additional message/notification/text display handling and other minor bug and formatting fixes

.github/dependabot.yaml

@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "monthly"

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

@@ -2,7 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: main
+    branches: [main]
   pull_request:
     branches: main
   # allow manual action trigger
@@ -37,7 +37,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/format-batch-update.yaml

@@ -0,0 +1,28 @@
+# Workflow derived from https://github.com/posit-dev/setup-air/tree/main/examples
+name: format-update
+
+on:
+  # This workflow is run manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  format-update:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          ref: ${{ github.head_ref }}
+
+      - name: Install
+        uses: posit-dev/setup-air@v1
+
+      - name: Format
+        run: air format .
+
+      - name: commit updates
+        uses: EndBug/add-and-commit@v9
+        with:
+          author_name: 'github-actions[bot]'
+          author_email: 'github-actions[bot]@users.noreply.github.com'
+          message: "air formatting"

.github/workflows/spellcheck-package.yaml

@@ -0,0 +1,34 @@
+on:
+  push:
+    branches: [develop]
+  pull_request:
+    branches: develop
+
+name: spelling-check
+
+jobs:
+  spelling-check:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install spellchecker
+        run: install.packages("spelling")
+        shell: Rscript {0}
+
+      - name: Spellcheck root directory (include vignettes)
+        id: spellcheck # Assign ID to this step for output
+        run: |
+          result <- spelling::spell_check_package()
+          result
+          if (length(result[[1]]) != 0) {
+            stop("Spelling errors found (fix or add to WORDLIST)")
+          }
+        shell: Rscript {0}

.github/workflows/test-coverage.yaml

@@ -8,31 +8,53 @@ on:
 
 name: test-coverage
 
+permissions:
+  contents: write
+  checks: write
+  pull-requests: write
+
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
+      - name: Capture Environment Info
+        run: |
+          Rscript -e '
+            env_vars <- Sys.getenv()
+            pkg_versions <- installed.packages()[, c("Package", "Version")]
+            sys_info <- Sys.info()
+            save(env_vars, pkg_versions, sys_info, file = "ci_env_info.RData")
+          '
+
+      - name: Upload Environment Info
+        uses: actions/upload-artifact@v6
+        with:
+          name: ci_env_info
+          path: ci_env_info.RData
+
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
             install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          print(cov)
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
       - name: Show testthat output
@@ -44,8 +66,23 @@ jobs:
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v6
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package
           if-no-files-found: ignore  # Suppress warnings if no files are found
+
+      - name: Upload coverage report
+        uses: actions/upload-artifact@v6
+        with:
+          name: coverage-report
+          path: ./cobertura.xml
+
+      - name: Comment coverage
+        uses: 5monkeys/cobertura-action@master
+        with:
+          report_name: coverage-report
+          path: ./cobertura.xml
+          minimum_coverage: 10
+          show_missing: true
+          link_missing_lines: true

DESCRIPTION

@@ -15,15 +15,15 @@ License: CC0
 URL: https://github.com/USEPA/TADAShinyAnalyze
 BugReports: https://github.com/USEPA/TADAShinyAnalyze/issues
 Imports: 
+    stats,
     config,
-    dplyr,
+    dplyr (>= 1.1.0),
     EPATADA,
+    TADACommunityHub,
     golem,
     gotop,
     htmltools,
     leaflet,
-    pkgload,
-    sf,
     shiny,
     shinyjs,
     utils,
@@ -42,15 +42,19 @@ Imports:
     readr,
     httr,
     slider,
-    rExpertQuery
+    rExpertQuery,
+    graphics
 Remotes:
-    USEPA/EPATADA@develop
+    USEPA/EPATADA,
+    USEPA/TADACommunityHub,
+    USEPA/rExpertQuery
 Suggests: 
     spelling,
     testthat (>= 3.0.0)
+Depends: 
+    R (>= 4.1.0)
 Config/testthat/edition: 3
 Encoding: UTF-8
 Language: en-US
 LazyData: true
 RoxygenNote: 7.3.3
-StagedInstall: FALSE

R/fct_helpers.R

@@ -19,7 +19,8 @@ criteria_join <- function(x, y, match_type = "Option 2",
       -TADA.MethodSpeciationName,
       -TADA.ComparableDataIdentifier
     ) |>
-    dplyr::mutate(dplyr::across(dplyr::any_of("TADA.ResultSampleFractionText"), as.character)) # temp solution, consider removing after TADA updates
+    EPATADA::TADA_CorrectColType()
+    #dplyr::mutate(dplyr::across(dplyr::any_of("TADA.ResultSampleFractionText"), as.character)) # temp solution, consider removing after TADA updates
 
   # Build join expression as a string
   join_cols <- c(
@@ -93,7 +94,7 @@ pH_join <- function(x, y){
 
   by <- dplyr::join_by(TADA.MonitoringLocationIdentifier, TADA.MonitoringLocationTypeName,
                        TADA.LatitudeMeasure, TADA.LongitudeMeasure,
-                       dplyr::closest(DateTime >= DateTime_lower), 
+                       closest(DateTime >= DateTime_lower), 
                        closest(DateTime <= DateTime_upper))
 
   x2 <- x |>
@@ -135,7 +136,7 @@ temp_join <- function(x, y){
 
   by <- dplyr::join_by(TADA.MonitoringLocationIdentifier, TADA.MonitoringLocationTypeName,
                        TADA.LatitudeMeasure, TADA.LongitudeMeasure,
-                       dplyr::closest(DateTime >= DateTime_lower), 
+                       closest(DateTime >= DateTime_lower), 
                        closest(DateTime <= DateTime_upper))
 
   x2 <- x |>
@@ -276,7 +277,7 @@ excursion_summary <- function(x, type){
                      Start_Date = min(ActivityStartDate, na.rm = TRUE),
                      End_Date = max(ActivityStartDate, na.rm = TRUE),
                      Minimum = min(TADA.ResultMeasureValue, na.rm = TRUE),
-                     Median = median(TADA.ResultMeasureValue, na.rm = TRUE),
+                     Median = stats::median(TADA.ResultMeasureValue, na.rm = TRUE),
                      Maximum = max(TADA.ResultMeasureValue, na.rm = TRUE),
                      Number_of_Excursions = modSum(Excursion),
                      .groups = "drop") |>
@@ -1232,7 +1233,7 @@ frequency_summary <- function(x, type){
     x_P2 <- x_P |>
       dplyr::group_by(dplyr::across(dplyr::all_of(id_cols2))) |>
       dplyr::mutate(FreqValue = FreqValue/100) |>
-      dplyr::mutate(Percentile = quantile(Result_Duration,
+      dplyr::mutate(Percentile = stats::quantile(Result_Duration,
                                           probs = dplyr::first(FreqValue))) |>
       dplyr::mutate(E_Value = Percentile) |>
       dplyr::ungroup()
@@ -1468,8 +1469,8 @@ window_before_period <- function(unit, value) {
   if (is.na(unit)) unit <- "n-day"
   if (unit == "n-hour")   return(lubridate::hours(max(value, 1) - 1))
   if (unit == "n-day")    return(lubridate::days(max(value, 1) - 1))
-  if (unit == "n-month")  return(lubridate::months(max(value, 1)) - lubridate::days(1))
-  if (unit == "n-season") return(lubridate::months(3L * max(value, 1)) - lubridate::days(1))
+  if (unit == "n-month")  return(months(max(value, 1)) - lubridate::days(1))
+  if (unit == "n-season") return(months(3L * max(value, 1)) - lubridate::days(1))
   lubridate::days(max(value, 1) - 1)
 }
 

R/mod_analysis_plots.R

@@ -435,8 +435,8 @@ mod_analysis_plots_server <- function(id,
 
       # Check if there's data to plot
       if(nrow(filtered_data4()) == 0) {
-        plot.new()
-        text(0.5, 0.5, "No data available for selected filters", 
+        graphics::plot.new()
+        graphics::text(0.5, 0.5, "No data available for selected filters", 
              cex = 1.2, col = "gray50")
         return(NULL)
       }
@@ -564,7 +564,7 @@ mod_analysis_plots_server <- function(id,
 
       # Helper: line type from AcuteChronic
       get_linetype <- function(vals) {
-        typ <- unique(tolower(na.omit(vals)))
+        typ <- unique(tolower(stats::na.omit(vals)))
         if ("acute" %in% typ) return("dotted")
         if ("chronic" %in% typ) return("dashed")
         return("solid")

R/mod_batch_analysis.R

@@ -794,6 +794,10 @@ mod_batch_analysis_server <- function(id, tadat){
       # Get selected locations - if NULL or empty, use all locations
       selected_locs <- tadat$selected_monitoring_locations
 
+      if (is.null(selected_locs) || length(selected_locs) == 0) {
+        # No selection - set to NULL to show empty state
+        tadat$exceedance_summary2 <- NULL
+      } else{
       # Filter based on location type for the exceedance results
       if (tadat$loc_select %in% "MLid") {
         exceedance_summary2 <- tadat$exceed_summary |>
@@ -806,7 +810,7 @@ mod_batch_analysis_server <- function(id, tadat){
 
         exceedance_summary2 <- tadat$exceed_summary |>
           dplyr::filter(ATTAINS.AssessmentUnitIdentifier %in% selected_aus)
-      }
+      }}
 
       # Handle NULL or empty parameter filter
       if (is.null(input$parameter_filter) || length(input$parameter_filter) == 0) {