Jupyter file clean up?

[Tom Brander]

So after a somewhat problematic upgrade I have a notebook up and running again after doing a pip3 upgrade process but I have lost the ability to run P2 based notebooks my older NB's are defaulting to 3

• I need to restore the ability to run the p2 kernel
  
• Also the console continues to complain about Missing extensions yet they seem to be operating fine, How can I clean this up?
  

[W 17:54:28.875 NotebookApp] 404 GET /nbextensions/latex_envs/latex_envs.js?v=20160421175358 (127.0.0.1) 6.36ms referer=http://localhost:8888/notebooks/Documents/InfluenceH/Propensity/Prob_testV2_analysis_TomB.ipynb

[W 17:54:28.966 NotebookApp] 404 GET /nbextensions/hide_input.js?v=20160421175358 (127.0.0.1) 1.91ms referer=http://localhost:8888/notebooks/Documents/InfluenceH/Propensity/Prob_testV2_analysis_TomB.ipynb

[W 17:54:28.967 NotebookApp] 404 GET /nbextensions/codefolding.js?v=20160421175358 (127.0.0.1) 1.45ms referer=http://localhost:8888/notebooks/Documents/InfluenceH/Propensity/Prob_testV2_analysis_TomB.ipynb

[W 17:54:29.282 NotebookApp] 404 GET /nbextensions/widgets/notebook/js/extension.js?v=20160421175358 (127.0.0.1) 1.69ms referer=http://localhost:8888/notebooks/Documents/InfluenceH/Propensity/Prob_testV2_analysis_TomB.ipynb

[I 17:54:30.114 NotebookApp] Kernel started: 034814d0-c438-4680-a026-b4543f61a3bf

[W 17:54:32.256 NotebookApp] 404 GET /notebooks/Documents/InfluenceH/Propensity/biblio.bib (127.0.0.1): No such file or directory: Documents/InfluenceH/Propensity/biblio.bib

At least now I have the Jupyter troubleshoot command... But I notice that it runs pip list rather than pip3 so I'm quite concerned overall that Jupyter is kind of confused...on the whole p2-vsp3 when both are on the system?

tom@tom-sam:~$ jupyter troubleshoot

$PATH:

/home/tom/gce/google-cloud-sdk/bin

/usr/local/sbin

/usr/local/bin

/usr/sbin

/usr/bin

/sbin

/bin

/usr/games

/usr/local/games

/home/tom/Downloads/google_appengine/

sys.path:

/usr/local/bin

/home/tom/src/csvkit

/home/tom/nbconvert

/usr/lib/python3.4

/usr/lib/python3.4/plat-x86_64-linux-gnu

/usr/lib/python3.4/lib-dynload

/usr/local/lib/python3.4/dist-packages

/usr/lib/python3/dist-packages

sys.executable:

/usr/bin/python3

sys.version:

3.4.3 (default, Oct 14 2015, 20:28:29) 

[GCC 4.8.4]

platform.platform():

Linux-3.13.0-85-generic-x86_64-with-Ubuntu-14.04-trusty

which -a jupyter:

/usr/local/bin/jupyter

pip list:

adium-theme-ubuntu (0.3.4)

agate (1.3.0)

agate-dbf (0.1.0)

agate-excel (0.1.0)

alabaster (0.7.6)

alembic (0.7.7)

apt-xapian-index (0.45)

argh (0.26.1)

astroid (1.3.6)

astropy (1.0.3)

Babel (2.1.1)

backports-abc (0.4)

backports.shutil-get-terminal-size (1.0.0)

backports.ssl-match-hostname (3.5.0.1)

beautifulsoup4 (4.4.0)

bokeh (0.9.3)

Bottleneck (1.0.0)

brewer2mpl (1.4.1)

ccsm (0.9.12)

certifi (2015.11.20.1)

cffi (1.2.1)

chardet (2.3.0)

classicmenu-indicator (0.7)

colorama (0.3.3)

command-not-found (0.3)

compizconfig-python (0.9.12)

configglue (1.1.2)

configobj (5.0.6)

configparser (3.3.0.post2)

cryptography (1.0.1)

csvkit (1.0.0, /home/tom/src/csvkit)

cycler (0.9.0)

Cython (0.23.2)

dataset (0.6.0)

dbf (0.94.3)

dbfread (2.0.5)

debtagshw (0.1)

decorator (4.0.6)

defer (1.0.6)

dirspec (13.10)

distribute (0.7.3)

dnspython (1.11.1)

docutils (0.12)

drivendata-submission-validator (1.0.0)

dulwich (0.10.0)

dummy (0.1.0)

duplicity (0.6.23)

ecdsa (0.13)

entrypoints (0.2)

enum34 (1.0.4)

et-xmlfile (1.0.1)

evernote (1.25.1)

fastimport (0.9.4)

Flask (0.10.1)

freetype-py (1.0.2)

funcsigs (0.4)

functools32 (3.2.3.post2)

gevent (1.0.2)

gevent-websocket (0.9.5)

ggplot (0.6.8)

glue (0.11.1)

GnuPGInterface (0.3.2)

GPy (0.6.0)

graphviz (0.4.7)

greenlet (0.4.9)

h5py (2.5.0)

holoviews (1.3.2)

html5lib (0.999999)

httplib2 (0.9.1)

husl (4.0.2)

idna (2.0)

ipaddress (1.0.14)

ipdb (0.8.1)

ipykernel (4.2.2)

ipython (4.2.0, /usr/local/lib/python2.7/dist-packages)

ipython-genutils (0.1.0)

ipywidgets (5.0.0)

isodate (0.5.4)

itsdangerous (0.24)

jdcal (1.2)

jedi (0.9.0)

Jinja2 (2.8)

joblib (0.8.4)

jsonpointer (1.9)

jsonrpc (1.2)

jsonschema (2.5.1)

jupyter (1.0.0)

jupyter-client (4.1.1)

jupyter-console (4.1.0)

jupyter-core (4.0.6)

keyring (5.3)

launchpadlib (1.10.2)

lazr.restfulclient (0.13.3)

lazr.uri (1.0.3)

linkenv (0.1.0)

lockfile (0.10.2)

logilab-astng (0.24.3)

logilab-common (1.0.2)

lxml (3.4.4)

Mako (1.0.1)

Markdown (2.6.2)

MarkupSafe (0.23)

matplotlib (1.5.1)

mercurial (3.5.1)

mistune (0.7.1)

mock (1.3.0)

moss (0.3.4)

mpld3 (0.2)

mysql-connector-python (1.1.6)

MySQL-python (1.2.5)

mysql-utilities (1.3.5)

nbconvert (4.3.0.dev0, /home/tom/nbconvert)

nbformat (4.0.1)

ndg-httpsclient (0.4.0)

networkx (1.10)

normality (0.2.2)

nose (1.3.7)

notebook (4.2.0)

numexpr (2.4.3)

numpy (1.10.4)

oauth (1.0.1)

oauth2 (1.9.0.post1)

oauthlib (1.0.0)

oneconf (0.3.7.14.4.1)

openpyxl (2.3.4)

openshot (1.4.3)

Orange (2.7.8)

PAM (0.4.2)

pandas (0.18.0)

pandas-datareader (0.2.1)

pandas-profiling (1.0.0a1)

param (1.3.2)

paramiko (1.15.2)

parsedatetime (2.1)

path.py (8.1.2)

pathtools (0.1.2)

patsy (0.4.0)

pbr (1.8.0)

pep8 (1.6.2)

pexpect (4.0.1)

pickleshare (0.5)

PIL (1.1.7)

Pillow (2.9.0)

pip (8.1.1)

piston-mini-client (0.7.5)

prettytable (0.7.2)

protobuf (2.6.1)

psutil (3.1.1)

psycopg2 (2.6.1)

ptyprocess (0.5)

py (1.4.30)

pyasn1 (0.1.8)

PyAVM (0.9.2)

pycparser (2.14)

pycrypto (2.6.1)

pycups (1.9.66)

pycurl (7.19.5.1)

pydot2 (1.0.33)

pyflakes (0.9.2)

Pygments (2.0.2)

pygobject (3.12.0)

pygpgme (0.3)

pyinotify (0.9.6)

pylint (1.4.4)

pymc (3.0)

PyMySQL (0.7.2)

pyOpenSSL (0.15.1)

pyparsing (2.0.7)

pyPdf (1.13)

PyPDF2 (1.25.1)

pypdfocr (0.8.2)

pyserial (2.7)

pysmbc (1.0.14.1)

pysqlite (2.6.3)

pystache (0.5.4)

pytest (2.7.2)

python-apt (0.9.3.5ubuntu2)

python-dateutil (2.5.1)

python-debian (0.1.21-nmu2ubuntu2)

python-slugify (1.1.3)

pytimeparse (1.1.5)

pytz (2016.3)

pyxdg (0.25)

PyYAML (3.11)

pyzmq (15.2.0)

qgrid (0.2.0)

qtconsole (4.1.1)

rabbitvcs (0.15.2)

redis (2.10.3)

reportlab (3.2.0)

requests (2.9.1)

requests-file (1.4)

roman (2.0.0)

rope (0.10.2)

scikit-learn (0.17)

scipy (0.16.0)

seaborn (0.6.0)

SecretStorage (2.0.0)

sessioninstaller (0.0.0)

setuptools (20.9.0)

simplegeneric (0.8.1)

simplejson (3.8.0)

singledispatch (3.4.0.3)

six (1.10.0)

sklearn-pandas (0.0.10)

smartypants (1.8.6)

snowballstemmer (1.2.0)

software-center-aptd-plugins (0.0.0)

Sphinx (1.3.1)

sphinx-bootstrap-theme (0.4.7)

sphinx-rtd-theme (0.1.9)

spyder (2.3.6)

SQLAlchemy (1.0.12)

sqlalchemy-migrate (0.9.7)

sqlparse (0.1.15)

statsmodels (0.6.1)

stevedore (1.8.0)

sympy (0.7.6)

system-service (0.1.6)

tables (3.2.0)

Tempita (0.5.2)

terminado (0.6)

Theano (0.7.0)

tornado (4.3)

traitlets (4.0.0)

Twisted (15.2.1)

Twisted-Core (13.2.0)

Twisted-Names (13.2.0)

Twisted-Web (13.2.0)

ubuntu-tweak (0.8.6)

UniConvertor (1.1.4)

Unidecode (0.4.18)

unity-lens-photos (1.0)

urllib3 (1.11)

vboxapi (1.0)

vincent (0.4.4)

virtualenv (13.1.2)

virtualenv-clone (0.2.6)

virtualenvwrapper (4.7.1)

wadllib (1.3.2)

watchdog (0.8.3)

websocket (0.2.1)

Werkzeug (0.10.4)

wheel (0.26.0)

widgetsnbextension (1.0.0)

wxPython (2.8.12.1)

wxPython-common (2.8.12.1)

xdiagnose (3.6.3build2)

xlrd (0.9.4)

XlsxWriter (0.7.3)

xlwt (1.0.0)

yolk (0.4.3)

zope.interface (4.1.2)

tom@tom-sam:~$ 

[Thomas Kluyver]

Hi Tom,

On 22 April 2016 at 17:27, Tom Brander <tombr...@gmail.com> wrote:

• I need to restore the ability to run the p2 kernel
  

See here:
http://ipython.readthedocs.org/en/stable/install/kernel_install.html#kernels-for-python-2-and-3

 

• Also the console continues to complain about Missing extensions yet they seem to be operating fine, How can I clean this up?
  

You should be able to disable them with command 'jupyter nbextension disable'. Use 'jupyter nbextension list' to see what it knows about.

At least now I have the Jupyter troubleshoot command... But I notice that it runs pip list rather than pip3 so I'm quite concerned overall that Jupyter is kind of confused...on the whole p2-vsp3 when both are on the system?

It should really be running 'python -m pip list', using the same Python it's running under. PRs welcome to fix that.

Thomas

[Tom Brander]

Fantastic! huge thanks!

[Tom Brander]

so using jupyter nbextension list I get (below)::

How do I specify the correct one to disable?

IE latex_envs/latex_envs has problems found

and 

usability/latex_envs/latex_envs  enabled is ok.. 

So something like juypyter nbextension disable latex_envs/latex_envs   Should be correct?

usability/codefolding/main  enabled 

      - Validating: OK

      hide_input  enabled 

      - Validating: problems found:

        - require?  X hide_input

      livereveal/main  enabled 

      - Validating: OK

      codefolding  enabled 

      - Validating: problems found:

        - require?  X codefolding

      latex_envs/latex_envs  enabled 

      - Validating: problems found:

        - require?  X latex_envs/latex_envs

      usability/latex_envs/latex_envs  enabled 

      - Validating: OK

[Thomas Kluyver]

On 22 April 2016 at 19:06, Tom Brander <tombr...@gmail.com> wrote:

So something like juypyter nbextension disable latex_envs/latex_envs   Should be correct?

Yep, that sounds right.

[Tom Brander]

Thanks all for all the help, it seems to me that my installation is quite hosed,, after running pip3 install jupyter --upgrade several times I'm still stuck showing 4.1 and getting console errors relation to same so I think I'm going to have to do major surgery and remove all jupyter files manually, which I hate to do...  That way I think I can truly make sure that I have all files gone from both the P2 and p3 versions gone...

If anyone has advice or a better idea I'm going out for a while before I get going on it!

tom@tom-sam:~$ jupyter notebook

[W 13:23:05.402 NotebookApp] server_extensions is deprecated, use nbserver_extensions

/usr/local/lib/python3.4/dist-packages/widgetsnbextension/__init__.py:30: UserWarning: To use the jupyter-js-widgets nbextension, you'll need to update

    the Jupyter notebook to version 4.2 or later.

  the Jupyter notebook to version 4.2 or later.""")

tom@tom-sam:~$ jupyter nbextension disable server_extensions

Disabling notebook extension server_extensions...

      - Validating: problems found:

        - require?  X server_extensions

and it still shows and :

tom@tom-sam:~$ jupyter --version

4.1.0

[Thomas Kluyver]

Note that each piece has a separate version number - try jupyter notebook --version.

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[Tom Brander]

Thanks  jupyter-notebook --version gave me 4.2

so progress..

How to get rid of this though?

[Thomas Kluyver]

On 22 April 2016 at 20:05, Tom Brander <tombr...@gmail.com> wrote:

How to get rid of this though?

[W 13:23:05.402 NotebookApp] server_extensions is deprecated, use nbserver_extensions

I think this is complaining about something in your config file (jupyter_notebook_config.py)

 

/usr/local/lib/python3.4/dist-packages/widgetsnbextension/__init__.py:30: UserWarning: To use the jupyter-js-widgets nbextension, you'll need to update

    the Jupyter notebook to version 4.2 or later.

  the Jupyter notebook to version 4.2 or later.""")

No idea about this one ;-)