Merge pull request #17 from william-hutchison/improve-continuous-deve…

…lopment

Improve continuous development

.github/workflows/rworkflows.yml

@@ -0,0 +1,49 @@
+name: rworkflows
+on:
+  push:
+    branches:
+  pull_request:
+    branches:
+jobs:
+  rworkflows:
+    permissions: write-all
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    container: ${{ matrix.config.cont }}
+    strategy:
+      fail-fast: ${{ false }}
+      matrix:
+        config:
+        - os: ubuntu-latest
+          bioc: devel
+          r: auto
+          cont: ghcr.io/bioconductor/bioconductor_docker:devel
+          rspm: ~
+        - os: macOS-latest
+          bioc: release
+          r: auto
+          cont: ~
+          rspm: ~
+        - os: windows-latest
+          bioc: release
+          r: auto
+          cont: ~
+          rspm: ~
+    steps:
+    - uses: neurogenomics/rworkflows@master
+      with:
+        run_bioccheck: ${{ true }}
+        run_rcmdcheck: ${{ true }}
+        as_cran: ${{ true }}
+        run_vignettes: ${{ true }}
+        has_testthat: ${{ true }}
+        run_covr: ${{ true }}
+        run_pkgdown: ${{ true }}
+        has_runit: ${{ false }}
+        has_latex: ${{ false }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run_docker: ${{ false }}
+        DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
+        runner_os: ${{ runner.os }}
+        cache_version: cache-v1
+        docker_registry: ghcr.io

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: tidySpatialExperiment
 Title: Brings SpatialExperiment to the tidyverse 
-Version: 0.99.9
+Version: 0.99.11
 Authors@R: c(
     person("William", "Hutchison", email = "[email protected]", role = c("aut", "cre"), 
            comment = c(ORCID = "0009-0001-6242-4269")),
@@ -67,7 +67,7 @@ Biarch: true
 biocViews: Infrastructure, RNASeq, GeneExpression, Sequencing, Spatial, Transcriptomics, SingleCell
 Encoding: UTF-8
 LazyData: false
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0
 Roxygen: list(markdown = TRUE)
 URL: https://github.com/william-hutchison/tidySpatialExperiment
 BugReports: https://github.com/william-hutchison/tidySpatialExperiment/issues

NAMESPACE

@@ -23,8 +23,6 @@ S3method(unnest,tidySpatialExperiment_nested)
 export(aggregate_cells)
 export(ellipse)
 export(rectangle)
-export(ellipse)
-export(rectangle)
 export(unnest_single_cell_experiment)
 import(tidySingleCellExperiment)
 importFrom(BiocGenerics,cbind)
@@ -58,8 +56,6 @@ importFrom(dplyr,select)
 importFrom(dplyr,select_if)
 importFrom(fansi,strwrap_ctl)
 importFrom(ggplot2,aes)
-importFrom(magrittr,"%$%")
-importFrom(magrittr,"%>%")
 importFrom(magrittr,equals)
 importFrom(magrittr,set_rownames)
 importFrom(methods,callNextMethod)

NEWS.md

@@ -1,5 +1,13 @@
 # tidySpatialExperiment 0.99.9
 
-* tidySpatialExperiment now features a NEWS file!
+* tidySpatialExperiment now features a `NEWS.md` file!
 * The package also now has its own pkgdown website.
 * Updated README to better reflect the development of tidyomics ecosystem. 
+
+# tidySpatialExperiment 0.99.10
+
+* Rectangular and elliptical gating added by Quentin Clayssen.
+
+# tidySpatialExperiment 0.99.11
+
+* Add rworkflow github actions to support continuous and collaborative development. 

R/methods.R

@@ -115,7 +115,6 @@ setMethod("join_features", "SpatialExperiment",  function(.data,
 #'
 #' @description Combine cells into groups based on shared variables and aggregate feature counts.
 #'
-#' @importFrom magrittr "%>%"
 #' @importFrom rlang enquo
 #' @importFrom tibble enframe
 #' @importFrom Matrix rowSums
@@ -184,7 +183,6 @@ aggregate_cells <- function(.data, .sample = NULL, slot = "data", assays = NULL,
 #'
 #' @description Determines whether points specified by spatial coordinates are within a defined rectangle.
 #'
-#' @importFrom magrittr "%>%"
 #' @importFrom dplyr mutate
 #'
 #' @name rectangle

R/utilities.R

@@ -2,7 +2,6 @@
 #'
 #' @keywords internal
 #'
-#' @importFrom magrittr "%>%"
 #' @importFrom tibble rowid_to_column
 #' @importFrom dplyr mutate
 #' @importFrom utils tail
@@ -108,7 +107,6 @@ setMethod("cbind", "SpatialExperiment", function(..., deparse.level = 1) {
 #'
 #' @keywords internal
 #'
-#' @importFrom magrittr "%$%"
 #' @importFrom tidyr pivot_longer
 #' @importFrom tibble as_tibble
 #' @importFrom purrr when