Merge pull request #127 from nmfs-opensci/dev

remove binder, return to apt2.txt to load pkgs after R installation

README.md

@@ -41,4 +41,4 @@ Then add `environment.yml`, `apt.txt` or `install.R` to the repo and those will
 
 The original [py-rocket 1.0](https://github.com/NASA-Openscapes/py-rocket) was developed by Luis Lopez and was built off a Rocker base image. Carl Boettiger and Eli Holmes later altered the image (py-rocket 2.0) so that the Python environment matched the Pangeo image structure but the image was still built off a Rocker image. Subsequently, Carl Boettiger developed [repo2docker-r](https://github.com/boettiger-lab/repo2docker-r) that creates a JupyterHub-compatible image that uses a [Jupyter docker stack image](https://jupyter-docker-stacks.readthedocs.io/en/latest/) as base. For py-rocker 3.0, Eli Holmes used Carl's ideas but used [repo2docker](https://repo2docker.readthedocs.io/en/latest/) and [repo2docker-action](https://github.com/jupyterhub/repo2docker-action) to build the base image. To do this, the [CryoCloud hub image](https://github.com/CryoInTheCloud/hub-image) repo was used for the basic structure and approach. Eli added the `rocker.sh` script and `appendix` modifications to install R and RStudio via the Rocker scripts (rather than using a Rocker image as base). Yuvi Panda (repo2docker) gave input throughout the process as snags were hit.
 
-**Why Rocker for the R/RStudio environment?** The Rocker images are the standard for R/RStudio contanier images. They are heavily tested and regularly updated. There is a large developer community that fixes problems and bugs. The stack has gone through major revisions to improve modularity and they constantly innovating (integration for machine-learning, CUDA, BLAS, spatial, etc., etc.). py-rocker is building off that work without using the images directly. Instead it uses the Dockerfile code and the installation scripts.  There are many other approaches to adding R and RStudio to images that work in JupyterHubs. See [repo2docker-r](https://github.com/boettiger-lab/repo2docker-r) that Carl developed and [r-conda](https://github.com/binder-examples/r-conda) for a conda native approach using repo2docker. py-rocket is not intended to create small images; it is intended to create images that emulate Rocker in the `/rstudio` environment on a JupyterHub.
+**Why Rocker for the R/RStudio environment?** The Rocker images are the standard for R/RStudio contanier images. They are heavily tested and regularly updated. There is a large developer community that fixes problems and bugs. The stack has gone through major revisions to improve modularity and they constantly innovating (integration for machine-learning, CUDA, BLAS, spatial, etc., etc.). py-rocket is building off that work without using the images directly. Instead it uses the Docker file code and the installation scripts.  There are many other approaches to adding R and RStudio to images that work in JupyterHubs. See [repo2docker-r](https://github.com/boettiger-lab/repo2docker-r) that Carl developed and [r-conda](https://github.com/binder-examples/r-conda) for a conda native approach using repo2docker. py-rocket is not intended to create small images; it is intended to create images that emulate Rocker in the `/rstudio` environment on a JupyterHub.

appendix

@@ -2,6 +2,8 @@ USER root
 
 # repo2docker does not set this. This is the default env in repo2docker type images
 ENV CONDA_ENV=notebook
+# Tell applications where to open desktop apps - this allows notebooks to pop open GUIs
+ENV DISPLAY=":1.0"
 
 # Install R, RStudio via Rocker scripts
 ENV R_VERSION="4.4.1"
@@ -13,9 +15,11 @@ RUN PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin && \
   chmod +x ${REPO_DIR}/rocker.sh && \
   ${REPO_DIR}/rocker.sh
 
-# Install any missing build packages. Most are installed when R installed but get any missing packages
-RUN apt-get update && \
-  apt-get install --yes --no-install-recommends build-essential gfortran && \
+# Install linux packages after R installation since the R install scripts get rid of packages
+# The package_list part is reading the file and doing clean-up to just have the list of packages
+RUN package_list=$(grep -v '^\s*#' ${REPO_DIR}/apt2.txt | grep -v '^\s*$' | sed 's/\r//g; s/#.*//; s/^[[:space:]]*//; s/[[:space:]]*$//' | awk '{$1=$1};1') && \
+  apt-get update && \
+  apt-get install --yes --no-install-recommends $package_list && \
   apt-get autoremove --purge && \
   apt-get clean && \
   rm -rf /var/lib/apt/lists/*
@@ -44,29 +48,17 @@ ENV NB_USER=${NB_USER}
 
 ## ONBUILD section. These commands are run in child Dockerfiles. These are run right after the FROM image is loaded
 
+ONBUILD RUN echo "py-rocket-base: looking for configuration files to use"
+
 ONBUILD USER ${NB_USER}
 
 # ${REPO_DIR} is owned by ${NB_USER}
 ONBUILD COPY --chown=${NB_USER}:${NB_USER} . ${REPO_DIR}/childimage
 
-# repo2docker will load files from a .binder or binder directory if
-# present. We check if those directories exist.
-ONBUILD RUN echo "Checking for 'binder' or '.binder' subfolder" \
-        ; cd "${REPO_DIR}/childimage/" \
-        ; if [ -d binder ] ; then \
-        echo "Using 'binder/' build context" \
-        ; elif [ -d .binder ] ; then \
-        echo "Using '.binder/' build context" \
-        ; else \
-        echo "Using './' build context" \
-        ; fi
-
 # Copy Desktop files into ${REPO_DIR}/Desktop if they exist. start will copy to Application dir and Desktop
 # Will not fail if Desktop dir exists but is empty
 ONBUILD RUN echo "Checking for 'Desktop directory'..." \
         ; cd "${REPO_DIR}/childimage/" \
-        ; [ -d binder ] && cd binder \
-        ; [ -d .binder ] && cd .binder \
         ; if test -d Desktop ; then \
             mkdir -p "${REPO_DIR}/Desktop" && \
             [ "$(ls -A Desktop 2>/dev/null)" ] && cp -r Desktop/* "${REPO_DIR}/Desktop/"; \
@@ -77,8 +69,6 @@ ONBUILD RUN echo "Checking for 'Desktop directory'..." \
 ONBUILD USER root
 ONBUILD RUN echo "Checking for 'apt.txt'..." \
         ; cd "${REPO_DIR}/childimage/" \
-        ; [ -d binder ] && cd binder \
-        ; [ -d .binder ] && cd .binder \
         ; if test -f "apt.txt" ; then \
         package_list=$(grep -v '^\s*#' apt.txt | grep -v '^\s*$' | sed 's/\r//g; s/#.*//; s/^[[:space:]]*//; s/[[:space:]]*$//' | awk '{$1=$1};1') \
         && apt-get update --fix-missing > /dev/null \
@@ -93,8 +83,6 @@ ONBUILD USER ${NB_USER}
 # sometimes package solving will get rid of pip installed packages. Make sure jupyter-remote-desktop-proxy does not disappear
 ONBUILD RUN echo "Checking for 'conda-lock.yml' or 'environment.yml'..." \
         ; cd "${REPO_DIR}/childimage/" \
-        ; [ -d binder ] && cd binder \
-        ; [ -d .binder ] && cd .binder \
         ; if test -f "conda-lock.yml" ; then echo "Using conda-lock.yml" & \
         conda-lock install --name ${CONDA_ENV} \
         && pip install --no-deps jupyter-remote-desktop-proxy \
@@ -114,17 +102,13 @@ ONBUILD RUN echo "Checking for 'conda-lock.yml' or 'environment.yml'..." \
 # to avoid wasting space.
 ONBUILD RUN echo "Checking for pip 'requirements.txt'..." \
         ; cd "${REPO_DIR}/childimage/" \
-        ; [ -d binder ] && cd binder \
-        ; [ -d .binder ] && cd .binder \
         ; if test -f "requirements.txt" ; then \
         ${NB_PYTHON_PREFIX}/bin/pip install --no-cache -r requirements.txt \
         ; fi
 
 # Add the r packages
 ONBUILD RUN echo "Checking for 'install.R" \
         ; cd "${REPO_DIR}/childimage/" \
-        ; [ -d binder ] && cd binder \
-        ; [ -d .binder ] && cd .binder \
         ; if test -f "install.R" ; then echo "Using install.R" & \
         Rscript install.R \
         ; fi
@@ -133,8 +117,6 @@ ONBUILD RUN echo "Checking for 'install.R" \
 # This is sourced in ${REPO_DIR}/start
 ONBUILD RUN echo "Checking for 'start'..." \
         ; cd "${REPO_DIR}/childimage/" \
-        ; [ -d binder ] && cd binder && cp start ${REPO_DIR}/childimage/start \
-        ; [ -d .binder ] && cd .binder && cp start ${REPO_DIR}/childimage/start \
         ; if test -f "start" ; then \
         chmod +x start \
         ; fi
@@ -145,8 +127,6 @@ ONBUILD RUN echo "Checking for 'start'..." \
 # leave behind.
 ONBUILD RUN echo "Checking for 'postBuild'..." \
         ; cd "${REPO_DIR}/childimage/" \
-        ; [ -d binder ] && cd binder \
-        ; [ -d .binder ] && cd .binder \
         ; if test -f "postBuild" ; then \
         chmod +x postBuild \
         && ./postBuild \

apt.txt → apt2.txt

@@ -28,7 +28,8 @@ mc
 
 # Regular build tools for compiling common stuff
 # most installed with R installation
-# need to install after R so these added to appendix
+build-essential
+gfortran
 
 # Dependencies for nbconvert and myst
 # texlive is installed by R installation

start

@@ -4,13 +4,11 @@ set -euo pipefail
 # Start - Set any environment variables here
 # These are inherited by all processes, *except* RStudio
 # USE export <parname>=value
-# Tell applications where to open desktop apps - this allows notebooks to pop open GUIs
-export DISPLAY=":1.0"
 # source this file to get the variables defined in the rocker Dockerfile
+# this is a series of export cmds
 source ${REPO_DIR}/env.txt
 # End - Set any environment variables here
 
-
 # The for loops will fail if they return null (no files). Set shell option nullglob
 shopt -s nullglob