Apply formatting

.github/dependabot.yml

@@ -3,7 +3,6 @@
 
 version: 2
 updates:
-
   # Set update schedule for GitHub Actions
   - package-ecosystem: "github-actions"
     directory: "/"

.github/workflows/link-checker-pr.yml

@@ -13,13 +13,15 @@ jobs:
         with:
           # Avoid using single or double quotes for multiline patterns
           files: |
-             **.md
+            **.md
           matrix: true
-  
+
   linkChecker:
     runs-on: ubuntu-latest
     needs: changedFiles
-    if: ${{ needs.changedFiles.outputs.files != '' && toJSON(fromJSON(needs.changedFiles.outputs.files)) != '[]' }}
+    if:
+      ${{ needs.changedFiles.outputs.files != '' &&
+      toJSON(fromJSON(needs.changedFiles.outputs.files)) != '[]' }}
     strategy:
       matrix:
         file: ${{ fromJSON(needs.changedFiles.outputs.files) }}

.github/workflows/link-checker.yml

@@ -5,7 +5,7 @@ on:
     branches:
       - main
   schedule:
-    - cron: '0 4 * * *'  
+    - cron: "0 4 * * *"
 jobs:
   linkChecker:
     runs-on: ubuntu-latest
@@ -16,7 +16,9 @@ jobs:
         id: lychee
         with:
           # note: args has a long default value; when you override it, make sure you don't accidentally forget to include the default options you want! see https://github.com/lycheeverse/lychee-action/blob/master/action.yml
-          args: --verbose --no-progress './**/*.md' './**/*.html' './**/*.rst' --accept '100..=103,200..=299, 429' --exclude nlesc.sharepoint.com
+          args:
+            --verbose --no-progress './**/*.md' './**/*.html' './**/*.rst'
+            --accept '100..=103,200..=299, 429' --exclude nlesc.sharepoint.com
         env:
           # This token is included to avoid github.com requests to error out with status 429 (too many requests). It only works for GitHub requests (also other GitHub REST API calls), not for the rest of the web.
           GITHUB_TOKEN: ${{secrets.TOKEN_GITHUB}}

.github/workflows/pdf.yml

@@ -16,7 +16,7 @@ jobs:
 
       - uses: actions/setup-node@v4
         with:
-          node-version: '20'
+          node-version: "20"
 
       - name: Install uploader
         run: npm install @iomeg/zenodo-upload
@@ -33,7 +33,7 @@ jobs:
             --user $(id -u):$(id -g) \
             -e "PDF_OUTPUT_NAME=guide-nlesc.pdf" \
             ghcr.io/kernoeb/docker-docsify-pdf:latest
-        
+
       - name: Upload PDF as an artifact
         if: always()
         uses: actions/upload-artifact@v4
@@ -43,6 +43,8 @@ jobs:
 
       - name: Upload PDF to Zenodo
         if: github.event_name == 'release'
-        run: npx --package @iomeg/zenodo-upload zenodo_upload 4020565 guide-nlesc.pdf "${github_ref:10}" ${{ secrets.ZENODO_TOKEN }}
+        run:
+          npx --package @iomeg/zenodo-upload zenodo_upload 4020565
+          guide-nlesc.pdf "${github_ref:10}" ${{ secrets.ZENODO_TOKEN }}
         env:
           github_ref: ${{ github.ref }}

CITATION.cff

@@ -1,6 +1,10 @@
 cff-version: 1.0.3
 title: Software Development Guide
-abstract: This is a guide to software development and projects at the Netherlands eScience Center. It both serves as a source of information for exactly how we work at the eScience Center, and as a basis for discussions and reaching consensus on this topic.
+abstract:
+  This is a guide to software development and projects at the Netherlands
+  eScience Center. It both serves as a source of information for exactly how we
+  work at the eScience Center, and as a basis for discussions and reaching
+  consensus on this topic.
 message: If you use this guide, please cite it.
 repository-code: https://github.com/NLeSC/guide
 license: CC-BY-4.0
@@ -109,7 +113,7 @@ authors:
   - affiliation: "Netherlands eScience Center"
     family-names: Zapata
     given-names: Felipe
-    orcid:  "https://orcid.org/0000-0001-8286-677X"
+    orcid: "https://orcid.org/0000-0001-8286-677X"
   - affiliation: "Netherlands eScience Center"
     family-names: Bakker
     given-names: Tom

README.md

@@ -2,22 +2,23 @@
 
 # Guide
 
-This is a guide to software development at the Netherlands eScience Center.
-It both serves as a source of information for how we work at the eScience
-Center, and as a basis for discussions and reaching consensus on this topic.
+This is a guide to software development at the Netherlands eScience Center. It
+both serves as a source of information for how we work at the eScience Center,
+and as a basis for discussions and reaching consensus on this topic.
 
 **Read The Turing Way instead**
 
 If you are looking for an overall picture of best practices, read
-[The Turing Way](https://book.the-turing-way.org/index.html) first.
-We joined forces with that guide for most of our generic research software
-engineering advice.
-Because The Turing Way is programming language agnostic, this guide provides
-addtional specific
-[language guides](language_guides/languages_overview.md).
-We also provide [technology guides](technology/technology_overview.md) on digital technologies we use often in our projects with research partners.
-*Please be aware that most remaining [best practices](/best_practices/overview.md) content is unmaintained,
-be careful when using it.*
-We plan on removing that content ([#286](https://github.com/NLeSC/guide/issues/286)).
+[The Turing Way](https://book.the-turing-way.org/index.html) first. We joined
+forces with that guide for most of our generic research software engineering
+advice. Because The Turing Way is programming language agnostic, this guide
+provides addtional specific
+[language guides](language_guides/languages_overview.md). We also provide
+[technology guides](technology/technology_overview.md) on digital technologies
+we use often in our projects with research partners. _Please be aware that most
+remaining [best practices](/best_practices/overview.md) content is unmaintained,
+be careful when using it._ We plan on removing that content
+([#286](https://github.com/NLeSC/guide/issues/286)).
 
-If you would like to contribute to this book see [CONTRIBUTING.md](CONTRIBUTING.md).
+If you would like to contribute to this book see
+[CONTRIBUTING.md](CONTRIBUTING.md).

_sidebar.md

@@ -1,18 +1,17 @@
-
-* [Introduction](/README.md)
-* [Language Guides](/language_guides/languages_overview.md)
-   * [Bash](/language_guides/bash.md)
-   * [JavaScript and TypeScript](/language_guides/javascript.md)
-   * [Python](/language_guides/python.md)
-   * [R](/language_guides/r.md)
-   * [C and C++](/language_guides/ccpp.md)
-   * [Fortran](/language_guides/fortran.md)
-* [Technology Guides](/technology/technology_overview.md)
-   * [GPU programming](/technology/gpu.md)
-   * [UX - User Experience](/technology/user_experience.md)
-   * [Datasets](/technology/datasets.md)
-* [Best practices](/best_practices/overview.md)
-   * [Releases](/best_practices/releases.md)
-   * [Documentation](/best_practices/documentation.md)
-   * [Standards](/best_practices/standards.md)
-* [Contributing to this Guide](/CONTRIBUTING.md)
+- [Introduction](/README.md)
+- [Language Guides](/language_guides/languages_overview.md)
+  - [Bash](/language_guides/bash.md)
+  - [JavaScript and TypeScript](/language_guides/javascript.md)
+  - [Python](/language_guides/python.md)
+  - [R](/language_guides/r.md)
+  - [C and C++](/language_guides/ccpp.md)
+  - [Fortran](/language_guides/fortran.md)
+- [Technology Guides](/technology/technology_overview.md)
+  - [GPU programming](/technology/gpu.md)
+  - [UX - User Experience](/technology/user_experience.md)
+  - [Datasets](/technology/datasets.md)
+- [Best practices](/best_practices/overview.md)
+  - [Releases](/best_practices/releases.md)
+  - [Documentation](/best_practices/documentation.md)
+  - [Standards](/best_practices/standards.md)
+- [Contributing to this Guide](/CONTRIBUTING.md)