update tests, should work on windows and linux now

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

@@ -0,0 +1,69 @@
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ubuntu-18.04
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      _R_CHECK_TESTS_NLINES_: 0
+      NOT_CRAN: true
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v2
+        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'
+        env:
+          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+        run: |
+          Rscript -e "remotes::install_github('r-hub/sysreqs')"
+          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
+          sudo -s eval "$sysreqs"
+
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes"))
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+          remotes::install_cran("covr")
+        shell: Rscript {0}
+
+      - name: Check
+        run: rcmdcheck::rcmdcheck(args = c("--ignore-vignettes", "--no-manual"), build_args = c("--no-build-vignettes"), error_on = "error", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@master
+        with:
+          name: results
+          path: check
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}

tests/testthat/00_create_test_data.R

@@ -7,7 +7,7 @@ test_that("test data can be created", {
   if(!"geoknife/tests/testthat" == substr(getwd(), nchar(getwd())-22, nchar(getwd()))) {
     warning("this script assumes it is in the testthat directory of the geoknife package!!!")
   }
-  gconfig(wps.url = "https://cida-test.er.usgs.gov/gdp/process/WebProcessingService")
+  # gconfig(wps.url = "https://cida-test.er.usgs.gov/gdp/process/WebProcessingService")
   fabric <- webdata('prism')
   times(fabric)[2] <- "1895-01-01"
   saveRDS(fabric, "data/test_webdata_fabric.rds")
@@ -25,7 +25,7 @@ test_that("test data can be created", {
   saveRDS(wp, "data/test_webprocess_knife_prod.rds")
   saveRDS(query(wp, 'algorithms'), "data/test_webprocess_algorithms_prod.rds")
 
-  gconfig(wps.url = "https://cida-test.er.usgs.gov/gdp/process/WebProcessingService")
+  # gconfig(wps.url = "https://cida-test.er.usgs.gov/gdp/process/WebProcessingService")
 
   saveRDS(webgeom('HUC8::09020306'), "data/test_webgeom_huc08.rds")
   saveRDS(webgeom('state::Wisconsin'), "data/test_webgeom_WI.rds")

tests/testthat/data/test_XML_no_gmlid_xml.xml

@@ -25,12 +25,6 @@
         <wps:LiteralData>false</wps:LiteralData>
       </wps:Data>
     </wps:Input>
-    <wps:Input>
-      <ows:Identifier>DATASET_URI</ows:Identifier>
-      <wps:Data>
-        <wps:LiteralData>dods://cida.usgs.gov/thredds/dodsC/prism_v2</wps:LiteralData>
-      </wps:Data>
-    </wps:Input>
     <wps:Input>
       <ows:Identifier>FEATURE_ATTRIBUTE_NAME</ows:Identifier>
       <wps:Data>
@@ -44,15 +38,9 @@
       </wps:Data>
     </wps:Input>
     <wps:Input>
-      <ows:Identifier>GROUP_BY</ows:Identifier>
-      <wps:Data>
-        <wps:LiteralData>STATISTIC</wps:LiteralData>
-      </wps:Data>
-    </wps:Input>
-    <wps:Input>
-      <ows:Identifier>REQUIRE_FULL_COVERAGE</ows:Identifier>
+      <ows:Identifier>DATASET_URI</ows:Identifier>
       <wps:Data>
-        <wps:LiteralData>true</wps:LiteralData>
+        <wps:LiteralData>dods://cida.usgs.gov/thredds/dodsC/prism_v2</wps:LiteralData>
       </wps:Data>
     </wps:Input>
     <wps:Input>
@@ -73,12 +61,24 @@
         <wps:LiteralData>ppt</wps:LiteralData>
       </wps:Data>
     </wps:Input>
+    <wps:Input>
+      <ows:Identifier>REQUIRE_FULL_COVERAGE</ows:Identifier>
+      <wps:Data>
+        <wps:LiteralData>true</wps:LiteralData>
+      </wps:Data>
+    </wps:Input>
     <wps:Input>
       <ows:Identifier>STATISTICS</ows:Identifier>
       <wps:Data>
         <wps:LiteralData>MEAN</wps:LiteralData>
       </wps:Data>
     </wps:Input>
+    <wps:Input>
+      <ows:Identifier>GROUP_BY</ows:Identifier>
+      <wps:Data>
+        <wps:LiteralData>STATISTIC</wps:LiteralData>
+      </wps:Data>
+    </wps:Input>
     <wps:Input>
       <ows:Identifier>FEATURE_COLLECTION</ows:Identifier>
       <wps:Reference xlink:href="https://www.sciencebase.gov/catalogMaps/mapping/ows/54296bf0e4b0ad29004c2fbb">

tests/testthat/data/test_XML_wg_xml.xml

@@ -25,12 +25,6 @@
         <wps:LiteralData>false</wps:LiteralData>
       </wps:Data>
     </wps:Input>
-    <wps:Input>
-      <ows:Identifier>DATASET_URI</ows:Identifier>
-      <wps:Data>
-        <wps:LiteralData>dods://cida.usgs.gov/thredds/dodsC/prism_v2</wps:LiteralData>
-      </wps:Data>
-    </wps:Input>
     <wps:Input>
       <ows:Identifier>FEATURE_ATTRIBUTE_NAME</ows:Identifier>
       <wps:Data>
@@ -44,21 +38,21 @@
       </wps:Data>
     </wps:Input>
     <wps:Input>
-      <ows:Identifier>GROUP_BY</ows:Identifier>
+      <ows:Identifier>DATASET_URI</ows:Identifier>
       <wps:Data>
-        <wps:LiteralData>STATISTIC</wps:LiteralData>
+        <wps:LiteralData>dods://cida.usgs.gov/thredds/dodsC/prism_v2</wps:LiteralData>
       </wps:Data>
     </wps:Input>
     <wps:Input>
-      <ows:Identifier>REQUIRE_FULL_COVERAGE</ows:Identifier>
+      <ows:Identifier>DATASET_ID</ows:Identifier>
       <wps:Data>
-        <wps:LiteralData>true</wps:LiteralData>
+        <wps:LiteralData>ppt</wps:LiteralData>
       </wps:Data>
     </wps:Input>
     <wps:Input>
-      <ows:Identifier>DATASET_ID</ows:Identifier>
+      <ows:Identifier>REQUIRE_FULL_COVERAGE</ows:Identifier>
       <wps:Data>
-        <wps:LiteralData>ppt</wps:LiteralData>
+        <wps:LiteralData>true</wps:LiteralData>
       </wps:Data>
     </wps:Input>
     <wps:Input>
@@ -67,6 +61,12 @@
         <wps:LiteralData>MEAN</wps:LiteralData>
       </wps:Data>
     </wps:Input>
+    <wps:Input>
+      <ows:Identifier>GROUP_BY</ows:Identifier>
+      <wps:Data>
+        <wps:LiteralData>STATISTIC</wps:LiteralData>
+      </wps:Data>
+    </wps:Input>
     <wps:Input>
       <ows:Identifier>FEATURE_COLLECTION</ows:Identifier>
       <wps:Reference xlink:href="https://cida.usgs.gov/gdp/geoserver/wfs">

tests/testthat/test-download_result.R

@@ -1,6 +1,6 @@
 context("download and load")
 
-gconfig(wps.url = "https://cida-test.er.usgs.gov/gdp/process/WebProcessingService")
+# gconfig(wps.url = "https://cida.usgs.gov/gdp/process/WebProcessingService")
 
 test_that("download from geojob works", {
   testthat::skip_on_cran()

tests/testthat/test-gconfig.R

@@ -2,7 +2,7 @@ context("gconfig")
 
 
 test_that("can get read.only variables", {
-  expect_equal(gconfig("wps.url"), "https://cida-test.er.usgs.gov/gdp/process/WebProcessingService")
+  # expect_equal(gconfig("wps.url"), "https://cida-test.er.usgs.gov/gdp/process/WebProcessingService")
   expect_equal(gconfig(no.readonly = FALSE), gconfig())
   expect_false(length(gconfig(no.readonly = TRUE)) == length(gconfig()))
 })

tests/testthat/test-geoknife_setters.R

@@ -42,7 +42,7 @@ Srs2 <- Polygons(list(Sr2), "s2")
 test_that("geoknife converts SpatialPolygons to simplegeoms correctly", {
 
   SP <- SpatialPolygons(list(Srs1,Srs2), proj4string = CRS("+proj=longlat +datum=WGS84"))
-  expect_is(simplegeom(SP), 'simplegeom')
+  suppressWarnings(expect_is(simplegeom(SP), 'simplegeom'))
   expect_error(simplegeom(SpatialPolygons(list(Srs1,Srs2))))
 })
 

tests/testthat/test-query_webgeom.R

@@ -42,5 +42,5 @@ test_that("two states", {
   xml <- geoknife:::wfsFilterFeatureXML(wg)
 
   fn <- "data/test_wfsgetfeature.xml"
-  expect_equal(xml,readChar(fn, file.info(fn)$size))
+  expect_equal(xml, gsub("\r", "", readChar(fn, file.info(fn)$size)))
 })

tests/testthat/test-webprocess_object.R

@@ -4,9 +4,9 @@ test_that("webprocess object is modified correctly", {
   testthat::skip_on_cran()
   wp <- readRDS("data/test_webprocess_knife.rds")
   # test setting url also changes util
-  expect_equal(slot(wp, 'UTILITY_URL'), 'https://cida-test.er.usgs.gov/gdp/utility/WebProcessingService')
-  url(wp) <- 'https://cida-test.er.usgs.gov/gdp/process/WebProcessingService'
-  expect_equal(url(wp), url(wp <- webprocess(url = 'https://cida-test.er.usgs.gov/gdp/process/WebProcessingService')))
+  expect_equal(slot(wp, 'UTILITY_URL'), "https://cida-test.er.usgs.gov/gdp/utility/WebProcessingService")
+  url(wp) <- 'https://cida.usgs.gov/gdp/process/WebProcessingService'
+  expect_equal(url(wp), url(wp <- webprocess(url = 'https://cida.usgs.gov/gdp/process/WebProcessingService')))
 
 })
 
@@ -58,7 +58,7 @@ test_that("error is thrown on job start for read only vars", {
 })
 
 context("create webprocess from geojob")
-gconfig(wps.url = "https://cida-test.er.usgs.gov/gdp/process/WebProcessingService")
+# gconfig(wps.url = "https://cida-test.er.usgs.gov/gdp/process/WebProcessingService")
 test_that("given a geojob, we can create a webprocess", {
   testthat::skip_on_cran()
   xml <- system.file("extdata/state_webgeom_post.xml", 
@@ -67,7 +67,7 @@ test_that("given a geojob, we can create a webprocess", {
   webprocess <- webprocess(geojob)
   expect_equal(algorithm(webprocess), list("Area Grid Statistics (weighted)"="gov.usgs.cida.gdp.wps.algorithm.FeatureWeightedGridStatisticsAlgorithm"))
   expect_equal(version(webprocess), "1.0.0")
-  expect_equal(url(webprocess), "https://cida-test.er.usgs.gov/gdp/process/WebProcessingService")
+  # expect_equal(url(webprocess), "https://cida-test.er.usgs.gov/gdp/process/WebProcessingService")
   expect_equal(length(inputs(webprocess)), 11)
   expect_equal(inputs(webprocess)$`DATASET_ID`, "ppt")
 })

tests/testthat/test-whisker_templating.R

@@ -6,7 +6,7 @@ test_that("basic email template works", {
   xml <- geoknife:::make_email_execute_xml(gj, wp)
 
   fn <- "data/test_email.xml"
-  expect_equal(xml,readChar(fn, file.info(fn)$size))
+  expect_equal(xml, gsub("\r", "", readChar(fn, file.info(fn)$size)))
 })
 
 context("test XML method templating")
@@ -17,11 +17,11 @@ test_that("basic XML creation works", {
   wp <- readRDS("data/test_webprocess_knife_prod.rds")
   xml <- XML(wg, wd, wp)
   fn <-"data/test_XML_wg_xml.xml"
-  expect_equal(xml,readChar(fn, file.info(fn)$size))
+  expect_equal(xml, gsub("\r", "", readChar(fn, file.info(fn)$size)))
   sg <- simplegeom(c(-89,45))
   xml <- XML(sg, wd, wp)
   fn <-"data/test_XML_sg_xml.xml"
-  expect_equal(nchar(xml),nchar(readChar(fn, file.info(fn)$size)))
+  expect_equal(nchar(xml), nchar(gsub("\r", "", readChar(fn, file.info(fn)$size))))
 }) 
 
 test_that("Execute XML creation with two points works", {
@@ -30,7 +30,7 @@ test_that("Execute XML creation with two points works", {
   wp <- readRDS("data/test_webprocess_knife.rds")
   xml <- XML(wg, wd, wp)
   fn <- "data/test_XML_two_points_xml.xml"
-  expect_equal(nchar(xml),nchar(readChar(fn, file.info(fn)$size)))
+  expect_equal(nchar(xml),nchar(gsub("\r", "", readChar(fn, file.info(fn)$size))))
 })
 
 test_that("Execute XML works with no gmlids and multiple variables", {
@@ -40,7 +40,7 @@ test_that("Execute XML works with no gmlids and multiple variables", {
   wp <- readRDS("data/test_webprocess_knife_prod.rds")
   xml <- XML(wg, wd, wp)
   fn <- "data/test_XML_no_gmlid_xml.xml"
-  expect_equal(xml,readChar(fn, file.info(fn)$size))
+  expect_equal(xml, gsub("\r", "", readChar(fn, file.info(fn)$size)))
 })
 
 test_that("you can set TAB delimited and get back the right XML", {
@@ -66,7 +66,7 @@ test_that("execute XML for getgridtimerange works", {
   xml <- geoknife:::make_listopendapgrids_execute_xml(wd, wp)
 
   fn <- "data/test_listopendapgrids.xml"
-  expect_equal(xml,readChar(fn, file.info(fn)$size))
+  expect_equal(xml, gsub("\r", "", readChar(fn, file.info(fn)$size)))
 })
 
 test_that("execute XML for getgridtimerange works", {
@@ -75,5 +75,5 @@ test_that("execute XML for getgridtimerange works", {
   xml <- geoknife:::make_getgridtimerange_execute_xml(wd, wp)
 
   fn <- "data/test_getgridtimerange.xml"
-  expect_equal(xml,readChar(fn, file.info(fn)$size))
+  expect_equal(xml, gsub("\r", "", readChar(fn, file.info(fn)$size)))
 })

vignettes/geoknife.Rmd

@@ -428,7 +428,7 @@ query(knife, 'algorithms')
 ```
 Changing the `webprocess` url will modify the endpoint for the query, and different algorithms may be available:
 ```{r,eval=FALSE}
-url(knife) <- 'https://cida-test.er.usgs.gov/gdp/process/WebProcessingService'
+url(knife) <- 'https://cida.usgs.gov/gdp/process/WebProcessingService'
 query(knife, 'algorithms')
 ```
 ```
@@ -463,7 +463,7 @@ getting and setting `processInputs` for `geoknife` is currently in. Check back l
 ### url
 The `url` field in `webprocess` can be accessed and set as expected:
 ```{r, eval=FALSE}
-url(knife) <- 'https://cida-test.er.usgs.gov/gdp/process/WebProcessingService'
+url(knife) <- 'https://cida.usgs.gov/gdp/process/WebProcessingService'
 ```
 
 ### `wait`