Merge pull request #23 from ISISComputingGroup/update_user_manual_links

rerpha · web-flow · commit c6e4436507d0 · 2025-06-10T17:02:52.000+01:00
Update user manual links
diff --git a/doc/Providing-Support.md b/doc/Providing-Support.md
@@ -132,7 +132,7 @@ There are a number of tips for [trouble shooting](#all_troubleshooting_links) al
   1. I can't use this button to get to more details/why doesn't this bit of the OPI work
       - Check they are in manager mode
   1. I need to add this device to my system
-      - Check [the user manual](https://github.com/ISISComputingGroup/ibex_user_manual/wiki) for IBEX, for SECI, if you don't know already ask someone else
+      - Check {external+ibex_user_manual:doc}`the user manual <index>` for IBEX, for SECI, if you don't know already ask someone else
   1. My motor won't move
       - Are both limits made?
           - Yes: Something has happened in the physical realm, refer it to EUSG via the MCR
@@ -178,7 +178,7 @@ There are a number of tips for [trouble shooting](#all_troubleshooting_links) al
   <summary>Script issues</summary>
 
   1. My script won't load
-     - If `g.load_script` is being used and you see errors of the form `E:  1: error description (error-name)`, these errors are coming from the linter. Detailed linter troubleshooting is available [here](https://github.com/ISISComputingGroup/ibex_user_manual/wiki/Error-Checking-Troubleshooting).
+     - If `g.load_script` is being used and you see errors of the form `E:  1: error description (error-name)`, these errors are coming from the linter. Detailed linter troubleshooting is available {external+ibex_user_manual:doc}`here <scripting/Error-Checking-Troubleshooting>`.
   1. My script isn't behaving in the way I expect it to
      - This is a best efforts, and not everyone can provide the same level of support
      - Look at it with respect to basic coding standards and obvious race condition points
diff --git a/doc/conf.py b/doc/conf.py
@@ -97,3 +97,8 @@
     "client/getting_started/GUI-Development-Workflow": "../../processes/git_and_github/Git-workflow.html",  # noqa E501
     "client/testing/Using-Mockito-for-Testing-in-the-GUI": "Mockito.html",
 }
+
+intersphinx_mapping = {
+    "ibex_user_manual": ("https://isiscomputinggroup.github.io/ibex_user_manual/", None),
+}
+
diff --git a/doc/deployment/Creating-a-release.md b/doc/deployment/Creating-a-release.md
@@ -72,7 +72,7 @@ Project is ready to be released not for a specific event, e.g. at the end of a s
 1. Update the "Latest Stable Release" link on the [IBEX wiki homepage](https://github.com/ISISComputingGroup/IBEX) to be the new `"Release X.x.m"` and commit to master.
 1. Remove all entries from `Upcoming Release Notes`, leaving a blank file with only the headers, e.g. "Instrument Specific Changes", etc. and commit to master.
 1. If applicable, update the dependencies since the last release and add them to the bottom of the release notes. To find the python dependencies list, run a `pip freeze` on a cleanly released `uktena`. Note that you will need to specify the scripts directory to run pip commands. i.e. `C:\Instrument\Apps\Python3\Scripts\Pip.exe freeze`
-1. Update the [user manual](https://github.com/ISISComputingGroup/ibex_user_manual/wiki) with any relevant changes
+1. Update the {external+ibex_user_manual:doc}`user manual <index>` with any relevant changes
 1. copy the release to `control-svcs`, this is so we can set git remotes for hotfixes etc. as part of the deploy. So if release is number 1.2.3
     - `robocopy "Kits$\CompGroup\ICP\Releases\1.2.3\EPICS\.git" "\\control-svcs.nd.rl.ac.uk\git$\releases\1.2.3\EPICS.git" /mir /nfl /ndl`
     - edit `EPICS.git\config` on the control-svcs version (you can browse straight to the `\\control-svcs` share above)
diff --git a/doc/deployment/deploy/Configure-Mini-Inst.md b/doc/deployment/deploy/Configure-Mini-Inst.md
@@ -3,15 +3,15 @@
 To install a mini inst, you need to install the EPICS backend and add the following in the `\NDXxxxxx\configurations\` area.
 
 - `startup.txt`: contains a list of the IOCs to start (use the IOC name as in the IOCs list)
-- `globals.txt`: add macro values you want the IOCs in `startup.txt` to start up with. [To do this, add a line per macro of the format `<IOC_name>__<macro_name>=<macro_value>`](https://github.com/ISISComputingGroup/ibex_user_manual/wiki/Create-and-Manage-Configurations#editing-a-global-setting)
+- `globals.txt`: add macro values you want the IOCs in `startup.txt` to start up with. To do this, {external+ibex_user_manual:ref}`add a line per macro of the format <manage_configs_globals>` `<IOC_name>__<macro_name>=<macro_value>`.
 
 ### Startup and shutdown
 
 You can start up the mini inst using the normal `start_ibex_server` and stop it with `stop_ibex_server`. It will look for the `startup.txt` and start up the mini inst instead of the full IBEX server if it exists.
 
 ### Updating config
 
-If you update a configuration in [globals.txt](https://github.com/ISISComputingGroup/ibex_user_manual/wiki/Create-and-Manage-Configurations#editing-a-global-setting) then don't forget to restart the IOC. This can be done either by running `start_ibex_server` but it is more efficient to console to the IOC and restart it using `ctrl+x`.
+If you update a configuration in {external+ibex_user_manual:ref}`globals.txt <manage_configs_globals>` then don't forget to restart the IOC. This can be done either by running `start_ibex_server` but it is more efficient to console to the IOC and restart it using `ctrl+x`.
 
 ### Adding Devices
 
diff --git a/doc/index.md b/doc/index.md
@@ -52,6 +52,6 @@ Processes
 ## External Documentation
 
 - [IBEX project wiki](https://github.com/isiscomputinggroup/ibex/wiki)
-- [IBEX user manual](https://github.com/isiscomputinggroup/ibex_user_manual/wiki)
+- {external+ibex_user_manual:doc}`IBEX user manual <index>`
 - [Python shared scripts (also known as shared instrument scripts)](https://github.com/ISISNeutronMuon/InstrumentScripts/wiki)
 - [Scientific Advisory Group (sharepoint)](https://stfc365.sharepoint.com/sites/IBEXSAG)
diff --git a/doc/overview/Links-and-Resources.md b/doc/overview/Links-and-Resources.md
@@ -26,7 +26,7 @@
 ## Links
 
 - [IBEX wiki](https://github.com/ISISComputingGroup/IBEX/wiki)
-- [IBEX User Manual](https://github.com/ISISComputingGroup/ibex_user_manual/wiki)
+- {external+ibex_user_manual:doc}`IBEX user manual <index>`
 - [IBEX Project Board for Issues](https://github.com/ISISComputingGroup/IBEX/projects/1)
 - [Stream Protocol Page](http://epics.web.psi.ch/software/streamdevice/doc/)
 - [genie_python reference](http://shadow.nd.rl.ac.uk/genie_python/sphinx/genie_python.html)
diff --git a/doc/overview/New-Starters.md b/doc/overview/New-Starters.md
@@ -81,11 +81,11 @@ Here's some useful bits and bobs for how our team operates and the conventions w
 
 While that's installing, get to know the IBEX components. Get to know EPICS. It's the software environment that IBEX uses to control the ISIS instruments. 
 
-Ironically, to get a well-explained overview of what IBEX is, and how to interact with it as a dev, the [IBEX User Manual](https://github.com/ISISComputingGroup/ibex_user_manual/wiki) is a really nice place to start. In particular, see:
+Ironically, to get a well-explained overview of what IBEX is, and how to interact with it as a dev, the {external+ibex_user_manual:doc}`IBEX user manual <index>` is a really nice place to start. In particular, see:
 
-- [IBEX Key Concepts](https://github.com/ISISComputingGroup/ibex_user_manual/wiki/Key-Concepts-in-IBEX)
-- [IBEX GUI Features](https://github.com/ISISComputingGroup/ibex_user_manual/wiki/IBEX-GUI-Features)
-- [How To Do Things In IBEX](https://github.com/ISISComputingGroup/ibex_user_manual/wiki/How-To-Do-Things-In-IBEX)
+- {external+ibex_user_manual:doc}`IBEX Key Concepts <Key-Concepts-in-IBEX>`
+- {external+ibex_user_manual:doc}`IBEX-GUI-Features`
+- {external+ibex_user_manual:doc}`How To Do Things In IBEX <How-To>`
 
 There are some training materials available that we use to train scientists on IBEX, which is also a nice way to get started:
 
diff --git a/doc/processes/dev_processes/Project-Documentation.md b/doc/processes/dev_processes/Project-Documentation.md
@@ -3,8 +3,8 @@
 We have three wikis:
 
 1. [IBEX wiki](https://github.com/ISISComputingGroup/IBEX/wiki)
-1. [IBEX user manual](https://github.com/ISISComputingGroup/ibex_user_manual/wiki)
-    - [on shadow](http://shadow.nd.rl.ac.uk/ibex_user_manual/Home)
+1. {external+ibex_user_manual:doc}`IBEX user manual <index>`
+    - [on shadow](http://shadow.nd.rl.ac.uk/ibex_user_manual/)
 1. [IBEX developer wiki](/index)
 
 ## IBEX wiki
diff --git a/doc/processes/meetings_with_scientists/Training-Instrument-Scientists-in-IBEX.md b/doc/processes/meetings_with_scientists/Training-Instrument-Scientists-in-IBEX.md
@@ -18,7 +18,7 @@ We record people who would like to attend the next training session by listing t
 - [Mantid](https://www.mantidproject.org/Documentation)
 - [IBEX](/overview/Links-and-Resources)
     - There are various slides at the end of the material: "Reference card", "GUI Reference Card" and "Useful Locations". These are supposed to provide a brief reference of the major IBEX features, GUI elements and a memo sheet for folder locations respectively. Print off a copy of each for each delegate.
-- [genie_python](https://github.com/ISISComputingGroup/ibex_user_manual/wiki/genie_python-and-IBEX-%28Introduction%29)
+- {external+ibex_user_manual:doc}`scripting/Genie-Python-Training`
 
 ## Planning the IBEX and genie_python training courses
 This section summarises the steps you will need to consider when planning the IBEX and genie_python training courses.
diff --git a/doc/scripting/Genie-Python.md b/doc/scripting/Genie-Python.md
@@ -13,5 +13,5 @@ genie_python/*
 
 ### User documentation
 
-- [Scripting in the user manual](https://github.com/ISISComputingGroup/ibex_user_manual/wiki/Scripting)
+- {external+ibex_user_manual:doc}`Scripting in the user manual <Scripting>`
 - [genie_python reference](http://shadow.nd.rl.ac.uk/genie_python/sphinx/genie_python.html)
diff --git a/doc/scripting/Matplotlib.md b/doc/scripting/Matplotlib.md
@@ -1,7 +1,7 @@
 # Matplotlib
 
 ```{seealso}
-[User-facing docs](https://github.com/ISISComputingGroup/ibex_user_manual/wiki/Matplotlib) on user manual.
+{external+ibex_user_manual:doc}`scripting/Matplotlib` on the user manual.
 ```
 
 We allow plotting in IBEX via `matplotlib`. These plots will appear in the IBEX client.
diff --git a/doc/scripting/genie_python/genie_python-linter.md b/doc/scripting/genie_python/genie_python-linter.md
@@ -1,6 +1,6 @@
 # `genie_python` script checking (linting)
 
-On `g.load_script` genie_python now runs pylint on the scripts. This help the user see errors before the script is run. However sometimes this causes its own issues. There is a [page in the user manual](https://github.com/ISISComputingGroup/ibex_user_manual/wiki/Error-Checking-Troubleshooting) describing what the user should do.
+On `g.load_script` genie_python now runs pylint on the scripts. This help the user see errors before the script is run. However sometimes this causes its own issues. There is a {external+ibex_user_manual:doc}`page in the user manual <scripting/Error-Checking-Troubleshooting>` describing what the user should do.
 
 Here are some more tips that we don't necessarily want to encourage. 
 
diff --git a/doc/specific_iocs/choppers/FZJ_Fermi_chopper.md b/doc/specific_iocs/choppers/FZJ_Fermi_chopper.md
@@ -2,4 +2,4 @@
 
 Used on MERLIN, MAPS, MARI.
 
-This material is now in the [user manual](https://github.com/ISISComputingGroup/ibex_user_manual/wiki/FZJ-Fermi-Chopper).
+This material is now {external+ibex_user_manual:doc}`here <device_specific/FZJ-Fermi-Chopper>`.
diff --git a/doc/specific_iocs/dae/DAE-Trouble-Shooting.md b/doc/specific_iocs/dae/DAE-Trouble-Shooting.md
@@ -255,7 +255,7 @@ Freddie may also have a patched version of the isisicp that fixes this issue.
 
 ### My blocks aren't being written to a run title properly
 
-See the documentation in the [user manual](https://github.com/ISISComputingGroup/ibex_user_manual/wiki/Add-blocks-to-run-title)
+See the documentation in the {external+ibex_user_manual:doc}`user manual <how_to/Add-blocks-to-run-title>`
 
 ### Exception in ICP log
 
diff --git a/doc/specific_iocs/motors/EnginX-Sample-Positioner.md b/doc/specific_iocs/motors/EnginX-Sample-Positioner.md
@@ -1,6 +1,6 @@
 # EnginX Sample Positioner
 
-The sample positioner on EnginX allows the sample to be moved into position. It is not controlled by IBEX through the motor record but instead via lvdcom this is to allow them to use the EnginX jog box. when plugged in the jog box allows the operator (once SECI mode is selected) to jog the positions of various axes at various speeds; the controller has a speed control and an enable jog button. There is user information for the sample positioner in the [user manual](https://github.com/ISISComputingGroup/ibex_user_manual/wiki/Engin-X-Sample-Stack).
+The sample positioner on EnginX allows the sample to be moved into position. It is not controlled by IBEX through the motor record but instead via lvdcom this is to allow them to use the EnginX jog box. when plugged in the jog box allows the operator (once SECI mode is selected) to jog the positions of various axes at various speeds; the controller has a speed control and an enable jog button. There is user information for the sample positioner in the {external+ibex_user_manual:doc}`user manual <inst_specific/Engin-X-Sample-Stack>`.
 
 Under the hood the IBEX `SamPos` IOC uses lvdcom to talk with the LabVIEW vi. The LabVIEW vi then talks through the table of motors to the galil controller. The controller runs a special program which allows the jog box to work as well as normal positioning.
 
diff --git a/doc/specific_iocs/power_supplies/Kepco.md b/doc/specific_iocs/power_supplies/Kepco.md
@@ -1,6 +1,6 @@
 # Kepco
 
-Summary of use is now in the [user manual](https://github.com/ISISComputingGroup/ibex_user_manual/wiki/Kepco-Power-Supply).
+Summary of use is now in the {external+ibex_user_manual:doc}`user manual <device_specific/Kepco-Power-Supply>`.
 
 ## Remote connection details
 
diff --git a/doc/specific_iocs/reflectometry/config_training/Reflectometry-Config-Training-‐-Overview-&-Setup.md b/doc/specific_iocs/reflectometry/config_training/Reflectometry-Config-Training-‐-Overview-&-Setup.md
@@ -6,7 +6,7 @@ This training unit presents a series of exercises which take you through the cre
 
 ## Useful Resources:
 
-- [Reflectometry View User Manual](https://github.com/ISISComputingGroup/ibex_user_manual/wiki/Reflectometry-View)
+- {external+ibex_user_manual:doc}`Reflectometry View User Manual <gui/Reflectometry-View>`
 - [Reflectometry Config Documentation & Reference Manual](../Reflectometry-Configuration)
 - [Reflectometry Glossary](../Reflectometry-Glossary)
 
diff --git a/doc/specific_iocs/temp_controllers/Lakeshore340.md b/doc/specific_iocs/temp_controllers/Lakeshore340.md
@@ -28,14 +28,14 @@ The MuSR Lakeshore 340 excitations need to be able to be controlled in two ways:
 
 ### Excitations Temperature Threshold File
 
-You can find examples in the Lakeshore 340 support module `lakeshore340\excitation_thresholds`. More details [here](https://github.com/ISISComputingGroup/ibex_user_manual/wiki/Lakeshore-340).
+You can find examples in the Lakeshore 340 support module `lakeshore340\excitation_thresholds`. More details {external+ibex_user_manual:doc}`here <device_specific/Lakeshore-340>`.
 
 ### Excitations IOC records and algorithm
 
 You can view a diagram describing how the original VI worked [here](https://github.com/ISISComputingGroup/IBEX/issues/5950#issuecomment-769071044).
 
 The `asub` record `THRESHOLDS:_CALC` calculates and sets the thresholds. The function the record contains also checks conditions such as the file containing invalid lines, the file not existing and whether the file is None.txt (the default which says to not do anything).
 
-The `THRESHOLDS:_CALC` record is triggered into processing by the setting of `A:TEMP:SP` and `THRESHOLDS:FILE` (written to via `dbpf` from `st-common.cmd`). For how the thresholds file is read see [here](https://github.com/ISISComputingGroup/ibex_user_manual/wiki/Lakeshore-340) and diagram below. Once the values are calculated they are set into `THRESHOLDS:TEMP` and `THRESHOLDS:EXCITATION` or if there is an error `THRESHOLDS:ERROR`. The IOC then waits for the temperature to reach the setpoint before writing the excitation to `EXCITATIONA:SP`, this mechanism is documented in the diagram below.
+The `THRESHOLDS:_CALC` record is triggered into processing by the setting of `A:TEMP:SP` and `THRESHOLDS:FILE` (written to via `dbpf` from `st-common.cmd`). For how the thresholds file is read see {external+ibex_user_manual:doc}`here <device_specific/Lakeshore-340>` and diagram below. Once the values are calculated they are set into `THRESHOLDS:TEMP` and `THRESHOLDS:EXCITATION` or if there is an error `THRESHOLDS:ERROR`. The IOC then waits for the temperature to reach the setpoint before writing the excitation to `EXCITATIONA:SP`, this mechanism is documented in the diagram below.
 
 ![IOC and flowchart diagram for excitations](LKSH340ExcitationsEPICS.png)
diff --git a/doc/system_components/configurations/PV-Sets.md b/doc/system_components/configurations/PV-Sets.md
@@ -2,7 +2,9 @@
 
 PV Sets are a feature that is rarely used, if at all. According to Freddie, it was originally made at the request of an instrument scientist on LARMOR. Later, said scientist said he might not need it anymore and then never came back with the issue. It can only be set for the Galil according to John and Freddie. However, there is a page called [Linmot](/specific_iocs/motors/Linmot) in the dev wiki which says that the Linmot IOC should have PV Sets for Engin-X and MAPS, however I could not find any PV Set in any Linmot ioc in any component.
 
-The User wiki has this to say about PV Sets: https://github.com/ISISComputingGroup/ibex_user_manual/wiki/Create-And-Manage-Configurations#ioc-pv-sets .
+:::{seealso}
+The {external+ibex_user_manual:ref}`manage_configs_pv_sets` documentation on the user manual.
+:::
 
 The logic to add pv sets exists in the back end, but there does not seem to be an implementation in the GUI beyond the view. If you manually add pv sets encoded in XML according to the schema in a component of your dev machine, then load that component, then the pv sets table will still be empty. The XML schemas in inst_servers describe how pv sets should look in XML. There is also no button that allows you to add a PV Set.
 

Original file line number	Diff line number	Diff line change
`@@ -97,3 +97,8 @@`
`97`	`97`	`"client/getting_started/GUI-Development-Workflow": "../../processes/git_and_github/Git-workflow.html", # noqa E501`
`98`	`98`	`"client/testing/Using-Mockito-for-Testing-in-the-GUI": "Mockito.html",`
`99`	`99`	`}`
	`100`	`+`
	`101`	`+intersphinx_mapping = {`
	`102`	`+ "ibex_user_manual": ("https://isiscomputinggroup.github.io/ibex_user_manual/", None),`
	`103`	`+}`
	`104`	`+`