pkgdown update

.Rbuildignore

@@ -6,3 +6,4 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

DESCRIPTION

@@ -59,3 +59,4 @@ Suggests:
     progress
 RoxygenNote: 7.1.2
 VignetteBuilder: knitr
+URL: http://andersenlab.org/easyXpress/

R/readXpress.R

@@ -133,7 +133,7 @@ readXpress <- function(filedir, rdafile, design = FALSE, px_per_um = 3.2937, len
     message("Design file not joined.\nPlease use 'design = TRUE' if you would like to join a design file.\n")
     raw_data <- raw_data_read %>%
       dplyr::mutate(well.id = paste(Metadata_Experiment, Metadata_Plate, Metadata_Well, sep = "_")) %>%
-      dplyr::select(well.id, everything())
+      dplyr::select(well.id, dplyr::everything())
     # Return raw_data_read as raw_data
     message("DONE")
     return(raw_data)
@@ -174,7 +174,7 @@ readXpress <- function(filedir, rdafile, design = FALSE, px_per_um = 3.2937, len
       #join to raw data
       suppressMessages(raw_data <- dplyr::left_join(raw_data_read, design_file) %>%
                          dplyr::mutate(well.id = paste(Metadata_Experiment, Metadata_Plate, Metadata_Well, sep = "_")) %>%
-                         dplyr::select(well.id, everything()))
+                         dplyr::select(well.id, dplyr::everything()))
       message("DONE")
       return(list(raw_data = raw_data, design = design_file))
     }
@@ -227,7 +227,7 @@ readXpress <- function(filedir, rdafile, design = FALSE, px_per_um = 3.2937, len
       #join to raw data
       suppressMessages(raw_data <- dplyr::left_join(raw_data_read, design_file, by = c("Metadata_Experiment", "Metadata_Plate", "Metadata_Well")) %>%
                          dplyr::mutate(well.id = paste(Metadata_Experiment, Metadata_Plate, Metadata_Well, sep = "_")) %>%
-                         dplyr::select(well.id, everything()))
+                         dplyr::select(well.id, dplyr::everything()))
       message("DONE")
       return(list(raw_data = raw_data, design = design_file))
     }

_pkgdown.yml

@@ -0,0 +1,4 @@
+url: http://andersenlab.org/easyXpress/
+template:
+  bootstrap: 5
+