Merge pull request #69 from r-spatial/JOSS

JOSS rgee: Address suggested changes of the review - rgee 1.0.0

.Rbuildignore

@@ -17,4 +17,4 @@
 ^vignettes\setup.Rmd
 ^vignettes\BestPractices.Rmd
 ^vignettes\thumb_down.png
-^vignettes\thumb_up.png
+^vignettes\thumb_up.png

.github/decrypt_secret.sh

@@ -1,15 +1,15 @@
 #!/bin/sh
 
 # Decrypt the file
-mkdir -p $HOME/.config/earthengine/data.colec.fbf/
+mkdir -p $HOME/.config/earthengine/ndef/
 
 # --batch to prevent interactive command --yes to assume "yes" for questions
 gpg --quiet --batch --yes --decrypt --passphrase="$RGEE_SECRET_PASSPHRASE" \
---output $HOME/.config/earthengine/data.colec.fbf/GCS_AUTH_FILE.json \
+--output $HOME/.config/earthengine/ndef/GCS_AUTH_FILE.json \
 ./tests/credentials/GCS_AUTH_FILE.json.gpg
 
 gpg --quiet --batch --yes --decrypt --passphrase="$RGEE_SECRET_PASSPHRASE" \
---output $HOME/.config/earthengine/data.colec.fbf/[email protected] ./tests/credentials/[email protected]
+--output $HOME/.config/earthengine/ndef/[email protected] ./tests/credentials/[email protected]
 
 gpg --quiet --batch --yes --decrypt --passphrase="$RGEE_SECRET_PASSPHRASE" \
---output $HOME/.config/earthengine/data.colec.fbf/credentials ./tests/credentials/credentials.gpg
+--output $HOME/.config/earthengine/ndef/credentials ./tests/credentials/credentials.gpg

.github/workflows/R-CMD-check.yaml

@@ -28,75 +28,65 @@ jobs:
     env:
       # otherwise remotes::fun() errors cause the build to fail. Example: Unavailability of binaries
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      CRAN: ${{ matrix.config.cran }}
+      RSPM: ${{ matrix.config.rspm }}
+      # prevent rgl issues because no X11 display is available
+      RGL_USE_NULL: true
       # macOS >= 10.15.4 linking
       SDKROOT: /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
 
     steps:
-      - name: CHECKOUT CODE
-        uses: actions/checkout@v2
-
-      - name: SETUP PYTHON
+      - uses: actions/checkout@v2
+      - name: Setup python
         uses: actions/setup-python@v1
         with:
-          python-version: 3.6
-
-      - name: SETUP R
-        uses: r-lib/actions/setup-r@master
+          python-version: '3.6'
+          architecture: 'x64'
+      - uses: r-lib/actions/setup-r@master
         with:
           r-version: ${{ matrix.config.r }}
 
-      - name: SETUP PANDOC
-        uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@master
 
-      - name: FIND ALL R PACKAGES DEPENDECIES OF RGEE
+      - name: Query dependencies
         run: |
           install.packages('remotes')
-          install.packages('knitr')
-          install.packages('pillar') # winbug
-          install.packages('vctrs')
           saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
         shell: Rscript {0}
 
-      - name: RETICULATE_PYTHON SETTING
+      - name: Install Python dependencies
+        if: runner.os == 'Windows'
         run: |
-          reticulate_dir <- path.expand("~/.Renviron")
-          fileConn <- file(reticulate_dir)
-          pyPATH <- Sys.getenv("pythonLocation")
-          writeLines(sprintf('RETICULATE_PYTHON="%s"', pyPATH), fileConn)
-          close(fileConn)
-        shell: Rscript {0}
-
-      - name: INSTALL PYTHON DEPENDENCIES
-        run: |
-          pip install --upgrade pip
-          pip install setuptools oauth2client earthengine-api numpy virtualenv
-
-      - name: CACHE R PACKAGES [LINUX and macOS]
+          %PYTHON%\\python.exe -m pip install setuptools numpy earthengine-api
+      - name: Cache R packages
         if: runner.os != 'Windows'
         uses: actions/cache@v1
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }}
           restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-
 
-      - name: PREBUILD TESTING
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        env:
+          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
         run: |
-          earthengine -h
+          Rscript -e "remotes::install_github('r-hub/sysreqs')"
+          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
+          sudo -s eval "$sysreqs"
 
-      - name: INSTALL dependencies and rcmdcheck
+      - name: Install dependencies
         run: |
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("rcmdcheck")
         shell: Rscript {0}
 
-      - name: CHECK
+      - name: Check
         env:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--no-examples"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
 
-      - name: UPLOAD CHECK RESULTS
+      - name: Upload check results
         if: failure()
         uses: actions/upload-artifact@master
         with:

.github/workflows/test-coverage.yaml

@@ -91,7 +91,7 @@ jobs:
         run: |
           earthengine -h
           ls $HOME/.config/earthengine/
-          ls $HOME/.config/earthengine/data.colec.fbf
+          ls $HOME/.config/earthengine/ndef
 
 
       - name: INSTALL rgdal WITH CONFIGURE

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rgee
 Title: R Bindings for Calling the 'Earth Engine' API
-Version: 0.6.2
+Version: 1.0.0
 Authors@R: 
     c(person(given = "Cesar",
              family = "Aybar",
@@ -75,14 +75,14 @@ Authors@R:
              comment = "Appel reviewed the package for JOSS, see 
                         https://github.com/openjournals/joss-reviews/issues/2272"))
 Description: Earth Engine <https://earthengine.google.com/> client library for R. All of the 'Earth Engine' API classes, 
-    modules, and functions are made available. Additional functions implemented include importing (exporting) of R (Earth Engine) 
+    modules, and functions are made available. Additional functions implemented include importing (exporting) of Earth Engine 
     spatial objects, extraction of time series, interactive map display, assets management interface, and metadata display.
     See <https://r-spatial.github.io/rgee/> for further details.
 License: Apache License (>= 2.0)
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.1
 Depends:
     R (>= 3.3.0)
 Imports:

NAMESPACE

@@ -5,6 +5,7 @@ S3method(ee_print,ee.featurecollection.FeatureCollection)
 S3method(ee_print,ee.geometry.Geometry)
 S3method(ee_print,ee.image.Image)
 S3method(ee_print,ee.imagecollection.ImageCollection)
+S3method(print,ee.computedobject.ComputedObject)
 export("%>%")
 export(Map)
 export(ee)
@@ -24,6 +25,7 @@ export(ee_clean_pyenv)
 export(ee_drive_to_local)
 export(ee_extract)
 export(ee_gcs_to_local)
+export(ee_get)
 export(ee_get_assethome)
 export(ee_get_date_ic)
 export(ee_get_date_img)
@@ -75,12 +77,12 @@ export(eedate_to_rdate)
 export(gcs_to_ee_image)
 export(gcs_to_ee_table)
 export(local_to_gcs)
-export(print.ee.computedobject.ComputedObject)
 export(raster_as_ee)
 export(rdate_to_eedate)
 export(sf_as_ee)
 export(stars_as_ee)
 exportClasses(EarthEngineMap)
+exportClasses(mapview)
 importFrom(cli,cat_line)
 importFrom(cli,rule)
 importFrom(cli,symbol)

NEWS.md

@@ -11,17 +11,47 @@ vignette: >
   %\VignetteIndexEntry{NEWS}
   %\VignetteEncoding{UTF-8}
 ---
+# rgee 1.0.0
+- We implement `ee_createAssetHome` to help users to define their *Earth Engine Assets home root folder* without leaving ee_Initialize(). (#70 Thanks @jhollist)
+- Fix a bug in `ee_Initialize(drive = TRUE, gcs = TRUE)` which do not permit users save credentials. (#72 Thanks @appelmar).
+- Removed `check_ring_dir` argument from `sf_as_ee`. Now `rgee` expect that users fix potential geometry problems before upload geometries to their Earth Engine assets.
+- Changes in "welcome to rgee"  message (located in `ee_Initialize`). We delete `stop("Initialization aborted")` and implement `ee_search_init_message`. It will permit to `rgee` to know if the user accepted to create the global var "EARTHENGINE_INIT_MESSAGE" without need to restart the R session.
+- Fix minor bugs in `sf_as_ee` and `gcs_to_ee_table`. The argument `command_line_tool_path` was added to give users the option to set the path of the Earth Engine command linetool. This new argument is only relevant to upload files using Google Cloud Storage. New diagnostic message were added.
+- Now `sf_as_ee` returns an `ee$Geometry$...` when `x` is a `sfg` or a single sfc object. If `x` is a sf or a `sfc` object with multiple geometries will return an `ee$FeatureCollection`. New unit test for `sf_as_ee`.
+- Changes in the documentation of `ee_as_stars` and `ee_as_raster` (#72 Thanks @appelmar).
+- Fix minor bugs in `raster_as_ee`, `stars_as_ee` and `gcs_to_ee_image`. The argument `command_line_tool_path` was added to give users the option to set the path of the Earth Engine command linetool. New diagnostic message were added. New unit test added.
+- Fixed a bug in `stars_as_ee` that didn't allow to read single-band images.
+- `ee_manage_asset_access` has a better approach to determine the user owner of the asset.
+- Add a new logical argument called 'strict' to `ee_manage_assetlist`, `ee_manage_copy`,
+`ee_manage_move`, `ee_manage_set_properties` and `ee_manage_delete_properties`. If TRUE, 
+the existence of the asset will be evaluate before to perform the task. By default TRUE.
+- If the `path_asset` is not specified in `ee_manage_assetlist`, rgee will assume that the
+path_asset is `ee_get_assethome`.
+- `raster_as_ee.R` was created in the /R folder to maintain an order between functions
+to upload and download images.
+- Fix a bug in the documentation of `print.ee.computedobject.ComputedObject()` (#72 Thanks @appelmar).
+- Fix a bug in `ee_install_set_pyenv` now users can set `py_path` without set 
+`py_env` and  vice versa.
+- `ee_extract` was adapted to work well with changes in `sf_as_ee`.
+- R CMD check is more friendly with users, the use of `--run-dontrun` is also 
+available (#72 Thanks @appelmar).
+- Fix a bug in `ee_get_date_ic`.
+- `Map$addLayer` now could display a legend when `eeObject` is an one-band `ee$Image` (By default legend = TRUE).
+- New function `ee_get`: Return the element at the specified position in a Earth Engine Collection.
+- New function `Map$addLayers`: Create interactive visualizations of ImageCollections.
+- - Earth Engine Python API updated to 0.1.227.
+
 # rgee 0.6.2
 - Earth Engine Python API updated to 0.1.226.
 - Fix some typos.
 - Fix a minor bug in ee_monitoring.
 - Users can mix mapview and EarthEnginemap objects in the same pipeline (see Examples in `Map$addLayer`).
 - Add `ee_as_mapview`, a function to convert `EarthEnginemap` objects to  `mapview` objects.
 - add a new logical argument called 'strict' to **ee_manage_delete**. If TRUE, the existence of the asset will be evaluate before to perform the task.
-- Fix a bug en ee_Initialize, now users without an Earth Engine Assets home root will see a message error.
+- Fix a bug in ee_Initialize, now users without an Earth Engine Assets home root will see a message.
 - Fix a minor bug when ee_Initialize change of user, now before to change of user the GCS and GD credentials will be deleted.
 - ee_check completely renovated. 
-  - New message display.
+  - New diagnostic messages.
   - Fix a minor bug when testing GCS credentials.
   - The file ee_check.py was deleted.
 - Roy Samapriya added as a contributor.  

R/AAAMapclass.R

@@ -9,6 +9,18 @@ setClass('EarthEngineMap',
                    map = 'ANY'))
 NULL
 
+#' Class mapview
+#'
+#' @slot object the spatial object
+#' @slot map the leaflet map object
+#'
+#' @exportClass mapview
+setClass('mapview',
+         slots = c(object = 'list',
+                   map = 'ANY'))
+NULL
+
+
 if ( !isGeneric('EarthEngineMap') ) {
   setGeneric('EarthEngineMap', function(x, ...)
     standardGeneric('EarthEngineMap'))