Merge pull request #15 from espm-157/main

sync

.devcontainer/Dockerfile

@@ -1,20 +1,30 @@
 # devcontainer-focused Rocker
 FROM ghcr.io/rocker-org/devcontainer/tidyverse:4.3
 
+
+ENV NB_USER=rstudio
+ENV VIRTUAL_ENV=/opt/venv
+ENV PATH=${PATH}:${VIRTUAL_ENV}/bin
+ADD https://raw.githubusercontent.com/rocker-org/rocker-versioned2/c1a472465532c8349cf0ad4f3f95c86e85787dc3/scripts/install_python.sh install_python.sh
+RUN bash install_python.sh && rm install_python.sh
+
+
 RUN apt-get update && apt-get -y install libxt6
-RUN /rocker_scripts/install_python.sh
 ADD https://raw.githubusercontent.com/rocker-org/rocker-versioned2/master/scripts/experimental/install_dev_osgeo.sh install_dev_osgeo.sh
 RUN bash install_dev_osgeo.sh && rm install_dev_osgeo.sh
 
+RUN chown -R rstudio:rstudio /opt/venv
+
 USER rstudio
 WORKDIR /home/rstudio
+RUN usermod -s /bin/bash rstudio
 
 COPY requirements.txt requirements.txt
 ENV PATH=$PATH:/home/rstudio/.local/bin
 
-RUN pip install --user -r requirements.txt && rm requirements.txt
+RUN python -m pip install -r requirements.txt && rm requirements.txt
 COPY install.R install.R
 RUN Rscript install.R && rm install.R
 
 # some teaching preferences
-RUN git config --global pull.rebase false
+RUN git config --global pull.rebase false

.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-resume.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+sudo rstudio-server start
+

.gitpod-setup.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+sudo cp /etc/rstudio/disable_auth_rserver.conf /etc/rstudio/rserver.conf
+cp /etc/environment env
+echo "USER=$USER" >> env
+sudo mv env /etc/environment
+
+mkdir -p ~/.local/share/rstudio/projects_settings
+export RPROJ"=$(ls -d $PWD/*.Rproj)"
+echo ${RPROJ} > ~/.local/share/rstudio/projects_settings/last-project-path
+
+sudo rstudio-server start
+

.gitpod.yml

@@ -1 +1,4 @@
 image:  ghcr.io/boettiger-lab/nasa-tops:latest
+tasks:
+    - name: rstudio-init
+      command: bash .gitpod-setup.sh