close update-actions / closes #47 (#48)

* github actions updated * reformat r-cmd-check * graceful fail na ok to proceed / a ne jen downloader * non routable IP address to test for timeout * why aim for less than 100%? * no aws in test coverage * update ubuntu versions / it is not 2018 anymore * cleanup of branch detritus / work is complete...
jlacko · Nov 9, 2022 · 1a3edab · 1a3edab
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commit 1a3edab
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -21,64 +21,32 @@ jobs:
         config:
           - {os: windows-latest, r: 'release'}
           - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-18.04, r: '3.6'} # ancient, but PROJ 4.9.3 needs to be supported...
-          - {os: ubuntu-20.04, r: 'release'}
-          - {os: ubuntu-20.04, r: 'devel'}
+          - {os: ubuntu-22.04, r: 'release'}
+          - {os: ubuntu-22.04, r: 'devel'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
+          extra-packages: any::rcmdcheck
+          needs: check
 
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
 
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
-        with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
 
diff --git a/.github/workflows/coverage.yaml b/.github/workflows/coverage.yaml
@@ -9,60 +9,41 @@ name: test-coverage
 
 jobs:
   test-coverage:
-    runs-on: ${{ matrix.config.os }}
-
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-
-    strategy:
-      fail-fast: false
-      matrix:
-        config:
-          - {os: ubuntu-20.04, r: 'release'}
-
+    runs-on: ubuntu-latest
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
-          r-version: ${{ matrix.config.r }}
-
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
+          use-public-rspm: true
 
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+          extra-packages: any::covr
+          needs: coverage
 
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install dependencies
+      - name: Test coverage
         run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
         shell: Rscript {0}
 
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
 
-      - name: Test coverage
-        run: covr::codecov()
-        shell: Rscript {0}
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
diff --git a/R/downloader.R b/R/downloader.R
@@ -5,7 +5,6 @@
 
 .downloader <- function(file) {
   network <- as.logical(Sys.getenv("NETWORK_UP", unset = TRUE)) # dummy variable to allow testing of network
-  aws <- as.logical(Sys.getenv("AWS_UP", unset = TRUE)) # dummy variable to allow testing of network
 
   remote_path <- "https://rczechia.jla-data.net/" # remote archive
 
@@ -20,11 +19,6 @@
       return(NULL)
     }
 
-    if (!.ok_to_proceed(remote_file) | !aws) { # AWS bucket down
-      message("Data source broken.")
-      return(NULL)
-    }
-
     # proceed to download via curl
     message("RCzechia: downloading remote dataset.")
     curl::curl_download(url = remote_file, destfile = local_file, quiet = T)

diff --git a/R/ok_to_proceed.R b/R/ok_to_proceed.R
@@ -11,12 +11,15 @@
       warning = function(w) conditionMessage(w)
     )
   }
+
   is_response <- function(x) {
     class(x) == "response"
   }
 
+  network <- as.logical(Sys.getenv("NETWORK_UP", unset = TRUE)) # dummy variable to allow testing of network
+
   # First check internet connection
-  if (!curl::has_internet()) {
+  if (!curl::has_internet() | !network) {
     message("No internet connection.")
     return(FALSE)
   }

diff --git a/tests/testthat/test-1-casti.R b/tests/testthat/test-1-casti.R
@@ -9,10 +9,6 @@ test_that("městské části", {
   expect_message(casti(), "internet") # zpráva o chybějícím internetu
   Sys.setenv("NETWORK_UP" = TRUE)
 
-  Sys.setenv("AWS_UP" = FALSE)
-  expect_message(casti(), "source") # zpráva o spadlém AWS
-  Sys.setenv("AWS_UP" = TRUE)
-
   expect_true(is.data.frame(casti()))
 
   expect_s3_class(casti(), "sf")

diff --git a/tests/testthat/test-1-chr-uzemi.R b/tests/testthat/test-1-chr-uzemi.R
@@ -10,10 +10,6 @@ test_that("chráněná území", {
   expect_message(chr_uzemi(), "internet") # zpráva o chybějícím internetu
   Sys.setenv("NETWORK_UP" = TRUE)
 
-  Sys.setenv("AWS_UP" = FALSE)
-  expect_message(chr_uzemi(), "source") # zpráva o spadlém AWS
-  Sys.setenv("AWS_UP" = TRUE)
-
   expect_true(is.data.frame(chr_uzemi()))
 
   expect_s3_class(chr_uzemi(), "sf")

diff --git a/tests/testthat/test-1-kraje.R b/tests/testthat/test-1-kraje.R
@@ -9,10 +9,6 @@ test_that("kraje", {
   expect_message(kraje(), "internet") # zpráva o chybějícím internetu
   Sys.setenv("NETWORK_UP" = TRUE)
 
-  Sys.setenv("AWS_UP" = FALSE)
-  expect_message(kraje(), "source") # zpráva o spadlém AWS
-  Sys.setenv("AWS_UP" = TRUE)
-
   expect_true(is.data.frame(kraje()))
   expect_true(is.data.frame(kraje("low")))
   expect_true(is.data.frame(kraje("high")))

diff --git a/tests/testthat/test-1-lesy.R b/tests/testthat/test-1-lesy.R
@@ -9,10 +9,6 @@ test_that("lesy", {
   expect_message(lesy(), "internet") # zpráva o chybějícím internetu
   Sys.setenv("NETWORK_UP" = TRUE)
 
-  Sys.setenv("AWS_UP" = FALSE)
-  expect_message(lesy(), "source") # zpráva o spadlém AWS
-  Sys.setenv("AWS_UP" = TRUE)
-
   expect_true(is.data.frame(lesy()))
 
   expect_s3_class(lesy(), "sf")

diff --git a/tests/testthat/test-1-obce.R b/tests/testthat/test-1-obce.R
@@ -9,10 +9,6 @@ test_that("obce body", {
   expect_message(obce_body(), "internet") # zpráva o chybějícím internetu
   Sys.setenv("NETWORK_UP" = TRUE)
 
-  Sys.setenv("AWS_UP" = FALSE)
-  expect_message(obce_body(), "source") # zpráva o spadlém AWS
-  Sys.setenv("AWS_UP" = TRUE)
-
   expect_true(is.data.frame(obce_body()))
 
   expect_s3_class(obce_body(), "sf")
@@ -38,10 +34,6 @@ test_that("obce polygony", {
   expect_message(obce_polygony(), "internet") # zpráva o chybějícím internetu
   Sys.setenv("NETWORK_UP" = TRUE)
 
-  Sys.setenv("AWS_UP" = FALSE)
-  expect_message(obce_polygony(), "source") # zpráva o spadlém AWS
-  Sys.setenv("AWS_UP" = TRUE)
-
   expect_true(is.data.frame(obce_polygony()))
 
   expect_s3_class(obce_polygony(), "sf")

diff --git a/tests/testthat/test-1-okresy.R b/tests/testthat/test-1-okresy.R
@@ -9,10 +9,6 @@ test_that("okresy", {
   expect_message(okresy(), "internet") # zpráva o chybějícím internetu
   Sys.setenv("NETWORK_UP" = TRUE)
 
-  Sys.setenv("AWS_UP" = FALSE)
-  expect_message(okresy(), "source") # zpráva o spadlém AWS
-  Sys.setenv("AWS_UP" = TRUE)
-
   expect_true(is.data.frame(okresy()))
   expect_true(is.data.frame(okresy("low")))
   expect_true(is.data.frame(okresy("high")))

diff --git a/tests/testthat/test-1-orp.R b/tests/testthat/test-1-orp.R
@@ -10,10 +10,6 @@ test_that("ORP", {
   expect_message(orp_polygony(), "internet") # zpráva o chybějícím internetu
   Sys.setenv("NETWORK_UP" = TRUE)
 
-  Sys.setenv("AWS_UP" = FALSE)
-  expect_message(orp_polygony(), "source") # zpráva o spadlém AWS
-  Sys.setenv("AWS_UP" = TRUE)
-
   expect_true(is.data.frame(orp_polygony()))
 
   expect_s3_class(orp_polygony(), "sf")

diff --git a/tests/testthat/test-1-relief.R b/tests/testthat/test-1-relief.R
@@ -9,10 +9,6 @@ test_that("reliéf", {
   expect_message(vyskopis(), "internet") # zpráva o chybějícím internetu
   Sys.setenv("NETWORK_UP" = TRUE)
 
-  Sys.setenv("AWS_UP" = FALSE)
-  expect_message(vyskopis(), "source") # zpráva o spadlém AWS
-  Sys.setenv("AWS_UP" = TRUE)
-
   expect_s4_class(vyskopis(), "RasterLayer")
   expect_s4_class(vyskopis("actual"), "RasterLayer")
   expect_s4_class(vyskopis("rayshaded"), "RasterLayer")

diff --git a/tests/testthat/test-1-republika.R b/tests/testthat/test-1-republika.R
@@ -9,10 +9,6 @@ test_that("republika", {
   expect_message(republika(), "internet") # zpráva o chybějícím internetu
   Sys.setenv("NETWORK_UP" = TRUE)
 
-  Sys.setenv("AWS_UP" = FALSE)
-  expect_message(republika(), "source") # zpráva o spadlém AWS
-  Sys.setenv("AWS_UP" = TRUE)
-
   expect_true(is.data.frame(republika()))
   expect_true(is.data.frame(republika("low")))
   expect_true(is.data.frame(republika("high")))

diff --git a/tests/testthat/test-1-transport.R b/tests/testthat/test-1-transport.R
@@ -10,10 +10,6 @@ test_that("silnice", {
   expect_message(silnice(), "internet") # zpráva o chybějícím internetu
   Sys.setenv("NETWORK_UP" = TRUE)
 
-  Sys.setenv("AWS_UP" = FALSE)
-  expect_message(silnice(), "source") # zpráva o spadlém AWS
-  Sys.setenv("AWS_UP" = TRUE)
-
   expect_true(is.data.frame(silnice()))
 
   expect_s3_class(silnice(), "sf")
@@ -40,10 +36,6 @@ test_that("železnice", {
   expect_message(zeleznice(), "internet") # zpráva o chybějícím internetu
   Sys.setenv("NETWORK_UP" = TRUE)
 
-  Sys.setenv("AWS_UP" = FALSE)
-  expect_message(zeleznice(), "source") # zpráva o spadlém AWS
-  Sys.setenv("AWS_UP" = TRUE)
-
   expect_true(is.data.frame(zeleznice()))
 
   expect_s3_class(zeleznice(), "sf")

diff --git a/tests/testthat/test-1-vodstvo.R b/tests/testthat/test-1-vodstvo.R
@@ -9,10 +9,6 @@ test_that("vodní plochy", {
   expect_message(plochy(), "internet") # zpráva o chybějícím internetu
   Sys.setenv("NETWORK_UP" = TRUE)
 
-  Sys.setenv("AWS_UP" = FALSE)
-  expect_message(plochy(), "source") # zpráva o spadlém AWS
-  Sys.setenv("AWS_UP" = TRUE)
-
   expect_true(is.data.frame(plochy()))
 
   expect_s3_class(plochy(), "sf")
@@ -38,19 +34,13 @@ test_that("řeky", {
   expect_message(reky(), "internet") # zpráva o chybějícím internetu
   Sys.setenv("NETWORK_UP" = TRUE)
 
-  Sys.setenv("AWS_UP" = FALSE)
-  expect_message(reky(), "source") # zpráva o spadlém AWS
-  Sys.setenv("AWS_UP" = TRUE)
-
   expect_error(reky(NA)) # parametr je povinný
   expect_error(reky(resolution = "bflm")) # nezámé rozlišení
   expect_error(reky(resolution = 42)) # nezámé rozlišení
   expect_error(reky(resolution = NA)) # nezámé rozlišení
   expect_error(reky("bflm")) # neznámý scope
   expect_error(reky(c("Praha", "Brno"))) # moc řek...
 
-
-
   expect_true(is.data.frame(reky()))
   expect_true(is.data.frame(reky(resolution = "high")))
   expect_true(is.data.frame(reky(resolution = "low")))

diff --git a/tests/testthat/test-1-volby.R b/tests/testthat/test-1-volby.R
@@ -9,10 +9,6 @@ test_that("obvody senátu", {
   expect_message(senat_obvody(), "internet") # zpráva o chybějícím internetu
   Sys.setenv("NETWORK_UP" = TRUE)
 
-  Sys.setenv("AWS_UP" = FALSE)
-  expect_message(senat_obvody(), "source") # zpráva o spadlém AWS
-  Sys.setenv("AWS_UP" = TRUE)
-
   expect_true(is.data.frame(senat_obvody()))
   expect_true(is.data.frame(senat_obvody("low")))
   expect_true(is.data.frame(senat_obvody("high")))
@@ -50,10 +46,6 @@ test_that("volební okrsky", {
   expect_message(volebni_okrsky(), "internet") # zpráva o chybějícím internetu
   Sys.setenv("NETWORK_UP" = TRUE)
 
-  Sys.setenv("AWS_UP" = FALSE)
-  expect_message(volebni_okrsky(), "source") # zpráva o spadlém AWS
-  Sys.setenv("AWS_UP" = TRUE)
-
   expect_true(is.data.frame(volebni_okrsky()))
   expect_true(is.data.frame(volebni_okrsky("low")))
   expect_true(is.data.frame(volebni_okrsky("high")))

diff --git a/tests/testthat/test-1-zip-codes.R b/tests/testthat/test-1-zip-codes.R
@@ -9,10 +9,6 @@ test_that("PSČ", {
   expect_message(zip_codes(), "internet") # zpráva o chybějícím internetu
   Sys.setenv("NETWORK_UP" = TRUE)
 
-  Sys.setenv("AWS_UP" = FALSE)
-  expect_message(zip_codes(), "source") # zpráva o spadlém AWS
-  Sys.setenv("AWS_UP" = TRUE)
-
   expect_true(is.data.frame(zip_codes()))
   expect_true(is.data.frame(zip_codes("low")))
   expect_true(is.data.frame(zip_codes("high")))