Add tzone attribute to all time columns

.Rbuildignore

@@ -73,3 +73,7 @@ vignettes/Reference_Lists.Rmd
 environment.yml
 ^\.positai$
 ^\.claude$
+requirements.txt
+^\.venv$
+.env
+

.gitignore

@@ -18,3 +18,5 @@ vignettes/*.R
 /.quarto/
 **/*.quarto_ipynb
 .positai
+/.venv/
+/.env/

.gitlab-ci.yml

@@ -8,7 +8,6 @@ workflow:
 default:
   tags:
     - chs-shared
-    - dind
 
 stages:
   - build
@@ -36,9 +35,12 @@ 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
   script:
     - echo ${CI_REGISTRY_PASSWORD} | docker login -u ${CI_REGISTRY_USER} --password-stdin $CI_REGISTRY

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: dataRetrieval
 Type: Package
 Title: Retrieval Functions for USGS and EPA Hydrology and Water Quality Data
-Version: 2.7.24.9001
+Version: 2.7.25
 Authors@R: c(
     person("Laura", "DeCicco", role = c("aut","cre"),
             email = "ldecicco@usgs.gov",

NEWS

@@ -17,7 +17,10 @@ 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

R/construct_api_requests.R

@@ -67,16 +67,6 @@ construct_api_requests <- function(
     skipGeometry = full_list[["skipGeometry"]]
   )
 
-  time_periods <- c(
-    "last_modified",
-    "datetime",
-    "time",
-    "begin",
-    "end",
-    "begin_utc",
-    "end_utc"
-  )
-
   full_list <- switch_arg_id(
     full_list,
     id_name = output_id,
@@ -655,3 +645,14 @@ add_api_token <- function(req) {
   }
   req
 }
+
+# Treat these columns as time:
+time_periods <- c(
+  "last_modified",
+  "datetime",
+  "time",
+  "begin",
+  "end",
+  "begin_utc",
+  "end_utc"
+)

R/read_waterdata_combined_meta.R

@@ -121,6 +121,14 @@
 #'                          monitoring_location_id = hucs$monitoring_location_id
 #' )
 #'
+#' # Query for instantaneous nitrate data for sites in Iowa
+#' sites_inst <- read_waterdata_combined_meta(
+#'   monitoring_location_id = "USGS-05418400",
+#'   parameter_code = "00065"
+#' )
+#'
+#' # parse individual thresholds lists:
+#' threshold_1 <- jsonlite::fromJSON(sites_inst$thresholds[1])
 #'
 #' }
 read_waterdata_combined_meta <- function(

R/read_waterdata_peaks.R

@@ -27,6 +27,11 @@
 #' `r dataRetrieval:::get_properties_for_docs("peaks", "peak_id")`.
 #' The default (`NA`) will return all columns of the data.
 #'
+#' @param allow_incomplete_dates Logical whether to allow incomplete dates
+#' in the "time" column to be converted to date objects (`TRUE`), or whether
+#' to use the available year, month, day to get a character date only using
+#' known values (`FALSE`). Default is `FALSE`. If `FALSE` but all dates are
+#' complete the "time" column will remain a Date object.
 #' @inheritParams check_arguments_api
 #' @inheritParams check_arguments_non_api
 #'
@@ -45,6 +50,10 @@
 #'                monitoring_location_id = wi_peaks$monitoring_location_id[1],
 #'                parameter_code = "00060")
 #'
+#' incomplete_dates <- read_waterdata_peaks(
+#'                monitoring_location_id = "USGS-06334330",
+#'                parameter_code = "00060")
+#'
 #' }
 read_waterdata_peaks <- function(
   monitoring_location_id = NA_character_,
@@ -64,6 +73,7 @@ read_waterdata_peaks <- function(
   time = NA_character_,
   bbox = NA,
   ...,
+  allow_incomplete_dates = FALSE,
   convertType = getOption("dataRetrieval.convertType"),
   no_paging = getOption("dataRetrieval.no_paging"),
   chunk_size = getOption("dataRetrieval.site_chunk_size_meta"),
@@ -75,7 +85,27 @@ read_waterdata_peaks <- function(
   rlang::check_dots_empty()
 
   args <- mget(names(formals()))
+  args[["allow_incomplete_dates"]] <- NULL
   return_list <- get_ogc_data(args, output_id, service)
 
+  if (anyNA(return_list[, c("year", "month", "day")])) {
+    if (allow_incomplete_dates) {
+      warning("Incomplete dates are included in time column.")
+    } else {
+      parse_time <- as.character(return_list$year)
+      parse_time[!is.na(return_list$month)] <- paste(
+        parse_time[!is.na(return_list$month)],
+        zeroPad(return_list$month[!is.na(return_list$month)], 2),
+        sep = "-"
+      )
+      parse_time[!is.na(return_list$day)] <- paste(
+        parse_time[!is.na(return_list$day)],
+        zeroPad(return_list$day[!is.na(return_list$day)], 2),
+        sep = "-"
+      )
+      return_list$time <- parse_time
+    }
+  }
+
   return(return_list)
 }

R/rejigger_cols.R

@@ -64,15 +64,17 @@ rejigger_cols <- function(df, properties, output_id) {
 #'
 cleanup_cols <- function(df, service) {
   if ("time" %in% names(df)) {
-    if (service == "daily") {
+    if (service %in% c("daily", "peaks")) {
       df$time <- as.Date(df$time)
     } else {
       attr(df$time, "tzone") <- "UTC"
     }
   }
 
-  if ("last_modified" %in% names(df)) {
-    attr(df$last_modified, "tzone") <- "UTC"
+  for (time_period_columns in time_periods) {
+    if (time_period_columns %in% names(df)) {
+      attr(df[[time_period_columns]], "tzone") <- "UTC"
+    }
   }
 
   df

docker/Dockerfile

@@ -1,8 +1,4 @@
-FROM code.chs.usgs.gov:5001/ctek/docker/r-lang/r-base:4.5
-
-# Disable the annoying bell on WSL2
-RUN sed -i 's/^# set bell-style none$/set bell-style none/' /etc/inputrc
-RUN echo 'set visualbell' >> /root/.vimrc
+FROM code.chs.usgs.gov:5001/ctek/docker/r-lang/r-base:4.6
 
 # Change the name of this environment to something which pleases you, if you
 # so please. But the name will not be relevant for most cases, as reticulate

inst/CITATION

@@ -37,9 +37,9 @@ bibentry(bibtype = "Manual",
   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 = "2.7.24",
+  version = "2.7.25",
   institution = "U.S. Geological Survey",
   year = 2026,
   doi = "10.5066/P9X4L3GE",
-  textVersion = "De Cicco, L.A., Hirsch, R.M., Lorenz, D., Watkins, W.D., Johnson, M., Blodgett, D.L., Hinman, E.D., Zemmels, J., 2026, dataRetrieval: R packages for discovering and retrieving water data available from Federal hydrologic web services, v.2.7.24, doi:10.5066/P9X4L3GE"
+  textVersion = "De Cicco, L.A., Hirsch, R.M., Lorenz, D., Watkins, W.D., Johnson, M., Blodgett, D.L., Hinman, E.D., Zemmels, J., 2026, dataRetrieval: R packages for discovering and retrieving water data available from Federal hydrologic web services, v.2.7.25, doi:10.5066/P9X4L3GE"
 )

tutorials/basic_slides_deck.qmd

@@ -201,7 +201,7 @@ or
 ```{bash}
 #| echo: true
 #| eval: false
-conda -c conda-forge install dataretrieval
+conda install conda-forge::dataretrieval
 ```
 
 Then each time you open Python, you'll need to load the library:
@@ -734,8 +734,6 @@ qw_data <- read_waterdata_samples(
 ncol(qw_data)
 ```
 
-R generates a few POSIXct columns to combine date, time, timezone information.
-
 ### Python
 
 ```{python}
@@ -1323,8 +1321,10 @@ ts_available <- read_waterdata_ts_meta(monitoring_location_id = "USGS-04183500")
 ### Python
 
 ```{python}
-#| eval: !expr evaluate_python
-ts_avail, ts_me = waterdata.get_time_series_metadata(monitoring_location_id="USGS-04183500")
+#| eval: false
+ts_avail, ts_me = waterdata.get_time_series_metadata(
+    monitoring_location_id="USGS-04183500"
+)
 ```
 
 :::

tutorials/quick_intro_deck.qmd

@@ -157,7 +157,7 @@ pip install dataretrieval
 ```{bash}
 #| echo: true
 #| eval: false
-conda -c conda-forge install dataretrieval
+conda install conda-forge::dataretrieval
 ```
 
 Then each time you open Python, you'll need to load the library:

vignettes/Contributing.Rmd

@@ -400,6 +400,31 @@ conda activate pyclass
 ```
 The slides will use the R package `reticulate` to manage flipping back and forth between R and Python. To help `reticulate` know where Python is installed, you will need to add an envionmnental variable to your .Renviorn file "RETICULATE_PYTHON". Run `usethis::edit_r_environ()`, then add the path to your Python installation, and restart R. RStudio can render both the R and Python in the Quarto slides. However, if you want to do troubleshooting on individual code chunks, you might want to switch to Positron which allows seamless transition between R and Python consoles.
 
+Let's say you need to update to a new version of dataretrieval:
+
+1. Open the Miniforge prompt
+
+2. Navigate to dataRetrieval directory
+
+3. Activate pyclass:
+```
+conda activate pyclass
+```
+
+4. Update package:
+```
+conda install conda-forge::dataretrieval
+```
+
+5. Restart your python session.
+
+
+Let's say you want to update all packages. In step 4 above, run:
+```
+mamba update
+```
+
+
 
 # References