Virtual Desktop First Pass -- DO NOT MERGE YET.

.gitlab-ci.yml

@@ -20,6 +20,7 @@ include:
   - DOCKERFILE_RELPATH: "geolab-gpu"
   # - DOCKERFILE_RELPATH: "mspass_shortcourse"
   # - DOCKERFILE_RELPATH: "mt_shortcourse"
+  - DOCKERFILE_RELPATH: "virtual_desktop"
 
 variables:
   CONTAINER_REGISTRY_PLATFORM: "AWS-PUB"

docs/.readthedocs.yaml

@@ -4,6 +4,7 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.12"
+    nodejs: "20"
   jobs:
     pre_build:
       # Generate the Sphinx configuration for this Jupyter Book so it builds.

docs/requirements.txt

@@ -1,4 +1,4 @@
-jupyter-book
+jupyter-book<2.0.0
 matplotlib
 numpy
 sphinx == 6.2.1

virtual_desktop/Dockerfile

@@ -0,0 +1,51 @@
+FROM public.ecr.aws/earthscope-dev/geolab/geolab-default:agu_wkshp-dc9cd124 AS stage 
+
+ENV NB_GID=1000
+
+FROM stage
+
+USER root
+
+COPY setup-scripts/setup-linux-desktop.bash /opt/setup-scripts/setup-linux-desktop.bash
+COPY setup-scripts/fix-permissions.bash /usr/local/bin/fix-permissions.bash
+
+# Set DISPLAY env variable, so processes know where to open GUI windows.
+# Allows python processes running in notebooks to open windows in the GUI.
+ENV DISPLAY=":1.0"
+
+# Setup Linux Desktop
+RUN chmod a+x /opt/setup-scripts/setup-linux-desktop.bash
+RUN chmod a+x /usr/local/bin/fix-permissions.bash
+
+RUN /opt/setup-scripts/setup-linux-desktop.bash
+
+COPY startup-scripts /usr/local/bin/start-notebook.d/
+
+# env variables used by downstream images for setting up desktop files or
+# mime associations. Consumed by the startup-scripts in startup-scripts/
+ENV DESKTOP_FILES_DIR=/opt/desktop-files
+ENV MIME_FILES_DIR=/opt/mime-files
+
+RUN mkdir -p ${DESKTOP_FILES_DIR} ${MIME_FILES_DIR}
+
+#install GMT
+RUN apt-get update -qq --yes > /dev/null \
+    && apt-get install --yes -qq gnupg2 > /dev/null \
+    && apt-get install gcc --yes \
+    && apt-get install gfortran --yes \
+    && apt-get install g++ --yes \
+    && apt-get install make \
+    && apt-get install ftp --yes \
+    # && apt-get install gmt gmt-dcw gmt-gshhg --yes\
+    # && apt-get install gedit --yes \
+    # && apt-get install man-db --yes \
+    # && apt-get install taup \
+    && apt-get clean
+
+USER ${NB_UID}
+
+# Pin jupyterhub and pydantic to older version
+# because of https://github.com/NASA-IMPACT/veda-jupyterhub/issues/52#issuecomment-2277453902
+RUN python -m pip install --no-cache "jupyterhub<5.0.0" "pydantic<2.0"
+RUN python -m pip install --no-cache jupyter-remote-desktop-proxy
+# RUN python -m pip install --no-cache git+https://github.com/sunu/jupyter-remote-qgis-proxy@e1a49e0ba98700c2f49fc092d5fc1e43ca5442eb

virtual_desktop/environment.yml

@@ -0,0 +1,33 @@
+# Environment we need *on top* of base PANGEO stack
+# Get list of pangeo packages from https://github.com/pangeo-data/pangeo-docker-images/blob/master/pangeo-notebook/packages.txt
+# BUT REMEMBER TO PICK THE HASH THAT CORRESPONDS TO OUR BASE IMAGE
+channels:
+  - conda-forge
+
+dependencies:
+  # Packages required by ES
+  - tiledb
+  - pip
+  - pip:
+  # Pin jupyterhub and pydantic to older version because of https://github.com/NASA-IMPACT/veda-jupyterhub/issues/52#issuecomment-2277453902
+    - awswrangler
+    - dascore
+    - earthscope-sdk==1.2.0b0
+    - earthscope-cli==1.0.1
+    - earthscopestraintools
+    - hypoinvpy
+    - gnssrefl
+    - jupyter_contrib_nbextensions
+    # - jupyterlab_jupyterbook_navigation
+    - jupyter-remote-desktop-proxy
+    - jupyter-resource-usage
+    - jupyter-server-proxy
+    # - jupyterhub<5.0.0
+    - nbgitpuller
+    - obspy==1.4.1
+    # - pydantic<2.0
+    - pygmt==0.14.2
+    - pynlloc
+    - pyocto
+    - pyrocko
+    - websockify

virtual_desktop/setup-scripts/fix-permissions.bash

@@ -0,0 +1,33 @@
+#!/bin/bash
+# Set permissions on a directory
+# After any installation, if a directory needs to be (human) user-writable, run this script on it.
+# It will make everything in the directory owned by the group ${NB_GID} and writable by that group.
+# Deployments that want to set a specific user id can preserve permissions
+# by adding the `--group-add users` line to `docker run`.
+
+# Uses find to avoid touching files that already have the right permissions,
+# which would cause a massive image explosion
+
+# Right permissions are:
+# group=${NB_GID}
+# AND permissions include group rwX (directory-execute)
+# AND directories have setuid,setgid bits set
+
+set -e
+
+for d in "$@"; do
+    find "${d}" \
+        ! \( \
+            -group "${NB_GID}" \
+            -a -perm -g+rwX \
+        \) \
+        -exec chgrp "${NB_GID}" -- {} \+ \
+        -exec chmod g+rwX -- {} \+
+    # setuid, setgid *on directories only*
+    find "${d}" \
+        \( \
+            -type d \
+            -a ! -perm -6000 \
+        \) \
+        -exec chmod +6000 -- {} \+
+done

virtual_desktop/setup-scripts/setup-linux-desktop.bash

@@ -0,0 +1,59 @@
+#!/bin/bash
+set -exuo pipefail
+# Requirements:
+# - Run as the root user
+
+# Install baseline packages to get X and xfce working
+apt-get update -qq --yes > /dev/null 
+apt-get install --yes --no-install-recommends -qq \
+    xfce4 \
+    xorg \
+    dbus-x11 \
+    xubuntu-icon-theme \
+    > /dev/null
+
+# Install tigervnc from apt repos - these are newer and more architecture
+# appropriate than whatever is bundled with jupyter-remote-desktop-proxy
+apt-get install --yes --no-install-recommends -qq \
+        tigervnc-standalone-server \
+        tigervnc-xorg-extension > /dev/null
+
+# Install add-apt-repositories so we can add PPA for latest firefox
+apt-get install --yes --no-install-recommends -qq \
+    software-properties-common gpg-agent > /dev/null
+
+# Install Firefox from a PPA - default Ubuntu's Firefox no longer
+# provides it via apt, using snap instead. That does not work inside
+# containers. We do this before our apt update in the script so that
+# needs to run only once.
+add-apt-repository ppa:mozillateam/ppa
+
+# Install Firefox from the PPA explicitly
+apt-get update -qq --yes > /dev/null
+apt-get install -qq --yes -t 'o=LP-PPA-mozillateam' --yes firefox
+
+#install GMT
+apt-get install gmt gmt-dcw gmt-gshhg --yes
+apt-get install gedit --yes
+apt-get install man-db --yes
+
+#install java and taup
+apt-get install -y openjdk-11-jre-headless
+wget https://zenodo.org/records/16884103/files/TauP-3.1.0.zip
+unzip TauP-3.1.0.zip
+export PATH="$PATH:TauP-3.1.0/bin"
+
+# Cleanup apt-get update side effects
+rm -rf /var/lib/apt/lists/*
+
+# Install packages required for linux desktop VPN setup to work
+# websockify and jupyter-server-proxy available from conda-forge, but
+# jupyter-remote-desktop-proxy is not.
+# Temporarily install nbgitpuller too, while we work on getting it upstream
+mamba install -c conda-forge --yes \
+      websockify \
+      jupyter-server-proxy \
+      nbgitpuller
+
+/usr/local/bin/fix-permissions.bash "${CONDA_DIR}"
+/usr/local/bin/fix-permissions.bash "/home/${NB_USER}"

virtual_desktop/startup-scripts/setup-mime-files.bash

@@ -0,0 +1,19 @@
+#!/bin/bash -l
+set -euo pipefail
+# This script is run on container startup, as a non-root user
+# It copies any .xml files it may find in a MIME_FILES_DIR to the user's
+# mime associations directory, allowing image authors to allow users to launch
+# a specific application by double clicking files of a specific type.
+# It's done at startup time because $HOME is often mounted over by a
+# persistent remote filesystem, hiding whatever is in the directory.
+
+# Set nullglob, so we don't error out if there are no MIME files to be found
+shopt -s nullglob
+
+MIME_DIR="${HOME}/.local/share/mime"
+MIME_PACKAGES_DIR="${MIME_DIR}/packages"
+mkdir -p "${MIME_PACKAGES_DIR}"
+for mime_file_path in ${MIME_FILES_DIR}/*.xml; do
+    cp "${mime_file_path}" "${MIME_PACKAGES_DIR}/."
+done
+update-mime-database "${MIME_DIR}"