Merge branch 'ELIXIR-Belgium:main' into linked-cohorts-showcase

.github/workflows/jekyll.yml

@@ -1,10 +1,10 @@
-
 name: Jekyll site CI
 
 on:
+  push:
   pull_request:
-    branches: [ main, master ]
-
+    branches: [ master, main ]
+  workflow_dispatch:
 
 permissions:
   contents: read
@@ -14,15 +14,14 @@ permissions:
 jobs:
   build:
     runs-on: ubuntu-latest
-
     steps:
       - name: Checkout
         uses: actions/checkout@v3
         with:
           ref: ${{ github.event.inputs.branch }}
 
       - name: Setup Ruby
-        uses: ruby/setup-ruby@v1.127.0
+        uses: ruby/setup-ruby@v1
         with:
           ruby-version: '3.1'
           bundler-cache: true
@@ -53,8 +52,33 @@ jobs:
           bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}"
         env:
           PAGES_REPO_NWO: ${{ github.repository }}
+          JEKYLL_BUILD_BRANCH: ${{ github.ref_name }}
           JEKYLL_ENV: ${{ steps.name.outputs.jekyll_env }}
           JEKYLL_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          JEKYLL_BASE_PATH: ${{ steps.pages.outputs.base_path }}
 
       - name: Upload artifact
-        uses: actions/upload-pages-artifact@v1
+        uses: actions/upload-pages-artifact@v1
+
+
+  deploy:
+    runs-on: ubuntu-latest
+    needs: build
+
+    if: |
+      github.event_name == 'workflow_dispatch' ||
+      (github.event_name == 'push' && github.event.repository.default_branch == github.ref_name)
+
+    concurrency:
+      group: "pages"
+      cancel-in-progress: true
+
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v1
+

.github/workflows/tool_list_conversion.yml

@@ -1,11 +1,11 @@
 name: Validation of the tools and page metadata
-
 on:
   pull_request:
     branches: [ master, main ]
   schedule:
     - cron:  '0 13 * * 1'
   workflow_dispatch:
+
 jobs:
   validation:
     runs-on: ubuntu-latest
@@ -22,38 +22,47 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install pyyaml requests python-frontmatter
+          pip install ruamel.yaml requests python-frontmatter
       - name: Run tool table 2 yaml
         run: | 
-          python var/conversions.py
+          python var/tools_validator.py
   
   registry-lookup:
     if: |
         github.repository_owner == 'elixir-europe' &&  github.event_name != 'pull_request'
   
     runs-on: ubuntu-latest
+
     strategy:
       matrix:
         python-version: [3.8]
+
     steps:
       - name: Checkout
         uses: actions/checkout@v3
+
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install pyyaml requests python-frontmatter
-      - name: Run tool table 2 yaml
+          pip install ruamel.yaml requests python-frontmatter
+
+      - name: Run regsitry lookup for the tools file
         run: | 
-          python var/conversions.py --reg --username ${{ secrets.FAIRSHARING_USERNAME }} --password "${{ secrets.FAIRSHARING_PASSWORD }}"
+          python var/tools_validator.py --reg --username ${{ secrets.FAIRSHARING_USERNAME }} --password "${{ secrets.FAIRSHARING_PASSWORD }}"
+
       - name: Fetch country names with corresponding iso
         run: |
           python var/country_list.py
+
       - name: Show differences
-        run: 'git diff --stat'
+        run: |
+          git diff --stat
+
       - name: Create Pull Request
         id: cpr
         uses: peter-evans/create-pull-request@v3
@@ -62,14 +71,12 @@ jobs:
           commit-message: Update tool/resource_list.yaml
           title: 'Automatic tool/resource-list update'
           body: |
-            This PR is automatically generated based on changes in the main_tool_and_resource_list.csv file or based on new links made between the tool table and TeSS.
+            This PR is automatically generated based on new links made between the tools and the registries: TeSS, Bio.tools and FAIRsharing.
 
             Please verify if these changes are valid.
           labels: |
             automatic PR
           reviewers: bedroesb
-          team-reviewers: |
-            maintainers
           branch: list_updates
           base: main
 

.gitignore

@@ -1,4 +1,5 @@
 _site/
 Gemfile.lock
+.jekyll-cache
 .jekyll-metadata
 .vscode/launch.json

CODE_OF_CONDUCT.md

@@ -52,7 +52,7 @@ As such, we do not tolerate behaviour that is disrespectful to our community mem
 We do not tolerate discrimination or harassment based on characteristics that include, but are not limited to: gender identity and expression, sexual orientation, disability, physical appearance, body size, citizenship, nationality, ethnic or social origin, pregnancy, familial status, veteran status, genetic information, religion or belief (or lack thereof), membership of a national minority, property, age, education, socio-economic status, technical choices, and experience level.
 
 Everyone who participates in the Infectious Diseases Toolkit activities is required to conform to this Code of Conduct.
-This Code of Conduct applies to all spaces managed by the Turing Way project including, but not limited to, in person focus groups and workshops, and communications online via GitHub.
+This Code of Conduct applies to all spaces managed by the Infectious Diseases Toolkit including, but not limited to, in person focus groups and workshops, and communications online via GitHub.
 By participating, contributors indicate their acceptance of the procedures by which the Infectious Diseases Toolkit project core development team resolves any Code of Conduct incidents, which may include storage and processing of their personal information.
 
 ### 2.1 Expected behaviour

Gemfile

@@ -1,7 +1,17 @@
 source "https://rubygems.org"
 
-# GitHub pages dependencies
-gem 'github-pages', group: :jekyll_plugins
+gem "elixir-toolkit-theme-plugins", "~> 0.1.9"
+gem "webrick", "~> 1.7"
+gem "jekyll", "~> 4.3.1"
+gem "jemoji", "~> 0.13.0"
+gem "kramdown-parser-gfm", "~> 1.1"
+
+group :jekyll_plugins do
+  gem "jekyll-redirect-from", "~> 0.16.0"
+  gem "jekyll-sitemap", "~> 1.4"
+  gem "jekyll-github-metadata", "~> 2.15"
+  gem "jekyll-relative-links", "~> 0.6"
+  gem "jekyll-seo-tag", "~> 2.8"
+  gem "jekyll-remote-theme"
+end
 
-# Webrick needed for Ruby v3.0+ compatibility
-gem "webrick"

README.md

@@ -1,50 +1,51 @@
-[![theme badge](https://img.shields.io/badge/ELIXIR%20toolkit%20theme-jekyll-blue?color=0d6efd)](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme)
+[![theme badge](https://img.shields.io/badge/ELIXIR%20toolkit%20theme-jekyll-blue?color=0d6efd)](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme) [![Validation of the tools and page metadata](https://github.com/elixir-europe/infectious-diseases-toolkit/actions/workflows/tool_list_conversion.yml/badge.svg)](https://github.com/elixir-europe/infectious-diseases-toolkit/actions/workflows/tool_list_conversion.yml) [![Jekyll site CI](https://github.com/elixir-europe/infectious-diseases-toolkit/actions/workflows/jekyll.yml/badge.svg)](https://github.com/elixir-europe/infectious-diseases-toolkit/actions/workflows/jekyll.yml)
 
-# Infectious Diseases Toolkit
+<img src="https://raw.githubusercontent.com/elixir-europe/infectious-diseases-toolkit/master/assets/img/main_logo.svg" alt="IDTk logo" width="650"/>
 
-The website is build on GitHub using Jekyll, a simple, static site generator based on ruby. When you have a local copy cloned onto your computer, it is possible to generate the website based on this repo. This makes it possible to preview changes live, every time you save a file from within the GitHub infectious-diseases-toolkit repo. Follow these steps to deploy the website based on your local clone (copy) of the jekyll-bootstrap-theme repo:
 
-Make sure you have cloned the infectious-diseases-toolkit repo:
 
-    git clone git@github.com:elixir-europe/infectious-diseases-toolkit.git
-    cd infectious-diseases-toolkit
+# Infectious Diseases Toolkit (IDTk)
 
+The Infectious Diseases Toolkit (IDTk) is a community effort to detail best practices related to infectious disease data management, and showcase solutions that were developed to deal with outbreaks. It was created as part of the [BeYond COVID (BY-COVID) project]( https://by-covid.org/). More information can be found in the [about](https://www.infectious-diseases-toolkit.org/about/) page.
 
-To run the website locally, you can either use [Docker](https://www.docker.com/) or use Jekyll directly after installing various dependencies.
+## Contribute
 
-### Run using Docker
+IDTk is an open [community](https://www.infectious-diseases-toolkit.org/about/contributors) project and if you'd like to help with this project, please check out the following pages for more information:
 
-If not already installed on your machine, install Docker. From the root of the ``infectious-diseases-toolkit`` directory, run:
-```
-docker run -it --rm -p 4000:4000 -v $PWD:/srv/jekyll jekyll/jekyll:latest /bin/bash -c "chmod a+w /srv/jekyll/Gemfile.lock && chmod 777 /srv/jekyll && jekyll serve -w"
-```
-This will start the docker container and serve the website locally.
+* [Code of Conduct](https://www.infectious-diseases-toolkit.org/CODE_OF_CONDUCT)
+* [How to contribute](https://www.infectious-diseases-toolkit.org/contribute/)
+* [Deploy the website locally](https://www.infectious-diseases-toolkit.org/contribute/working-with-git#the-advantage-of-working-locally-previewing-your-changes-through-your-web-browser)
 
-### Run using Jekyll directly
+ The content of the material is developed in Markdown and a templating system ([Jekyll](http://jekyllrb.com/)) is used to format the Markdown pages and generate a website at ([https://www.infectious-diseases-toolkit.org](https://www.infectious-diseases-toolkit.org)). However, there are multiple [ways to contribute](https://elixir-belgium.github.io/infectious-diseases-toolkit-sandbox/contribute/#ways-of-contributing), and it is not a requirement that you are able to use these systems in order to contribute!
 
-1. If not already present on your machine, install ruby. Note that incompatibility issues may arise with ruby 3.0.0 (released 25.12.20) or newer versions.
 
+## How to reach us
 
-1. Install Jekyll
-If you have never installed or run a Jekyll site locally on your computer, follow these instructions to install Jekyll:
-   * Install Jekyll on MacOS/Ubuntu/Other_Linux/Windows: [https://jekyllrb.com/docs/installation/](https://jekyllrb.com/docs/installation/)
+**Have a suggestion or spotted an error?**
+* Feel free to open a [GitHub issue](https://github.com/elixir-europe/infectious-diseases-toolkit/issues)
+* Or email the IDTk editors at [idtk-editors@elixir-europe.org](mailto:rdm-editors@elixir-europe.org )
 
-1. Install Bundler and Jekyll
 
-    ```
-    gem install jekyll bundler
-    ```
+## IDTk is a BY-COVID project
 
-1. Install dependencies
+The BY-COVID project aims to make COVID-19 data accessible not only to researchers, but to anyone that to anyone that could benefit from it, such as policy makers or hospital staff.
 
-    ```
-    bundle install
-    ```
+Going beyond SARS-CoV-2 data, the project will provide a framework for making data from other infectious diseases open and accessible to everyone.
 
-1. deploy website
 
-    ```
-    bundle exec jekyll serve
-    ```
+## Licence
 
-Additional information can be found at the following link: [https://docs.github.com/en/free-pro-team@latest/github/working-with-github-pages/testing-your-github-pages-site-locally-with-jekyll](https://docs.github.com/en/free-pro-team@latest/github/working-with-github-pages/testing-your-github-pages-site-locally-with-jekyll)
+The documents and data from the IDTk are made available under a CC-BY licence. Software are made available under an MIT license. More information about our licence can be found on our [licence](LICENSE) page.
+
+## How to cite the IDTk
+We have not published the story of IDTk yet. Until then, please refer to:
+
+
+<div style="padding:30px;"><p><i>Infectious Diseases Toolkit. A deliverable from the EU-funded BY-COVID project (grant agreement number 101046203). URL: <a href="https://www.infectious-diseases-toolkit.org/">https://www.infectious-diseases-toolkit.org/</a>.</i></p>
+</div>
+
+All of the material from the IDTk is made publicly available under Open Source Initiative licences. The process documents and data are made available under a CC-BY license. Software is made available under an MIT licence. For full details on licensing, please see our [licence document](/LICENSE).
+
+## Acknowledgements
+
+The IDTk is developed as part of the project BY-COVID, which received funding from the European Union’s Horizon Europe Research and Innovation Programme (grant number: 101046203). It is built based on experience and ways of working from the [RDMkit](https://rdmkit.elixir-europe.org/), and makes use of the [ELIXIR Toolkit Theme](https://elixir-belgium.github.io/elixir-toolkit-theme/) for deployment.

TEMPLATE-page.md

@@ -3,7 +3,7 @@ title: <!---Page title--->
 description: <!---Short description of the page--->
 search_exclude: true #leave as “true” until the page is complete and ready to be made public
 contributors: [<!---REPLACE THIS with comma separated list of contributors--->]
-page_id: <!---REPLACE THIS with a shortened page name, with lower case letters and spaces, or an acronym in upper and lower case letters--->
+page_id: "<!---REPLACE THIS with a shortened page name in snake-case: lowercase and underscores--->"
 related_pages: 
   showcase: [<!---REPLACE THIS with the page IDs of the showcase pages that you want to list here as related pages--->]
   human_biomolecular_data: [<!---REPLACE THIS with the page IDs of the human_biomolecular_data pages that you want to list here as related pages--->]

_config.yml

@@ -7,17 +7,15 @@ topnav_title: SANDBOX
 description: "Find tools and guidelines to help you access, analyse and share infectious disease data, and respond quickly to disease outbreaks."
 # Metadata description of the website
 
-remote_theme: ELIXIR-Belgium/elixir-toolkit-theme@1.26.0
+remote_theme: ELIXIR-Belgium/elixir-toolkit-theme@gray-tiles
 
 # gtag: G-TNT17YGXQ4
 
 theme_variables:
   privacy_statement_url: /about/privacy
-  theme_color: da366e
-  topnav:
-    brand_logo: assets/img/main_logo.png
+  theme_color: 457B9D
   fonts:
-    - https://fonts.googleapis.com/css2?family=IBM+Plex+Sans:ital,wght@0,100;0,200;0,300;0,400;0,500;0,600;0,700;1,100;1,200;1,300;1,400;1,500;1,600;1,700&display=swap
+    - https://fonts.googleapis.com/css2?family=PT+Sans:ital,wght@0,400;0,700;1,400;1,700&display=swap
 
 exclude:
   - README.md
@@ -48,6 +46,7 @@ defaults:
       type: "pages"
     values:
       sidebar: contribute
+      search_exclude: true
   -
     scope:
       path: "pathogen-characterisation"
@@ -117,6 +116,8 @@ defaults:
       search_exclude: true
       no_robots: true
 plugins:
+  - elixir-toolkit-theme-plugins
   - jemoji
+  - jekyll-redirect-from
   - jekyll-sitemap
   - jekyll-github-metadata