Merge pull request #335 from ranghetti/devel

RC v. 1.3.7
ranghetti · Jul 6, 2020 · b0d8d41 · b0d8d41
2 parents 74acccd + dc47fbe
commit b0d8d41
Show file tree

Hide file tree

Showing 125 changed files with 380 additions and 257 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: sen2r
 Type: Package
 Title: Find, Download and Process Sentinel-2 Data
-Version: 1.3.6.9002
+Version: 1.3.7
 Authors@R: c(person("Luigi", "Ranghetti",
                     email = "[email protected]",
                     role = c("aut", "cre"),
@@ -51,6 +51,7 @@ Suggests:
   geojsonlint,
   httptest,
   knitr,
+  markdown,
   rmarkdown,
   sys,
   tools,

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,22 @@
+# Version 1.3.7
+
+## Major changes
+- Some additional products are now supported: `CLD`, `SNW`, `AOT`, `WVP` (see documentation for description). The GUI and internal functions were modified to support their selection and generation.
+
+## Minor changes
+- Add indices Red / Green / Blue Chromatic Coordinate (`Rcc`, `Gcc`, `Bcc`) and Excess Green (`ExG`) (#330).
+- All methods based on runtime GDAL are now discouraged and never called by default (before this version, they were used in case GDAL was found on `paths.json`).
+- Output GeoTIFF files are now tiled.
+
+## Documentation
+- New products were documented in function references and in the article ["Output file structure"](https://sen2r.ranghetti.info/articles/outstructure).
+- Function references explicit discourage the use of GDAL-based methods.
+- The documentation site links to the personal page https://luigi.ranghetti.info/.
+
+## Bug fixes
+- Fix #318, #323 and #329.
+
+
 # Version 1.3.6
 
 ## Bug fixes 

diff --git a/R/gipp.R b/R/gipp.R
@@ -55,9 +55,14 @@ gipp_init <- function(gipp_sen2r_path = NA, force = FALSE, dem_warning = FALSE)
       sen2cor_version_raw1
     )
     # define L2A_GIPP.xml path
-    gipp_sen2cor_path <- normalize_path(
-      file.path("~/sen2cor", sen2cor_version, "cfg/L2A_GIPP.xml")
-    )
+    gipp_sen2cor_path <- normalize_path(file.path(
+      if (Sys.info()["sysname"] == "Windows") {
+        file.path(Sys.getenv("USERPROFILE"), "Documents")
+      } else {
+        "~"
+      },
+      "sen2cor", sen2cor_version, "cfg/L2A_GIPP.xml"
+    ))
     # (this assumes Sen2Cor to be installed and configured to be used with sen2r)
 
     if (!file.exists(gipp_sen2cor_path)) {

diff --git a/R/s2_gui.R b/R/s2_gui.R
@@ -145,6 +145,7 @@ s2_gui <- function(param_list = NULL,
   tabItem <- shinydashboard::tabItem
   tabItems <- shinydashboard::tabItems
   tagList <- shiny::tagList
+  tags <- shiny::tags
   textInput <- shiny::textInput
   toggle <- shinyjs::toggle
   uiOutput <- shiny::uiOutput
@@ -171,7 +172,35 @@ s2_gui <- function(param_list = NULL,
   # shiny
   s2_gui.ui <- dashboardPage(
     title = "sen2r: Find, Download and Process Sentinel-2 Data",
-    header = dashboardHeader(),
+    header = dashboardHeader(
+
+      tags$li(class ="dropdown", tags$a(
+        href="http://sen2r.ranghetti.info",
+        shiny::icon("book"),
+        style="margin:0;padding-top:11px;padding-bottom:11px;padding-left:10px;padding-right:10px;font-size:30px;",
+        target="_blank"
+      )),
+      tags$li(class ="dropdown", tags$a(
+        href="https://github.com/ranghetti/sen2r",
+        shiny::icon("github"),
+        style="margin:0;padding-top:11px;padding-bottom:11px;padding-left:10px;padding-right:10px;font-size:30px;",
+        target="_blank"
+      )),
+      tags$li(class ="dropdown", tags$a(
+        href="https://luigi.ranghetti.info",
+        shiny::icon("user"),
+        style="margin:0;padding-top:11px;padding-bottom:11px;padding-left:10px;padding-right:10px;font-size:30px;",
+        target="_blank"
+      )),
+      tags$li(class ="dropdown", tags$a(
+        href="http://www.irea.cnr.it",
+        tags$img(src="www/images/irea_logo.png"),
+        style="margin:0;padding-top:2px;padding-bottom:2px;padding-left:10px;padding-right:10px;",
+        target="_blank"
+      ))
+
+
+    ),
     sidebar = dashboardSidebar(
 
       # logo

diff --git a/R/str_pad2.R b/R/str_pad2.R
@@ -1,6 +1,7 @@
 #' @title Pad a string.
 #' @description Vectorised over `string`, `width` and `pad`.
-#'  This is an internal function doing the same thing of [stringr::str_pad]
+#'  This is an internal function doing the same thing of `str_pad()`
+#'  function in package `stringr`
 #'  (except for parameters `'width'` and `'length'` which must be of length 1),
 #'  but without depending on package `stringi`.
 #' @param string A character vector.

diff --git a/README.Rmd b/README.Rmd
@@ -107,20 +107,20 @@ sen2r()
 ```
 
 <p style="text-align:center;">
-  <a href="https://raw.githubusercontent.com/ranghetti/sen2r/devel/man/figures/sen2r_gui_sheet1.png" target="_blank">
+  <a href="https://raw.githubusercontent.com/ranghetti/sen2r/master/man/figures/sen2r_gui_sheet1.png" target="_blank">
     <img src="man/figures/sen2r_gui_sheet1_small.png">
   </a>
-  <a href="https://raw.githubusercontent.com/ranghetti/sen2r/devel/man/figures/sen2r_gui_sheet2.png" target="_blank">
+  <a href="https://raw.githubusercontent.com/ranghetti/sen2r/master/man/figures/sen2r_gui_sheet2.png" target="_blank">
     <img src="man/figures/sen2r_gui_sheet2_small.png">
   </a>
   <br/>
-  <a href="https://raw.githubusercontent.com/ranghetti/sen2r/devel/man/figures/sen2r_gui_sheet3.png" target="_blank">
+  <a href="https://raw.githubusercontent.com/ranghetti/sen2r/master/man/figures/sen2r_gui_sheet3.png" target="_blank">
     <img src="man/figures/sen2r_gui_sheet3_small.png">
   </a>
-  <a href="https://raw.githubusercontent.com/ranghetti/sen2r/devel/man/figures/sen2r_gui_sheet4.png" target="_blank">
+  <a href="https://raw.githubusercontent.com/ranghetti/sen2r/master/man/figures/sen2r_gui_sheet4.png" target="_blank">
     <img src="man/figures/sen2r_gui_sheet4_small.png">
   </a>
-  <a href="https://raw.githubusercontent.com/ranghetti/sen2r/devel/man/figures/sen2r_gui_sheet5.png" target="_blank">
+  <a href="https://raw.githubusercontent.com/ranghetti/sen2r/master/man/figures/sen2r_gui_sheet5.png" target="_blank">
     <img src="man/figures/sen2r_gui_sheet5_small.png">
   </a>
 </p>

diff --git a/README.md b/README.md
@@ -117,15 +117,15 @@ sen2r()
 
 <p style="text-align:center;">
 
-<a href="https://raw.githubusercontent.com/ranghetti/sen2r/devel/man/figures/sen2r_gui_sheet1.png" target="_blank">
+<a href="https://raw.githubusercontent.com/ranghetti/sen2r/master/man/figures/sen2r_gui_sheet1.png" target="_blank">
 <img src="man/figures/sen2r_gui_sheet1_small.png"> </a>
-<a href="https://raw.githubusercontent.com/ranghetti/sen2r/devel/man/figures/sen2r_gui_sheet2.png" target="_blank">
+<a href="https://raw.githubusercontent.com/ranghetti/sen2r/master/man/figures/sen2r_gui_sheet2.png" target="_blank">
 <img src="man/figures/sen2r_gui_sheet2_small.png"> </a> <br/>
-<a href="https://raw.githubusercontent.com/ranghetti/sen2r/devel/man/figures/sen2r_gui_sheet3.png" target="_blank">
+<a href="https://raw.githubusercontent.com/ranghetti/sen2r/master/man/figures/sen2r_gui_sheet3.png" target="_blank">
 <img src="man/figures/sen2r_gui_sheet3_small.png"> </a>
-<a href="https://raw.githubusercontent.com/ranghetti/sen2r/devel/man/figures/sen2r_gui_sheet4.png" target="_blank">
+<a href="https://raw.githubusercontent.com/ranghetti/sen2r/master/man/figures/sen2r_gui_sheet4.png" target="_blank">
 <img src="man/figures/sen2r_gui_sheet4_small.png"> </a>
-<a href="https://raw.githubusercontent.com/ranghetti/sen2r/devel/man/figures/sen2r_gui_sheet5.png" target="_blank">
+<a href="https://raw.githubusercontent.com/ranghetti/sen2r/master/man/figures/sen2r_gui_sheet5.png" target="_blank">
 <img src="man/figures/sen2r_gui_sheet5_small.png"> </a>
 
 </p>

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,20 +1,18 @@
-# sen2r v. 1.3.6
+# sen2r v. 1.3.7
 
 ## Test environments
 * [local installation] Ubuntu 18.04, 64 bit, R 3.6.3
-* [local installation] Archlinux, 64 bit, R 4.0.0
+* [local installation] Archlinux, 64 bit, R 4.0.2
 * [local installation] Windows 10, 64 bit, R 4.0.0
 * [local installation] Windows 10, 64 bit, R 3.6.3
 * [travis-ci] Ubuntu 16.04.6 LTS, 64 bit, R 3.6.2 (devel, release and oldrelease)
-* [win-builder] R unstable (r78617), 4.0.0 and 3.6.3 (devel, release and oldrelease)
+* [win-builder] R unstable, 4.0.2 and 3.6.3 (devel, release and oldrelease)
 
 ## R CMD check results
 There were no ERRORs or WARNINGs.
 
 A note was returned:
 ```
-Days since last update: 3
+Number of updates in past 6 months: 7
 ```
-this because this is a bug-fixing release:
-the bug I need to fix affects the major part of Windows users, 
-so this patch is urgent.
+this because this package is quite recente and under active development.
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/CODE-OF-CONDUCT.html b/docs/CODE-OF-CONDUCT.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/articles/docker.html b/docs/articles/docker.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/installation.html b/docs/articles/installation.html
diff --git a/docs/articles/outstructure.html b/docs/articles/outstructure.html
diff --git a/docs/articles/sen2r_cmd.html b/docs/articles/sen2r_cmd.html
diff --git a/docs/articles/sen2r_gui.html b/docs/articles/sen2r_gui.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/man/figures/sen2r_gui_sheet1_small.png b/docs/man/figures/sen2r_gui_sheet1_small.png
diff --git a/docs/man/figures/sen2r_gui_sheet2_small.png b/docs/man/figures/sen2r_gui_sheet2_small.png
diff --git a/docs/man/figures/sen2r_gui_sheet3_small.png b/docs/man/figures/sen2r_gui_sheet3_small.png
diff --git a/docs/man/figures/sen2r_gui_sheet4_small.png b/docs/man/figures/sen2r_gui_sheet4_small.png
diff --git a/docs/man/figures/sen2r_gui_sheet5_small.png b/docs/man/figures/sen2r_gui_sheet5_small.png