Merge pull request #79 from bczernecki/dev

fixes for CRAN policy

.Rbuildignore

@@ -12,3 +12,7 @@
 ^\.github$
 ^\.Rhistory$
 ^\.lintr$
+vignettes/articles/usecase.Rmd
+^pkgdown$
+^.codecov.yml$
+

.codecov.yml

@@ -0,0 +1,8 @@
+coverage:
+  status:
+    patch:
+      default:
+        target: 60%
+    project:
+      default:
+        target: 60%

.github/workflows/R-CMD-check.yaml

@@ -32,8 +32,9 @@ jobs:
         config:
           - {os: macOS-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-18.04,   r: 'release'}
-          - {os: ubuntu-18.04,   r: '3.6'}
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-20.04,   r: 'release'}
+          - {os: ubuntu-20.04,   r: '3.6'}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
@@ -74,14 +75,15 @@ jobs:
           while read -r cmd
           do
             eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "18.04"))')
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
 
       - name: Install dependencies
         run: |
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("rcmdcheck")
           remotes::install_cran("covr")
           remotes::install_cran("xml2")
+          remotes::install_cran("DT")
         shell: Rscript {0}
 
       - name: Session info
@@ -94,7 +96,7 @@ jobs:
       - name: Check
         env:
           _R_CHECK_CRAN_INCOMING_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--run-donttest"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
 
       - name: Show testthat output
@@ -103,12 +105,31 @@ jobs:
         shell: bash
 
       - name: Upload check results
-        if: failure()
+        if: always()
         uses: actions/upload-artifact@main
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check
 
-      - name: Test coverage
-        run: covr::codecov()
-        shell: Rscript {0}
+      - name: Codecov
+        run: |
+          covr::codecov()
+        shell: Rscript {0}
+
+      - name: Test coverage report
+        if: always()
+        run: |
+          covr_report <- covr::package_coverage(wrap = TRUE)
+          covr::report(x = covr_report, file = 'covr_report.html')
+          print(getwd())
+          print(dir())
+        shell: Rscript {0}
+
+      - name: Upload test coverage report
+        if: always()
+        uses: actions/upload-artifact@v3
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: |
+            covr_report.html
+            lib

.github/workflows/html5-check.yaml

@@ -0,0 +1,48 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master, dev, devel]
+  pull_request:
+    branches: [main, master, dev, devel]
+
+name: HTML5 check
+
+jobs:
+  HTML5-check:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'devel'
+          http-user-agent: 'release'
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          dependencies: 'character()'
+
+      - name: Install pdflatex
+        run: sudo apt-get install texlive-latex-base texlive-fonts-recommended texlive-fonts-extra texlive-latex-extra
+
+      - name: Install tidy and pandoc
+        run: sudo apt install tidy pandoc
+
+      - name: Install dependencies
+        run: R -e 'install.packages(c("knitr", "rmarkdown", "XML", "httr", "data.table", "maps", "dplyr", "tidyr", "xml2", "testthat"))'
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          args: 'c("--as-cran")'
+          build_args: 'character()'
+          error-on: '"note"'
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+          _R_CHECK_CRAN_INCOMING_: false
+          LANG: "en_US.UTF.8"

.github/workflows/pkgdown.yaml

@@ -0,0 +1,39 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+name: pkgdown
+on:
+  push:
+    branches: [main, master, dev, devel]
+  pull_request:
+    branches: [main, master, dev, devel]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    container: bczernecki/meteo:latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - name: Checkout Project
+        uses: actions/checkout@v1
+
+      - name: Checked for installed packages
+        run: |
+          sudo apt-get install -y libfontconfig1-dev libharfbuzz-dev libfribidi-dev rsync
+          R -e 'install.packages(c("pkgdown", "openair", "rnaturalearthdata"))'
+          R -e 'installed.packages()[, 1:3]'
+          
+      - name: Build book
+        run: |
+          Rscript -e 'pkgdown::build_site()'
+
+      - name: Deploy to GitHub pages 🚀
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -10,3 +10,5 @@ climate.Rproj
 .DS_Store
 covr_report.html
 lib
+docs
+pkgdown

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: climate
 Title: Interface to Download Meteorological (and Hydrological) Datasets
-Version: 1.0.5
+Version: 1.1.0
 Authors@R: c(person(given = "Bartosz",
            family = "Czernecki",
            role = c("aut", "cre"),
@@ -27,9 +27,9 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.1
 Depends: 
-    R (>= 3.1)
+    R (>= 3.5.0)
 Imports: 
     XML,
     httr,

NAMESPACE

@@ -13,7 +13,7 @@ export(meteo_noaa_co2)
 export(meteo_noaa_hourly)
 export(meteo_ogimet)
 export(nearest_stations_imgw)
-export(nearest_stations_nooa)
+export(nearest_stations_noaa)
 export(nearest_stations_ogimet)
 export(ogimet_daily)
 export(ogimet_hourly)

NEWS.md

@@ -1,3 +1,12 @@
+# climate 1.1.0
+
+* A new approach for handling CRAN policy for resolving problems if network issues are detected or some of the external services are temporarily down. 
+* Adding `allow_failure` argument used by default that turns off automatic debugging but avoid warnings and errors for most typical use cases
+* re-factoring of unit tests
+* documentation build with CI/CD
+* updating vignettes and examples, including the way to use climate with Python
+
+
 # climate 1.0.5
 
 * `meteo_imgw` family of functions supports multiple names as argument - bug fix

R/clean_metadata_hydro.R

@@ -11,8 +11,8 @@ clean_metadata_hydro = function(address, interval) {
   test_url(link = address, output = temp)
   a = readLines(temp, warn = FALSE)
 
-  a = iconv(a, from = "cp1250", to = "ASCII//TRANSLIT") # usuwamy polskie znaki, bo to robi spore "kuku"
-  a = gsub(a, pattern = "\\?", replacement = "") # usuwamy znaki zapytania powstale po konwersji
+  a = iconv(a, from = "cp1250", to = "ASCII//TRANSLIT") # remove polish characters
+  a = gsub(a, pattern = "\\?", replacement = "") # removing extra characters after conversion
 
   # additional workarounds for mac os but not only...
   a = gsub(x = a, pattern = "'", replacement = "")
@@ -40,8 +40,8 @@ clean_metadata_hydro = function(address, interval) {
       b = cbind(b, tmp)
     }
     b = list("H" = data.frame(parameters = b[, 1]),
-              "Q" = data.frame(parameters = b[, 2]),
-              "T" = data.frame(parameters = b[, 3]))
+             "Q" = data.frame(parameters = b[, 2]),
+             "T" = data.frame(parameters = b[, 3]))
   }
-  b
+  return(b)
 }

R/clean_metadata_meteo.R

@@ -8,22 +8,15 @@
 #' @importFrom stats na.omit
 #' @keywords internal
 #'
-#' @examples
-#' \donttest{
-#'   my_add = paste0("https://danepubliczne.imgw.pl/data/dane_pomiarowo_obserwacyjne/",
-#'                   "dane_meteorologiczne/dobowe/synop/s_d_format.txt")
-#'   climate:::clean_metadata_meteo(address = my_add, rank = "synop", interval = "hourly")
-#' }
-#'
 
 clean_metadata_meteo = function(address, rank = "synop", interval = "hourly") {
 
   temp = tempfile()
   test_url(link = address, output = temp)
   a = readLines(temp, warn = FALSE)
 
-  a = iconv(a, from = "cp1250", to = "ASCII//TRANSLIT") # usuwamy polskie znaki, bo to robi spore "kuku"
-  a = gsub(a, pattern = "\\?", replacement = "") # usuwamy znaki zapytania powstale po konwersji
+  a = iconv(a, from = "cp1250", to = "ASCII//TRANSLIT")
+  a = gsub(a, pattern = "\\?", replacement = "")
 
   # additional workarounds for mac os but not only...
   a = gsub(x = a, pattern = "'", replacement = "")

R/get_coord_from_string.R

@@ -27,7 +27,7 @@ get_coord_from_string = function(txt, pattern = "Longitude") {
   wsp = suppressWarnings(as.numeric(tmp)[1] + (as.numeric(tmp)[2] * 5 / 3) / 100)
 
   if (hemisphere %in% c("W", "S")) {
-    wsp = wsp * -1
+    wsp = wsp*-1
   }
 return(wsp)
 }

R/hydro_imgw_annual.R

@@ -12,24 +12,55 @@
 #' "short" - default, values with shorten names,
 #' "full" - full English description,
 #' "polish" - original names in the dataset
+#' @param allow_failure logical - whether to proceed or stop on failure. By default set to TRUE (i.e. don't stop on error). For debugging purposes change to FALSE
 #' @param ... other parameters that may be passed to the 'shortening' function that shortens column names
 #' @importFrom XML readHTMLTable
 #' @importFrom utils download.file unzip read.csv
 #' @importFrom data.table fread
 #' @export
 #' @examples
 #' \donttest{
-#'   yearly = hydro_imgw_annual(year = 2000, value = "H", station = "ANNOPOL")
-#'   head(yearly)
+#' hydro_yearly = hydro_imgw_annual(year = 2000, value = "H", station = "ANNOPOL")
 #' }
 hydro_imgw_annual = function(year,
                              coords = FALSE,
                              value = "H",
                              station = NULL,
-                             col_names = "short", ...) {
- # options(RCurlOptions = list(ssl.verifypeer = FALSE)) # required on windows for RCurl
-  translit = check_locale()
+                             col_names = "short", 
+                             allow_failure = TRUE,
+                             ...) {
+
+  if (allow_failure) {
+    tryCatch(hydro_imgw_annual_bp(year,
+                                  coords,
+                                  value,
+                                  station,
+                                  col_names, 
+                                  ...),
+             error = function(e){
+               message(paste("Problems with downloading data.",
+                             "Run function with argument allow_failure = FALSE",
+                             "to see more details"))})
+  } else {
+    hydro_imgw_annual_bp(year,
+                         coords,
+                         value,
+                         station,
+                         col_names, 
+                         ...)
+  }
+}
 
+#' @keywords internal
+#' @noRd
+hydro_imgw_annual_bp = function(year = year,
+                                coords = coords,
+                                value = value,
+                                station = station,
+                                col_names = col_names,
+                                ...) {
+
+  translit = check_locale()
   base_url = "https://danepubliczne.imgw.pl/data/dane_pomiarowo_obserwacyjne/dane_hydrologiczne/"
   interval = "semiannual_and_annual"
   interval_pl = "polroczne_i_roczne"