Add CI

.github/workflows/check_links.yaml

@@ -0,0 +1,51 @@
+# Check that all links are valid, i.e. not broken
+name: Check links
+
+# Check links on the 21st day of the month.
+# 21st as the first letter of this repo is the 21st letter in the alphabet.
+on:
+  push:
+  pull_request:
+  schedule:
+  - cron: "0 0 21 * *"
+
+
+jobs:
+  check-links:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      # The link checker will only work if mlc_config.json is a valid JSON
+      - name: Validate JSON
+        uses: docker://orrosenblatt/validate-json-action:latest
+        env:
+          INPUT_SCHEMA: .github/workflows/valid_json_schema.json
+          INPUT_JSONS: mlc_config.json
+
+      # These are status code that cannot be ignored.
+      #
+      # If there is a valid external link that fails,
+      # add it to mlc_config.json
+      - name: External links must be checked, do not allow '0' in the 'aliveStatusCodes' of mlc_config.json
+        run: if [[ $(grep --regexp "[^0-9]0[^0-9]" mlc_config.json | wc --lines) == "1" ]]; then echo "FOUND"; exit 42; fi
+
+      - name: Internal links must checked, do not allow '400' in the 'aliveStatusCodes' of mlc_config.json
+        run: if [[ $(grep --regexp "[^0-9]400[^0-9]" mlc_config.json | wc --lines) == "1" ]]; then echo "FOUND"; exit 42; fi
+
+
+      # For an indented block, a link to a broken image is ignored, as the link checker assumes it to be code.
+      # In our case, it is not: for us, it is usually an admonition (i.e. a 'question' or 'info' block)
+      # Here all indented text is unindented
+      # https://github.com/UPPMAX/UPPMAX-documentation/issues/114
+      - name: unindent text
+        run: ./scripts/unindent_text.sh
+
+      - uses: gaurav-nelson/github-action-markdown-link-check@v1
+        with:
+          config-file: 'mlc_config.json'
+          use-quiet-mode: 'yes'
+          use-verbose-mode: 'no'
+

.github/workflows/check_markdown.yaml

@@ -0,0 +1,44 @@
+# Check that there is correct markdown in all files
+name: Check markdown
+
+# Check spelling on the 21st day of the month.
+# 21st as the first letter of this repo is the 21st letter in the alphabet.
+on:
+  push:
+  pull_request:
+  schedule:
+  - cron: "0 0 21 * *"
+
+jobs:
+  check_markdown:
+
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+
+      - name: Set up Git repository
+        uses: actions/checkout@v4
+
+      # Indented blocks are ignored, as the linter assumes it to be code.
+      # In our case, it is not: for us, it is usually an admonition (i.e. a 'question' or 'info' block)
+      # Here all indented text is unindented
+      # https://github.com/UPPMAX/UPPMAX-documentation/issues/114
+      - name: unindent text
+        run: ./scripts/unindent_text.sh
+
+      - uses: articulate/actions-markdownlint@v1
+        with:
+          config: .markdownlint.jsonc
+          ignore: .markdownlintignore
+
+      # There are many linters with the same name,
+      # this is the linter whose documentation to look into :-)
+      - name: CLI to the linter is at https://github.com/igorshubovych/markdownlint-cli
+        run: echo "CLI to the linter is at https://github.com/igorshubovych/markdownlint-cli"
+
+      # There are many linters with the same name,
+      # this is the linter whose documentation to look into :-)
+      - name: Linter is at https://github.com/DavidAnson/markdownlint
+        run: echo "Linter is at https://github.com/DavidAnson/markdownlint"
+

.github/workflows/check_spelling.yaml

@@ -0,0 +1,30 @@
+# Check that there is correct spelling in all files
+name: Check spelling
+
+# Check spelling on the 21st day of the month.
+# 21st as the first letter of this repo is the 21st letter in the alphabet.
+on:
+  push:
+  pull_request:
+  schedule:
+  - cron: "0 0 21 * *"
+
+
+jobs:
+  check_spelling:
+
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+
+      - name: Set up Git repository
+        uses: actions/checkout@v4
+
+      - name: Do not check raw evaluation results
+        run: rm evaluations/20240827/survey_feedback.md
+
+      - uses: igsekor/[email protected]
+
+
+

.github/workflows/valid_json_schema.json

@@ -0,0 +1,6 @@
+{
+    "properties": {
+        "foo": { "type": "string" },
+        "bar": { "type": "number" }
+    }
+}

.markdownlint.jsonc

@@ -0,0 +1,43 @@
+// Example markdownlint configuration with all properties set to their default value
+{
+
+  // Default state for all rules
+  "default": true,
+
+  // MkDocs assumes 4 spaces for indentation.
+  // Markdown assumes 4 spaces for indentation.
+  // That markdownlint has a different default is the error of markdownlint
+  "MD007": { "indent": 4 },
+
+  // Standard markdown does not allow for two correct consecutive blank lines 
+  // i an admonitions (a.o. the 'question' admonition):
+  //
+  // ???- question "A question"
+  //
+  //     ```
+  //     echo "indented code here :-)
+  //     ````
+  //     [blank line 1 here]
+  // [blank line 2 here]
+  //
+  // Hence we allow 2 consecutive blank lines
+  //
+  "MD012": {
+    // Consecutive blank lines, CHANGED FROM 1
+    "maximum": 2
+  },
+
+  // Standard markdown does not allow for valid indent code like this:
+  //
+  // ???- question "A question"
+  //
+  //     ```
+  //     echo "indented code here :-)
+  //     ````
+  //     
+  // Hence we allow valid indented code.
+  //
+  // MD046/code-block-style : Code block style : https://github.com/DavidAnson/markdownlint/blob/v0.34.0/doc/md046.md
+  "MD046": false
+
+}

.markdownlintignore

@@ -0,0 +1,3 @@
+docs/index.md
+docs/software/software-table.md
+evaluations/**/*_feedback.md

.spellcheck.yml

@@ -0,0 +1,45 @@
+matrix:
+- name: markdown
+  dictionary:
+    wordlists:
+    - .wordlist.txt
+    output: wordlist.dic
+    encoding: utf-8
+  pipeline:
+  - pyspelling.filters.markdown:
+      markdown_extensions:
+      - markdown.extensions.extra:
+  - pyspelling.filters.html:
+      comments: true
+      attributes:
+      - alt
+      ignores:
+      - ':matches(code, pre)'
+      - 'code'
+      - 'pre'
+      - 'blockquote'
+  sources:
+  - '**/*.md'
+  default_encoding: utf-8
+- name: Quarto markdown
+  dictionary:
+    wordlists:
+    - .wordlist.txt
+    output: wordlist.dic
+    encoding: utf-8
+  pipeline:
+  - pyspelling.filters.markdown:
+      markdown_extensions:
+      - markdown.extensions.extra:
+  - pyspelling.filters.html:
+      comments: true
+      attributes:
+      - alt
+      ignores:
+      - ':matches(code, pre)'
+      - 'code'
+      - 'pre'
+      - 'blockquote'
+  sources:
+  - '**/*.md'
+  default_encoding: utf-8

.wordlist.txt

@@ -0,0 +1,124 @@
+Richel
+Richèl
+UPPMAX
+config
+Dardel
+github
+html
+https
+json
+jsonc
+linter
+markdownlint
+markdownlintignore
+mlc
+Servicedesk
+txt
+uppmax
+Uppsala
+UU
+wordlist
+yml
+Awk
+bianca
+bilderbeek
+Bioinformatics
+BSc
+CentOS
+Centre
+clustername
+Codecademy
+CodeRefinery
+Conda
+CPUs
+dataset
+emacs
+ENCCS
+EuroCC
+faq
+FileZilla
+formalisms
+GDPR
+gedit
+genomic
+GPUs
+gvim
+HPC
+icm
+MSc
+NAISS
+naiss
+nano
+NGI
+personuppgifter
+Rackham
+RedHat
+richel
+scp
+se
+sexualized
+Skydd
+Slurm
+SNIC
+snic
+socio
+Sunet
+SUNET
+SUPR
+supr
+Swegen
+ThinLinc
+Transfering
+uu
+VPN
+www
+Bourne
+cd
+chmod
+Crex
+Deamons
+docx
+Domus
+Lutra
+MacOS
+Miarka
+Nvidia
+rackham
+Richèl's
+subdirectories
+tmp
+Vulpes
+connectivist
+cowsay
+distros
+Easybuild
+et
+filesystem
+hdd
+linuxjourney
+macbook
+marcusl
+multiuser
+Nextflow
+pre
+Rackham's
+reproducibility
+RStudio
+Spack
+tcsh
+Thunar
+VSCode
+VSCodium
+webbrowser
+wikipedia
+IDEs
+slurm
+bioinformaticians
+filezilla
+ide
+mins
+
+
+
+
+

README.md

@@ -164,4 +164,15 @@ You can share your feedback at this repository by:
 - `[Deenadayalan et al., 2008]`
   Deenadayalan, Yamini, et al. 
   "How to run an effective journal club: a systematic review." 
-  Journal of evaluation in clinical practice 14.5 (2008): 898-911.
+  Journal of evaluation in clinical practice 14.5 (2008): 898-911.
+
+## Files used by continuous integration scripts
+
+Filename                              |Descriptions
+--------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------
+[mlc_config.json](mlc_config.json)    |Configuration of the link checker, use `markdown-link-check --config mlc_config.json --quiet docs/**/*.md` to do link checking locally
+[.spellcheck.yml](.spellcheck.yml)    |Configuration of the spell checker, use `pyspelling -c .spellcheck.yml` to do spellcheck locally
+[.wordlist.txt](.wordlist.txt)        |Whitelisted words for the spell checker, use `pyspelling -c .spellcheck.yml` to do spellcheck locally
+[.markdownlint.jsonc](.markdownlint.jsonc)|Configuration of the markdown linter, use `markdownlint "**/*.md"` to do markdown linting locally. The name of this file is a default name.
+[.markdownlintignore](.markdownlintignore)|Files ignored by the markdown linter, use `markdownlint "**/*.md"` to do markdown linting locally. The name of this file is a default name.
+