From b58116a761962a15012a98f9547b650cc362f0ab Mon Sep 17 00:00:00 2001
From: Eli Holmes <eli.holmes@noaa.gov>
Date: Sat, 19 Oct 2024 17:18:25 -0700
Subject: [PATCH] text py-rocket with pangeo notebook

---
 draft_images/pangeo/Dockerfile      | 30 +++++++++++
 draft_images/pangeo/apt.txt         | 79 +++++++++++++++++++++++++++++
 draft_images/pangeo/environment.yml | 45 ++++++++++++++--
 draft_images/pangeo/rocker.sh       | 41 +++++++++++++++
 4 files changed, 191 insertions(+), 4 deletions(-)
 create mode 100644 draft_images/pangeo/apt.txt
 create mode 100644 draft_images/pangeo/rocker.sh

diff --git a/draft_images/pangeo/Dockerfile b/draft_images/pangeo/Dockerfile
index 74872d4..f6528e0 100644
--- a/draft_images/pangeo/Dockerfile
+++ b/draft_images/pangeo/Dockerfile
@@ -1 +1,31 @@
 FROM pangeo/pangeo-notebook:latest
+
+USER root
+
+ENV REPO_DIR="/srv/repo"
+RUN mkdir -p ${REPO_DIR}
+COPY . ${REPO_DIR}
+
+# Install R, RStudio via Rocker scripts
+ENV R_VERSION="4.4.1"
+ENV R_DOCKERFILE="verse_${R_VERSION}"
+RUN PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin && \
+  chmod +x ${REPO_DIR}/rocker.sh && \
+  ${REPO_DIR}/rocker.sh
+
+# Install extra cmd line packages after R installation
+# The package_list part is reading the file and doing clean-up to just have the list of packages
+RUN package_list=$(grep -v '^\s*#' ${REPO_DIR}/apt.txt | grep -v '^\s*$' | 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/*
+
+# Revert to default user
+USER ${NB_USER}
+
+COPY environment.yml environment.yml
+RUN mamba env update --name notebook -f environment.yml && mamba clean --all
+RUN rm environment.yml
+
diff --git a/draft_images/pangeo/apt.txt b/draft_images/pangeo/apt.txt
new file mode 100644
index 0000000..959a342
--- /dev/null
+++ b/draft_images/pangeo/apt.txt
@@ -0,0 +1,79 @@
+# Need to install after R installation
+
+# Basic unix tools
+man
+man-db
+manpages-posix
+manpages-dev
+manpages-posix-dev
+
+# Download tools
+curl
+wget
+
+# Core text editors on a *nix box: vim and emacs
+vim
+emacs-nox
+emacs-goodies-el
+
+# A couple of CLI editors that are easier than vim
+# micro  # currently not working on 18.04
+nano
+jed
+jed-extra
+
+# powerful terminal-based file manager, better than the one in JLab
+mc
+
+# for easily managing multiple repositories with one command (perl-doc
+# is needed for its help pages to work)
+mr
+perl-doc
+
+# Regular build tools for compiling common stuff
+build-essential
+gfortran
+
+# Dependencies for nbconvert and myst
+# texlive is installed by R installation but not some of the common packages
+texlive-latex-recommended
+
+# Other useful document-related tools
+# pandoc installed by R installation
+imagemagick
+
+# Some useful git utilities use basic Ruby
+ruby
+
+# Other niceties for command-line work and life
+ack   # powerful grep-like tool
+pydf  # colorized disk usage
+tmux
+screen
+htop
+nnn   # cmd line file manager
+zsh
+rsync
+tig  # console UI for git
+multitail
+tree
+
+## This section adds tools needed for desktop environment
+dbus-x11
+xorg
+xubuntu-icon-theme
+xfce4
+xfce4-goodies
+xclip
+xsel
+
+# GUI text editors
+emacs
+vim-gtk3
+gedit
+
+# Git clients and tools
+git-gui
+gitg
+qgit
+meld
\ No newline at end of file
diff --git a/draft_images/pangeo/environment.yml b/draft_images/pangeo/environment.yml
index 27f9e09..bf5fcc4 100644
--- a/draft_images/pangeo/environment.yml
+++ b/draft_images/pangeo/environment.yml
@@ -1,9 +1,46 @@
-name: pangeo
+name: py-rocket-base
+
 channels:
- - conda-forge
+  - conda-forge
+  - nodefaults
+
 dependencies:
-  - qgis
-  - pip
+  # This provides memory usage stats on JupyterLab and classic notebook
+  - jupyter-resource-usage~=1.0.1
+  # https://syncthing.net/ provides a dropbox-like interface for syncing directories across users,
+  # hubs and machines. Used along with `jupyter-syncthing-proxy`.
+  # - jupyter-syncthing-proxy==1.0.3
+  # - syncthing~=1.22.1
+  # gh-scoped-creds allows users to securely push to GitHub from their repo.
+  # https://blog.jupyter.org/securely-pushing-to-github-from-a-jupyterhub-3ee42dfdc54f has
+  # some more information
+  - gh-scoped-creds==4.1
+  # More git tools from github-cli
+  - gh~=2.32.1
+
+  # R/RStudio Support
+  - jupyter-rsession-proxy
+  
+  # VS Code support
+  - jupyter-vscode-proxy~=0.5
+  - code-server~=4.23
+
+
+  # JupyterBook Addons
+  - sphinx~=7.3
+  - sphinxcontrib-bibtex
+
+  # Resolves warning "No ICDs were found": https://github.com/CryoInTheCloud/hub-image/issues/50
+  - ocl-icd-system
+  # needed for Linux desktop to work
+  - websockify>=0.10
+  # Includes new subcommands (`switch` & `restore`) and vulnerability fixes
+  # over the version available via ubuntu sources
+  - git>=2.39
+
+  # Desktop server
+  # Not all packages will be available from conda-forge, we install from pip when we need to.
+  - pip~=23.3.2
   - pip:
     # Access linux desktop from inside JupyterHub
     - jupyter-desktop-server==0.1.3
diff --git a/draft_images/pangeo/rocker.sh b/draft_images/pangeo/rocker.sh
new file mode 100644
index 0000000..ea0a5c4
--- /dev/null
+++ b/draft_images/pangeo/rocker.sh
@@ -0,0 +1,41 @@
+#!/bin/bash
+set -e
+
+# This script will copy in the rocker_scripts to install things and
+# Install rocker-verse using the TAG_${R_VERSION}.Dockerfile file
+# It will run just the ENV and RUN commands in that file
+# Variables defined here will only be available in this script.
+
+# Copy in the rocker files. Work in ${REPO_DIR} to make sure I don't clobber anything
+cd ${REPO_DIR}
+ROCKER_DOCKERFILE_NAME="${R_DOCKERFILE}.Dockerfile"
+# For degugging use: wget https://github.com/eeholmes/rocker-versioned2/archive/refs/tags/R4.4.1.tar.gz
+wget https://github.com/rocker-org/rocker-versioned2/archive/refs/tags/R${R_VERSION}.tar.gz
+tar zxvf R${R_VERSION}.tar.gz && \
+mv rocker-versioned2-R${R_VERSION}/scripts /rocker_scripts && \
+mv rocker-versioned2-R${R_VERSION}/dockerfiles/${ROCKER_DOCKERFILE_NAME} /rocker_scripts/original.Dockerfile && \
+rm R${R_VERSION}.tar.gz && \
+rm -rf rocker-versioned2-R${R_VERSION}
+
+cd /
+# Read the Dockerfile and process each line
+while IFS= read -r line; do
+    # Check if the line starts with ENV or RUN
+    if [[ "$line" == ENV* ]]; then
+        # Assign variable
+        var_assignment=$(echo "$line" | sed 's/^ENV //g')
+        # Replace ENV DEFAULT_USER="jovyan"
+        if [[ "$var_assignment" == DEFAULT_USER* ]]; then
+            var_assignment="DEFAULT_USER=${NB_USER}"
+        fi
+        # Run this way eval "export ..." otherwise the " will get turned to %22
+        eval "export $var_assignment"
+        # Write the exported variable to env.txt
+        echo "export $var_assignment" >> ${REPO_DIR}/env.txt
+    elif [[ "$line" == RUN* ]]; then
+        # Run the command from the RUN line
+        cmd=$(echo "$line" | sed 's/^RUN //g')
+        echo "Executing: $cmd"
+        eval "$cmd" # || echo ${cmd}" encountered an error, but continuing..."
+    fi
+done < /rocker_scripts/original.Dockerfile
\ No newline at end of file