Structure iocs

Author: Tom-Willemsen

doc/Deployment.md

@@ -1,4 +1,6 @@
-# Releases
+# Releases & Deployment
+
+## Releases
 
 ```{toctree}
 :glob:
@@ -8,9 +10,9 @@ deployment/Creating-a-release
 deployment/Manual-system-tests
 ```
 
-# Deployment
+## Deployment
 
-## IBEX
+### IBEX
 
 ```{toctree}
 :glob:
@@ -25,7 +27,7 @@ deployment/Reviewing-Deploy-Tickets
 deployment/Deploy-script-workflow
 ```
 
-## Supporting software
+### Supporting software
 
 ```{toctree}
 :glob:
@@ -37,7 +39,7 @@ deployment/Upgrade-Java
 deployment/Upgrade-ISISICP
 ```
 
-# Patching
+## Patching
 
 ```{toctree}
 :glob:
@@ -49,11 +51,21 @@ deployment/Release-Single-IOC
 deployment/Modifying-Plugins-on-a-Deployed-Client
 ```
 
-# VHD Build & Deployments
+## VHD Build & Deployments
 
 ```{toctree}
 :glob:
 :titlesonly:
 
 deployment/Mount-or-create-IBEX-VHDs
 ```
+
+## Containers
+
+```{toctree}
+:glob:
+:titlesonly:
+
+deployment/Containerising-an-IOC
+deployment/Containerising-the-Archiver-Appliance
+```

doc/Gui.md

@@ -41,4 +41,27 @@ client/System-Testing-with-Squish
 client/Test-naming
 ```
 
-# Web Dashboard
+## Eclipse
+
+```{toctree}
+:glob:
+:titlesonly:
+
+client/Common-Eclipse-Tasks
+client/Common-Eclipse-Issues
+client/Creating-the-IBEX-Developer-Version-of-Eclipse
+client/Eclipse-RCP
+client/Eclipse-logging
+client/Eclipse-preferences
+client/Checkstyle-setup
+client/Dictionary-setup
+```
+
+## CS-Studio in the GUI
+
+```{toctree}
+:glob:
+:titlesonly:
+
+client/GUI-CSS
+```

doc/IOCs.md

@@ -0,0 +1,36 @@
+# Devices & IOCs
+
+These are the list of categories for an IOC. The IOC can appear in multiple categories if it is relevant. There are details relating to specific device IOCs listed from within the categories where applicable. Most IOC control a device which has [manuals](Manuals).
+
+```{toctree}
+:glob:
+:titlesonly:
+:maxdepth: 1
+
+iocs/Cells
+iocs/Choppers
+iocs/Cryogenics
+iocs/Daq
+iocs/Gas-And-Liquid-Handling-Systems
+iocs/Imaging-Cameras
+iocs/Jaws-and-slits
+iocs/Loading-Rigs
+iocs/Magnets
+iocs/Fluxgates
+iocs/Motor-IOCs
+iocs/Miscellaneous-Motion-Control
+iocs/Multimeters
+iocs/PLCs
+iocs/Polarisers-and-Analysers
+iocs/Power-Distribution-Units
+iocs/Power-Supplies
+iocs/Pressure-Monitors
+iocs/Rheometers
+iocs/Sample-Changers
+iocs/Sensors
+iocs/Signal-Generators
+iocs/Temperature-Controllers
+iocs/Water-Baths
+iocs/Other
+iocs/Partially-Supported-Devices
+```

doc/Instrument-Details.md

@@ -1,7 +1,10 @@
-# Instrument Details
+# Instrument Migration Notes
 
+```{warning}
 These instrument details pages provide historical context about the devices on a specific instrument,
-at the time they were migrated to IBEX.
+at the time they were migrated to IBEX. **These pages may not be up to date with the latest instrument
+configuration.**
+```
 
 ```{toctree} Instrument Details
 :glob:

doc/Python.md

@@ -0,0 +1 @@
+# Python

doc/Server.md

@@ -0,0 +1 @@
+# IBEX Server

doc/Web.md

@@ -0,0 +1,9 @@
+# Web
+
+```{toctree}
+:glob:
+:titlesonly:
+
+webdashboard/Web-Dashboard
+webdashboard/PVWS
+```

doc/_static/css/custom.css

@@ -0,0 +1,14 @@
+.wy-table-responsive table td, .wy-table-responsive table th {
+    white-space: inherit;
+}
+
+a:hover {
+    color: #01afec;
+}
+
+.wy-menu-vertical p.caption {
+    color: #01afec;
+}
+.wy-nav-content {
+    max-width: 1200px !important;
+}

doc/uncategorised/Checkstyle-setup.md renamed to doc/client/Checkstyle-setup.md

@@ -1,4 +1,4 @@
-> [Wiki](Home) > [The GUI](The-GUI) > [Eclipse](GUI-Eclipse) > [Check Style setup](Checkstyle-setup)
+# Checkstyle setup
 
 Check style is set up by:
 

doc/client/Common-Eclipse-Issues.md

@@ -1,38 +1,38 @@
-> [Wiki](Home) > [The GUI](The-GUI) > [Eclipse](GUI-Eclipse) > Common Eclipse issues
+# Common Eclipse issues
 
 Sometimes the error messages that Eclipse gives are a little opaque, so here are some possible solutions for some of the more common issues.
 
-### plugin execution not covered by lifecycle configuration
+## Plugin execution not covered by lifecycle configuration
 
 Go to window -> preferences -> Maven -> Errors/Warnings. Change "Plugin execution not covered by lifecycle configuration" to ignore in the drop down.
 
-### The type XXXXXXX cannot be resolved. It is indirectly referenced from required .class files ###
+## The type XXXXXXX cannot be resolved. It is indirectly referenced from required .class files
 
-#### Errors appear for single plugin
+### Errors appear for single plugin
 Possible solutions (in order of desperation):
 
 * Check the error message: you may need to add a dependency to the plugin that contains XXXXXXX. For example: if the error message is ```The type org.eclipse.ui.plugin.AbstractUIPlugin cannot be resolved. It is indirectly referenced from required .class files``` then the org.eclipse.ui plugin requires adding.bundle to the required bundle in the manifest file of your plugin.
 * Delete the complaining plugin from the workspace and then re-import it.
 * Remove JRE System Library from the complaining plug-in's Java Build Path then re-add it.
 * This can also occur in similar cases to the **Invalid class hierarchy**.
 
-#### Errors appear across entire project
+### Errors appear across entire project
 
 Suggests that eclipse has got itself into a funny state. Try `Project > Clean` first, if that does not get rid of the problems, try:
 1. Reset the targetplatform: Open file in `uk.ac.stfc.isis.ibex.targetplatform`, reload dependencies if they are in error, then click `Reload Target Platform` top right
 2. Synchronize the runnable product: open `ibex.product` in `uk.ac.stfc.isis.ibex.e4.client.product`, click `Synchronize this configuration with the product's defining plug-in.`
 3. Confirm the problems have disappeared. (you may need to repeat step 1 & 2 a couple of times)
 4. Launch application from `ibex.product` (little green arrow on the top right) and confirm the client starts
 
-### Invalid class hierarchy ###
+## Invalid class hierarchy
 
 * Make sure that you don't have any circular dependencies. That is package A imports package B imports package A.
 * If you have several layers of derived dependencies, particularly containing CSStudio or eclipse classes, make sure the correct bundles have been imported. Dependencies are not necessarily re-exported from the intermediate layers by default. There are two solutions:
     * Add the base bundle to the list of dependencies of your new class via the manifest file
     * Go through the classes you derive from. In their bundles go to the dependencies menu and click on the plugin you're deriving from. Click properties and check the box that says "Reexport this dependency". Once the intermediate layers all reexport their dependencies then it should become available to your class.
 
 
-### Product XXXXXXXXXXX.product could not be found ###
+## Product XXXXXXXXXXX.product could not be found
 
 Typically is followed by a lot of errors relating to bundle resolution, for example:
 
@@ -75,21 +75,20 @@ Possible solution:
 
 * Check the offending plug-in has been added to one of the feature projects as a plug-in
 
-### New plugin is not available (and possibly crashing existing plugins) ###
+## New plugin is not available (and possibly crashing existing plugins)
 
 This might be difficult to find as an error, and it may not exist for other developers - even on the same branch!
 Adding the plugin directly to your configuration solves this.
 
-### Plugins compile fine but dependencies cause errors at runtime ###
+## Plugins compile fine but dependencies cause errors at runtime
 
 If you can run the application fine but are seeing a `java.lang.NoClassDefFoundError` at runtime, try re-setting the target platform, synchronizing `client.product` (under "testing" in the product overview), and doing a clean.
 
-### Menu items are missing ###
+## Menu items are missing
 
 This is usually because a dependency is missing. See "I really cannot work out why the GUI won't start!" below.
 
-### I really cannot work out why the GUI won't start! ###
-#### Also for runtime error "No application ID" ####
+## No application ID
 
 Starting the GUI via Eclipse just doesn't seem to work and I cannot see why!
 
@@ -111,20 +110,20 @@ Sometimes eclipse will tell you that you have errors in various projects when yo
 - In `uk.ac.stfc.isis.ibex.targetplatform`, open `uk.ac.stfc.isis.ibex.targetplatform.target` and click "set as target platform". 
 - If all else fails, delete all the projects from eclipse's workspace and reimport them.
 
-#### The GUI starts but looks strange and some items (e.g. menu bar, perspective buttons) are missing ####
+## The GUI starts but looks strange and some items (e.g. menu bar, perspective buttons) are missing
 
 This can happen if the wrong ".product" file is run and not all plugins are defined in the application.
 
 * Make sure you *only* run ibex.product in uk.ac.stfc.isis.ibex.**client**.product *not* any other ".product" file in the workspace e.g. uk.ac.stfc.isis.ibex.product
 
-### I can't see changes in a new branch
+## I can't see changes in a new branch
 
 Sometimes when you check out a new branch in the ibex GUI repository, you won't see any changes in the GUI. You can fix this by following the steps below:
 
 1. In Eclipse, remove all the projects from the workspace and close Eclipse.
 1. Then, while checked out to the branch you want to see the changes on, perform a `git clean -fdx && git reset HEAD --hard` to reset the git repository. This will remove any changes you have made to the branch.
 1. Restart Eclipse and repeat the steps to get the GUI working from [Building the GUI](https://github.com/ISISComputingGroup/ibex_developers_manual/wiki/Building-the-GUI).
 
-### Build fails with `[ERROR] Failed to resolve target definition ... targetplatform.target: Could not find "org.eclipse.e4.tools.spies.feature.feature.group..." in the repositories of the current location`
+## Build fails with `[ERROR] Failed to resolve target definition ... targetplatform.target: Could not find "org.eclipse.e4.tools.spies.feature.feature.group..." in the repositories of the current location`
 
 This probably means that our pinned target has gone out of date and needs updating. Open the Eclipse IDE and click on `org.eclipse.tools/latest` and click `update` this should fail and show `Unable to locate installable unit ...`. To fix this remove the plugin and then add it from the `software site `, work with `org.eclipse.e4.core.tools.update - http://download.eclipse.org/e4/snapshots/org.eclipse.e4.tools/latest` then you add `Eclipse E4 - All Spies`.

doc/client/Common-Eclipse-Tasks.md

@@ -1,4 +1,4 @@
-> [Wiki](Home) > [The GUI](The-GUI) > [Eclipse](GUI-Eclipse) > Common Eclipse tasks
+# Common Eclipse tasks
 
 ## Add A New Plugin
 

doc/client/Creating-the-IBEX-Developer-Version-of-Eclipse.md

@@ -1,73 +1,3 @@
-> [Wiki](Home) > [The GUI](The-GUI) > [Eclipse](GUI-Eclipse) > Creating the IBEX developer version of Eclipse
+# Creating the IBEX developer version of Eclipse
 
 The recommended IBEX developer version of Eclipse can be found at `\\isis\inst$\Kits$\CompGroup\ICP\Developer Tools`.
-
-# Old instructions (no longer in use)
-
-We are no longer using these instructions as several plugins are no longer relevant to the project (for example, RCPTT) or do not support modern versions of java/eclipse (e.g. checkstyle).
-
-The instructions are left here in case they are useful for a future "IBEX developer eclipse" with bundled plugins.
-
-```
-## Download and install plugins
-
-* Download the latest version of Eclipse for RCP and RAP developers from https://www.eclipse.org/downloads/, unzip somewhere appropriate and start Eclipse
-* Set the workspace to ../workspace (or another suitable relative path)
-* Modify eclipse/plugins/org.eclipse.platform_4.5.0.v20150603-2000/splash.bmp (replacing 4.5.0... with the current version number) to make clear this is the IBEX version of Eclipse
-* From Help -> Eclipse Marketplace install RCP Testing Tool
-* From Help -> Eclipse Marketplace install EclEmma
-* From Help -> Install New Software add a repository with the name ObjectAid UML Explorer and URL http://www.objectaid.com/update, then install ObjectAid Class Diagram only (uncheck the other 3 options)
-* From Help -> Eclipse Marketplace install Eclipse Checkstyle Plug-in
-* Configure Checkstyle, Window -> Preferences -> Checkstyle, select New, Internal Configuration then import the IBEX Checkstyle file (found in the root of base\uk.ac.stfc.isis.ibex.client.tycho.parent) NOTE - This is why we can't use EPF exports, the Checkstyle configurations get lost
-* Be sure to call the new Checkstyle configuration "IBEX Checks".
-* Set the IBEX checkstyle to be the default
-* From Help -> Eclipse Marketplace install Unnecessary Code Detector
-* Configure Unnecessary Code Detector, Window -> Preferences -> UCDetector, change the 'Active mode' to 'Unused only [built-in]'
-* From Help -> Eclipse Marketplace install JAutodoc
-* Configure JAutodoc, Window -> Preferences -> Java -> JAutodoc. Change the visibility to be public and package then add the standard IBEX header (copied from a pre-existing code) 
-* Run an update from Help -> Check for Updates
-
-Save actions
-------------
-
-* From Window -> Preferences -> Java -> Editor -> Save Actions choose Perform the selection actions on save, then Format source code (Format edited lines), Organize imports, Additional actions
-* In Window -> Preferences -> Java -> Compiler -> Errors/Warning -> Annotations -> Unhandled Token in ``@SupressWarnings`` set to ignore
-* From Window -> Preferences -> Java -> Code Style -> Organize Imports set the 'Number of static imports' to 2
-
-Formatting
-----------
-
-There are a number of changes to the formatting. The easiest way to get the correct code formatting is to start with the most recent previous developer's edition, choose Window -> Preferences -> Java -> Code Style -> Formatter. IBEX should be active, choose to Edit then Export.
-
-To recreate the formatter from scratch these are the known steps. Start by going to 'New', start with 'Java Conventions' and save the formatting as 'IBEX'. Then edit this profile.
-
-* Under 'Indentation' Tab policy -> Spaces only, Tab size -> 4
-* Under 'Indentation' check Statements within 'case' body
-* Under 'Comments' uncheck 'Format line comments on first column'
-* Under 'Comments'' check 'Enable header comment formatting'
-* Under 'Comments'' uncheck 'New line after @param tags'
-* Under 'Line Wrapping' select 'enum declaration'. For 'Constants and ''implements' clause' set the line wrapping to 'Wrap all elements, every element on new line' and check the 'Force split' box
-* Under 'Line Wrapping' select 'enum declaration'. For 'Constant arguments' set the line wrapping to 'Wrap where necessary' and leave 'Force split' unchecked
-
-Code templates
---------------
-
-In Window -> Preferences -> Java -> Code Style -> Code Templates
-
-* Check 'Automatically add comments for new methods and types'
-* Remove all ``@author`` tags
-* Change 'Overriding methods' to the same comment as 'Methods'
-* For 'New Java files' add the licence header
-* 'Method body' comment becomes ``// ${body_statement}``
-* 'Constructor body' comment becomes ``// ${body_statement}``
-* 'Catch block body' comment becomes ``// ${exception_var}.printStackTrace();``
-
-Finally
--------
-
-* From Window -> Preferences -> Maven -> Errors/Warnings choose 'Ignore' for 'Plugin execution not covered by lifecycle configuration'
-* From Window -> Preferences -> General -> Error Reporting set 'Send mode' to 'Never send reports'
-* Tidy up - check for paths tied to your own user account and either remove the offending line or delete the file
-* Zip up both the workspace and the eclipse folder, to get all plugins and settings
-
-```

doc/uncategorised/Dictionary-setup.md renamed to doc/client/Dictionary-setup.md

@@ -1,4 +1,4 @@
-> [Wiki](Home) > [The GUI](The-GUI) > [Eclipse](GUI-Eclipse) > [Dictionary setup](Dictionary-setup)
+# Dictionary setup
 
 Spelling error highlights fix
 

doc/client/Eclipse-RCP.md

@@ -1,4 +1,4 @@
-> [Wiki](Home) > [The GUI](The-GUI) > [Eclipse](GUI-Eclipse) > Eclipse RCP
+# Eclipse RCP
 
 We have two books which should serve as a reasonable introduction to the Eclipse RCP platform: 'Eclipse Rich Client Platform' by McAffer, Lemieux and Aniszczyk, and 'Eclipse 4 Application Development' by Vogel. Most of the contents of the latter book can be found on the Vogella website along with a large number of additional Eclipse RCP and JFace tutorials.
 

doc/client/Eclipse-logging.md

@@ -1,6 +1,4 @@
-> [Wiki](Home) > [The GUI](The-GUI) > [Eclipse](GUI-Eclipse) > Eclipse logging
-
-# Logging in the IBEX GUI (Eclipse Client)
+# Eclipse logging
 
 ## Log4j
 We are using the [log4j2](http://logging.apache.org/log4j/2.x/manual/index.html) framework for our logging.

doc/client/Eclipse-preferences.md

@@ -1,4 +1,4 @@
-> [Wiki](Home) > [The GUI](The-GUI) > [Eclipse](GUI-Eclipse) > Eclipse preferences
+# Eclipse preferences
 
 There are two sorts of settings.