v0.4.0 CRAN release

appelmar · Jul 15, 2021 · 2b5a868 · 2b5a868
1 parent 3cb7e23
commit 2b5a868
Show file tree

Hide file tree

Showing 13 changed files with 140 additions and 278 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -9,6 +9,7 @@
 ^src/gdalcubes/\.clang-format$
 ^src/gdalcubes/\.dockerignore$
 ^src/gdalcubes/\.travis.yml$
+^src/gdalcubes/\.github$
 ^src/gdalcubes/\.git$
 ^vignettes/MOD11A2$
 ^vignettes/MOD11A2\.db$
@@ -70,6 +71,7 @@
 ^Dockerfile$
 ^.*Dockerfile$
 ^\.dockerignore$
-^.github$
-^.pkgdown.R$
-^.test$
+^\.docker$
+^\.github$
+^\.pkgdown.R$
+^\.test.*$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: gdalcubes
 Title: Earth Observation Data Cubes from Satellite Image Collections
-Version: 0.3.9999
-Date: 2021-02-08
+Version: 0.4.0
+Date: 2021-07-08
 Authors@R: c(
     person(given = "Marius",
            family = "Appel",
@@ -46,13 +46,13 @@ Description: Processing collections of Earth observation images as on-demand mul
     multithreading. All computational parts are implemented in C++, linking to the 'GDAL', 'netCDF', 'CURL', and 'SQLite' libraries. 
     See Appel and Pebesma (2019) <doi:10.3390/data4030092> for further details.
 Depends: R (>= 3.4)
-Imports: Rcpp, jsonlite, ncdf4
+Imports: Rcpp, RcppProgress, jsonlite, ncdf4
 License: MIT + file LICENSE
 URL: https://github.com/appelmar/gdalcubes_R
 BugReports: https://github.com/appelmar/gdalcubes_R/issues/
 Encoding: UTF-8
 RoxygenNote: 7.1.1
-LinkingTo: Rcpp, RcppThread
+LinkingTo: Rcpp, RcppProgress
 Suggests: 
     knitr,
     magrittr,

diff --git a/NAMESPACE b/NAMESPACE
@@ -64,13 +64,12 @@ export(size)
 export(srs)
 export(st_as_stars.cube)
 export(stac_image_collection)
-export(translate_cog)
-export(translate_gtiff)
 export(window_time)
 export(write_chunk_from_array)
 export(write_ncdf)
 export(write_tif)
 export(zonal_statistics)
+import(RcppProgress)
 import(jsonlite)
 import(ncdf4)
 importFrom(Rcpp,sourceCpp)

diff --git a/NEWS.md b/NEWS.md
@@ -1,18 +1,16 @@
 
-# gdalcubes 0.3.2 (under development)
+# gdalcubes 0.4.0 (2021-07-08)
 
 * new operator `ncdf_cube()` to read data cubes from (intermediate) results
 * new operator `rename_bands()` to change band names
 * image collection creation from STAC API queries with `stac_image_collection()`
 * progress bar can now be disabled with `gdalcubes_options()`
-* new progress bar
-* removed `RcppProgress` package dependency
-* C++ multithreading now uses `RcppThread` 
 * removed `gdalcubes_set_threads()` in favor of `gdalcubes_options()` 
 * removed `gdalcubes_debug_output()` in favor of `gdalcubes_options()` 
 * removed `gdalcubes_set_ncdf_compression()` in favor of `gdalcubes_options()` 
 * removed `gdalcubes_use_cache()` in favor of `gdalcubes_options()` 
-
+* removed image collection operations `translate_COG()` and `translate_gtiff()`
+* fix installation issues on MacOS and GCC11 warnings
 
 
 # gdalcubes 0.3.1 (2020-08-25)

diff --git a/R/gdalcubes.R b/R/gdalcubes.R
@@ -17,7 +17,7 @@
 #' @importFrom graphics axis box image.default layout lcm par plot rasterImage rect title legend lines
 #' @importFrom stats quantile rnorm
 #' @importFrom utils head download.file
-#' @import jsonlite ncdf4 
+#' @import RcppProgress jsonlite ncdf4 
 #' 
 #' 
 #' 

diff --git a/R/image_collection_ops.R b/R/image_collection_ops.R
diff --git a/R/zzz.R b/R/zzz.R
@@ -16,7 +16,7 @@
   .pkgenv$ncdf_write_bounds = TRUE 
   .pkgenv$use_overview_images = TRUE
   if (interactive()) {
-    .pkgenv$show_progress = FALSE
+    .pkgenv$show_progress = TRUE
   }
   else {
     .pkgenv$show_progress = FALSE

diff --git a/README.md b/README.md
@@ -262,7 +262,7 @@ x
     ## resolution : 1000, 1000  (x, y)
     ## extent     : -6582280, -5799280, -764014.4, -205014.4  (xmin, xmax, ymin, ymax)
     ## crs        : +proj=merc +a=6378137 +b=6378137 +lat_ts=0 +lon_0=0 +x_0=0 +y_0=0 +k=1 +units=m +nadgrids=@null +wktext +no_defs 
-    ## names      : cube_4a86d5076049c2013, cube_4a86d5076049c2014, cube_4a86d5076049c2015, cube_4a86d5076049c2016, cube_4a86d5076049c2017, cube_4a86d5076049c2018, cube_4a86d5076049c2019
+    ## names      : cube_2a3ac18d60def2013, cube_2a3ac18d60def2014, cube_2a3ac18d60def2015, cube_2a3ac18d60def2016, cube_2a3ac18d60def2017, cube_2a3ac18d60def2018, cube_2a3ac18d60def2019
 
 ``` r
 suppressPackageStartupMessages(library(stars))
@@ -351,17 +351,17 @@ raster_cube(L8.col, v.overview) %>%
   query_points(x,y,t, v.overview$space$srs)
 ```
 
-    ##         B04       B05
-    ## 1  431.5464  455.1081
-    ## 2  205.4124 2851.5982
-    ## 3  258.9569 2527.4188
-    ## 4  249.7894 3129.4676
-    ## 5  259.1570 3277.0765
-    ## 6       NaN       NaN
-    ## 7       NaN       NaN
-    ## 8  167.8571 2888.4166
-    ## 9       NaN       NaN
-    ## 10      NaN       NaN
+    ##          B04       B05
+    ## 1   176.5942 3032.5324
+    ## 2        NaN       NaN
+    ## 3  3878.2453 4828.9001
+    ## 4   309.5338  221.7426
+    ## 5        NaN       NaN
+    ## 6   213.2422 3180.3651
+    ## 7   725.4656 3244.4685
+    ## 8        NaN       NaN
+    ## 9   731.5507 2186.4171
+    ## 10       NaN       NaN
 
 ``` r
 raster_cube(L8.col, v.overview) %>%
@@ -370,30 +370,30 @@ raster_cube(L8.col, v.overview) %>%
 ```
 
     ## $B04
-    ##        2013     2014     2015      2016     2017     2018     2019
-    ## 1  221.9795 431.5464 315.9992  388.2862 490.8458      NaN 188.7578
-    ## 2  214.8850 192.7086 262.5035  205.4124 231.8854 232.1024 918.7678
-    ## 3  282.3089 230.5423 264.7602  263.5589 225.6577 258.9569 196.1888
-    ## 4       NaN 247.1129 287.4146  249.7894 423.3914 257.3268      NaN
-    ## 5       NaN 259.1570      NaN 4162.9515 188.5636 293.4895 216.6074
-    ## 6       NaN      NaN      NaN       NaN      NaN      NaN      NaN
-    ## 7       NaN      NaN      NaN       NaN      NaN      NaN      NaN
-    ## 8  168.4943 203.5209 249.7479  674.5761 169.0721 227.1009 167.8571
-    ## 9       NaN      NaN      NaN       NaN      NaN      NaN      NaN
-    ## 10      NaN      NaN      NaN       NaN      NaN      NaN      NaN
+    ##        2013      2014     2015     2016     2017      2018      2019
+    ## 1  168.1739  166.4379 199.2356 218.3613 176.5942  164.1710  152.0536
+    ## 2       NaN       NaN      NaN      NaN      NaN       NaN       NaN
+    ## 3  342.9068  198.0663 188.4386 171.4423 234.2039  176.9131 3878.2453
+    ## 4       NaN  309.5338 653.0165 490.7659 334.7592  662.8106       NaN
+    ## 5       NaN       NaN      NaN      NaN      NaN       NaN       NaN
+    ## 6  158.2323  213.2422 288.2853 228.0108 222.6970  175.8526  152.9250
+    ## 7       NaN  233.6421 286.0872 725.4656 234.8174 1012.2984       NaN
+    ## 8       NaN       NaN      NaN      NaN      NaN       NaN       NaN
+    ## 9  570.6068 1094.3404 698.8447 286.1469 731.5507       NaN  193.9442
+    ## 10      NaN  242.1999 295.2309 283.9409 256.7757  270.4900       NaN
     ## 
     ## $B05
-    ##         2013      2014      2015      2016      2017     2018      2019
-    ## 1   181.1607  455.1081  355.2088  404.1128  385.7219      NaN  126.5602
-    ## 2  2971.5674 2993.9556 3041.8152 2851.5982 3162.7466 3070.888 3082.5338
-    ## 3  2842.5738 2752.5699 2840.5063 2970.3880 2998.9544 2527.419 2808.5265
-    ## 4        NaN 3155.3942 3341.5062 3129.4676 3349.6015 3404.804       NaN
-    ## 5        NaN 3277.0765       NaN 5617.8526 3158.9640 3422.652 3237.7933
-    ## 6        NaN       NaN       NaN       NaN       NaN      NaN       NaN
-    ## 7        NaN       NaN       NaN       NaN       NaN      NaN       NaN
-    ## 8  2841.4007 2891.8610 2888.1330 3083.6199 2823.1811 2904.574 2888.4166
-    ## 9        NaN       NaN       NaN       NaN       NaN      NaN       NaN
-    ## 10       NaN       NaN       NaN       NaN       NaN      NaN       NaN
+    ##        2013      2014      2015      2016      2017      2018      2019
+    ## 1  2881.747 3006.7054 2988.5880 3004.6927 3032.5324 2856.9048 2918.1521
+    ## 2       NaN       NaN       NaN       NaN       NaN       NaN       NaN
+    ## 3  3117.646 3057.9624 2891.6479 2843.5118 3050.4765 2869.4212 4828.9001
+    ## 4       NaN  221.7426  337.6181  220.5666  227.3253  435.6817       NaN
+    ## 5       NaN       NaN       NaN       NaN       NaN       NaN       NaN
+    ## 6  2991.214 3180.3651 3131.6213 3199.9639 3090.0413 3103.3886 3027.6535
+    ## 7       NaN 2994.1378 3212.3224 3244.4685 2994.0125 2884.8660       NaN
+    ## 8       NaN       NaN       NaN       NaN       NaN       NaN       NaN
+    ## 9   663.193 1116.9384  650.0309  848.6397 2186.4171       NaN  394.6935
+    ## 10      NaN 3167.8636 3493.6315 3106.9801 3229.5042 3434.0334       NaN
 
 To compute time series of summary statistics over spatial polygons, we
 need to specify polygon geometries (e.g., as an `sf` object) and specify

diff --git a/configure b/configure
@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for gdalcubes 0.3.2.
+# Generated by GNU Autoconf 2.69 for gdalcubes 0.4.0.
 #
 # Report bugs to <marius.appel@uni-muenster.de>.
 #
@@ -580,8 +580,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='gdalcubes'
 PACKAGE_TARNAME='gdalcubes'
-PACKAGE_VERSION='0.3.2'
-PACKAGE_STRING='gdalcubes 0.3.2'
+PACKAGE_VERSION='0.4.0'
+PACKAGE_STRING='gdalcubes 0.4.0'
 PACKAGE_BUGREPORT='marius.appel@uni-muenster.de'
 PACKAGE_URL=''
 
@@ -1257,7 +1257,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures gdalcubes 0.3.2 to adapt to many kinds of systems.
+\`configure' configures gdalcubes 0.4.0 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1319,7 +1319,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of gdalcubes 0.3.2:";;
+     short | recursive ) echo "Configuration of gdalcubes 0.4.0:";;
    esac
   cat <<\_ACEOF
 
@@ -1415,7 +1415,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-gdalcubes configure 0.3.2
+gdalcubes configure 0.4.0
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -1717,7 +1717,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by gdalcubes $as_me 0.3.2, which was
+It was created by gdalcubes $as_me 0.4.0, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -4503,7 +4503,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by gdalcubes $as_me 0.3.2, which was
+This file was extended by gdalcubes $as_me 0.4.0, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -4556,7 +4556,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-gdalcubes config.status 0.3.2
+gdalcubes config.status 0.4.0
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 

diff --git a/configure.ac b/configure.ac
@@ -1,6 +1,6 @@
 # Process this file with autoconf to produce a configure script.
 
-AC_INIT(gdalcubes, 0.3.2, marius.appel@uni-muenster.de)
+AC_INIT(gdalcubes, 0.4.0, marius.appel@uni-muenster.de)
 AC_LANG(C++)
 
 # find R home and set CC/CFLAGS