Add docs section

Nothing is changed on the level of the virus or toolbox information.
data-intuitive · Feb 23, 2024 · 3d2e482 · 3d2e482
2 parents e39c09a + cfe71ab
commit 3d2e482
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diff --git a/.github/workflows/release-to-virusbank.yml b/.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
diff --git a/.github/workflows/release_to_netlify.yml b/.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'

diff --git a/.gitignore b/.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
diff --git a/README.md b/README.md
@@ -1,35 +1,46 @@
 # VirusBank Phylotree project
 
-## Requirements and setup
 
-In order to *render* this site/app, the following are required:
+Update
 
-0.  `wget`
+## Introduction
 
-1.  Quarto
+This repository contains the code *and* content for the PhyloViz part of
+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/`.
 
-2.  `yq`:
+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.
 
-    ``` 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
-    ```
+This can be illustrated using three situations that the site/app is
+created for:
 
-## Rendering
+### A new tool is available for a virus
 
-## Setup
+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.
 
-### Toolbox page
+### Adding a virus to an existing family
 
-The toolbox page is based on a YAML file.
+If tools are developed or made available for a virus that was not yet
+listed, we should be able to quickly add this information and let this
+be reflected where relevant.
 
-### Virus family pages
+### Updating information about a virus
 
-Every virus family is contained in a *folder* of its own. Inside this
-folder, everything related to this specific family can be found.
+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.
 
-### Virus pages
+These scenarios (and others) have been taken into account for the design
+of the site/app.
 
-## Various remarks
+## Documentation
 
-- `d3` is loaded by Quarto already, there is not need to load it again
+Documentation has been integrated in the app itself and [is stored onder
+`docs/`](https://steady-beijinho-13360d.netlify.app//docs).
diff --git a/README.qmd b/README.qmd
@@ -3,39 +3,26 @@ title: VirusBank Phylotree project
 format: gfm
 ---
 
-## Requirements and setup
+## Introduction
 
-In order to _render_ this site/app, the following are required:
+This repository contains the code _and_ content for the PhyloViz part of 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/`.
 
-0. `wget`
+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.
 
-1. Quarto
+[Quarto]: https://quarto.org
 
-2. `yq`:
+This can be illustrated using three situations that the site/app is created for:
 
-    ```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
+- __A new tool is available for a virus__: 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.
 
-## Setup
+- __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 to quickly add this information and let this be reflected where relevant.
 
-### Toolbox page
+- __Updating information about a virus__: 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.
 
-The toolbox page is based on a YAML file.
+These scenarios (and others) have been taken into account for the design of the site/app.
 
-### 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
+## Documentation
 
+Documentation has been integrated in the app itself and [is stored onder `docs/`](https://steady-beijinho-13360d.netlify.app//docs).
 
diff --git a/_quarto.yml b/_quarto.yml
@@ -4,6 +4,8 @@ project:
 website:
   title: "VirusBank"
   repo-url: https://github.com/data-intuitive/VirusBank
+  sidebar:
+    contents: docs/*
 format:
   html:
     title-block-banner: virus.jpg
@@ -72,7 +74,7 @@ format:
           })
         }
         window.addEventListener("load", cleanUpDOM);
-        
+
         </script>
 
     sidebar: false
@@ -81,8 +83,9 @@ format:
     mainfont: "Mukta"
     font-size: 16em
     css: styles.css
+    scss: pimp.scss
     toc: false
-    resources: 
+    resources:
       - families.json
       - tree.newick
       - family.xlsx

diff --git a/bin/find_empty_toolbox_qmd.sh b/bin/find_empty_toolbox_qmd.sh
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+find . -type f -empty | grep "\-toolbox"
diff --git a/bin/install_nodejs.sh b/bin/install_nodejs.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+sudo apt-get update
+sudo apt-get install nodejs
+
+npm install xlsx liquidjs exceljs
diff --git a/bin/install_quarto.sh b/bin/install_quarto.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+wget https://github.com/quarto-dev/quarto-cli/releases/download/v1.4.550/quarto-1.4.550-linux-amd64.deb -O /tmp/quarto.deb
+sudo dpkg -i /tmp/quarto.deb
+
+sudo apt-get install r-base r-base-dev -y
+quarto install tinytex
+
+Rscript -e 'dir.create(Sys.getenv("R_LIBS_USER"), recursive = TRUE)'
+Rscript -e '.libPaths(Sys.getenv("R_LIBS_USER"))'
+Rscript -e 'install.packages("rmarkdown)'
diff --git a/docs/excel.png b/docs/excel.png
diff --git a/docs/family-page.png b/docs/family-page.png
diff --git a/docs/img/add_virus_1.png b/docs/img/add_virus_1.png
diff --git a/docs/img/add_virus_2.png b/docs/img/add_virus_2.png
diff --git a/docs/img/failure_1.png b/docs/img/failure_1.png
diff --git a/docs/img/failure_2.png b/docs/img/failure_2.png
diff --git a/docs/img/failure_3.png b/docs/img/failure_3.png
diff --git a/docs/img/gh-actions.png b/docs/img/gh-actions.png
diff --git a/docs/img/gh-branch_create.png b/docs/img/gh-branch_create.png
diff --git a/docs/img/gh-branch_created.png b/docs/img/gh-branch_created.png
diff --git a/docs/img/gh-branch_new.png b/docs/img/gh-branch_new.png
diff --git a/docs/img/gh-codespaces_1.png b/docs/img/gh-codespaces_1.png
diff --git a/docs/img/gh-codespaces_2.png b/docs/img/gh-codespaces_2.png
diff --git a/docs/img/gh-codespaces_3.png b/docs/img/gh-codespaces_3.png
diff --git a/docs/img/gh-codespaces_created.png b/docs/img/gh-codespaces_created.png
diff --git a/docs/img/gh-codespaces_created_1.png b/docs/img/gh-codespaces_created_1.png
diff --git a/docs/img/gh-cs_commit_1.png b/docs/img/gh-cs_commit_1.png
diff --git a/docs/img/gh-cs_commit_2.png b/docs/img/gh-cs_commit_2.png
diff --git a/docs/img/gh-cs_commit_3.png b/docs/img/gh-cs_commit_3.png
diff --git a/docs/img/gh-cs_commit_4.png b/docs/img/gh-cs_commit_4.png
diff --git a/docs/img/gh-cs_commit_5.png b/docs/img/gh-cs_commit_5.png
diff --git a/docs/img/gh-cs_commit_6.png b/docs/img/gh-cs_commit_6.png
diff --git a/docs/img/gh-cs_commit_7.png b/docs/img/gh-cs_commit_7.png
diff --git a/docs/img/gh-cs_extension_0.png b/docs/img/gh-cs_extension_0.png
diff --git a/docs/img/gh-cs_extension_1.png b/docs/img/gh-cs_extension_1.png
diff --git a/docs/img/gh-cs_extension_2.png b/docs/img/gh-cs_extension_2.png
diff --git a/docs/img/gh-cs_pr.png b/docs/img/gh-cs_pr.png
diff --git a/docs/img/gh-main.png b/docs/img/gh-main.png
diff --git a/docs/img/gh-main_branches.png b/docs/img/gh-main_branches.png
diff --git a/docs/img/gh-pr.png b/docs/img/gh-pr.png
diff --git a/docs/img/gh-pr_conflict.png b/docs/img/gh-pr_conflict.png
diff --git a/docs/img/gh-pr_created.png b/docs/img/gh-pr_created.png
diff --git a/docs/img/gh-pr_cs-again.png b/docs/img/gh-pr_cs-again.png
diff --git a/docs/img/gh-pr_merge_1.png b/docs/img/gh-pr_merge_1.png
diff --git a/docs/img/gh-pr_new.png b/docs/img/gh-pr_new.png
diff --git a/docs/img/gh-pr_new_branches.png b/docs/img/gh-pr_new_branches.png
diff --git a/docs/img/offline_1.png b/docs/img/offline_1.png
diff --git a/docs/img/offline_2.png b/docs/img/offline_2.png
diff --git a/docs/img/offline_3.png b/docs/img/offline_3.png
diff --git a/docs/img/offline_4.png b/docs/img/offline_4.png
diff --git a/docs/img/offline_5.png b/docs/img/offline_5.png
diff --git a/docs/img/offline_6.png b/docs/img/offline_6.png
diff --git a/docs/img/offline_7.png b/docs/img/offline_7.png
diff --git a/docs/img/xlsx_1.png b/docs/img/xlsx_1.png
diff --git a/docs/img/xlsx_2.png b/docs/img/xlsx_2.png
diff --git a/docs/img/xlsx_3.png b/docs/img/xlsx_3.png
diff --git a/docs/img/xlsx_4.png b/docs/img/xlsx_4.png
diff --git a/docs/index.qmd b/docs/index.qmd
@@ -0,0 +1,21 @@
+---
+title: VirusBank documentation
+format:
+  html:
+    toc: true
+    sidebar: true
+    page-layout: article
+---
+
+Table of contents:
+
+1. [Introduction](/docs/introduction.qmd)
+2. [Information on how it ties together](/docs/internals.qmd)
+3. [What one needs to know concerning the UI/UX](docs/ui-ux.qmd)
+3. [Some information on specific components and styling](/docs/ui-ux.qmd)
+4. [Some common scenarios in detail](/docs/scenarios.qmd)
+5. [General information on how to use Github for the scenarios](docs/use-github.qmd)
+
+
+A rendered version of the repository [`README` file](/docs/readme.qmd).
+