v. 1.3.2 (#285)

.Rbuildignore

@@ -13,3 +13,5 @@
 ^LICENSE\.md$
 ^cran\-comments\.md$
 ^CRAN-RELEASE$
+^doc$
+^Meta$

.gitignore

@@ -23,3 +23,5 @@ vignettes/*.pdf
 *.knit.md
 .Rproj.user
 *.Rproj
+doc
+Meta

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: sen2r
 Type: Package
 Title: Find, Download and Process Sentinel-2 Data
-Version: 1.3.1.9004
+Version: 1.3.2
 Authors@R: c(person("Luigi", "Ranghetti",
                     email = "[email protected]",
                     role = c("aut", "cre"),

NEWS.md

@@ -1,3 +1,25 @@
+# Version 1.3.2
+
+## New features
+* Add argument `req_res` to `safe_isvalid()` and `rm_invalid_safe()`: now the presence of the JP2 images required by the processing chain is checked by default. L2A products without all the three resolutions will not be used.
+* Add output field `"res"` to the default `safe_getMetadata()` output, with the list of the available resolutions ("`all`" is returned in case of L1C products).
+
+## New function arguments
+* Add argument `timeout` to `sen2cor()` to limit the maximum Sen2cor execution time (after that time, Sen2Cor is stopped). This is useful to avoid blocking processing chains due to internal Sen2Cor errors.
+
+## Dependencies
+* Add new suggested dependency **`sys`** (it is used to call Sen2Cor using `sys::exec_wait()` instead than `system()`, allowing exporting Sen2Cor output to log files).
+* Add new suggested dependency **`rgdal`** (since it is implicitly called by internal functions), as requested by CRAN policy.
+* Move **`units`** and **`tools`** to suggested dependencies.
+* Prepare to move **`shiny*`** and **`leaflet*`** dependencies to suggested (this will be done in a future release).
+
+## Minor changes
+* Allow choosing if ordering SAFE products from `dhus` or `apihub` (experimental).
+* Replace all `GET()` calls with `RETRY()`, so to avoid errors in case of temporary unavailability of services.
+* Allow Sen2Cor running with oldname SAFE (although the usage of these products is generally deprecated).
+* Bug fixes (#272, #276).
+
+
 # Version 1.3.1
 
 ## Major changes
@@ -35,7 +57,7 @@
 - Internal function `sen2r_process_report()` to manage processing reports returned by `sen2r()`.
 
 ## Deprecated functions
-- Internal function `init_python()` was deprecated (Python is no longer managed by **reticulate**).
+- Internal function `init_python()` was deprecated (Python is no longer managed by **`reticulate`**).
 
 ## Changes in default argument values
 - New argument `bigtiff` for BigTIFF management in functions `s2_translate()`, `s2_merge()`, `s2_mask()`, `s2_rgb()` and `s2_calcindices()`.

README.Rmd

@@ -92,13 +92,11 @@ For detailed instructions about using it, see the page ["Run in a Docker contain
 
 The simplest way to use
 <span style="color:#5793dd;vertical-align:top;font-size:90%;font-weight:normal;">sen</span><span style="color:#6a7077;vertical-align:baseline;font-size:115%;font-weight:bolder;">2</span><span style="color:#2f66d5;vertical-align:baseline;font-size:90%;font-weight:bold;">r</span>
-is to execute it in interactive mode:
+is to execute it in interactive mode (see [this vignette](http://sen2r.ranghetti.info/articles/sen2r_gui.html)):
 ```{r, eval = FALSE}
 library(sen2r)
 sen2r()
 ```
-this opens a GUI which allows to set the required processing parameters,
-and then launches the main function.
 
 <p style="text-align:center;">
   <a href="https://raw.githubusercontent.com/ranghetti/sen2r/devel/man/figures/sen2r_gui_sheet1.png" target="_blank">
@@ -124,32 +122,28 @@ Alternatively,
 can be launched with a list of parameters (created with
 [`s2_gui()`](http://sen2r.ranghetti.info/reference/s2_gui.html))
 or passing manually the parameters as arguments of the function
-(see [the documentation of the function](http://sen2r.ranghetti.info/reference/sen2r.html) for further details).
+(see [this vignette](http://sen2r.ranghetti.info/articles/sen2r_cmd.html) for further details).
 
-Other specific functions can be used to run single steps separately:
+Other specific functions can be used to run single steps separately.
+This is a list of the principal processing functions 
+(the complete list can be found in the Reference page):
 
 * [`s2_list()`](http://sen2r.ranghetti.info/reference/s2_list.html)
     to retrieve the list of available Sentinel-2 products based on input parameters;
 * [`s2_download()`](http://sen2r.ranghetti.info/reference/s2_download.html)
     to download Sentinel-2 products;
+* [`s2_order()`](http://sen2r.ranghetti.info/reference/s2_order.html)
+    to order products from the Long Term Archive;
 * [`sen2cor()`](reference/sen2cor.html)
     to correct level-1C products using [Sen2Cor](http://step.esa.int/main/third-party-plugins-2/sen2cor);
-* [`s2_translate()`](http://sen2r.ranghetti.info/reference/s2_translate.html)
-    to convert Sentinel-2 products from SAFE format to a format managed by GDAL;
-* [`s2_merge()`](http://sen2r.ranghetti.info/reference/s2_merge.html)
-    to merge Sentinel-2 tiles which have the same date and orbit;
-* [`gdal_warp()`](http://sen2r.ranghetti.info/reference/gdal_warp.html)
-    to clip, reproject and warp raster files (this is a wrapper to call
-    [gdal_translate](http://www.gdal.org/gdal_translate.html) or
-    [gdalwarp](http://www.gdal.org/gdalwarp.html) based on input parameters);
 * [`s2_mask()`](http://sen2r.ranghetti.info/reference/s2_mask.html)
     to apply a cloud mask to Sentinel-2 products;
 * [`s2_rgb()`](http://sen2r.ranghetti.info/reference/s2_rgb.html)
     to generate RGB images from Sentinel-2 Surface Reflectance multiband raster files;
 * [`s2_calcindices()`](http://sen2r.ranghetti.info/reference/s2_calcindices.html)
-    to compute maps of spectral indices from Sentinel-2 Surface Reflectance multiband raster files;
-* [`s2_thumbnails()`](http://sen2r.ranghetti.info/reference/s2_thumbnails.html)
-    to generate RGB thumbnails (JPEG or PNG) of the products.
+    to compute maps of spectral indices from Sentinel-2 Surface Reflectance multiband raster files.
+
+Output products follow a specific naming convention (see [here](http://sen2r.ranghetti.info/articles/outstructure.html) for details).
 
 ## Credits
 
@@ -186,4 +180,3 @@ By participating in this project you agree to abide by its terms.
 Users are encouraged to use GitHub issues in case of errors with the package.
 Before opening a new issue, please read
  <a href="https://github.com/ranghetti/sen2r/issues/186" target="_blank">these notes</a>.
-

README.md

@@ -97,17 +97,14 @@ container”](http://sen2r.ranghetti.info/articles/docker.html) page.
 
 The simplest way to use
 <span style="color:#5793dd;vertical-align:top;font-size:90%;font-weight:normal;">sen</span><span style="color:#6a7077;vertical-align:baseline;font-size:115%;font-weight:bolder;">2</span><span style="color:#2f66d5;vertical-align:baseline;font-size:90%;font-weight:bold;">r</span>
-is to execute it in interactive mode:
+is to execute it in interactive mode (see [this
+vignette](http://sen2r.ranghetti.info/articles/sen2r_gui.html)):
 
 ``` r
 library(sen2r)
 sen2r()
 ```
 
-this opens a GUI which allows to set the required processing parameters,
-and then launches the main
-function.
-
 <p style="text-align:center;">
 
 <a href="https://raw.githubusercontent.com/ranghetti/sen2r/devel/man/figures/sen2r_gui_sheet1.png" target="_blank">
@@ -127,32 +124,24 @@ Alternatively,
 [`sen2r()`](http://sen2r.ranghetti.info/reference/sen2r.html) can be
 launched with a list of parameters (created with
 [`s2_gui()`](http://sen2r.ranghetti.info/reference/s2_gui.html)) or
-passing manually the parameters as arguments of the function (see [the
-documentation of the
-function](http://sen2r.ranghetti.info/reference/sen2r.html) for further
-details).
+passing manually the parameters as arguments of the function (see [this
+vignette](http://sen2r.ranghetti.info/articles/sen2r_cmd.html) for
+further details).
 
-Other specific functions can be used to run single steps separately:
+Other specific functions can be used to run single steps separately.
+This is a list of the principal processing functions (the complete list
+can be found in the Reference page):
 
   - [`s2_list()`](http://sen2r.ranghetti.info/reference/s2_list.html) to
     retrieve the list of available Sentinel-2 products based on input
     parameters;
   - [`s2_download()`](http://sen2r.ranghetti.info/reference/s2_download.html)
     to download Sentinel-2 products;
+  - [`s2_order()`](http://sen2r.ranghetti.info/reference/s2_order.html)
+    to order products from the Long Term Archive;
   - [`sen2cor()`](reference/sen2cor.html) to correct level-1C products
     using
     [Sen2Cor](http://step.esa.int/main/third-party-plugins-2/sen2cor);
-  - [`s2_translate()`](http://sen2r.ranghetti.info/reference/s2_translate.html)
-    to convert Sentinel-2 products from SAFE format to a format managed
-    by GDAL;
-  - [`s2_merge()`](http://sen2r.ranghetti.info/reference/s2_merge.html)
-    to merge Sentinel-2 tiles which have the same date and
-    orbit;
-  - [`gdal_warp()`](http://sen2r.ranghetti.info/reference/gdal_warp.html)
-    to clip, reproject and warp raster files (this is a wrapper to call
-    [gdal\_translate](http://www.gdal.org/gdal_translate.html) or
-    [gdalwarp](http://www.gdal.org/gdalwarp.html) based on input
-    parameters);
   - [`s2_mask()`](http://sen2r.ranghetti.info/reference/s2_mask.html) to
     apply a cloud mask to Sentinel-2 products;
   - [`s2_rgb()`](http://sen2r.ranghetti.info/reference/s2_rgb.html) to
@@ -161,10 +150,11 @@ Other specific functions can be used to run single steps separately:
     files;
   - [`s2_calcindices()`](http://sen2r.ranghetti.info/reference/s2_calcindices.html)
     to compute maps of spectral indices from Sentinel-2 Surface
-    Reflectance multiband raster
-    files;
-  - [`s2_thumbnails()`](http://sen2r.ranghetti.info/reference/s2_thumbnails.html)
-    to generate RGB thumbnails (JPEG or PNG) of the products.
+    Reflectance multiband raster files.
+
+Output products follow a specific naming convention (see
+[here](http://sen2r.ranghetti.info/articles/outstructure.html) for
+details).
 
 ## Credits
 
@@ -186,17 +176,17 @@ International license](https://creativecommons.org/licenses/by-sa/4.0)
 
 To cite this library, please use the following entry:
 
-Ranghetti, L. and Busetto, L. (2019). *sen2r: Find, Download and Process
-Sentinel-2 Data*. R package version 1.2.0. DOI:
+Ranghetti, L. and Busetto, L. (2020). *sen2r: Find, Download and Process
+Sentinel-2 Data*. R package version 1.3.2. DOI:
 [10.5281/zenodo.1240384](https://dx.doi.org/10.5281/zenodo.1240384).
 URL: <http://sen2r.ranghetti.info>.
 
 ``` bibtex
 @Manual{sen2r,
   title  = {sen2r: Find, Download and Process Sentinel-2 Data},
   author = {Luigi Ranghetti and Lorenzo Busetto},
-  year   = {2019},
-  note   = {R package version 1.2.0},
+  year   = {2020},
+  note   = {R package version 1.3.2},
   doi    = {10.5281/zenodo.1240384},
   url    = {http://sen2r.ranghetti.info},
 }

cran-comments.md

@@ -1,4 +1,4 @@
-# sen2r v. 1.3.1
+# sen2r v. 1.3.2
 
 ## Test environments
 * [local installation] Ubuntu 18.04, 64 bit, R 3.6.2
@@ -10,15 +10,12 @@
 * [R-hub] macOS 10.11 El Capitan, R-release (experimental)
 
 ## R CMD check results
-There were no ERRORs or WARNINGs.
+There were no ERRORs, WARNINGs or NOTEs on all the tested platforms,
+with the exception of win-builder oldrelease,
+which returned the following warning:
 
-There was 1 NOTE:
-Days since last update: 3
+Found the following significant warnings:
+  Warning: namespace 'rgdal' is not available and has been replaced
 
-In the previous version 1.3.0 a bug was discovered:
-in case the environmental variables PYTHONHOME and PYTHONPATH were not
-previously set, Python-based utilities called by the package crash.
-The bug interests portions of code which are commonly called by users, 
-and it can affect a large part of Windows users:
-this is the reason why releasing this new version 1.3.1, 
-which corrects this bug, is so urgent.
+This warning is quite strange, being rgdal a well-known R package working also
+on R 3.5.2, for which binaries for r-oldrel are available and updated.