initial commit

.github/workflows/build.yaml

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+name: Build and Deploy
+
+on:
+  push:
+    branches:
+      - master
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout master
+      uses: actions/checkout@v1
+      with:
+        submodules: true
+
+    - name: Hugo Deploy GitHub Pages
+      uses: benmatselby/hugo-deploy-gh-pages@master
+      env:
+        HUGO_EXTENDED: true
+        TARGET_REPO: FAIRDataPipeline/FAIRDataPipeline.github.io
+        TOKEN: ${{ secrets.FDP_HUGO }}

.gitignore

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+/resources

archetypes/default.md

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+---
+title: "{{ replace .Name "-" " " | title }}"
+date: {{ .Date }}
+draft: true
+---
+

config.toml

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+# hugo server --minify --themesDir ... --baseURL=http://0.0.0.0:1313/theme/hugo-book/
+
+baseURL = 'https://FAIRDataPipeline.github.io/'
+title = 'FAIRDataPipeline'
+theme = 'hugo-book'
+enableEmoji = true
+
+# Book configuration
+disablePathToLower = true
+enableGitInfo = true
+pygmentsUseClasses = true
+
+# Needed for mermaid/katex shortcodes
+[markup]
+[markup.goldmark.renderer]
+  unsafe = true
+
+[markup.tableOfContents]
+  startLevel = 1
+
+[menu]
+# [[menu.before]]
+[[menu.after]]
+  name = "SCRC UoG"
+  url = "https://www.gla.ac.uk/research/az/scrc/"
+  weight = 10
+
+[[menu.after]]
+  name = "Data Registry"
+  url = "https://data.scrc.uk/"
+  weight = 20
+
+[params]
+  # (Optional, default true) Controls table of contents visibility on right side of pages.
+  # Start and end levels can be controlled with markup.tableOfContents setting.
+  # You can also specify this parameter per page in front matter.
+  BookToC = true
+
+  # (Optional, default none) Set the path to a logo for the book. If the logo is
+  # /static/logo.png then the path would be logo.png
+  # BookLogo = 'logo.png'
+
+  # (Optional, default none) Set leaf bundle to render as side menu
+  # When not specified file structure and weights will be used
+  # BookMenuBundle = '/menu'
+
+  # (Optional, default docs) Specify root page to render child pages as menu.
+  # Page is resoled by .GetPage function: https://gohugo.io/functions/getpage/
+  # For backward compatibility you can set '*' to render all sections to menu. Acts same as '/'
+  BookSection = 'docs'
+
+  # Set source repository location.
+  # Used for 'Last Modified' and 'Edit this page' links.
+  BookRepo = 'https://github.com/FAIRDataPipeline/FDP_hugo'
+
+  # Enable "Edit this page" links for 'doc' page type.
+  # Disabled by default. Uncomment to enable. Requires 'BookRepo' param.
+  # Edit path must point to root directory of repo.
+  BookEditPath = 'tree/master/content'
+
+  # Configure the date format used on the pages
+  # - In git information
+  # - In blog posts
+  BookDateFormat = 'January 2, 2006'
+
+  # (Optional, default true) Enables search function with flexsearch,
+  # Index is built on fly, therefore it might slowdown your website.
+  # Configuration for indexing can be adjusted in i18n folder per language.
+  BookSearch = false
+
+  SearchEnabled = true
+
+  # (Optional, default true) Enables comments template on pages
+  # By default partals/docs/comments.html includes Disqus template
+  # See https://gohugo.io/content-management/comments/#configure-disqus
+  # Can be overwritten by same param in page frontmatter
+  BookComments = true
+
+  # /!\ This is an experimental feature, might be removed or changed at any time
+  # (Optional, experimental, default false) Enables portable links and link checks in markdown pages.
+  # Portable links meant to work with text editors and let you write markdown without {{< relref >}} shortcode
+  # Theme will print warning if page referenced in markdown does not exists.
+  BookPortableLinks = true
+
+  # /!\ This is an experimental feature, might be removed or changed at any time
+  # (Optional, experimental, default false) Enables service worker that caches visited pages and resources for offline use.
+  BookServiceWorker = true
+
+  # To change the fenced code block theme. 
+  # 1. Put this in config.toml: 
+  # pygmentsUseClasses = true
+  # 2. Run this:
+  # hugo gen chromastyles --style=arduino > syntax.css 
+  # 3. Copy the css into a new stylesheet, themes/hugo-book/assets/_scriptstyle.scss
+  # 4. Add an import to the new stylesheet in _custom.scss:
+  # @import "scriptstyle";
+
+    BookLogo = "logo.jpg"

content/_index.md

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+---
+title: Introduction
+type: docs
+---
+
+# SCRC
+
+## Who are we?
+
+The Scottish COVID-19 Response Consortium is formed of [dozens of individuals from over 30 academic and commercial organisations](https://www.gla.ac.uk/research/az/scrc/ourpeople/#members).
+
+Researchers in these organisations jointly responded to a call by the [Royal Society](https://royalsociety.org/topics-policy/health-and-wellbeing/ramp/) to develop more epidemiological models of COVID-19 spread - [RAPID ASSISTANCE IN MODELLING THE PANDEMIC: RAMP](https://epcced.github.io/ramp/) - in order to develop a more robust and clearer understanding of the impacts of different exit strategies from lockdown. Scientists from several other organisations across the UK and abroad have now joined the consortium to provide additional expertise in specific areas.
+
+## Our outputs:
+
+During and since the initial three months of RAMP work, our major achievements have been:
+
+- Seven [software epidemiological models](https://scottishcovidresponse.github.io/docs/models/) in four different programming languages and using multiple scientific approaches. These models have been assessed favourably in internal review against a [software checklist](https://github.com/ScottishCovidResponse/modelling-resources/blob/main/software-checklist.md) we developed.
+- Data APIs in five languages (python, Julia, R, Java and C++) that simplify provenance recording, allowing input data to be verified as it is used, and model outputs to be traced back to the model code and input data that were used to produce them.
+- A set of curated, traceable source data useful for epidemiological modelling on COVID-19.
+- A database to hold metadata and index the data.
+- Data processing code in `R` to populate the database.
+
+These are discoverable via our [GitHub organisation](https://github.com/ScottishCovidResponse).