R/fix automation (#441)

- Remove references to RasterAPI in the non-expression-based R methods
- Fix and simplify the R package build automation, including updating failing tests. The R packages will now appear with our release artefacts 👍
- Added caching and use of Posit public package manager in Github actions to avoid downloading Spark source every time and building R package dependencies from source
- Skip coverage checks if being run _outside_ of the main build workflow

.github/actions/r_build/action.yml

@@ -6,23 +6,54 @@ runs:
     - name: Setup R build environment
       shell: bash
       run: |
-        sudo apt-get update && sudo apt-get install -y curl libcurl4-openssl-dev pkg-config libharfbuzz-dev libfribidi-dev 
-    - name: Download and unpack Spark
+        sudo apt-get update && sudo apt-get install -y curl libcurl4-openssl-dev pkg-config libharfbuzz-dev libfribidi-dev
+    - name: Create download location for Spark
       shell: bash
       run: |
-        sudo mkdir -p /usr/spark-download/raw
         sudo mkdir -p /usr/spark-download/unzipped
+        sudo mkdir -p /usr/spark-download/raw
         sudo chown -R $USER: /usr/spark-download/
-        wget -P /usr/spark-download/raw https://archive.apache.org/dist/spark/spark-3.2.1/spark-3.2.1-bin-hadoop2.7.tgz 
+    - name: Cache Spark download
+      id: cache-spark
+      uses: actions/cache@v3
+      with:
+        path: /usr/spark-download/unzipped
+        key: r_build-spark
+    - if: ${{ steps.cache-spark.outputs.cache-hit != 'true' }}
+      name: Download and unpack Spark
+      shell: bash
+      run: |
+        wget -P /usr/spark-download/raw https://archive.apache.org/dist/spark/spark-3.2.1/spark-3.2.1-bin-hadoop2.7.tgz
         tar zxvf /usr/spark-download/raw/spark-3.2.1-bin-hadoop2.7.tgz -C /usr/spark-download/unzipped
-
-
-    - name: Build R package
+    - name: Create R environment
       shell: bash
       run: |
-        cd R
         sudo mkdir -p /usr/lib/R/site-library
         sudo chown -R $USER: /usr/lib/R/site-library
+    - name: Setup R
+      uses: r-lib/actions/setup-r@v2
+      with:
+        r-version: ${{ matrix.R }}
+        use-public-rspm: true
+    - name: Install R dependencies
+      shell: bash
+      run: |
+        cd R
+        Rscript --vanilla install_deps.R
+    - name: Generate R bindings
+      shell: bash
+      run: |
+        cd R
+        Rscript --vanilla generate_R_bindings.R ../src/main/scala/com/databricks/labs/mosaic/functions/MosaicContext.scala
+    - name: Build R docs
+      shell: bash
+      run: |
+        cd R
+        Rscript --vanilla generate_docs.R
+    - name: Build R package
+      shell: bash
+      run: |
+        cd R
         Rscript --vanilla build_r_package.R
     - name: Test R package
       shell: bash

.github/actions/scala_build/action.yml

@@ -27,8 +27,9 @@ runs:
         - name: Build the scala JAR - skip tests is true
           if: inputs.skip_tests == 'true'
           shell: bash
-          run: sudo mvn -q clean install -DskipTests
+          run: sudo mvn -q clean install -DskipTests -Dscoverage.skip
         - name: Publish test coverage
+          if: inputs.skip_tests == 'false'
           uses: codecov/codecov-action@v1
         - name: Copy Scala artifacts to GH Actions run
           shell: bash

.github/workflows/build_main.yml

@@ -26,5 +26,7 @@ jobs:
         uses: ./.github/actions/scala_build
       - name: build python
         uses: ./.github/actions/python_build
+      - name: build R
+        uses: ./.github/actions/r_build
       - name: upload artefacts
         uses: ./.github/actions/upload_artefacts

R/.gitignore

@@ -1 +1,2 @@
 **/.Rhistory
+**/*.tar.gz

R/build_r_package.R

@@ -1,54 +1,15 @@
-repos = c(
-   "https://cran.ma.imperial.ac.uk" = "https://cran.ma.imperial.ac.uk"
-  ,"https://www.stats.bris.ac.uk/R" = "https://www.stats.bris.ac.uk/R"
-  ,"https://cran.rstudio.com/"  = "https://cran.rstudio.com/" 
-)
-
-mirror_is_up <- function(x){
-  out <- tryCatch({
-    available.packages(contrib.url(x))
-  }
-  ,error = function(cond){return(0)}
-  ,warning = function(cond){return(0)}
-  ,finally = function(cond){}
-  )
-  return(length(out))
-}
-
-mirror_status = lapply(repos, mirror_is_up)
-for(repo in names(mirror_status)){
-  if (mirror_status[[repo]] > 1){
-    repo <<- repo
-    break
-  }
-}
-
-install.packages("pkgbuild", repos=repo)
-install.packages("roxygen2", repos=repo)
-install.packages("sparklyr", repos=repo)
 spark_location <- "/usr/spark-download/unzipped/spark-3.2.1-bin-hadoop2.7"
 Sys.setenv(SPARK_HOME = spark_location)
 
 library(SparkR, lib.loc = c(file.path(spark_location, "R", "lib")))
 
 
 library(pkgbuild)
-library(roxygen2)
 library(sparklyr)
 
 
 
 build_mosaic_bindings <- function(){
-  # build functions
-  scala_file_path <- "../src/main/scala/com/databricks/labs/mosaic/functions/MosaicContext.scala"
-  system_cmd <- paste0(c("Rscript --vanilla generate_R_bindings.R", scala_file_path), collapse = " ")
-  system(system_cmd)
-
-  # build doc
-  roxygen2::roxygenize("sparkR-mosaic/sparkrMosaic")
-  roxygen2::roxygenize("sparklyr-mosaic/sparklyrMosaic")
-
-
   ## build package
   pkgbuild::build("sparkR-mosaic/sparkrMosaic")
   pkgbuild::build("sparklyr-mosaic/sparklyrMosaic")

R/generate_docs.R

@@ -0,0 +1,14 @@
+spark_location <- "/usr/spark-download/unzipped/spark-3.2.1-bin-hadoop2.7"
+Sys.setenv(SPARK_HOME = spark_location)
+
+library(SparkR, lib.loc = c(file.path(spark_location, "R", "lib")))
+library(roxygen2)
+
+build_mosaic_docs <- function(){
+  # build doc
+  roxygen2::roxygenize("sparkR-mosaic/sparkrMosaic")
+  roxygen2::roxygenize("sparklyr-mosaic/sparklyrMosaic")
+
+}
+
+build_mosaic_docs()

R/install_deps.R

@@ -0,0 +1,5 @@
+options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/focal/latest"))
+
+install.packages("pkgbuild")
+install.packages("roxygen2")
+install.packages("sparklyr")

R/sparkR-mosaic/enableMosaic.R

@@ -17,14 +17,11 @@
 enableMosaic <- function(
   geometryAPI="JTS"
   ,indexSystem="H3"
-  ,rasterAPI="GDAL"
 ){
   geometry_api <- sparkR.callJStatic(x="com.databricks.labs.mosaic.core.geometry.api.GeometryAPI", methodName="apply", geometryAPI)
   indexing_system <- sparkR.callJStatic(x="com.databricks.labs.mosaic.core.index.IndexSystemFactory", methodName="getIndexSystem", indexSystem)
 
-  raster_api <- sparkR.callJStatic(x="com.databricks.labs.mosaic.core.raster.api.RasterAPI", methodName="apply", rasterAPI)
-
-  mosaic_context <- sparkR.newJObject(x="com.databricks.labs.mosaic.functions.MosaicContext", indexing_system, geometry_api, raster_api)
+  mosaic_context <- sparkR.newJObject(x="com.databricks.labs.mosaic.functions.MosaicContext", indexing_system, geometry_api)
   functions <<- sparkR.callJMethod(mosaic_context, "functions")
   # register the sql functions for use in sql() commands
   sparkR.callJMethod(mosaic_context, "register")

R/sparkR-mosaic/sparkrMosaic/DESCRIPTION

@@ -8,7 +8,7 @@ Description: This package extends SparkR to bring the Databricks Mosaic for geos
 License: Databricks
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.3
 Collate: 
     'enableMosaic.R'
     'generics.R'

R/sparkR-mosaic/tests.R

@@ -1,5 +1,3 @@
-repo<-"https://cran.ma.imperial.ac.uk/"
-
 spark_location <- "/usr/spark-download/unzipped/spark-3.2.1-bin-hadoop2.7"
 Sys.setenv(SPARK_HOME = spark_location)
 library(SparkR, lib.loc = c(file.path(spark_location, "R", "lib")))
@@ -66,15 +64,15 @@ sdf <- withColumn(sdf, "transformed_geom", st_transform(column("geom_with_srid")
 # Grid functions
 sdf <- withColumn(sdf, "grid_longlatascellid", grid_longlatascellid(lit(1), lit(1), lit(1L)))
 sdf <- withColumn(sdf, "grid_pointascellid", grid_pointascellid(column("point_wkt"), lit(1L)))
-sdf <- withColumn(sdf, "grid_boundaryaswkb", grid_boundaryaswkb( SparkR::cast(lit(1), "long")))
+sdf <- withColumn(sdf, "grid_boundaryaswkb", grid_boundaryaswkb(column("grid_pointascellid")))
 sdf <- withColumn(sdf, "grid_polyfill", grid_polyfill(column("wkt"), lit(1L)))
 sdf <- withColumn(sdf, "grid_tessellateexplode", grid_tessellateexplode(column("wkt"), lit(1L)))
 sdf <- withColumn(sdf, "grid_tessellate", grid_tessellate(column("wkt"), lit(1L)))
 
 # Deprecated
 sdf <- withColumn(sdf, "point_index_lonlat", point_index_lonlat(lit(1), lit(1), lit(1L)))
 sdf <- withColumn(sdf, "point_index_geom", point_index_geom(column("point_wkt"), lit(1L)))
-sdf <- withColumn(sdf, "index_geometry", index_geometry( SparkR::cast(lit(1), "long")))
+sdf <- withColumn(sdf, "index_geometry", index_geometry(column("point_index_geom")))
 sdf <- withColumn(sdf, "polyfill", polyfill(column("wkt"), lit(1L)))
 sdf <- withColumn(sdf, "mosaic_explode", mosaic_explode(column("wkt"), lit(1L)))
 sdf <- withColumn(sdf, "mosaicfill", mosaicfill(column("wkt"), lit(1L)))

R/sparklyr-mosaic/sparklyrMosaic/DESCRIPTION

@@ -8,7 +8,7 @@ Description: This package extends sparklyr to bring the Databricks Mosaic for ge
 License: Databricks
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.3
 Collate: 
     'enableMosaic.R'
     'sparkFunctions.R'