Merge pull request #1806 from alan-turing-institute/update_docs

Update docs

docs/requirements.txt

@@ -1,29 +1,29 @@
 #
-# This file is autogenerated by pip-compile with Python 3.11
+# This file is autogenerated by pip-compile with Python 3.12
 # by the following command:
 #
 #    pip-compile requirements.in
 #
 accessible-pygments==0.0.4
     # via pydata-sphinx-theme
-alabaster==0.7.13
+alabaster==0.7.16
     # via sphinx
-babel==2.12.1
+babel==2.14.0
     # via
     #   pydata-sphinx-theme
     #   sphinx
-beautifulsoup4==4.12.2
+beautifulsoup4==4.12.3
     # via pydata-sphinx-theme
-certifi==2023.7.22
+certifi==2024.2.2
     # via requests
-charset-normalizer==3.1.0
+charset-normalizer==3.3.2
     # via requests
-docutils==0.19
+docutils==0.20.1
     # via
     #   myst-parser
     #   pydata-sphinx-theme
     #   sphinx
-emoji==2.2.0
+emoji==2.11.0
     # via -r requirements.in
 idna==3.7
     # via requests
@@ -33,55 +33,55 @@ jinja2==3.1.3
     # via
     #   myst-parser
     #   sphinx
-markdown-it-py==2.2.0
+markdown-it-py==3.0.0
     # via
     #   mdit-py-plugins
     #   myst-parser
-markupsafe==2.1.2
+markupsafe==2.1.5
     # via jinja2
-mdit-py-plugins==0.3.5
+mdit-py-plugins==0.4.0
     # via myst-parser
 mdurl==0.1.2
     # via markdown-it-py
-myst-parser==1.0.0
+myst-parser==2.0.0
     # via -r requirements.in
-packaging==23.1
+packaging==24.0
     # via
     #   pydata-sphinx-theme
     #   sphinx
-pydata-sphinx-theme==0.13.3
+pydata-sphinx-theme==0.15.2
     # via -r requirements.in
-pygments==2.15.1
+pygments==2.17.2
     # via
     #   accessible-pygments
     #   pydata-sphinx-theme
     #   sphinx
-pyyaml==6.0
+pyyaml==6.0.1
     # via myst-parser
 requests==2.31.0
     # via sphinx
 snowballstemmer==2.2.0
     # via sphinx
-soupsieve==2.4.1
+soupsieve==2.5
     # via beautifulsoup4
-sphinx==6.2.1
+sphinx==7.2.6
     # via
     #   -r requirements.in
     #   myst-parser
     #   pydata-sphinx-theme
-sphinxcontrib-applehelp==1.0.4
+sphinxcontrib-applehelp==1.0.8
     # via sphinx
-sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-devhelp==1.0.6
     # via sphinx
-sphinxcontrib-htmlhelp==2.0.1
+sphinxcontrib-htmlhelp==2.0.5
     # via sphinx
 sphinxcontrib-jsmath==1.0.1
     # via sphinx
-sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-qthelp==1.0.7
     # via sphinx
-sphinxcontrib-serializinghtml==1.1.5
+sphinxcontrib-serializinghtml==1.1.10
     # via sphinx
-typing-extensions==4.6.1
+typing-extensions==4.11.0
     # via pydata-sphinx-theme
-urllib3==2.0.7
+urllib3==2.2.1
     # via requests

docs/source/roles/researcher/user_guide.md

@@ -381,7 +381,7 @@ After going through the account setup procedure, you should have access to:
 - Multifactor authentication
 
 ```{tip}
-If you aren't sure about any of these then please return to the [**Set up your account**](#set-up-your-account) section above.
+If you aren't sure about any of these then please return to the [**Set up your account**](#-set-up-your-account) section above.
 ```
 
 ### {{house}} Log into the research environment
@@ -470,7 +470,7 @@ Once connected to it, you can analyse the sensitive data belonging to your proje
 
   ```{caution}
   We recommend _not_ including special characters in your password as the keyboard layout expected by the login screen may be different from the one you're using.
-  - if you want to reset your password, follow the steps defined in the [Password and MFA](#password-and-mfa) section above.
+  - if you want to reset your password, follow the steps defined in the [Password and MFA](#-password-and-mfa) section above.
   - if you want to continue with special characters in your password, please test that they are being entered correctly by typing them in the username field.
   ```
 
@@ -531,7 +531,7 @@ If you need anything that is not already installed, please discuss this with the
 
 ```{attention}
 This secure research desktop SRD is your interface to a single computer running in the cloud.
-You may have access to [additional SRDs](#access-additional-srds) so be careful to check which machine you are working in as files and installed packages may not be the same across the machines.
+You may have access to [additional SRDs](#-access-additional-srds) so be careful to check which machine you are working in as files and installed packages may not be the same across the machines.
 ```
 
 ### {{musical_keyboard}} Keyboard mapping
@@ -545,7 +545,7 @@ You may find that the keyboard mapping on your computer is not the same as the o
 Click on `Desktop` and `Applications > Settings > Keyboard` to change the layout.
 
 ```{tip}
-We recommend opening an application that allows text entry (such as `Libre Office Writer` , see [Access applications](#access-applications) below) to check what keys the remote desktop thinks you're typing – especially if you need to use special characters.
+We recommend opening an application that allows text entry (such as `Libre Office Writer` , see [Access applications](#-access-applications) below) to check what keys the remote desktop thinks you're typing – especially if you need to use special characters.
 ```
 
 ### {{unlock}} Access applications
@@ -676,7 +676,7 @@ Depending on the type of data you are accessing, different `R` and `python` pack
 - {ref}`Tier 2 <policy_tier_2>` (medium security) environments have full mirrors of `PyPI` and `CRAN` available.
 - {ref}`Tier 3 <policy_tier_3>` (high security) environments only have pre-authorised packages available.
 
-If you need to use a package that is not on the allowlist see the section on how to [bring software or data into the environment](#bring-in-new-files-to-the-sre) below.
+If you need to use a package that is not on the allowlist see the section on how to [bring software or data into the environment](#-bring-in-new-files-to-the-sre) below.
 
 (role_researcher_user_guide_shared_storage)=
 
@@ -832,7 +832,7 @@ We recommend that you make your repositories public to facilitate collaboration
 
 If you have not used GitLab before:
 
-- There is a small tutorial available as an [Appendix](#appendix-b-gitlab-tutorial-notes) to this user guide.
+- There is a small tutorial available as an [Appendix](#-appendix-b-gitlab-tutorial-notes) to this user guide.
 - You can find the official documentation on the [GitLab website](https://docs.gitlab.com/ee/user/index.html).
 - Ask your team mates for help.
 - Ask the designated contact for your SRE.