Update workflow and formatting (#121)

* update description * ok let's go * test windows too * Update r.yml * Update r.yml * Update r.yml * Update r.yml
zktuong · Dec 6, 2024 · 6e64612 · 6e64612
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diff --git a/.github/workflows/r.yml b/.github/workflows/r.yml
@@ -7,87 +7,50 @@ on:
   push:
     branches:
       - "master"
-      - "*"
-
-env:
-  cache-version: "cache-v1"
 
 jobs:
   build:
     strategy:
       max-parallel: 5
       matrix:
         config:
-          - { r-version: release, os: ubuntu-latest }
-          - { r-version: release, os: macos-latest }
+          - { os: ubuntu-latest }
+          - { os: windows-latest }
+          - { os: macos-latest }
     runs-on: ${{ matrix.config.os }}
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      NOT_CRAN: true
-      TZ: UTC
-      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-node@v2
+      - uses: actions/checkout@v4
 
-      - name: Install ubuntu system dependencies
-        if: matrix.config.os == 'ubuntu-latest'
-        run: |
-          sudo apt-get install git libcurl4-openssl-dev libssl-dev libicu-dev libxml2-dev make pandoc libgit2-dev libharfbuzz-dev libfribidi-dev libglpk-dev
-      - name: Install macOS system dependencies
-        if: matrix.config.os == 'macos-latest'
-        run: |
-          brew install cairo pkg-config autoconf automake libtool
-
-      - name: Set up R
-        uses: r-lib/actions/setup-r@v2
+      - uses: r-lib/actions/setup-r@v2
+        id: install-r
         with:
-          r-version: ${{ matrix.config.r-version}}
-
-      - name: Setup r-lib/remotes
-        run: |
-          install.packages(c("remotes", "devtools"))
-        shell: Rscript {0}
+          use-public-rspm: true
 
-      - id: bioc
-        name: Check bioc version
-        run: |
-          echo "##[set-output name=mainbiocversion;]$(Rscript -e 'cat(unlist(tools:::.BioC_version_associated_with_R_version()))' | awk '{print $1}')"
-          echo "##[set-output name=subbiocversion;]$(Rscript -e 'cat(unlist(tools:::.BioC_version_associated_with_R_version()))' | awk '{print $2}')"
-          echo "##[set-output name=biocversion;]$(Rscript -e 'cat(as.character(tools:::.BioC_version_associated_with_R_version()))' | awk '{print $1}')"
-        shell: bash -l {0}
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Cache ubuntu R packages
-        if: "!contains(github.event.head_commit.message, '/nocache') && matrix.config.os == 'ubuntu-latest'"
-        uses: actions/cache@v2
+      - name: Cache R packages
+        uses: actions/cache@v4
         with:
           path: /home/runner/work/_temp/Library
-          key: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.bioc.outputs.mainbiocversion}}_${{ steps.bioc.outputs.subbiocversion}}-r-${{ matrix.config.r-version}}-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.bioc.outputs.mainbiocversion}}_${{ steps.bioc.outputs.subbiocversion}}-r-${{ matrix.config.r-version}}-
+          key: ${{ runner.OS }}-R-${{ steps.install-r.outputs.installed-r-version }}-cache-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: |
+            ${{ runner.OS }}-R-${{ steps.install-r.outputs.installed-r-version }}-cache-
 
-      - name: Cache macOS R packages
-        if: "!contains(github.event.head_commit.message, '/nocache') && matrix.config.os != 'ubuntu-latest'"
-        uses: actions/cache@v2
+      - name: Install and check
+        uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.bioc.outputs.mainbiocversion}}_${{ steps.bioc.outputs.subbiocversion}}-r-${{ matrix.config.r-version}}-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.bioc.outputs.mainbiocversion}}_${{ steps.bioc.outputs.subbiocversion}}-r-${{ matrix.config.r-version}}-
-
-      - name: Install dependencies
-        run: |
-          install.packages(c("rcmdcheck", "covr"))
-          remotes::install_deps(dependencies = TRUE)
-        shell: Rscript {0}
-
-      - name: Check
-        run: |
-          Rscript -e 'rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")'
-        shell: bash -l {0}
+          extra-packages: |
+            any::rcmdcheck
+            covr
+            pkgdown
+          needs: check
 
       - name: Test coverage
-        if: github.actor == 'zktuong'
+        if: github.actor == 'zktuong' && matrix.config.os == 'ubuntu-latest'
         run: |
           Rscript -e 'covr::codecov(token = "${{ secrets.CODECOV_TOKEN }}")'
         shell: bash -l {0}
diff --git a/.github/workflows/vignette.yml b/.github/workflows/vignette.yml
@@ -21,41 +21,26 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         id: install-r
+        with:
+          use-public-rspm: true
 
       - uses: r-lib/actions/setup-pandoc@v2
 
-      - id: bioc
-        name: Check bioc version
-        run: |
-          echo "##[set-output name=mainbiocversion;]$(Rscript -e 'cat(unlist(tools:::.BioC_version_associated_with_R_version()))' | awk '{print $1}')"
-          echo "##[set-output name=subbiocversion;]$(Rscript -e 'cat(unlist(tools:::.BioC_version_associated_with_R_version()))' | awk '{print $2}')"
-          echo "##[set-output name=biocversion;]$(Rscript -e 'cat(as.character(tools:::.BioC_version_associated_with_R_version()))' | awk '{print $1}')"
-        shell: bash -l {0}
-
-      - name: Install pak and query dependencies
-        run: |
-          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
-          saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), ".github/r-depends.rds")
-        shell: Rscript {0}
-
       - name: Cache R packages
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
-          path: |
-            ${{ env.R_LIBS_USER }}
-            !${{ env.R_LIBS_USER }}/pak
-          key: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.bioc.outputs.mainbiocversion}}_${{ steps.bioc.outputs.subbiocversion}}-r-${{ matrix.config.r-version}}-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.bioc.outputs.mainbiocversion}}_${{ steps.bioc.outputs.subbiocversion}}-r-${{ matrix.config.r-version}}-
+          path: /home/runner/work/_temp/Library
+          key: ${{ runner.OS }}-R-${{ steps.install-r.outputs.installed-r-version }}-cache-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: |
+            ${{ runner.OS }}-R-${{ steps.install-r.outputs.installed-r-version }}-cache-
 
-      - name: Install dependencies
-        run: |
-          pak::local_install_dev_deps(upgrade = TRUE, dependencies = c("all", "Config/Needs/website"))
-          pak::pkg_install("pkgdown")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: pkgdown
 
       - name: Install package
         run: R CMD INSTALL .

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -27,9 +27,10 @@ Suggests:
 	scater,
 	testthat,
 	covr,
-	plyr
-LazyData: true
-RoxygenNote: 7.2.3
+	plyr,
+    styler
+LazyData: false
+RoxygenNote: 7.3.2
 Collate: 
     'combine_cpdb.R'
     'correlationSpot.R'

diff --git a/R/combine_cpdb.R b/R/combine_cpdb.R
@@ -4,20 +4,18 @@
 #' @return combine results from multiple cellphonedb runs.
 #' @import dplyr
 #' @import purrr
-#' @examples
-#' \donttest{
-#' combine_cpdb(means, means2, means3)
-#' combine_cpdb(pvals, pvals2, pvals3)
-#' combine_cpdb(decon, decon2, decon3)
-#' }
 #' @export
 combine_cpdb <- function(...) {
     output <- list(...)
-    anames <- c("id_cp_interaction", "interacting_pair", "partner_a", "partner_b",
+    anames <- c(
+        "id_cp_interaction", "interacting_pair", "partner_a", "partner_b",
         "gene_a", "gene_b", "secreted", "receptor_a", "receptor_b", "annotation_strategy",
-        "is_integrin")
-    bnames <- c("gene_name", "uniprot", "is_complex", "protein_name", "complex_name",
-        "id_cp_interaction")
+        "is_integrin"
+    )
+    bnames <- c(
+        "gene_name", "uniprot", "is_complex", "protein_name", "complex_name",
+        "id_cp_interaction"
+    )
     if (all(colnames(output[[1]])[1:11] == anames)) {
         out <- output %>%
             reduce(full_join, by = anames)
@@ -26,4 +24,4 @@ combine_cpdb <- function(...) {
             reduce(full_join, by = bnames)
     }
     return(out)
-}
+}
diff --git a/R/correlationSpot.R b/R/correlationSpot.R
@@ -20,10 +20,15 @@
 #' @return SpatialFeaturePlot
 #' @export
 
-correlationSpot <- function(st, genes = NULL, celltypes = NULL, geneset = NULL, mode = c("high",
-    "low", "both"), cutoff = 0.5, standardize = TRUE, dims = 1:30, k.params = 10,
-    resolution = 1, rna_slot = "SCT", label_slot = "predictions", by = c("image",
-        "expression"), average_by_cluster = FALSE, ...) {
+correlationSpot <- function(
+    st, genes = NULL, celltypes = NULL, geneset = NULL, mode = c(
+        "high",
+        "low", "both"
+    ), cutoff = 0.5, standardize = TRUE, dims = 1:30, k.params = 10,
+    resolution = 1, rna_slot = "SCT", label_slot = "predictions", by = c(
+        "image",
+        "expression"
+    ), average_by_cluster = FALSE, ...) {
     requireNamespace("Seurat")
     requireNamespace("FNN")
 
@@ -213,4 +218,4 @@ correlationSpot <- function(st, genes = NULL, celltypes = NULL, geneset = NULL,
 
     g <- Seurat::SpatialFeaturePlot(st, features = "correlation", ...)
     return(g)
-}
+}
diff --git a/R/data.R b/R/data.R
@@ -157,4 +157,4 @@
 #' interaction_scores_v5 - Dataframe of CellPhoneDB output interaction_scores.txt file
 #' @rdname kidneyimmune
 #' @docType data
-"interaction_scores_v5"
+"interaction_scores_v5"