Merge branch 'master' of https://github.com/matsim-vsp/covid-sim

matsim-vsp · Jun 16, 2023 · d4e32e8 · d4e32e8
2 parents 95b8bc6 + ded0974
commit d4e32e8
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diff --git a/.github/workflows/autobuild.yml b/.github/workflows/autobuild.yml
@@ -7,8 +7,8 @@ on:
   # Triggers the workflow on push or pull request events but only for the gh-pages branch
   push:
     branches: [master]
-#  pull_request:
-#    branches: [master]
+  #  pull_request:
+  #    branches: [master]
   schedule:
     # * is a special character in YAML so you have to quote this string
     # run every night:
@@ -27,12 +27,12 @@ jobs:
   # This workflow contains a single job called "build"
   build:
     # The type of runner that the job will run on
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       # Runs a set of commands using the runners shell
       - name: CI Autobuild

diff --git a/docs/.gitignore b/docs/.gitignore
@@ -0,0 +1,12 @@
+pids
+logs
+node_modules
+npm-debug.log
+coverage/
+run
+dist
+.DS_Store
+.nyc_output
+.basement
+config.local.js
+basement_dist
diff --git a/docs/package.json b/docs/package.json
@@ -0,0 +1,19 @@
+{
+  "name": "covid-sim",
+  "version": "0.0.1",
+  "description": "",
+  "main": "index.js",
+  "authors": {
+    "name": "",
+    "email": ""
+  },
+  "repository": "/covid-sim",
+  "scripts": {
+    "dev": "vuepress dev src",
+    "build": "vuepress build src && cp -r ./src/.vuepress/dist/* ../public/docs"
+  },
+  "license": "MIT",
+  "devDependencies": {
+    "vuepress": "^1.5.3"
+  }
+}
diff --git a/docs/src/.vuepress/components/Foo/Bar.vue b/docs/src/.vuepress/components/Foo/Bar.vue
@@ -0,0 +1,15 @@
+<template>
+  <p class="demo">
+    {{ msg }}
+  </p>
+</template>
+
+<script>
+  export default {
+    data () {
+      return {
+        msg: 'Hello this is <Foo-Bar>'
+      }
+    }
+  }
+</script>
diff --git a/docs/src/.vuepress/components/OtherComponent.vue b/docs/src/.vuepress/components/OtherComponent.vue
@@ -0,0 +1,3 @@
+<template>
+  <p class="demo">This is another component</p>
+</template>
diff --git a/docs/src/.vuepress/components/demo-component.vue b/docs/src/.vuepress/components/demo-component.vue
@@ -0,0 +1,15 @@
+<template>
+  <p class="demo">
+    {{ msg }}
+  </p>
+</template>
+
+<script>
+  export default {
+    data() {
+      return {
+        msg: 'Hello this is <demo-component>'
+      }
+    }
+  }
+</script>
diff --git a/docs/src/.vuepress/config.js b/docs/src/.vuepress/config.js
@@ -0,0 +1,67 @@
+const { description } = require('../../package')
+
+module.exports = {
+
+  base: '/docs/',
+  /**
+   * Ref：https://v1.vuepress.vuejs.org/config/#title
+   */
+  title: 'COVID-SIM Documentation',
+  /**
+   * Ref：https://v1.vuepress.vuejs.org/config/#description
+   */
+  description: description,
+
+  /**
+   * Extra tags to be injected to the page HTML `<head>`
+   *
+   * ref：https://v1.vuepress.vuejs.org/config/#head
+   */
+  head: [
+    ['meta', { name: 'theme-color', content: '#3eaf7c' }],
+    ['meta', { name: 'apple-mobile-web-app-capable', content: 'yes' }],
+    ['meta', { name: 'apple-mobile-web-app-status-bar-style', content: 'black' }]
+  ],
+
+  /**
+   * Theme configuration, here is the default theme configuration for VuePress.
+   *
+   * ref：https://v1.vuepress.vuejs.org/theme/default-theme-config.html
+   */
+  themeConfig: {
+    repo: '',
+    editLinks: true,
+    docsDir: '',
+    editLinkText: '',
+    lastUpdated: true,
+    nav: [
+      {
+        text: 'Documentation',
+        link: '/documentation/',
+      }
+    ],
+    sidebar: {
+      '/documentation/': [
+        {
+          title: 'Documentation',
+          collapsable: true,
+          children: [
+            '',
+            'run-setup',
+            'configuration',
+            'website',
+            'plots',
+          ]
+        }
+      ],
+    }
+  },
+
+  /**
+   * Apply plugins，ref：https://v1.vuepress.vuejs.org/zh/plugin/
+   */
+  plugins: [
+    '@vuepress/plugin-back-to-top',
+    '@vuepress/plugin-medium-zoom',
+  ]
+}
diff --git a/docs/src/.vuepress/enhanceApp.js b/docs/src/.vuepress/enhanceApp.js
@@ -0,0 +1,14 @@
+/**
+ * Client app enhancement file.
+ *
+ * https://v1.vuepress.vuejs.org/guide/basic-config.html#app-level-enhancements
+ */
+
+export default ({
+  Vue, // the version of Vue being used in the VuePress app
+  options, // the options for the root Vue instance
+  router, // the router instance for the app
+  siteData // site metadata
+}) => {
+  // ...apply enhancements for the site.
+}
diff --git a/docs/src/.vuepress/styles/index.styl b/docs/src/.vuepress/styles/index.styl
@@ -0,0 +1,8 @@
+/**
+ * Custom Styles here.
+ *
+ * ref：https://v1.vuepress.vuejs.org/config/#index-styl
+ */
+
+.home .hero img
+  max-width 450px!important
diff --git a/docs/src/.vuepress/styles/palette.styl b/docs/src/.vuepress/styles/palette.styl
@@ -0,0 +1,10 @@
+/**
+ * Custom palette here.
+ *
+ * ref：https://v1.vuepress.vuejs.org/zh/config/#palette-styl
+ */
+
+$accentColor = #3eaf7c
+$textColor = #2c3e50
+$borderColor = #eaecef
+$codeBgColor = #282c34
diff --git a/docs/src/config/README.md b/docs/src/config/README.md
@@ -0,0 +1,15 @@
+---
+sidebar: auto
+---
+
+# Config
+
+## foo
+
+- Type: `string`
+- Default: `/`
+
+## bar
+
+- Type: `string`
+- Default: `/`
diff --git a/docs/src/documentation/README.md b/docs/src/documentation/README.md
@@ -0,0 +1,3 @@
+# Introduction
+
+Here you can find all the information for covid-sim.info. Among other things, how you can set up a new run, what configuration options are available, etc.
diff --git a/docs/src/documentation/configuration.md b/docs/src/documentation/configuration.md
@@ -0,0 +1,90 @@
+# Configuration
+
+Each run has a `config.yaml` file. In this file settings can be made. The following settings are possible:
+
+## YAML File
+
+| name | required | data type | description |
+|------|-----------|----------|-------------|
+| viewerVersion | false | number | There are several versions of covid-sim. The current version is 2. Possible versions are: 1 and 2. |
+| city | true | string | Covid-sim can map data from different cities. Possible are: berlin and cologne. |
+| info | true | string | Specifies the name of the file in which the run IDs are assigned to the settings. |
+| readme | true | string | For the description to be displayed above the plots, the name of the Markdown file can be specified, which is located in the same folder as the YAML file. |
+| zipFolder | true | string | For the data of the runs, the folder with the results can be specified here, which is located in the same folder as the YAML file. |
+| timestamp | true | string | Specifies the date in the format `YYYY-MM-DD` on which the run was set up. |
+| offset | false| number[] | desc... |
+| startDate | false | string | Specifies the start date in the format `YYYY-MM-DD` when the run starts. One of the two values `startDate` and `defaultStartDate` must be set. |
+| endDate | false | string | Specifies the start date in the format `YYYY-MM-DD` when the run ends. |
+| defaultStartDate | false | string | One of the two values `startDate` and `defaultStartDate` must be set. |
+| startDates | false | string[] | Are required if no `offset` has been specified. |
+| ignoredPlots | false | string[] | Plots can be hidden for specific runs. For this purpose, the short name of the plot must be specified at this point. For the respective short names see: [Plots](plots.md#plots). |
+| graphStartDate | true | string | Specifies the date in the format `YYYY-MM-DD` when the plots start. |
+| heatMapMaxValue | false | number | So that the results of different runs can be compared with the heatmap. A maximum value must be set, which can be adjusted here. |
+| rValueDate | false | string | The date for the displayed R-value can be set in the format 'YYYY-MM-DD'. The default date is: `2020-10-15`. |
+| optionGroups | true | [optionGroups](#optiongroups)[] | desc... |
+
+### optionGroups
+
+| name | required | data type | description |
+|------|-----------|----------|-------------|
+| day | false | number | desc... |
+| heading | true | string | desc... |
+| subheading | false | string | desc... |
+| measures | true | [measures](#measures)[] | desc... |
+      
+### measures
+
+| name | required | data type | description |
+|------|-----------|----------|-------------|
+| measure | true | string | desc... |
+| title | true | string | desc... |
+| order | false | string | desc... |
+| options | false | number[] | desc... |
+| asPercent | false | boolean | desc... |
+
+### Example
+This is an example YAML file which belongs to this [run](https://covid-sim.info/cologne/2022-11-16/3-variants).
+
+```yaml
+---
+readme: notes.md
+zip: summaries.zip
+info: _info.txt
+zipFolder: summaries
+timestamp: 2022-11-18
+viewerVersion: 2
+city: cologne
+runName: calibration
+defaultStartDate: 2020-02-25
+graphStartDate: 2022-08-01
+endDate: 2024-09-30
+startDates:
+- 2020-02-25
+optionGroups:
+- day: -1
+  heading: ""
+  subheading: ""
+  measures:
+  - title: Vac Camp
+    measure: vacCamp
+  - title: Strain A
+    measure: StrainA
+  - title: Strain A Date
+    measure: strainADate
+  - title: Esc
+    measure: esc
+  - title: Esc L
+    measure: escL
+  - title: Ci Corr
+    measure: ciCorr
+  - title: Days
+    measure: days
+  - title: Strain Rnd
+    measure: strainRnd
+  - title: Line B
+    measure: lineB
+  - title: Iga
+    measure: iga
+  - title: Seasonal
+    measure: seasonal
+```