Merge pull request #95 from drieslab/dev

Fix gh actions
drieslab · Nov 19, 2023 · dce5511 · dce5511
2 parents c6b3bd3 + 8ea8b6b
commit dce5511
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diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -1,5 +1,7 @@
 # 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
+name: pkgdown
+
 on:
   push:
     branches: [main, master]
@@ -9,8 +11,6 @@ on:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
-
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
@@ -22,19 +22,35 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-pandoc@v2
+      - name: Checkout repo for workflow access
+        uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v2
+      - name: Setup pandoc
+        uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Setup R environment
+        uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - name: Set up dependencies (general)
+        uses: r-lib/actions/setup-r-dependencies@v2
+        env:
+          _R_CHECK_FORCE_SUGGESTS: false
+          _R_CHECK_RD_XREFS: false
         with:
+          dependencies: '"hard"' # do not use suggested dependencies
           extra-packages: any::pkgdown, local::.
           needs: website
 
+      - name: Set up dependencies (GiottoData)
+        run: |
+          suppressWarnings({
+            remotes::install_github('drieslab/GiottoData@suite_modular', build = FALSE)
+          })
+        shell: Rscript {0}
+
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -51,6 +51,7 @@ Suggests:
     geometry,
     GiottoData,
     HDF5Array (>= 1.18.1),
+    raster,
     remotes,
     rhdf5,
     rlang,

diff --git a/R/methods-IDs.R b/R/methods-IDs.R
@@ -9,8 +9,6 @@ NULL
 #' the single-cell level) and feature IDs of a giotto object or subobject
 #' @aliases spatIDs featIDs
 #' @param x an object
-#' @param spat_unit (optional) specify which spatial unit
-#' @param feat_type (optional) specify which feature type
 #' @param ... additional parameters to pass
 #' @include classes.R
 #' @usage
@@ -29,6 +27,7 @@ NULL
 
 
 #' @rdname spatIDs-generic
+#' @param spat_unit (optional) specify which spatial unit
 #' @export
 setMethod('spatIDs', signature(x = 'giotto'),
           function(x, spat_unit = NULL, ...) {
@@ -103,6 +102,7 @@ setMethod('spatIDs', signature(x = 'nnNetObj'),
 
 
 #' @rdname spatIDs-generic
+#' @param feat_type (optional) specify which feature type
 #' @export
 setMethod('featIDs', signature(x = 'giotto'),
           function(x, feat_type = NULL, ...) {

diff --git a/R/methods-coerce.R b/R/methods-coerce.R
@@ -14,37 +14,14 @@
 #' @family As coercion functions
 NULL
 
-#' @title Coerce to sp
-#' @name as.sp
+#' @title R spatial conversions
+#' @name r_spatial_conversions
 #' @param x The object to coerce
 #' @param drop When TRUE, returned object will be the sp object instead of
 #' wrapped in a `giottoPoints` or `giottoPolygon` object
 #' @family As coercion functions
 NULL
 
-#' @title Coerce to sf
-#' @name as.sf
-#' @param x The object to coerce
-#' @param drop When TRUE, returned object will be the sf object instead of
-#' wrapped in a `giottoPoints` or `giottoPolygon` object
-#' @family As coercion functions
-NULL
-
-#' @title Coerce to stars
-#' @name as.stars
-#' @param x The object to coerce
-#' @param drop When TRUE, returned object will be the stars object instead of
-#' wrapped in a `giottoPoints` or `giottoPolygon` object
-#' @family As coercion functions
-NULL
-
-#' @title Coerce to terra
-#' @name as.terra
-#' @param x The object to coerce
-#' @param drop When TRUE, returned object will be the terra object instead of
-#' wrapped in a `giottoPoints` or `giottoPolygon` object
-#' @family As coercion functions
-NULL
 
 # ---------------------------------------------------------------- #
 
@@ -102,36 +79,36 @@ as.data.table.giottoPoints <- function(x, ...) {
 # * to sp ####
 # Spatial class covers both SpatialPolygonsDataFrame and SpatialPointsDataFrame
 
-#' @rdname as.sp
+#' @rdname r_spatial_conversions
 #' @export
 setMethod('as.sp', signature('sf'), function(x) {
   GiottoUtils::package_check('sp')
   as(x, "Spatial")
 })
 
-#' @rdname as.sp
+#' @rdname r_spatial_conversions
 #' @export
 setMethod('as.sp', signature('SpatVector'), function(x) {
   GiottoUtils::package_check('sp')
   GiottoUtils::package_check('raster') # needed for this conversion
   as(x, "Spatial")
 })
 
-#' @rdname as.sp
+#' @rdname r_spatial_conversions
 #' @export
 setMethod('as.sp', signature('stars'), function(x) {
   GiottoUtils::package_check('sp')
   as(x, "Spatial")
 })
 
-#' @rdname as.sp
+#' @rdname r_spatial_conversions
 #' @export
 setMethod('as.sp', signature('Spatial'), function(x) {
   GiottoUtils::package_check('sp')
   x
 })
 
-#' @rdname as.sp
+#' @rdname r_spatial_conversions
 #' @export
 setMethod('as.sp', signature('giottoPolygon'), function(x, drop = TRUE) {
   if (isTRUE(drop)) {
@@ -142,7 +119,7 @@ setMethod('as.sp', signature('giottoPolygon'), function(x, drop = TRUE) {
   }
 })
 
-#' @rdname as.sp
+#' @rdname r_spatial_conversions
 #' @export
 setMethod('as.sp', signature('giottoPoints'), function(x, drop = TRUE) {
   s <- as.sp(x[])
@@ -157,34 +134,34 @@ setMethod('as.sp', signature('giottoPoints'), function(x, drop = TRUE) {
 
 
 # * to sf ####
-#' @rdname as.sf
+#' @rdname r_spatial_conversions
 #' @export
 setMethod('as.sf', signature('SpatVector'), function(x) {
   spatvector_to_sf(x)
 })
 
-#' @rdname as.sf
+#' @rdname r_spatial_conversions
 #' @export
 setMethod('as.sf', signature('Spatial'), function(x) {
   GiottoUtils::package_check('sf')
   sf::st_as_sf(x)
 })
 
-#' @rdname as.sf
+#' @rdname r_spatial_conversions
 #' @export
 setMethod('as.sf', signature('stars'), function(x) {
   GiottoUtils::package_check('sf')
   sf::st_as_sf(x)
 })
 
-#' @rdname as.sf
+#' @rdname r_spatial_conversions
 #' @export
 setMethod('as.sf', signature('sf'), function(x) {
   GiottoUtils::package_check('sf')
   x
 })
 
-#' @rdname as.sf
+#' @rdname r_spatial_conversions
 #' @export
 setMethod('as.sf', signature('giottoPolygon'),
           function(x, drop = TRUE) {
@@ -197,7 +174,7 @@ setMethod('as.sf', signature('giottoPolygon'),
             }
           })
 
-#' @rdname as.sf
+#' @rdname r_spatial_conversions
 #' @export
 setMethod('as.sf', signature('giottoPoints'),
           function(x, drop = TRUE) {
@@ -215,7 +192,7 @@ setMethod('as.sf', signature('giottoPoints'),
 
 # st_as_stars does not handle SpatVector. Only SpatRaster
 # however, conversions from sf work fine
-#' @rdname as.stars
+#' @rdname r_spatial_conversions
 #' @export
 setMethod('as.stars', signature('SpatVector'),
           function(x) {
@@ -224,31 +201,31 @@ setMethod('as.stars', signature('SpatVector'),
               stars::st_as_stars()
           })
 
-#' @rdname as.stars
+#' @rdname r_spatial_conversions
 #' @export
 setMethod('as.stars', signature('sf'),
           function(x) {
             GiottoUtils::package_check('stars')
             stars::st_as_stars(x)
           })
 
-#' @rdname as.stars
+#' @rdname r_spatial_conversions
 #' @export
 setMethod('as.stars', signature('Spatial'),
           function(x) {
             GiottoUtils::package_check('stars')
             stars::st_as_stars(x)
           })
 
-#' @rdname as.stars
+#' @rdname r_spatial_conversions
 #' @export
 setMethod('as.stars', signature('stars'),
           function(x) {
             GiottoUtils::package_check('stars')
             x
           })
 
-#' @rdname as.stars
+#' @rdname r_spatial_conversions
 #' @export
 setMethod('as.stars', signature('giottoPolygon'),
           function(x, drop = TRUE) {
@@ -260,7 +237,7 @@ setMethod('as.stars', signature('giottoPolygon'),
             }
           })
 
-#' @rdname as.stars
+#' @rdname r_spatial_conversions
 #' @export
 setMethod('as.stars', signature('giottoPoints'),
           function(x, drop = TRUE) {
@@ -276,21 +253,21 @@ setMethod('as.stars', signature('giottoPoints'),
 
 # * to terra ####
 
-#' @rdname as.terra
+#' @rdname r_spatial_conversions
 #' @export
 setMethod('as.terra', signature('SpatVector'),
           function(x) {
             x
           })
 
-#' @rdname as.terra
+#' @rdname r_spatial_conversions
 #' @export
 setMethod('as.terra', signature('sf'),
           function(x) {
             terra::vect(x)
           })
 
-#' @rdname as.terra
+#' @rdname r_spatial_conversions
 #' @param type whether data is 'vector' or 'raster'
 #' @export
 setMethod('as.terra', signature('stars'),
@@ -314,25 +291,25 @@ setMethod('as.terra', signature('stars'),
             return(x)
           })
 
-#' @rdname as.terra
+#' @rdname r_spatial_conversions
 #' @export
 setMethod('as.terra', signature('Spatial'), function(x) {
   terra::vect(x)
 })
 
-#' @rdname as.terra
+#' @rdname r_spatial_conversions
 #' @export
 setMethod('as.terra', signature('giottoPolygon'),
-          function(x, drop = TRUE, ...) {
+          function(x, drop = TRUE) {
             if (isTRUE(drop)) {
-              return(as.terra(x[], ...))
+              return(as.terra(x[]))
             } else {
-              x <- do_gpoly(x = x, what = as.terra, args = list(...))
+              x <- do_gpoly(x = x, what = as.terra, args = list())
               return(x)
             }
           })
 
-#' @rdname as.terra
+#' @rdname r_spatial_conversions
 #' @export
 setMethod('as.terra', signature('giottoPoints'),
           function(x, drop = TRUE) {

diff --git a/man/as.data.table.Rd b/man/as.data.table.Rd
diff --git a/man/as.sf.Rd b/man/as.sf.Rd