Merge pull request #87 from ldecicco-USGS/main

Fix colors
DOI-USGS · May 16, 2024 · e1d6ce2 · e1d6ce2
2 parents 81c7fb8 + b55c213
commit e1d6ce2
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Showing 6 changed files with 128 additions and 62 deletions.
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -1,7 +1,10 @@
-image: ${CI_DEPENDENCY_PROXY_GROUP_IMAGE_PREFIX}/rocker/geospatial@sha256:d09a38602a306da8ac3e90beed95cf0b30e0f69aca1432379e65e62de9a4db3e
-
+workflow:
+  rules:
+    - if: $CI_COMMIT_TAG
+    - if: $CI_COMMIT_BRANCH
+
 stages:
-  - getready
+  - build
   - check
   - test
   - end
@@ -25,55 +28,62 @@ variables:
   GITHUB_PAT: $GITHUB_PAT
   PAGES_OUTDIR: "$CI_PROJECT_DIR/public"
 
-cache:
-  key: ${CI_JOB_NAME}
-  paths:
-    - $R_LIBS_USER
-
-getready:
-  stage: getready
+build-image:
+  stage: build
+  image: ${DEVOPS_REGISTRY}usgs/docker:20
+  services:
+  - name: ${DEVOPS_REGISTRY}usgs/docker:20-dind
+    alias: docker
+  rules:
+    - changes:
+      - docker/Dockerfile
+      - .gitlab-ci.yml
   script:
-    - mkdir -p $R_LIBS_USER
-    - mkdir -p $APT_CACHE
-    - echo "options(Ncpus=$(nproc --all), repos=c(CRAN='$CRAN'))" >> $R_PROFILE
-    - Rscript -e "install.packages(c('devtools','pkgdown', 'connectapi', 'vctrs'))"
-  cache:
-    paths:
-     - $R_LIBS_USER
-  artifacts:
-    paths:
-     - $R_LIBS_USER
+    - 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 ${CI_REGISTRY_IMAGE}:BUILD_${CI_COMMIT_SHORT_SHA}
+        -t ${CI_REGISTRY_IMAGE}:latest
+        .
+    # If this is building a git tag, create the corresponding docker tag
+    - if [ -n "${CI_COMMIT_TAG}" ]; then docker tag ${CI_REGISTRY_IMAGE}:BUILD_${CI_COMMIT_SHORT_SHA} ${CI_REGISTRY_IMAGE}:${CI_COMMIT_TAG}; fi
+    - docker push --all-tags ${CI_REGISTRY_IMAGE}
 
 buildcheck:
   stage: check
+  image: ${CI_REGISTRY_IMAGE}:latest
+  dependencies:
+    - build-image
   script:
-    - mkdir -p $BUILD_LOGS_DIR
-    - apt-get update
-    - apt-get -o dir::cache::archives=${APT_CACHE} install -y --no-install-recommends qpdf pandoc pandoc-citeproc
     - R CMD build . --no-build-vignettes --no-manual
     - R -e 'devtools::check(document = FALSE, args = "--no-tests", error_on = "error", check_dir = Sys.getenv("BUILD_LOGS_DIR"))'
   artifacts:
+    expire_in: 1 week
     paths:
       - $BUILD_LOGS_DIR
 
 unittests:
   stage: test
+  image: ${CI_REGISTRY_IMAGE}:latest
   dependencies:
-    - getready
+    - 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")'
   artifacts:
     when: always
+    expire_in: 1 week
     paths: 
       - test-out.xml
     reports:
       junit: test-out.xml
 
 covertests:
   stage: test
+  image: ${CI_REGISTRY_IMAGE}:latest
   dependencies:
-    - getready
+    - build-image
     - buildcheck
   script:
     - R -e 'x <- covr::package_coverage(); covr::to_cobertura(x); x; '
@@ -82,10 +92,12 @@ covertests:
       coverage_report:
         coverage_format: cobertura
         path: cobertura.xml
+    expire_in: 1 week
   coverage: '/Coverage: \d+.\d+\%/'
 
 pages:
   stage: end
+  image: ${CI_REGISTRY_IMAGE}:latest
   only: 
     - main
   script:

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: HASP
 Type: Package
 Title: Hydrologic AnalySis Package
-Version: 1.0.2
+Version: 1.0.3
 Authors@R: c(person("Laura", "DeCicco", 
                      role = c("aut", "cre"),
                      email = "ldecicco@usgs.gov",

diff --git a/NEWS b/NEWS
@@ -1,3 +1,7 @@
+HASP 1.0.3
+===========
+* Fix some color options in monthly plot
+
 HASP 1.0.2
 ===========
 * Minor bug fix that happens in the first week of the year

diff --git a/R/frequency_analysis.R b/R/frequency_analysis.R
@@ -274,11 +274,11 @@ stats_by_interval <- function(interval,
 #'                                                  plot_title = "L2701 Groundwater Level",
 #'                                                  flip = TRUE,
 #'                                                  percentile_colors = c(
-#'                                                      "#d7191c",
-#'                                                      "#fdae61",
-#'                                                      "#ffffbf",
-#'                                                      "#abdda4",
-#'                                                      "#2b83ba"
+#'                                                      "red",
+#'                                                      "yellow",
+#'                                                      "green",
+#'                                                      "blue",
+#'                                                      "orange"
 #'                                                  ))
 #'                                                  
 #' monthly_frequency_custom_colors
@@ -288,7 +288,7 @@ stats_by_interval <- function(interval,
 #'                                                       parameter_cd = "62610",
 #'                                                       y_axis_label = label,
 #'                                                       plot_title = "L2701 Groundwater Level",
-#'                                                       flip = TRUE,
+#'                                                       flip = FALSE,
 #'                                                       include_edges = TRUE)
 #' monthly_frequency_edge_bins
 #' 
@@ -381,13 +381,26 @@ monthly_frequency_plot <- function(gw_level_dv,
                c("p75", "p90"), c("p90", "p95"))
   groups <- c("5 - 10", "10 - 25", "25 - 75", "75 - 90", "90 - 95")
   # define default colors
-  color_list <- c("firebrick3", "orange2", "green2", "steelblue1", "blue")
-  # set plot colors and markers
-  rectangle_colors <- c("5 - 10" = color_list[1],
-                        "10 - 25" = color_list[2],
-                        "25 - 75" = color_list[3],
-                        "75 - 90" = color_list[4],
-                        "90 - 95" = color_list[5])
+
+  color_list <- c("darkred", "orange2", "green2", "steelblue1", "blue")
+
+  if(include_edges){
+    color_list <- c("firebrick3", color_list, "darkblue")
+  } 
+
+  # custom colors and shapes
+  if (length(percentile_colors) >= 5) {
+    color_list <- percentile_colors
+  } else if (is.na(percentile_colors) == FALSE) {
+    warning(
+      paste0(
+        "percentile_colors argument was provided but was invalid,",
+        " should be a vector of length 5 or 7 in which each item in",
+        " the vector represents a color."
+      )
+    )
+  }
+
   # set scale breaks
   scale_breaks <- c("90 - 95",
                     "75 - 90",
@@ -408,16 +421,27 @@ monthly_frequency_plot <- function(gw_level_dv,
     cols <- append(cols, list(c("p95", "maxMed")))
     groups <- c("0 - 5", groups, "95 - 100")
     # expand color list
-    color_list <- c("darkred", color_list, "darkblue")
+
     # expand rectangle colors
     rectangle_colors <- c("0 - 5" = color_list[1],
-                          rectangle_colors,
+                          "5 - 10" = color_list[2],
+                          "10 - 25" = color_list[3],
+                          "25 - 75" = color_list[4],
+                          "75 - 90" = color_list[5],
+                          "90 - 95" = color_list[6],
                           "95 - 100" = color_list[7])
     # expand the scale breaks
     scale_breaks <- c("95 - 100",
                       scale_breaks,
                       "0 - 5")
-  }  
+  } else {
+    # set plot colors and markers
+    rectangle_colors <- c("5 - 10" = color_list[1],
+                          "10 - 25" = color_list[2],
+                          "25 - 75" = color_list[3],
+                          "75 - 90" = color_list[4],
+                          "90 - 95" = color_list[5])
+  }
 
   plot_list <- data.frame()
 
@@ -460,19 +484,6 @@ monthly_frequency_plot <- function(gw_level_dv,
                                     points_plot)
   }
 
-  # custom colors and shapes
-  if (length(percentile_colors) >= 5) {
-    color_list <- percentile_colors
-  } else if (is.na(percentile_colors) == FALSE) {
-    warning(
-      paste0(
-        "percentile_colors argument was provided but was invalid,",
-        " should be a vector of length 5 or 7 in which each item in",
-        " the vector represents a color."
-      )
-    )
-  }
-
   point_shapes <- c("Monthly median" = 17,
                     "Data point" = 18)
   point_colors <- c("Monthly median" = "black",
@@ -508,7 +519,8 @@ monthly_frequency_plot <- function(gw_level_dv,
                    x = month,
                    y = value,
                    shape = group,
-                   color = group
+                   color = group,
+                   size = group
                  ))
   }
 

diff --git a/docker/Dockerfile b/docker/Dockerfile
@@ -0,0 +1,38 @@
+FROM code.chs.usgs.gov:5001/ctek/docker/r-lang/r-base:4.4
+
+# Necessary R libraries
+RUN apt-get update -qq && apt-get -y --no-install-recommends install \
+  r-cran-dataretrieval \
+  r-cran-devtools \
+  r-cran-connectapi \
+  r-cran-covr \
+  r-cran-tidyverse \
+  r-cran-ggpp \
+  r-cran-scales \
+  r-cran-ggpmisc \
+  r-cran-checkmate \
+  r-cran-whisker \
+  r-cran-xfun \
+  r-cran-usethis \
+  r-cran-envstats \
+  r-cran-readxl \
+  r-cran-shiny \
+  r-cran-shinycssloaders \
+  r-cran-shinydashboard \
+  r-cran-shinyace \
+  r-cran-openxlsx \
+  r-cran-oce \
+  r-cran-kableextra \
+  r-cran-dt \
+  r-cran-leaflet \
+  r-cran-rkt \
+  r-cran-zyp \
+  r-cran-plotly \
+  r-cran-rlang \
+  r-cran-knitr \
+  r-cran-waterdata \
+  r-cran-rsconnect \
+  && rm -rf /var/lib/apt/lists/*
+
+
+
diff --git a/man/monthly_frequency_plot.Rd b/man/monthly_frequency_plot.Rd