Use patches in the macos profile and remove the standard one (Closes #8)

.github/workflows/build.yaml

@@ -0,0 +1,72 @@
+name: build
+on:
+  push:
+    branches:
+    - main
+    - develop
+
+    paths:
+    # Only rebuild website when apps have changed
+    - '.github/**'
+    - 'advanced-tooling/**'
+    - 'dask-gateway/**'
+    - 'how-to/**'
+    - 'container/**'
+jobs:
+
+
+  container-coder:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin
+    - name: build & push image
+      run: |
+        cd container/coder
+        version=$(cat codemeta.json | jq -r .version )
+        IMAGE_ID=ghcr.io/eoap/dev-platform-eoap/eoap-coder
+        docker build . --file Dockerfile.coder --tag eoap-coder
+        docker tag eoap-coder $IMAGE_ID:${version}
+        docker push $IMAGE_ID:${version}
+
+  container-build:
+
+    #needs: []
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        step: ["application-package-patterns", "advanced-tooling", "how-to"]
+
+    steps:
+    - uses: actions/checkout@v2
+    - run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin
+    - name: build & push image
+      run: |
+        version=$(cat ${{ matrix.step }}/codemeta.json | jq -r .version )
+        IMAGE_ID=ghcr.io/eoap/dev-platform-eoap/${{ matrix.step }}-coder
+        docker build ${{ matrix.step }} --file ${{ matrix.step }}/Dockerfile.coder --tag ${{ matrix.step }}
+        docker tag ${{ matrix.step }} $IMAGE_ID:${version}
+        docker push $IMAGE_ID:${version}
+
+  container-dask:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        step: ["client", "coder", "worker"]
+
+    steps:
+    - uses: actions/checkout@v2
+    - run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin
+    - name: build & push image
+      run: |
+        version=$(cat dask-gateway/codemeta.json | jq -r .version )
+        IMAGE_ID=ghcr.io/eoap/dev-platform-eoap/dask-gateway-${{ matrix.step }}
+        docker build dask-gateway --file dask-gateway/Dockerfile.${{ matrix.step }} --tag eoap-dask-gateway-${{ matrix.step }}
+        docker tag eoap-dask-gateway-${{ matrix.step }} $IMAGE_ID:${version}
+        docker push $IMAGE_ID:${version}

.pre-commit-config.yaml

@@ -0,0 +1,35 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.2.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-merge-conflict
+      - id: debug-statements
+      - id: detect-private-key
+      - id: no-commit-to-branch
+        args:
+          - --pattern=master|main
+      - id: requirements-txt-fixer
+
+  - repo: https://github.com/myint/autoflake
+    rev: v1.4
+    hooks:
+      - id: autoflake
+        args:
+          - --in-place
+          - --remove-unused-variables
+          - --remove-all-unused-imports
+  - repo: https://github.com/PyCQA/flake8
+    rev: 4.0.1
+    hooks:
+      - id: flake8
+        args:
+          - --max-line-length=188
+          - --max-doc-length=190
+
+  - repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+      - id: black
+        args:
+          - --line-length=140

README.md

@@ -71,7 +71,7 @@ cd mastering-app-package
 skaffold dev
 ```
 
-Wait for the deployment to stablize (1-2 minutes) and the open your browser on the link printed, usually http://127.0.0.1:8000.
+Wait for the deployment to stablize (1-2 minutes) and then open your browser on the link printed, usually http://127.0.0.1:8000.
 
 The typical output is: 
 

advanced-tooling/Dockerfile.coder

@@ -0,0 +1,156 @@
+FROM docker.io/library/python:3.10.12@sha256:bac3a0e0d16125977e351c861e2f4b12ecafeaa6f72431dc970d0b9155103232
+
+RUN \
+    apt-get update && \
+    apt-get install -y \
+    build-essential \
+    curl \
+    gcc \
+    vim \
+    tree \
+    file
+
+RUN \
+    echo "**** install node repo ****" && \
+    curl -s https://deb.nodesource.com/gpgkey/nodesource.gpg.key | apt-key add - && \
+    echo 'deb https://deb.nodesource.com/node_14.x jammy main' \
+        > /etc/apt/sources.list.d/nodesource.list && \
+    echo "**** install build dependencies ****" && \
+    apt-get update && \
+    apt-get install -y \
+    nodejs && \
+    apt remove yq jq -y
+
+RUN \
+    echo "**** install runtime dependencies ****" && \
+    apt-get install -y \
+    git \
+    libatomic1 \
+    nano \
+    net-tools \
+    sudo \
+    podman \
+    wget \
+    python3 \
+    python3-pip 
+
+RUN \
+    echo "**** install code-server ****" && \
+    if [ -z ${CODE_RELEASE+x} ]; then \
+        CODE_RELEASE=$(curl -sX GET https://api.github.com/repos/coder/code-server/releases/latest \
+        | awk '/tag_name/{print $4;exit}' FS='[""]' | sed 's|^v||'); \
+    fi && \
+    mkdir -p /app/code-server && \
+    curl -o \
+        /tmp/code-server.tar.gz -L \
+        "https://github.com/coder/code-server/releases/download/v${CODE_RELEASE}/code-server-${CODE_RELEASE}-linux-amd64.tar.gz" && \
+    tar xf /tmp/code-server.tar.gz -C \
+        /app/code-server --strip-components=1 && \
+    echo "**** patch 4.0.2 ****" && \
+    if [ "${CODE_RELEASE}" = "4.0.2" ] && [ "$(uname -m)" !=  "x86_64" ]; then \
+        cd /app/code-server && \
+        npm i --production @node-rs/argon2; \
+    fi && \
+    echo "**** clean up ****" && \
+    apt-get purge --auto-remove -y \
+        build-essential \
+        nodejs && \
+    apt-get clean && \
+    rm -rf \
+        /config/* \
+        /tmp/* \
+        /var/lib/apt/lists/* \
+        /var/tmp/* \
+        /etc/apt/sources.list.d/nodesource.list
+
+ENV USER=jovyan \
+    UID=1001 \
+    GID=100 \
+    HOME=/workspace \
+    PATH=/opt/conda/bin:/app/code-server/bin/:$PATH:/app/code-server/
+
+
+# RUN \
+#     echo "**** install conda ****" && \
+#     wget https://repo.anaconda.com/miniconda/Miniconda3-py39_4.12.0-Linux-x86_64.sh -O miniconda.sh -q && \
+#     sh miniconda.sh -b -p /opt/conda && \
+#     conda install -n base -c conda-forge mamba && \
+#     conda config --system --append channels conda-forge && \
+#     conda config --system --append channels terradue && \
+#     conda config --system --append channels eoepca && \
+#     conda config --system --append channels r && \
+#     conda config --system --set auto_update_conda false && \
+#     conda config --system --set show_channel_urls true && \
+#     conda config --system --set channel_priority "flexible"
+
+
+# RUN \
+#     mamba install -n base cwltool cwl-wrapper==0.12.2 nodejs && \
+#     mamba clean -a
+
+RUN \
+    echo "**** install yq, aws cli ****" && \
+    VERSION="v4.12.2"                                                                               && \
+    BINARY="yq_linux_amd64"                                                                         && \
+    wget --quiet https://github.com/mikefarah/yq/releases/download/${VERSION}/${BINARY}.tar.gz -O - |\
+    tar xz && mv ${BINARY} /usr/bin/yq                                                              && \
+    pip install awscli                                                            && \
+    pip install awscli-plugin-endpoint                                              
+
+RUN \
+    echo "**** install jupyter-hub native proxy ****" && \
+    pip install jhsingle-native-proxy>=0.0.9 && \
+    echo "**** install bash kernel ****" && \
+    pip install bash_kernel && \
+    python -m bash_kernel.install
+
+RUN \
+    echo "**** adds user jovyan ****" && \
+    useradd -m -s /bin/bash -N -u $UID $USER 
+
+COPY entrypoint.sh /opt/entrypoint.sh
+
+RUN chmod +x /opt/entrypoint.sh
+
+# RUN chown -R jovyan:100 /opt/conda
+
+# RUN \
+#     echo "**** required by cwltool docker pull even if running with --podman ****" && \
+#     ln -s /usr/bin/podman /usr/bin/docker
+
+ENTRYPOINT ["/opt/entrypoint.sh"]
+
+EXPOSE 8888
+
+RUN echo "**** install kubectl ****" && \
+    curl -s -LO "https://dl.k8s.io/release/$(curl -L -s https://dl.k8s.io/release/stable.txt)/bin/linux/amd64/kubectl" && \
+    chmod +x kubectl && \
+    mkdir -p /workspace/.venv/bin && \
+    mv ./kubectl /usr/local/bin/kubectl
+
+
+RUN curl -s -L https://github.com/pypa/hatch/releases/latest/download/hatch-x86_64-unknown-linux-gnu.tar.gz | tar -xzvf - -C /usr/local/bin/ && \
+    chmod +x /usr/local/bin/hatch
+
+RUN curl -s -L https://github.com/go-task/task/releases/download/v3.41.0/task_linux_amd64.tar.gz | tar -xzvf - -C /usr/local/bin/ && \
+    chmod +x /usr/local/bin/task
+
+RUN curl -s -L https://storage.googleapis.com/skaffold/releases/latest/skaffold-linux-amd64 > /usr/local/bin/skaffold && \
+    chmod +x /usr/local/bin/skaffold
+
+RUN pip3 install tomlq && tomlq --version
+
+RUN rm -f /usr/bin/yq && \
+    rm -f /usr/local/bin/yq && \
+    curl -s -LO https://github.com/mikefarah/yq/releases/download/v4.45.1/yq_linux_amd64.tar.gz && \
+    tar -xvf yq_linux_amd64.tar.gz && \
+    mv yq_linux_amd64 /usr/local/bin/yq && \
+    cp -v /usr/local/bin/yq /usr/bin/yq && \
+    chmod +x /usr/bin/yq /usr/local/bin/yq
+
+RUN curl -s -L https://github.com/jqlang/jq/releases/download/jq-1.7.1/jq-linux-amd64 > /usr/bin/jq && \
+    chmod +x /usr/bin/jq
+
+RUN pip install --upgrade uv
+
+USER jovyan

advanced-tooling/codemeta.json

@@ -0,0 +1,3 @@
+{
+    "version": "0.1.0"
+}

advanced-tooling/entrypoint.sh

@@ -0,0 +1,37 @@
+#!/bin/bash
+
+collect_port=0
+port="8888"
+delim='='
+
+for var in "$@"
+do
+    echo "$var"
+
+    if [ "$collect_port" == "1" ]; then
+       echo "Collecting external port $var"
+       port=$var
+       collect_port=0
+    fi
+
+    splitarg=${var%%$delim*}
+
+    if [ "$splitarg" == "--port" ]; then
+       if [ ${#splitarg} == ${#var} ]; then
+         collect_port=1
+       else
+         port=${var#*$delim}
+         echo "Setting external port $port"
+       fi
+    fi
+done
+
+destport=$((port + 1))
+
+echo "Using internal port $destport"
+
+if [ -z "$CODE_SERVER_WS" ]; then
+    CODE_SERVER_WS="/workspace"
+fi
+
+jhsingle-native-proxy --port $port --destport $destport code-server {--}auth none {--}bind-addr 0.0.0.0:$destport {--}user-data-dir /workspace $CODE_SERVER_WS

advanced-tooling/files/init.sh

@@ -19,27 +19,9 @@ echo '{"workbench.colorTheme": "Visual Studio Dark"}' > /workspace/User/settings
 
 python -m venv /workspace/.venv
 source /workspace/.venv/bin/activate
-/workspace/.venv/bin/python -m pip install --no-cache-dir tomlq calrissian
-# /workspace/.venv/bin/python -m ipykernel install --user --name mastering_env --display-name "Python (Mastering Application Package)"
-
-echo "**** install kubectl ****" 
-curl -s -LO "https://dl.k8s.io/release/$(curl -L -s https://dl.k8s.io/release/stable.txt)/bin/linux/amd64/kubectl"  
-chmod +x kubectl 
-mkdir -p /workspace/.venv/bin                                                                                                   
-mv ./kubectl /workspace/.venv/bin/kubectl
-
-
-curl -s -L https://github.com/pypa/hatch/releases/latest/download/hatch-x86_64-unknown-linux-gnu.tar.gz | tar -xzvf - -C /workspace/.venv/bin/
-chmod +x /workspace/.venv/bin/hatch
-curl -s -L https://github.com/go-task/task/releases/download/v3.41.0/task_linux_amd64.tar.gz | tar -xzvf - -C /workspace/.venv/bin/
-chmod +x /workspace/.venv/bin/task
-
-curl -s -L https://storage.googleapis.com/skaffold/releases/latest/skaffold-linux-amd64 > /workspace/.venv/bin/skaffold
-chmod +x /workspace/.venv/bin/skaffold
-
-curl -s -LO https://github.com/mikefarah/yq/releases/download/v4.45.1/yq_linux_amd64.tar.gz 
-tar -xvf yq_linux_amd64.tar.gz
-mv yq_linux_amd64 /workspace/.venv/bin/yq
+/workspace/.venv/bin/pip install --upgrade uv
+/workspace/.venv/bin/python -m uv pip install --no-cache-dir tomlq calrissian
+/workspace/.venv/bin/python -m ipykernel install --user --name advanced_tooling --display-name "Python (Application Package Patterns)"
 
 export AWS_DEFAULT_REGION="us-east-1"
 

advanced-tooling/skaffold.yaml

@@ -2,7 +2,18 @@ apiVersion: skaffold/v4beta9
 kind: Config
 metadata:
   name: eoap-advanced-tooling
-
+
+build:
+  tagPolicy:
+    envTemplate:
+      template: 2h
+
+  artifacts:
+    - image: ttl.sh/eoap-advanced-tooling-coder 
+      context: .
+      docker:
+        dockerfile: Dockerfile.coder
+
 deploy:
   helm:
     releases:
@@ -11,17 +22,19 @@ deploy:
         namespace: eoap-advanced-tooling
         createNamespace: true
         setValues:
-          coder.coderImage: eoepca/pde-code-server:1.0.0
+          coder.coderImage: ttl.sh/eoap-advanced-tooling-coder:2h
           coder.workspace: advanced-tooling
-          coderstorageClassName: standard
+          coder.storageClassName: standard #openebs-kernel-nfs-scw
           coder.workspaceStorage: 10Gi
           coderResources.limits.cpu: '2'
           coderResources.limits.memory: '6442450944'
           coderResources.requests.cpu: '1'
           coderResources.requests.memory: '4294967296'
           coder.securityContext.privileged: false
           calrissian.enabled: true
+          calrissian.storageClassName: standard #openebs-kernel-nfs-scw
           skaffold.enabled: true
+          kaniko.enabled: true
 
         setFiles: {
           initScript: ./files/init.sh,