4-0              conda-forge
    graphite2:       1.3.9-0               conda-forge
    h5py:            2.7.1-py36_1          conda-forge
    harfbuzz:        1.4.3-0               conda-forge
    hdf5:            1.8.18-1              conda-forge
    icu:             58.1-1                conda-forge
    imageio:         2.2.0-py36_0          conda-forge
    intel-openmp:    2018.0.0-h15fc484_7              
    jpeg:            9b-1                  conda-forge
    jsoncpp:         0.10.6-1              conda-forge
    libffi:          3.2.1-3               conda-forge
    libgcc-ng:       7.2.0-h7cc24e2_2                 
    libgfortran:     3.0.0-1                          
    libgfortran-ng:  7.2.0-h9f7466a_2                 
    libiconv:        1.14-4                conda-forge
    libpng:          1.6.28-1              conda-forge
    libstdcxx-ng:    7.2.0-h7a57d05_2                 
    libtiff:         4.0.7-0               conda-forge
    libxml2:         2.9.5-0               conda-forge
    matplotlib:      1.5.3-np113py36_8     conda-forge
    mayavi:          4.5.0-np113py36_2     conda-forge
    mkl:             2018.0.0-hb491cac_4              
    ncurses:         5.9-10                conda-forge
    nibabel:         2.2.0-py36_0          conda-forge
    numpy:           1.13.3-py36ha12f23b_0            
    olefile:         0.44-py36_0           conda-forge
    openssl:         1.0.2l-0              conda-forge
    pango:           1.40.4-0              conda-forge
    pcre:            8.39-0                conda-forge
    pillow:          4.3.0-py36_0          conda-forge
    pip:             9.0.1-py36_0          conda-forge
    pixman:          0.34.0-0              conda-forge
    pydicom:         0.9.9-py36_0          conda-forge
    pyface:          5.1.0-py36_1          conda-forge
    pygments:        2.2.0-py36_0          conda-forge
    pyparsing:       2.2.0-py36_0          conda-forge
    pyqt:            4.11.4-py36_2         conda-forge
    pysurfer:        0.8.0-py36_0          conda-forge
    python:          3.6.3-0               conda-forge
    python-dateutil: 2.6.1-py36_0          conda-forge
    pytz:            2017.2-py36_0         conda-forge
    qt:              4.8.7-7               conda-forge
    readline:        6.2-0                 conda-forge
    scipy:           0.19.1-py36h9976243_3            
    setuptools:      36.6.0-py36_1         conda-forge
    sip:             4.18-py36_1           conda-forge
    six:             1.11.0-py36_1         conda-forge
    sqlite:          3.13.0-1              conda-forge
    tbb:             2018_20170919-0       conda-forge
    tk:              8.5.19-2              conda-forge
    tornado:         4.5.2-py36_0          conda-forge
    traits:          4.6.0-py36_1          conda-forge
    traitsui:        5.1.0-py36_0          conda-forge
    vtk:             7.1.1-py36_202        conda-forge
    wheel:           0.30.0-py_1           conda-forge
    xz:              5.2.3-0               conda-forge
    zlib:            1.2.8-3               conda-forge

Proceed ([y]/n)? y

libgcc-ng-7.2. 100% |########################################| Time: 0:00:00  48.42 MB/s
libgfortran-ng 100% |########################################| Time: 0:00:00  55.96 MB/s
libstdcxx-ng-7 100% |########################################| Time: 0:00:00  58.65 MB/s
numpy-1.13.3-p 100% |########################################| Time: 0:00:00  58.05 MB/s
olefile-0.44-p 100% |########################################| Time: 0:00:00   2.35 MB/s
pillow-4.3.0-p 100% |########################################| Time: 0:00:00   3.81 MB/s
imageio-2.2.0- 100% |########################################| Time: 0:00:00  11.56 MB/s
matplotlib-1.5 100% |########################################| Time: 0:00:00  10.32 MB/s
mayavi-4.5.0-n 100% |########################################| Time: 0:00:01   6.80 MB/s
pysurfer-0.8.0 100% |########################################| Time: 0:00:00   6.53 MB/s
#
# To activate this environment, use:
# > source activate pysurfer
#
# To deactivate an active environment, use:
# > source deactivate
#

1reaction

christianbrodbeckcommented, Oct 24, 2017

It was too good to be true 😃