Add additional web output and figure handling

.github/workflows/run-model-and-publish.yml

@@ -1,58 +0,0 @@
-# This is a basic workflow to help you get started with Actions
-
-name: RUN_MODEL_AND_PUBLISH
-
-# Controls when the action will run. Triggers the workflow on push or pull request
-# events but only for the master branch
-
-# This workflow can be started manually by using the GitHub API
-# send a POST request to https://api.github.com/repos/ImperialCollegeLondon/covid19model/dispatches
-# with a an Authorization token <GitHub_Token> header and JSON payload:
-# {"event_type": "run-and-publish"}
-on:
-  repository_dispatch:
-    types: run-and-publish
-
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
-jobs:
-  # This workflow contains a single job called "build"
-  run-and-publish:
-    # Set secret to enable the workflow
-    # The type of runner that the job will run on
-    runs-on: ubuntu-18.04
-
-    # Steps represent a sequence of tasks that will be executed as part of the job
-    steps:
-    # should throw an error if the token is not set, to enable the action only for repos which have set this token
-    - name: Check if access token is set
-      env:
-        SECRET_TEST: ${{ secrets.GH_PAGES_ACCESS_TOKEN }}
-      run: "[ -z \"$SECRET_TEST\" ] && exit 1 || exit 0 "
-    # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-    - uses: actions/checkout@v2
-
-    # Docker build
-    - name: Build docker image
-      run: |
-        docker build -f docker/Dockerfile -t covid19model:latest .
-
-    - name: Download the newest data from the ECDC
-      run: |
-        docker run --rm -v $(pwd):/var/model --user $(id -u):$(id -g) covid19model:latest Rscript data/fetch-ecdc.R
-
-    - name: Perform the full model run, aprox. 90 minutes
-      run: |
-        docker run --rm -v $(pwd):/var/model --user $(id -u):$(id -g) --env FULL=TRUE covid19model:latest
-
-    - name: Fix SVG font families for publishing
-      run: |
-        docker run --rm -v $(pwd):/var/model --user $(id -u):$(id -g) covid19model:latest Rscript web-fix-fonts.R
-
-    - name: Deploy
-      uses: peaceiris/actions-gh-pages@v3
-      with:
-        personal_token: ${{ secrets.GH_PAGES_ACCESS_TOKEN }}
-        external_repository: ImperialCollegeLondon/covid19estimates
-        publish_branch: master
-        publish_dir: ./web
-        keep_files: true

base.r

@@ -5,6 +5,7 @@ library(gdata)
 library(dplyr)
 library(tidyr)
 library(EnvStats)
+library(optparse)
 
 countries <- c(
   "Denmark",
@@ -23,17 +24,43 @@ countries <- c(
   "Netherlands"
 )
 
+# Commandline options and parsing
+parser <- OptionParser()
+parser <- add_option(parser, c("-D", "--debug"), action="store_true",
+                     help="Perform a debug run of the model")
+parser <- add_option(parser, c("-F", "--full"), action="store_true",
+                     help="Perform a full run of the model")
+cmdoptions <- parse_args(parser, args = commandArgs(trailingOnly = TRUE), positional_arguments = TRUE)
+
 # Default run parameters for the model
-DEBUG = FALSE
-FULL = FALSE
+if(is.null(cmdoptions$options$debug)) {
+  DEBUG = Sys.getenv("DEBUG") == "TRUE"
+} else {
+  DEBUG = cmdoptions$options$debug
+}
 
-args = commandArgs(trailingOnly=TRUE)
-if(length(args) == 0) {
-  args = 'base'
-} 
-StanModel = args[1]
+if(is.null(cmdoptions$options$full)) {
+  FULL = Sys.getenv("FULL") == "TRUE"
+} else {
+  FULL = cmdoptions$options$full
+}
 
+if(DEBUG && FULL) {
+  stop("Setting both debug and full run modes at once is invalid")
+}
+
+if(length(cmdoptions$args) == 0) {
+  StanModel = 'base'
+} else {
+  StanModel = cmdoptions$args[1]
+}
+ 
 print(sprintf("Running %s",StanModel))
+if(DEBUG) {
+  print("Running in DEBUG mode")
+} else if (FULL) {
+  print("Running in FULL mode")
+}
 
 ## Reading all data
 d=readRDS('data/COVID-19-up-to-date.rds')
@@ -65,7 +92,6 @@ covariates$self_isolating_if_ill[covariates$self_isolating_if_ill > covariates$l
 
 forecast = 0
 
-DEBUG = FALSE
 N2 = 90 # increase if you need more forecast
 
 dates = list()
@@ -202,10 +228,8 @@ m = stan_model(paste0('stan-models/',StanModel,'.stan'))
 if(DEBUG) {
   fit = sampling(m,data=stan_data,iter=40,warmup=20,chains=2)
 } else if (FULL) {
-  fit = sampling(m,data=stan_data,iter=4000,warmup=2000,chains=8,thin=4,control = list(adapt_delta = 0.90, max_treedepth = 10))
+  fit = sampling(m,data=stan_data,iter=4000,warmup=2000,chains=4,thin=4,control = list(adapt_delta = 0.95, max_treedepth = 10))
 } else { 
-  # uncomment the line below for a full run to replicate results and comment the second line below 
-  # fit = sampling(m,data=stan_data,iter=4000,warmup=2000,chains=4,thin=4,control = list(adapt_delta = 0.95, max_treedepth = 10))
   fit = sampling(m,data=stan_data,iter=200,warmup=100,chains=4,thin=4,control = list(adapt_delta = 0.95, max_treedepth = 10))
 }  
 
@@ -242,3 +266,5 @@ verify_result <- system(paste0("Rscript web-verify-output.r ", filename,'.Rdata'
 if(verify_result != 0){
   stop("Verification of web output failed!")
 }
+system("Rscript web-fix-fonts.r")
+

docker/Dockerfile

@@ -7,7 +7,7 @@ RUN apt-get update && apt-get install -y \
 	fonts-adf-verana
 
 RUN install2.r --error --deps TRUE \
-	gdata EnvStats ggpubr svglite jsonlite \
+	gdata EnvStats ggpubr svglite jsonlite optparse \
 	&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds
 
 WORKDIR /var/model

environment.yml

@@ -9,5 +9,6 @@ dependencies:
   - r-tidyr
   - r-dplyr
   - r-rstan
+  - r-optparse
 channels:
   - conda-forge

make-table.r

@@ -118,6 +118,10 @@ total_infected[order(total_infected$countries),c("countries","value")]
 total_infected <- total_infected[,c("countries","value")]
 write.csv(total_infected,paste0("results/total_infected_",date_till_percentage,".csv"),row.names=F)
 
+# Store copy for web output
+dir.create("web/data/", showWarnings = FALSE, recursive = TRUE)
+write.csv(total_infected,paste0("web/data/total_infected.csv"),row.names=F)
+
 fraction_obs_infected <- do.call(rbind, fraction_obs_infected)
 fraction_obs_infected_df <- as.data.frame(fraction_obs_infected)
 names(fraction_obs_infected_df) <- dates_italy

web-fix-fonts.R

@@ -4,6 +4,7 @@ for( f in filenames ){
   
   x <- readLines(f)
   y <- gsub( "Aerial", "Arial, Helvetica, sans-serif", x )
+  y <- gsub( "Arimo", "Arial, Helvetica, sans-serif", x )
   cat(y, file=f, sep="\n")
   
 }