Merge pull request #666 from olivroy/clean

Upkeep

.github/.gitignore

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

.github/workflows/rcmdcheck.yml → .github/workflows/R-CMD-check.yaml

@@ -9,7 +9,7 @@ on:
     # * is a special character in YAML so you have to quote this string
     - cron: "0 4 * * 0" # every week
 
-name: rcmdcheck
+name: R-CMD-check
 
 jobs:
   R-CMD-check:
@@ -25,13 +25,14 @@ jobs:
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -40,7 +41,7 @@ jobs:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
-          extra-repositories: "http://cran.uni-muenster.de/pebesma"
+          extra-repositories: "https://cran.uni-muenster.de/pebesma"
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:

.github/workflows/pkgdown.yml → .github/workflows/pkgdown.yaml

@@ -22,14 +22,14 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
-          extra-repositories: "http://cran.uni-muenster.de/pebesma"
+          extra-repositories: "https://cran.uni-muenster.de/pebesma"
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
@@ -42,7 +42,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

.github/workflows/test-coverage.yaml

@@ -15,7 +15,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -31,7 +31,7 @@ jobs:
           covr::codecov(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
         shell: Rscript {0}
 
@@ -44,7 +44,7 @@ jobs:
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

DESCRIPTION

@@ -47,10 +47,10 @@ Suggests:
     OpenStreetMap,
     PCICt,
     RNetCDF (>= 1.8-2),
-	clue,
+    clue,
     covr,
-	cubble (>= 0.3.0),
-	cubelyr,
+    cubble (>= 0.3.0),
+    cubelyr,
     digest,
     dplyr (>= 0.7-0),
     exactextractr,
@@ -70,7 +70,7 @@ Suggests:
     ncmeta (>= 0.0.3),
     pbapply,
     plm,
-	randomForest,
+    randomForest,
     raster,
     rmarkdown,
     sp,

NEWS.md

@@ -232,7 +232,7 @@
 
 * handle `normalize_path` for choosing to `proxy`; #391
 
-* ignore units when there are different units accross bands of a subdataset
+* ignore units when there are different units across bands of a subdataset
 
 * speed up `st_rgb()` using faster `st_apply()` approach; #315, #390
 
@@ -264,13 +264,13 @@
 
 * `st_apply()` and other methods for `stars_proxy` objects handle ... ; #374
 
-* add `st_bbox()`, `st_crs()` methods for terra's `SpatVector` objects; https://github.com/mtennekes/tmap/issues/536
+* add `st_bbox()`, `st_crs()` methods for terra's `SpatVector` objects; https://github.com/r-tmap/tmap/issues/536
 
-* add `st_bbox()`, `st_crs()` and `st_as_stars()` methods for terra's `SpatRaster` objects; https://github.com/mtennekes/tmap/issues/536
+* add `st_bbox()`, `st_crs()` and `st_as_stars()` methods for terra's `SpatRaster` objects; https://github.com/r-tmap/tmap/issues/536
 
 * allow for multi-resolution attributes in `stars_proxy` objects (e.g., all gray scale sentinel-2 bands); see vignettes 2 and 7 for examples.
 
-* `plot()` defaults to a categorical color scale when plotting a factor variable; https://github.com/mtennekes/tmap/issues/526
+* `plot()` defaults to a categorical color scale when plotting a factor variable; https://github.com/r-tmap/tmap/issues/526
 
 * `st_extract()` extracts space-time points if `time_column` is specified, and handles time intervals; #352
 
@@ -328,7 +328,7 @@
 
 # version 0.4-3
 
-* fix bug in `st_as_stars.Raster`; set crs to the one assigned by raster; https://github.com/mtennekes/tmap/issues/471
+* fix bug in `st_as_stars.Raster`; set crs to the one assigned by raster; https://github.com/r-tmap/tmap/issues/471
 
 * add `s2` to Suggests:
 
@@ -358,7 +358,7 @@
 
 * x/y range subsetting of `stars_proxy` objects now only reads that range, similar to how crop already did this.
 
-* `st_warp()` preserves levels and colors; https://github.com/mtennekes/tmap/issues/429
+* `st_warp()` preserves levels and colors; https://github.com/r-tmap/tmap/issues/429
 
 * `st_crop()` works with bounding boxes larger than the downsampled bounding box; #276
 
@@ -386,7 +386,7 @@
 
 * handle full `crs` objects as `refsys` element in a spatial dimensions, rather than proj4string only
 
-* `st_raster_type(x)` reveals the raster type of `x`; #248, https://github.com/mtennekes/tmap/issues/368
+* `st_raster_type(x)` reveals the raster type of `x`; #248, https://github.com/r-tmap/tmap/issues/368
 
 * add `st_as_stars.OpenStreetMap()` method; #241 by @mtennekes
 
@@ -474,7 +474,7 @@
 
 * support for `PCICt` 360- and 365-day calendars; #29
 
-* remove import of `ncdf4` in favour of `RNetCDF`, now in line with practice in `ncmeta` package. Thanks to David Blodgett for motivation and testing (see #87, #94). 
+* remove import of `ncdf4` in favor of `RNetCDF`, now in line with practice in `ncmeta` package. Thanks to David Blodgett for motivation and testing (see #87, #94). 
 
 * `st_as_sf` uses date/time column names when appropriate
 
@@ -486,7 +486,7 @@
 
 * depend on sf 0.7-2
 
-* add logz support for log-scale keys to `plot` and `image`
+* add `logz` support for log-scale keys to `plot` and `image`
 
 # version 0.2-0
 

PROPOSAL.md

@@ -42,7 +42,7 @@ to finish computation within acceptable time? How can we quickly
 and easily develop an analysis by testing it on a small portion of
 the spatiotemporal datasets, before deploying it on the massive
 data set?  How can we use pipe-based workflows or dplyr-verbs on such
-data sets? How can we visualy explore high-dimensional raster data?
+data sets? How can we visually explore high-dimensional raster data?
 
 Today, people use R for large spatiotemporal data, but hit
 limits related to usability, user interface, and scalability. The
@@ -103,17 +103,17 @@ data is distributed.
 
 Relevant work outside R includes
 
-* [GDAL](http://www.gdal.org/), in particular gdal [virtual tiles](http://www.gdal.org/gdalbuildvrt.html) for building arbitrary large grid data sets from many individual files,
-* [SciDB](http://www.paradigm4.com/), an open source array database which has no spatial or temporal capabilities, but a strongly scalable architecture, and extremely flexible array manipulation methods
+* [GDAL](https://gdal.org/), in particular gdal [virtual tiles](https://gdal.org/programs/gdalbuildvrt.html) for building arbitrary large grid data sets from many individual files,
+* [SciDB](https://paradigm4.com/), an open source array database which has no spatial or temporal capabilities, but a strongly scalable architecture, and extremely flexible array manipulation methods
 * [SciDB4geo](https://github.com/appelmar/scidb4geo), a SciDB Plugin
 for Managing Spatial and Temporal Reference Information of Arrays, and
-[SciDB4gdal](https://github.com/appelmar/scidb4geo), a GDAL driver for SciDB arrays, two activities to make SciDB databases aware of space and time
-* [PostGIS Raster](http://postgis.net/docs/RT_reference.html), a raster data extension of [PostGIS](http://www.postgis.net/)
-* [Rasdaman](http://www.rasdaman.com/), an array database dedicate to images, which is partially open source.
+[SciDB4gdal](https://github.com/appelmar/scidb4gdal), a GDAL driver for SciDB arrays, two activities to make SciDB databases aware of space and time
+* [PostGIS Raster](https://postgis.net/docs/RT_reference.html), a raster data extension of [PostGIS](https://www.postgis.net/)
+* [Rasdaman](https://www.rasdaman.com/), an array database dedicate to images, which is partially open source.
 
 Since there is a definite trend that
 [downloading Earth observation data is no longer
-feasible](http://r-spatial.org/2016/11/29/openeo.html), we will
+feasible](https://r-spatial.org/2016/11/29/openeo.html), we will
 have to work towards solutions where the data are accessed over
 a web service interface. Cloud services such as AWS are starting
 to give access to the large remote sensing imagery archives of e.g.
@@ -174,4 +174,4 @@ We will use most funding to develop the R package and web service API. Total cos
 
 ## Dissemination: 
 
-We will regularly post blogs about the project on [r-spatial.org](http://r-spatial.org/), use twitter, post to [r-sig-geo](https://stat.ethz.ch/mailman/listinfo/r-sig-geo), stackoverflow, and communicate through github issues or gitter discussion. The project will live on GitHub, in the [r-spatial](https://github.com/r-spatial/) organisation. We will work under a permissive open source license, probably LGPL-2.1. Pull requests will be encouraged. R consortium blogs will be provided at start and end. Publications in _the R Journal_ and other scientific outlets are foreseen.
+We will regularly post blogs about the project on [r-spatial.org](https://r-spatial.org/), use twitter, post to [r-sig-geo](https://stat.ethz.ch/mailman/listinfo/r-sig-geo), stackoverflow, and communicate through github issues or gitter discussion. The project will live on GitHub, in the [r-spatial](https://github.com/r-spatial/) organisation. We will work under a permissive open source license, probably LGPL-2.1. Pull requests will be encouraged. R consortium blogs will be provided at start and end. Publications in _the R Journal_ and other scientific outlets are foreseen.

R/datasets.R

@@ -14,13 +14,13 @@
 
 #' Monthly Gridded Meteorological Observations
 #'
-#' These are the monthly observational data used for BCSD downscaling. See: http://gdo-dcp.ucllnl.org/downscaled_cmip_projections/dcpInterface.html#About for more information." ;
+#' These are the monthly observational data used for BCSD downscaling. See: <https://gdo-dcp.ucllnl.org/downscaled_cmip_projections/dcpInterface.html#About> for more information." ;
 #' "Atmospheric Temperature, Air Temperature Atmosphere, Precipitation, Rain, Maximum Daily Temperature, Minimum  Daily Temperature" ;
 #'
 "bcsd_obs"
 
 #' Sentinel-2 sample tile
 #'
-#' Sentinel-2 sample tile, downloaded from https://scihub.copernicus.eu/
+#' Sentinel-2 sample tile, downloaded from <https://scihub.copernicus.eu/>
 #' reads the four 10-m bands: B2 (490 nm), B3 (560 nm), B4 (665 nm) and B8 (842 nm)
 "stars_sentinel2"

R/mdim.R

@@ -109,7 +109,7 @@ mdim_use_bounds = function(dims, x, bnds, center = TRUE) {
 #' @param raster names of the raster variables (default: first two dimensions)
 #' @param offset integer; offset for each dimension (pixels) of sub-array to read, defaults to 0 for each dimension(requires sf >= 1.0-9)
 #' @param count integer; size for each dimension (pixels) of sub-array to read (default: read all); a value of NA will read the corresponding dimension entirely; counts are relative to the step size (requires sf >= 1.0-9)
-#' @param step integer; step size for each dimension (pixels) of sub-aray to read; defaults to 1 for each dimension (requires sf >= 1.0-9)
+#' @param step integer; step size for each dimension (pixels) of sub-array to read; defaults to 1 for each dimension (requires sf >= 1.0-9)
 #' @param proxy logical; return proxy object? (not functional yet)
 #' @param debug logical; print debug info?
 #' @param bounds logical or character: if \code{TRUE} tries to infer from "bounds" attribute; if character, 

R/mosaic.R

@@ -7,7 +7,7 @@
 #' @param options character; options to the gdalbuildvrt command
 #' @param file_ext character; file extension, determining the format used to write to (".tif" implies GeoTIFF)
 #' @return the stars method returns a stars object with the composite of the input; the \code{character} method returns the file name of the file with the mosaic; see also the GDAL documentation of \code{gdalbuildvrt}
-#' @details the gdal function buildvrt builds a mosaic of input images; these imput images can be multi-band, but not higher-dimensional data cubes or stars objects with multiple attributes
+#' @details the gdal function buildvrt builds a mosaic of input images; these input images can be multi-band, but not higher-dimensional data cubes or stars objects with multiple attributes
 #' 
 #' uses \link[sf]{gdal_utils} to internally call \code{buildvrt}; no executables external to R are called.
 #' @export

R/ncdf.R

@@ -32,7 +32,7 @@
 #' curvilinear coordinates if they are not supplied.
 #' @param eps numeric; dimension value increases are considered identical when they differ less than \code{eps}
 #' @param ignore_bounds logical; should bounds values for dimensions, if present, be ignored?
-#' @param make_time if \code{TRUE} (the default), an atttempt is made to provide a date-time class from the "time" variable
+#' @param make_time if \code{TRUE} (the default), an attempt is made to provide a date-time class from the "time" variable
 #' @param make_units if \code{TRUE} (the default), an attempt is made to set the units property of each variable
 #' @param proxy logical; if \code{TRUE}, an object of class \code{stars_proxy} is read which contains array
 #' metadata only; if \code{FALSE} the full array data is read in memory. If not set, defaults to \code{TRUE}
@@ -45,7 +45,7 @@
 #' @details
 #' If \code{var} is not set the first set of variables on a shared grid is used.
 #'
-#' \code{start} and \code{count} columns of ncsub must correspond to the variable dimemsion (nrows)
+#' \code{start} and \code{count} columns of ncsub must correspond to the variable dimension (nrows)
 #' and be valid index using \code{\link[RNetCDF]{var.get.nc}} convention (start is 1-based). If the count value
 #' is \code{NA} then all steps are included. Axis order must match that of the variable/s being read.
 #' @export

R/plot.R

@@ -49,7 +49,7 @@ kw_dflt = function(x, key.pos) {
 #' @param breaks numeric vector with actual color breaks, or a \code{style} name used in \link[classInt]{classIntervals}.
 #' @param col colors to use for grid cells, or color palette function
 #' @param ... further arguments: for \code{plot}, passed on to \code{image.stars}; for \code{image}, passed on to \code{image.default} or \code{rasterImage}.
-#' @param key.pos numeric; side to plot a color key: 1 bottom, 2 left, 3 top, 4 right; set to \code{NULL} to omit key. Ignored if multiple columns are plotted in a single function call. Default depends on plot size, map aspect, and, if set, parameter \code{asp}. If it has lenght 2, the second value, ranging from 0 to 1, determines where the key is placed in the available space (default: 0.5, center).
+#' @param key.pos numeric; side to plot a color key: 1 bottom, 2 left, 3 top, 4 right; set to \code{NULL} to omit key. Ignored if multiple columns are plotted in a single function call. Default depends on plot size, map aspect, and, if set, parameter \code{asp}. If it has length 2, the second value, ranging from 0 to 1, determines where the key is placed in the available space (default: 0.5, center).
 #' @param key.width amount of space reserved for width of the key (labels); relative or absolute (using lcm)
 #' @param key.length amount of space reserved for length of the key (labels); relative or absolute (using lcm)
 #' @param key.lab character; label for color key in case of multiple subplots, use \code{""} to suppress

R/proxy.R

@@ -332,7 +332,7 @@ st_as_stars.stars_proxy = function(.x, ..., downsample = 0, url = attr(.x, "url"
 		ret # nocov end
 	} else {
 		cl = attr(.x, "call_list")
-		# FIXME: this means we ALLWAYS process after (possibly partial) reading; 
+		# FIXME: this means we ALWAYS process after (possibly partial) reading; 
 		# there are cases where this is not right. Hence:
 		# TODO: only warn when there is a reason to warn.
 		if (!all(downsample == 0))

R/stars.R

@@ -166,7 +166,7 @@ pretty_cut = function(lim, n, inside = FALSE, ...) {
 #' @param values value(s) to populate the raster values with
 #' @param n the (approximate) target number of grid cells
 #' @param pretty logical; should cell coordinates have \link{pretty} values?
-#' @param inside logical; should all cells entirely fall inside the bbox, potentially not covering it completely (\code{TRUE}), or allways cover the bbox (\code{FALSE}), or find a good approximation (\code{NA}, default)?
+#' @param inside logical; should all cells entirely fall inside the bbox, potentially not covering it completely (\code{TRUE}), or always cover the bbox (\code{FALSE}), or find a good approximation (\code{NA}, default)?
 #' @param proxy logical; should a \code{stars_proxy} object be created? (requires gdal_create binary when sf < 1.0-6)
 #' @details For the \code{bbox} method: if \code{pretty} is \code{TRUE}, raster cells may extend the coordinate range of \code{.x} on all sides. If in addition to \code{nx} and \code{ny}, \code{dx} and \code{dy} are also missing, these are set to a single value computed as \code{sqrt(diff(xlim)*diff(ylim)/n)}. 
 #' 

R/warp.R

@@ -22,7 +22,7 @@ default_target_grid = function(x, crs, cellsize = NA_real_, segments = NA) {
 	envelope = if (!is.na(segments) && !has_global_longitude(x)) # FIXME: should this branch be retained?
 				st_segmentize(envelope, st_length(st_cast(envelope, "LINESTRING"))/segments)
 			else {
-				# https://github.com/mtennekes/tmap/issues/526 :
+				# https://github.com/r-tmap/tmap/issues/526 :
 				old_crs = st_crs(envelope)
 				st_crs(envelope) = NA_crs_
 				st_set_crs(st_segmentize(envelope, st_length(st_cast(envelope, "LINESTRING"))/segments), old_crs)