Merge branch 'master' into asalikhov/remove_py2

.flake8

+[flake8]
+ignore = W605,W503,W504,H306,H238,H301,H202
+max-line-length = 120
+per-file-ignores =
+    test/test_packages.py:E501

.github/workflows/docker.yml

+name: Build Docker Images
+
+on:
+  pull_request:
+    paths-ignore:
+      - "*.md"
+      - "binder/**"
+      - "docs/**"
+      - "examples/**"
+  push:
+    branches:
+      - master
+    paths-ignore:
+      - "*.md"
+      - "binder/**"
+      - "docs/**"
+      - "examples/**"
+
+jobs:
+  build:
+    name: Build Docker Images
+    runs-on: ubuntu-latest
+    if: >
+      !contains(github.event.head_commit.message, 'ci skip') &&
+      !contains(github.event.pull_request.title, 'ci skip')
+    steps:
+      - name: Clone Main Repo
+        uses: actions/checkout@v2
+        with:
+          path: main
+      - name: Clone Wiki
+        uses: actions/checkout@v2
+        with:
+          repository: ${{github.repository}}.wiki
+          path: wiki
+      - name: Set Up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+      - name: Install Dev Dependencies
+        run: |
+          python -m pip install --upgrade pip
+          make -C main dev-env hadolint-install
+      - name: Lint Dockerfiles
+        run: make -C main hadolint-all
+      - name: Run pre-commit hooks
+        run: make -C main pre-commit-all
+      - name: Build Docker Images
+        run: make -C main build-test-all
+      - name: Run Post-Build Hooks
+        run: make -C main hook-all
+        env:
+          COMMIT_MSG: "${{github.event.head_commit.message}}"
+          WIKI_PATH: ../wiki
+      - name: Login to Docker Hub
+        if: github.ref == 'refs/heads/master'
+        run: >
+          echo '${{secrets.DOCKERHUB_PASSWORD}}' | docker login --username
+          '${{secrets.DOCKERHUB_USERNAME}}' --password-stdin
+      - name: Push Images to DockerHub
+        if: github.ref == 'refs/heads/master'
+        run: make -C main push-all
+      - name: Push Wiki to GitHub
+        if: github.ref == 'refs/heads/master'
+        # Pass GITHUB_REPOSITORY directly to avoid conflict with GitHub Actions built-in env var
+        run: make -C main git-commit GITHUB_REPOSITORY='${{ github.repository }}.wiki'
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          LOCAL_PATH: ../wiki

.github/workflows/sphinx.yml

+name: Build Sphinx Documentation
+
+on:
+  pull_request:
+    paths:
+      - "docs/**"
+      - ".github/workflows/sphinx.yml"
+  push:
+    branches:
+      - master
+    paths:
+      - "docs/**"
+      - ".github/workflows/sphinx.yml"
+
+jobs:
+  build:
+    name: Build Sphinx Documentation
+    runs-on: ubuntu-latest
+    if: >
+      !contains(github.event.head_commit.message , 'ci skip') &&
+      !contains(github.event.pull_request.title, 'ci skip')
+    steps:
+      - name: Checkout Repo
+        uses: actions/checkout@v2
+      - name: Set Up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.x
+      - name: Install Dev Dependencies
+        run: |
+          python -m pip install --upgrade pip
+          make dev-env
+      - name: Build Documentation
+        run: make docs
+      - name: Extract Source Strings
+        if: github.ref == 'refs/heads/master'
+        working-directory: docs
+        run: |
+          make gettext
+          sphinx-intl update -p _build/gettext -l en
+      - name: Push Strings to Master
+        if: github.ref == 'refs/heads/master'
+        run: make git-commit
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_REPOSITORY: ${{ github.repository }}
+          LOCAL_PATH: ./docs/locale/en

.pre-commit-config.yaml

+---
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.1.0
+    hooks:
+      - id: check-yaml
+        files: .*\.(yaml|yml)$
+  - repo: https://github.com/adrienverge/yamllint.git
+    rev: v1.23.0
+    hooks:
+      - id: yamllint
+        args: ['-d {extends: relaxed, rules: {line-length: disable}}', '-s']
+        files: \.(yaml|yml)$
+  - repo: https://github.com/openstack-dev/bashate.git
+    rev: 2.0.0
+    hooks:
+      - id: bashate
+        args: ['--ignore=E006']
+  - repo: https://gitlab.com/pycqa/flake8
+    rev: 3.8.3
+    hooks:
+      - id: flake8
+  - repo: https://github.com/pre-commit/mirrors-autopep8
+    rev: v1.5.4
+    hooks:
+      - id: autopep8

.travis.yml

----
-dist: bionic
-language: python
-python:
-  - 3.7
-sudo: required
-services:
-  - docker
-
-jobs:
-  include:
-    - stage: diff-test
-      install:
-        - pip install --upgrade pip
-        - make dev-env
-        - make lint-install
-      script:
-        - set -e
-        - if [ $(make n-docs-diff) -ne 0 ]; then make docs; fi;
-        - if [ $(make n-other-diff) -ne 0 ]; then make lint-build-test-all DARGS="--build-arg TEST_ONLY_BUILD=1"; fi;
-    - stage: push-tx
-      install:
-        - pip install --upgrade pip
-        - make dev-env
-      script:
-        - if [ $(make n-docs-diff DIFF_RANGE=$TRAVIS_COMMIT_RANGE) -ne 0 ]; then make tx-en; fi;
-    - stage: full-test
-      install:
-        - pip install --upgrade pip
-        - make dev-env
-        - make lint-install
-      script:
-        - set -e
-        - make docs
-        - make lint-build-test-all DARGS="--build-arg TEST_ONLY_BUILD=1"
-
-stages:
-  - name: diff-test
-    if: type = pull_request
-  - name: push-tx
-    if: type = push AND branch = master
-  - name: full-test
-    if: type = cron AND branch = master
-
-env:
-  global:
-    # yamllint disable-line
-    secure: 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

Makefile

@@ -4,9 +4,8 @@
 
 # Use bash for inline if-statements in arch_patch target
 SHELL:=bash
-OWNER:=jupyter
 ARCH:=$(shell uname -m)
-DIFF_RANGE?=master...HEAD
+OWNER?=jupyter
 
 # Need to list the images in build dependency order
 ifeq ($(ARCH),ppc64le)
@@ -24,8 +23,9 @@ endif
 
 ALL_IMAGES:=$(ALL_STACKS)
 
-# Linter
+# Dockerfile Linter
 HADOLINT="${HOME}/hadolint"
+HADOLINT_VERSION="v1.18.0"
 
 help:
 # http://marmelab.com/blog/2016/02/29/auto-documented-makefile.html
@@ -74,24 +74,38 @@ dev/%: ## run a foreground container for a stack
 	docker run -it --rm -p $(PORT):8888 $(DARGS) $(OWNER)/$(notdir $@) $(ARGS)
 
 dev-env: ## install libraries required to build docs and run tests
-	pip install -r requirements-dev.txt
+	@pip install -r requirements-dev.txt
 
-lint/%: ARGS?=
-lint/%: ## lint the dockerfile(s) for a stack
-	@echo "Linting Dockerfiles in $(notdir $@)..."
-	@git ls-files --exclude='Dockerfile*' --ignored $(notdir $@) | grep -v ppc64 | xargs -L 1 $(HADOLINT) $(ARGS)
-	@echo "Linting done!"
-
-lint-all: $(foreach I,$(ALL_IMAGES),lint/$(I) ) ## lint all stacks
+docs: ## build HTML documentation
+	make -C docs html
 
-lint-build-test-all: $(foreach I,$(ALL_IMAGES),lint/$(I) arch_patch/$(I) build/$(I) test/$(I) ) ## lint, build and test all stacks
-
-lint-install: ## install hadolint
-	@echo "Installing hadolint at $(HADOLINT) ..."
-	@curl -sL -o $(HADOLINT) "https://github.com/hadolint/hadolint/releases/download/v1.18.0/hadolint-$(shell uname -s)-$(shell uname -m)"
-	@chmod 700 $(HADOLINT)
-	@echo "Installation done!"
-	@$(HADOLINT) --version	
+git-commit: LOCAL_PATH?=.
+git-commit: GITHUB_SHA?=$(shell git rev-parse HEAD)
+git-commit: GITHUB_REPOSITORY?=jupyter/docker-stacks
+git-commit: GITHUB_TOKEN?=
+git-commit: ## commit outstading git changes and push to remote
+	@git config --global user.name "GitHub Actions"
+	@git config --global user.email "actions@users.noreply.github.com"
+
+	@echo "Publishing outstanding changes in $(LOCAL_PATH) to $(GITHUB_REPOSITORY)" 
+	@cd $(LOCAL_PATH) && \
+		git remote add publisher https://$(GITHUB_TOKEN)@github.com/$(GITHUB_REPOSITORY).git && \
+		git checkout master && \
+		git add -A -- . && \
+		git commit -m "[ci skip] Automated publish for $(GITHUB_SHA)" || exit 0
+	@cd $(LOCAL_PATH) && git push -u publisher master
+
+hook/%: export COMMIT_MSG?=$(shell git log -1 --pretty=%B)
+hook/%: export GITHUB_SHA?=$(shell git rev-parse HEAD)
+hook/%: export WIKI_PATH?=../wiki
+hook/%: ## run post-build hooks for an image
+	BUILD_TIMESTAMP="$$(date -u +%FT%TZ)" \
+	DOCKER_REPO="$(OWNER)/$(notdir $@)" \
+	IMAGE_NAME="$(OWNER)/$(notdir $@):latest" \
+	IMAGE_SHORT_NAME="$(notdir $@)" \
+	$(SHELL) $(notdir $@)/hooks/run_hook
+
+hook-all: $(foreach I,$(ALL_IMAGES),hook/$(I) ) ## run post-build hooks for all images
 
 img-clean: img-rm-dang img-rm ## clean dangling and jupyter images
 
@@ -107,20 +121,40 @@ img-rm-dang: ## remove dangling images (tagged None)
 	@echo "Removing dangling images ..."
 	-docker rmi --force $(shell docker images -f "dangling=true" -q) 2> /dev/null
 
-docs: ## build HTML documentation
-	make -C docs html
+hadolint/%: ARGS?=
+hadolint/%: ## lint the dockerfile(s) for a stack
+	@echo "Linting Dockerfiles in $(notdir $@)..."
+	@git ls-files --exclude='Dockerfile*' --ignored $(notdir $@) | grep -v ppc64 | xargs -L 1 $(HADOLINT) $(ARGS)
+	@echo "Linting done!"
+
+hadolint-all: $(foreach I,$(ALL_IMAGES),hadolint/$(I) ) ## lint all stacks
+
+hadolint-build-test-all: $(foreach I,$(ALL_IMAGES),hadolint/$(I) arch_patch/$(I) build/$(I) test/$(I) ) ## lint, build and test all stacks
 
-n-docs-diff: ## number of docs/ files changed since branch from master
-	@git diff --name-only $(DIFF_RANGE) -- docs/ ':!docs/locale' | wc -l | awk '{print $$1}'
+hadolint-install: ## install hadolint
+	@echo "Installing hadolint at $(HADOLINT) ..."
+	@curl -sL -o $(HADOLINT) "https://github.com/hadolint/hadolint/releases/download/$(HADOLINT_VERSION)/hadolint-$(shell uname -s)-$(shell uname -m)"
+	@chmod 700 $(HADOLINT)
+	@echo "Installation done!"
+	@$(HADOLINT) --version
 
+pre-commit-all: ## run pre-commit hook on all files
+	@pre-commit run --all-files
 
-n-other-diff: ## number of files outside docs/ changed since branch from master
-	@git diff --name-only $(DIFF_RANGE) -- ':!docs/' | wc -l | awk '{print $$1}'
+pre-commit-install: ## set up the git hook scripts
+	@pre-commit --version
+	@pre-commit install
 
 pull/%: DARGS?=
 pull/%: ## pull a jupyter image
 	docker pull $(DARGS) $(OWNER)/$(notdir $@)
 
+push/%: DARGS?=
+push/%: ## push all tags for a jupyter image
+	docker push $(DARGS) $(OWNER)/$(notdir $@)
+
+push-all: $(foreach I,$(ALL_IMAGES),push/$(I) ) ## push all tagged images
+
 run/%: DARGS?=
 run/%: ## run a bash in interactive mode in a stack
 	docker run -it --rm $(DARGS) $(OWNER)/$(notdir $@) $(SHELL)
@@ -129,20 +163,6 @@ run-sudo/%: DARGS?=
 run-sudo/%: ## run a bash in interactive mode as root in a stack
 	docker run -it --rm -u root $(DARGS) $(OWNER)/$(notdir $@) $(SHELL)
 
-tx-en: ## rebuild en locale strings and push to master (req: GH_TOKEN)
-	@git config --global user.email "travis@travis-ci.org"
-	@git config --global user.name "Travis CI"
-	@git checkout master
-
-	@make -C docs clean gettext
-	@cd docs && sphinx-intl update -p _build/gettext -l en
-
-	@git add docs/locale/en
-	@git commit -m "[ci skip] Update en source strings (build: $$TRAVIS_JOB_NUMBER)"
-
-	@git remote add origin-tx https://$${GH_TOKEN}@github.com/jupyter/docker-stacks.git
-	@git push -u origin-tx master
-
 test/%: ## run tests against a stack (only common tests or common tests + specific tests)
 	@if [ ! -d "$(notdir $@)/test" ]; then TEST_IMAGE="$(OWNER)/$(notdir $@)" pytest -m "not info" test; \
 	else TEST_IMAGE="$(OWNER)/$(notdir $@)" pytest -m "not info" test $(notdir $@)/test; fi

all-spark-notebook/Dockerfile

@@ -17,17 +17,17 @@ RUN apt-get update && \
     fonts-dejavu \
     gfortran \
     gcc && \
-    rm -rf /var/lib/apt/lists/*
+    apt-get clean && rm -rf /var/lib/apt/lists/*
 
 USER $NB_UID
 
 # R packages
 RUN conda install --quiet --yes \
-    'r-base=3.6.3' \
+    'r-base=4.0.3' \
     'r-ggplot2=3.3*' \
     'r-irkernel=1.1*' \
     'r-rcurl=1.98*' \
-    'r-sparklyr=1.2*' \
+    'r-sparklyr=1.4*' \
     && \
     conda clean --all -f -y && \
     fix-permissions "${CONDA_DIR}" && \

all-spark-notebook/README.md

-[![docker pulls](https://img.shields.io/docker/pulls/jupyter/all-spark-notebook.svg)](https://hub.docker.com/r/jupyter/all-spark-notebook/) [![docker stars](https://img.shields.io/docker/stars/jupyter/all-spark-notebook.svg)](https://hub.docker.com/r/jupyter/all-spark-notebook/) [![image metadata](https://images.microbadger.com/badges/image/jupyter/all-spark-notebook.svg)](https://microbadger.com/images/jupyter/all-spark-notebook "jupyter/all-spark-notebook image metadata")
+[![docker pulls](https://img.shields.io/docker/pulls/jupyter/all-spark-notebook.svg)](https://hub.docker.com/r/jupyter/all-spark-notebook/)
+[![docker stars](https://img.shields.io/docker/stars/jupyter/all-spark-notebook.svg)](https://hub.docker.com/r/jupyter/all-spark-notebook/)
+[![image metadata](https://images.microbadger.com/badges/image/jupyter/all-spark-notebook.svg)](https://microbadger.com/images/jupyter/all-spark-notebook "jupyter/all-spark-notebook image metadata")
 
 # Jupyter Notebook Python, Scala, R, Spark Stack
 
-Please visit the documentation site for help using and contributing to this image and others.
+GitHub Actions in the https://github.com/jupyter/docker-stacks project builds and pushes this image
+to Docker Hub.
 
-* [Jupyter Docker Stacks on ReadTheDocs](http://jupyter-docker-stacks.readthedocs.io/en/latest/index.html)
-* [Selecting an Image :: Core Stacks :: jupyter/all-spark-notebook](http://jupyter-docker-stacks.readthedocs.io/en/latest/using/selecting.html#jupyter-all-spark-notebook)
-* [Image Specifics :: Apache Spark](http://jupyter-docker-stacks.readthedocs.io/en/latest/using/specifics.html#apache-spark)
+Please visit the project documentation site for help using and contributing to this image and
+others.
+
+- [Jupyter Docker Stacks on ReadTheDocs](http://jupyter-docker-stacks.readthedocs.io/en/latest/index.html)
+- [Selecting an Image :: Core Stacks :: jupyter/all-spark-notebook](http://jupyter-docker-stacks.readthedocs.io/en/latest/using/selecting.html#jupyter-all-spark-notebook)
+- [Image Specifics :: Apache Spark](http://jupyter-docker-stacks.readthedocs.io/en/latest/using/specifics.html#apache-spark)

all-spark-notebook/hooks/index.tmpl

-INDEX_ROW="|\`${BUILD_TIMESTAMP}\`|\`jupyter/${IMAGE_SHORT_NAME}:${GIT_SHA_TAG}\`|[Git diff](https://github.com/jupyter/docker-stacks/commit/${SOURCE_COMMIT})<br />[Dockerfile](https://github.com/jupyter/docker-stacks/blob/${SOURCE_COMMIT}/${IMAGE_SHORT_NAME}/Dockerfile)<br />[Build manifest](./${IMAGE_SHORT_NAME}-${GIT_SHA_TAG})|"
-sed "/|-|/a ${INDEX_ROW}" -i "$INDEX_FILE"
\ No newline at end of file

all-spark-notebook/hooks/post_push

-#!/bin/bash
-set -e
-
-# Tag the latest build with the short git sha. Push the tag in addition
-# to the "latest" tag already pushed.
-GIT_SHA_TAG=${SOURCE_COMMIT:0:12}
-docker tag $IMAGE_NAME $DOCKER_REPO:$GIT_SHA_TAG
-docker push $DOCKER_REPO:$GIT_SHA_TAG
-
-# Create a working directory.
-BUILD_TIMESTAMP=$(date -u +%FT%TZ)
-WORKDIR=$(mktemp -d)
-GIT_URI="git@github.com:jupyter/docker-stacks.wiki.git"
-GIT_SANDBOX="${WORKDIR}/docker-stacks.wiki"
-IMAGE_SHORT_NAME=$(basename $DOCKER_REPO)
-MANIFEST_FILE="${GIT_SANDBOX}/manifests/${IMAGE_SHORT_NAME}-${GIT_SHA_TAG}.md"
-INDEX_FILE="${GIT_SANDBOX}/Home.md"
-
-# Configure git so it can push back to GitHub.
-eval $(ssh-agent -s)
-ssh-add <(base64 -d <(echo "$DEPLOY_KEY"))
-ssh-add -l
-git config --global user.email "jupyter@googlegroups.com"
-git config --global user.name "Jupyter Docker Stacks"
-
-# Glone the GitHub project wiki.
-pushd "$WORKDIR"
-git clone "$GIT_URI"
-popd
-
-# Render the build manifest template.
-mkdir -p $(dirname "$MANIFEST_FILE")
-source hooks/manifest.tmpl
-source hooks/index.tmpl
-
-# Push the wiki update back to GitHub.
-pushd "$GIT_SANDBOX"
-git add .
-git commit -m "DOC: Build ${MANIFEST_FILE}"
-git push -u origin master
-popd
-
-# Shutdown the ssh agent for good measure.
-ssh-agent -k
-
-# Invoke all downstream build triggers.
-set +e
-for url in $(echo $NEXT_BUILD_TRIGGERS | sed "s/,/ /g")
-do
-    curl -X POST $url
-done
\ No newline at end of file

all-spark-notebook/hooks/manifest.tmpl → all-spark-notebook/hooks/run_hook

+#!/bin/bash
+set -e
+
+# Apply tags
+GIT_SHA_TAG=${GITHUB_SHA:0:12}
+docker tag $IMAGE_NAME "$DOCKER_REPO:$GIT_SHA_TAG"
+
+# Update index
+INDEX_ROW="|\`${BUILD_TIMESTAMP}\`|\`jupyter/${IMAGE_SHORT_NAME}:${GIT_SHA_TAG}\`|[Git diff](https://github.com/jupyter/docker-stacks/commit/${GITHUB_SHA})<br />[Dockerfile](https://github.com/jupyter/docker-stacks/blob/${GITHUB_SHA}/${IMAGE_SHORT_NAME}/Dockerfile)<br />[Build manifest](./${IMAGE_SHORT_NAME}-${GIT_SHA_TAG})|"
+sed "/|-|/a ${INDEX_ROW}" -i "${WIKI_PATH}/Home.md"
+
+# Build manifest
+MANIFEST_FILE="${WIKI_PATH}/manifests/${IMAGE_SHORT_NAME}-${GIT_SHA_TAG}.md"
+mkdir -p $(dirname "$MANIFEST_FILE")
+
 cat << EOF > "$MANIFEST_FILE"
 * Build datetime: ${BUILD_TIMESTAMP}
-* DockerHub build code: ${BUILD_CODE}
 * Docker image: ${DOCKER_REPO}:${GIT_SHA_TAG}
 * Docker image size: $(docker images ${IMAGE_NAME} --format "{{.Size}}")
-* Git commit SHA: [${SOURCE_COMMIT}](https://github.com/jupyter/docker-stacks/commit/${SOURCE_COMMIT})
+* Git commit SHA: [${GITHUB_SHA}](https://github.com/jupyter/docker-stacks/commit/${GITHUB_SHA})
 * Git commit message:
 \`\`\`
 ${COMMIT_MSG}

all-spark-notebook/test/test_spark_notebooks.py

@@ -21,7 +21,10 @@ def test_nbconvert(container, test_file):
     output_dir = "/tmp"
     timeout_ms = 600
     LOGGER.info(f"Test that {test_file} notebook can be executed ...")
-    command = f"jupyter nbconvert --to markdown --ExecutePreprocessor.timeout={timeout_ms} --output-dir {output_dir} --execute {cont_data_dir}/{test_file}.ipynb"
+    command = "jupyter nbconvert --to markdown " + \
+        f"--ExecutePreprocessor.timeout={timeout_ms} " + \
+        f"--output-dir {output_dir} " + \
+        f"--execute {cont_data_dir}/{test_file}.ipynb"
     c = container.run(
         volumes={host_data_dir: {"bind": cont_data_dir, "mode": "ro"}},
         tty=True,

base-notebook/Dockerfile

@@ -4,7 +4,7 @@
 # Ubuntu 20.04 (focal)
 # https://hub.docker.com/_/ubuntu/?tab=tags&name=focal
 # OS/ARCH: linux/amd64
-ARG ROOT_CONTAINER=ubuntu:focal-20200703@sha256:d5a6519d9f048100123c568eb83f7ef5bfcad69b01424f420f17c932b00dea76
+ARG ROOT_CONTAINER=ubuntu:focal-20200925@sha256:2e70e9c81838224b5311970dbf7ed16802fbfe19e7a70b3cbfa3d7522aa285b4
 
 ARG BASE_CONTAINER=$ROOT_CONTAINER
 FROM $BASE_CONTAINER
@@ -19,6 +19,17 @@ SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 
 USER root
 
+# Miniconda installation
+# Default values can be overridden at build time
+# (ARGS are in lower case to distinguish them from ENV)
+# Check https://repo.anaconda.com/miniconda/
+# Miniconda archive to install
+ARG miniconda_version="4.8.3"
+# Archive MD5 checksum
+ARG miniconda_checksum="d63adf39f2c220950a063e0529d4ff74"
+# Conda version that can be different from the archive
+ARG conda_version="4.9.0"
+
 # Install all OS dependencies for notebook server that starts but lacks all
 # features (e.g., download as all possible file formats)
 ENV DEBIAN_FRONTEND noninteractive
@@ -53,9 +64,12 @@ COPY fix-permissions /usr/local/bin/fix-permissions
 RUN chmod a+rx /usr/local/bin/fix-permissions
 
 # Enable prompt color in the skeleton .bashrc before creating the default NB_USER
-RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc
+# hadolint ignore=SC2016
+RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc && \
+   # Add call to conda init script see https://stackoverflow.com/a/58081608/4413446
+   echo 'eval "$(command conda shell.bash hook 2> /dev/null)"' >> /etc/skel/.bashrc 
 
-# Create NB_USER wtih name jovyan user with UID=1000 and in the 'users' group
+# Create NB_USER with name jovyan user with UID=1000 and in the 'users' group
 # and make sure these dirs are writable by the `users` group.
 RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
     sed -i.bak -e 's/^%admin/#%admin/' /etc/sudoers && \
@@ -76,15 +90,15 @@ RUN mkdir /home/$NB_USER/work && \
     fix-permissions /home/$NB_USER
 
 # Install conda as jovyan and check the md5 sum provided on the download site
-ENV MINICONDA_VERSION=4.8.3 \
-    MINICONDA_MD5=d63adf39f2c220950a063e0529d4ff74 \
-    CONDA_VERSION=4.8.3
+ENV MINICONDA_VERSION="${miniconda_version}" \
+    CONDA_VERSION="${conda_version}"
 
 WORKDIR /tmp
 RUN wget --quiet https://repo.continuum.io/miniconda/Miniconda3-py38_${MINICONDA_VERSION}-Linux-x86_64.sh && \
-    echo "${MINICONDA_MD5} *Miniconda3-py38_${MINICONDA_VERSION}-Linux-x86_64.sh" | md5sum -c - && \
+    echo "${miniconda_checksum} *Miniconda3-py38_${MINICONDA_VERSION}-Linux-x86_64.sh" | md5sum -c - && \
     /bin/bash Miniconda3-py38_${MINICONDA_VERSION}-Linux-x86_64.sh -f -b -p $CONDA_DIR && \
     rm Miniconda3-py38_${MINICONDA_VERSION}-Linux-x86_64.sh && \
+    # Conda configuration see https://conda.io/projects/conda/en/latest/configuration.html
     echo "conda ${CONDA_VERSION}" >> $CONDA_DIR/conda-meta/pinned && \
     conda config --system --prepend channels conda-forge && \
     conda config --system --set auto_update_conda false && \
@@ -92,7 +106,7 @@ RUN wget --quiet https://repo.continuum.io/miniconda/Miniconda3-py38_${MINICONDA
     conda config --system --set channel_priority strict && \
     if [ ! $PYTHON_VERSION = 'default' ]; then conda install --yes python=$PYTHON_VERSION; fi && \
     conda list python | grep '^python ' | tr -s ' ' | cut -d '.' -f 1,2 | sed 's/$/.*/' >> $CONDA_DIR/conda-meta/pinned && \
-    conda install --quiet --yes conda && \
+    conda install --quiet --yes "conda=${CONDA_VERSION}" && \
     conda install --quiet --yes pip && \
     conda update --all --quiet --yes && \
     conda clean --all -f -y && \
@@ -114,9 +128,9 @@ RUN conda install --quiet --yes 'tini=0.18.0' && \
 # Do all this in a single RUN command to avoid duplicating all of the
 # files across image layers when the permissions change
 RUN conda install --quiet --yes \
-    'notebook=6.0.3' \
+    'notebook=6.1.4' \
     'jupyterhub=1.1.0' \
-    'jupyterlab=2.1.5' && \
+    'jupyterlab=2.2.8' && \
     conda clean --all -f -y && \
     npm cache clean --force && \
     jupyter notebook --generate-config && \

base-notebook/Dockerfile.ppc64le

@@ -107,9 +107,9 @@ RUN conda install --quiet --yes 'tini=0.18.0' && \
 # Do all this in a single RUN command to avoid duplicating all of the
 # files across image layers when the permissions change
 RUN conda install --quiet --yes \
-    'notebook=6.0.3' \
+    'notebook=6.1.3' \
     'jupyterhub=1.1.0' \
-    'jupyterlab=2.1.1' && \
+    'jupyterlab=2.2.5' && \
     conda clean --all -f -y && \
     npm cache clean --force && \
     jupyter notebook --generate-config && \

base-notebook/README.md

-[![docker pulls](https://img.shields.io/docker/pulls/jupyter/base-notebook.svg)](https://hub.docker.com/r/jupyter/base-notebook/) [![docker stars](https://img.shields.io/docker/stars/jupyter/base-notebook.svg)](https://hub.docker.com/r/jupyter/base-notebook/) [![image metadata](https://images.microbadger.com/badges/image/jupyter/base-notebook.svg)](https://microbadger.com/images/jupyter/base-notebook "jupyter/base-notebook image metadata")
+[![docker pulls](https://img.shields.io/docker/pulls/jupyter/base-notebook.svg)](https://hub.docker.com/r/jupyter/base-notebook/)
+[![docker stars](https://img.shields.io/docker/stars/jupyter/base-notebook.svg)](https://hub.docker.com/r/jupyter/base-notebook/)
+[![image metadata](https://images.microbadger.com/badges/image/jupyter/base-notebook.svg)](https://microbadger.com/images/jupyter/base-notebook "jupyter/base-notebook image metadata")
 
 # Base Jupyter Notebook Stack
 
-Please visit the documentation site for help using and contributing to this image and others.
+GitHub Actions in the https://github.com/jupyter/docker-stacks project builds and pushes this image
+to Docker Hub.
 
-* [Jupyter Docker Stacks on ReadTheDocs](http://jupyter-docker-stacks.readthedocs.io/en/latest/index.html)
-* [Selecting an Image :: Core Stacks :: jupyter/base-notebook](http://jupyter-docker-stacks.readthedocs.io/en/latest/using/selecting.html#jupyter-base-notebook)
+Please visit the project documentation site for help using and contributing to this image and
+others.
+
+- [Jupyter Docker Stacks on ReadTheDocs](http://jupyter-docker-stacks.readthedocs.io/en/latest/index.html)
+- [Selecting an Image :: Core Stacks :: jupyter/base-notebook](http://jupyter-docker-stacks.readthedocs.io/en/latest/using/selecting.html#jupyter-base-notebook)

base-notebook/fix-permissions

@@ -18,18 +18,18 @@
 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 {} \;
+    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

base-notebook/hooks/index.tmpl

-INDEX_ROW="|\`${BUILD_TIMESTAMP}\`|\`jupyter/${IMAGE_SHORT_NAME}:${GIT_SHA_TAG}\`<br />\`jupyter/${IMAGE_SHORT_NAME}:${PY_VERSION_TAG}\`<br />\`jupyter/${IMAGE_SHORT_NAME}:${NB_VERSION_TAG}\`<br />\`jupyter/${IMAGE_SHORT_NAME}:${LAB_VERSION_TAG}\`<br />\`jupyter/${IMAGE_SHORT_NAME}:${HUB_VERSION_TAG}\`|[Git diff](https://github.com/jupyter/docker-stacks/commit/${SOURCE_COMMIT})<br />[Dockerfile](https://github.com/jupyter/docker-stacks/blob/${SOURCE_COMMIT}/${IMAGE_SHORT_NAME}/Dockerfile)<br />[Build manifest](./${IMAGE_SHORT_NAME}-${GIT_SHA_TAG})|"
-sed "/|-|/a ${INDEX_ROW}" -i "$INDEX_FILE"
\ No newline at end of file

base-notebook/hooks/manifest.tmpl

-cat << EOF > "$MANIFEST_FILE"
-* Build datetime: ${BUILD_TIMESTAMP}
-* DockerHub build code: ${BUILD_CODE}
-* Docker image: ${DOCKER_REPO}:${GIT_SHA_TAG}
-* Docker image size: $(docker images ${IMAGE_NAME} --format "{{.Size}}")
-* Git commit SHA: [${SOURCE_COMMIT}](https://github.com/jupyter/docker-stacks/commit/${SOURCE_COMMIT})
-* Git commit message:
-\`\`\`
-${COMMIT_MSG}
-\`\`\`
-
-## Python Packages
-
-\`\`\`
-$(docker run --rm ${IMAGE_NAME} python --version)
-\`\`\`
-
-\`\`\`
-$(docker run --rm ${IMAGE_NAME} conda info)
-\`\`\`
-
-\`\`\`
-$(docker run --rm ${IMAGE_NAME} conda list)
-\`\`\`
-
-## Apt Packages
-
-\`\`\`
-$(docker run --rm ${IMAGE_NAME} apt list --installed)
-\`\`\`
-EOF
\ No newline at end of file

base-notebook/hooks/post_checkout

-#!/bin/bash
-if [[ "$COMMIT_MSG" = *"skip ci"* || "$COMMIT_MSG" = *"ci skip"* ]]; then
-    exit 1;
-fi
\ No newline at end of file

base-notebook/hooks/post_push

-#!/bin/bash
-set -e
-
-# Apply and push all tags
-source hooks/apply_tags
-docker push $DOCKER_REPO
-
-# Create a working directory.
-BUILD_TIMESTAMP=$(date -u +%FT%TZ)
-WORKDIR=$(mktemp -d)
-GIT_URI="git@github.com:jupyter/docker-stacks.wiki.git"
-GIT_SANDBOX="${WORKDIR}/docker-stacks.wiki"
-IMAGE_SHORT_NAME=$(basename $DOCKER_REPO)
-MANIFEST_FILE="${GIT_SANDBOX}/manifests/${IMAGE_SHORT_NAME}-${GIT_SHA_TAG}.md"
-INDEX_FILE="${GIT_SANDBOX}/Home.md"
-
-# Configure git so it can push back to GitHub.
-eval $(ssh-agent -s)
-ssh-add <(base64 -d <(echo "$DEPLOY_KEY"))
-ssh-add -l
-git config --global user.email "jupyter@googlegroups.com"
-git config --global user.name "Jupyter Docker Stacks"
-
-# Glone the GitHub project wiki.
-pushd "$WORKDIR"
-git clone "$GIT_URI"
-popd
-
-# Render the build manifest template.
-mkdir -p $(dirname "$MANIFEST_FILE")
-source hooks/manifest.tmpl
-source hooks/index.tmpl
-
-# Push the wiki update back to GitHub.
-pushd "$GIT_SANDBOX"
-git add .
-git commit -m "DOC: Build ${MANIFEST_FILE}"
-git push -u origin master
-popd
-
-# Shutdown the ssh agent for good measure.
-ssh-agent -k
-
-# Invoke all downstream build triggers.
-set +e
-for url in $(echo $NEXT_BUILD_TRIGGERS | sed "s/,/ /g")
-do
-    curl -X POST $url
-done
\ No newline at end of file

base-notebook/hooks/apply_tags → base-notebook/hooks/run_hook

 #!/bin/bash
 set -e
 
-# Tag the latest build with the short git sha as well as version of key runtimes
-# and packages. 
-GIT_SHA_TAG=${SOURCE_COMMIT:0:12}
+# Apply tags
+GIT_SHA_TAG=${GITHUB_SHA:0:12}
 docker tag $IMAGE_NAME "$DOCKER_REPO:$GIT_SHA_TAG"
 PY_VERSION_TAG="python-$(docker run --rm ${IMAGE_NAME} python --version 2>&1 | awk '{print $2}')"
 docker tag $IMAGE_NAME "$DOCKER_REPO:$PY_VERSION_TAG"
@@ -12,4 +11,43 @@ docker tag $IMAGE_NAME "$DOCKER_REPO:${NB_VERSION_TAG%% }"
 LAB_VERSION_TAG="lab-$(docker run --rm -a STDOUT ${IMAGE_NAME} jupyter-lab --version | tr -d '\r')"
 docker tag $IMAGE_NAME "$DOCKER_REPO:${LAB_VERSION_TAG%%\r}"
 HUB_VERSION_TAG="hub-$(docker run --rm -a STDOUT ${IMAGE_NAME} jupyterhub --version | tr -d '\r')"
-docker tag $IMAGE_NAME "$DOCKER_REPO:${HUB_VERSION_TAG%%\r}"
\ No newline at end of file
+docker tag $IMAGE_NAME "$DOCKER_REPO:${HUB_VERSION_TAG%%\r}"
+
+# Update index
+INDEX_FILE="${WIKI_PATH}/Home.md"
+INDEX_ROW="|\`${BUILD_TIMESTAMP}\`|\`jupyter/${IMAGE_SHORT_NAME}:${GIT_SHA_TAG}\`<br />\`jupyter/${IMAGE_SHORT_NAME}:${PY_VERSION_TAG}\`<br />\`jupyter/${IMAGE_SHORT_NAME}:${NB_VERSION_TAG}\`<br />\`jupyter/${IMAGE_SHORT_NAME}:${LAB_VERSION_TAG}\`<br />\`jupyter/${IMAGE_SHORT_NAME}:${HUB_VERSION_TAG}\`|[Git diff](https://github.com/jupyter/docker-stacks/commit/${GITHUB_SHA})<br />[Dockerfile](https://github.com/jupyter/docker-stacks/blob/${GITHUB_SHA}/${IMAGE_SHORT_NAME}/Dockerfile)<br />[Build manifest](./${IMAGE_SHORT_NAME}-${GIT_SHA_TAG})|"
+sed "/|-|/a ${INDEX_ROW}" -i "$INDEX_FILE"
+
+# Build manifest
+MANIFEST_FILE="${WIKI_PATH}/manifests/${IMAGE_SHORT_NAME}-${GIT_SHA_TAG}.md"
+mkdir -p $(dirname "$MANIFEST_FILE")
+cat << EOF > "$MANIFEST_FILE"
+* Build datetime: ${BUILD_TIMESTAMP}
+* Docker image: ${DOCKER_REPO}:${GIT_SHA_TAG}
+* Docker image size: $(docker images ${IMAGE_NAME} --format "{{.Size}}")
+* Git commit SHA: [${GITHUB_SHA}](https://github.com/jupyter/docker-stacks/commit/${GITHUB_SHA})
+* Git commit message:
+\`\`\`
+${COMMIT_MSG}
+\`\`\`
+
+## Python Packages
+
+\`\`\`
+$(docker run --rm ${IMAGE_NAME} python --version)
+\`\`\`
+
+\`\`\`
+$(docker run --rm ${IMAGE_NAME} conda info)
+\`\`\`
+
+\`\`\`
+$(docker run --rm ${IMAGE_NAME} conda list)
+\`\`\`
+
+## Apt Packages
+
+\`\`\`
+$(docker run --rm ${IMAGE_NAME} apt list --installed)
+\`\`\`
+EOF

base-notebook/jupyter_notebook_config.py

@@ -7,7 +7,7 @@ import os
 import errno
 import stat
 
-c = get_config()
+c = get_config()  # noqa: F821
 c.NotebookApp.ip = '0.0.0.0'
 c.NotebookApp.port = 8888
 c.NotebookApp.open_browser = False
@@ -52,4 +52,4 @@ distinguished_name = req_distinguished_name
 # Change default umask for all subprocesses of the notebook server if set in
 # the environment
 if 'NB_UMASK' in os.environ:
-    os.umask(int(os.environ['NB_UMASK'], 8))
\ No newline at end of file
+    os.umask(int(os.environ['NB_UMASK'], 8))

base-notebook/start.sh

@@ -80,7 +80,7 @@ if [ $(id -u) == 0 ] ; then
     if [ "$NB_UID" != $(id -u $NB_USER) ] || [ "$NB_GID" != $(id -g $NB_USER) ]; then
         echo "Set user $NB_USER UID:GID to: $NB_UID:$NB_GID"
         if [ "$NB_GID" != $(id -g $NB_USER) ]; then
-            groupadd -g $NB_GID -o ${NB_GROUP:-${NB_USER}}
+            groupadd -f -g $NB_GID -o ${NB_GROUP:-${NB_USER}}
         fi
         userdel $NB_USER
         useradd --home /home/$NB_USER -u $NB_UID -g $NB_GID -G 100 -l $NB_USER

base-notebook/test/test_container_options.py

@@ -11,11 +11,13 @@ LOGGER = logging.getLogger(__name__)
 def test_cli_args(container, http_client):
     """Container should respect notebook server command line args
     (e.g., disabling token security)"""
-    container.run(
-        command=['start-notebook.sh', '--NotebookApp.token=""']
+    c = container.run(
+        command=["start-notebook.sh", "--NotebookApp.token=''"]
     )
     resp = http_client.get('http://localhost:8888')
     resp.raise_for_status()
+    logs = c.logs(stdout=True).decode('utf-8')
+    LOGGER.debug(logs)
     assert 'login_submit' not in resp.text
 
 
@@ -70,23 +72,28 @@ def test_nb_user_change(container):
     running_container = container.run(
         tty=True,
         user="root",
-        environment=[f"NB_USER={nb_user}",
-                      "CHOWN_HOME=yes"],
+        environment=[
+            f"NB_USER={nb_user}",
+            "CHOWN_HOME=yes"
+        ],
         working_dir=f"/home/{nb_user}",
         command=['start.sh', 'bash', '-c', 'sleep infinity']
     )
-    
+
+    # Give the chown time to complete. Use sleep, not wait, because the
+    # container sleeps forever.
+    time.sleep(10)
     LOGGER.info(f"Checking if the user is changed to {nb_user} by the start script ...")
     output = running_container.logs(stdout=True).decode("utf-8")
-    assert f"Set username to: {nb_user}" in output, f"User is not changed to {nb_user}" 
-    
+    assert f"Set username to: {nb_user}" in output, f"User is not changed to {nb_user}"
+
     LOGGER.info(f"Checking {nb_user} id ...")
     command = "id"
     expected_output = f"uid=1000({nb_user}) gid=100(users) groups=100(users)"
     cmd = running_container.exec_run(command, user=nb_user)
     output = cmd.output.decode("utf-8").strip("\n")
     assert output == expected_output, f"Bad user {output}, expected {expected_output}"
-    
+
     LOGGER.info(f"Checking if {nb_user} owns his home folder ...")
     command = f'stat -c "%U %G" /home/{nb_user}/'
     expected_output = f"{nb_user} users"
@@ -100,10 +107,11 @@ def test_chown_extra(container):
     c = container.run(
         tty=True,
         user='root',
-        environment=['NB_UID=1010',
-                     'NB_GID=101',
-                     'CHOWN_EXTRA=/opt/conda',
-                     'CHOWN_EXTRA_OPTS=-R',
+        environment=[
+            'NB_UID=1010',
+            'NB_GID=101',
+            'CHOWN_EXTRA=/opt/conda',
+            'CHOWN_EXTRA_OPTS=-R'
         ],
         command=['start.sh', 'bash', '-c', 'stat -c \'%n:%u:%g\' /opt/conda/LICENSE.txt']
     )
@@ -113,16 +121,18 @@ def test_chown_extra(container):
 
 
 def test_chown_home(container):
-    """Container should change the NB_USER home directory owner and 
+    """Container should change the NB_USER home directory owner and
     group to the current value of NB_UID and NB_GID."""
     c = container.run(
         tty=True,
         user='root',
-        environment=['CHOWN_HOME=yes',
-                     'CHOWN_HOME_OPTS=-R',
+        environment=[
+            'CHOWN_HOME=yes',
+            'CHOWN_HOME_OPTS=-R'
         ],
         command=['start.sh', 'bash', '-c', 'chown root:root /home/jovyan && ls -alsh /home']
     )
+    c.wait(timeout=120)
     assert "Changing ownership of /home/jovyan to 1000:100 with options '-R'" in c.logs(stdout=True).decode('utf-8')
 
 

base-notebook/test/test_pandoc.py

@@ -3,8 +3,6 @@
 
 import logging
 
-import pytest
-
 LOGGER = logging.getLogger(__name__)
 
 
@@ -17,4 +15,3 @@ def test_pandoc(container):
     logs = c.logs(stdout=True).decode("utf-8")
     LOGGER.debug(logs)
     assert "<p><strong>BOLD</strong></p>" in logs
-

conftest.py

@@ -13,6 +13,7 @@ from requests.adapters import HTTPAdapter
 
 LOGGER = logging.getLogger(__name__)
 
+
 @pytest.fixture(scope='session')
 def http_client():
     """Requests session with retries and backoff."""
@@ -48,6 +49,7 @@ class TrackedContainer(object):
     **kwargs: dict, optional
         Default keyword arguments to pass to docker.DockerClient.containers.run
     """
+
     def __init__(self, docker_client, image_name, **kwargs):
         self.container = None
         self.docker_client = docker_client
@@ -78,7 +80,7 @@ class TrackedContainer(object):
         LOGGER.info(f"Running {self.image_name} with args {all_kwargs} ...")
         self.container = self.docker_client.containers.run(self.image_name, **all_kwargs)
         return self.container
-    
+
     def remove(self):
         """Kills and removes the tracked docker container."""
         if self.container:

datascience-notebook/Dockerfile

@@ -14,26 +14,34 @@ SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 
 USER root
 
+# Julia installation
+# Default values can be overridden at build time
+# (ARGS are in lower case to distinguish them from ENV)
+# Check https://julialang.org/downloads/
+ARG julia_version="1.5.2"
+# SHA256 checksum
+ARG julia_checksum="6da704fadcefa39725503e4c7a9cfa1a570ba8a647c4bd8de69a118f43584630"
+
 # R pre-requisites
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
     fonts-dejavu \
     gfortran \
     gcc && \
-    rm -rf /var/lib/apt/lists/*
+    apt-get clean && rm -rf /var/lib/apt/lists/*
 
 # Julia dependencies
 # install Julia packages in /opt/julia instead of $HOME
-ENV JULIA_DEPOT_PATH=/opt/julia
-ENV JULIA_PKGDIR=/opt/julia
-ENV JULIA_VERSION=1.4.1
+ENV JULIA_DEPOT_PATH=/opt/julia \
+    JULIA_PKGDIR=/opt/julia \
+    JULIA_VERSION="${julia_version}"
 
 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 "fd6d8cadaed678174c3caefb92207a3b0e8da9f926af6703fb4d1e4e4f50610a *julia-${JULIA_VERSION}-linux-x86_64.tar.gz" | sha256sum -c - && \
+    echo "${julia_checksum} *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
@@ -50,26 +58,23 @@ USER $NB_UID
 
 # R packages including IRKernel which gets installed globally.
 RUN conda install --quiet --yes \
-    'r-base=3.6.3' \
+    'r-base=4.0.3'  \
     'r-caret=6.0*' \
     'r-crayon=1.3*' \
     'r-devtools=2.3*' \
-    'r-forecast=8.12*' \
+    'r-forecast=8.13*' \ 
     'r-hexbin=1.28*' \
-    'r-htmltools=0.4*' \
-    'r-htmlwidgets=1.5*' \
+    'r-htmltools=0.5*' \
+    'r-htmlwidgets=1.5*' \ 
     'r-irkernel=1.1*' \
     'r-nycflights13=1.0*' \
-    'r-plyr=1.8*' \
     'r-randomforest=4.6*' \
     'r-rcurl=1.98*' \
-    'r-reshape2=1.4*' \
-    'r-rmarkdown=2.1*' \
+    'r-rmarkdown=2.4*' \
     'r-rsqlite=2.2*' \
-    'r-shiny=1.4*' \
+    'r-shiny=1.5*' \
     'r-tidyverse=1.3*' \
-    'rpy2=3.1*' \
-    && \
+    'rpy2=3.3*' && \
     conda clean --all -f -y && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"

datascience-notebook/README.md

-[![docker pulls](https://img.shields.io/docker/pulls/jupyter/datascience-notebook.svg)](https://hub.docker.com/r/jupyter/datascience-notebook/) [![docker stars](https://img.shields.io/docker/stars/jupyter/datascience-notebook.svg)](https://hub.docker.com/r/jupyter/datascience-notebook/) [![image metadata](https://images.microbadger.com/badges/image/jupyter/datascience-notebook.svg)](https://microbadger.com/images/jupyter/datascience-notebook "jupyter/datascience-notebook image metadata")
+[![docker pulls](https://img.shields.io/docker/pulls/jupyter/datascience-notebook.svg)](https://hub.docker.com/r/jupyter/datascience-notebook/)
+[![docker stars](https://img.shields.io/docker/stars/jupyter/datascience-notebook.svg)](https://hub.docker.com/r/jupyter/datascience-notebook/)
+[![image metadata](https://images.microbadger.com/badges/image/jupyter/datascience-notebook.svg)](https://microbadger.com/images/jupyter/datascience-notebook "jupyter/datascience-notebook image metadata")
 
 # Jupyter Notebook Data Science Stack
 
-Please visit the documentation site for help using and contributing to this image and others.
+GitHub Actions in the https://github.com/jupyter/docker-stacks project builds and pushes this image
+to Docker Hub.
 
-* [Jupyter Docker Stacks on ReadTheDocs](http://jupyter-docker-stacks.readthedocs.io/en/latest/index.html)
-* [Selecting an Image :: Core Stacks :: jupyter/datascience-notebook](http://jupyter-docker-stacks.readthedocs.io/en/latest/using/selecting.html#jupyter-datascience-notebook)
+Please visit the project documentation site for help using and contributing to this image and
+others.
+
+- [Jupyter Docker Stacks on ReadTheDocs](http://jupyter-docker-stacks.readthedocs.io/en/latest/index.html)
+- [Selecting an Image :: Core Stacks :: jupyter/datascience-notebook](http://jupyter-docker-stacks.readthedocs.io/en/latest/using/selecting.html#jupyter-datascience-notebook)

datascience-notebook/hooks/index.tmpl

-INDEX_ROW="|\`${BUILD_TIMESTAMP}\`|\`jupyter/${IMAGE_SHORT_NAME}:${GIT_SHA_TAG}\`<br />\`jupyter/${IMAGE_SHORT_NAME}:${PY_VERSION_TAG}\`<br />\`jupyter/${IMAGE_SHORT_NAME}:${JULIA_VERSION_TAG}\`<br />\`jupyter/${IMAGE_SHORT_NAME}:${R_VERSION_TAG}\`<br />\`jupyter/${IMAGE_SHORT_NAME}:${NB_VERSION_TAG}\`<br />\`jupyter/${IMAGE_SHORT_NAME}:${LAB_VERSION_TAG}\`<br />\`jupyter/${IMAGE_SHORT_NAME}:${HUB_VERSION_TAG}\`|[Git diff](https://github.com/jupyter/docker-stacks/commit/${SOURCE_COMMIT})<br />[Dockerfile](https://github.com/jupyter/docker-stacks/blob/${SOURCE_COMMIT}/${IMAGE_SHORT_NAME}/Dockerfile)<br />[Build manifest](./${IMAGE_SHORT_NAME}-${GIT_SHA_TAG})|"
-sed "/|-|/a ${INDEX_ROW}" -i "$INDEX_FILE"
\ No newline at end of file

datascience-notebook/hooks/post_push

-#!/bin/bash
-set -e
-
-# Apply and push all tags
-source hooks/apply_tags
-docker push $DOCKER_REPO
-
-# Tag the latest build with the short git sha. Push the tag in addition
-# to the "latest" tag already pushed.
-GIT_SHA_TAG=${SOURCE_COMMIT:0:12}
-docker tag $IMAGE_NAME $DOCKER_REPO:$GIT_SHA_TAG
-docker push $DOCKER_REPO:$GIT_SHA_TAG
-
-# Create a working directory.
-BUILD_TIMESTAMP=$(date -u +%FT%TZ)
-WORKDIR=$(mktemp -d)
-GIT_URI="git@github.com:jupyter/docker-stacks.wiki.git"
-GIT_SANDBOX="${WORKDIR}/docker-stacks.wiki"
-IMAGE_SHORT_NAME=$(basename $DOCKER_REPO)
-MANIFEST_FILE="${GIT_SANDBOX}/manifests/${IMAGE_SHORT_NAME}-${GIT_SHA_TAG}.md"
-INDEX_FILE="${GIT_SANDBOX}/Home.md"
-
-# Configure git so it can push back to GitHub.
-eval $(ssh-agent -s)
-ssh-add <(base64 -d <(echo "$DEPLOY_KEY"))
-ssh-add -l
-git config --global user.email "jupyter@googlegroups.com"
-git config --global user.name "Jupyter Docker Stacks"
-
-# Glone the GitHub project wiki.
-pushd "$WORKDIR"
-git clone "$GIT_URI"
-popd
-
-# Render the build manifest template.
-mkdir -p $(dirname "$MANIFEST_FILE")
-source hooks/manifest.tmpl
-source hooks/index.tmpl
-
-# Push the wiki update back to GitHub.
-pushd "$GIT_SANDBOX"
-git add .
-git commit -m "DOC: Build ${MANIFEST_FILE}"
-git push -u origin master
-popd
-
-# Shutdown the ssh agent for good measure.
-ssh-agent -k
-
-# Invoke all downstream build triggers.
-set +e
-for url in $(echo $NEXT_BUILD_TRIGGERS | sed "s/,/ /g")
-do
-    curl -X POST $url
-done

datascience-notebook/hooks/apply_tags → datascience-notebook/hooks/run_hook

 #!/bin/bash
 set -e
 
-# Tag the latest build with the short git sha as well as version of key runtimes
-# and packages. 
-GIT_SHA_TAG=${SOURCE_COMMIT:0:12}
+# Apply tags
+GIT_SHA_TAG=${GITHUB_SHA:0:12}
 docker tag $IMAGE_NAME "$DOCKER_REPO:$GIT_SHA_TAG"
 PY_VERSION_TAG="python-$(docker run --rm ${IMAGE_NAME} python --version 2>&1 | awk '{print $2}')"
 docker tag $IMAGE_NAME "$DOCKER_REPO:$PY_VERSION_TAG"
@@ -17,3 +16,63 @@ LAB_VERSION_TAG="lab-$(docker run --rm -a STDOUT ${IMAGE_NAME} jupyter-lab --ver
 docker tag $IMAGE_NAME "$DOCKER_REPO:${LAB_VERSION_TAG%%\r}"
 HUB_VERSION_TAG="hub-$(docker run --rm -a STDOUT ${IMAGE_NAME} jupyterhub --version | tr -d '\r')"
 docker tag $IMAGE_NAME "$DOCKER_REPO:${HUB_VERSION_TAG%%\r}"
+
+
+# Update index
+INDEX_ROW="|\`${BUILD_TIMESTAMP}\`|\`jupyter/${IMAGE_SHORT_NAME}:${GIT_SHA_TAG}\`<br />\`jupyter/${IMAGE_SHORT_NAME}:${PY_VERSION_TAG}\`<br />\`jupyter/${IMAGE_SHORT_NAME}:${JULIA_VERSION_TAG}\`<br />\`jupyter/${IMAGE_SHORT_NAME}:${R_VERSION_TAG}\`<br />\`jupyter/${IMAGE_SHORT_NAME}:${NB_VERSION_TAG}\`<br />\`jupyter/${IMAGE_SHORT_NAME}:${LAB_VERSION_TAG}\`<br />\`jupyter/${IMAGE_SHORT_NAME}:${HUB_VERSION_TAG}\`|[Git diff](https://github.com/jupyter/docker-stacks/commit/${GITHUB_SHA})<br />[Dockerfile](https://github.com/jupyter/docker-stacks/blob/${GITHUB_SHA}/${IMAGE_SHORT_NAME}/Dockerfile)<br />[Build manifest](./${IMAGE_SHORT_NAME}-${GIT_SHA_TAG})|"
+sed "/|-|/a ${INDEX_ROW}" -i "${WIKI_PATH}/Home.md"
+
+# Build manifest
+MANIFEST_FILE="${WIKI_PATH}/manifests/${IMAGE_SHORT_NAME}-${GIT_SHA_TAG}.md"
+mkdir -p $(dirname "$MANIFEST_FILE")
+
+cat << EOF > "$MANIFEST_FILE"
+* Build datetime: ${BUILD_TIMESTAMP}
+* Docker image: ${DOCKER_REPO}:${GIT_SHA_TAG}
+* Docker image size: $(docker images ${IMAGE_NAME} --format "{{.Size}}")
+* Git commit SHA: [${GITHUB_SHA}](https://github.com/jupyter/docker-stacks/commit/${GITHUB_SHA})
+* Git commit message:
+\`\`\`
+${COMMIT_MSG}
+\`\`\`
+
+## Julia Packages
+
+\`\`\`
+$(docker run --rm ${IMAGE_NAME} julia -E 'using InteractiveUtils; versioninfo()')
+\`\`\`
+
+\`\`\`
+$(docker run --rm ${IMAGE_NAME} julia -E 'import Pkg; Pkg.status()')
+\`\`\`
+
+## Python Packages
+
+\`\`\`
+$(docker run --rm ${IMAGE_NAME} python --version)
+\`\`\`
+
+\`\`\`
+$(docker run --rm ${IMAGE_NAME} conda info)
+\`\`\`
+
+\`\`\`
+$(docker run --rm ${IMAGE_NAME} conda list)
+\`\`\`
+
+## R Packages
+
+\`\`\`
+$(docker run --rm ${IMAGE_NAME} R --version)
+\`\`\`
+
+\`\`\`
+$(docker run --rm ${IMAGE_NAME} R --silent -e 'installed.packages(.Library)[, c(1,3)]')
+\`\`\`
+
+## Apt Packages
+
+\`\`\`
+$(docker run --rm ${IMAGE_NAME} apt list --installed)
+\`\`\`
+EOF

datascience-notebook/test/test_julia.py

@@ -2,18 +2,16 @@
 # Distributed under the terms of the Modified BSD License.
 import logging
 
-import pytest
-
 LOGGER = logging.getLogger(__name__)
 
 
 def test_julia(container):
     """Basic julia test"""
-    LOGGER.info(f"Test that julia is correctly installed ...")
+    LOGGER.info("Test that julia is correctly installed ...")
     running_container = container.run(
         tty=True, command=["start.sh", "bash", "-c", "sleep infinity"]
     )
-    command = f"julia --version"
+    command = "julia --version"
     cmd = running_container.exec_run(command)
     output = cmd.output.decode("utf-8")
     assert cmd.exit_code == 0, f"Command {command} failed {output}"

docs/conf.py

@@ -21,11 +21,6 @@
 # import sys
 # sys.path.insert(0, os.path.abspath('.'))
 
-# For conversion from markdown to html
-import recommonmark.parser
-from recommonmark.transform import AutoStructify
-
-
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -199,4 +194,4 @@ linkcheck_anchors = False
 # -- Translation ----------------------------------------------------------
 
 gettext_uuid = True
-locale_dirs = ['locale/']
\ No newline at end of file
+locale_dirs = ['locale/']

docs/contributing/features.md

 # New Features
 
-Thank you for contributing to the Jupyter Docker Stacks! We review pull requests of new features (e.g., new packages, new scripts, new flags) to balance the value of the images to the Jupyter community with the cost of maintaining the images over time.
+Thank you for contributing to the Jupyter Docker Stacks! We review pull requests of new features
+(e.g., new packages, new scripts, new flags) to balance the value of the images to the Jupyter
+community with the cost of maintaining the images over time.
 
 ## Suggesting a New Feature
 
 Please follow the process below to suggest a new feature for inclusion in one of the core stacks:
 
-1. [Open a GitHub issue](https://github.com/jupyter/docker-stacks/issues) describing the feature you'd like to contribute.
-2. Discuss with the maintainers whether the addition makes sense in [one of the core stacks](../using/selecting.md#Core-Stacks), as a [recipe in the documentation](recipes.md), as a [community stack](stacks.md), or as something else entirely.
+1. [Open a GitHub issue](https://github.com/jupyter/docker-stacks/issues) describing the feature
+   you'd like to contribute.
+2. Discuss with the maintainers whether the addition makes sense in
+   [one of the core stacks](../using/selecting.md#Core-Stacks), as a
+   [recipe in the documentation](recipes.md), as a [community stack](stacks.md), or as something
+   else entirely.
 
 ## Selection Criteria
 
 Roughly speaking, we evaluate new features based on the following criteria:
 
-* **Usefulness to Jupyter users**: Is the feature generally applicable across domains? Does it work with Jupyter Notebook, JupyterLab, JupyterHub, etc.?
-* **Fit with the image purpose**: Does the feature match the theme of the stack in which it will be added? Would it fit better in a new, community stack?
-* **Complexity of build / runtime configuration**: How many lines of code does the feature require in one of the Dockerfiles or startup scripts? Does it require new scripts entirely? Do users need to adjust how they use the images?
-* **Impact on image metrics**: How many bytes does the feature and its dependencies add to the image(s)? How many minutes do they add to the build time?
-* **Ability to support the addition**: Can existing maintainers answer user questions and address future build issues? Are the contributors interested in helping with long-term maintenance? Can we write tests to ensure the feature continues to work over time?
+- **Usefulness to Jupyter users**: Is the feature generally applicable across domains? Does it work
+  with Jupyter Notebook, JupyterLab, JupyterHub, etc.?
+- **Fit with the image purpose**: Does the feature match the theme of the stack in which it will be
+  added? Would it fit better in a new, community stack?
+- **Complexity of build / runtime configuration**: How many lines of code does the feature require
+  in one of the Dockerfiles or startup scripts? Does it require new scripts entirely? Do users need
+  to adjust how they use the images?
+- **Impact on image metrics**: How many bytes does the feature and its dependencies add to the
+  image(s)? How many minutes do they add to the build time?
+- **Ability to support the addition**: Can existing maintainers answer user questions and address
+  future build issues? Are the contributors interested in helping with long-term maintenance? Can we
+  write tests to ensure the feature continues to work over time?
 
 ## Submitting a Pull Request
 
 If there's agreement that the feature belongs in one or more of the core stacks:
 
 1. Implement the feature in a local clone of the `jupyter/docker-stacks` project.
-2. Please build the image locally before submitting a pull request. Building the image locally shortens the debugging cycle by taking some load off [Travis CI](http://travis-ci.org/), which graciously provides free build services for open source projects like this one.  If you use `make`, call:
-    ```bash
-    make build/somestack-notebook
-    ```
-3. [Submit a pull request](https://github.com/PointCloudLibrary/pcl/wiki/A-step-by-step-guide-on-preparing-and-submitting-a-pull-request) (PR) with your changes.
-4. Watch for Travis to report a build success or failure for your PR on GitHub.
+2. Please build the image locally before submitting a pull request. Building the image locally
+   shortens the debugging cycle by taking some load off GitHub Actions, which graciously provide
+   free build services for open source projects like this one. If you use `make`, call:
+   ```bash
+   make build/somestack-notebook
+   ```
+3. [Submit a pull request](https://github.com/PointCloudLibrary/pcl/wiki/A-step-by-step-guide-on-preparing-and-submitting-a-pull-request)
+   (PR) with your changes.
+4. Watch for GitHub to report a build success or failure for your PR on GitHub.
 5. Discuss changes with the maintainers and address any build issues.

docs/contributing/lint.md

-# Image Lint
+# Lint
+
+In order to enforce some rules **linters** are used in this project.
+Linters can be run either during the **development phase** (by the developer) and during **integration phase** (by Travis).
+To integrate and enforce this process in the project lifecycle we are using **git hooks** through [pre-commit][pre-commit].
+
+## Pre-commit hook
+
+### Installation
+
+pre-commit is a Python package that needs to be installed.
+This can be achieved by using the generic task used to install all Python development dependencies.
+
+```sh
+# Install all development dependencies for the project
+$ make dev-env
+# It can also be installed directly
+$ pip install pre-commit
+```
+
+Then the git hooks scripts configured for the project in `.pre-commit-config.yaml` need to be installed in the local git repository.
+
+```sh
+$ make pre-commit-install
+```
+
+### Run
+
+Now pre-commit (and so configured hooks) will run automatically on `git commit` on each changed file.
+However it is also possible to trigger it against all files.
+
+```sh
+$ make pre-commit-all
+```
+
+## Image Lint
 
 To comply with [Docker best practices][dbp], we are using the [Hadolint][hadolint] tool to analyse each `Dockerfile` .
 
-## Installation
+### Installation
 
 There is a specific `make` target to install the linter.
 By default `hadolint` will be installed in `${HOME}/hadolint`.
 
 ```bash
-$ make lint-install
+$ make hadolint-install
 
 # Installing hadolint at /Users/romain/hadolint ...
 # Installation done!
 # Haskell Dockerfile Linter v1.17.6-0-gc918759
 ```
 
-## Lint
+### Linting
 
-### Per Stack
+#### Per Stack
 
 The linter can be run per stack.
 
 ```bash
-$ make lint/scipy-notebook  
+$ make hadolint/scipy-notebook
 
 # Linting Dockerfiles in scipy-notebook...
 # scipy-notebook/Dockerfile:4 DL3006 Always tag the version of an image explicitly
@@ -34,28 +69,28 @@ $ make lint/scipy-notebook
 # make: *** [lint/scipy-notebook] Error 1
 ```
 
-Optionally you can pass arguments to the linter.
+Optionally you can pass arguments to the hadolint.
 
 ```bash
 # Use a different export format
-$ make lint/scipy-notebook ARGS="--format codeclimate"  
+$ make hadolint/scipy-notebook ARGS="--format codeclimate"
 ```
 
-### All the Stacks
+#### All the Stacks
 
 The linter can be run against all the stacks.
 
 ```bash
-$ make lint-all
+$ make hadolint-all
 ```
 
-## Ignoring Rules
+### Ignoring Rules
 
-Sometimes it is necessary to ignore [some rules][rules]. 
+Sometimes it is necessary to ignore [some rules][rules].
 The following rules are ignored by default and sor for all images in the `.hadolint.yaml` file.
 
-- [`DL3006`][DL3006]: We use a specific policy to manage image tags. 
-  - `base-notebook` `FROM` clause is fixed but based on an argument (`ARG`). 
+- [`DL3006`][DL3006]: We use a specific policy to manage image tags.
+  - `base-notebook` `FROM` clause is fixed but based on an argument (`ARG`).
   - Building downstream images from (`FROM`) the latest is done on purpose.
 - [`DL3008`][DL3008]: System packages are always updated (`apt-get`) to the latest version.
 
@@ -75,4 +110,5 @@ RUN cd /tmp && echo "hello!"
 [dbp]: https://docs.docker.com/develop/develop-images/dockerfile_best-practices
 [rules]: https://github.com/hadolint/hadolint#rules
 [DL3006]: https://github.com/hadolint/hadolint/wiki/DL3006
-[DL3008]: https://github.com/hadolint/hadolint/wiki/DL3008
\ No newline at end of file
+[DL3008]: https://github.com/hadolint/hadolint/wiki/DL3008
+[pre-commit]: https://pre-commit.com/
\ No newline at end of file

docs/contributing/packages.md

 # Package Updates
 
-We actively seek pull requests which update packages already included in the project Dockerfiles. This is a great way for first-time contributors to participate in developing the Jupyter Docker Stacks.
+We actively seek pull requests which update packages already included in the project Dockerfiles.
+This is a great way for first-time contributors to participate in developing the Jupyter Docker
+Stacks.
 
 Please follow the process below to update a package version:
 
-1. Locate the Dockerfile containing the library you wish to update (e.g., [base-notebook/Dockerfile](https://github.com/jupyter/docker-stacks/blob/master/base-notebook/Dockerfile), [scipy-notebook/Dockerfile](https://github.com/jupyter/docker-stacks/blob/master/scipy-notebook/Dockerfile))
-2. Adjust the version number for the package. We prefer to pin the major and minor version number of packages so as to minimize rebuild side-effects when users submit pull requests (PRs). For example, you'll find the Jupyter Notebook package, `notebook`, installed using conda with `notebook=5.4.*`.
-3. Please build the image locally before submitting a pull request. Building the image locally shortens the debugging cycle by taking some load off [Travis CI](http://travis-ci.org/), which graciously provides free build services for open source projects like this one. If you use `make`, call:
-    ```bash
-    make build/somestack-notebook
-    ```
-4. [Submit a pull request](https://github.com/PointCloudLibrary/pcl/wiki/A-step-by-step-guide-on-preparing-and-submitting-a-pull-request) (PR) with your changes.
-5. Watch for Travis to report a build success or failure for your PR on GitHub.
-6. Discuss changes with the maintainers and address any build issues. Version conflicts are the most common problem. You may need to upgrade additional packages to fix build failures.
+1. Locate the Dockerfile containing the library you wish to update (e.g.,
+   [base-notebook/Dockerfile](https://github.com/jupyter/docker-stacks/blob/master/base-notebook/Dockerfile),
+   [scipy-notebook/Dockerfile](https://github.com/jupyter/docker-stacks/blob/master/scipy-notebook/Dockerfile))
+2. Adjust the version number for the package. We prefer to pin the major and minor version number of
+   packages so as to minimize rebuild side-effects when users submit pull requests (PRs). For
+   example, you'll find the Jupyter Notebook package, `notebook`, installed using conda with
+   `notebook=5.4.*`.
+3. Please build the image locally before submitting a pull request. Building the image locally
+   shortens the debugging cycle by taking some load off GitHub Actions, which graciously provide
+   free build services for open source projects like this one. If you use `make`, call:
+   ```bash
+   make build/somestack-notebook
+   ```
+4. [Submit a pull request](https://github.com/PointCloudLibrary/pcl/wiki/A-step-by-step-guide-on-preparing-and-submitting-a-pull-request)
+   (PR) with your changes.
+5. Watch for GitHub to report a build success or failure for your PR on GitHub.
+6. Discuss changes with the maintainers and address any build issues. Version conflicts are the most
+   common problem. You may need to upgrade additional packages to fix build failures.
 
 ## Notes
 
-In order to help identifying packages that can be updated you can use the following helper tool.
-It will list all the packages installed in the `Dockerfile` that can be updated -- dependencies are filtered to focus only on requested packages.
+In order to help identifying packages that can be updated you can use the following helper tool. It
+will list all the packages installed in the `Dockerfile` that can be updated -- dependencies are
+filtered to focus only on requested packages.
 
 ```bash
 $ make check-outdated/base-notebook
 
 # INFO     test_outdated:test_outdated.py:80 3/8 (38%) packages could be updated
-# INFO     test_outdated:test_outdated.py:82 
+# INFO     test_outdated:test_outdated.py:82
 # Package     Current    Newest
 # ----------  ---------  --------
 # conda       4.7.12     4.8.2

docs/contributing/tests.md

 # Image Tests
 
-We greatly appreciate pull requests that extend the automated tests that vet the basic functionality of the Docker images.
+We greatly appreciate pull requests that extend the automated tests that vet the basic functionality
+of the Docker images.
 
 ## How the Tests Work
 
-Travis executes `make build-test-all` against pull requests submitted to the `jupyter/docker-stacks` repository. This `make` command builds every docker image. After building each image, the `make` command executes `pytest` to run both image-specific tests like those in [base-notebook/test/](https://github.com/jupyter/docker-stacks/tree/master/base-notebook/test) and common tests defined in [test/](https://github.com/jupyter/docker-stacks/tree/master/test). Both kinds of tests make use of global [pytest fixtures](https://docs.pytest.org/en/latest/fixture.html) defined in the [conftest.py](https://github.com/jupyter/docker-stacks/blob/master/conftest.py) file at the root of the projects.
+GitHub executes `make build-test-all` against pull requests submitted to the `jupyter/docker-stacks`
+repository. This `make` command builds every docker image. After building each image, the `make`
+command executes `pytest` to run both image-specific tests like those in
+[base-notebook/test/](https://github.com/jupyter/docker-stacks/tree/master/base-notebook/test) and
+common tests defined in [test/](https://github.com/jupyter/docker-stacks/tree/master/test). Both
+kinds of tests make use of global [pytest fixtures](https://docs.pytest.org/en/latest/fixture.html)
+defined in the [conftest.py](https://github.com/jupyter/docker-stacks/blob/master/conftest.py) file
+at the root of the projects.
 
 ## Contributing New Tests
 
 Please follow the process below to add new tests:
 
-1. If the test should run against every image built, add your test code to one of the modules in [test/](https://github.com/jupyter/docker-stacks/tree/master/test) or create a new module.
-2. If your test should run against a single image, add your test code to one of the modules in `some-notebook/test/` or create a new module.
+1. If the test should run against every image built, add your test code to one of the modules in
+   [test/](https://github.com/jupyter/docker-stacks/tree/master/test) or create a new module.
+2. If your test should run against a single image, add your test code to one of the modules in
+   `some-notebook/test/` or create a new module.
 3. Build one or more images you intend to test and run the tests locally. If you use `make`, call:
-    ```bash
-    make build/somestack-notebook
-    make test/somestack-notebook
-    ```
-4. [Submit a pull request](https://github.com/PointCloudLibrary/pcl/wiki/A-step-by-step-guide-on-preparing-and-submitting-a-pull-request) (PR) with your changes.
-5. Watch for Travis to report a build success or failure for your PR on GitHub.
-6. Discuss changes with the maintainers and address any issues running the tests on Travis.
+   ```bash
+   make build/somestack-notebook
+   make test/somestack-notebook
+   ```
+4. [Submit a pull request](https://github.com/PointCloudLibrary/pcl/wiki/A-step-by-step-guide-on-preparing-and-submitting-a-pull-request)
+   (PR) with your changes.
+5. Watch for GitHub to report a build success or failure for your PR on GitHub.
+6. Discuss changes with the maintainers and address any issues running the tests on GitHub.

docs/maintaining/tasks.md

@@ -4,41 +4,61 @@
 
 To build new images on Docker Cloud and publish them to the Docker Hub registry, do the following:
 
-1. Make sure Travis is green for a PR.
+1. Make sure GitHub Actions status checks pas for the PR.
 2. Merge the PR.
-3. Monitor the Docker Cloud build status for each of the stacks, starting with [jupyter/base-notebook](https://cloud.docker.com/app/jupyter/repository/docker/jupyter/base-notebook/general) and ending with [jupyter/all-spark-notebook](https://cloud.docker.com/app/jupyter/repository/docker/jupyter/all-spark-notebook/general). See the [stack hierarchy diagram](../using/selecting.html#image-relationships) for the current, complete build order.
-4. Manually click the retry button next to any build that fails to resume that build and any dependent builds.
-5. Try to avoid merging another PR to master until all outstanding builds complete. There's no way at present to propagate the git SHA to build through the Docker Cloud build trigger API. Every build trigger works off of master HEAD.
+3. Monitor the Docker Cloud build status for each of the stacks, starting with
+   [jupyter/base-notebook](https://cloud.docker.com/app/jupyter/repository/docker/jupyter/base-notebook/general)
+   and ending with
+   [jupyter/all-spark-notebook](https://cloud.docker.com/app/jupyter/repository/docker/jupyter/all-spark-notebook/general).
+   See the [stack hierarchy diagram](../using/selecting.html#image-relationships) for the current,
+   complete build order.
+4. Manually click the retry button next to any build that fails to resume that build and any
+   dependent builds.
+5. Try to avoid merging another PR to master until all outstanding builds complete. There's no way
+   at present to propagate the git SHA to build through the Docker Cloud build trigger API. Every
+   build trigger works off of master HEAD.
 
 ## Updating the Ubuntu Base Image
 
-When there's a security fix in the Ubuntu base image or after some time passes, it's a good idea to update the pinned SHA in the [jupyter/base-notebook Dockerfile](https://github.com/jupyter/docker-stacks/blob/master/base-notebook/Dockerfile). Submit it as a regular PR and go through the build process. Expect the build to take a while to complete: every image layer will rebuild.
+When there's a security fix in the Ubuntu base image or after some time passes, it's a good idea to
+update the pinned SHA in the
+[jupyter/base-notebook Dockerfile](https://github.com/jupyter/docker-stacks/blob/master/base-notebook/Dockerfile).
+Submit it as a regular PR and go through the build process. Expect the build to take a while to
+complete: every image layer will rebuild.
 
 ## Adding a New Core Image to Docker Cloud
 
 When there's a new stack definition, do the following before merging the PR with the new stack:
 
-1. Ensure the PR includes an update to the stack overview diagram [in the documentation](https://github.com/jupyter/docker-stacks/blob/master/docs/using/selecting.md#image-relationships). The image links to the [blockdiag source](http://interactive.blockdiag.com/) used to create it.
-2. Ensure the PR updates the Makefile which is used to build the stacks in order on Travis CI.
-3. Create a new repository in the `jupyter` org on Docker Cloud named after the stack folder in the git repo.
+1. Ensure the PR includes an update to the stack overview diagram
+   [in the documentation](https://github.com/jupyter/docker-stacks/blob/master/docs/using/selecting.md#image-relationships).
+   The image links to the [blockdiag source](http://interactive.blockdiag.com/) used to create it.
+2. Ensure the PR updates the Makefile which is used to build the stacks in order on GitHub Actions.
+3. Create a new repository in the `jupyter` org on Docker Cloud named after the stack folder in the
+   git repo.
 4. Grant the `stacks` team permission to write to the repo.
-5. Click *Builds* and then *Configure Automated Builds* for the repository.
+5. Click _Builds_ and then _Configure Automated Builds_ for the repository.
 6. Select `jupyter/docker-stacks` as the source repository.
-7. Choose *Build on Docker Cloud's infrastructure using a Small node* unless you have reason to believe a bigger host is required.
-8. Update the *Build Context* in the default build rule to be `/<name-of-the-stack>`.
-9. Toggle *Autobuild* to disabled unless the stack is a new root stack (e.g., like `jupyter/base-notebook`).
+7. Choose _Build on Docker Cloud's infrastructure using a Small node_ unless you have reason to
+   believe a bigger host is required.
+8. Update the _Build Context_ in the default build rule to be `/<name-of-the-stack>`.
+9. Toggle _Autobuild_ to disabled unless the stack is a new root stack (e.g., like
+   `jupyter/base-notebook`).
 10. If the new stack depends on the build of another stack in the hierarchy:
-    1. Hit *Save* and then click *Configure Automated Builds*.
-    2. At the very bottom, add a build trigger named *Stack hierarchy trigger*.
+    1. Hit _Save_ and then click _Configure Automated Builds_.
+    2. At the very bottom, add a build trigger named _Stack hierarchy trigger_.
     3. Copy the build trigger URL.
-    4. Visit the parent repository *Builds* page and click *Configure Automated Builds*.
-    5. Add the URL you copied to the *NEXT_BUILD_TRIGGERS* environment variable comma separated list of URLs, creating that environment variable if it does not already exist.
-    6. Hit *Save*.
+    4. Visit the parent repository _Builds_ page and click _Configure Automated Builds_.
+    5. Add the URL you copied to the _NEXT_BUILD_TRIGGERS_ environment variable comma separated list
+       of URLs, creating that environment variable if it does not already exist.
+    6. Hit _Save_.
 11. If the new stack should trigger other dependent builds:
-    1. Add an environment variable named *NEXT_BUILD_TRIGGERS*.
-    2. Copy the build trigger URLs from the dependent builds into the *NEXT_BUILD_TRIGGERS* comma separated list of URLs.
-    3. Hit *Save*.
-12. Adjust other *NEXT_BUILD_TRIGGERS* values as needed so that the build order matches that in the stack hierarchy diagram.
+    1. Add an environment variable named _NEXT_BUILD_TRIGGERS_.
+    2. Copy the build trigger URLs from the dependent builds into the _NEXT_BUILD_TRIGGERS_ comma
+       separated list of URLs.
+    3. Hit _Save_.
+12. Adjust other _NEXT_BUILD_TRIGGERS_ values as needed so that the build order matches that in the
+    stack hierarchy diagram.
 
 ## Adding a New Maintainer Account
 
@@ -61,22 +81,22 @@ If automated builds on Docker Cloud have got you down, do the following to push
 First enable translation on Transifex:
 
 1. Visit https://www.transifex.com/project-jupyter/jupyter-docker-stacks-1/languages/
-2. Click *Edit Languages* in the top right.
+2. Click _Edit Languages_ in the top right.
 3. Select the language from the dropdown.
-4. Click *Apply*.
+4. Click _Apply_.
 
 Then setup a subproject on ReadTheDocs for the language:
 
 1. Visit https://readthedocs.org/dashboard/import/manual/
-2. Enter *jupyter-docker-stacks-language_abbreviation* for the project name.
+2. Enter _jupyter-docker-stacks-language_abbreviation_ for the project name.
 3. Enter https://github.com/jupyter/docker-stacks for the URL.
-4. Check *Edit advanced project options*.
-5. Click *Next*.
-6. Select the *Language* from the dropdown on the next screen.
-7. Click *Finish*.
+4. Check _Edit advanced project options_.
+5. Click _Next_.
+6. Select the _Language_ from the dropdown on the next screen.
+7. Click _Finish_.
 
 Finally link the new language subproject to the top level doc project:
 
 1. Visit https://readthedocs.org/dashboard/jupyter-docker-stacks/translations/
-2. Select the subproject you created from the *Project* dropdown.
-3. Click *Add*.
+2. Select the subproject you created from the _Project_ dropdown.
+3. Click _Add_.

docs/using/recipes.md

@@ -48,7 +48,7 @@ packages desired. Next, create a new Dockerfile like the one shown below.
 # Start from a core stack version
 FROM jupyter/datascience-notebook:9f9e5ca8fe5a
 # Install from requirements.txt file
-COPY requirements.txt /tmp/
+COPY --chown=${NB_UID}:${NB_GID} requirements.txt /tmp/
 RUN pip install --requirement /tmp/requirements.txt && \
     fix-permissions $CONDA_DIR && \
     fix-permissions /home/$NB_USER
@@ -60,7 +60,7 @@ For conda, the Dockerfile is similar:
 # Start from a core stack version
 FROM jupyter/datascience-notebook:9f9e5ca8fe5a
 # Install from requirements.txt file
-COPY requirements.txt /tmp/
+COPY --chown=${NB_UID}:${NB_GID} requirements.txt /tmp/
 RUN conda install --yes --file /tmp/requirements.txt && \
     fix-permissions $CONDA_DIR && \
     fix-permissions /home/$NB_USER
@@ -118,7 +118,7 @@ RUN conda create --quiet --yes -p $CONDA_DIR/envs/$conda_env python=$py_ver ipyt
 # alternatively, you can comment out the lines above and uncomment those below
 # if you'd prefer to use a YAML file present in the docker build context
 
-# COPY environment.yml /home/$NB_USER/tmp/
+# COPY --chown=${NB_UID}:${NB_GID} environment.yml /home/$NB_USER/tmp/
 # RUN cd /home/$NB_USER/tmp/ && \
 #     conda env create -p $CONDA_DIR/envs/$conda_env -f environment.yml && \
 #     conda clean --all -f -y

docs/using/specifics.md

@@ -2,21 +2,81 @@
 
 This page provides details about features specific to one or more images.
 
-## Apache Spark
+## Apache Spark™
 
-**Specific Docker Image Options**
+### Specific Docker Image Options
 
 * `-p 4040:4040` - The `jupyter/pyspark-notebook` and `jupyter/all-spark-notebook` images open [SparkUI (Spark Monitoring and Instrumentation UI)](http://spark.apache.org/docs/latest/monitoring.html) at default port `4040`, this option map `4040` port inside docker container to `4040` port on host machine . Note every new spark context that is created is put onto an incrementing port (ie. 4040, 4041, 4042, etc.), and it might be necessary to open multiple ports. For example: `docker run -d -p 8888:8888 -p 4040:4040 -p 4041:4041 jupyter/pyspark-notebook`.
 
-**Usage Examples**
+### Build an Image with a Different Version of Spark
+
+You can build a `pyspark-notebook` image (and also the downstream `all-spark-notebook` image) with a different version of Spark by overriding the default value of the following arguments at build time.
+
+* Spark distribution is defined by the combination of the Spark and the Hadoop version and verified by the package checksum, see [Download Apache Spark](https://spark.apache.org/downloads.html) for more information. At this time the build will only work with the set of versions available on the Apache Spark download page, so it will not work with the archived versions.
+  * `spark_version`: The Spark version to install (`3.0.0`).
+  * `hadoop_version`: The Hadoop version (`3.2`).
+  * `spark_checksum`: The package checksum (`BFE4540...`).
+* Spark is shipped with a version of Py4J that has to be referenced in the `PYTHONPATH`.
+  * `py4j_version`: The Py4J version (`0.10.9`), see the tip below.
+* Spark can run with different OpenJDK versions.
+  * `openjdk_version`: The version of (JRE headless) the OpenJDK distribution (`11`), see [Ubuntu packages](https://packages.ubuntu.com/search?keywords=openjdk).
+
+For example here is how to build a `pyspark-notebook` image with Spark `2.4.6`, Hadoop `2.7` and OpenJDK `8`.
+
+```bash
+# From the root of the project
+# Build the image with different arguments
+docker build --rm --force-rm \
+    -t jupyter/pyspark-notebook:spark-2.4.6 ./pyspark-notebook \
+    --build-arg spark_version=2.4.6 \
+    --build-arg hadoop_version=2.7 \
+    --build-arg spark_checksum=3A9F401EDA9B5749CDAFD246B1D14219229C26387017791C345A23A65782FB8B25A302BF4AC1ED7C16A1FE83108E94E55DAD9639A51C751D81C8C0534A4A9641 \
+    --build-arg openjdk_version=8 \
+    --build-arg py4j_version=0.10.7
+
+# Check the newly built image
+docker images jupyter/pyspark-notebook:spark-2.4.6
+
+# REPOSITORY                 TAG                 IMAGE ID            CREATED             SIZE
+# jupyter/pyspark-notebook   spark-2.4.6         7ad7b5a9dbcd        4 minutes ago       3.44GB
+
+# Check the Spark version
+docker run -it --rm jupyter/pyspark-notebook:spark-2.4.6 pyspark --version
+
+# Welcome to
+#       ____              __
+#      / __/__  ___ _____/ /__
+#     _\ \/ _ \/ _ `/ __/  '_/
+#    /___/ .__/\_,_/_/ /_/\_\   version 2.4.6
+#       /_/
+#                         
+# Using Scala version 2.11.12, OpenJDK 64-Bit Server VM, 1.8.0_265
+```
+
+**Tip**: to get the version of Py4J shipped with Spark:
+
+ * Build a first image without changing `py4j_version` (it will not prevent the image to build it will just prevent Python to find the `pyspark` module),
+ * get the version (`ls /usr/local/spark/python/lib/`),
+ * set the version `--build-arg py4j_version=0.10.7`.
+
+```bash
+docker run -it --rm jupyter/pyspark-notebook:spark-2.4.6 ls /usr/local/spark/python/lib/ 
+# py4j-0.10.7-src.zip  PY4J_LICENSE.txt  pyspark.zip
+# You can now set the build-arg
+# --build-arg py4j_version=
+```
+
+*Note: At the time of writing there is an issue preventing to use Spark `2.4.6` with Python `3.8`, see [this answer on SO](https://stackoverflow.com/a/62173969/4413446) for more information.*
+
+### Usage Examples
 
 The `jupyter/pyspark-notebook` and `jupyter/all-spark-notebook` images support the use of [Apache Spark](https://spark.apache.org/) in Python, R, and Scala notebooks. The following sections provide some examples of how to get started using them.
 
-### Using Spark Local Mode
+#### Using Spark Local Mode
 
 Spark **local mode** is useful for experimentation on small data when you do not have a Spark cluster available.
 
-#### In Python
+##### In Python
 
 In a Python notebook.
 
@@ -33,7 +93,7 @@ rdd.sum()
 # 5050
 ```
 
-#### In R
+##### In R
 
 In a R notebook with [SparkR][sparkr].
 
@@ -71,9 +131,7 @@ sdf_len(sc, 100, repartition = 1) %>%
 # 5050
 ```
 
-#### In Scala
-
-##### In a Spylon Kernel
+##### In Scala
 
 Spylon kernel instantiates a `SparkContext` for you in variable `sc` after you configure Spark
 options in a `%%init_spark` magic cell.
@@ -91,18 +149,7 @@ rdd.sum()
 // 5050
 ```
 
-##### In an Apache Toree Kernel
-
-Apache Toree instantiates a local `SparkContext` for you in variable `sc` when the kernel starts.
-
-```scala
-// Sum of the first 100 whole numbers
-val rdd = sc.parallelize(0 to 100)
-rdd.sum()
-// 5050
-```
-
-### Connecting to a Spark Cluster in Standalone Mode
+#### Connecting to a Spark Cluster in Standalone Mode
 
 Connection to Spark Cluster on **[Standalone Mode](https://spark.apache.org/docs/latest/spark-standalone.html)** requires the following set of steps:
 
@@ -117,7 +164,7 @@ Connection to Spark Cluster on **[Standalone Mode](https://spark.apache.org/docs
 
 **Note**: In the following examples we are using the Spark master URL `spark://master:7077` that shall be replaced by the URL of the Spark master.
 
-#### In Python
+##### In Python
 
 The **same Python version** need to be used on the notebook (where the driver is located) and on the Spark workers.
 The python version used at driver and worker side can be adjusted by setting the environment variables `PYSPARK_PYTHON` and / or `PYSPARK_DRIVER_PYTHON`, see [Spark Configuration][spark-conf] for more information.
@@ -135,7 +182,7 @@ rdd.sum()
 # 5050
 ```
 
-#### In R
+##### In R
 
 In a R notebook with [SparkR][sparkr].
 
@@ -172,9 +219,7 @@ sdf_len(sc, 100, repartition = 1) %>%
 # 5050
 ```
 
-#### In Scala
-
-##### In a Spylon Kernel
+##### In Scala
 
 Spylon kernel instantiates a `SparkContext` for you in variable `sc` after you configure Spark
 options in a `%%init_spark` magic cell.
@@ -192,29 +237,6 @@ rdd.sum()
 // 5050
 ```
 
-##### In an Apache Toree Scala Notebook
-
-The Apache Toree kernel automatically creates a `SparkContext` when it starts based on configuration information from its command line arguments and environment variables. You can pass information about your cluster via the `SPARK_OPTS` environment variable when you spawn a container.
-
-For instance, to pass information about a standalone Spark master, you could start the container like so:
-
-```bash
-docker run -d -p 8888:8888 -e SPARK_OPTS='--master=spark://master:7077' \
-       jupyter/all-spark-notebook
-```
-
-Note that this is the same information expressed in a notebook in the Python case above. Once the kernel spec has your cluster information, you can test your cluster in an Apache Toree notebook like so:
-
-```scala
-// should print the value of --master in the kernel spec
-println(sc.master)
-
-// Sum of the first 100 whole numbers
-val rdd = sc.parallelize(0 to 100)
-rdd.sum()
-// 5050
-```
-
 ## Tensorflow
 
 The `jupyter/tensorflow-notebook` image supports the use of

examples/docker-compose/notebook/Dockerfile

@@ -4,12 +4,13 @@
 # Pick your favorite docker-stacks image
 FROM jupyter/minimal-notebook:55d5ca6be183
 
-USER jovyan
-
-# Add permanent pip/conda installs, data files, other user libs here
-# e.g., RUN pip install jupyter_dashboards
-
 USER root
 
 # Add permanent apt-get installs and other root commands here
 # e.g., RUN apt-get install npm nodejs
+
+USER $NB_UID
+
+# Switch back to jovyan to avoid accidental container runs as root
+# Add permanent pip/conda installs, data files, other user libs here
+# e.g., RUN pip install jupyter_dashboards

examples/make-deploy/Dockerfile

@@ -4,12 +4,13 @@
 # Pick your favorite docker-stacks image
 FROM jupyter/minimal-notebook:2d125a7161b5
 
-USER jovyan
-
-# Add permanent pip/conda installs, data files, other user libs here
-# e.g., RUN pip install jupyter_dashboards
-
 USER root
 
 # Add permanent apt-get installs and other root commands here
 # e.g., RUN apt-get install npm nodejs
+
+USER $NB_UID
+
+# Switch back to jovyan to avoid accidental container runs as root
+# Add permanent pip/conda installs, data files, other user libs here
+# e.g., RUN pip install jupyter_dashboards

minimal-notebook/Dockerfile

@@ -24,13 +24,14 @@ RUN apt-get update && apt-get install -yq --no-install-recommends \
     texlive-xetex \
     texlive-fonts-recommended \
     texlive-plain-generic \
-    # Optional dependency
-    texlive-fonts-extra \
     # ----
     tzdata \
     unzip \
-    nano \
+    nano-tiny \
     && apt-get clean && rm -rf /var/lib/apt/lists/*
 
+# Create alternative for nano -> nano-tiny
+RUN update-alternatives --install /usr/bin/nano nano /usr/bin/nano-tiny 10
+
 # Switch back to jovyan to avoid accidental container runs as root
 USER $NB_UID

minimal-notebook/README.md

-[![docker pulls](https://img.shields.io/docker/pulls/jupyter/minimal-notebook.svg)](https://hub.docker.com/r/jupyter/minimal-notebook/) [![docker stars](https://img.shields.io/docker/stars/jupyter/minimal-notebook.svg)](https://hub.docker.com/r/jupyter/minimal-notebook/) [![image metadata](https://images.microbadger.com/badges/image/jupyter/minimal-notebook.svg)](https://microbadger.com/images/jupyter/minimal-notebook "jupyter/minimal-notebook image metadata")
+[![docker pulls](https://img.shields.io/docker/pulls/jupyter/minimal-notebook.svg)](https://hub.docker.com/r/jupyter/minimal-notebook/)
+[![docker stars](https://img.shields.io/docker/stars/jupyter/minimal-notebook.svg)](https://hub.docker.com/r/jupyter/minimal-notebook/)
+[![image metadata](https://images.microbadger.com/badges/image/jupyter/minimal-notebook.svg)](https://microbadger.com/images/jupyter/minimal-notebook "jupyter/minimal-notebook image metadata")
 
 # Minimal Jupyter Notebook Stack
 
-Please visit the documentation site for help using and contributing to this image and others.
+GitHub Actions in the https://github.com/jupyter/docker-stacks project builds and pushes this image
+to Docker Hub.
 
-* [Jupyter Docker Stacks on ReadTheDocs](http://jupyter-docker-stacks.readthedocs.io/en/latest/index.html)
-* [Selecting an Image :: Core Stacks :: jupyter/minimal-notebook](http://jupyter-docker-stacks.readthedocs.io/en/latest/using/selecting.html#jupyter-minimal-notebook)
+Please visit the project documentation site for help using and contributing to this image and
+others.
+
+- [Jupyter Docker Stacks on ReadTheDocs](http://jupyter-docker-stacks.readthedocs.io/en/latest/index.html)
+- [Selecting an Image :: Core Stacks :: jupyter/minimal-notebook](http://jupyter-docker-stacks.readthedocs.io/en/latest/using/selecting.html#jupyter-minimal-notebook)

minimal-notebook/hooks/index.tmpl

-INDEX_ROW="|\`${BUILD_TIMESTAMP}\`|\`jupyter/${IMAGE_SHORT_NAME}:${GIT_SHA_TAG}\`|[Git diff](https://github.com/jupyter/docker-stacks/commit/${SOURCE_COMMIT})<br />[Dockerfile](https://github.com/jupyter/docker-stacks/blob/${SOURCE_COMMIT}/${IMAGE_SHORT_NAME}/Dockerfile)<br />[Build manifest](./${IMAGE_SHORT_NAME}-${GIT_SHA_TAG})|"
-sed "/|-|/a ${INDEX_ROW}" -i "$INDEX_FILE"
\ No newline at end of file

minimal-notebook/hooks/manifest.tmpl

-cat << EOF > "$MANIFEST_FILE"
-* Build datetime: ${BUILD_TIMESTAMP}
-* DockerHub build code: ${BUILD_CODE}
-* Docker image: ${DOCKER_REPO}:${GIT_SHA_TAG}
-* Docker image size: $(docker images ${IMAGE_NAME} --format "{{.Size}}")
-* Git commit SHA: [${SOURCE_COMMIT}](https://github.com/jupyter/docker-stacks/commit/${SOURCE_COMMIT})
-* Git commit message:
-\`\`\`
-${COMMIT_MSG}
-\`\`\`
-
-## Python Packages
-
-\`\`\`
-$(docker run --rm ${IMAGE_NAME} python --version)
-\`\`\`
-
-\`\`\`
-$(docker run --rm ${IMAGE_NAME} conda info)
-\`\`\`
-
-\`\`\`
-$(docker run --rm ${IMAGE_NAME} conda list)
-\`\`\`
-
-## Apt Packages
-
-\`\`\`
-$(docker run --rm ${IMAGE_NAME} apt list --installed)
-\`\`\`
-EOF
\ No newline at end of file

minimal-notebook/hooks/post_push

-#!/bin/bash
-set -e
-
-# Tag the latest build with the short git sha. Push the tag in addition
-# to the "latest" tag already pushed.
-GIT_SHA_TAG=${SOURCE_COMMIT:0:12}
-docker tag $IMAGE_NAME $DOCKER_REPO:$GIT_SHA_TAG
-docker push $DOCKER_REPO:$GIT_SHA_TAG
-
-# Create a working directory.
-BUILD_TIMESTAMP=$(date -u +%FT%TZ)
-WORKDIR=$(mktemp -d)
-GIT_URI="git@github.com:jupyter/docker-stacks.wiki.git"
-GIT_SANDBOX="${WORKDIR}/docker-stacks.wiki"
-IMAGE_SHORT_NAME=$(basename $DOCKER_REPO)
-MANIFEST_FILE="${GIT_SANDBOX}/manifests/${IMAGE_SHORT_NAME}-${GIT_SHA_TAG}.md"
-INDEX_FILE="${GIT_SANDBOX}/Home.md"
-
-# Configure git so it can push back to GitHub.
-eval $(ssh-agent -s)
-ssh-add <(base64 -d <(echo "$DEPLOY_KEY"))
-ssh-add -l
-git config --global user.email "jupyter@googlegroups.com"
-git config --global user.name "Jupyter Docker Stacks"
-
-# Glone the GitHub project wiki.
-pushd "$WORKDIR"
-git clone "$GIT_URI"
-popd
-
-# Render the build manifest template.
-mkdir -p $(dirname "$MANIFEST_FILE")
-source hooks/manifest.tmpl
-source hooks/index.tmpl
-
-# Push the wiki update back to GitHub.
-pushd "$GIT_SANDBOX"
-git add .
-git commit -m "DOC: Build ${MANIFEST_FILE}"
-git push -u origin master
-popd
-
-# Shutdown the ssh agent for good measure.
-ssh-agent -k
-
-# Invoke all downstream build triggers.
-set +e
-for url in $(echo $NEXT_BUILD_TRIGGERS | sed "s/,/ /g")
-do
-    curl -X POST $url
-done
\ No newline at end of file

minimal-notebook/hooks/run_hook

+#!/bin/bash
+set -e
+
+# Apply tags
+GIT_SHA_TAG=${GITHUB_SHA:0:12}
+docker tag $IMAGE_NAME "$DOCKER_REPO:$GIT_SHA_TAG"
+
+# Update index
+INDEX_ROW="|\`${BUILD_TIMESTAMP}\`|\`jupyter/${IMAGE_SHORT_NAME}:${GIT_SHA_TAG}\`|[Git diff](https://github.com/jupyter/docker-stacks/commit/${GITHUB_SHA})<br />[Dockerfile](https://github.com/jupyter/docker-stacks/blob/${GITHUB_SHA}/${IMAGE_SHORT_NAME}/Dockerfile)<br />[Build manifest](./${IMAGE_SHORT_NAME}-${GIT_SHA_TAG})|"
+sed "/|-|/a ${INDEX_ROW}" -i "${WIKI_PATH}/Home.md"
+
+# Build manifest
+MANIFEST_FILE="${WIKI_PATH}/manifests/${IMAGE_SHORT_NAME}-${GIT_SHA_TAG}.md"
+mkdir -p $(dirname "$MANIFEST_FILE")
+
+cat << EOF > "$MANIFEST_FILE"
+* Build datetime: ${BUILD_TIMESTAMP}
+* Docker image: ${DOCKER_REPO}:${GIT_SHA_TAG}
+* Docker image size: $(docker images ${IMAGE_NAME} --format "{{.Size}}")
+* Git commit SHA: [${GITHUB_SHA}](https://github.com/jupyter/docker-stacks/commit/${GITHUB_SHA})
+* Git commit message:
+\`\`\`
+${COMMIT_MSG}
+\`\`\`
+
+## Python Packages
+
+\`\`\`
+$(docker run --rm ${IMAGE_NAME} python --version)
+\`\`\`
+
+\`\`\`
+$(docker run --rm ${IMAGE_NAME} conda info)
+\`\`\`
+
+\`\`\`
+$(docker run --rm ${IMAGE_NAME} conda list)
+\`\`\`
+
+## Apt Packages
+
+\`\`\`
+$(docker run --rm ${IMAGE_NAME} apt list --installed)
+\`\`\`
+EOF

minimal-notebook/test/test_inkscape.py

+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+
+import logging
+
+LOGGER = logging.getLogger(__name__)
+
+
+def test_inkscape(container):
+    """Inkscape shall be installed to be able to convert SVG files."""
+    LOGGER.info("Test that inkscape is working by printing its version ...")
+    c = container.run(
+        tty=True, command=["start.sh", "bash", "-c", "inkscape --version"]
+    )
+    c.wait(timeout=10)
+    logs = c.logs(stdout=True).decode("utf-8")
+    LOGGER.debug(logs)
+    assert "Inkscape" in logs, "Inkscape not installed or not working"

minimal-notebook/test/test_nbconvert.py

@@ -9,15 +9,17 @@ import os
 LOGGER = logging.getLogger(__name__)
 
 
-@pytest.mark.parametrize("format", ["html", "pdf"])
-def test_nbconvert(container, format):
+@pytest.mark.parametrize("test_file, output_format,", [
+    ("notebook_math", "pdf"), ("notebook_math", "html"),
+    ("notebook_svg", "pdf"), ("notebook_svg", "html"),
+])
+def test_nbconvert(container, test_file, output_format):
     """Check if nbconvert is able to convert a notebook file"""
     host_data_dir = os.path.join(os.path.dirname(os.path.realpath(__file__)), "data")
     cont_data_dir = "/home/jovyan/data"
-    test_file = "notebook1"
     output_dir = "/tmp"
-    LOGGER.info(f"Test that an example notebook can be converted to {format.upper()} ...")
-    command = f"jupyter nbconvert {cont_data_dir}/{test_file}.ipynb --output-dir {output_dir} --to {format}"
+    LOGGER.info(f"Test that the example notebook {test_file} can be converted to {output_format.upper()} ...")
+    command = f"jupyter nbconvert {cont_data_dir}/{test_file}.ipynb --output-dir {output_dir} --to {output_format}"
     c = container.run(
         volumes={host_data_dir: {"bind": cont_data_dir, "mode": "ro"}},
         tty=True,
@@ -27,5 +29,5 @@ def test_nbconvert(container, format):
     assert rv == 0 or rv["StatusCode"] == 0, f"Command {command} failed"
     logs = c.logs(stdout=True).decode("utf-8")
     LOGGER.debug(logs)
-    expected_file = f"{output_dir}/{test_file}.{format}"
+    expected_file = f"{output_dir}/{test_file}.{output_format}"
     assert expected_file in logs, f"Expected file {expected_file} not generated"

pyspark-notebook/Dockerfile

@@ -11,20 +11,30 @@ SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 USER root
 
 # Spark dependencies
-ENV APACHE_SPARK_VERSION=3.0.0 \
-    HADOOP_VERSION=3.2
+# Default values can be overridden at build time
+# (ARGS are in lower case to distinguish them from ENV)
+ARG spark_version="3.0.1"
+ARG hadoop_version="3.2"
+ARG spark_checksum="E8B47C5B658E0FBC1E57EEA06262649D8418AE2B2765E44DA53AAF50094877D17297CC5F0B9B35DF2CEEF830F19AA31D7E56EAD950BBE7F8830D6874F88CFC3C"
+ARG py4j_version="0.10.9"
+ARG openjdk_version="11"
+
+ENV APACHE_SPARK_VERSION="${spark_version}" \
+    HADOOP_VERSION="${hadoop_version}"
 
 RUN apt-get -y update && \
-    apt-get install --no-install-recommends -y openjdk-11-jre-headless ca-certificates-java && \
-    rm -rf /var/lib/apt/lists/*
+    apt-get install --no-install-recommends -y \
+    "openjdk-${openjdk_version}-jre-headless" \
+    ca-certificates-java && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
 
-# Using the preferred mirror to download Spark
+# Spark installation
 WORKDIR /tmp
-
+# Using the preferred mirror to download Spark
 # hadolint ignore=SC2046
 RUN wget -q $(wget -qO- https://www.apache.org/dyn/closer.lua/spark/spark-${APACHE_SPARK_VERSION}/spark-${APACHE_SPARK_VERSION}-bin-hadoop${HADOOP_VERSION}.tgz\?as_json | \
     python -c "import sys, json; content=json.load(sys.stdin); print(content['preferred']+content['path_info'])") && \
-    echo "BFE45406C67CC4AE00411AD18CC438F51E7D4B6F14EB61E7BF6B5450897C2E8D3AB020152657C0239F253735C263512FFABF538AC5B9FFFA38B8295736A9C387 *spark-${APACHE_SPARK_VERSION}-bin-hadoop${HADOOP_VERSION}.tgz" | sha512sum -c - && \
+    echo "${spark_checksum} *spark-${APACHE_SPARK_VERSION}-bin-hadoop${HADOOP_VERSION}.tgz" | sha512sum -c - && \
     tar xzf "spark-${APACHE_SPARK_VERSION}-bin-hadoop${HADOOP_VERSION}.tgz" -C /usr/local --owner root --group root --no-same-owner && \
     rm "spark-${APACHE_SPARK_VERSION}-bin-hadoop${HADOOP_VERSION}.tgz"
 
@@ -33,16 +43,17 @@ RUN ln -s "spark-${APACHE_SPARK_VERSION}-bin-hadoop${HADOOP_VERSION}" spark
 
 # Configure Spark
 ENV SPARK_HOME=/usr/local/spark
-ENV PYTHONPATH=$SPARK_HOME/python:$SPARK_HOME/python/lib/py4j-0.10.9-src.zip \
+ENV PYTHONPATH="${SPARK_HOME}/python:${SPARK_HOME}/python/lib/py4j-${py4j_version}-src.zip" \
     SPARK_OPTS="--driver-java-options=-Xms1024M --driver-java-options=-Xmx4096M --driver-java-options=-Dlog4j.logLevel=info" \
     PATH=$PATH:$SPARK_HOME/bin
 
 USER $NB_UID
 
 # Install pyarrow
-RUN conda install --quiet -y 'pyarrow' && \
+RUN conda install --quiet --yes --satisfied-skip-solve \
+    'pyarrow=1.0.*' && \
     conda clean --all -f -y && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 
-WORKDIR $HOME
\ No newline at end of file
+WORKDIR $HOME

pyspark-notebook/README.md

-[![docker pulls](https://img.shields.io/docker/pulls/jupyter/pyspark-notebook.svg)](https://hub.docker.com/r/jupyter/pyspark-notebook/) [![docker stars](https://img.shields.io/docker/stars/jupyter/pyspark-notebook.svg)](https://hub.docker.com/r/jupyter/pyspark-notebook/) [![image metadata](https://images.microbadger.com/badges/image/jupyter/pyspark-notebook.svg)](https://microbadger.com/images/jupyter/pyspark-notebook "jupyter/pyspark-notebook image metadata")
+[![docker pulls](https://img.shields.io/docker/pulls/jupyter/pyspark-notebook.svg)](https://hub.docker.com/r/jupyter/pyspark-notebook/)
+[![docker stars](https://img.shields.io/docker/stars/jupyter/pyspark-notebook.svg)](https://hub.docker.com/r/jupyter/pyspark-notebook/)
+[![image metadata](https://images.microbadger.com/badges/image/jupyter/pyspark-notebook.svg)](https://microbadger.com/images/jupyter/pyspark-notebook "jupyter/pyspark-notebook image metadata")
 
 # Jupyter Notebook Python, Spark Stack
 
-Please visit the documentation site for help using and contributing to this image and others.
+GitHub Actions in the https://github.com/jupyter/docker-stacks project builds and pushes this image
+to Docker Hub.
 
-* [Jupyter Docker Stacks on ReadTheDocs](http://jupyter-docker-stacks.readthedocs.io/en/latest/index.html)
-* [Selecting an Image :: Core Stacks :: jupyter/pyspark-notebook](http://jupyter-docker-stacks.readthedocs.io/en/latest/using/selecting.html#jupyter-pyspark-notebook)
-* [Image Specifics :: Apache Spark](http://jupyter-docker-stacks.readthedocs.io/en/latest/using/specifics.html#apache-spark)
+Please visit the project documentation site for help using and contributing to this image and
+others.
+
+- [Jupyter Docker Stacks on ReadTheDocs](http://jupyter-docker-stacks.readthedocs.io/en/latest/index.html)
+- [Selecting an Image :: Core Stacks :: jupyter/pyspark-notebook](http://jupyter-docker-stacks.readthedocs.io/en/latest/using/selecting.html#jupyter-pyspark-notebook)
+- [Image Specifics :: Apache Spark](http://jupyter-docker-stacks.readthedocs.io/en/latest/using/specifics.html#apache-spark)

pyspark-notebook/hooks/index.tmpl

-INDEX_ROW="|\`${BUILD_TIMESTAMP}\`|\`jupyter/${IMAGE_SHORT_NAME}:${GIT_SHA_TAG}\`|[Git diff](https://github.com/jupyter/docker-stacks/commit/${SOURCE_COMMIT})<br />[Dockerfile](https://github.com/jupyter/docker-stacks/blob/${SOURCE_COMMIT}/${IMAGE_SHORT_NAME}/Dockerfile)<br />[Build manifest](./${IMAGE_SHORT_NAME}-${GIT_SHA_TAG})|"
-sed "/|-|/a ${INDEX_ROW}" -i "$INDEX_FILE"
\ No newline at end of file

pyspark-notebook/hooks/post_push

-#!/bin/bash
-set -e
-
-# Tag the latest build with the short git sha. Push the tag in addition
-# to the "latest" tag already pushed.
-GIT_SHA_TAG=${SOURCE_COMMIT:0:12}
-docker tag $IMAGE_NAME $DOCKER_REPO:$GIT_SHA_TAG
-docker push $DOCKER_REPO:$GIT_SHA_TAG
-
-# Create a working directory.
-BUILD_TIMESTAMP=$(date -u +%FT%TZ)
-WORKDIR=$(mktemp -d)
-GIT_URI="git@github.com:jupyter/docker-stacks.wiki.git"
-GIT_SANDBOX="${WORKDIR}/docker-stacks.wiki"
-IMAGE_SHORT_NAME=$(basename $DOCKER_REPO)
-MANIFEST_FILE="${GIT_SANDBOX}/manifests/${IMAGE_SHORT_NAME}-${GIT_SHA_TAG}.md"
-INDEX_FILE="${GIT_SANDBOX}/Home.md"
-
-# Configure git so it can push back to GitHub.
-eval $(ssh-agent -s)
-ssh-add <(base64 -d <(echo "$DEPLOY_KEY"))
-ssh-add -l
-git config --global user.email "jupyter@googlegroups.com"
-git config --global user.name "Jupyter Docker Stacks"
-
-# Glone the GitHub project wiki.
-pushd "$WORKDIR"
-git clone "$GIT_URI"
-popd
-
-# Render the build manifest template.
-mkdir -p $(dirname "$MANIFEST_FILE")
-source hooks/manifest.tmpl
-source hooks/index.tmpl
-
-# Push the wiki update back to GitHub.
-pushd "$GIT_SANDBOX"
-git add .
-git commit -m "DOC: Build ${MANIFEST_FILE}"
-git push -u origin master
-popd
-
-# Shutdown the ssh agent for good measure.
-ssh-agent -k
-
-# Invoke all downstream build triggers.
-set +e
-for url in $(echo $NEXT_BUILD_TRIGGERS | sed "s/,/ /g")
-do
-    curl -X POST $url
-done
\ No newline at end of file

pyspark-notebook/hooks/manifest.tmpl → pyspark-notebook/hooks/run_hook

+#!/bin/bash
+set -e
+
+# Apply tags
+GIT_SHA_TAG=${GITHUB_SHA:0:12}
+docker tag $IMAGE_NAME "$DOCKER_REPO:$GIT_SHA_TAG"
+
+# Update index
+INDEX_ROW="|\`${BUILD_TIMESTAMP}\`|\`jupyter/${IMAGE_SHORT_NAME}:${GIT_SHA_TAG}\`|[Git diff](https://github.com/jupyter/docker-stacks/commit/${GITHUB_SHA})<br />[Dockerfile](https://github.com/jupyter/docker-stacks/blob/${GITHUB_SHA}/${IMAGE_SHORT_NAME}/Dockerfile)<br />[Build manifest](./${IMAGE_SHORT_NAME}-${GIT_SHA_TAG})|"
+sed "/|-|/a ${INDEX_ROW}" -i "${WIKI_PATH}/Home.md"
+
+# Build manifest
+MANIFEST_FILE="${WIKI_PATH}/manifests/${IMAGE_SHORT_NAME}-${GIT_SHA_TAG}.md"
+mkdir -p $(dirname "$MANIFEST_FILE")
+
 cat << EOF > "$MANIFEST_FILE"
 * Build datetime: ${BUILD_TIMESTAMP}
-* DockerHub build code: ${BUILD_CODE}
 * Docker image: ${DOCKER_REPO}:${GIT_SHA_TAG}
 * Docker image size: $(docker images ${IMAGE_NAME} --format "{{.Size}}")
-* Git commit SHA: [${SOURCE_COMMIT}](https://github.com/jupyter/docker-stacks/commit/${SOURCE_COMMIT})
+* Git commit SHA: [${GITHUB_SHA}](https://github.com/jupyter/docker-stacks/commit/${GITHUB_SHA})
 * Git commit message:
 \`\`\`
 ${COMMIT_MSG}

pyspark-notebook/test/test_spark.py

 # Copyright (c) Jupyter Development Team.
 # Distributed under the terms of the Modified BSD License.
-import time
 import logging
 
-import pytest
 
 LOGGER = logging.getLogger(__name__)
 
+
 def test_spark_shell(container):
     """Checking if Spark (spark-shell) is running properly"""
     c = container.run(
@@ -18,6 +17,7 @@ def test_spark_shell(container):
     LOGGER.debug(logs)
     assert 'res0: Int = 2' in logs
 
+
 def test_pyspark(container):
     """PySpark should be in the Python path"""
     c = container.run(

r-notebook/Dockerfile

@@ -16,7 +16,7 @@ RUN apt-get update && \
     r-cran-rodbc \
     gfortran \
     gcc && \
-    rm -rf /var/lib/apt/lists/*
+    apt-get clean && rm -rf /var/lib/apt/lists/*
 
 # Fix for devtools https://github.com/conda-forge/r-devtools-feedstock/issues/4
 RUN ln -s /bin/tar /bin/gtar
@@ -25,22 +25,22 @@ USER $NB_UID
 
 # R packages
 RUN conda install --quiet --yes \
-    'r-base=4.0.0' \
+    'r-base=4.0.3' \
     'r-caret=6.*' \
     'r-crayon=1.3*' \
     'r-devtools=2.3*' \
-    'r-forecast=8.12*' \
+    'r-forecast=8.13*' \
     'r-hexbin=1.28*' \
-    'r-htmltools=0.4*' \
+    'r-htmltools=0.5*' \
     'r-htmlwidgets=1.5*' \
     'r-irkernel=1.1*' \
     'r-nycflights13=1.0*' \
     'r-randomforest=4.6*' \
     'r-rcurl=1.98*' \
-    'r-rmarkdown=2.2*' \
+    'r-rmarkdown=2.4*' \
     'r-rodbc=1.3*' \
     'r-rsqlite=2.2*' \
-    'r-shiny=1.4*' \
+    'r-shiny=1.5*' \
     'r-tidyverse=1.3*' \
     'unixodbc=2.3.*' \
     'r-tidymodels=0.1*' \

r-notebook/README.md

-[![docker pulls](https://img.shields.io/docker/pulls/jupyter/r-notebook.svg)](https://hub.docker.com/r/jupyter/r-notebook/) [![docker stars](https://img.shields.io/docker/stars/jupyter/r-notebook.svg)](https://hub.docker.com/r/jupyter/r-notebook/) [![image metadata](https://images.microbadger.com/badges/image/jupyter/r-notebook.svg)](https://microbadger.com/images/jupyter/r-notebook "jupyter/r-notebook image metadata")
+[![docker pulls](https://img.shields.io/docker/pulls/jupyter/r-notebook.svg)](https://hub.docker.com/r/jupyter/r-notebook/)
+[![docker stars](https://img.shields.io/docker/stars/jupyter/r-notebook.svg)](https://hub.docker.com/r/jupyter/r-notebook/)
+[![image metadata](https://images.microbadger.com/badges/image/jupyter/r-notebook.svg)](https://microbadger.com/images/jupyter/r-notebook "jupyter/r-notebook image metadata")
 
 # Jupyter Notebook R Stack
 
-* [Jupyter Docker Stacks on ReadTheDocs](http://jupyter-docker-stacks.readthedocs.io/en/latest/index.html)
-* [Selecting an Image :: Core Stacks :: jupyter/r-notebook](http://jupyter-docker-stacks.readthedocs.io/en/latest/using/selecting.html#jupyter-r-notebook)
+GitHub Actions in the https://github.com/jupyter/docker-stacks project builds and pushes this image
+to Docker Hub.
+
+Please visit the project documentation site for help using and contributing to this image and
+others.
+
+- [Jupyter Docker Stacks on ReadTheDocs](http://jupyter-docker-stacks.readthedocs.io/en/latest/index.html)
+- [Selecting an Image :: Core Stacks :: jupyter/r-notebook](http://jupyter-docker-stacks.readthedocs.io/en/latest/using/selecting.html#jupyter-r-notebook)

r-notebook/hooks/index.tmpl

-INDEX_ROW="|\`${BUILD_TIMESTAMP}\`|\`jupyter/${IMAGE_SHORT_NAME}:${GIT_SHA_TAG}\`|[Git diff](https://github.com/jupyter/docker-stacks/commit/${SOURCE_COMMIT})<br />[Dockerfile](https://github.com/jupyter/docker-stacks/blob/${SOURCE_COMMIT}/${IMAGE_SHORT_NAME}/Dockerfile)<br />[Build manifest](./${IMAGE_SHORT_NAME}-${GIT_SHA_TAG})|"
-sed "/|-|/a ${INDEX_ROW}" -i "$INDEX_FILE"
\ No newline at end of file

r-notebook/hooks/post_push

-#!/bin/bash
-set -e
-
-# Tag the latest build with the short git sha. Push the tag in addition
-# to the "latest" tag already pushed.
-GIT_SHA_TAG=${SOURCE_COMMIT:0:12}
-docker tag $IMAGE_NAME $DOCKER_REPO:$GIT_SHA_TAG
-docker push $DOCKER_REPO:$GIT_SHA_TAG
-
-# Create a working directory.
-BUILD_TIMESTAMP=$(date -u +%FT%TZ)
-WORKDIR=$(mktemp -d)
-GIT_URI="git@github.com:jupyter/docker-stacks.wiki.git"
-GIT_SANDBOX="${WORKDIR}/docker-stacks.wiki"
-IMAGE_SHORT_NAME=$(basename $DOCKER_REPO)
-MANIFEST_FILE="${GIT_SANDBOX}/manifests/${IMAGE_SHORT_NAME}-${GIT_SHA_TAG}.md"
-INDEX_FILE="${GIT_SANDBOX}/Home.md"
-
-# Configure git so it can push back to GitHub.
-eval $(ssh-agent -s)
-ssh-add <(base64 -d <(echo "$DEPLOY_KEY"))
-ssh-add -l
-git config --global user.email "jupyter@googlegroups.com"
-git config --global user.name "Jupyter Docker Stacks"
-
-# Glone the GitHub project wiki.
-pushd "$WORKDIR"
-git clone "$GIT_URI"
-popd
-
-# Render the build manifest template.
-mkdir -p $(dirname "$MANIFEST_FILE")
-source hooks/manifest.tmpl
-source hooks/index.tmpl
-
-# Push the wiki update back to GitHub.
-pushd "$GIT_SANDBOX"
-git add .
-git commit -m "DOC: Build ${MANIFEST_FILE}"
-git push -u origin master
-popd
-
-# Shutdown the ssh agent for good measure.
-ssh-agent -k
-
-# Invoke all downstream build triggers.
-set +e
-for url in $(echo $NEXT_BUILD_TRIGGERS | sed "s/,/ /g")
-do
-    curl -X POST $url
-done
\ No newline at end of file

datascience-notebook/hooks/manifest.tmpl → r-notebook/hooks/run_hook

+#!/bin/bash
+set -e
+
+# Apply tags
+GIT_SHA_TAG=${GITHUB_SHA:0:12}
+docker tag $IMAGE_NAME "$DOCKER_REPO:$GIT_SHA_TAG"
+
+# Update index
+INDEX_ROW="|\`${BUILD_TIMESTAMP}\`|\`jupyter/${IMAGE_SHORT_NAME}:${GIT_SHA_TAG}\`|[Git diff](https://github.com/jupyter/docker-stacks/commit/${GITHUB_SHA})<br />[Dockerfile](https://github.com/jupyter/docker-stacks/blob/${GITHUB_SHA}/${IMAGE_SHORT_NAME}/Dockerfile)<br />[Build manifest](./${IMAGE_SHORT_NAME}-${GIT_SHA_TAG})|"
+sed "/|-|/a ${INDEX_ROW}" -i "${WIKI_PATH}/Home.md"
+
+# Build manifest
+MANIFEST_FILE="${WIKI_PATH}/manifests/${IMAGE_SHORT_NAME}-${GIT_SHA_TAG}.md"
+mkdir -p $(dirname "$MANIFEST_FILE")
+
 cat << EOF > "$MANIFEST_FILE"
 * Build datetime: ${BUILD_TIMESTAMP}
-* DockerHub build code: ${BUILD_CODE}
 * Docker image: ${DOCKER_REPO}:${GIT_SHA_TAG}
 * Docker image size: $(docker images ${IMAGE_NAME} --format "{{.Size}}")
-* Git commit SHA: [${SOURCE_COMMIT}](https://github.com/jupyter/docker-stacks/commit/${SOURCE_COMMIT})
+* Git commit SHA: [${GITHUB_SHA}](https://github.com/jupyter/docker-stacks/commit/${GITHUB_SHA})
 * Git commit message:
 \`\`\`
 ${COMMIT_MSG}
 \`\`\`
 
-## Julia Packages
+## R Packages
 
 \`\`\`
-$(docker run --rm ${IMAGE_NAME} julia -E 'using InteractiveUtils; versioninfo()')
+$(docker run --rm ${IMAGE_NAME} R --version)
 \`\`\`
 
 \`\`\`
-$(docker run --rm ${IMAGE_NAME} julia -E 'import Pkg; Pkg.status()')
+$(docker run --rm ${IMAGE_NAME} R --silent -e 'installed.packages(.Library)[, c(1,3)]')
 \`\`\`
 
 ## Python Packages
@@ -33,19 +47,9 @@ $(docker run --rm ${IMAGE_NAME} conda info)
 $(docker run --rm ${IMAGE_NAME} conda list)
 \`\`\`
 
-## R Packages
-
-\`\`\`
-$(docker run --rm ${IMAGE_NAME} R --version)
-\`\`\`
-
-\`\`\`
-$(docker run --rm ${IMAGE_NAME} R --silent -e 'installed.packages(.Library)[, c(1,3)]')
-\`\`\`
-
 ## Apt Packages
 
 \`\`\`
 $(docker run --rm ${IMAGE_NAME} apt list --installed)
 \`\`\`
-EOF
\ No newline at end of file
+EOF

requirements-dev.txt

 docker
+pre-commit
 pytest
-recommonmark==0.5.0
+recommonmark
 requests
 sphinx>=1.6
 sphinx-intl
 tabulate
 transifex-client
-

scipy-notebook/Dockerfile

@@ -7,10 +7,10 @@ LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
 
 USER root
 
-# ffmpeg for matplotlib anim & dvipng for latex labels
+# ffmpeg for matplotlib anim & dvipng+cm-super for latex labels
 RUN apt-get update && \
-    apt-get install -y --no-install-recommends ffmpeg dvipng && \
-    rm -rf /var/lib/apt/lists/*
+    apt-get install -y --no-install-recommends ffmpeg dvipng cm-super && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
 
 USER $NB_UID
 
@@ -18,31 +18,29 @@ USER $NB_UID
 RUN conda install --quiet --yes \
     'beautifulsoup4=4.9.*' \
     'conda-forge::blas=*=openblas' \
-    'bokeh=2.0.*' \
+    'bokeh=2.2.*' \
     'bottleneck=1.3.*' \
-    'cloudpickle=1.4.*' \
+    'cloudpickle=1.6.*' \
     'cython=0.29.*' \
-    'dask=2.15.*' \
+    'dask=2.30.*' \
     'dill=0.3.*' \
     'h5py=2.10.*' \
-    'hdf5=1.10.*' \
     'ipywidgets=7.5.*' \
     'ipympl=0.5.*'\
-    'matplotlib-base=3.2.*' \
-    # numba update to 0.49 fails resolving deps.
-    'numba=0.48.*' \
+    'matplotlib-base=3.3.*' \
+    'numba=0.51.*' \
     'numexpr=2.7.*' \
-    'pandas=1.0.*' \
+    'pandas=1.1.*' \
     'patsy=0.5.*' \
-    'protobuf=3.11.*' \
+    'protobuf=3.13.*' \
     'pytables=3.6.*' \
-    'scikit-image=0.16.*' \
+    'scikit-image=0.17.*' \
     'scikit-learn=0.23.*' \
-    'scipy=1.4.*' \
-    'seaborn=0.10.*' \
+    'scipy=1.5.*' \
+    'seaborn=0.11.*' \
     'sqlalchemy=1.3.*' \
-    'statsmodels=0.11.*' \
-    'sympy=1.5.*' \
+    'statsmodels=0.12.*' \
+    'sympy=1.6.*' \
     'vincent=0.4.*' \
     'widgetsnbextension=3.5.*'\
     'xlrd=1.2.*' \

scipy-notebook/README.md

-[![docker pulls](https://img.shields.io/docker/pulls/jupyter/scipy-notebook.svg)](https://hub.docker.com/r/jupyter/scipy-notebook/) [![docker stars](https://img.shields.io/docker/stars/jupyter/scipy-notebook.svg)](https://hub.docker.com/r/jupyter/scipy-notebook/) [![image metadata](https://images.microbadger.com/badges/image/jupyter/scipy-notebook.svg)](https://microbadger.com/images/jupyter/scipy-notebook "jupyter/scipy-notebook image metadata")
+[![docker pulls](https://img.shields.io/docker/pulls/jupyter/scipy-notebook.svg)](https://hub.docker.com/r/jupyter/scipy-notebook/)
+[![docker stars](https://img.shields.io/docker/stars/jupyter/scipy-notebook.svg)](https://hub.docker.com/r/jupyter/scipy-notebook/)
+[![image metadata](https://images.microbadger.com/badges/image/jupyter/scipy-notebook.svg)](https://microbadger.com/images/jupyter/scipy-notebook "jupyter/scipy-notebook image metadata")
 
 # Jupyter Notebook Scientific Python Stack
 
-Please visit the documentation site for help using and contributing to this image and others.
+GitHub Actions in the https://github.com/jupyter/docker-stacks project builds and pushes this image
+to Docker Hub.
 
-* [Jupyter Docker Stacks on ReadTheDocs](http://jupyter-docker-stacks.readthedocs.io/en/latest/index.html)
-* [Selecting an Image :: Core Stacks :: jupyter/scipy-notebook](http://jupyter-docker-stacks.readthedocs.io/en/latest/using/selecting.html#jupyter-scipy-notebook)
+Please visit the project documentation site for help using and contributing to this image and
+others.
+
+- [Jupyter Docker Stacks on ReadTheDocs](http://jupyter-docker-stacks.readthedocs.io/en/latest/index.html)
+- [Selecting an Image :: Core Stacks :: jupyter/scipy-notebook](http://jupyter-docker-stacks.readthedocs.io/en/latest/using/selecting.html#jupyter-scipy-notebook)

scipy-notebook/hooks/index.tmpl

-INDEX_ROW="|\`${BUILD_TIMESTAMP}\`|\`jupyter/${IMAGE_SHORT_NAME}:${GIT_SHA_TAG}\`|[Git diff](https://github.com/jupyter/docker-stacks/commit/${SOURCE_COMMIT})<br />[Dockerfile](https://github.com/jupyter/docker-stacks/blob/${SOURCE_COMMIT}/${IMAGE_SHORT_NAME}/Dockerfile)<br />[Build manifest](./${IMAGE_SHORT_NAME}-${GIT_SHA_TAG})|"
-sed "/|-|/a ${INDEX_ROW}" -i "$INDEX_FILE"
\ No newline at end of file

scipy-notebook/hooks/manifest.tmpl

-cat << EOF > "$MANIFEST_FILE"
-* Build datetime: ${BUILD_TIMESTAMP}
-* DockerHub build code: ${BUILD_CODE}
-* Docker image: ${DOCKER_REPO}:${GIT_SHA_TAG}
-* Docker image size: $(docker images ${IMAGE_NAME} --format "{{.Size}}")
-* Git commit SHA: [${SOURCE_COMMIT}](https://github.com/jupyter/docker-stacks/commit/${SOURCE_COMMIT})
-* Git commit message:
-\`\`\`
-${COMMIT_MSG}
-\`\`\`
-
-## Python Packages
-
-\`\`\`
-$(docker run --rm ${IMAGE_NAME} python --version)
-\`\`\`
-
-\`\`\`
-$(docker run --rm ${IMAGE_NAME} conda info)
-\`\`\`
-
-\`\`\`
-$(docker run --rm ${IMAGE_NAME} conda list)
-\`\`\`
-
-## Apt Packages
-
-\`\`\`
-$(docker run --rm ${IMAGE_NAME} apt list --installed)
-\`\`\`
-EOF
\ No newline at end of file

scipy-notebook/hooks/post_push

-#!/bin/bash
-set -e
-
-# Tag the latest build with the short git sha. Push the tag in addition
-# to the "latest" tag already pushed.
-GIT_SHA_TAG=${SOURCE_COMMIT:0:12}
-docker tag $IMAGE_NAME $DOCKER_REPO:$GIT_SHA_TAG
-docker push $DOCKER_REPO:$GIT_SHA_TAG
-
-# Create a working directory.
-BUILD_TIMESTAMP=$(date -u +%FT%TZ)
-WORKDIR=$(mktemp -d)
-GIT_URI="git@github.com:jupyter/docker-stacks.wiki.git"
-GIT_SANDBOX="${WORKDIR}/docker-stacks.wiki"
-IMAGE_SHORT_NAME=$(basename $DOCKER_REPO)
-MANIFEST_FILE="${GIT_SANDBOX}/manifests/${IMAGE_SHORT_NAME}-${GIT_SHA_TAG}.md"
-INDEX_FILE="${GIT_SANDBOX}/Home.md"
-
-# Configure git so it can push back to GitHub.
-eval $(ssh-agent -s)
-ssh-add <(base64 -d <(echo "$DEPLOY_KEY"))
-ssh-add -l
-git config --global user.email "jupyter@googlegroups.com"
-git config --global user.name "Jupyter Docker Stacks"
-
-# Glone the GitHub project wiki.
-pushd "$WORKDIR"
-git clone "$GIT_URI"
-popd
-
-# Render the build manifest template.
-mkdir -p $(dirname "$MANIFEST_FILE")
-source hooks/manifest.tmpl
-source hooks/index.tmpl
-
-# Push the wiki update back to GitHub.
-pushd "$GIT_SANDBOX"
-git add .
-git commit -m "DOC: Build ${MANIFEST_FILE}"
-git push -u origin master
-popd
-
-# Shutdown the ssh agent for good measure.
-ssh-agent -k
-
-# Invoke all downstream build triggers.
-set +e
-for url in $(echo $NEXT_BUILD_TRIGGERS | sed "s/,/ /g")
-do
-    curl -X POST $url
-done
\ No newline at end of file