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Update docs #1806

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Apr 15, 2024
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50 changes: 25 additions & 25 deletions docs/requirements.txt
Original file line number Diff line number Diff line change
@@ -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
12 changes: 6 additions & 6 deletions docs/source/roles/researcher/user_guide.md
Original file line number Diff line number Diff line change
@@ -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.