Update documentation and version (#402)

ranghetti · May 4, 2021 · 96e3ae6 · 96e3ae6
1 parent 347e635
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -3,6 +3,7 @@
 on:
   push:
     branches:
+      - master
       - devel
   pull_request:
     branches:

diff --git a/.github/workflows/R-CMD-check_sf_develop.yaml b/.github/workflows/R-CMD-check_sf_develop.yaml
@@ -3,6 +3,7 @@
 on:
   push:
     branches:
+      - master
       - devel
 
 name: R-CMD-check_sf_develop

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: sen2r
 Type: Package
 Title: Find, Download and Process Sentinel-2 Data
-Version: 1.4.2.9002
+Version: 1.4.3
 Authors@R: c(person("Luigi", "Ranghetti",
                     email = "[email protected]",
                     role = c("aut", "cre"),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,23 @@
+# Version 1.4.3
+
+## Minor changes
+- Use API URLs `https://apihub.copernicus.eu/apihub` instead of 
+    `https://scihub.copernicus.eu/apihub` as required after changes at 
+    SciHub side (https://scihub.copernicus.eu/news/News00868).
+- Manage multiple SciHub credentials when ordering SAFE archives from LTA
+    (experimental).
+
+## Documentation
+- Replace `http://` with `https://` in documentation _URLs. 
+
+## Checks
+- Replace Travis with GitHub Actions (and fix tests accordingly).
+
+## Bug fixes
+- Avoid topology errors on S2 footprints (to fix errors using `{sf}` 1.0).
+- Manage situations like in #397 (too many nodes for ESA API query).
+
+
 # Version 1.4.2
 
 ## Bug fixes

diff --git a/R/abs2rel.R b/R/abs2rel.R
@@ -25,15 +25,15 @@
 #'
 #' @examples
 #' # the reference path
-#' (ref_path <- system.file(package="sen2r"))
+#' (ref_path <- system.file(package="sf"))
 #' # a path with a common parent with ref_path
-#' (in_path_1 <- system.file(package="gdalUtils"))
+#' (in_path_1 <- system.file(package="rgdal"))
 #' # a path included in ref_path
-#' (in_path_2 <- system.file("R/abs2rel.R", package="sen2r"))
+#' (in_path_2 <- system.file("DESCRIPTION", package="sf"))
 #' # a path external to ref_path (in Linux)
 #' (in_path_3 <- system.file(package="base"))
 #' # an unexisting path
-#' (in_path_4 <- gsub("sen2r","r2sen",ref_path))
+#' (in_path_4 <- gsub("sf$","unexistingpackage",ref_path))
 #'
 #' abs2rel(in_path_1, ref_path)
 #'

diff --git a/R/s2_list.R b/R/s2_list.R
@@ -237,7 +237,7 @@ s2_list <- function(spatial_extent = NULL,
     )
   }
 
-  spatial_extent <- suppressWarnings(sf::st_union(spatial_extent))
+  spatial_extent <- suppressMessages(sf::st_union(spatial_extent))
   if (any(!st_is_valid(spatial_extent))) {
     spatial_extent <- st_make_valid(spatial_extent)
   }

diff --git a/R/sen2r.R b/R/sen2r.R
@@ -1262,9 +1262,9 @@ sen2r <- function(param_list = NULL,
         error = function(e) {st_sfc(st_polygon(), crs = 4326)}
       )
     })
-    s2_dt_centroid <- round(st_coordinates(
+    s2_dt_centroid <- suppressMessages(round(st_coordinates(
       st_centroid(st_transform(do.call("c",s2_footprint_sf_l), 3857))
-    ), -3) # rounded to 1 km
+    ), -3)) # rounded to 1 km
     s2_dt[,c("centroid_x", "centroid_y") := list(s2_dt_centroid[,"X"], s2_dt_centroid[,"Y"])]
   } else {
     s2_dt[,c("centroid_x", "centroid_y") := list(numeric(), numeric())]
@@ -1281,9 +1281,9 @@ sen2r <- function(param_list = NULL,
                "id_tile", "creation_datetime", "footprint"), 
       format = "data.table"
     )
-    s2_existing_dt_centroid <- round(st_coordinates(
+    s2_existing_dt_centroid <- suppressMessages(round(st_coordinates(
       st_centroid(st_transform(st_as_sfc(s2_existing_dt$footprint, crs = 4326), 3857))
-    ), -3) # rounded to 1 km
+    ), -3)) # rounded to 1 km
     s2_existing_dt[,c("centroid_x", "centroid_y") := list(s2_existing_dt_centroid[,"X"], s2_existing_dt_centroid[,"Y"])]
     # make a vector with only metadata to be used for the comparison
     s2_meta_pasted <- s2_dt[,list("V1" = paste(
@@ -1374,7 +1374,7 @@ sen2r <- function(param_list = NULL,
   }
   # if extent and footprint are defined, filter SAFEs on footprints
   if (all(!is(pm$extent, "logical"), !anyNA(pm$extent), !is.na(s2_dt$footprint))) {
-    extent_dissolved <- st_union(pm$extent)
+    extent_dissolved <- suppressMessages(st_union(pm$extent))
     if (any(!st_is_valid(extent_dissolved))) {
       extent_dissolved <- st_make_valid(extent_dissolved)
     }
@@ -2089,9 +2089,9 @@ sen2r <- function(param_list = NULL,
           fill = TRUE
         )
         if (nrow(s2_downloaded_dt)>0) {
-          s2_downloaded_dt_centroid <- round(st_coordinates(
+          s2_downloaded_dt_centroid <- suppressMessages(round(st_coordinates(
             st_centroid(st_transform(st_as_sfc(s2_downloaded_dt$footprint, crs = 4326), 3857))
-          ), -3) # rounded to 1 km
+          ), -3)) # rounded to 1 km
           s2_downloaded_dt[,c("centroid_x", "centroid_y") := list(
             s2_downloaded_dt_centroid[,"X"], 
             s2_downloaded_dt_centroid[,"Y"]

diff --git a/README.Rmd b/README.Rmd
@@ -1,8 +1,7 @@
 ---
 output:
   github_document:
-    toc: yes
-    toc_depth: 2
+    toc: no
   fig_caption: no
 ---
 
@@ -20,7 +19,7 @@ knitr::opts_chunk$set(
 [![CRAN Status](https://www.r-pkg.org/badges/version-ago/sen2r)](https://cran.r-project.org/package=sen2r)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1240384.svg)](https://doi.org/10.5281/zenodo.1240384)
 [![CRAN RStudio mirror downloads](https://cranlogs.r-pkg.org/badges/last-month/sen2r?color=green)](https://cran.rstudio.com/web/packages/ggplot2/index.html)
-[![R-CMD-check](https://github.com/ranghetti/sen2r/workflows/R-CMD-check/badge.svg)](https://github.com/ranghetti/sen2r/actions)
+[![R-CMD-check](https://github.com/ranghetti/sen2r/workflows/R-CMD-check/badge.svg)](https://github.com/ranghetti/sen2r/actions/workflows/R-CMD-check.yaml)
 [![Coverage Status](http://img.shields.io/codecov/c/github/ranghetti/sen2r/master.svg)](http://codecov.io/github/ranghetti/sen2r?branch=master)
 [![Docker Automated build](https://img.shields.io/docker/automated/ranghetti/sen2r.svg)](https://hub.docker.com/r/ranghetti/sen2r)
 [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](http://www.gnu.org/licenses/gpl-3.0)

diff --git a/README.md b/README.md
@@ -1,11 +1,4 @@
 
-  - [sen2r: Find, Download and Process Sentinel-2
-    Data](#sen2r-find-download-and-process-sentinel-2-data)
-      - [Installation](#installation)
-      - [Usage](#usage)
-      - [Credits](#credits)
-      - [Contributing](#contributing)
-
 <!-- IMPORTANT: do NOT edit README.Rmd! Edit index.Rmd instead, -->
 
 <!-- and generate README.Rmd using utils/code/create_README.sh  -->
@@ -15,7 +8,7 @@ Status](https://www.r-pkg.org/badges/version-ago/sen2r)](https://cran.r-project.
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1240384.svg)](https://doi.org/10.5281/zenodo.1240384)
 [![CRAN RStudio mirror
 downloads](https://cranlogs.r-pkg.org/badges/last-month/sen2r?color=green)](https://cran.rstudio.com/web/packages/ggplot2/index.html)
-[![R-CMD-check](https://github.com/ranghetti/sen2r/workflows/R-CMD-check/badge.svg)](https://github.com/ranghetti/sen2r/actions)
+[![R-CMD-check](https://github.com/ranghetti/sen2r/workflows/R-CMD-check/badge.svg)](https://github.com/ranghetti/sen2r/actions/workflows/R-CMD-check.yaml)
 [![Coverage
 Status](http://img.shields.io/codecov/c/github/ranghetti/sen2r/master.svg)](http://codecov.io/github/ranghetti/sen2r?branch=master)
 [![Docker Automated

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,4 +1,4 @@
-# sen2r v. 1.4.2
+# sen2r v. 1.4.3
 
 ## Test environments
 * [local installation] Ubuntu 18.04, 64 bit, R 4.0.4
@@ -7,19 +7,4 @@
 * [win-builder] R unstable, 4.0.4 and 3.6.3 (devel, release and oldrelease)
 
 ## R CMD check results
-There were no ERRORs nor WARNINGs.
-
-There was 1 NOTE:
-Days since last update: 2
-
-This submission is finalised to fix an error found by CRAN checks 
-on the last release submitted 2 days ago (see below).
-
-## CRAN review
-> Dear maintainer,
-Please see the problems shown on
-<https://cran.r-project.org/web/checks/check_results_sen2r.html>.
-Please correct before 2021-03-18 to safely retain your package on CRAN.
-
-The error were fixed
-(see commit 6010b3f327f3c71392e47c2adc12071f50c29ee7).
+There were no ERRORs, WARNINGs nor NOTEs.
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/ISSUE_TEMPLATE.html b/docs/ISSUE_TEMPLATE.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
-Original file line number
+Diff line change
@@ Expand Up / @@ -3,6 +3,7 @@ @@
     on:
       push:
         branches:
+          - master
           - devel
       pull_request:
         branches:
@@ Expand Down @@