Merge pull request #88 from brown-ccv/base_packages

Base packages in dev/templates were updated and tested in mpa2065.

.github/workflows/basepackages-recurring-tag.yml

@@ -0,0 +1,52 @@
+name: tag-image-basepackages
+on: [workflow_dispatch]
+
+env:
+  CLASS: basepackages
+  TARGET: r_julia
+  SQLITE: false
+  PYTHON_VERSION: "3.9.17"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/[email protected]
+
+      - name: Set Up GCloud
+        uses: google-github-actions/[email protected]
+        with:
+          project_id: ${{ secrets.GCP_PROJECT_ID_JH_DOCKER }}
+          service_account_key: ${{ secrets.GCP_SA_KEY_JH_DOCKER }}
+          export_default_credentials: true
+
+      - name: Create Julia Environment Files
+        if: env.TARGET == 'r_julia'
+        run: |
+          sudo --preserve-env=CLASS docker-compose up julia_build
+
+      - name: Upload Julia Env Files to Google Storage Bucket
+        if: env.TARGET == 'r_julia'
+        run: |
+          gsutil cp -r requirements/classes/basepackages/julia_env gs://jupyterhub-environment-files/recurring-/basepackages/past/${GITHUB_SHA}/julia
+          gsutil cp -r requirements/classes/basepackages/julia_env gs://jupyterhub-environment-files/recurring-/basepackages/latest/julia
+
+      - name: Configure Docker
+        run: gcloud auth configure-docker
+
+      - name: Build and Push JH Image
+        run: |
+          COMPOSE_DOCKER_CLI_BUILD=1 DOCKER_BUILDKIT=1 docker-compose up jh_image
+          docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/basepackages:${GITHUB_REF##*/}
+          docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/basepackages:${GITHUB_SHA}
+          docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/basepackages:latest
+          docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/basepackages:recurring-
+          docker push gcr.io/jupyterhub-docker-images/basepackages:latest
+          docker push gcr.io/jupyterhub-docker-images/basepackages:recurring-
+          docker push gcr.io/jupyterhub-docker-images/basepackages:${GITHUB_REF##*/}
+          docker push gcr.io/jupyterhub-docker-images/basepackages:${GITHUB_SHA}
+
+      - name: Upload Conda Env Files to Google Storage Bucket
+        run: |
+          gsutil cp -r requirements/out gs://jupyterhub-environment-files/recurring-/basepackages/past/${GITHUB_SHA}/conda
+          gsutil cp -r requirements/out gs://jupyterhub-environment-files/recurring-/basepackages/latest/conda

.github/workflows/basepackages.yml

@@ -0,0 +1,46 @@
+name: build-image-basepackages
+on: 
+  push:
+      paths:
+      - 'requirements/classes/basepackages/**'
+      - 'Dockerfile'
+      - 'docker-compose.yml'
+      - 'scripts/**'
+      - '.github/workflows/basepackages.yml'
+
+env:
+  CLASS: basepackages
+  TARGET: r_julia
+  SQLITE: false
+  PYTHON_VERSION: "3.9.17"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/[email protected]
+
+      - name: Set Up GCloud
+        uses: google-github-actions/[email protected]
+        with:
+          project_id: ${{ secrets.GCP_PROJECT_ID_JH_DOCKER }}
+          service_account_key: ${{ secrets.GCP_SA_KEY_JH_DOCKER }}
+          export_default_credentials: true
+
+      - name: Create Julia Environment Files
+        if: env.TARGET == 'r_julia'
+        run: |
+          sudo --preserve-env=CLASS docker-compose up julia_build
+
+      - name: Configure Docker
+        run: gcloud auth configure-docker
+      - uses: satackey/[email protected]
+        # Ignore the failure of a step and avoid terminating the job.
+        continue-on-error: true
+      - name: Build and Push JH Image
+        run: |
+          COMPOSE_DOCKER_CLI_BUILD=1 DOCKER_BUILDKIT=1 docker-compose up jh_image
+          docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/basepackages:${GITHUB_REF##*/}
+          docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/basepackages:latest
+          docker push gcr.io/jupyterhub-docker-images/basepackages:latest
+          docker push gcr.io/jupyterhub-docker-images/basepackages:${GITHUB_REF##*/}

.github/workflows/mpa2065-fall-tag.yml

@@ -5,29 +5,31 @@ env:
   CLASS: mpa2065
   TARGET: r_julia
   SQLITE: true
-  PYTHON_VERSION: "3.10"
+  PYTHON_VERSION: "3.9.17"
 
 jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3.5.3
 
       - name: Set Up GCloud
-        uses: google-github-actions/[email protected].0
+        uses: google-github-actions/[email protected].2
         with:
           project_id: ${{ secrets.GCP_PROJECT_ID_JH_DOCKER }}
           service_account_key: ${{ secrets.GCP_SA_KEY_JH_DOCKER }}
           export_default_credentials: true
 
       - name: Create Julia Environment Files
+        if: env.TARGET == 'r_julia'
         run: |
           sudo --preserve-env=CLASS docker-compose up julia_build
 
       - name: Upload Julia Env Files to Google Storage Bucket
+        if: env.TARGET == 'r_julia'
         run: |
-          gsutil cp -r requirements/classes/mpa2065/julia_env gs://jupyterhub-environment-files/fall-2022/mpa2065/past/${GITHUB_SHA}/julia
-          gsutil cp -r requirements/classes/mpa2065/julia_env gs://jupyterhub-environment-files/fall-2022/mpa2065/latest/julia
+          gsutil cp -r requirements/classes/mpa2065/julia_env gs://jupyterhub-environment-files/fall-2023/mpa2065/past/${GITHUB_SHA}/julia
+          gsutil cp -r requirements/classes/mpa2065/julia_env gs://jupyterhub-environment-files/fall-2023/mpa2065/latest/julia
 
       - name: Configure Docker
         run: gcloud auth configure-docker
@@ -38,13 +40,13 @@ jobs:
           docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/mpa2065:${GITHUB_REF##*/}
           docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/mpa2065:${GITHUB_SHA}
           docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/mpa2065:latest
-          docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/mpa2065:fall-2022
+          docker tag jupyterhub-docker-images_jh_image:latest gcr.io/jupyterhub-docker-images/mpa2065:fall-2023
           docker push gcr.io/jupyterhub-docker-images/mpa2065:latest
-          docker push gcr.io/jupyterhub-docker-images/mpa2065:fall-2022
+          docker push gcr.io/jupyterhub-docker-images/mpa2065:fall-2023
           docker push gcr.io/jupyterhub-docker-images/mpa2065:${GITHUB_REF##*/}
           docker push gcr.io/jupyterhub-docker-images/mpa2065:${GITHUB_SHA}
 
       - name: Upload Conda Env Files to Google Storage Bucket
         run: |
-          gsutil cp -r requirements/out gs://jupyterhub-environment-files/fall-2022/mpa2065/past/${GITHUB_SHA}/conda
-          gsutil cp -r requirements/out gs://jupyterhub-environment-files/fall-2022/mpa2065/latest/conda
+          gsutil cp -r requirements/out gs://jupyterhub-environment-files/fall-2023/mpa2065/past/${GITHUB_SHA}/conda
+          gsutil cp -r requirements/out gs://jupyterhub-environment-files/fall-2023/mpa2065/latest/conda

.github/workflows/mpa2065.yml

@@ -13,35 +13,31 @@ env:
   CLASS: mpa2065
   TARGET: r_julia
   SQLITE: true
-  PYTHON_VERSION: "3.10"
+  PYTHON_VERSION: "3.9.17"
 
 jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-
-      - name: Create Julia Environment Files
-        run: |
-          sudo --preserve-env=CLASS docker-compose up julia_build
-      - name: Upload Julia Env Files
-        uses: actions/upload-artifact@v2
-        with:
-          name: julia-environment-files
-          path: requirements/classes/${{ env.CLASS }}/julia_env
+      - uses: actions/[email protected]
 
       - name: Set Up GCloud
-        uses: google-github-actions/[email protected].0
+        uses: google-github-actions/[email protected].2
         with:
           project_id: ${{ secrets.GCP_PROJECT_ID_JH_DOCKER }}
           service_account_key: ${{ secrets.GCP_SA_KEY_JH_DOCKER }}
           export_default_credentials: true
 
+      - name: Create Julia Environment Files
+        if: env.TARGET == 'r_julia'
+        run: |
+          sudo --preserve-env=CLASS docker-compose up julia_build
+
       - name: Configure Docker
         run: gcloud auth configure-docker
-      - uses: satackey/[email protected]
-        # Ignore the failure of a step and avoid terminating the job.
-        continue-on-error: true
+#      - uses: satackey/[email protected]
+#        # Ignore the failure of a step and avoid terminating the job.
+#        continue-on-error: true
       - name: Build and Push JH Image
         run: |
           COMPOSE_DOCKER_CLI_BUILD=1 DOCKER_BUILDKIT=1 docker-compose up jh_image

Dockerfile

@@ -1,6 +1,6 @@
 # Copyright (c) Jupyter Development Team.
 # Distributed under the terms of the Modified BSD License.
-ARG ROOT_CONTAINER="jupyter/base-notebook:lab-3.4.5"
+ARG ROOT_CONTAINER="jupyter/base-notebook:lab-4.0.4"
 FROM ${ROOT_CONTAINER} as base
 
 ARG CLASS
@@ -68,11 +68,11 @@ RUN mktexlsr
 
 #------------ Install VSCode Server a Root----------------------------
 
-ENV VS_CODE_VERSION=4.5.1
+ENV VS_CODE_VERSION=4.16.1
 RUN mkdir /opt/code-server 
 WORKDIR /opt/code-server 
 RUN wget -qO- https://github.com/coder/code-server/releases/download/v${VS_CODE_VERSION}/code-server-${VS_CODE_VERSION}-linux-amd64.tar.gz | tar zxvf - --strip-components=1
-ENV	PATH=/opt/code-server:$PATH
+ENV	PATH=/opt/code-server:/opt/code-server/bin:$PATH
 
 #------------ Install Lab Extensions in base environment as NB_USER----------------------------
 
@@ -230,8 +230,8 @@ USER root
 
 ENV JULIA_DEPOT_PATH=/opt/julia
 ENV JULIA_PKGDIR=/opt/julia
-ENV JULIA_VERSION=1.8.5
-ENV JULIA_TAG=v1.8
+ENV JULIA_VERSION=1.9.2
+ENV JULIA_TAG=v1.9.2
 
 COPY requirements/classes/${CLASS}/julia_env/Project.toml $JULIA_PKGDIR/environments/$JULIA_TAG/
 COPY requirements/classes/${CLASS}/julia_env/Manifest.toml $JULIA_PKGDIR/environments/$JULIA_TAG/
@@ -242,7 +242,7 @@ WORKDIR /tmp
 # hadolint ignore=SC2046
 RUN mkdir "/opt/julia-${JULIA_VERSION}" && \
     wget -q https://julialang-s3.julialang.org/bin/linux/x64/$(echo "${JULIA_VERSION}" | cut -d. -f 1,2)"/julia-${JULIA_VERSION}-linux-x86_64.tar.gz" && \
-    echo "e71a24816e8fe9d5f4807664cbbb42738f5aa9fe05397d35c81d4c5d649b9d05 *julia-${JULIA_VERSION}-linux-x86_64.tar.gz" | sha256sum -c - && \
+    echo "4c2d799f442d7fe718827b19da2bacb72ea041b9ce55f24eee7b1313f57c4383 *julia-${JULIA_VERSION}-linux-x86_64.tar.gz" | sha256sum -c - && \
     tar xzf "julia-${JULIA_VERSION}-linux-x86_64.tar.gz" -C "/opt/julia-${JULIA_VERSION}" --strip-components=1 && \
     rm "/tmp/julia-${JULIA_VERSION}-linux-x86_64.tar.gz"
 RUN ln -fs /opt/julia-*/bin/julia /usr/local/bin/julia

README.md

@@ -59,8 +59,9 @@ To add a new class:
  - `-c`: class name (string) 
  - `-s`: class season/semester (fall, summer, spring) 
  - `-t`: target in docker file (string  – `base`, `r_lang` or `r_julia`) 
- - `-p`: python version (i.e 3.7 if ommited defaults to 3.10)
- - `-q`: wheter to install sqlite kernel (ommit the `-q` tag if sqlite is not required)
+ - `-p`: python version (i.e 3.7 if ommited defaults to 3.9.17)
+ - `-q`: whether to install sqlite kernel (ommit the `-q` tag if sqlite is not required)
+ - `-y`: class year
 
 ```bash
 # e.g

dev/add_class.sh

@@ -2,22 +2,24 @@
 set -e
 
 #default version of Python to use
-PYTHON_VERSION=3.10
+PYTHON_VERSION=3.9.17
 
 usage () { echo "Usage:"
-           echo "     -h – help"
-           echo "     -c – Class name"
+           echo "     -h - help"
+           echo "     -c - Class name"
            echo "     -s - Season (fall, spring, recurring)"
-           echo "     -t – Target stage in docker file (base, r_lang, or r_julia)"
-           echo "     -p – Python version (optional, if not given uses default)"
-           echo "     -q – Whether to install SQLITE Kernel"; }
+           echo "     -t - Target stage in docker file (base, r_lang, or r_julia)"
+           echo "     -p - Python version (optional, if not given uses default)"
+           echo "     -q - Whether to install SQLITE Kernel"
+           echo "     -y - Class year"; }
 
-while getopts c:s:t:p:qh option; do
+while getopts c:s:t:p:y:qh option; do
     case "${option}" in
         c) CLASS=${OPTARG};;
         s) SEASON=${OPTARG};;
         t) TARGET=${OPTARG};;
         p) PYTHON_VERSION=${OPTARG};;
+        y) YEAR=${OPTARG};;
         q) ADD_SQLITE=true;;
         h) usage; exit;;
     esac
@@ -31,7 +33,7 @@ if ((OPTIND < 6))
 then
     echo "Incomplete options specified. Make sure to pass at least the class name (-c) and target stage (-t)."
 else
-    export YEAR=$(date +'%Y')
+    export YEAR=$YEAR
     export CLASS=$CLASS
     export TARGET=$TARGET
     export SEASON=$SEASON

dev/sandbox/Dockerfile

@@ -1,4 +1,4 @@
-FROM ubuntu:20.04
+FROM ubuntu:22.04
 
 LABEL maintainer "Paul Stey <[email protected]>"
 LABEL image jh_sandbox
@@ -21,9 +21,9 @@ RUN usermod -aG sudo ccv
 USER ccv
 
 RUN cd /home/ccv \
-    && wget https://repo.anaconda.com/archive/Anaconda3-2020.02-Linux-x86_64.sh \
-    && bash Anaconda3-2020.02-Linux-x86_64.sh -b \
-    && rm Anaconda3-2020.02-Linux-x86_64.sh
+    && wget https://repo.anaconda.com/archive/Anaconda3-2023.07-2-Linux-x86_64.sh \
+    && bash Anaconda3-2023.07-2-Linux-x86_64.sh -b \
+    && rm Anaconda3-2023.07-2-Linux-x86_64.sh
 
 ENV PATH="/home/ccv/anaconda3/bin:${PATH}"
 

dev/templates/class_tag.yml

@@ -11,10 +11,10 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3.5.3
 
       - name: Set Up GCloud
-        uses: google-github-actions/[email protected].0
+        uses: google-github-actions/[email protected].2
         with:
           project_id: ${{ secrets.GCP_PROJECT_ID_JH_DOCKER }}
           service_account_key: ${{ secrets.GCP_SA_KEY_JH_DOCKER }}

dev/templates/class_workflow.yml

@@ -7,6 +7,7 @@ on:
       - 'docker-compose.yml'
       - 'scripts/**'
       - '.github/workflows/${CLASS}.yml'
+  workflow_dispatch:
 
 env:
   CLASS: ${CLASS}
@@ -18,10 +19,10 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3.5.3
 
       - name: Set Up GCloud
-        uses: google-github-actions/[email protected].0
+        uses: google-github-actions/[email protected].2
         with:
           project_id: ${{ secrets.GCP_PROJECT_ID_JH_DOCKER }}
           service_account_key: ${{ secrets.GCP_SA_KEY_JH_DOCKER }}

dev/templates/requirements.txt

@@ -27,25 +27,25 @@ bottleneck
 pytables
 
 # these are the base r packages in the r-notebook image ( YOU PROBABLY WANT THESE IF YOUR TARGET IN DOCKER IS r_lang OR r_julia )
-r-base=4.0.0
+r-base=4.2.*
 r-caret=6.*
-r-crayon=1.3*
-r-devtools=2.3*
-r-forecast=8.12*
-r-hexbin=1.28*
-r-htmltools=0.4*
-r-htmlwidgets=1.5*
-r-irkernel=1.1*
-r-nycflights13=1.0*
-r-randomforest=4.6*
+r-crayon=1.*
+r-devtools=2.*
+r-forecast=8.*
+r-hexbin=1.*
+r-htmltools=0.*
+r-htmlwidgets=1.*
+r-irkernel=1.*
+r-nycflights13=1.*
+r-randomforest=4.*
 r-rcurl=1.98*
-r-rmarkdown=2.2*
-r-rodbc=1.3*
-r-rsqlite=2.2*
-r-shiny=1.4*
-r-tidyverse=1.3*
-unixodbc=2.3.*
-r-tidymodels=0.1*
+r-rmarkdown=2.*
+r-rodbc=1.*
+r-rsqlite=2.*
+r-shiny=1.*
+r-tidyverse
+unixodbc=2.*
+r-tidymodels=1.*
 
 # required for environment and plugins ( DO NOT REMOVE THESE!!! )
 ipython