Virtual Desktop First Pass -- DO NOT MERGE YET. #41

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sarahwilson523 wants to merge 24 commits into main from virtual_desktop

.gitlab-ci.yml

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+Diff line change
@@ Expand Up / @@ -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"
@@ Expand Down @@

docs/.readthedocs.yaml

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+Diff line change
@@ Expand Up / @@ -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.
@@ Expand Down @@

docs/requirements.txt

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

virtual_desktop/Dockerfile

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+    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

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+    # 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

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+    #!/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

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+    #!/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
+    # 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}"
+    #install java and taup
+    WORKDIR= /opt
+    apt-get install -y openjdk-11-jre-headless
+    wget -P /opt/TauP-3.1.0.zip https://zenodo.org/records/16884103/files/TauP-3.1.0.zip
+    unzip /opt/TauP-3.1.0.zip
+    export PATH="$PATH:/opt/TauP-3.1.0/bin"

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

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+    #!/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}"

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