More misspelling updates (#1073)

Fix these pages mispellings and add lots of spelling words to this list.

source/glossary.rst

@@ -14,7 +14,7 @@ Glossary
      Runs on the cluster but is not a compute-node.
 
    Web-node
-     A term used for when a site or institution has enough funds/personel to run the OOD login on a dedicated server and not on a login-node. 
+     A term used for when a site or institution has enough funds/personnel to run the OOD login on a dedicated server and not on a login-node. 
 
    PUN
     The Per User Nginx. An Nginx instance running as the user.

source/how-tos/app-development/app-sharing.rst

@@ -23,7 +23,7 @@ Apps may be shared via a variety of methods including:
 System Installed Apps
 ---------------------
 
-Admins may install apps to the system by copying the application directory to ``/var/www/ood/apps/sys``. Default directory permissions (``755``) will allow all users with access to OnDemand to see and run that app. Apps may have their access restricted by changing the permissions on individual application directories. For example if a site does not wish to show licensed software to un-licensed users they might do the following:
+Admins may install apps to the system by copying the application directory to ``/var/www/ood/apps/sys``. Default directory permissions (``755``) will allow all users with access to OnDemand to see and run that app. Apps may have their access restricted by changing the permissions on individual application directories. For example if a site does not wish to show licensed software to unlicensed users they might do the following:
 
   .. code-block:: sh
 
@@ -95,7 +95,7 @@ These changes take effect immediately, although when a user is added or removed
 Code Sharing
 ------------
 
-Code sharing is when an application's source code is shared between two or more users who run it as a personal development application. Models for this sharing can include using a web-based file repository such as Github, emailing Zip'd app directories, or a group readable directory symlinked to each user's ``~/ondemand/dev/`` directory.
+Code sharing is when an application's source code is shared between two or more users who run it as a personal development application. Models for this sharing can include using a web-based file repository such as Github, emailing zipped app directories, or a group readable directory symlinked to each user's ``~/ondemand/dev/`` directory.
 
 For an example of the later consider:
 
@@ -138,7 +138,7 @@ Enabling The App Sharing Dashboard
    for finding an app.
 #. Set ``OOD_APP_CATALOG_URL=https://link.to.online/app/catalog`` to link
    externally to an advertised listing of apps available.
-#. Pin usr apps to the dashboard and group them by category.
+#. Pin user (``usr``) apps to the dashboard and group them by category.
 
 .. code:: yaml
 
@@ -185,7 +185,7 @@ approach has these benefits (assuming users named ``efranz`` and ``an0047``:
    permissions on this directory. Thus by setting ``750`` on
    ``/var/www/ood/apps/usr/an0047`` this ensures that an0047 can only share
    apps with users in his primary group. At times we have created a \
-   supplemental group (shinyusr) and chgrp the share directory to this group so
+   supplemental group (``shinyusr``) and chgrp the share directory to this group so
    that the developer can share apps with every user in this group.
 #. The developer who can share apps can modify permissions on the app
    directories themselves i.e.
@@ -206,9 +206,9 @@ In summary, to enable a new user to create shared apps, run these commands:
 Example of Executable Sharing
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-This is with two users Eric (efranz) and Bob (an0047).
+This is with two users Eric (``efranz``) and Bob (``an0047``).
 
-Eric has a dev app "MATLAB", and interactive plugin app. Eric can
+Eric has a development app "MATLAB", and interactive plugin app. Eric can
 
 1. Launch MATLAB
 2. View and Edit the code
@@ -224,11 +224,11 @@ i.e. ``~efranz/ondemand/dev/matlab``:
 .. figure:: /images/app-sharing-2.png
    :align: center
 
-If Eric shares the git repo path or URL with Bob, Bob can clone this into his
+If Eric shares the git repository path or URL with Bob, Bob can clone this into his
 home directory if he is enabled as a developer. This is called "Source Code Sharing".
 
 Eric can share this app with Bob by selecting "My Shared Apps" and cloning the MATLAB
-repo to deploy ``~efranz/ondemand/share/matlab``
+repository to deploy ``~efranz/ondemand/share/matlab``
 
 .. figure:: /images/app-sharing-3.png
    :align: center

source/how-tos/app-development/enabling-development-mode.rst

@@ -6,9 +6,9 @@ Enabling App Development
 Enable in OnDemand v1.6+:
 .........................
 
-Here are example steps to enable a user "efranz", assuming efranz's home directory is at ``/home/efranz``:
+Here are example steps to enable a user ``efranz``, assuming ``efranz``'s home directory is at ``/home/efranz``:
 
-#. Create a symlink so OnDemand finds efranz's apps:
+#. Create a symlink so OnDemand finds ``efranz``'s apps:
 
    .. code:: sh
 
@@ -17,33 +17,33 @@ Here are example steps to enable a user "efranz", assuming efranz's home directo
       sudo ln -s /home/efranz/ondemand/dev gateway
 
 
-#. Have efranz access the Dashboard, and efranz will see the Develop dropdown
+#. Have ``efranz`` access the Dashboard, and they will see the Develop drop-down.
 
 
 Enable in OnDemand v1.4 & v1.5:
 ...............................
 
-Here are example steps to enable a user "efranz", assuming efranz's home directory is at ``/home/efranz``:
+Here are example steps to enable a user ``efranz``, assuming ``efranz``'s home directory is at ``/home/efranz``:
 
-#. Create a symlink so OnDemand finds efranz's apps:
+#. Create a symlink so OnDemand finds ``efranz``'s apps:
 
    .. code:: sh
 
       sudo mkdir -p /var/www/ood/apps/dev/efranz
       cd /var/www/ood/apps/dev/efranz
       sudo ln -s /home/efranz/ondemand/dev gateway
 
-#. Create dev directory ``/home/efranz/ondemand/dev`` where efranz's dev apps will go (or ask efranz to do that)
-#. Have efranz access the Dashboard, and efranz will see the Develop dropdown
+#. Create ``dev`` directory ``/home/efranz/ondemand/dev`` where ``efranz``'s development apps will go (or ask ``efranz`` to do that).
+#. Have ``efranz`` access the Dashboard, and they will see the Develop drop-down.
 
 
 Enable in OnDemand v1.3:
 ........................
 
-Here are example steps to enable a user "efranz", assuming efranz's home directory is at ``/home/efranz``:
+Here are example steps to enable a user ``efranz``, assuming ``efranz``'s home directory is at ``/home/efranz``:
 
-#. Create dev directory ``/home/efranz/ondemand/dev`` where efranz's dev apps will go (or ask efranz to do that)
-#. Have efranz access the Dashboard, and efranz will see the Develop dropdown. (if this doesn't happen, )
+#. Create ``dev`` directory ``/home/efranz/ondemand/dev`` where ``efranz``'s development apps will go (or ask ``efranz`` to do that).
+#. Have ``efranz`` access the Dashboard, and they will see the Develop drop-down. (if this doesn't happen, )
 
 .. note::
 
@@ -55,13 +55,13 @@ Specify dedicated host for development (optional)
 
 The default host for the shell app is typically a login node. If this node does not contain a similar environment as the host OnDemand is installed on, including access to Software Collection (SCL) packages, it may be useful to provide developers a dedicated development host they can SSH to. This could even be the OnDemand host itself. If you configure the OnDemand dashboard to know about the dedicated development host, the dashboard will present links to open the shell app to this host.
 
-To specify a dedicated development host so OnDemand, set ``OOD_DEV_SSH_HOST`` environment variable for the dashboard in the file ``/etc/ood/config/apps/dashboard/env``. For example at OSC one of our OnDemand installs uses ondemand-test.osc.edu for the development host so we have this line: `OOD_DEV_SSH_HOST="ondemand-test.osc.edu" <https://github.com/OSC/osc-ood-config/blob/bde54e4c5a9fd756f74ac981f8c607320e9a0bf0/ondemand.osc.edu/apps/dashboard/env#L20>`_
+To specify a dedicated development host so OnDemand, set ``OOD_DEV_SSH_HOST`` environment variable for the dashboard in the file ``/etc/ood/config/apps/dashboard/env``. For example at OSC one of our OnDemand installs uses ``ondemand-test.osc.edu`` for the development host so we have this line: `OOD_DEV_SSH_HOST="ondemand-test.osc.edu" <https://github.com/OSC/osc-ood-config/blob/bde54e4c5a9fd756f74ac981f8c607320e9a0bf0/ondemand.osc.edu/apps/dashboard/env#L20>`_
 
 
 Make everyone a developer by default (optional)
 ...............................................
 
-To revert to the way developer enabling worked in OnDemand 1.3, change the nginx_stage app_root configuration for dev apps by modifying /etc/ood/config/nginx_stage.yml and replacing
+To revert to the way developer enabling worked in OnDemand 1.3, change the ``nginx_stage`` app_root configuration for development apps by modifying ``/etc/ood/config/nginx_stage.yml`` and replacing
 
 .. code-block:: yaml
    :emphasize-lines: 2
@@ -83,11 +83,11 @@ with
      usr: '/var/www/ood/apps/usr/%{owner}/gateway/%{name}'
      sys: '/var/www/ood/apps/sys/%{name}'
 
-Then users can just create the directory ``~/ondemand/dev`` and the Develop dropdown will appear.
+Then users can just create the directory ``~/ondemand/dev`` and the Develop drop-down will appear.
 
 .. warning:: If you do this, it is recommended that you treat the node that OnDemand is running on as a login node, as you are effectively giving those users shell access by letting them run arbitrary code on the OnDemand node (of course the UID of the processes are still their regular unprivileged user UID).
 
-If you do this, you still might want to restrict who sees the Develop dropdown in the Dashboard. To do that you can explicitly show or hide the dropdown in the Dashboard by setting ``Configuration.app_development_enabled`` to true based on one or more Ruby statements in the initializer ``/etc/ood/config/apps/dashboard/initializers/ood.rb``. Code in the initializer runs as the user. This code also has access to the `ood_support library <http://www.rubydoc.info/github/OSC/ood_support>`__ in which we provide some helper classes to work with User's and Groups. For example:
+If you do this, you still might want to restrict who sees the Develop drop-down in the Dashboard. To do that you can explicitly show or hide the drop-down in the Dashboard by setting ``Configuration.app_development_enabled`` to true based on one or more Ruby statements in the initializer ``/etc/ood/config/apps/dashboard/initializers/ood.rb``. Code in the initializer runs as the user. This code also has access to the `ood_support library <http://www.rubydoc.info/github/OSC/ood_support>`__ in which we provide some helper classes to work with User's and Groups. For example:
 
 
     .. code-block:: ruby

source/how-tos/debug/debug-apache.rst

@@ -47,7 +47,7 @@ and the ServerName you may have configured.
 Showing virtualhosts can help debug Apache request routing.  The output from these
 commands will show you how Apache is routing based off of the ServerName in the VirtualHost.
 
-If you're seeing the default Apache webpage you likely have to :ref:`configure the ServerName <ood-portal-generator-servername>`
+If you're seeing the default Apache web-page you likely have to :ref:`configure the ServerName <ood-portal-generator-servername>`
 which corresponds directly to `Apache's ServerName configuration`_ (and restart Apache).
 
 Or you're using the wrong hostname in your browser.
@@ -71,7 +71,7 @@ Performance Tuning
 
 If you're servicing many clients at time (more than 50) you will likely need to change the
 `Apache Httpd's MPM configuration`_. The default configuration may degrade service when
-Httpd has to serve many clients (I.e., when you have a lot of customers using Open OnDemand).
+httpd has to serve many clients (I.e., when you have a lot of customers using Open OnDemand).
 
 We suggest configurations similar to this. 
 
@@ -84,7 +84,7 @@ We suggest configurations similar to this.
 
   The example configuration below can handle about 256 simultaneous requests.
   Use this as an example and increase or decrease `MaxRequestWorkers` accordingly
-  (based on your resources, cpus & memory and how much traffic you anticipate) then recalculate
+  (based on your resources, CPUs & memory and how much traffic you anticipate) then recalculate
   `ServerLimit`, `ThreadsPerChild` and whatever else you may want to change.
 
 

source/install-ihpc-apps.rst

@@ -131,8 +131,8 @@ interactive apps that are currently deployed at OSC and other contributing insti
      - https://github.com/OSC/bc_osc_qgis
      - yes
      - noVNC
-   * - RELION (for REgularised LIkelihood OptimisatioN)
-     - Shanghai Jiao Tong University (SJTU)
+   * - RELION (for ``REgularised LIkelihood OptimisatioN``)
+     - Shanghai ``Jiao Tong University (SJTU)``
      - https://github.com/SJTU-HPC/bc_relion
      - yes
      - 

source/release-notes/v1.3-release-notes.rst

@@ -7,9 +7,9 @@ Highlights in 1.3:
 
 - `RPM based installation`_
 - `Store configuration under /etc instead of under app directories`_
-- `Config changes no longer require app rebuilds`_
-- `Xfce support Interactive Desktops`_
-- `Cluster config verification script`_
+- `Configuration changes no longer require app rebuilds`_
+- `XFCE support Interactive Desktops`_
+- `Cluster configuration verification script`_
 - `Ignore apps if they have a period in directory name`_
 - `Enable multiple Dashboard announcements with embedded HTML`_
 - `Open "help" links in new window`_
@@ -235,7 +235,7 @@ RPM based installation
 
 This is the biggest change and constitutes the bulk of this release's work. RPM
 based installation will now be the default and documented way to install and
-update OnDemand. The latest rpms that are in use at OSC can be accessed from
+update OnDemand. The latest RPMs that are in use at OSC can be accessed from
 https://yum.osc.edu/ondemand/latest/ and the stable releases will be available
 in specific release version directories, such as
 https://yum.osc.edu/ondemand/1.3/.
@@ -248,32 +248,32 @@ configuration for OnDemand:
 
 1. All configuration can be moved to files under /etc/ood
 2. Modifications to configuration only require Passenger app, Per User NINGX,
-   or Apache server restart (with the exception of the ood-portal-generater
-   config)
+   or Apache server restart (with the exception of the ood-portal-generator
+   configuration)
 
 Since all configuration is stored under /etc/ood this directory can be easily
 managed by Puppet or versioned in a git repository.
 
-Config changes no longer require app rebuilds
+Configuration changes no longer require app rebuilds
 ..................................................................
 
 It is now much faster to make and test configuration changes. For most
 configuration changes, you can make the change and then select "Restart Web
-Server" from the "Help" or "Develop" dropdown to see the change.
+Server" from the "Help" or "Develop" drop-down to see the change.
 
-Xfce support Interactive Desktops
+XFCE support Interactive Desktops
 ..................................................................
 
-We now have documentation for enabling Xfce 4+ as the desktop environment for
-OnDemand Interactive Desktops. Xfce is the desktop environment we now use
+We now have documentation for enabling XFCE 4+ as the desktop environment for
+OnDemand Interactive Desktops. XFCE is the desktop environment we now use
 internally at OSC. See :ref:`enable-desktops-modify-form-attributes` for
-documentation on how to use Xfce in OnDemand.
+documentation on how to use XFCE in OnDemand.
 
-Cluster config verification script
+Cluster configuration verification script
 ..................................................................
 
 A Rake task has been added to the Dashboard app that will submit and check the
-status of jobs for each cluster specified in the cluster config. This provides
+status of jobs for each cluster specified in the cluster configuration. This provides
 a quick way to verify that OnDemand has been properly configured for a new
 cluster and should speed up installation. See :ref:`resource-manager-test` in
 the cluster configuration documentation for more details.
@@ -289,13 +289,13 @@ directory in the app deployment directory, e.g., :file:`../.hidden-app/`.
 Enable multiple Dashboard announcements with embedded HTML
 ..................................................................
 
-Site-wide dashboard announcement support in OnDemand has been expanded. Orinally we supported a file ``/etc/ood/config/announcement.md`` but now a YAML file ``/etc/ood/config/announcement.yml`` can be used. A collection of markdown and yaml announcements in ``/etc/ood/config/announcements.d/`` can be added. The yaml file provides extra benefits:
+Site-wide dashboard announcement support in OnDemand has been expanded. Originally we supported a file ``/etc/ood/config/announcement.md`` but now a YAML file ``/etc/ood/config/announcement.yml`` can be used. A collection of markdown and YAML announcements in ``/etc/ood/config/announcements.d/`` can be added. The YAML file provides extra benefits:
 
-#. Pre process file using ERB so that ERB tags can provide per-request dynamic modification of the announcement
+#. Preprocess file using ERB so that ERB tags can provide per-request dynamic modification of the announcement
 #. Control the color of announcement with ``:type`` which is the Bootstrap alert name (``warning``, ``info``, ``success``, or ``danger``)
 #. Control whether announcement appears or not by setting ``:msg`` to a string or ``nil``
 
-The ability to use ERB means we can set the msg to nil after a certain time period. For example:
+The ability to use ERB means we can set the ``msg`` to nil after a certain time period. For example:
 
 .. code-block:: erb
 
@@ -333,7 +333,7 @@ Better debugging of Interactive Apps by logging shell commands
 ..................................................................
 
 Whenever an Interactive Session is started from the Dashboard, the shell
-command used to submit the job is logged to the user's NGINX config to help
+command used to submit the job is logged to the user's NGINX configuration to help
 with debugging Interactive Apps.
 
 Job Composer: Optionally hide Account field in Job Options
@@ -345,7 +345,7 @@ resource manager (whether it is ``-A`` or ``-P`` or ``--account``, etc.). Howeve
 sites do not use this, and others use different mechanisms for accounting. Long
 term we want to support flexible configuration of this web form, but for now we
 have added the ability to hide this Account field from the web form. This field
-is hidden by adding to the Job Composer's env file:
+is hidden by adding to the Job Composer's ``env`` file:
 ``OOD_SHOW_JOB_OPTIONS_ACCOUNT_FIELD=0``
 
 Active Jobs: display list of nodes that a job is running on