Add datascience notebook and github actions

.github/workflows/main.yaml

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+name: Build kernel images
+
+on: 
+  push:
+    branches:
+      - main
+
+  pull_request:
+    branches:
+      - main
+
+jobs:
+
+  build-python-images:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        # version: ["3.8.8", "3.9.13", "3.10.5"] 3.10.5 fails with dependency conflicts
+        # We may need to have separate requirements.txt for each version, or replace
+        # dependencies on the fly
+        version: ["3.7.12", "3.8.13", "3.9.13", "3.10.9"]
+        directory: ["datascience-notebook"]
+        # The datascience-notebook base image does not support ARM
+        # We would need to build and maintain our own base image
+        # architecture: ["arm", "amd"]
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      # TODO: Log into DockerHub to prevent rate limiting
+
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v2
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
+
+      - name: Create context
+        run: |
+          docker context create github-action
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+        with:
+          endpoint: github-action
+          version: v0.10.4
+        env:
+          DOCKER_CONTEXT: github-action
+
+      - name: Cache Docker layers
+        uses: actions/cache@v3
+        id: docker-cache
+        with:
+          path: "/tmp/buildx-cache"
+          key: "${{ runner.os }}-buildx-${{ matrix.directory }}-${{ matrix.version }}"
+          restore-keys: "${{ runner.os }}-buildx-"
+
+      - name: Build arguments
+        id: build-args
+        run: |
+          # Image Name
+          container_registry=ghcr.io/${{ github.repository_owner }}
+          image_name=kernel-${{ matrix.directory }}
+          full_image_name="${container_registry}/${image_name}"
+
+          # Image Tags
+          image_sha_tag="${GITHUB_SHA:0:12}" # first 12 numbers of the SHA
+          image_version_tag="python-$(version=${{ matrix.version }} && echo ${version%.*} )" # removes patch version
+
+          full_image_name_tagged=''
+
+          if [ "${GITHUB_EVENT_NAME}" = 'push' ]; then
+            full_image_name_tagged="${full_image_name}:${image_version_tag}"
+          elif [ "${GITHUB_EVENT_NAME}" = 'pull_request' ]; then
+            full_image_name_tagged="${full_image_name}:${image_version_tag}-${image_sha_tag}"
+          fi
+
+          echo "::set-output name=FULL_IMAGE_NAME::${full_image_name}"
+          echo "::set-output name=FULL_IMAGE_NAME_TAGGED::${full_image_name_tagged}"
+
+          echo "::set-output name=BUILD_URL::https://github.com/${GITHUB_REPOSITORY}/actions/runs/${GITHUB_RUN_ID}"
+          echo "::set-output name=BUILD_TIMESTAMP::$(date --utc --iso-8601=seconds)"
+
+          echo "full_image_name: $full_image_name"
+          echo "image_version_tag: $image_version_tag"
+          echo "image_sha_tag: $image_sha_tag"
+          echo "full_image_name_tagged: $full_image_name_tagged"
+
+      - name: Build image
+        env:
+          DOCKER_CONTEXT: github-action
+        run: |
+          (
+            cd ${GITHUB_WORKSPACE}/kernels/${{ matrix.directory }}
+
+            docker buildx build \
+              --pull \
+              --push \
+              --platform=linux/amd64 \
+              --progress plain \
+              --cache-from 'type=local,src=/tmp/buildx-cache' \
+              --cache-to 'type=local,dest=/tmp/buildx-cache' \
+              --tag '${{ steps.build-args.outputs.FULL_IMAGE_NAME_TAGGED }}' \
+              --build-arg PYTHON_VERSION=${{ matrix.version }} \
+              --build-arg 'NBL_ARG_BUILD_TIMESTAMP=${{ steps.build-args.outputs.BUILD_TIMESTAMP }}' \
+              --build-arg 'NBL_ARG_BUILD_URL=${{ steps.build-args.outputs.BUILD_URL }}' \
+              --build-arg 'NBL_ARG_REVISION=${{ github.sha }}' \
+              --build-arg 'NBL_ARG_VERSION=${{ github.ref }}' \
+              .
+          )

kernels/datascience-notebook/.pythonrc

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+import pandas as pd
+
+import dx
+
+dx.set_option("DISPLAY_MAX_ROWS", 50_000)
+dx.set_option("DISPLAY_MAX_COLUMNS", 100)
+dx.set_option("ENABLE_DATALINK", True)
+dx.set_option("ENABLE_ASSIGNMENT", False)

kernels/datascience-notebook/Dockerfile

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+# syntax = docker/dockerfile:1.4.3
+ARG BASE_IMAGE=jupyter/datascience-notebook
+ARG PYTHON_VERSION=3.9.13
+# hadolint ignore=DL3006
+FROM ${BASE_IMAGE}:python-${PYTHON_VERSION}
+
+USER root
+
+# datascience-notebook:python-3.9.13 includes psutil 5.9.2 with cooked C lib, but
+# later pip installs end up installing 5.9.4, but for some
+# reason 'import psutil' will end up getting the python 5.9.4 but the
+# C lib from 5.9.2, and, unlike Smeagol, it hateses the precious.
+RUN pip uninstall -y psutil
+
+# Set up log file for magics
+RUN touch /var/log/noteable_magics.log && \
+  chown 4004:4004 /var/log/noteable_magics.log
+
+# When image is run, run the code with the environment
+# activated:
+SHELL ["/bin/bash", "-c"]
+
+WORKDIR /tmp
+
+# hadolint ignore=DL3008,DL3015
+RUN apt-get update && \
+  apt-get install -y jq procps git unixodbc-dev g++ \
+  && rm -rf /var/lib/apt/lists/*
+
+ENV NB_USER="noteable" \
+  NB_UID=4004 \
+  NB_GID=4004
+
+# Create the default unprivileged user
+RUN groupadd --gid 4004 noteable && \
+  useradd --uid 4004 --shell /bin/false --create-home --no-log-init --gid noteable noteable && \
+  chown --recursive noteable:noteable /home/noteable
+
+RUN mkdir /etc/ipython && chown noteable:noteable /etc/ipython
+RUN mkdir -p /etc/noteable && chown noteable:noteable /etc/noteable
+
+RUN chown noteable:noteable "${CONDA_DIR}" && \
+  fix-permissions "${CONDA_DIR}"
+
+# `rust` is required for install of some packages under arm (and future x86 packages)
+# hadolint ignore=SC1091
+RUN wget -O rustup.sh -q https://sh.rustup.rs && \
+    sh rustup.sh -y && \
+    rm rustup.sh && \
+    source "$HOME/.cargo/env"
+
+# Run non-privileged user
+USER noteable
+
+ENV PATH="/home/noteable/.local/bin:${PATH}" \
+  HOME="/home/noteable" \
+  XDG_CACHE_HOME="/home/noteable/.cache/" \
+  GOOGLE_APPLICATION_CREDENTIALS="/vault/secrets/gcp-credentials"
+
+ARG PYTHON_VERSION
+
+# hadolint ignore=DL3045
+COPY environment-${PYTHON_VERSION}.txt  ./environment.txt
+
+# hadolint ignore=SC2034
+RUN mamba install --file environment.txt
+
+# hadolint ignore=DL3045
+COPY requirements-${PYTHON_VERSION}.txt ./requirements.txt
+
+# hadolint ignore=SC1008,SC2155,DL3042,SC2102
+RUN pip install -I --no-cache-dir -r requirements.txt
+
+# Copy over any python commands that need to run on startup
+# that aren't covered by IPython extensions
+COPY .pythonrc /home/noteable/.pythonrc
+
+# Enable the widgets nbextension
+# hadolint ignore=SC1008
+RUN jupyter nbextension enable --py --sys-prefix widgetsnbextension
+
+# Smoke test to ensure packages were installed properly
+# hadolint ignore=SC1008
+RUN if [ "$PYTHON_VERSION" != "3.7.12" ]; then python -c "import noteable_magics"; fi
+
+RUN git config --global user.name "Noteable Kernel" && \
+  git config --global user.email "[email protected]" && \
+  git config --global safe.directory /etc/noteable/project && \
+  git config --global credential.helper /git_credential_helper.py && \
+  git config --global credential.useHttpPath true
+
+# https://ipython.readthedocs.io/en/stable/config/intro.html#systemwide-configuration
+COPY ipython_config.py /etc/ipython
+
+# Set standard working directory for noteable project
+WORKDIR /etc/noteable/project
+
+# Add the entrypoint script to the $PATH
+COPY run.sh /usr/local/bin
+COPY secrets_helper.py /tmp/secrets_helper.py
+COPY git_credential_helper.py /git_credential_helper.py
+COPY git-wrapper.sh /usr/local/bin/git
+
+EXPOSE 50001-50005
+
+# Use tini to manage passing signals to the child kernel process
+# -g will ensure signals are passed to the entire child process *group*, 
+# not just the immediate child process (bash)
+# https://github.com/krallin/tini#process-group-killing
+ENTRYPOINT ["tini", "-g", "--"]
+CMD ["run.sh"]
+
+# Labels
+ARG NBL_ARG_BUILD_TIMESTAMP="undefined"
+ARG NBL_ARG_REVISION="undefined"
+ARG NBL_ARG_PYTHON_VERSION="3.9.6"
+ARG NBL_ARG_BUILD_URL="undefined"
+ARG NBL_ARG_VERSION="undefined"
+LABEL org.opencontainers.image.created="${NBL_ARG_BUILD_TIMESTAMP}" \
+  org.opencontainers.image.revision="${NBL_ARG_REVISION}" \
+  org.opencontainers.image.source="https://github.com/noteable-io/polymorph" \
+  org.opencontainers.image.title="noteable-python-${NBL_ARG_PYTHON_VERSION}" \
+  org.opencontainers.image.url="${NBL_ARG_BUILD_URL}" \
+  org.opencontainers.image.vendor="Noteable" \
+  org.opencontainers.image.version="${NBL_ARG_VERSION}"