Merge pull request #160 from jr-leary7/dev

still trying to resolve CI/CD issues ugh

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

@@ -1,4 +1,5 @@
 # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Additional formatting taken from: https://github.com/r-lib/actions/blob/v2-branch/check-r-package/action.yaml
 
 on:
   push:
@@ -25,23 +26,56 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-pandoc@v2
+      - name: Checkout repo
+        uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v2
+      - name: Setup Pandoc
+        uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - name: Setup dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck
           needs: check
 
-      - uses: r-lib/actions/check-r-package@v2
+      - name: Check
+        id: rcmdcheck
+        run: |
+          ## --------------------------------------------------------------------
+          options(crayon.enabled = TRUE)
+          cat("check-dir-path=", file.path(getwd(), "check"), "\n", file = Sys.getenv("GITHUB_OUTPUT"), sep = "", append = TRUE)
+          check_results <- rcmdcheck::rcmdcheck(args = c("--no-vignettes", "--no-manual", "--as-cran"), build_args = c("--no-build-vignettes", "--no-manual"), check_dir = "check", error_on = "error")
+        shell: Rscript {0}
+        working-directory: '.'
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          echo ::group::Show testthat output
+          find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+          echo ::endgroup::
+        shell: bash
+        working-directory: '.'
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: ${{ steps.rcmdcheck.outputs.check-dir-path }}
+
+      - name: Upload snapshots
+        uses: actions/upload-artifact@v3
         with:
-          upload-snapshots: true
-          args: 'c("--ignore-vignettes", "--no-manual")'
-          build_args: 'c("--no-build-vignettes")'
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-testthat-snapshots
+          path: ${{ steps.rcmdcheck.outputs.check-dir-path }}/**/tests*/testthat/_snaps
+          if-no-files-found: ignore

.github/workflows/bioc-check.yaml

@@ -5,12 +5,12 @@ on:
   push:
     branches: main
 
-name: bioc-check
+name: Bioc-check
 
 jobs:
   bioc-check:
     runs-on: macos-latest
-    name: BiocCheck
+    name: Bioc-check
     steps:
       - uses: actions/checkout@v3
       - uses: r-lib/actions/setup-pandoc@v2

.github/workflows/test-coverage.yaml

@@ -8,7 +8,7 @@ name: test-coverage
 
 jobs:
   test-coverage:
-    runs-on: ubuntu-latest
+    runs-on: macos-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 

R/GetResultsDE.R

@@ -2,16 +2,16 @@
 #'
 #' @name getResultsDE
 #' @author Jack Leary
-#' @description This function turns the nested list differential expression results of \code{\link{testDynamic}} and turns them into a tidy \code{data.frame}.
+#' @description This function turns the nested list differential expression results of \code{\link{testDynamic}} and turns them into a tidy data.frame.
 #' @import magrittr
 #' @importFrom purrr map_dfr
 #' @importFrom dplyr arrange desc mutate across if_else with_groups relocate
 #' @importFrom tidyselect everything
 #' @importFrom stats p.adjust p.adjust.methods
 #' @param test.dyn.res The nested list returned by \code{\link{testDynamic}}. Defaults to NULL.
-#' @param p.adj.method (Optional) The method used to adjust \emph{p}-values for multiple hypothesis testing. Defaults to "holm".
-#' @param fdr.cutoff (Optional) The FDR threshold for determining statistical significance. Defaults to 0.01.
-#' @return A data.frame containing differential expression results & modeling statistics for each gene.
+#' @param p.adj.method The method used to adjust \emph{p}-values for multiple hypothesis testing. Defaults to "holm".
+#' @param fdr.cutoff The FDR threshold for determining statistical significance. Defaults to 0.01.
+#' @return A data.frame containing differential expression results & test statistics for each gene.
 #' @export
 #' @seealso \code{\link{testDynamic}}
 #' @seealso \code{\link[stats]{p.adjust}}
@@ -34,7 +34,7 @@ getResultsDE <- function(test.dyn.res = NULL,
                                                    dplyr::mutate(dplyr::across(tidyselect::everything(), \(z) unname(unlist(z))))
                                                })
                               }) %>%
-               dplyr::arrange(P_Val, dplyr::desc(Test_Stat)) %>%
+               dplyr::arrange(dplyr::desc(Test_Stat)) %>%
                dplyr::mutate(P_Val_Adj = stats::p.adjust(P_Val, method = p.adj.method),
                              Gene_Dynamic_Lineage = dplyr::if_else(P_Val_Adj < fdr.cutoff, 1, 0, missing = 0)) %>%
                dplyr::with_groups(Gene,

R/testSlope.R

@@ -8,9 +8,9 @@
 #' @importFrom dplyr arrange desc mutate if_else with_groups
 #' @importFrom stats p.adjust
 #' @param test.dyn.res The list returned by \code{\link{testDynamic}} - no extra processing required. Defaults to NULL.
-#' @param p.adj.method The method used to adjust the \emph{p}-values for each slope. Defaults to "holm".
+#' @param p.adj.method The method used to adjust the \emph{p}-values for each coefficient. Defaults to "holm".
 #' @param fdr.cutoff The FDR threshold for determining statistical significance. Defaults to 0.01.
-#' @return A dataframe containing the genes, breakpoints, and slope \emph{p}-values from each model.
+#' @return A dataframe containing the genes, breakpoints, and coefficient \emph{p}-values from each model.
 #' @seealso \code{\link{testDynamic}}
 #' @seealso \code{\link[stats]{p.adjust}}
 #' @export
@@ -25,7 +25,7 @@ testSlope <- function(test.dyn.res = NULL,
   if (is.null(test.dyn.res)) { stop("You forgot to provide results from testDynamic() to testSlope().") }
   # create table of results
   slope_df <- purrr::map_dfr(test.dyn.res, \(x) purrr::map_dfr(x, \(y) data.frame(y["MARGE_Slope_Data"][[1]]))) %>%
-              dplyr::arrange(P_Val, dplyr::desc(abs(Test_Stat))) %>%
+              dplyr::arrange(dplyr::desc(abs(Test_Stat))) %>%
               dplyr::mutate(P_Val_Adj = stats::p.adjust(P_Val, method = p.adj.method)) %>%
               dplyr::arrange(Gene, Breakpoint) %>%
               dplyr::mutate(Gene_Dynamic_Lineage_Slope = dplyr::if_else(P_Val_Adj < fdr.cutoff, 1, 0, missing = 0)) %>%

README.Rmd

@@ -24,6 +24,7 @@ knitr::opts_chunk$set(warning = FALSE,
 
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/jr-leary7/scLANE/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jr-leary7/scLANE/actions/workflows/R-CMD-check.yaml)
+[![Bioc-check](https://github.com/jr-leary7/scLANE/actions/workflows/bioc-check.yaml/badge.svg)](https://github.com/jr-leary7/scLANE/actions/workflows/bioc-check.yaml)
 ![release](https://img.shields.io/github/v/release/jr-leary7/scLANE?color=purple)
 ![last commit](https://img.shields.io/github/last-commit/jr-leary7/scLANE/main?color=darkgreen)
 [![codecov](https://codecov.io/gh/jr-leary7/scLANE/branch/main/graph/badge.svg?token=U2U5RTF2VW)](https://codecov.io/gh/jr-leary7/scLANE)