Merge pull request DOI-USGS#749 from DOI-USGS/develop

Develop to main

Author: ldecicco-USGS

.Rbuildignore

@@ -94,4 +94,5 @@ vignettes/dataretrieval_discrete_changes_images/*
 ^ci$
 ^public$
 ^docker$
-vignettes/WQX_3.Rmd
+vignettes/WQX_3.Rmd
+vignettes/samples_data.Rmd

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

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main]
+    branches: [main, develop]
   pull_request:
-    branches: [main]
+    branches: [main, develop]
 
 name: R-CMD-check
 
@@ -32,15 +32,16 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@6012817847b5f064d0882d67a7b5e2ca6639afb2
 
-      - uses: r-lib/actions/setup-r@15cf1013badbaf6d25f100593ad5d7d75e65d64b
+      - uses: r-lib/actions/setup-r@473c68190595b311a74f208fba61a8d8c0d4c247
         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@96b1dc658a45175f93ed5f33fda2b2cebbb12ee8
         with:
-          extra-packages: any::rcmdcheck
+          extra-packages: |
+            any::rcmdcheck
           needs: check
 
       - uses: r-lib/actions/check-r-package@3e56ca41aa267855f36891af7a495d24bfaa8373

.github/workflows/pkgdown.yaml

@@ -40,7 +40,15 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@473c68190595b311a74f208fba61a8d8c0d4c247
         with:
-          extra-packages: any::pkgdown, local::.
+          extra-packages: |
+            any::pkgdown
+            any::rcmdcheck
+            any::DT
+            any::data.table
+            any::dplyr
+            any::tidyr
+            any::gridExtra
+            local::.
           needs: website
 
       - name: Build site

.gitlab-ci.yml

@@ -42,7 +42,6 @@ build-image:
   rules:
     - changes:
       - docker/Dockerfile
-      - .gitlab-ci.yml
   script:
     - echo ${CI_REGISTRY_PASSWORD} | docker login -u ${CI_REGISTRY_USER} --password-stdin $CI_REGISTRY
     - docker pull ${CI_REGISTRY_IMAGE}:latest || true
@@ -81,22 +80,33 @@ unittests:
         coverage_format: cobertura
         path: cobertura.xml
   coverage: '/Coverage: \d+.\d+\%/'
-        
+
+longtest:
+  stage: test
+  dependencies:
+    - build-image
+    - buildcheck
+  script:
+    - Rscript -e 'testthat::test_local(path = "tests/manual")'
+  rules:
+    - if: $RUN_LONG_TESTS == "FALSE"
+      when: always
+    - when: never
+  
 pages:
   stage: end
   cache: []
-  only: 
-    - main
   script:
     - Rscript -e 'pkgdown::build_site(override = list(destination = "public"))'
-    - Rscript -e 'source("deploy_simple.R")'
   artifacts:
     paths:
       - $PAGES_OUTDIR
     expire_in: 1 week
 
 Validate Inventory:
     stage: end
+    only: 
+      - main
     image: ${INTERNAL_REGISTRY}software/software-management:latest
     script:
       - software-management review

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: dataRetrieval
 Type: Package
 Title: Retrieval Functions for USGS and EPA Hydrology and Water Quality Data
-Version: 2.7.17.9000
+Version: 2.7.18
 Authors@R: c(
     person("Laura", "DeCicco", role = c("aut","cre"),
             email = "[email protected]",
@@ -37,24 +37,19 @@ Copyright: This software is in the public domain because it contains materials
     that originally came from the United States Geological Survey, an agency of
     the United States Department of Interior. 
 Depends:
-    R (>= 3.5.0)
+    R (>= 4.1.0)
 Imports:
-    httr (>= 1.0.0),
     curl,
     lubridate (>= 1.5.0),
     stats,
     utils,
     xml2,
     readr (>= 1.4.0),
-    jsonlite
+    jsonlite,
+    httr2
 Suggests:
     covr,
     dplyr,
-    ggplot2,
-    tidyr,
-    data.table,
-    DT,
-    gridExtra,
     knitr,
     rmarkdown,
     sf,

NAMESPACE

@@ -3,9 +3,11 @@
 export(addWaterYear)
 export(calcWaterYear)
 export(checkWQPdates)
+export(check_param)
 export(constructNWISURL)
 export(constructUseURL)
 export(constructWQPURL)
+export(construct_USGS_sample_request)
 export(countyCd)
 export(countyCdLookup)
 export(create_NWIS_bib)
@@ -40,10 +42,12 @@ export(readNWISuv)
 export(readWQPdata)
 export(readWQPqw)
 export(readWQPsummary)
+export(read_USGS_samples)
 export(renameNWISColumns)
 export(setAccess)
 export(stateCd)
 export(stateCdLookup)
+export(summarize_USGS_samples)
 export(whatNWISdata)
 export(whatNWISsites)
 export(whatWQPdata)

NEWS

@@ -1,6 +1,10 @@
 dataRetrieval 2.7.18
 ===================
+* Switched from httr to httr2
 * Added a way to include a custom user-agent suffix via an enviornmental variable "CUSTOM_DR_UA"
+* Added function for USGS discrete data samples_data service: read_USGS_samples
+* Restructured stateCdLookup and countyCdLookup to use web services that only
+list states and counties that have water quality data.
 
 dataRetrieval 2.7.17
 ===================

R/checkWQPdates.R

@@ -16,7 +16,9 @@
 checkWQPdates <- function(values) {
   dateNames <- c(
     "startDateLo", "startDateHi",
-    "startDate", "endDate"
+    "startDate", "endDate",
+    "activityStartDateLower",
+    "activityStartDateUpper"
   )
 
   if (any(names(values) %in% dateNames)) {