From 2691cc8fb8e080768f93ae4ead5cf50b27167414 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 12 Apr 2024 15:06:18 +0000 Subject: [PATCH 1/3] Bump myst-parser from 1.0.0 to 2.0.0 in /docs Bumps [myst-parser](https://github.com/executablebooks/MyST-Parser) from 1.0.0 to 2.0.0. - [Release notes](https://github.com/executablebooks/MyST-Parser/releases) - [Changelog](https://github.com/executablebooks/MyST-Parser/blob/master/CHANGELOG.md) - [Commits](https://github.com/executablebooks/MyST-Parser/compare/v1.0.0...v2.0.0) --- updated-dependencies: - dependency-name: myst-parser dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- docs/requirements.txt | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index 9b683ebca1..5356681948 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -33,17 +33,17 @@ 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 # 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 # via From dd5946e89b62c0dccd77c364b7d55b5ea16a4ced Mon Sep 17 00:00:00 2001 From: Jim Madge Date: Mon, 15 Apr 2024 14:15:11 +0100 Subject: [PATCH 2/3] Update dependencies --- docs/requirements.txt | 44 +++++++++++++++++++++---------------------- 1 file changed, 22 insertions(+), 22 deletions(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index 5356681948..e045e60539 100644 --- a/docs/requirements.txt +++ b/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 @@ -37,7 +37,7 @@ 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==0.4.0 # via myst-parser @@ -45,43 +45,43 @@ mdurl==0.1.2 # via markdown-it-py 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 From 4813d84b60a3fed4d08e839d26bbcb8afed99cf5 Mon Sep 17 00:00:00 2001 From: Jim Madge Date: Mon, 15 Apr 2024 14:15:23 +0100 Subject: [PATCH 3/3] Fix crossreferences --- docs/source/roles/researcher/user_guide.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/source/roles/researcher/user_guide.md b/docs/source/roles/researcher/user_guide.md index e8bd0df1d4..5b36c5e328 100644 --- a/docs/source/roles/researcher/user_guide.md +++ b/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 ` (medium security) environments have full mirrors of `PyPI` and `CRAN` available. - {ref}`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.