Merge pull request #674 from ldecicco-USGS/main

Add NMC links to readme
DOI-USGS · Sep 20, 2023 · e3272cb · e3272cb
2 parents b920321 + 6b39008
commit e3272cb
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -30,19 +30,19 @@ jobs:
     steps:
       - uses: actions/checkout@c0a81a463886bb75afe234e07a9fd5bb79219196
 
-      - uses: r-lib/actions/setup-pandoc@52330cc136b963487918a8867f948ddf954e9e63
+      - uses: r-lib/actions/setup-pandoc@756399d909bf9c180bbdafe8025f794f51f2da02
 
-      - uses: r-lib/actions/setup-r@52330cc136b963487918a8867f948ddf954e9e63
+      - uses: r-lib/actions/setup-r@756399d909bf9c180bbdafe8025f794f51f2da02
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@52330cc136b963487918a8867f948ddf954e9e63
+      - uses: r-lib/actions/setup-r-dependencies@756399d909bf9c180bbdafe8025f794f51f2da02
         with:
           extra-packages: any::rcmdcheck
           needs: check
 
-      - uses: r-lib/actions/check-r-package@52330cc136b963487918a8867f948ddf954e9e63
+      - uses: r-lib/actions/check-r-package@756399d909bf9c180bbdafe8025f794f51f2da02
         with:
           upload-snapshots: true
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -14,30 +14,14 @@ jobs:
     steps:
       - uses: actions/checkout@c0a81a463886bb75afe234e07a9fd5bb79219196
 
-      - uses: r-lib/actions/setup-r@52330cc136b963487918a8867f948ddf954e9e63
+      - uses: r-lib/actions/setup-r@756399d909bf9c180bbdafe8025f794f51f2da02
 
-      - uses: r-lib/actions/setup-pandoc@52330cc136b963487918a8867f948ddf954e9e63
+      - uses: r-lib/actions/setup-pandoc@756399d909bf9c180bbdafe8025f794f51f2da02
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v1
+      - uses: r-lib/actions/setup-r-dependencies@756399d909bf9c180bbdafe8025f794f51f2da02
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: macOS-r-4.0-2-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: macOS-r-4.0-2-
-
-      - name: Install dependencies
-        run: |
-          options(pkgType = "binary")
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("covr")
-        shell: Rscript {0}
+          extra-packages: any::rcmdcheck
+          needs: check
 
       - name: Test coverage
         run: covr::codecov()

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -27,7 +27,7 @@ getready:
   stage: getready
   script:
     - mkdir -p $R_LIBS_USER
-    - Rscript -e "install.packages(c('stringi', 'devtools','pkgdown', 'connectapi', 'patchwork'))"
+    - Rscript -e "install.packages(c('rlang', 'stringi', 'devtools','pkgdown', 'connectapi', 'patchwork'))"
     - Rscript -e "devtools::install_deps(dependencies = TRUE, quiet = TRUE)"
   cache:
     paths:

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: dataRetrieval
 Type: Package
 Title: Retrieval Functions for USGS and EPA Hydrology and Water Quality Data
-Version: 2.7.12
+Version: 2.7.13
 Authors@R: c(
     person("Laura", "DeCicco", role = c("aut","cre"),
             email = "[email protected]",
@@ -40,7 +40,7 @@ Imports:
     stats,
     utils,
     xml2,
-    readr (>= 1.0.0),
+    readr (>= 1.4.0),
     jsonlite
 Suggests:
     covr,

diff --git a/NEWS b/NEWS
@@ -1,6 +1,7 @@
 dataRetrieval 2.7.13
 ===================
 * Added pcode_to_name function to get WQP characteristics from USGS parameter codes.
+* Required readr version 1.4 or greater
 
 dataRetrieval 2.7.12
 ===================

diff --git a/R/findNLDI.R b/R/findNLDI.R
@@ -232,7 +232,7 @@ valid_ask <- function(all, type) {
 
 #' @title R Client for the Network Linked Data Index
 #' @description Provides a formal client to the USGS
-#' \href{https://labs.waterdata.usgs.gov/about-nldi/index.html}{Network Linked Data Index}.
+#' Network Linked Data Index.
 #' @details The function is useful for topology and location based
 #' feature discovery. A user must specify an origin feature, optional navigation
 #' direction(s) along the network, as well as features to identify along the

diff --git a/R/importRDB1.R b/R/importRDB1.R
@@ -156,9 +156,9 @@ importRDB1 <- function(obs_url,
       skip = meta.rows + 2,
       col_names = FALSE
     )
-    if (utils::packageVersion("readr") > 1.4) {
-      args_list[["show_col_types"]] <- FALSE
-    }
+
+    args_list[["show_col_types"]] <- FALSE
+
     if (convertType) {
       args_list[["guess_max"]] <- data.rows
       args_list[["col_types"]] <- readr::cols()

diff --git a/README.Rmd b/README.Rmd
@@ -20,6 +20,10 @@ knitr::opts_chunk$set(
 
 # dataRetrieval <img src="man/figures/hex_logo.png" class="logo"  alt="dataRetrieval" style="width:90px;height:auto;" align="right" />
 
+[![CRAN version](http://www.r-pkg.org/badges/version/dataRetrieval)](https://cran.r-project.org/package=EGRET)
+[![](http://cranlogs.r-pkg.org/badges/dataRetrieval)](https://cran.r-project.org/package=dataRetrieval)
+[![](http://cranlogs.r-pkg.org/badges/grand-total/dataRetrieval)](https://cran.r-project.org/package=dataRetrieval)
+
 The `dataRetrieval` package was created to simplify the process of loading hydrologic data into the R environment. It is designed to retrieve the major data types of U.S. Geological Survey (USGS) hydrology data that are available on the Web, as well as data from the Water Quality Portal (WQP), which currently houses water quality data from the Environmental Protection Agency (EPA), U.S. Department of Agriculture (USDA), and USGS. Direct USGS data is obtained from a service called the National Water Information System (NWIS). 
 
 For complete tutorial information, see:
@@ -28,6 +32,10 @@ For complete tutorial information, see:
 
 [https://waterdata.usgs.gov/blog/dataretrieval/](https://waterdata.usgs.gov/blog/dataretrieval/)
 
+[dataRetrieval Introduction 1](https://rconnect.usgs.gov/NMC_dataRetrieval_1)
+
+[dataRetrieval Introduction 2](https://rconnect.usgs.gov/NMC_dataRetrieval_2)
+
 
 # Sample Workflow
 

diff --git a/README.md b/README.md
@@ -1,5 +1,10 @@
 # dataRetrieval <img src="man/figures/hex_logo.png" class="logo"  alt="dataRetrieval" style="width:90px;height:auto;" align="right" />
 
+[![CRAN
+version](http://www.r-pkg.org/badges/version/dataRetrieval)](https://cran.r-project.org/package=EGRET)
+[![](http://cranlogs.r-pkg.org/badges/dataRetrieval)](https://cran.r-project.org/package=dataRetrieval)
+[![](http://cranlogs.r-pkg.org/badges/grand-total/dataRetrieval)](https://cran.r-project.org/package=dataRetrieval)
+
 The `dataRetrieval` package was created to simplify the process of
 loading hydrologic data into the R environment. It is designed to
 retrieve the major data types of U.S. Geological Survey (USGS) hydrology
@@ -15,6 +20,12 @@ For complete tutorial information, see:
 
 <https://waterdata.usgs.gov/blog/dataretrieval/>
 
+[dataRetrieval Introduction
+1](https://rconnect.usgs.gov/NMC_dataRetrieval_1)
+
+[dataRetrieval Introduction
+2](https://rconnect.usgs.gov/NMC_dataRetrieval_2)
+
 # Sample Workflow
 
 ## USGS
@@ -92,24 +103,23 @@ Please consider reporting bugs and asking questions on the Issues page:
 
 ``` r
 citation(package = "dataRetrieval")
-#> 
 #> To cite dataRetrieval in publications, please use:
 #> 
 #>   De Cicco, L.A., Hirsch, R.M., Lorenz, D., Watkins, W.D., Johnson, M.,
-#>   2022, dataRetrieval: R packages for discovering and retrieving water
-#>   data available from Federal hydrologic web services, v.2.7.12,
+#>   2023, dataRetrieval: R packages for discovering and retrieving water
+#>   data available from Federal hydrologic web services, v.2.7.13,
 #>   doi:10.5066/P9X4L3GE
 #> 
 #> A BibTeX entry for LaTeX users is
 #> 
 #>   @Manual{,
-#>     author = {Laura A. {De Cicco} and David Lorenz and Robert M. Hirsch and William Watkins and Mike Johnson},
+#>     author = {Laura DeCicco and Robert Hirsch and David Lorenz and David Watkins and Mike Johnson},
 #>     title = {dataRetrieval: R packages for discovering and retrieving water data available from U.S. federal hydrologic web services},
 #>     publisher = {U.S. Geological Survey},
 #>     address = {Reston, VA},
-#>     version = {2.7.12},
+#>     version = {2.7.13},
 #>     institution = {U.S. Geological Survey},
-#>     year = {2022},
+#>     year = {2023},
 #>     doi = {10.5066/P9X4L3GE},
 #>     url = {https://code.usgs.gov/water/dataRetrieval},
 #>   }

diff --git a/inst/CITATION b/inst/CITATION
@@ -1,20 +1,26 @@
 citHeader("To cite dataRetrieval in publications, please use:")
 
 bibentry(bibtype = "Manual",
- author = personList(
-              as.person("Laura A. De Cicco"),
-              as.person("David Lorenz"),
-              as.person("Robert M. Hirsch"),
-              as.person("William Watkins"),
-              as.person("Mike Johnson")
-              ),
+ author = c(
+    person("Laura", "DeCicco", role = c("aut","cre"),
+            email = "[email protected]",
+            comment=c(ORCID="0000-0002-3915-9487")),
+    person("Robert", "Hirsch", role = c("aut"),
+            comment=c(ORCID="0000-0002-4534-075X")),
+    person("David","Lorenz", role=c("aut")),
+    person("David","Watkins", role=c("aut"),
+            email = "[email protected]",
+            comment=c(ORCID="0000-0002-7544-0700")),
+    person("Mike", "Johnson", role=c("aut"),
+            email = "[email protected]",
+            comment=c(ORCID="0000-0002-5288-8350"))),
   title = "dataRetrieval: R packages for discovering and retrieving water data available from U.S. federal hydrologic web services",
   publisher = "U.S. Geological Survey",
   address="Reston, VA",
-  version = "2.7.12",
+  version = "2.7.13",
   institution = "U.S. Geological Survey",
-  year = 2022,
+  year = 2023,
   doi = "10.5066/P9X4L3GE",
   url = "https://code.usgs.gov/water/dataRetrieval",
-  textVersion = "De Cicco, L.A., Hirsch, R.M., Lorenz, D., Watkins, W.D., Johnson, M., 2022, dataRetrieval: R packages for discovering and retrieving water data available from Federal hydrologic web services, v.2.7.12, doi:10.5066/P9X4L3GE"
+  textVersion = "De Cicco, L.A., Hirsch, R.M., Lorenz, D., Watkins, W.D., Johnson, M., 2023, dataRetrieval: R packages for discovering and retrieving water data available from Federal hydrologic web services, v.2.7.13, doi:10.5066/P9X4L3GE"
 )
diff --git a/man/findNLDI.Rd b/man/findNLDI.Rd
diff --git a/tests/testthat/tests_imports.R b/tests/testthat/tests_imports.R
@@ -63,7 +63,7 @@ test_that("External importRDB1 tests", {
   ))
   site_data <- importRDB1(url)
 
-  expect_equal(site_data$station_nm, "\"G\" CANAL NEAR OLENE,OREG.")
+  expect_equal(site_data$station_nm, "G CANAL NEAR OLENE, OR")
 
   site <- "040854588204"
 
@@ -74,7 +74,7 @@ test_that("External importRDB1 tests", {
   ))
   site_data <- importRDB1(url)
 
-  expect_equal(site_data$station_nm, "\"FISHER CR AT 32 & HIGHLAND RD AT HOWARDS GROVE, W")
+  expect_equal(site_data$station_nm, "FISHER CR AT 32 & HIGHLAND RD AT HOWARDS GROVE, W")
 })
 
 context("importRDB")

diff --git a/tests/testthat/tests_nldi.R b/tests/testthat/tests_nldi.R
@@ -65,7 +65,7 @@ test_that("NLDI starting sources...", {
   # GENERAL START: STABLE
   expect_equal(findNLDI(origin = list("comid" = 101), warn = FALSE)$origin$sourceName, "NHDPlus comid")
   # GENERAL START: NON-STABLE
-  expect_equal(findNLDI(origin = list("wade" = "NMwr_S148023"), warn = FALSE)$origin$sourceName, "Water Data Exchange 2.0 Sites")
+  expect_equal(findNLDI(origin = list("nwissite" = "USGS-05427850"), warn = FALSE)$origin$sourceName, "NWIS Surface Water Sites")
   # ERROR: TWO STARTS
   expect_error(findNLDI(nwis = 1000, comid = 101, warn = FALSE))
   # NON EXISTING SITE