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nbconvert disabled in IPython 5.1.0 easyconfig using Python 2.7.12 #3825

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boegel opened this issue Nov 17, 2016 · 1 comment
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nbconvert disabled in IPython 5.1.0 easyconfig using Python 2.7.12 #3825

boegel opened this issue Nov 17, 2016 · 1 comment
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@boegel
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boegel commented Nov 17, 2016

I was forced to exclude the nbconvert extension from the IPython 5.1.0 easyconfig using Python 2.7.12 as a base in #3823, because it was responsible for the sanity check failing.

Any sanity check command trying to access the IPython module failed with an error like this:

== 2016-11-17 16:36:01,157 extensioneasyblock.py:136 WARNING Sanity check for ipywidgets failed: ipywidgets failed to install, cmd 'python -c 'import ipywidgets'' (stdin: None) output: Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/IPython/5.1.0-intel-2016b-Python-2.7.12/lib/python2.7/site-packages/ipywidgets/__init__.py", line 20, in <module>
    from IPython import get_ipython
  File "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/IPython/5.1.0-intel-2016b-Python-2.7.12/lib/python2.7/site-packages/IPython/__init__.py", line 48, in <module>
    from .core.application import Application
  File "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/IPython/5.1.0-intel-2016b-Python-2.7.12/lib/python2.7/site-packages/IPython/core/application.py", line 25, in <module>
    from IPython.core import release, crashhandler
  File "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/IPython/5.1.0-intel-2016b-Python-2.7.12/lib/python2.7/site-packages/IPython/core/crashhandler.py", line 28, in <module>
    from IPython.core import ultratb
  File "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/IPython/5.1.0-intel-2016b-Python-2.7.12/lib/python2.7/site-packages/IPython/core/ultratb.py", line 128, in <module>
    from IPython.utils.terminal import get_terminal_size
  File "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/IPython/5.1.0-intel-2016b-Python-2.7.12/lib/python2.7/site-packages/IPython/utils/terminal.py", line 22, in <module>
    from backports.shutil_get_terminal_size import get_terminal_size as _get_terminal_size
ImportError: No module named shutil_get_terminal_size

The problem was that the entrypoints Python package (https://pypi.python.org/pypi/entrypoints), which is required for nbconvert, pulls in the configparser package (https://pypi.python.org/pypi/configparser) as a dependency, which also provides a backports package.

The import from backports.shutil_get_terminal_size fails because it is hitting the backports namespace provided by configparser rather than the one provided by the backports.shutil_get_terminal_size package (https://pypi.python.org/pypi/backports.shutil_get_terminal_size).

At this time, I have no idea why this suddenly pops up now, especially since the tests reports in #3424 show that this originally was no problem, even though all components responsible for this problem were already included...

@boegel
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boegel commented Apr 20, 2017

fixed in #4504

@boegel boegel closed this as completed Apr 20, 2017
wpoely86 added a commit to wpoely86/easybuild-easyconfigs that referenced this issue May 8, 2017
* origin/develop: (235 commits)
  add checksum for ViennaRNA 2.3.5 source tarball
  adding easyconfigs: ViennaRNA-2.3.5-intel-2017a.eb
  add toyplot extension in ipyrad easyconfig file
  add patch file for configparser as extension in IPython easyconfig
  adding easyconfigs: ipyrad-0.6.15-intel-2017a-Python-2.7.13.eb, h5py-2.7.0-intel-2017a-Python-2.7.13.eb, pkgconfig-1.2.2-intel-2017a-Python-2.7.13.eb, pkg-config-0.29.2-GCCcore-6.3.0.eb
  adding easyconfigs: IPython-5.3.0-intel-2017a-Python-2.7.13.eb
  Change source_urls of pycrypto to https://pypi.python.org/packages/source/p/pycrypto/: A crypto library should be downloaded via https, python.org seems more reliable than dlitz.net, dlitz.net is currently not online.
  re-add nbconvert extension in IPython easyconfigs
  add patch to avoid configparser declaring ownership of backports namespace, fixes easybuilders#3825
  adding easyconfigs: GSL-2.3-intel-2017a.eb
  adding easyconfigs: PyZMQ-16.0.2-intel-2017a-Python-2.7.13-zmq4.eb, ZeroMQ-4.2.2-intel-2017a.eb, OpenPGM-5.2.122-intel-2017a.eb, libsodium-1.0.12-intel-2017a.eb
  adding easyconfigs: numba-0.32.0-intel-2017a-Python-2.7.13.eb
  install libiconv with GCCcore rather than intel toolchain
  adding easyconfigs: libiconv-1.15-intel-2017a.eb
  v6.0
  adding easyconfigs: g2lib-1.4.0-intel-2017a.eb, g2clib-1.6.0-intel-2017a.eb
  adding easyconfigs: HDF-4.2.12-intel-2017a.eb
  adding easyconfigs: UDUNITS-2.2.24-intel-2017a.eb
  adding easyconfigs: cURL-7.54.0-GCCcore-6.3.0.eb
  adding easyconfigs: makedepend-1.0.5-GCCcore-6.3.0.eb, xorg-macros-1.19.1-GCCcore-6.3.0.eb, xproto-7.0.31-GCCcore-6.3.0.eb
  ...
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