Merge branch 'master' into asalikhov/ubuntu_jammy

.github/pull_request_template.md

@@ -0,0 +1,14 @@
+## Describe your changes
+
+## Issue ticket if applicable
+
+<!-- Example - Fix: https://github.com/jupyter/docker-stacks/issues/0 -->
+
+## Checklist (especially for first-time contributors)
+
+- [ ] I have performed a self-review of my code
+- [ ] If it is a core feature, I have added thorough tests
+- [ ] I will try not to use force-push to make the review process easier for reviewers
+- [ ] I have updated the documentation for significant changes
+
+<!-- markdownlint-disable-file MD041 -->

.github/workflows/docker.yml

@@ -67,10 +67,10 @@ jobs:
       # https://github.com/docker/build-push-action/tree/master#usage
       # https://github.com/docker/build-push-action/blob/master/docs/advanced/multi-platform.md
       - name: Set up QEMU (for docker buildx) 🐳
-        uses: docker/setup-qemu-action@27d0a4f181a40b142cce983c5393082c365d1480 # dependabot updates to latest release
+        uses: docker/setup-qemu-action@8b122486cedac8393e77aa9734c3528886e4a1a8 # dependabot updates to latest release
 
       - name: Set up Docker Buildx (for multi-arch builds) 🐳
-        uses: docker/setup-buildx-action@94ab11c41e45d028884a99163086648e898eed25 # dependabot updates to latest release
+        uses: docker/setup-buildx-action@dc7b9719a96d48369863986a06765841d7ea23f6 # dependabot updates to latest release
 
       - name: Checkout Repo ⚡️
         uses: actions/checkout@v3
@@ -97,7 +97,7 @@ jobs:
       - name: Checkout Wiki Repo 📃
         uses: actions/checkout@v3
         with:
-          repository: ${{github.repository}}.wiki
+          repository: ${{ github.repository }}.wiki
           path: wiki/
 
       - name: Create tags and manifest 🏷
@@ -107,15 +107,15 @@ jobs:
         if: github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' || github.event_name == 'schedule'
         uses: stefanzweifel/git-auto-commit-action@49620cd3ed21ee620a48530e81dba0d139c9cb80 # dependabot updates to latest release
         with:
-          commit_message: "Automated wiki publish for ${{github.sha}}"
+          commit_message: "Automated wiki publish for ${{ github.sha }}"
           repository: wiki/
 
       - name: Login to Docker Hub 🔐
         if: github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' || github.event_name == 'schedule'
-        uses: docker/login-action@dd4fa0671be5250ee6f50aedf4cb05514abda2c7 # dependabot updates to latest release
+        uses: docker/login-action@49ed152c8eca782a232dede0303416e8f356c37b # dependabot updates to latest release
         with:
-          username: ${{secrets.DOCKERHUB_USERNAME}}
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
-          password: ${{secrets.DOCKERHUB_TOKEN}}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Push Images to Docker Hub 📤
         if: github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' || github.event_name == 'schedule'

.github/workflows/hub-overview.yml

@@ -34,8 +34,8 @@ jobs:
       - name: push README to Dockerhub for base-notebook 🐳
         uses: christian-korneck/update-container-description-action@d36005551adeaba9698d8d67a296bd16fa91f8e8 # dependabot updates to latest release
         env:
-          DOCKER_USER: ${{secrets.DOCKERHUB_USERNAME}}
+          DOCKER_USER: ${{ secrets.DOCKERHUB_USERNAME }}
-          DOCKER_PASS: ${{secrets.DOCKERHUB_TOKEN}}
+          DOCKER_PASS: ${{ secrets.DOCKERHUB_TOKEN }}
         with:
           destination_container_repo: jupyter/base-notebook
           provider: dockerhub

.pre-commit-config.yaml

@@ -14,7 +14,7 @@
 repos:
   # Autoupdate: Python code
   - repo: https://github.com/asottile/pyupgrade
-    rev: v2.32.0
+    rev: v2.32.1
     hooks:
       - id: pyupgrade
         args: [--py39-plus]
@@ -35,7 +35,7 @@ repos:
 
   # Check python code static typing
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.942
+    rev: v0.950
     hooks:
       - id: mypy
         args: [--config, ./mypy.ini]

CONTRIBUTING.md

@@ -1,5 +1,3 @@
-<!-- markdownlint-disable MD041 -->
-
 Thanks for contributing! Please see the
 **Contributor Guide** section in [the documentation](https://jupyter-docker-stacks.readthedocs.io/en/latest/) for
 information about how to contribute
@@ -8,3 +6,5 @@ information about how to contribute
 [tests](https://jupyter-docker-stacks.readthedocs.io/en/latest/contributing/tests.html),
 [features](https://jupyter-docker-stacks.readthedocs.io/en/latest/contributing/features.html),
 [community-maintained stacks](https://jupyter-docker-stacks.readthedocs.io/en/latest/contributing/stacks.html).
+
+<!-- markdownlint-disable-file MD041 -->

all-spark-notebook/Dockerfile

@@ -27,7 +27,13 @@ RUN apt-get update --yes && \
 USER ${NB_UID}
 
 # R packages including IRKernel which gets installed globally.
-RUN mamba install --quiet --yes \
+RUN arch=$(uname -m) && \
+    if [ "${arch}" == "aarch64" ]; then \
+        # Prevent libmamba from sporadically hanging on arm64 under QEMU
+        # <https://github.com/mamba-org/mamba/issues/1611>
+        export G_SLICE=always-malloc; \
+    fi && \
+    mamba install --quiet --yes \
     'r-base' \
     'r-ggplot2' \
     'r-irkernel' \

base-notebook/Dockerfile

@@ -119,7 +119,8 @@ RUN set -x && \
     if [ "${arch}" == "aarch64" ]; then \
         # Prevent libmamba from sporadically hanging on arm64 under QEMU
         # <https://github.com/mamba-org/mamba/issues/1611>
-        ./micromamba config set extract_threads 1; \
+        # We don't use `micromamba config set` since it instead modifies ~/.condarc.
+        echo "extract_threads: 1" >> "${CONDA_DIR}/.condarc"; \
     fi && \
     # Install the packages
     ./micromamba install \
@@ -165,7 +166,8 @@ RUN sed -re "s/c.ServerApp/c.NotebookApp/g" \
 # This healtcheck works well for `lab`, `notebook`, `nbclassic`, `server` and `retro` jupyter commands
 # https://github.com/jupyter/docker-stacks/issues/915#issuecomment-1068528799
 HEALTHCHECK  --interval=15s --timeout=3s --start-period=5s --retries=3 \
-    CMD wget -O- --no-verbose --tries=1 http://localhost:8888${JUPYTERHUB_SERVICE_PREFIX:-/}api || exit 1
+    CMD wget -O- --no-verbose --tries=1 --no-check-certificate \
+    http${GEN_CERT:+s}://localhost:8888${JUPYTERHUB_SERVICE_PREFIX:-/}api || exit 1
 
 # Switch back to jovyan to avoid accidental container runs as root
 USER ${NB_UID}

datascience-notebook/Dockerfile

@@ -61,7 +61,13 @@ USER ${NB_UID}
 
 # R packages including IRKernel which gets installed globally.
 # r-e1071: dependency of the caret R package
-RUN mamba install --quiet --yes \
+RUN arch=$(uname -m) && \
+    if [ "${arch}" == "aarch64" ]; then \
+        # Prevent libmamba from sporadically hanging on arm64 under QEMU
+        # <https://github.com/mamba-org/mamba/issues/1611>
+        export G_SLICE=always-malloc; \
+    fi && \
+    mamba install --quiet --yes \
     'r-base' \
     'r-caret' \
     'r-crayon' \
@@ -75,23 +81,23 @@ RUN mamba install --quiet --yes \
     'r-nycflights13' \
     'r-randomforest' \
     'r-rcurl' \
+    'r-rmarkdown' \
     'r-rodbc' \
     'r-rsqlite' \
     'r-shiny' \
+    'r-tidyverse' \
     'rpy2' \
     'unixodbc' && \
     mamba clean --all -f -y && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 
-# These packages are not easy to install under arm
+# `r-tidymodels` is not easy to install under arm
 RUN set -x && \
     arch=$(uname -m) && \
     if [ "${arch}" == "x86_64" ]; then \
         mamba install --quiet --yes \
-            'r-rmarkdown' \
+            'r-tidymodels' && \
-            'r-tidymodels' \
-            'r-tidyverse' && \
             mamba clean --all -f -y && \
             fix-permissions "${CONDA_DIR}" && \
             fix-permissions "/home/${NB_USER}"; \

pyspark-notebook/Dockerfile

@@ -61,7 +61,13 @@ RUN fix-permissions "/etc/ipython/"
 USER ${NB_UID}
 
 # Install pyarrow
-RUN mamba install --quiet --yes \
+RUN arch=$(uname -m) && \
+    if [ "${arch}" == "aarch64" ]; then \
+        # Prevent libmamba from sporadically hanging on arm64 under QEMU
+        # <https://github.com/mamba-org/mamba/issues/1611>
+        export G_SLICE=always-malloc; \
+    fi && \
+    mamba install --quiet --yes \
     'pyarrow' && \
     mamba clean --all -f -y && \
     fix-permissions "${CONDA_DIR}" && \

r-notebook/Dockerfile

@@ -27,7 +27,13 @@ USER ${NB_UID}
 
 # R packages including IRKernel which gets installed globally.
 # r-e1071: dependency of the caret R package
-RUN mamba install --quiet --yes \
+RUN arch=$(uname -m) && \
+    if [ "${arch}" == "aarch64" ]; then \
+        # Prevent libmamba from sporadically hanging on arm64 under QEMU
+        # <https://github.com/mamba-org/mamba/issues/1611>
+        export G_SLICE=always-malloc; \
+    fi && \
+    mamba install --quiet --yes \
     'r-base' \
     'r-caret' \
     'r-crayon' \
@@ -52,7 +58,6 @@ RUN mamba install --quiet --yes \
     fix-permissions "/home/${NB_USER}"
 
 # `r-tidymodels` is not easy to install under arm
-# hadolint ignore=SC2039
 RUN set -x && \
     arch=$(uname -m) && \
     if [ "${arch}" == "x86_64" ]; then \

scipy-notebook/Dockerfile

@@ -26,7 +26,13 @@ RUN apt-get update --yes && \
 USER ${NB_UID}
 
 # Install Python 3 packages
-RUN mamba install --quiet --yes \
+RUN arch=$(uname -m) && \
+    if [ "${arch}" == "aarch64" ]; then \
+        # Prevent libmamba from sporadically hanging on arm64 under QEMU
+        # <https://github.com/mamba-org/mamba/issues/1611>
+        export G_SLICE=always-malloc; \
+    fi && \
+    mamba install --quiet --yes \
     'altair' \
     'beautifulsoup4' \
     'bokeh' \

tensorflow-notebook/Dockerfile

@@ -11,7 +11,13 @@ LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
 SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 
 # Install Tensorflow
-RUN mamba install --quiet --yes \
+RUN arch=$(uname -m) && \
+    if [ "${arch}" == "aarch64" ]; then \
+        # Prevent libmamba from sporadically hanging on arm64 under QEMU
+        # <https://github.com/mamba-org/mamba/issues/1611>
+        export G_SLICE=always-malloc; \
+    fi && \
+    mamba install --quiet --yes \
     'tensorflow' && \
     mamba clean --all -f -y && \
     fix-permissions "${CONDA_DIR}" && \

tests/datascience-notebook/test_julia.py

@@ -10,12 +10,9 @@ LOGGER = logging.getLogger(__name__)
 def test_julia(container: TrackedContainer) -> None:
     """Basic julia test"""
     LOGGER.info("Test that julia is correctly installed ...")
-    running_container = container.run_detached(
+    logs = container.run_and_wait(
+        timeout=5,
         tty=True,
-        command=["start.sh", "bash", "-c", "sleep infinity"],
+        command=["start.sh", "bash", "-c", "julia --version"],
     )
-    command = "julia --version"
+    LOGGER.debug(logs)
-    cmd = running_container.exec_run(command)
-    output = cmd.output.decode("utf-8")
-    LOGGER.debug(output)
-    assert cmd.exit_code == 0, f"Command {command} failed {output}"