Add docs section

.github/workflows/release-to-virusbank.yml

@@ -1,6 +1,6 @@
 on:
   push:
-    branches: [ main ]
+    branches: [main]
 
 name: Render and deploy to Netlify and VirusBank
 
@@ -15,11 +15,16 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
-      - name: Assemble alpha/toolbox.json 
+      - name: Assemble alpha/toolbox.json
         uses: mikefarah/yq@master
         with:
           cmd: yq -M -o=json src/toolbox.yaml > toolbox/toolbox.json
 
+      - name: Create families.json based src/families.yaml
+        uses: mikefarah/yq@master
+        with:
+          cmd: yq -M -o=json src/families.yaml > families.json
+
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: "4.2"
@@ -32,22 +37,22 @@ jobs:
       - name: Install Quarto
         uses: quarto-dev/quarto-actions/setup@v2
         with:
-          version: 1.4.449
+          version: 1.4.549
           tinytex: true
 
       - name: Render Quarto Project
         uses: quarto-dev/quarto-actions/render@v2
         with:
           to: html
-  
+
       - name: Deploy to Netlify 🚀
         uses: data-intuitive/netlify-deploy-site@v1
         with:
           auth: ${{ secrets.NETLIFY_AUTH_TOKEN }}
           site: ${{ env.NETLIFY_SITE_ID }}
-          dir: '_site'
+          dir: "_site"
           prod: true
-          message: 'Deploy production ${{ github.ref }}'
+          message: "Deploy production ${{ github.ref }}"
 
       - name: Deploy preview to VirusBank
         id: deploy_virusbank
@@ -56,6 +61,6 @@ jobs:
           server: ftp.virusbankplatformorg.webhosting.be
           username: floor@virusbankplatformorg
           password: ${{ secrets.FTP_AUTH_SECRET }}
-          local-dir: './_site/'
+          local-dir: "./_site/"
           log-level: standard
           # dangerous-clean-slate: true

.github/workflows/release_to_netlify.yml

@@ -1,6 +1,6 @@
 on:
-  push:
-    branches-ignore: [ main ]
+  # push:
+  #   branches-ignore: [ main ]
   pull_request:
     types:
       - opened
@@ -20,11 +20,16 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
-      - name: Assemble alpha/toolbox.json 
+      - name: Create toolbox.json based on src/toolbox.yaml
         uses: mikefarah/yq@master
         with:
           cmd: yq -M -o=json src/toolbox.yaml > toolbox/toolbox.json
 
+      - name: Create families.json based src/families.yaml
+        uses: mikefarah/yq@master
+        with:
+          cmd: yq -M -o=json src/families.yaml > families.json
+
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: "4.2"
@@ -37,24 +42,24 @@ jobs:
       - name: Install Quarto
         uses: quarto-dev/quarto-actions/setup@v2
         with:
-          version: 1.4.449
+          version: 1.4.549
           tinytex: true
 
       - name: Render Quarto Project
         uses: quarto-dev/quarto-actions/render@v2
         with:
           to: html
-  
+
       - name: Deploy preview 🚀
         id: deploy_preview
         if: github.event_name == 'pull_request'
         uses: data-intuitive/netlify-deploy-site@v1
         with:
           auth: ${{ secrets.NETLIFY_AUTH_TOKEN }}
           site: ${{ env.NETLIFY_SITE_ID }}
-          dir: '_site'
+          dir: "_site"
           alias: "${{ env.BRANCH_NAME }}"
-          message: 'Deploy production ${{ github.ref }}'
+          message: "Deploy production ${{ github.ref }}"
 
       - uses: thollander/actions-comment-pull-request@v2
         if: github.event_name == 'pull_request'

.gitignore

@@ -1,4 +1,13 @@
-alpha/index.html
-alpha/index_files/
+.Rhistory
+_material
+
+# node
+node_modules
+package.json
+package-lock.json
+
+# quarto
 /.quarto/
 _site
+index_files
+_extensions

README.md

@@ -1,211 +1,46 @@
 # VirusBank Phylotree project
 
-# Introduction
+
+Update
+
+## Introduction
 
 This repository contains the code *and* content for the PhyloViz part of
-the VirusBank platform. The idea is that as much as possible of the site
-is generated, either during pre-rendering or during a site visit. Next
-to that, all functionality that is generic is handled as such and can be
-found under `_js/`.
+the \[VirusBank platform\](https://virusbankplatform.be. The idea is
+that as much as possible of the site is generated, either during
+pre-rendering or page load. Next to that, all functionality that is
+generic is handled as such and can be found under `_js/`.
 
-We use [Quarto]() for rendering the site from source code and content to
-what you see on the internet. Quarto files have the `.qmd` extension and
-typically contain a YAML header (the part between the `---` lines). By
-using Quarto, it’s possible for instance to include files from `_js/`
-into another file using a `{{< include … >}}` statement.
+We use [Quarto](https://quarto.org) for rendering the site from source
+code and content to what you see on the internet. Quarto files have the
+`.qmd` extension and typically contain a YAML header (the part between
+the `---` lines). By using Quarto, it’s possible for instance to include
+files from `_js/` into another file using a `` statement.
 
 This can be illustrated using three situations that the site/app is
 created for:
 
-## A new tool is available for a virus
+### A new tool is available for a virus
 
-Adding a new tool for a virus should be extrememly easy, especially if
-we keep in mind that developing tools is the core business of the
-VirusBank.
+Adding a new tool for a virus should be easy, especially if we keep in
+mind that developing tools is the core business of the VirusBank.
 
-## Adding a virus to an existing family
+### Adding a virus to an existing family
 
 If tools are developed or made available for a virus that was not yet
-listed, we should be able quickly add it this information and let this
+listed, we should be able to quickly add this information and let this
 be reflected where relevant.
 
-## Adding a new virus family
+### Updating information about a virus
 
-Also this should be easy. The hard task should be collecting tools and
-curated information about the viruses at hand, not updating the site and
-visualization.
+Next to structure information about a virus, we also store and show
+semi-structured data: transmission and symptoms, for instance. This
+information should be easy to add or update.
 
 These scenarios (and others) have been taken into account for the design
 of the site/app.
 
-# Details
-
-## Structure
-
-Each virus family is stored in a *directory* or *folder*, for instance:
-`flaviviridae/`. Inside this folder, there are a couple of files that
-are required to bootstrap the family page:
-
-- `tree.newick`: The newick-format tree file downloaded from the ICTV
-  website
-- `family.xlsx`: The Excel file containing annotations for the viruses
-  of interest. The IDs should match those in the `tree.newick` file.
-
-Based on these two files, the following files are generated using
-`_js/update_family.js`:
-
-- `index.qmd`: This will become the main family overview page. This page
-  in turn *includes* all the virus page content
-- `_details.qmd`: The part of the page where individual virus
-  information is shown in tabs. This file is included in `index.qmd`
-- For every virus in the family (say `VIR`), multiple files are
-  generated:
-  - `VIR.qmd`: the main virus page, basically a number of *includes* of
-    the files below
-  - `_VIR.qmd`: The content for the Virus page, also included in the
-    virus family `_details.qmd` and displayed as tabs
-  - `_VIR-symptoms.qmd`: The text description of the symptoms for `VIR`
-  - `_VIR-symptoms.qmd`: A pointer to the symptoms figure, usually
-    stored under `img/`
-  - `_VIR-transmission.qmd`: A text description of the transmission of
-    `VIR`. This is kept empty for now because the figure is
-    self-explanatory.
-  - `_VIR-transmission-fig.qmd`: A figure explaining the transmission of
-    `VIR`. The image itself is usually stored under `img/`
-  - `_VIR-relevance.qmd`: A text description of the medical relevance of
-    `VIR`
-  - `_VIR-relevance-fig.qmd`: A pointer to a figure for the medical
-    relevance (and optionally a caption)
-
-Graphically, the includes can be depicted as follows:
-
-``` mermaid
-graph LR
-
-  subgraph _js/
-    _js/_ojs_data.qmd
-    _js/virus-breadcrumb.qmd
-    _js/family-breadcrumb.qmd
-  end
-
-  _details.qmd --&gt; index.qmd
-  _js/_ojs_data.qmd --&gt; index.qmd
-  _js/_ojs_data.qmd --&gt; VIR.qmd
-  _js/virus-breadcrumb.qmd --&gt; VIR.qmd
-  _js/family-breadcrumb.qmd --&gt; index.qmd
-
-  _VIR.qmd --&gt; _details.qmd
-  _VIR.qmd --&gt; VIR.qmd
-
-  _VIR-symptoms.qmd --&gt; _VIR.qmd
-  _VIR-symptoms.qmd --&gt; _VIR.qmd
-  _VIR-transmission.qmd --&gt; _VIR.qmd
-  _VIR-transmission-fig.qmd --&gt; _VIR.qmd
-  _VIR-relevance.qmd --&gt; _VIR.qmd
-  _VIR-relevance-fig.qmd --&gt; _VIR.qmd
-```
-
-The includes themselves are not parametrized, but the YAML header
-`VIR.qmd` is, for example `alphaviruses/CHIKV.qmd` contains the
-following header:
-
-``` yaml
----
-params:
-  family: alphaviruses
-  virus: Chikungunya virus (CHIKV)
----
-```
-
-Based on this the correct toolbox entries are shown, for instance.
-
-## Build and rendering
-
-As mentioned already, different build stages are performed and each
-generates different aspects of the site.
-
-### Rendering step 1: Bootstrap
-
-Remember that we start off with `family.xlsx` and `tree.newick` for ever
-family. That’s all we need. The bootstrap step generates all the other
-files mentioned above based on the information in `family.xlsx`:
-
-- The `index.qmd` file as well as the `_details.qmd` for the family
-- Per virus, it generates the different `_VIR-...` files.
-
-Please note that this step also generates the content files itself, even
-though we do not have content yet. Instead, placeholder text and figures
-are inserted to be replaced later.
-
-In order to build this step, one needs NodeJS installed and the `npm`
-package manager. The package manager can be used to install two
-packages:
-
-``` sh
-npm install xlsx liquid
-```
-
-This has to be done just once.
-
-Next, we create a directory for the virus family, say
-`virusbankviridae`:
-
-``` sh
-mkdir virusbankviridae
-```
-
-and store the correct `family.xlsx` and `tree.newick` in this directory.
-
-The following steps are required to bootstrap the site for this
-*family*:
-
-``` sh
-node _js/update_family.js -i virusbankviridae
-```
-
-**TODO**: Add a script to build *all* families that are available and
-let the CI run these steps.
-
-## How the site is built
-
-# Development
-
-## Requirements and setup
-
-In order to *render* this site/app locally, the following are required:
-
-0.  `wget`
-
-1.  Quarto
-
-2.  `yq`:
-
-    ``` sh
-    sudo wget -qO /usr/local/bin/yq https://github.com/mikefarah/yq/releases/latest/download/yq_linux_amd64
-    sudo chmod a+x /usr/local/bin/yq
-    ```
-
-## Rendering
-
-## Setup
-
-### Toolbox page
-
-The toolbox page is based on a YAML file.
-
-### Virus family pages
-
-Every virus family is contained in a *folder* of its own. Inside this
-folder, everything related to this specific family can be found.
-
-### Virus pages
-
-## Various remarks
-
-- `d3` is loaded by Quarto already, there is not need to load it again
-
-## Things to add
+## Documentation
 
-- What is *including* what and why
-- How to update *existing* info
-- How to add new info
+Documentation has been integrated in the app itself and [is stored onder
+`docs/`](https://steady-beijinho-13360d.netlify.app//docs).