Merge pull request #3333 from nsoranzo/followup_on_3294

More IPython to Jupyter changes

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

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/(?<nbtype>[^/]+)/api/kernels(?<rest>.*?)$ {
         proxy_pass http://localhost:8800/galaxy/gie_proxy/jupyter/$nbtype/api/kernels$rest;
         proxy_redirect off;

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