Prepping for CRAN release

.Rbuildignore

@@ -67,7 +67,9 @@ vignettes/changes_slides.Rmd
 vignettes/daily_data_statistics.Rmd
 vignettes/continuous_pr.Rmd
 vignettes/quick_slides.Rmd
+vignettes/Reference_Lists.Rmd
 ^[.]?air[.]toml$
 ^\.vscode$
+environment.yml
 ^\.positai$
 ^\.claude$

.gitignore

@@ -12,11 +12,9 @@ docs
 /doc/
 /Meta/
 /Temp/
+/public/
 vignettes/*.html
 vignettes/*.R
-
-
 /.quarto/
-
 **/*.quarto_ipynb
 .positai

.gitlab-ci.yml

@@ -8,7 +8,6 @@ workflow:
 default:
   tags:
     - chs-shared
-    - dind
 
 stages:
   - build
@@ -36,30 +35,41 @@ variables:
 build-image:
   stage: build
   cache: []
-  image: ${DEVOPS_REGISTRY}usgs/docker:20
+  tags:
+    - chs-shared
+    - dind
+  image: ${DEVOPS_REGISTRY}usgs/docker:29
   services:
-  - name: ${DEVOPS_REGISTRY}usgs/docker:20-dind
+  - name: ${DEVOPS_REGISTRY}usgs/docker:29-dind
     alias: docker
-  rules:
-    - changes:
-      - docker/Dockerfile
   script:
     - echo ${CI_REGISTRY_PASSWORD} | docker login -u ${CI_REGISTRY_USER} --password-stdin $CI_REGISTRY
     - docker pull ${CI_REGISTRY_IMAGE}:latest || true
-    - cd docker
-    - docker build
-        -t ${CI_REGISTRY_IMAGE}:latest
-        .
+    - docker build 
+        -f docker/Dockerfile -t ${CI_REGISTRY_IMAGE}:latest .
     - docker push --all-tags ${CI_REGISTRY_IMAGE}
+  artifacts:
+    expire_in: 5 minutes
 
 buildcheck:
   stage: check
   cache: []
   dependencies:
     - build-image
   script:
-    - Rscript -e 'devtools::install(quick = TRUE, upgrade = "never")'
-    - Rscript -e 'devtools::check(document = FALSE, args = "--no-tests", check_dir = Sys.getenv("BUILD_LOGS_DIR"), vignettes = FALSE)'
+    - |
+      Rscript -e "
+        rcmdcheck::rcmdcheck(
+          args = c('--no-manual', '--no-tests'),
+          build_args = c('--no-manual', '--no-resave-data'),
+          check_dir = '.',
+          error_on = 'warning'
+        )
+      "
+  artifacts:
+    paths:
+      - "*.tar.gz"
+    expire_in: 1 hour
 
 unittests:
   stage: test
@@ -68,11 +78,19 @@ unittests:
     - build-image
     - buildcheck
   script:
-    - R -e 'library(testthat); options(testthat.output_file = file.path(Sys.getenv("CI_PROJECT_DIR"), "test-out.xml")); devtools::test(reporter = "junit")'
-    - R -e 'x <- covr::package_coverage(); covr::to_cobertura(x); x; '
+    - |
+      Rscript -e '
+        library(testthat)
+        options(testthat.output_file = file.path(Sys.getenv("CI_PROJECT_DIR"), "test-out.xml"))
+        test_local(reporter = "junit")'
+    - |
+      Rscript -e '
+        x <- covr::package_coverage()
+        covr::to_cobertura(x)
+        x'
   artifacts:
     when: always
-    expire_in: 1 week
+    expire_in: 1 hour
     paths: 
       - test-out.xml
     reports:
@@ -93,33 +111,39 @@ longtest:
     - if: $RUN_LONG_TESTS == "FALSE"
       when: always
     - when: never
-
+  artifacts:
+    expire_in: 5 minutes
+
 pages:
   stage: end
   dependencies:
     - build-image
     - buildcheck
   script:
-    - Rscript -e 'devtools::install(quick = TRUE, upgrade = "never")'
-    - Rscript -e 'pkgdown::build_site(override = list(destination = "public"))'
-    - Rscript -e 'file.copy(from = "./public/articles/logo.png", to = "./public/reference/logo.png")'
+    - |
+      Rscript -e '
+        source_file <- list.files()[grep(".tar.gz", list.files())]
+        install.packages(source_file, type = "source", dependencies = FALSE)
+        pkgdown::build_site(override = list(destination = "public"))
+        file.copy(from = "./public/articles/logo.png", to = "./public/reference/logo.png")'
     - quarto render
-
   artifacts:
     paths:
       - $PAGES_OUTDIR
-    expire_in: 1 week
+    expire_in: 1 hour
 
 Validate Inventory:
-    stage: end
-    only: 
-      - main
-    image: ${INTERNAL_REGISTRY}software/software-management:latest
-    script:
-      - software-management review
-        --project "${CI_PROJECT_PATH}"
-        --ref "${CI_COMMIT_BRANCH}"
-        --type "provisional"
-        --token "${GIT_TOKEN_CUSTOM}"
-    tags:
-        - chs-shared
+  stage: end
+  only: 
+    - main
+  image: ${INTERNAL_REGISTRY}software/software-management:latest
+  script:
+    - software-management review
+      --project "${CI_PROJECT_PATH}"
+      --ref "${CI_COMMIT_BRANCH}"
+      --type "provisional"
+      --token "${GIT_TOKEN_CUSTOM}"
+  tags:
+      - chs-shared
+  artifacts:
+    expire_in: 5 minutes

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: dataRetrieval
 Type: Package
 Title: Retrieval Functions for USGS and EPA Hydrology and Water Quality Data
-Version: 2.7.24
+Version: 2.7.25
 Authors@R: c(
     person("Laura", "DeCicco", role = c("aut","cre"),
             email = "ldecicco@usgs.gov",
@@ -68,5 +68,5 @@ Encoding: UTF-8
 BuildVignettes: true
 VignetteBuilder: knitr
 BugReports: https://github.com/DOI-USGS/dataRetrieval/issues
-RoxygenNote: 7.3.3
 Roxygen: list(markdown = TRUE)
+Config/roxygen2/version: 8.0.0

NAMESPACE

@@ -55,6 +55,8 @@ export(read_waterdata_latest_daily)
 export(read_waterdata_metadata)
 export(read_waterdata_monitoring_location)
 export(read_waterdata_parameter_codes)
+export(read_waterdata_peaks)
+export(read_waterdata_ratings)
 export(read_waterdata_samples)
 export(read_waterdata_stats_daterange)
 export(read_waterdata_stats_por)

NEWS

@@ -1,3 +1,28 @@
+dataRetrieval 2.7.25
+===================
+* Added read_waterdata_ratings to access USGS rating curves with
+new modern endpoint.
+* Added read_waterdata_peaks to access USGS peak data with
+new modern endpoint.
+* Increase flexibility of chunking by monitoring_location_id by 
+including it as an argument in each relevant waterdata OGC function.
+* Clean up deprecated code.
+* Updated retry strategy to include retry_on_failure = TRUE.
+* Added countries, methods, method-categories, method-citations, and
+citations to possible values in read_waterdata_metadata.
+* Added field_measurements_series_id argument to read_waterdata_field_measurement
+* Removed NWIS tests
+* Introduce an error if user inputs a numeric to any of the "time" arguments.
+Because it is impossible to tell if they intended Dates or POSIX, we cannot
+know for sure and therefore could add incorrect filters to the query.
+* The "id" column that comes back from read_waterdata_fiel_meta was changed to
+field_measurements_series_id to match the expectation of `read_waterdata_field_measurements`
+* New argument added to read_waterdata_stats_por: "normal_type" accepts
+"DOY" and "MOY"
+* New argument added to read_waterdata_stats_daterange: "interval_type" accepts
+"M" (month), "CY" (calendar year), and "WY" (water year).
+
+
 dataRetrieval 2.7.24
 ===================
 * Let dataRetrieval take care of chunking up requests by monitoring_location_id.

R/AAA.R

@@ -7,6 +7,11 @@ pkg.env <- new.env()
   options("dataRetrieval.api_version" = "v0")
   options("dataRetrieval.api_version_stat" = "v0")
   options("dataRetrieval.attach_request" = TRUE)
+  options("dataRetrieval.convertType" = TRUE)
+  options("dataRetrieval.no_paging" = FALSE)
+  options("dataRetrieval.site_chunk_size_meta" = 250)
+  options("dataRetrieval.site_chunk_size_data" = 10)
+  options("dataRetrieval.limit" = 50000)
 
   services <- c(
     "server",
@@ -19,7 +24,8 @@ pkg.env <- new.env()
     "continuous",
     "field-measurements-metadata",
     "combined-metadata",
-    "channel-measurements"
+    "channel-measurements",
+    "peaks"
   )
   collections <- c(
     "parameter-codes",
@@ -32,7 +38,12 @@ pkg.env <- new.env()
     "coordinate-method-codes",
     "medium-codes",
     "counties",
+    "countries",
     "hydrologic-unit-codes",
+    "methods",
+    "method-categories",
+    "method-citations",
+    "citations",
     "states",
     "national-aquifer-codes",
     "reliability-codes",
@@ -52,7 +63,12 @@ pkg.env <- new.env()
     "coordinate_method_code",
     "medium_code",
     "county",
+    "country",
     "hydrologic_unit_code",
+    "methods",
+    "method_categories",
+    "method_citations",
+    "citations",
     "state",
     "national_aquifer_code",
     "reliability_code",
@@ -90,20 +106,6 @@ wqp_message_beta <- function() {
   message("WQX3 services are in-development, use with caution.")
 }
 
-only_legacy <- function(service) {
-  legacy <- service %in%
-    c(
-      "Organization",
-      "ActivityMetric",
-      "SiteSummary",
-      "Project",
-      "ProjectMonitoringLocationWeighting",
-      "ResultDetectionQuantitationLimit",
-      "BiologicalMetric"
-    )
-  return(legacy)
-}
-
 is_legacy <- function(service) {
   legacy <- service %in%
     c(

R/constructNWISURL.R

@@ -144,26 +144,6 @@ constructNWISURL <- function(
         url <- get_or_post(url, POST = POST, end_date = endDate)
       }
     },
-    measurements = {
-      url <- get_or_post(
-        baseURL,
-        POST = POST,
-        site_no = siteNumbers,
-        .multi = "comma"
-      )
-      url <- get_or_post(url, POST = POST, range_selection = "date_range")
-      if (nzchar(startDate)) {
-        url <- get_or_post(url, POST = POST, begin_date = startDate)
-      }
-      if (nzchar(endDate)) {
-        url <- get_or_post(url, POST = POST, end_date = endDate)
-      }
-      if (expanded) {
-        url <- get_or_post(url, POST = POST, format = "rdb_expanded")
-      } else {
-        url <- get_or_post(url, POST = POST, format = "rdb")
-      }
-    },
     stat = {
       # for statistics service