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changed ipython to jupyter #3294

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merged 3 commits into from Dec 16, 2016

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@annefou
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commented Dec 9, 2016

When converting jupyter notebook to html, ipython command is used instead of jupyter
(ipython is becoming obsolete).

Anne Fouilloux
changed ipython to jupyter
When converting jupyter notebook to html, ipython command is used instead of jupyter
(ipython is becoming obsolete).
@bgruening

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commented Dec 9, 2016

Thanks @annefou! And welcome to Galaxy!

@galaxybot galaxybot added the triage label Dec 9, 2016

@galaxybot galaxybot added this to the 17.01 milestone Dec 9, 2016

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commented Dec 9, 2016

Thanks @annefou!
If you want to dig further, there are more occurrences of "IPython" in the files you modified and in the rest of the Galaxy codebase.

$ ack -i -l --ignore-dir={.venv,database,eggs,.git,doc/build} ipython .

gives me the following list of files:

config/galaxy.ini.sample
config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample
config/plugins/interactive_environments/jupyter/static/js/jupyter.js
config/plugins/interactive_environments/jupyter/templates/jupyter.mako
doc/source/admin/interactive_environments.rst
doc/source/admin/interactive_environments.svg
doc/source/dev/faq.rst
doc/source/dev/interactive_environments.rst
doc/source/releases/15.10.rst
doc/source/releases/16.04.rst
lib/galaxy/config.py
lib/galaxy/datatypes/text.py
lib/galaxy/visualization/plugins/plugin.py
lib/galaxy/visualization/plugins/registry.py
lib/galaxy/web/framework/middleware/sentry.py
lib/galaxy/web/proxy/js/Dockerfile
test/docker/base/Dockerfile
test/unit/visualizations/plugins/test_VisualizationsRegistry.py

But you can ignore at least config/plugins/interactive_environments/jupyter/static/js/jupyter.js .

If you don't have time/are not interested in fixing those too, that's perfectly fine, we can merge this pull request and open an issue to track the other files.

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commented Dec 9, 2016

Ok, I'll look at it more carefully and see what else needs to be updated.

@jmchilton

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commented Dec 12, 2016

@galaxybot test this

Anne Fouilloux added some commits Dec 12, 2016

Anne Fouilloux
Changed ipython with jupyter
not only for converting jupyter notebook to HTML (with nbconvert) but also
where ipython/IPython was referenced.

Some files still contain ipython but this is mostly related to documentation or
to the IE docker container itself.
Anne Fouilloux
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev
 to take into account the latest changes done on the galaxyproject
# `pip install jinja2 pygments ipython` in Galaxy's virtualenv.
#trust_ipython_notebook_conversion = False
# `pip install jinja2 pygments jupyter` in Galaxy's virtualenv.
#trust_jupyter_notebook_conversion = False

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bgruening Dec 12, 2016

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@jmchilton do we need to implement some fallbacks for changing config names?

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jmchilton Dec 16, 2016

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Yup - I'll follow up with a new a PR for that.

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commented Dec 12, 2016

LGTM. One question is if we need to implement some fallback for the changed config parameter name. Hope that @jmchilton can answer this.

Thanks @annefou!

jmchilton added a commit to jmchilton/galaxy that referenced this pull request Dec 16, 2016

@jmchilton jmchilton merged commit 553f781 into galaxyproject:dev Dec 16, 2016

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@jmchilton

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commented Dec 16, 2016

Awesome sauce @annefou - thanks a ton for the original fix and going the extra mile and fixing it everywhere. This is really appreciated!

nsoranzo added a commit to nsoranzo/galaxy that referenced this pull request Dec 19, 2016

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