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nbconvert disabled in IPython 5.1.0 easyconfig using Python 2.7.12 #3825
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boegel
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boegel
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fixed in #4504 |
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* 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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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:The problem was that the
entrypoints
Python package (https://pypi.python.org/pypi/entrypoints), which is required fornbconvert
, pulls in theconfigparser
package (https://pypi.python.org/pypi/configparser) as a dependency, which also provides abackports
package.The import from
backports.shutil_get_terminal_size
fails because it is hitting thebackports
namespace provided byconfigparser
rather than the one provided by thebackports.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...
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