Updated R packages and add DVC (#6)

mapme-initiative · Jul 23, 2024 · 09da841 · 09da841
1 parent 3ff17a3
commit 09da841
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Showing 4 changed files with 24 additions and 5 deletions.
diff --git a/.github/workflows/docker-mapme.yml b/.github/workflows/docker-mapme.yml
@@ -9,7 +9,7 @@ on:
   pull_request:
     branches: [main, master]
 env:
-  tag: 1.2.0
+  tag: 1.2.1
 
 jobs:
 

diff --git a/scripts/install_rspatial.sh b/scripts/install_rspatial.sh
@@ -13,10 +13,13 @@ LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
 
 # install sf and terra dev versions
 Rscript -e 'remotes::install_github(c("r-spatial/sf", "rspatial/terra", "USDAForestService/gdalraster", "appelmar/gdalcubes"))'
+Rscript -e 'remotes::install_github("mapme-initiative/mapme.indicators", dependencies = TRUE)' 
+Rscript -e 'remotes::install_github("mapme-initiative/mapme.pipelines", dependencies = TRUE)' 
 
 # install r packages as binaries
 install2.r --error --skipmissing --skipinstalled --ncpus $NCPUS \
     classInt \
+    config \
     devtools \
     exactextractr \
     gdalcubes \
@@ -26,6 +29,7 @@ install2.r --error --skipmissing --skipinstalled --ncpus $NCPUS \
     hdf5r \
     here \
     leaflet \
+    logger \
     lwgeom \
     mapview \
     ncdf4 \
@@ -44,8 +48,9 @@ install2.r --error --skipmissing --skipinstalled --ncpus $NCPUS \
     spatialreg \
     spdep \
     stars \
+    targets \
     testthat \
-    tmap 
+    tmap  
 
 # install mapme.biodiversity from CRAN
 install2.r --error --skipmissing --skipinstalled --deps TRUE --ncpus $NCPUS mapme.biodiversity

diff --git a/scripts/install_rspatial_dev.sh b/scripts/install_rspatial_dev.sh
@@ -14,10 +14,13 @@ LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
 # install sf and terra dev versions
 Rscript -e 'remotes::install_github(c("r-spatial/sf", "rspatial/terra", "USDAForestService/gdalraster"))'
 Rscript -e 'remotes::install_github("mapme-initiative/mapme.biodiversity", dependencies = TRUE)' 
+Rscript -e 'remotes::install_github("mapme-initiative/mapme.indicators", dependencies = TRUE)' 
+Rscript -e 'remotes::install_github("mapme-initiative/mapme.pipelines", dependencies = TRUE)' 
 
 # install r packages as binaries
 install2.r --error --skipmissing --skipinstalled -n $NCPUS \
     classInt \
+    config \
     devtools \
     exactextractr \
     gdalcubes \
@@ -27,6 +30,7 @@ install2.r --error --skipmissing --skipinstalled -n $NCPUS \
     hdf5r \
     here \
     leaflet \
+    logger \
     lwgeom \
     mapview \
     ncdf4 \
@@ -45,6 +49,7 @@ install2.r --error --skipmissing --skipinstalled -n $NCPUS \
     spatialreg \
     spdep \
     stars \
+    targets \
     testthat \
     tmap 
 

diff --git a/scripts/install_sysdeps.sh b/scripts/install_sysdeps.sh
@@ -94,10 +94,19 @@ apt_install \
         screen \
         wget
 
+# install DVC
+wget https://dvc.org/deb/dvc.list -O /etc/apt/sources.list.d/dvc.list \
+  && wget -qO - https://dvc.org/deb/iterative.asc | gpg --dearmor > packages.iterative.gpg \
+  && install -o root -g root -m 644 packages.iterative.gpg /etc/apt/trusted.gpg.d \
+  && rm -f packages.iterative.gpg \
+  && apt update \
+  && apt install dvc 
+
 # geoparquet sysdeps
-wget https://apache.jfrog.io/artifactory/arrow/"$(lsb_release --id --short | tr '[:upper:]' '[:lower:]')"/apache-arrow-apt-source-latest-"$(lsb_release --codename --short)".deb
-apt_install -y -V ./apache-arrow-apt-source-latest-"$(lsb_release --codename --short)".deb
-apt-get update && apt-get install -y -V libarrow-dev libparquet-dev libarrow-dataset-dev	
+wget https://apache.jfrog.io/artifactory/arrow/"$(lsb_release --id --short | tr '[:upper:]' '[:lower:]')"/apache-arrow-apt-source-latest-"$(lsb_release --codename --short)".deb \
+  && apt_install -y -V ./apache-arrow-apt-source-latest-"$(lsb_release --codename --short)".deb \
+  && apt-get update \
+  && apt-get install -y -V libarrow-dev libparquet-dev libarrow-dataset-dev	
 
 locale-gen en_US.UTF-8