Merge pull request #1365 from alan-turing-institute/develop

Release v4.0.3 candidate

CONTRIBUTING.md

@@ -26,6 +26,7 @@ Jump to the following sections:
     - [Working in a private repository](#working-in-a-private-repository)
     - [Who's involved in the project](#whos-involved-in-the-project)
     - [Make a change with a pull request](#making-a-change-with-a-pull-request)
+    - [Make a change to the documentation](#making-a-change-to-the-documentation)
 
 ## A DevOps development philosophy
 
@@ -219,6 +220,21 @@ You can update your [fork](https://docs.github.com/en/get-started/quickstart/for
 
 GitHub has a [nice introduction](https://docs.github.com/en/get-started/quickstart/github-flow) to the pull request workflow, but please [get in touch](#get-in-touch) if you have any questions :balloon:.
 
+### Making a change to the documentation
+
+The docs, including for older releases, are available [here](https://alan-turing-institute.github.io/data-safe-haven).
+
+You should follow the same instructions as above to [make a change with a pull request](#making-a-change-with-a-pull-request) when editing the documentation.
+
+To test your changes, build the docs locally by checking out your fork of the repo, navigating to the `docs` folder and `make`ing them:
+
+```{bash}
+cd data-safe-haven/docs
+make html
+```
+
+This will add the contents to a folder called `_output` inside `docs`. Open the index html from a browser and you should be able to navigate the docs and view your changes.
+
 ### Who's involved in the project
 
 As some users have `GitHub` IDs that make it a little difficult to know who they are in real life and it's sometimes nice to know **who** you're working with on the project, hopefully this table will help you put names to faces and IDs :sparkles:

VERSIONING.md

@@ -62,6 +62,8 @@ We usually deploy the latest available version of the Data Safe Haven for each o
 | April 2020       | DSG 2020-04 (event cancelled) | [v2.0.0-beta](https://github.com/alan-turing-institute/data-safe-haven/releases/tag/v2.0.0-beta) |
 | June 2020        | DSSG 2020                     | [v3.0.0-beta](https://github.com/alan-turing-institute/data-safe-haven/releases/tag/v3.0.0-beta) |
 | December 2021    | DSG 2021-12                   | [v3.3.1](https://github.com/alan-turing-institute/data-safe-haven/releases/tag/v3.3.1)           |
+| December 2022    | DSG 2022-12                   | [v4.0.2](https://github.com/alan-turing-institute/data-safe-haven/releases/tag/v4.0.2)           |
+| February 2023    | DSG 2023-02                   | [v4.0.3](https://github.com/alan-turing-institute/data-safe-haven/releases/tag/v4.0.3)           |
 
 ## Versions that have undergone formal security evaluation
 

deployment/CheckRequirements.ps1

@@ -9,7 +9,7 @@ Import-Module $PSScriptRoot/common/Logging -Force -ErrorAction Stop
 
 # Requirements
 $PowershellMinVersion = "7.0.0"
-$PowershellMaxVersion = "7.2.7"
+$PowershellMaxVersion = "7.2.8"
 $ModuleVersionRequired = @{
     "Az.Accounts"                                  = @("ge", "2.9.0")
     "Az.Automation"                                = @("ge", "1.7.3")

deployment/secure_research_environment/cloud_init/cloud-init-srd.mustache.yaml

@@ -415,7 +415,7 @@ write_files:
         BLOBFUSE_CACHE_DIR="/tmp/blobfuse-cache-backup"
         rm -rf $BLOBFUSE_CACHE_DIR
         mkdir -p $BLOBFUSE_CACHE_DIR
-        CACHE_SPACE_MB=$(echo "$(df -BM | grep /mnt | awk '{print $2}' | sed 's/M//') / 2" | bc) # set the cache size to half the size of /mnt which scales with VM size
+        CACHE_SPACE_MB=$(echo "$(findmnt -nb -o size /) / 1024^2 / 50" | bc) # set the cache size to 2% of the OS disk size
         /usr/bin/blobfuse $1 -o rw --tmp-path=$BLOBFUSE_CACHE_DIR --cache-size-mb=$CACHE_SPACE_MB --no-symlinks=true --config-file=/opt/configuration/credentials-backup.secret --log-level=LOG_DEBUG -o attr_timeout=240 -o entry_timeout=240 -o negative_timeout=120 -o allow_other
       fi
 
@@ -426,7 +426,7 @@ write_files:
         BLOBFUSE_CACHE_DIR="/tmp/blobfuse-cache-egress"
         rm -rf $BLOBFUSE_CACHE_DIR
         mkdir -p $BLOBFUSE_CACHE_DIR
-        CACHE_SPACE_MB=$(echo "$(df -BM | grep /mnt | awk '{print $2}' | sed 's/M//') / 2" | bc) # set the cache size to half the size of /mnt which scales with VM size
+        CACHE_SPACE_MB=$(echo "$(findmnt -nb -o size /) / 1024^2 / 50" | bc) # set the cache size to 2% of the OS disk size
         /usr/bin/blobfuse $1 -o rw --tmp-path=$BLOBFUSE_CACHE_DIR --cache-size-mb=$CACHE_SPACE_MB --no-symlinks=true --config-file=/opt/configuration/credentials-egress.secret --log-level=LOG_DEBUG -o attr_timeout=240 -o entry_timeout=240 -o negative_timeout=120 -o allow_other
       fi
 
@@ -437,7 +437,7 @@ write_files:
         BLOBFUSE_CACHE_DIR="/tmp/blobfuse-cache-ingress"
         rm -rf $BLOBFUSE_CACHE_DIR
         mkdir -p $BLOBFUSE_CACHE_DIR
-        CACHE_SPACE_MB=$(echo "$(df -BM | grep /mnt | awk '{print $2}' | sed 's/M//') / 2" | bc) # set the cache size to half the size of /mnt which scales with VM size
+        CACHE_SPACE_MB=$(echo "$(findmnt -nb -o size /) / 1024^2 / 50" | bc) # set the cache size to 2% of the OS disk size
         /usr/bin/blobfuse $1 -o ro --tmp-path=$BLOBFUSE_CACHE_DIR --cache-size-mb=$CACHE_SPACE_MB --no-symlinks=true --config-file=/opt/configuration/credentials-ingress.secret --log-level=LOG_DEBUG -o attr_timeout=240 -o entry_timeout=240 -o negative_timeout=120 -o allow_other
       fi
 

deployment/secure_research_environment/remote/secure_research_desktop/scripts/check_drive_mounts.sh

@@ -10,26 +10,27 @@ END="\033[0m"
 MOUNT_POINTS=("/data" "/home" "/scratch" "/shared" "/output")
 echo -e "${BLUE}Checking drives are mounted...${END}"
 for MOUNT_POINT in "${MOUNT_POINTS[@]}"; do
-    ls ${MOUNT_POINT}/* > /dev/null 2>&1
-    if [ "$(mount | grep $MOUNT_POINT)" ]; then
+    ls "${MOUNT_POINT}"/* > /dev/null 2>&1
+    if (findmnt "$MOUNT_POINT" > /dev/null 2>&1); then
         echo -e "${BLUE} [o] ${MOUNT_POINT} is mounted...${END}"
     else
         echo -e "${RED} [ ] ${MOUNT_POINT} not mounted. Attempting to mount...${END}"
-        if [ -e /etc/systemd/system/${MOUNT_POINT}.mount ]; then
-            systemctl start $(echo $MOUNT_POINT | sed 's|/||').mount
+        MOUNT_UNIT="$(echo "$MOUNT_POINT" | tr -d '/').mount"
+        if [ -e "/etc/systemd/system/${MOUNT_UNIT}" ]; then
+            systemctl start "${MOUNT_UNIT}"
         else
-            mount $MOUNT_POINT
+            mount "$MOUNT_POINT"
         fi
     fi
 done
 sleep 30
 
 echo -e "${BLUE}Rechecking drives are mounted...${END}"
 for MOUNT_POINT in "${MOUNT_POINTS[@]}"; do
-    ls ${MOUNT_POINT}/* > /dev/null 2>&1
-    if [ "$(mount | grep $MOUNT_POINT)" ]; then
+    ls "${MOUNT_POINT}"/* > /dev/null 2>&1
+    if (findmnt "$MOUNT_POINT" > /dev/null 2>&1); then
         echo -e "${BLUE} [o] ${MOUNT_POINT} is mounted...${END}"
-        df -h  | grep $MOUNT_POINT
+        df -h  | grep "$MOUNT_POINT"
     else
         echo -e "${RED} [x] ${MOUNT_POINT} is not currently mounted...${END}"
     fi

docs/deployment/snippets/14_run_smoke_tests.partial.md

@@ -10,4 +10,4 @@ They are automatically uploaded to the SRD during the deployment step.
     - if any of the tests fail, check the `README.md` in this folder for help in diagnosing the issues
 - Copy `tests/test_jupyter.ipynb` to your home directory
     - activate each of the available Python versions in turn
-    - run `jupyter notebook` in each case and check that you can run the notebook and that all versions and paths match throughout
+    - run `jupyter notebook` in each case and check that you can run the notebook and that all versions and paths match throughout. See {ref}`Available Python Versions <available_python_and_r_versions>`.

docs/roles/researcher/snippets/04_using_srd.partial.md

@@ -78,6 +78,8 @@ For example:
 :align: center
 ```
 
+(available_python_and_r_versions)=
+
 ### {{snake}} Available Python and R versions
 
 Typing `R` at the command line will give you the system version of `R` with many custom packages pre-installed.