From 96678f57ccef01f322a6c6525defaa73333e56d0 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Mon, 19 Dec 2016 12:16:35 +0000 Subject: [PATCH] More IPython to Jupyter changes Follow-up on #3294. --- config/galaxy.ini.sample | 12 ++++++------ doc/source/admin/interactive_environments.rst | 7 +------ doc/source/dev/faq.rst | 2 +- 3 files changed, 8 insertions(+), 13 deletions(-) diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample index aefbbf7e8d0..cf97086f132 100644 --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -328,7 +328,7 @@ paste.app_factory = galaxy.web.buildapp:app_factory # Interactive environment plugins root directory: where to look for interactive # environment plugins. By default none will be loaded. Set to # config/plugins/interactive_environments to load Galaxy's stock plugins -# (currently just IPython). These will require Docker to be configured and +# (currently just Jupyter). These will require Docker to be configured and # have security considerations, so proceed with caution. The path is relative to the # Galaxy root dir. To use an absolute path begin the path with '/'. This is a comma # separated list. @@ -553,7 +553,7 @@ nglims_config_file = tool-data/nglims.yaml # URL (with schema http/https) of the Galaxy instance as accessible within your # local network - if specified used as a default by pulsar file staging and -# IPython Docker container for communicating back with Galaxy via the API. +# Jupyter Docker container for communicating back with Galaxy via the API. #galaxy_infrastructure_url = http://localhost:8080 # If the above URL cannot be determined ahead of time in dynamic environments @@ -671,8 +671,8 @@ nglims_config_file = tool-data/nglims.yaml # services based on Galaxy's session cookie. It will attempt to do this by # default though you do need to install node+npm and do an npm install from # `lib/galaxy/web/proxy/js`. It is generally more robust to configure this -# externally managing it however Galaxy is managed. If True Galaxy will only -# launch the proxy if it is actually going to be used (e.g. for IPython). +# externally, managing it however Galaxy is managed. If True, Galaxy will only +# launch the proxy if it is actually going to be used (e.g. for Jupyter). #dynamic_proxy_manage=True # As of 16.04 Galaxy supports multiple proxy types. The original NodeJS @@ -781,9 +781,9 @@ nglims_config_file = tool-data/nglims.yaml # See: https://developer.mozilla.org/en-US/docs/Web/HTTP/Access_control_CORS #allowed_origin_hostnames = None -# Set the following to True to use IPython nbconvert to build HTML from IPython +# Set the following to True to use Jupyter nbconvert to build HTML from Jupyter # notebooks in Galaxy histories. This process may allow users to execute -# arbitrary code or serve arbitrary HTML. If enabled, IPython must be +# arbitrary code or serve arbitrary HTML. If enabled, Jupyter must be # available and on Galaxy's PATH, to do this run # `pip install jinja2 pygments jupyter` in Galaxy's virtualenv. #trust_jupyter_notebook_conversion = False diff --git a/doc/source/admin/interactive_environments.rst b/doc/source/admin/interactive_environments.rst index 96c3aa256f3..7e5e067a46b 100644 --- a/doc/source/admin/interactive_environments.rst +++ b/doc/source/admin/interactive_environments.rst @@ -1,11 +1,6 @@ Galaxy Interactive Environments (GIEs) ====================================== -GIEs were a new feature back in Galaxy 15.05, leading with the release of the -IPython IE. They were presented at GCC2015, and the RStudio IE was released as -part of 15.07. The IPython IE was superceded by a Project Jupyter IE in -Galaxy XXXXX. - A GIE is a Docker container, launched by Galaxy, proxied by Galaxy, with some extra sugar inside the container to allow users to interact easily with their Galaxy histories. @@ -181,7 +176,7 @@ Please note you will need to be using apache2.4 with ``mod_proxy_wstunnel``. proxy_redirect off; } - # Project Jupyter / IPython specific. Other IEs may require their own routes. + # Project Jupyter specific. Other IEs may require their own routes. location ~ ^/galaxy/gie_proxy/jupyter/(?[^/]+)/api/kernels(?.*?)$ { proxy_pass http://localhost:8800/galaxy/gie_proxy/jupyter/$nbtype/api/kernels$rest; proxy_redirect off; diff --git a/doc/source/dev/faq.rst b/doc/source/dev/faq.rst index 596084defe0..9935b07866d 100644 --- a/doc/source/dev/faq.rst +++ b/doc/source/dev/faq.rst @@ -7,7 +7,7 @@ to provide relatively concrete answers for specific Galaxy development scenarios ... interact with the Galaxy database interactively? ---------------------------------------------------- -This can be done with either IPython/Jupyter or a plain python console, depending on your preferences:: +This can be done with either IPython or a plain Python console, depending on your preferences:: python -i scripts/db_shell.py