jupytext command throws NameError: name '_' is not defined in a conda environment

[bnjasim]

jupytext is installed and the paired notebooks is working great. (As I update the notebook, the associated .py file is also updated automatically. cool!). But running any of the commands jupytext notebook.ipynb --to md --output - throws a NameError.

Here is the stacktrace:
Traceback (most recent call last): File "/home/binu.jasim/miniconda3/envs/pytorch/bin/jupytext", line 7, in <module> from jupytext.cli import jupytext File "/home/binu.jasim/miniconda3/envs/pytorch/lib/python3.6/site-packages/jupytext/__init__.py", line 26, in <module> from .contentsmanager import TextFileContentsManager File "/home/binu.jasim/miniconda3/envs/pytorch/lib/python3.6/site-packages/jupytext/contentsmanager.py", line 11, in <module> from notebook.services.contents.filemanager import FileContentsManager File "/home/binu.jasim/miniconda3/envs/pytorch/lib/python3.6/site-packages/notebook/services/contents/filemanager.py", line 22, in <module> from .manager import ContentsManager File "/home/binu.jasim/miniconda3/envs/pytorch/lib/python3.6/site-packages/notebook/services/contents/manager.py", line 39, in <module> class ContentsManager(LoggingConfigurable): File "/home/binu.jasim/miniconda3/envs/pytorch/lib/python3.6/site-packages/notebook/services/contents/manager.py", line 73, in ContentsManager untitled_notebook = Unicode(_("Untitled"), config=True, NameError: name '_' is not defined

conda list shows:
# packages in environment at /home/binu.jasim/miniconda3/envs/pytorch: _nb_ext_conf 0.4.0 py36_1 alabaster 0.7.10 py36h306e16b_0 anaconda-client 1.6.14 py36_0 asn1crypto 0.24.0 py36_0 babel 2.5.3 py36_0 backcall 0.1.0 py36_0 bleach 2.1.3 py36_0 boto 2.49.0 <pip> boto3 1.9.0 <pip> botocore 1.12.0 <pip> bz2file 0.98 <pip> bzip2 1.0.6 h9a117a8_4 ca-certificates 2018.03.07 0 certifi 2018.4.16 py36_0 certifi 2018.8.24 <pip> cffi 1.11.5 py36h9745a5d_0 chardet 3.0.4 py36h0f667ec_1 clyent 1.2.2 py36h7e57e65_1 cmake 3.9.4 h142f0e9_0 colorama 0.3.9 <pip> cryptography 2.2.2 py36h14c3975_0 curl 7.59.0 h84994c4_0 cycler 0.10.0 py36h93f1223_0 cymem 1.31.2 <pip> cytoolz 0.9.0.1 <pip> dbus 1.13.2 h714fa37_1 decorator 4.3.0 py36_0 dill 0.2.8.2 <pip> docutils 0.14 py36hb0f60f5_0 en-core-web-sm 2.0.0 <pip> entrypoints 0.2.3 py36h1aec115_2 expat 2.2.5 he0dffb1_0 fontconfig 2.12.6 h49f89f6_0 fr-core-news-sm 2.0.0 <pip> freetype 2.8 hab7d2ae_1 gensim 3.5.0 <pip> gitdb2 2.0.4 <pip> GitPython 2.1.11 <pip> glib 2.56.1 h000015b_0 gmp 6.1.2 h6c8ec71_1 googletrans 2.3.0 <pip> gst-plugins-base 1.14.0 hbbd80ab_1 gstreamer 1.14.0 hb453b48_1 html5lib 1.0.1 py36h2f9c1c0_0 icu 58.2 h9c2bf20_1 idna 2.7 <pip> idna 2.6 py36h82fb2a8_1 imagesize 1.0.0 py36_0 intel-openmp 2018.0.0 8 ipykernel 4.8.2 py36_0 ipython 6.3.1 py36_0 ipython_genutils 0.2.0 py36hb52b0d5_0 ipywidgets 7.2.1 py36_0 jedi 0.12.0 py36_0 jinja2 2.10 py36ha16c418_0 jmespath 0.9.3 <pip> jpeg 9b h024ee3a_2 jsonschema 2.6.0 py36h006f8b5_0 jupyter-tensorboard 0.1.7 <pip> jupyter_client 5.2.3 py36_0 jupyter_core 4.4.0 py36h7c827e3_0 jupytext 0.6.4 <pip> kiwisolver 1.0.1 py36h764f252_0 libcurl 7.59.0 h1ad7b7a_0 libedit 3.1 heed3624_0 libffi 3.2.1 hd88cf55_4 libgcc-ng 7.2.0 hdf63c60_3 libgfortran-ng 7.2.0 hdf63c60_3 libpng 1.6.34 hb9fc6fc_0 libsodium 1.0.16 h1bed415_0 libssh2 1.8.0 h9cfc8f7_4 libstdcxx-ng 7.2.0 hdf63c60_3 libuv 1.20.0 h14c3975_0 libxcb 1.13 h1bed415_1 libxml2 2.9.8 hf84eae3_0 magma-cuda90 2.3.0 1 pytorch Markdown 2.6.11 <pip> markupsafe 1.0 py36hd9260cd_1 matplotlib 2.2.2 py36h0e671d2_1 mistune 0.8.3 py36h14c3975_1 mkl 2018.0.2 1 mkl-include 2018.0.2 1 mkl_fft 1.0.1 py36h3010b51_0 mkl_random 1.0.1 py36h629b387_0 mock 2.0.0 <pip> msgpack 0.5.6 <pip> msgpack-numpy 0.4.3.1 <pip> murmurhash 0.28.0 <pip> nb_anacondacloud 1.4.0 py36_0 nb_conda 2.2.1 py36h8118bb2_0 nb_conda_kernels 2.1.0 py36_0 nbconvert 5.3.1 py36hb41ffb7_0 nbdime 1.0.2 <pip> nbformat 4.4.0 py36h31c9010_0 nbpresent 3.0.2 py36h5f95a39_1 ncurses 6.0 h9df7e31_2 notebook 5.4.1 py36_0 numpy 1.14.2 py36hdbf6ddf_1 numpy 1.15.1 <pip> numpydoc 0.8.0 py36_0 openssl 1.0.2o h14c3975_1 packaging 17.1 py36_0 pandas 0.23.3 py36h04863e7_0 pandoc 1.19.2.1 hea2e7c5_1 pandocfilters 1.4.2 py36ha6701b7_1 parso 0.2.0 py36_0 pbr 4.2.0 <pip> pcre 8.42 h439df22_0 pexpect 4.5.0 py36_0 pickleshare 0.7.4 py36h63277f8_0 Pillow 5.1.0 <pip> pip 9.0.3 py36_0 plac 0.9.6 <pip> preshed 1.0.1 <pip> prompt_toolkit 1.0.15 py36h17d85b1_0 protobuf 3.6.0 <pip> ptyprocess 0.5.2 py36h69acd42_0 pycparser 2.18 py36hf9f622e_1 pygments 2.2.0 py36h0d3125c_0 pyopenssl 17.5.0 py36h20ba746_0 pyparsing 2.2.0 py36hee85983_1 pyqt 5.9.2 py36h751905a_0 pysocks 1.6.8 py36_0 python 3.6.5 hc3d631a_0 python-dateutil 2.7.3 <pip> python-dateutil 2.7.2 py36_0 pytz 2018.4 py36_0 PyYAML 3.13 <pip> pyyaml 3.12 py36hafb9ca4_1 pyzmq 17.0.0 py36h14c3975_0 qt 5.9.5 h7e424d6_0 readline 7.0 ha6073c6_4 regex 2017.4.5 <pip> requests 2.18.4 py36he2e5f8d_1 requests 2.19.1 <pip> rhash 1.3.5 hbf7ad62_1 s3transfer 0.1.13 <pip> scipy 1.1.0 <pip> sconce 0.0.2 <pip> send2trash 1.5.0 py36_0 sentencepiece 0.1.3 <pip> setuptools 39.0.1 py36_0 simplegeneric 0.8.1 py36_2 sip 4.19.8 py36hf484d3e_0 six 1.11.0 py36h372c433_1 smart-open 1.6.0 <pip> smmap2 2.0.4 <pip> snowballstemmer 1.2.1 py36h6febd40_0 spacy 2.0.12 <pip> sphinx 1.7.3 py36_0 sphinxcontrib 1.0 py36h6d0f590_1 sphinxcontrib-websupport 1.0.1 py36hb5cb234_1 sqlite 3.23.1 he433501_0 tensorboard 1.10.0 <pip> tensorboardX 1.2 <pip> terminado 0.8.1 py36_1 testfixtures 6.3.0 <pip> testpath 0.3.1 py36h8cadb63_0 thinc 6.10.3 <pip> tk 8.6.7 hc745277_3 toolz 0.9.0 <pip> torch 0.5.0a0+21e0fc8 <pip> torchfile 0.1.0 <pip> torchtext 0.3.0 <pip> tornado 5.0.2 py36_0 tqdm 4.23.0 py36_0 traitlets 4.3.2 py36h674d592_0 typing 3.6.4 py36_0 ujson 1.35 <pip> Unidecode 1.0.22 <pip> urllib3 1.23 <pip> urllib3 1.22 py36hbe7ace6_0 visdom 0.1.8.4 <pip> wcwidth 0.1.7 py36hdf4376a_0 webencodings 0.5.1 py36h800622e_1 websocket-client 0.48.0 <pip> Werkzeug 0.14.1 <pip> wheel 0.31.0 py36_0 widgetsnbextension 3.2.1 py36_0 wrapt 1.10.11 <pip> xz 5.2.3 h55aa19d_2 yaml 0.1.7 had09818_2 zeromq 4.2.5 h439df22_0 zlib 1.2.11 ha838bed_2

[grst]

The problem is associated with an old version of the notebook package and can probably be fixed
by inserting

from notebook import transutils

in the code.

cf. rossant/ipymd#87

[bnjasim]

@grst Thanks. That solved it.

Edited the ~/miniconda3/envs/pytorch/lib/python3.6/site-packages/notebook/services/contents/manager.py file and added from notebook import transutils and it works now.

[mwouts]

Thanks @bnjasim for reporting.

For some reason I had incorrectly changed the order of imports. This is now corrected in version 0.6.5.

@bnjasim , would you mind to

1. revert the local change you mentionned above,
2. test that your reproduce the issue,
3. and then install the new version with

pip install jupytext==0.6.5

and confirm that the issue is gone? Thanks!

[bnjasim]

@mwouts Cool. It works now!