Merge pull request #106 from pharmaverse/Enhancement-implement-CI-wor…

…kflows-based-on-admiralci

Enhancement: implemented relevant CI workflows from admiralci

.github/workflows/main.yml

@@ -0,0 +1,80 @@
+# Source: https://github.com/pharmaverse/admiralci
+# Stripped down version of admiralci checks. Good for
+# the developement process. When package is ready to
+# be published, revisit and add release-related
+# workflows.
+name: admiral CI/CD Workflows
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+concurrency:
+  group: admiral-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  R_VERSION: "release"
+
+jobs:
+  get_r_version:
+    name: Get R version
+    runs-on: ubuntu-latest
+    outputs:
+      r-version: ${{ steps.get_r_version.outputs.R_VERSION }}
+    steps:
+      - name: Get R Version for Downstream Container Jobs
+        id: get_r_version
+        run: echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT
+        shell: bash
+  spellcheck:
+    name: Spelling
+    uses: pharmaverse/admiralci/.github/workflows/spellcheck.yml@main
+    if: github.event_name == 'pull_request'
+    needs: get_r_version
+    with:
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
+  linter:
+    name: Lint
+    uses: pharmaverse/admiralci/.github/workflows/lintr.yml@main
+    needs: get_r_version
+    if: github.event_name == 'pull_request'
+    with:
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
+  man-pages:
+    name: Man Pages
+    uses: pharmaverse/admiralci/.github/workflows/man-pages.yml@main
+    if: github.event_name == 'pull_request'
+    needs: get_r_version
+    with:
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
+  tests:
+    name: Tests
+    runs-on: ubuntu-latest
+    needs: get_r_version
+    container:
+      image: "ghcr.io/pharmaverse/admiralci-${{ needs.get_r_version.outputs.r-version }}:latest"
+    steps:
+        - name: Checkout code
+          uses: actions/checkout@v2
+
+        - name: Install dependencies
+          run: |
+            Rscript -e 'remotes::install_deps(dependencies = TRUE)'
+
+        - name: Run tests
+          shell: Rscript {0}
+          run: |
+            devtools::load_all(".")
+            devtools::test()
+  check:
+    name: Check
+    uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main
+    if: github.event_name == 'pull_request'
+    with:
+        error-on: error

.lintr

@@ -4,6 +4,7 @@ linters:
     object_name_linter = object_name_linter(
         styles = c("snake_case", "SNAKE_CASE")
     ),
-    object_usage_linter = NULL
+    object_usage_linter = NULL,
+    trailing_blank_lines_linter = NULL
   )
 encoding: "UTF-8"

DESCRIPTION

@@ -60,3 +60,4 @@ Suggests:
     lintr (>= 3.1.2),
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
+Language: en-US

NAMESPACE

@@ -6,6 +6,7 @@ export(as_factor_preserve_label)
 export(calculate_summary_stats)
 export(create_conc)
 export(create_dose)
+export(filter_breaks)
 export(flexible_violinboxplot)
 export(format_data)
 export(general_lineplot)
@@ -58,7 +59,10 @@ importFrom(ggplot2,geom_errorbar)
 importFrom(ggplot2,geom_line)
 importFrom(ggplot2,geom_point)
 importFrom(ggplot2,ggplot)
+importFrom(ggplot2,ggplot_build)
+importFrom(ggplot2,ggplot_gtable)
 importFrom(ggplot2,labs)
+importFrom(grid,convertUnit)
 importFrom(htmlwidgets,JS)
 importFrom(logger,log_debug)
 importFrom(logger,log_error)

R/calculate_summary_stats.R

@@ -3,7 +3,7 @@
 #' This function calculates various summary statistics for formatted output of PKNCA::pk.nca().
 #'
 #' @param input_groups A character vector specifying the columns to group by.
-#'                     Here. the hierachrical order matters
+#'                     Here. the hierarchical order matters
 #' @param res_pknca     A data frame containing results of
 #'                     Non Compartmental Analysis using PKNCA package
 #' @return A data frame with summary statistics for each group and parameter.

R/filter_breaks.R

@@ -16,11 +16,11 @@ filter_breaks <- function(breaks = NA,
                           plot = plot,
                           min_cm_distance = 0.5,
                           axis = "x") {
-  
+
   breaks <- unique(na.omit(sort(breaks)))
   plot_build <- ggplot_build(plot)
   plot_table <- ggplot_gtable(plot_build)
-  
+
   # Extract axis scale information
   if (axis == "x") {
     scale_range <- plot_build$layout$panel_params[[1]]$x.range
@@ -29,21 +29,23 @@ filter_breaks <- function(breaks = NA,
   } else {
     stop("Error: Invalid axis specified. Use 'x' or 'y'.")
   }
-  
+
   # Identify the panel grob
   panel_index <- which(sapply(plot_table$grobs,
                               function(x) grepl("panel", x$name)))
-  
+
   if (length(panel_index) == 0) {
     stop("Error: Panel grob not found.")
   }
   panel <- plot_table$grobs[[panel_index]]
-  
+
   # Extract the panel border grob to get the width or height
-  panel_border <- panel$children[[which(sapply(panel$children,
-                                               function(x) {
-                                                 grepl("panel.border", x$name)}))]]
-
+  panel_border <- panel$children[[
+    which(sapply(panel$children, function(x) {
+      grepl("panel.border", x$name)
+    }))
+  ]]
+
   # Convert panel width or height to cm
   if (axis == "x") {
     panel_size_cm <- grid::convertUnit(panel_border$width,
@@ -54,15 +56,15 @@ filter_breaks <- function(breaks = NA,
                                        unitTo =  "cm",
                                        valueOnly = TRUE)
   }
-  
+
   # Calculate the distance between breaks in cm
   break_distances <- diff(breaks) / diff(scale_range) * panel_size_cm
-  
+
   # Filter only breaks that satisfy the minimum distance
   filt_breaks <- breaks[1]
-  
+
   for (i in 2:length(breaks)) {
-    
+
     # Take latest selected break and calculate its distance
     b0 <- filt_breaks[length(filt_breaks)]
     bdist <- (breaks[i] - b0) / diff(scale_range) * panel_size_cm

R/general_lineplot.R

@@ -72,7 +72,7 @@ general_lineplot <- function(
       DOSEA = factor(DOSEA),
       id_var = interaction(!!!syms(colorby_var), sep = ", ")
     )
-  
+
   # If there are predose records duplicate them in the previous line so they are considered
   if ("ARRLT" %in% names(preprocessed_data) &&
         any(preprocessed_data$ARRLT < 0 & preprocessed_data$AFRLT > 0)) {
@@ -113,8 +113,7 @@ general_lineplot <- function(
   } else {
     "AFRLT"
   }
-
-
+
   plt <- tern::g_ipp(
     df = preprocessed_data,
     xvar = time,
@@ -139,21 +138,23 @@ general_lineplot <- function(
 
   if (xaxis_scale == "Log") {
     plt <- plt +
-      scale_y_continuous(trans = scales::pseudo_log_trans(base = 10, sigma = 1)) +   
+      scale_y_continuous(trans = scales::pseudo_log_trans(base = 10, sigma = 1)) +
       labs(y = paste0("Log 10 - ", plt$labels$y))
-    
+
     custom_label <- function(x) {
-      
+
       ifelse(x == 1e-3, 0, scales::trans_format("log10", scales::math_format(10^x)))
     }
-
-    plt <- plt %+% dplyr::mutate(preprocessed_data, AVAL = ifelse(AVAL == 1e-3, 0, AVAL)) %>% 
-      + 
-      scale_y_continuous(
-        trans = scales::pseudo_log_trans(base = 10, sigma = 1),
-        breaks = c(-Inf, 10^seq(from = -3, to = ceiling(log10(max(plt$data["AVAL"], na.rm = T))))) %>% 
-          filter_breaks(plot = plt, min_cm_distance = 20, axis = "y"),
-        labels = scales::trans_format("log10", scales::math_format(10^.x))
+
+    plt <- plt %+% dplyr::mutate(preprocessed_data, AVAL = ifelse(AVAL == 1e-3, 0, AVAL)) %>%
+      +
+        scale_y_continuous(
+          trans = scales::pseudo_log_trans(base = 10, sigma = 1),
+          breaks = c(
+            -Inf, 10^seq(from = -3, to = ceiling(log10(max(plt$data["AVAL"], na.rm = TRUE))))
+          ) %>%
+            filter_breaks(plot = plt, min_cm_distance = 20, axis = "y"),
+          labels = scales::trans_format("log10", scales::math_format(10^.x))
         )
   }
   return(plt)

R/imports.R

@@ -1,2 +1,2 @@
 #' @importFrom logger log_trace log_debug log_info log_warn log_error log_fatal
-NULL
+NULL

R/reshape_PKNCA_results.R

@@ -6,7 +6,7 @@
 #'
 #' @param res_nca The output of PKNCA::pk.nca
 #'
-#' @returns A data frame (finalres2) which provides an easy overview on the results from the NCA
+#' @returns A data frame which provides an easy overview on the results from the NCA
 #'          in each profile/subject and how it was computed lambda (half life) and the results
 #'          of the NCA parameters (cmax, AUC, AUClast)
 #'

R/zzz.R

@@ -4,4 +4,4 @@
   logger::log_formatter(logger::formatter_glue)
   logger::log_threshold(logger::TRACE)
   logger::log_appender(logger::appender_console, namespace = "global")
-}
+}

README.md

@@ -77,7 +77,7 @@ devtools::load_all()
 aNCA::run_app()
 ```
 
-Have fun running your tailored Non-Compartemental Analysis!
+Have fun running your tailored Non-Compartmental Analysis!
 
 <!--
 ## Contribute as developer

inst/WORDLIST

@@ -0,0 +1,40 @@
+ADNCA
+ADPP
+AFRLT
+AUClast
+AVAL
+BLQ
+Bärtschi
+CDISC
+DOSEA
+DOSNO
+EVID
+IQROUTE
+NCA
+PCSPEC
+PKNCA
+Pharmacokinetic
+Pre
+RO
+RStudio
+STUDYID
+USUBJID
+USUBJIDs
+analyte
+analytes
+anonymized
+anonymizes
+cmax
+csv
+ggplot
+nca
+pharmacokinetic
+pknca
+plotly
+pptest
+pre
+sas
+summarization
+timepoint
+visualizable
+xpt

inst/shiny/tabs/nca.R

@@ -681,7 +681,7 @@ output$preslopesettings <- DT::renderDataTable({
       scrollX = TRUE,
       scrollY = TRUE,
       lengthMenu = list(c(10, 25, -1), c("10", "25", "All")),
-      pageLength = -1, 
+      pageLength = -1,
       fixedHeader = TRUE
     )
   ) %>%

tests/testthat/test-general_lineplot.R

@@ -13,7 +13,7 @@ sample_data <- data.frame(
   AVALU = rep("ng/mL", 24),
   DOSEA = rep(35, 24)
 )
-# testthat::test_file("tests/testhat/test-general_lineplot.R")
+
 describe("general_lineplot functions correctly", {
   it("returns a ggplot object", {
     p <- general_lineplot(