Merge branch 'main' into nomultithread-fix-typo

Author: bcumming

.github/actions/spelling/allow.txt

@@ -10,12 +10,9 @@ CHARMM
 CHF
 COSMA
 CPE
-cpe
 CPMD
-CSCS
 CWP
 CXI
-capstor
 Ceph
 Containerfile
 DNS
@@ -46,7 +43,6 @@ HPCP
 HPE
 HSN
 Hartree
-iopsstor
 Jax
 Jira
 Keycloak
@@ -101,23 +97,32 @@ acl
 biomolecular
 bristen
 bytecode
+capstor
 clariden
 concretise
 concretizer
 containerised
+cpe
+cscs
 customised
 diagonalisation
 eiger
 filesystems
 groundstate
+ijulia
 inodes
+iopsstor
 lexer
 libfabric
+miniconda
+mpi
 multitenancy
+nsight
 podman
-prioritised
 prgenv
+prioritised
 proactively
+pytorch
 quickstart
 santis
 sbatch

.github/workflows/spelling.yaml

@@ -0,0 +1,62 @@
+name: Check Spelling
+
+# Based on example in https://github.com/check-spelling/spell-check-this.
+on:
+  push:
+    branches: ['main']
+  pull_request_target:
+    branches: ['main']
+    types: ['opened', 'reopened', 'synchronize']
+  issue_comment:
+    types: ['created']
+
+jobs:
+  spelling:
+    name: Check Spelling
+    permissions:
+      contents: read
+      pull-requests: write
+      actions: read
+      security-events: write
+    outputs:
+      followup: ${{ steps.spelling.outputs.followup }}
+    runs-on: ubuntu-latest
+    if: ${{ contains(github.event_name, 'pull_request') || github.event_name == 'push' }}
+    concurrency:
+      group: spelling-${{ github.event.pull_request.number || github.ref }}
+      cancel-in-progress: true
+    steps:
+    - name: check-spelling
+      id: spelling
+      uses: check-spelling/check-spelling@2d5f9dd9d2d43584d36e4ae03a3508eff411eda9
+      with:
+        suppress_push_for_open_pull_request: ${{ github.actor != 'dependabot[bot]' && 1 }}
+        checkout: true
+        check_file_names: 0
+        only_check_changed_files: 1
+        post_comment: 1
+        use_magic_file: 1
+        warnings: bad-regex,binary-file,deprecated-feature,large-file,limited-references,no-newline-at-eof,noisy-file,non-alpha-in-dictionary,token-is-substring,unexpected-line-ending,whitespace-in-dictionary,minified-file,unsupported-configuration,no-files-to-check
+        use_sarif: ${{ (!github.event.pull_request || (github.event.pull_request.head.repo.full_name == github.repository)) && 1 }}
+        extra_dictionary_limit: 20
+        extra_dictionaries:
+          cspell:software-terms/dict/softwareTerms.txt
+          cspell:bash/dict/bash-words.txt
+          cspell:companies/dict/companies.txt
+          cspell:filetypes/filetypes.txt
+
+  comment-pr:
+    name: Check Spelling Report (PR)
+    runs-on: ubuntu-latest
+    needs: spelling
+    permissions:
+      actions: read
+      contents: read
+      pull-requests: write
+    if: (success() || failure()) && needs.spelling.outputs.followup && contains(github.event_name, 'pull_request')
+    steps:
+    - name: comment
+      uses: check-spelling/check-spelling@2d5f9dd9d2d43584d36e4ae03a3508eff411eda9
+      with:
+        checkout: true
+        task: ${{ needs.spelling.outputs.followup }}

docs/access/jupyterlab.md

@@ -148,7 +148,7 @@ To run Julia code in Jupyter notebooks, you can use the provided uenv for this l
 !!! important "pass a [`julia`][ref-uenv-julia] uenv and the view `jupyter`."
 
 When Julia is first used within Jupyter, IJulia and one or more Julia kernel need to be installed. 
-Type the following command in a shell within JupyterHub to install IJulia, the default Julia kernel and, on systems whith Nvidia GPUs, a Julia kernel running under Nvidia Nsight Systems:
+Type the following command in a shell within JupyterHub to install IJulia, the default Julia kernel and, on systems with Nvidia GPUs, a Julia kernel running under Nvidia Nsight Systems:
 ```bash
 install_ijulia
 ```

docs/accounts/account-create.md

@@ -38,7 +38,7 @@ After your password has been set, you will be redirected to a page where you log
 
 ![](../images/access/first-login.png)
 
-From here you will need to set up [multi-factor authentification][ref-mfa-configure-otp] (MFA).
+From here you will need to set up [multi-factor authentication][ref-mfa-configure-otp] (MFA).
 
 Once MFA has been configured, you will finally be redirected to the CSCS portal as shown:
 

docs/services/cicd.md

@@ -21,7 +21,7 @@ Version 2 is faster, easier to use, and more efficient in resource management th
 
 !!! warning "Deprecation notice"
     If you're using **version 1**, we recommend you to port your applications to use the new version.
-    We will communicate soon the exact date of the decomission of version 1 (not before Quarter 4 of 2025).
+    We will communicate soon the exact date of the decommissioning of version 1 (not before Quarter 4 of 2025).
 
 === "Version 2"
 

docs/services/firecrest.md

@@ -55,6 +55,6 @@ By default, uenv will generate color output according to the following:
 The default repo location for downloaded uenv images.
 The repo is selected according to the following process:
 
-* if the `--repo` CLI arguement overrides 
+* if the `--repo` CLI argument is given, use that setting
 * else if `repo` is set in the config file, use that setting
 * else use the default value of `$SCRATCH/.uenv-images`

docs/software/uenv/configure.md

@@ -106,11 +106,11 @@ However, it is not desirable to build every recipe on every possible target syst
 For example:
 
 * An ICON development environment would only be deployed on the weather and climate platform
-* A GROMACS recipe would not be deployed on the weather and climate platrofm
+* A GROMACS recipe would not be deployed on the weather and climate platform
 * Development builds only need to run on test and staging clusters
 
 A YAML file `config.yaml` is maintained in the [github.com/eth-cscs/alps-uenv](https://github.com/eth-cscs/alps-uenv/blob/main/config.yaml) repository that maps
-recipes to deployed versions on mucroarchitectures.
+recipes to deployed versions on microarchitectures.
 
 ### Permissions
 
@@ -215,13 +215,13 @@ However,
 * access to some packages is restricted by applying access rules to the package path
 * e.g. access to `uenv-sources/vasp` is restricted to members of the vasp6 group
 
-Permissons to acces restricted resources is set on a per-pipeline basis
+Permissions to access restricted resources is set on a per-pipeline basis
 
 * For example, only the `alps-uenv` pipeline has access to the VASP source code, while the [`uenv build`][ref-uenv-build] pipeline does not.
 
 | Package | Access | Path | Notes | Contact |
 |---------|--------|------|-------| ------- |
-| `cray-mpich` | anonymous | `uenv-sources/cray-mpich` | `cray-mpich`, `cray-gtl`, `cray-pals`, `cray-mpi` | Simon Pintarelli, Benjamin Comming|
+| `cray-mpich` | anonymous | `uenv-sources/cray-mpich` | `cray-mpich`, `cray-gtl`, `cray-pals`, `cray-mpi` | Simon Pintarelli, Benjamin Cumming|
 | `namd` | `uenv-sources-csstaff` | `uenv-sources/namd` | NAMD requires an account to download the source code | Rocco Meli |
 | `vasp` | `vasp6`, `cscs-uenv-admin` | `uenv-sources/vasp` | VASP requires a paid license to access source | Simon Frasch |
 | `vmd` | `uenv-sources-csstaff` | `uenv-sources/vmd` | VMD requires an account to download the source code | Alberto Invernizzi |

docs/software/uenv/deploy.md

@@ -317,7 +317,7 @@ A daily process removes files that have not been **accessed (either read or writ
 !!! warning "Do not artificially update the access time of files"
     It is not allowed to automatically or artificially update the access time of files to avoid the cleanup policy, and CSCS scans for these activities.
 
-    Please move data to a file system that is suitable for persistant storage instead.
+    Please move data to a file system that is suitable for persistent storage instead.
 
 In addition to the automatic deletion of old files, if occupancy exceeds 60% the following steps are taken to maintain performance of the file system: