Merge branch 'main' of https://github.com/espm-157/nasa-topst-env-jus…

…tice

.devcontainer/install.R

@@ -1,11 +1,11 @@
+#! /usr/local/bin/Rscript
 # install R dependencies
 
 # We could use renv.lock approach here instead, but will force re-creation of environment from scratch
 # Does not provide a good way to ensure that sf/terra/gdalcubes are installed from source while other packages can be binary
 
-install.packages(c("rstac", "spData"))
-remotes::install_github("boettiger-lab/earthdatalogin")
+install.packages(c("rstac", "spData", "earthdatalogin", "quarto"))
 remotes::install_github('r-tmap/tmap')
 
-#install.packages(c("IRkernel", "languageserver", "httpgd"))
-#IRkernel::installspec()
+install.packages(c("IRkernel", "languageserver", "httpgd"))
+IRkernel::installspec()

.devcontainer/setup.sh

@@ -2,11 +2,5 @@
 
 sudo cp /etc/rstudio/disable_auth_rserver.conf /etc/rstudio/rserver.conf
 sudo sudo bash -c 'echo "USER=rstudio" >>/etc/environment'
-sudo /init &
-
-## set startup dir
-mkdir -p ~/.local/share/rstudio/projects_settings
-export RPROJ"=$(ls ${CODESPACE_VSCODE_FOLDER}/*.Rproj)"
-echo ${RPROJ} > ~/.local/share/rstudio/projects_settings/last-project-path
-
+sudo /init &> /dev/null &
 

.devcontainer/welcome.sh

@@ -1,3 +1,8 @@
+mkdir -p ~/.local/share/rstudio/projects_settings
+export RPROJ"=$(ls ${CODESPACE_VSCODE_FOLDER}/*.Rproj)"
+echo ${RPROJ} > ~/.local/share/rstudio/projects_settings/last-project-path
+
+
 # Construct the message
 message="## [Open in RStudio](https://$CODESPACE_NAME-8787.app.github.dev)
 "

.gitpod-setup.sh

@@ -0,0 +1,7 @@
+sudo useradd rstudio -u 1000 -s /bin/bash
+mkdir -p ~/.local/share/rstudio/projects_settings
+sudo mkdir -p /home/rstudio/.local/share/rstudio/projects_settings
+export RPROJ"=$(ls -d $PWD/*.Rproj)"
+sudo echo ${RPROJ} > ~/.local/share/rstudio/projects_settings/last-project-path
+sudo cp ~/.local/share/rstudio/projects_settings/last-project-path /home/rstudio/.local/share/rstudio/projects_settings/last-project-path
+sudo chown -R rstudio:rstudio /home/rstudio/.local/share/rstudio

.gitpod.yml

@@ -0,0 +1,8 @@
+image:  ghcr.io/boettiger-lab/nasa-tops:latest
+tasks:
+    - name: rstudio-init
+      init: bash .devcontainer/setup.sh
+    - name: setup
+      init: bash .gitpod-setup.sh
+    - name: rstudio-server
+      init: sudo rstudio-server start