Develop (#250)

* fix rsconnect deployment and renv.lock

.Rbuildignore

@@ -7,5 +7,4 @@
 ^app\.R$
 ^man-roxygen$
 ^\.github$
-^deploy$
 ^rsconnect$

.Rprofile

@@ -1 +1,3 @@
+# renv::settings$ignored.packages(c("devtools", "Covid19Mirai"), persist = FALSE)
 source("renv/activate.R")
+

.github/workflows/ci-cd.yml

@@ -1,13 +1,15 @@
+name: CI-CD
+# renv with GitHub actions: https://rstudio.github.io/renv/articles/ci.html#github-actions
+
 # Triggered on push and pull request events, schedule for data update
 on:
   push:
   pull_request:
   schedule:
   # every day at 21 UTC
   - cron: "0 21 * * *"
-name: CI-CD
 
-# renv with GitHub actions: https://rstudio.github.io/renv/articles/ci.html#github-actions
+
 
 jobs:
   CI-CD:
@@ -29,6 +31,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
+
       - name: Checkout repo
         uses: actions/checkout@v3
 
@@ -39,16 +42,16 @@ jobs:
           # Enable RStudio Package Manager to speed up package installation
           use-public-rspm: true
 
-      - name: Activate renv and restore packages with cache
-        uses: r-lib/actions/setup-renv@v2
-
       # - name: Install system dependencies
-      #   env:
-      #     RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+      #   # This is not taken care of (yet) by r-lib/actions/setup-renv
+      #   # Package distro used to get the distro for the used ubuntu-latest
       #   run: |
-      #     Rscript -e "renv::install('r-hub/sysreqs')"
-      #     sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
-      #     sudo -s eval "$sysreqs"
+      #     Rscript -e "install.packages(c('remotes', 'distro'))"
+      #     while read -r cmd
+      #     do
+      #       eval sudo $cmd
+      #     done < <(Rscript -e 'writeLines(with(distro::distro(), remotes::system_requirements(id, short_version)))')
+
       - name: Activate renv and restore packages with cache
         uses: r-lib/actions/setup-renv@v2
 
@@ -77,7 +80,7 @@ jobs:
           git push origin
       - name: Deploy to shinyapps.io
         # Continuous deployment only for pushes to the main / master branch
-        if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master'
+        # if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master'
         env:
           SHINYAPPS_ACCOUNT: ${{ secrets.SHINYAPPS_ACCOUNT }}
           SHINYAPPS_TOKEN: ${{ secrets.SHINYAPPS_TOKEN }}

DESCRIPTION

@@ -31,20 +31,22 @@ Imports:
     grid,
     leaflet,
     leaflet.extras,
-    rgdal,
     shinycssloaders,
     lubridate,
     sp,
     markdown,
     scales,
     COVID19,
     grDevices,
+    pkgload,
     rlang,
     zoo
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Suggests: 
-    testthat,
-    pkgload,
-    rsconnect
+    rsconnect,
+    spelling,
+    testthat (>= 3.0.0),
+    sf,
+    packrat

NAMESPACE

@@ -49,7 +49,6 @@ export(get_timeseries_global_data)
 export(get_timeseries_province_data)
 export(get_timeseries_single_data)
 export(lab_percent)
-export(load_countries_data_map)
 export(lw_vars_calc)
 export(merge_pop_data)
 export(new_total_colors)

R/run_app.R

@@ -5,14 +5,15 @@
 #' @export
 #' @importFrom shiny shinyApp
 #' @importFrom golem with_golem_options
+#'
 run_app <- function(
   ...
 ) {
   with_golem_options(
     app = shinyApp(
-      ui = app_ui, 
+      ui = app_ui,
       server = app_server
-    ), 
+    ),
     golem_opts = list(...)
   )
 }

R/utils.R

@@ -307,146 +307,7 @@ new_total_colors <- c(
   "new" = "#ea8b5b"
 )
 
-#' load countries  data
-#' @param destpath path to file
-#'
-#' @returns countries shapefile
-#' @export
-load_countries_data_map <- function(destpath = system.file("./countries_data", package = "Covid19Mirai")){
-  # Resource https://www.naturalearthdata.com/downloads/50m-cultural-vectors/50m-admin-0-countries-2/
-  url <- "https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/50m/cultural/ne_50m_admin_0_countries.zip"
-  zip_path <- file.path(destpath,"ne_50m_admin_0_countries.zip")
-  dsn_path <- file.path(destpath, "ne_50m_admin_0_countries")
-
-  if (!file.exists(zip_path)) {
-    download.file(url = url, destfile = zip_path)
-    unzip(zip_path, exdir = dsn_path)
-  }
-
-  countries <- rgdal::readOGR(dsn = dsn_path,
-                              layer = "ne_50m_admin_0_countries",
-                              encoding = "utf-8", use_iconv = T,
-                              verbose = FALSE)
-  assign_new_level =  function(countrymap , lev, from, to, regexpress = FALSE) {
-    if (regexpress) {
-      if (!any(grepl(from, as.character(countrymap[[lev]]))))
-        stop("wrong expression, not present in map: ", from)
-      from = grep(from, as.character(countrymap[[lev]]), value = TRUE)
-    }
-    if (!any(countrymap[[lev]] == from))
-      stop("wrong name, not present in map: ", from)
-    levels(countrymap[[lev]])[levels(countrymap[[lev]])==from] <- to
-    countrymap[[lev]][countrymap[[lev]] == from] = to
-    countrymap
-  }
-  #rename continents
-  countries = assign_new_level(countries, "CONTINENT", "North America", "Northern America")
-  countries = assign_new_level(countries, "CONTINENT", "South America", "LatAm & Carib.")
-  #rename NAME, i.e. countries
-  #countries = assign_new_level(countries, "NAME", "Macao", "Macau")
-  #countries = assign_new_level(countries, "NAME", "Macao", "Macau")
-  countries = assign_new_level(countries, "NAME", "Macedonia", "North Macedonia")
-  countries = assign_new_level(countries, "NAME", "Czechia", "Czech Republic")
-  countries = assign_new_level(countries, "NAME", "Dominican Rep.", "Dominican Republic")
-  countries = assign_new_level(countries, "NAME", "United Kingdom", "UK")
-  countries = assign_new_level(countries, "NAME", "United States of America", "USA")
-  countries = assign_new_level(countries, "NAME", "United Arab Emirates", "UAE")
-  countries = assign_new_level(countries, "NAME", "^St-Barth", "St. Barth", regexpress = TRUE)
-  countries = assign_new_level(countries, "NAME", "Faeroe Is.", "Faeroe Islands")
-  countries = assign_new_level(countries, "NAME", "Bosnia and Herz.", "Bosnia and Herzegovina")
-  countries = assign_new_level(countries, "NAME", "Vatican", "Vatican City")
-  countries = assign_new_level(countries, "NAME", "St. Vin. and Gren.", "St. Vincent Grenadines")
-  countries = assign_new_level(countries, "NAME", "Dem. Rep. Congo", "Republic of the Congo")
-  #countries = assign_new_level(countries, "NAME", "Central African Rep.", "CAR")
-  countries = assign_new_level(countries, "NAME", "Ivoire", "Cote d'Ivoire", regexpress = TRUE)
-  countries = assign_new_level(countries, "NAME", "St-Martin", "St Martin")
-  countries = assign_new_level(countries, "NAME", "Cayman Is.", "Cayman Islands")
-  countries = assign_new_level(countries, "NAME", "Eq. Guinea", "Equatorial Guinea")
-  countries = assign_new_level(countries, "NAME", "Central African Rep.", "CAR")
-  countries = assign_new_level(countries, "NAME", "eSwatini", "Eswatini")
-  countries = assign_new_level(countries, "NAME", "Cabo Verde", "Cape Verde")
-  countries = assign_new_level(countries, "NAME", "S. Sudan", "South Sudan")
-  countries = assign_new_level(countries, "NAME", "Fr. Polynesia", "French Polynesia")
-  countries = assign_new_level(countries, "NAME", "Antigua and Barb.", "Antigua and Barbuda")
-  countries = assign_new_level(countries, "NAME", "Cook Is.", "Cook Islands")
-  countries = assign_new_level(countries, "NAME", "Falkland Is.", "Falkland Islands")
-  countries = assign_new_level(countries, "NAME", "U.S. Virgin Is.", "U.S. Virgin Islands")
-
-  countries
-}
 
-#' load countries data to match with get_datahub
-#' @param destpath path to file
-#'
-#' @returns countries shapefile
-#' @noRd
-load_countries_datahub_map <- function(destpath = system.file("./countries_data", package = "Covid19Mirai")){
-  # Resource https://www.naturalearthdata.com/downloads/50m-cultural-vectors/50m-admin-0-countries-2/
-  url <- "https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/50m/cultural/ne_50m_admin_0_countries.zip"
-  zip_path <- file.path(destpath,"ne_50m_admin_0_countries.zip")
-  dsn_path <- file.path(destpath, "ne_50m_admin_0_countries")
-
-  if (!file.exists(zip_path)) {
-    download.file(url = url, destfile = zip_path)
-    unzip(zip_path, exdir = dsn_path)
-  }
-
-  countries <- rgdal::readOGR(dsn = dsn_path,
-                              layer = "ne_50m_admin_0_countries",
-                              encoding = "utf-8", use_iconv = T,
-                              verbose = FALSE)
-  assign_new_level =  function(countrymap , lev, from, to, regexpress = FALSE) {
-    if (regexpress) {
-      if (!any(grepl(from, as.character(countrymap[[lev]]))))
-        stop("wrong expression, not present in map: ", from)
-      from = grep(from, as.character(countrymap[[lev]]), value = TRUE)
-    }
-    if (!any(countrymap[[lev]] == from))
-      stop("wrong name, not present in map: ", from)
-    levels(countrymap[[lev]])[levels(countrymap[[lev]])==from] <- to
-    countrymap[[lev]][countrymap[[lev]] == from] = to
-    countrymap
-  }
-  #rename continents
-  countries = assign_new_level(countries, "CONTINENT", "North America", "Northern America")
-  countries = assign_new_level(countries, "CONTINENT", "South America", "LatAm & Carib.")
-  #rename NAME, i.e. countries
-  #countries = assign_new_level(countries, "NAME", "Macao", "Macau")
-  #countries = assign_new_level(countries, "NAME", "Macao", "Macau")
-  countries = assign_new_level(countries, "NAME", "Macedonia", "North Macedonia")
-  countries = assign_new_level(countries, "NAME", "Czechia", "Czech Republic")
-  countries = assign_new_level(countries, "NAME", "Dominican Rep.", "Dominican Republic")
-  countries = assign_new_level(countries, "NAME", "United Kingdom", "UK")
-  countries = assign_new_level(countries, "NAME", "United States of America", "USA")
-  #countries = assign_new_level(countries, "NAME", "United Arab Emirates", "UAE") # now has new name
-  countries = assign_new_level(countries, "NAME", "^St-Barth", "St. Barth", regexpress = TRUE) # not needed but ok
-  countries = assign_new_level(countries, "NAME", "Faeroe Is.", "Faeroe Islands")
-  countries = assign_new_level(countries, "NAME", "Bosnia and Herz.", "Bosnia and Herzegovina")
-  countries = assign_new_level(countries, "NAME", "Vatican", "Vatican City")
-  countries = assign_new_level(countries, "NAME", "St. Vin. and Gren.", "St. Vincent Grenadines")
-  countries = assign_new_level(countries, "NAME", "Dem. Rep. Congo", "Republic of the Congo")
-  #countries = assign_new_level(countries, "NAME", "Central African Rep.", "CAR")
-  countries = assign_new_level(countries, "NAME", "Ivoire", "Cote d'Ivoire", regexpress = TRUE)
-  countries = assign_new_level(countries, "NAME", "St-Martin", "St Martin")
-  countries = assign_new_level(countries, "NAME", "Cayman Is.", "Cayman Islands")
-  countries = assign_new_level(countries, "NAME", "Eq. Guinea", "Equatorial Guinea")
-  countries = assign_new_level(countries, "NAME", "Central African Rep.", "Central African Republic")
-  countries = assign_new_level(countries, "NAME", "eSwatini", "Swaziland")
-  countries = assign_new_level(countries, "NAME", "Cabo Verde", "Cape Verde")
-  countries = assign_new_level(countries, "NAME", "S. Sudan", "South Sudan")
-  countries = assign_new_level(countries, "NAME", "Fr. Polynesia", "French Polynesia")
-  countries = assign_new_level(countries, "NAME", "Antigua and Barb.", "Antigua and Barbuda")
-  countries = assign_new_level(countries, "NAME", "Cook Is.", "Cook Islands")
-  countries = assign_new_level(countries, "NAME", "Falkland Is.", "Falkland Islands")
-  countries = assign_new_level(countries, "NAME", "U.S. Virgin Is.", "U.S. Virgin Islands") # new name
-  countries = assign_new_level(countries, "NAME", "St. Kitts and Nevis", "Saint Kitts and Nevis" ) # new name
-  countries = assign_new_level(countries, "NAME", "Principe", "Sao Tome and Principe", regexpress = TRUE )
-  countries = assign_new_level(countries, "NAME", "N. Mariana Is.", "Northern Mariana Islands")
-  countries = assign_new_level(countries, "NAME", "Marshall Is.", "Marshall Iselands")
-  countries = assign_new_level(countries, "NAME", "St. Pierre and Miquelon", "St. Pierre and Miquelon")
-
-  countries
-}
 
 #' Sort type by max
 #'

deploy/deploy-shinyapps.R

@@ -5,10 +5,15 @@ rsconnect::setAccountInfo(
   Sys.getenv("SHINYAPPS_TOKEN"),
   Sys.getenv("SHINYAPPS_SECRET")
 )
+
+# to be added since rsconnect >1
+options(rsconnect.packrat = FALSE)
+
 rsconnect::deployApp(
   account = "miraisolutions",
   appName = "Covid19",
-  forceUpdate = TRUE
+  forceUpdate = TRUE, # to be added since rsconnect >1
+  quarto = FALSE # to be added since rsconnect >1
   # exclude hidden files and renv directory (if present)
   # appFiles = setdiff(list.files(), "renv")
 )