Merge pull request #2 from jaytmiller/port-to-github

Port back to GitHub

deployments/common/Dockerfile

@@ -40,7 +40,7 @@ RUN /opt/common-scripts/apt-install \
         sysstat \
         net-tools \
         rename
-	#        libexpat1
+        #        libexpat1
 
 # S/W Development Tools
 RUN /opt/common-scripts/apt-install \
@@ -49,6 +49,7 @@ RUN /opt/common-scripts/apt-install \
         automake \
         libtool \
         make \
+        cmake \
         vim \
         emacs-nox \
         fftw3-dev \
@@ -87,10 +88,6 @@ RUN /opt/common-scripts/apt-install \
 #    apt-get remove --yes libpdfbox-java libfontbox-java && \
 #    apt autoremove --yes
 
-# ------------------------------------------------------------------------
-# This must be run after conda installs
-RUN /opt/common-scripts/fix-certs
-
 # ------------------------------------------------------------------------
 RUN curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip" && \
     unzip awscliv2.zip && \
@@ -112,7 +109,13 @@ USER root
 
 COPY --chown=${NB_UID}:${NB_GID}  common-scripts/ /opt/common-scripts
 COPY --chown=${NB_UID}:${NB_GID}  common-env/ /opt/common-env
-RUN cat /opt/common-scripts/global_bashrc >> /etc/bash.bashrc
+
+COPY bash.bashrc /tmp
+RUN cat /tmp/bash.bashrc >> /etc/bash.bashrc
+
+# For ENV_BASH definition for non-login shells
+COPY bash.env /etc/bash.env
+ENV BASH_ENV=/etc/bash.env
 
 # ----------------------------------------------------------------------
 # Common conda environments
@@ -128,11 +131,11 @@ COPY default-home-contents/   /etc/default-home-contents
 # ----------------------------------------------------------------------
 # YYYY SEC
 
-RUN npm set config set cafile /etc/ssl/certs/stsci-tls-ca-bundle.pem
-
 RUN npm install -g --prod yarn             && \
     npm install -g --prod yarn-audit-fix   && \
     npm install -g minimist                && \
-    yarn config set cafile /etc/ssl/certs/stsci-tls-ca-bundle.pem && \
     npm cache clean --force && \
     yarn cache clean --force
+
+COPY --chown=${NB_UID}:${NB_GID}  tools/  /opt/tools/
+COPY --chown=${NB_UID}:${NB_GID} VERSION /opt

deployments/common/Dockerfile.base

@@ -0,0 +1,44 @@
+ARG ROOT_CONTAINER=ubuntu:jammy
+ARG BASE_CONTAINER=$ROOT_CONTAINER
+FROM $BASE_CONTAINER
+
+USER root
+
+ARG TZ='America/New_York'
+ARG DEBIAN_FRONTEND=noninteractive
+
+ARG USE_FROZEN=1
+ENV USE_FROZEN=$USE_FROZEN
+
+ARG PIP_SWITCHES="--no-cache-dir"
+ENV PIP_SWITCHES=$PIP_SWITCHES
+
+# Enable easy swap of conda with e.g. mamba
+ARG CONDA_VER=conda
+ENV CONDA_VER=${CONDA_VER}
+
+# Clearing caches at the end of each RUN saves image space
+# but seems to mess up dependency debug tools like pipdeptree.
+# NOT setting this is also a requirement of effective Docker
+# buildkit cache use.  ATM jupyter/docker-stacks will still wipe
+# out caches created prior to the common base image regardless.
+ARG CLEAR_PKG_CACHES="1"
+ENV CLEAR_PKG_CACHES=${CLEAR_PKG_CACHES}
+
+# These are duplicated in jupyter/docker-stacks so need to be changed
+# in both locations.  Better than hard coding in scripts though.
+ENV NB_UID=1000
+ENV NB_GID=100
+
+# ------------------------------------------------------------------------
+
+COPY --chown=${NB_UID}:${NB_GID} common-scripts/apt-install  /opt/common-scripts/apt-install
+RUN /opt/common-scripts/apt-install \
+    apt-utils \
+    tzdata \
+    ca-certificates \
+    openssl \
+    wget \
+    vim \
+    npm \
+    nodejs

deployments/common/Dockerfile.trailer

@@ -1,12 +1,13 @@
 # ========================= vvvvv Generic vvvvv  =========================
 
+USER $NB_UID
+
 # Fix JS encoding issue that prevents widgets from displaying properly in notebook mode
 # See https://github.com/jupyter/notebook/issues/6033 for details
 RUN sed -i 's/data-base-url="{{base_url | urlencode}}"/data-base-url="{{base_url}}"/g' `ls -1 ${CONDA_DIR}/lib/python*/site-packages/notebook/templates/notebook.html`
 
 # ----------------------------------------------------------------------
 
-USER $NB_UID
 RUN /opt/common-scripts/kernel-setup   # set up Ipython / JupyterLab kernels
 
 # ----------------------------------------------------------------------
@@ -15,7 +16,7 @@ RUN /opt/common-scripts/kernel-setup   # set up Ipython / JupyterLab kernels
 
 USER root
 
-RUN find /home/${NB_USER} ! -uid ${NB_UID} | xargs chown ${NB_UID}:${NB_GID}
+RUN ( find /home/${NB_USER} ! -uid ${NB_UID} | xargs chown ${NB_UID}:${NB_GID} ) || true
 
 # remove this step once nbgitpuller enabled; these contents will be in the
 #  jupyterhub-user-content repo.   Install deployment-specific $HOME files.
@@ -24,20 +25,22 @@ RUN  cp -r /home/jovyan/.local /etc/default-home-contents && \
      cp -r /home/jovyan/.jupyter /etc/default-home-contents
 COPY global_bashrc /home/jovyan
 RUN  cat /home/jovyan/global_bashrc >> /etc/bash.bashrc  && \
+     cat /home/jovyan/global_bashrc >> /etc/bash.env  && \
      rm /home/jovyan/global_bashrc
 
-# Fix certs in conda for application level SSL, e.g. pass image-test running on CI-node
-RUN /opt/common-scripts/fix-certs
-
 # Copy any remaining environments files not caught by more precise as-needed build copies
 COPY --chown=${NB_UID}:${NB_GID} environments/    /opt/environments/
 
+# ----------------------------------------------------------------------
+
+COPY --chown=${NB_UID}:${NB_GID}  MISSION_VERSION /opt
+
 # ----------------------------------------------------------------------
 # YYYY SEC
 
 USER root
 #RUN  /opt/common-scripts/npm-audit  /usr/share/npm/node_modules/socks-proxy-agent  fix  && \
-RUN   /opt/common-scripts/env-clean
+#RUN   /opt/common-scripts/env-clean
 
 #RUN  find /opt/conda -name yarn.lock | grep jupyterlab/staging | xargs rm -f || true
 
@@ -46,6 +49,16 @@ RUN   /opt/common-scripts/env-clean
 # common home directory files.   post-start-hook may not include everything required
 # for running on AWS,  just common functions needed for both AWS and standalone/CI.
 
+# Enable deletion of non-empty directories from lab GUI
+RUN echo "-------------------------------- STSCI Config Overwrites --------------------------------" \
+      >> /etc/jupyter/jupyter_notebook_config.py &&\
+    echo "c.FileContentsManager.delete_to_trash = False" >> /etc/jupyter/jupyter_notebook_config.py &&\
+    echo "c.FileContentsManager.always_delete_dir = True" >> /etc/jupyter/jupyter_notebook_config.py &&\
+    echo "-------------------------------- STSCI Config Overwrites --------------------------------" \
+      >> /etc/jupyter/jupyter_server_config.py &&\
+    echo "c.FileContentsManager.delete_to_trash = False" >> /etc/jupyter/jupyter_server_config.py &&\
+    echo "c.FileContentsManager.always_delete_dir = True" >> /etc/jupyter/jupyter_server_config.py
+
 USER $NB_USER
 WORKDIR /home/$NB_USER
 RUN /opt/environments/post-start-hook  docker   # docker == do not run hub-specific functions of hook

deployments/common/VERSION

@@ -0,0 +1 @@
+1.1.0

deployments/common/bash.bashrc

@@ -0,0 +1,19 @@
+export PS1="${debian_chroot:+($debian_chroot)}\u@notebook:\w\$ "
+
+# Enable conda
+. "/opt/conda/etc/profile.d/conda.sh"
+
+# Activate base by default
+conda activate base
+
+#export PATH="/opt/TurboVNC/bin:$PATH"
+
+# Utility scripts for users,  mainly python environment management
+export PATH="/opt/tools:$PATH"
+
+export LD_LIBRARY_PATH=/usr/local/lib
+
+# make non-login shell (notebook !) use same environment, picking up default kernel
+export BASH_ENV=/etc/bash.bashrc
+
+alias ls="ls --color=auto"

deployments/common/bash.env

@@ -0,0 +1,33 @@
+# System-wide .bashrc file for non-login bash(1) shells.
+
+# if the command-not-found package is installed, use it
+if [ -x /usr/lib/command-not-found -o -x /usr/share/command-not-found/command-not-found ]; then
+        function command_not_found_handle {
+                # check because c-n-f could've been removed in the meantime
+                if [ -x /usr/lib/command-not-found ]; then
+                   /usr/lib/command-not-found -- "$1"
+                   return $?
+                elif [ -x /usr/share/command-not-found/command-not-found ]; then
+                   /usr/share/command-not-found/command-not-found -- "$1"
+                   return $?
+                else
+                   printf "%s: command not found\n" "$1" >&2
+                   return 127
+                fi
+        }
+fi
+
+# Enable conda
+. "/opt/conda/etc/profile.d/conda.sh"
+
+# Activate base by default
+conda activate base
+
+#export PATH="/opt/TurboVNC/bin:$PATH"
+
+# Utility scripts for users,  mainly python environment management
+export PATH="/opt/tools:$PATH"
+
+export LD_LIBRARY_PATH=/usr/local/lib
+
+alias ls="ls --color=auto"

deployments/common/common-env/jupyter.pip

@@ -16,9 +16,7 @@ jupyterlab-pygments
 jupyter-server
 bqplot-image-gl
 jupyter-server-proxy
-jupyter_bokeh
 jupyter-packaging
-ipywidgets_bokeh
 ipyevents
 ipympl
 ipyvolume
@@ -27,3 +25,6 @@ ipywebrtc
 ipykernel
 jupyter-resource-usage
 git+https://github.com/spacetelescope/nersc-refresh-announcements@octarine-updates
+sidecar
+y-py
+ypy-websocket

deployments/common/common-env/required.pip

@@ -0,0 +1,7 @@
+# packages required for the framework to work
+
+# needed to install a kernel
+ipykernel
+
+# needed to run headless notebook tests
+papermill

deployments/common/common-scripts/copy-default-home

@@ -0,0 +1,22 @@
+#! /bin/bash -e
+
+# This script conditionally initializes user $HOME,  once.
+# To re-init you must rm ${HOME}/.sp-initialized
+
+if [ ! -f ${HOME}/.sp-initialized ]; then
+    echo "Initializing $HOME with config defaults."
+    #echo "Deleting initial config directories to remove user added files."
+    #( cd /etc/default-home-contents/; find . -type d ) | xargs rm -rf || true
+    echo "Copying initial config files."
+    rsync -r  /etc/default-home-contents/ ${HOME}
+    cat > ${HOME}/.sp-initialized  <<EOF
+Remove this file to re-initialize default configuration. The only
+configuration which will be affected can be seen in
+/etc/default-home-contents/, so you may need to remove custom
+configuration files yourself, if you've added any. Our policy is not
+to delete anything from your home directory.
+EOF
+else
+    echo "Skipping default config init,  $HOME already initialized."
+fi
+

deployments/common/common-scripts/env-clean

@@ -10,9 +10,10 @@ if [[ "${CLEAR_PKG_CACHES}" == "1" ]]; then
     ${CONDA_VER} clean -fya
     # ${CONDA_VER} build purge-all
     rm -rf $HOME/.cache/pip
+    rm -rf $HOME/.cache/pip-tools
     echo "===== Clearing jupyterlab and npm caches..."
     jupyter lab clean -y
     npm cache clean --force
     yarn cache clean --force
-    rm -rf "/home/${NB_USER}/.node-gyp"
+    rm -rf $HOME/.node-gyp
 fi