diff --git a/.github/workflows/test-terra-jupyter-base.yml b/.github/workflows/test-terra-jupyter-base.yml index 6afe3760..921ffe64 100644 --- a/.github/workflows/test-terra-jupyter-base.yml +++ b/.github/workflows/test-terra-jupyter-base.yml @@ -64,7 +64,7 @@ jobs: credentials_json: ${{ secrets.TD_GCP_SA_KEY }} create_credentials_file: true - - name: Set up Cloud SDK + - name: Set up Google Cloud CLI uses: google-github-actions/setup-gcloud@v3 with: project_id: ${{ secrets.GCP_PROJECT_ID }} @@ -98,5 +98,6 @@ jobs: --volume $GITHUB_WORKSPACE/terra-jupyter-base/tests:/tests \ --workdir=/tests \ --entrypoint="" \ + --env PIP_USER=false \ terra-jupyter-base:smoke-test \ - /bin/sh -c "pip3 install pytest; pytest" + /bin/bash -c '"$CONDA_ENV_HOME"/bin/python -m pip install pytest && "$CONDA_ENV_HOME"/bin/python -m pytest' diff --git a/.gitignore b/.gitignore index c7b1ac97..6cbca952 100644 --- a/.gitignore +++ b/.gitignore @@ -17,4 +17,7 @@ package-lock.json .python_history .keras/ .ammonite/ -.metals/ \ No newline at end of file +.metals/ +# service-account keys fetched from vault at build time +image-build-account.json +dspci-wb-gcr-service-account.json diff --git a/README.md b/README.md index f2560ccf..99b27a40 100644 --- a/README.md +++ b/README.md @@ -5,8 +5,11 @@ This repo provides docker images for running jupyter notebook in [Terra](https:/ Make sure to go through the [contributing guide](https://github.com/DataBiosphere/terra-docker/blob/master/CONTRIBUTING.md#contributing) as you make changes to this repo. # Terra Base Images + [terra-base](terra-base/README.md) +[terra-jupyter-base](terra-jupyter-base/README.md) + [terra-jupyter-python](terra-jupyter-python/README.md) [terra-jupyter-r](terra-jupyter-r/README.md) @@ -17,6 +20,12 @@ Make sure to go through the [contributing guide](https://github.com/DataBiospher [terra-jupyter-bioconductor](terra-jupyter-bioconductor/README.md) +## Image dependencies + +![Image dependencies](dependencies.png) +To update this map, install the PlantUML intelliJ extension, then edit the `mind.puml` file. + + # How to create your own Custom image to use with notebooks on Terra Custom docker images need to use a Terra base image (see above) in order to work with the service that runs notebooks on Terra. * You can use any of the base images above @@ -83,12 +92,27 @@ Detailed documentation on how to integrate the terra-docker image with Leonardo - Ensure that the `terra-docker-versions-candidate.json` file (which is what the UI sources the dropdown from) in the `terra-docjker-image-documentation-[env]` bucket correclty references your new docker image - [Update the terra-docker version candidate json](https://broadworkbench.atlassian.net/wiki/spaces/IA/pages/2519564289/Integrating+new+Terra+docker+images+with+Leonardo#6.-Update-terra-docker-versions-candidate.json) +## UV and updating dependencies +This repo uses [uv](https://pypi.org/project/uv/) to manage python dependencies. +The uv.lock file at the root of the directory ensures package versions across all the docker images are compatible. +Each image has a pyproject.toml file that defines the additional dependencies for that image. +- To make a general update to all dependencies, cd into the image directory and run `uv update`. +- If you want to update a specific dependency, you can run `uv add [package name]@[version]` to update to a specific version or just `uv add [package name]` to update to the latest version. +- Because the uv.lock file is at the root of the repo, you will need to run `uv sync` in each image directory after making changes to the dependencies to update the lockfile. + +IMPORTANT NOTE: The terra-base image has a separate uv.lock file because its pyproject.toml defines dependencies for the isolated jupyter server environment, which has different dependencies than the other images. +This means that if you are updating dependencies for the terra-base image, you will need to cd into the terra-base directory to update the uv.lock file for that image. +For all other images, the uv.lock file at the root of the repo is used and therefore docker image must be built from the root of the repo. + ## Testing your image manually -Build the image: -run `docker build [your_dir] -t [name]`. +#### Build the image from the root of the repo: +This is necessary to ensure the workspace `uv.lock` file can be accessed. +The one exception is if you are building the `terra-base` image, you will need to cd into the `terra-base` directory and build from there) + +run `docker build -f [your_dir]/Dockerfile . -t [name]`. -`docker build terra-base -t terra-base` +`docker build -f terra-jupyter-base/Dockerfile . -t us.gcr.io/broad-dsp-gcr-public/terra-base:{tag}` If you're on an M1 and building an image from a locally built image, replace the current FROM command: @@ -111,7 +135,8 @@ You can gain root access and open a bash terminal as follows: docker run --rm -it -u root -p 8000:8000 --entrypoint /bin/bash us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:0.0.7 ``` -Running locally is conventient for quick development and exploring the image. However it has some limitations compared to running through Terra. Namely: +Running locally is convenient for quick development and exploring the image. +However it has some limitations compared to running through Terra. Namely: - there are no service account credentials when run locally - there are no environment variables like `GOOGLE_PROJECT`, `WORKSPACE_NAME`, `WORKSPACE_BUCKET`, etc when running locally - there is no workspace-syncing when run locally @@ -168,10 +193,6 @@ The scripts folder has scripts used for building. - `generate_package_docs.py` This script is run once by build.sh each time an image is built. It is used to generate a .json with the versions for the packages in the image. - `generate_version_docs.py` This script is run each time an image is built. It builds a new file master version file for the UI to look up the current versions to reference. -## Image dependencies - -Note that this dependency graph needs to be updated! -![Image dependencies](dependencies.png) ## Push Images to GCR diff --git a/build.sh b/build.sh index 9d3d67d0..6339ef9f 100755 --- a/build.sh +++ b/build.sh @@ -1,10 +1,17 @@ #!/bin/bash # Run `gcloud auth configure-docker --quiet` before running this script # Example: ./build.sh terra-jupyter-base +# Example: ./build.sh terra-jupyter-base true +# Example: KEEP_LOCAL_IMAGE=true ./build.sh terra-jupyter-base true +# +# Optional environment variables: +# KEEP_LOCAL_IMAGE true keeps the pulled image in the local docker store after the build set -e -x +set -o pipefail IMAGE_DIR=$1 -SKIP_GCP_AUTH=$2 +SKIP_GCP_AUTH=${2:-${SKIP_GCP_AUTH:-}} +KEEP_LOCAL_IMAGE=${KEEP_LOCAL_IMAGE:-false} VERSION=$(cat config/conf.json | jq -r ".image_data | .[] | select(.name == \"$IMAGE_DIR\") | .version") TAG_NAME=$(git log --pretty=format:'%h' -n 1) @@ -26,36 +33,84 @@ if [[ $VAULT_LOCATION == *"jenkins"* ]]; then VAULT_LOCATION="/etc/vault-token-dsde" fi -if [[ -z "${SKIP_GCP_AUTH}" ]] || [["${SKIP_GCP_AUTH}" != "true"]]; then +if [[ "${SKIP_GCP_AUTH}" != "true" ]]; then + # Docker silently creates the mount source as a directory when it does not + # exist, which makes vault fail with "is a directory" instead of anything + # useful. Check up front so the error names the real problem. + if [[ ! -f "$VAULT_LOCATION" ]]; then + echo "No vault token file at $VAULT_LOCATION (it must be a file, not a directory)." + echo "Create one with:" + echo " docker run -it --rm -v \$HOME:/root -e VAULT_ADDR=https://clotho.broadinstitute.org:8200 \\" + echo " broadinstitute/dsde-toolbox:latest vault login -method=github" + echo "Or re-run with SKIP_GCP_AUTH=true to use your existing gcloud credentials." + #unreserved exit code for checking in jenkins + exit 16 + fi + # will fail if you are not gcloud authed as dspci-wb-gcr-service-account or secret/dsde/firecloud/common/image-build-account.json # the below works locally but not on jenkins for some reason, using a different account until a resolution is found # docker run --rm -v $VAULT_LOCATION:/root/.vault-token:ro broadinstitute/dsde-toolbox:latest vault read --format=json secret/dsde/dsp-techops/common/dspci-wb-gcr-service-account.json | jq .data > dspci-wb-gcr-service-account.json # gcloud auth activate-service-account --key-file=dspci-wb-gcr-service-account.json docker run --rm -v $VAULT_LOCATION:/root/.vault-token:ro broadinstitute/dsde-toolbox:latest vault read --format=json secret/dsde/firecloud/common/image-build-account.json | jq .data > image-build-account.json + + # jq happily writes an empty file when the vault read produced nothing, which + # surfaces later as a confusing "Could not read json file" from gcloud. + if [[ ! -s image-build-account.json ]]; then + echo "vault read produced an empty image-build-account.json; see the error above." + #unreserved exit code for checking in jenkins + exit 16 + fi + gcloud auth activate-service-account --key-file=image-build-account.json gcloud auth configure-docker --quiet fi -docker image build ./$IMAGE_DIR \ +# Build and push in a single buildx step. +# +# Leonardo's registry client only accepts Docker schema 2 media types, so an OCI +# manifest or index makes its image auto-detection fail with MANIFEST_UNKNOWN. A +# plain `docker build && docker push` emits an OCI index whenever the daemon uses +# the containerd image store, which is the default in recent Docker versions. +# --platform pins the target arch; otherwise the manifest records the +# builder host's arch even when the FROM line is pinned to amd64 +# --provenance attestations are published as an extra manifest, which turns +# --sbom the push into an index even for a single-platform image +# oci-mediatypes false forces application/vnd.docker.distribution.manifest.v2+json +docker buildx build ./$IMAGE_DIR \ + --platform linux/amd64 \ + --provenance=false \ + --sbom=false \ + --output type=image,oci-mediatypes=false,push=true \ --tag $GCR_IMAGE_REPO/$IMAGE_DIR:$TAG_NAME \ --tag $GCR_IMAGE_REPO/$IMAGE_DIR:$VERSION \ --tag $GCR_IMAGE_REPO/$IMAGE_DIR:latest -docker push $GCR_IMAGE_REPO/$IMAGE_DIR:$TAG_NAME -docker push $GCR_IMAGE_REPO/$IMAGE_DIR:$VERSION -docker push $GCR_IMAGE_REPO/$IMAGE_DIR:latest +# Fail the build rather than publishing something Leonardo cannot read. +MANIFEST_TYPE=$(docker buildx imagetools inspect --raw $GCR_IMAGE_REPO/$IMAGE_DIR:$VERSION | jq -r '.mediaType') +if [ "$MANIFEST_TYPE" != "application/vnd.docker.distribution.manifest.v2+json" ]; then + echo "Pushed manifest is $MANIFEST_TYPE, expected application/vnd.docker.distribution.manifest.v2+json." + echo "Leonardo will not be able to auto-detect this image." + #unreserved exit code for checking in jenkins + exit 15 +fi + +# buildx pushed straight to the registry without loading the image into the local +# store, so pull it back for the doc-generation container below. +docker pull $GCR_IMAGE_REPO/$IMAGE_DIR:$VERSION docker kill $IMAGE_DIR || true docker rm -f $IMAGE_DIR || true docker run --rm -itd -u root -e PIP_USER=false --entrypoint='/bin/bash' --name $IMAGE_DIR $GCR_IMAGE_REPO/$IMAGE_DIR:$VERSION gcloud auth list -python scripts/generate_package_docs.py "$IMAGE_DIR" +python3 scripts/generate_package_docs.py "$IMAGE_DIR" docker kill $IMAGE_DIR || true docker rm -f $IMAGE_DIR || true -docker image rm -f $GCR_IMAGE_REPO/$IMAGE_DIR:$VERSION -docker image rm -f $GCR_IMAGE_REPO/$IMAGE_DIR:$TAG_NAME +if [[ "${KEEP_LOCAL_IMAGE}" != "true" ]]; then + docker image rm -f $GCR_IMAGE_REPO/$IMAGE_DIR:$VERSION + docker image rm -f $GCR_IMAGE_REPO/$IMAGE_DIR:$TAG_NAME +fi echo "Successfully completed build script for $IMAGE_DIR" diff --git a/build_smoke_test_image.sh b/build_smoke_test_image.sh index a4e6f2b9..74cc4c2e 100755 --- a/build_smoke_test_image.sh +++ b/build_smoke_test_image.sh @@ -1,7 +1,7 @@ #!/bin/bash # Perform a local build of an image for smoke-testing purposes. Also build its tree of base images, when missing. # -# Example: ./build_smoke_test_image.sh terra-jupyter-python +# Example: ./build_smoke_test_image.sh terra-jupyter-base # # Current working directory must be the directory in which this script resides (one level above all the Dockerfiles). # It walks down each relevant image directory, making changes to the FROM statements, @@ -13,9 +13,10 @@ set -o nounset set -o xtrace build_smoke_test_image() { - local IMAGE_TYPE=$1 + local IMAGE_TYPE=${1:-"terra-jupyter-base"} pushd ${IMAGE_TYPE} - local BASE_IMAGES=$( egrep '^FROM (\S+)' Dockerfile |tr -s ' ' | cut -d ' ' -f 2 ) + # The image is the first FROM argument that is not an option such as --platform=${BASE_PLATFORM} + local BASE_IMAGES=$( awk '/^FROM/ { for (i=2; i<=NF; i++) if ($i !~ /^--/) { print $i; break } }' Dockerfile ) local BASE_IMAGE for BASE_IMAGE in ${BASE_IMAGES}; do @@ -43,4 +44,4 @@ build_smoke_test_image() { # Log available disk space prior to building image df -kh -build_smoke_test_image $1 +build_smoke_test_image "${1:-}" diff --git a/config/conf.json b/config/conf.json index 11f76fb5..1fb7d0bd 100644 --- a/config/conf.json +++ b/config/conf.json @@ -30,7 +30,7 @@ "automated_flags" : { "generate_docs" : true, "include_in_ui" : true, - "build" : true, + "build" : false, "include_in_custom_dataproc" : true, "include_in_custom_gce" : true } @@ -51,7 +51,7 @@ "automated_flags" : { "generate_docs" : true, "include_in_ui" : true, - "build" : true, + "build" : false, "include_in_custom_dataproc" : true, "include_in_custom_gce" : false } @@ -72,7 +72,7 @@ "automated_flags" : { "generate_docs" : true, "include_in_ui" : true, - "build" : true, + "build" : false, "include_in_custom_dataproc" : true, "include_in_custom_gce" : true } @@ -86,10 +86,10 @@ "packages" : { }, - "version" : "1.1.4", + "version" : "2.0.1", "automated_flags" : { "generate_docs" : true, - "include_in_ui" : false, + "include_in_ui" : true, "build" : true, "include_in_custom_dataproc" : true, "include_in_custom_gce" : true @@ -108,7 +108,7 @@ "automated_flags" : { "generate_docs" : true, "include_in_ui" : true, - "build" : true, + "build" : false, "include_in_custom_dataproc" : true, "include_in_custom_gce" : true } @@ -122,9 +122,9 @@ "packages" : { }, - "version" : "2.2.7", + "version" : "3.0.0", "automated_flags" : { - "include_in_ui" : false, + "include_in_ui" : true, "generate_docs" : true, "build" : true, "include_in_custom_dataproc" : true, @@ -146,7 +146,7 @@ "automated_flags" : { "include_in_ui" : true, "generate_docs" : true, - "build" : true, + "build" : false, "include_in_custom_dataproc" : true, "include_in_custom_gce" : true } diff --git a/mind.puml b/mind.puml index 536de18b..3a1a9a4a 100644 --- a/mind.puml +++ b/mind.puml @@ -1,9 +1,8 @@ @startmindmap * terra-jupyter-base ** terra-jupyter-python -*** terra-jupyter-gatk *** terra-jupyter-hail ** terra-jupyter-r -*** terra-jupyter-gatk *** terra-jupyter-bioconductor +*** terra-jupyter-gatk @endmindmap diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 00000000..2e37594e --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,20 @@ +[project] +name = "terra-docker" +version = "2.0.0" +description = "Collection of inter-dependent docker images for Terra notebooks and services" +readme = "README.md" +requires-python = ">=3.13, <3.14" +dependencies = [ + "setuptools<71", + "terra-jupyter-base", + "terra-jupyter-python" +] + +[tool.uv.workspace] +# NOTE: We explicitly exclude terra-base from this because that defines the dependencies +# for the isolated jupyter server NOT the conda environment for the notebooks +members = ["terra-jupyter-base", "terra-jupyter-python"] + +[tool.uv.sources] +terra-jupyter-base = { workspace = true } +terra-jupyter-python = { workspace = true } diff --git a/terra-jupyter-base/CHANGELOG.md b/terra-jupyter-base/CHANGELOG.md index 103fc50f..07d8f0fd 100644 --- a/terra-jupyter-base/CHANGELOG.md +++ b/terra-jupyter-base/CHANGELOG.md @@ -1,3 +1,27 @@ +## 2.0.1 - 2026-10-16 +- Fix vulnerabilities reported in 2.0.0 + - Conda base env: upgrade `anyio` (>= 4.14.2), `pyjwt` (>= 2.14.0) and `cryptography` (>= 50.0.0) + - Drop `python3-openssl`, which pulled in Ubuntu's `python3-cryptography` 46.0.5 + - Remove the unused `/usr/bin/pebble` (Go 1.26.7) shipped by the `ubuntu:26.04` base + - google-cloud-cli: upgrade its bundled `cryptography` (>= 50.0.0) and `pyopenssl` (>= 26.4.0), and remove the + optional `gcloud-crc32c` binary (Go 1.26.6); `gcloud storage` falls back to the bundled `google_crc32c` + - npm: replace its bundled `brace-expansion` (5.0.12) and `undici` (6.29.1) + - nbclassic: replace its bundled `underscore` with 1.13.8 + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:2.0.1` + +## 2.0.0 - 2026-10-16 +- Build off Ubuntu 26.04 with base image `nvidia/cuda:13.4.2-base-ubuntu26.04` (merged with terra-base) +- Python 3.13 (Miniconda `py313_26.7.1-1`) for conda base, the Jupyter server venv and the user's conda env + - Downgraded from 3.14: Tensorflow and several scientific packages used by the child images have no Python 3.14 wheels yet + - Ubuntu's `/usr/bin/python3` (3.14) is not used for notebooks; `python3-pip` is no longer installed +- Jupyter server runs in an isolated uv venv at `/etc/jupyter` (`pyproject.toml` / `uv.lock`), Notebook 7 + nbclassic +- User's conda env at `/opt/conda/envs/python3`, registered as the `python3` kernel in `/usr/local/share/jupyter/kernels` +- R and the CRAN `resolute-cran40` apt repository; the R kernel is registered by terra-jupyter-r +- google-cloud-cli and OpenJDK 25 + +Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:2.0.0` + ## 1.1.4 - 2025-04-24 - Build off Ubuntu 22 with base image `gcr.io/deeplearning-platform-release/tf2-cu123.2-17.py310` diff --git a/terra-jupyter-base/Dockerfile b/terra-jupyter-base/Dockerfile index ba484718..15e8f9c4 100644 --- a/terra-jupyter-base/Dockerfile +++ b/terra-jupyter-base/Dockerfile @@ -1,159 +1,583 @@ -# adapted from https://hub.docker.com/r/jupyter/base-notebook/ AKA https://github.com/jupyter/docker-stacks/tree/master/base-notebook +# `terra-base` image: (soon to be removed) merged with into terra-jupyter-base +# package list, on the latest gpu-enabled base image on Ubuntu 26. +ARG BASE_PLATFORM=linux/amd64 +# ARG BASE_PLATFORM=linux/amd64 +FROM --platform=${BASE_PLATFORM} nvidia/cuda:13.4.2-base-ubuntu26.04 -FROM gcr.io/deeplearning-platform-release/tf2-cu123.2-17.py310 - -USER root +# want the command to fail due to an error at any stage in the pipe: https://github.com/hadolint/hadolint/wiki/DL4006 +SHELL ["/usr/bin/bash", "-o", "pipefail", "-c"] ####################### -# Prerequisites +# General Environment Variables ####################### -ENV DEBIAN_FRONTEND noninteractive +ENV DEBIAN_FRONTEND=noninteractive +# LC_ALL is set after the prerequisites step below, once locale-gen has generated en_US.UTF-8 -RUN apt-get update && apt-get install -yq --no-install-recommends \ - # gnupg requirement - dirmngr \ - gnupg \ - # curl requirement +# Version of python to be installed and used (conda base, the jupyter server venv and the user's +# conda env). 3.13 rather than 3.14: tensorflow and several scientific packages the child images +# install have no Python 3.14 wheels yet. Ubuntu 26.04's own /usr/bin/python3 stays at 3.14. +# NOTE TensorFlow only supports up to python 3.13 +ENV PYTHON_VERSION=3.13 +# Paired conda installer +# See https://repo.anaconda.com/miniconda/ for list of miniconda +ENV CONDA_INSTALLER=https://repo.anaconda.com/miniconda/Miniconda3-py313_26.7.1-1-Linux-x86_64.sh +ENV JUPYTER_VERSION=7.6.3 +ENV JUPYTER_PORT=8000 +ENV NODE_MAJOR=26 + +USER root + +################# +# Install Prerequisites +################# +# terra-base prerequisites + the packages terra-jupyter-base added on top (carried over from the +# old deeplearning image), installed in a single layer. +# Package names verified against Ubuntu 26.04 (resolute) + the CUDA 13.4 repo. +# Entries that are commented out are kept for reference with the reason they were dropped; +# "pulled in by X" means apt still installs it as a dependency of X, so listing it is redundant +# and only pins a soname that breaks on the next Ubuntu release. +# +# The nvidia/cuda Ubuntu base is a minimized image: /etc/dpkg/dpkg.cfg.d/excludes drops every man +# page and /usr/bin/man is diverted to a stub. That makes man-db (below) useless and makes +# update-alternatives warn "skip creation of /usr/share/man/man1/lzma.1.gz ..." for every +# alternative that links a man page. Re-enable man pages before installing (the same thing +# Ubuntu's `unminimize` does for man pages, without restoring all of /usr/share/doc). +RUN sed -i '\|^path-exclude=/usr/share/man/\*|d' /etc/dpkg/dpkg.cfg.d/excludes \ + && if [ "$(dpkg-divert --truename /usr/bin/man)" = "/usr/bin/man.REAL" ]; then \ + rm -f /usr/bin/man && dpkg-divert --quiet --remove --rename /usr/bin/man; \ + fi \ + && apt-get update && apt-get install -yq --no-install-recommends \ + # basic necessities \ + sudo \ ca-certificates \ - # useful utilities for debugging within the docker + curl \ + jq \ + # gnupg requirement \ + gnupg \ + dirmngr \ + # useful utilities for debugging within docker itself \ nano \ + less \ procps \ lsb-release \ - # python requirements - checkinstall \ + # gcc compiler (gcc-15 on Ubuntu 26.04) \ build-essential \ + locales \ + # for ssh-agent and ssh-add \ + keychain \ + # extras \ + wget \ + bzip2 \ + git \ + ########## terra-jupyter-base ########## \ + # debugging / terminal utilities \ + htop \ + tree \ + rsync \ + screen \ + tmux \ + # tmux/screen utmp helper (only a Recommends, so list it explicitly) \ + libutempter0 \ + dialog \ + bsdextrautils \ + inotify-tools \ + pciutils \ + man-db \ + apt-utils \ + pkg-config \ + llvm \ + # editors \ + emacs \ + vim \ + # xxd is no longer a dependency of vim on 26.04, keep it explicitly \ + xxd \ + # Python build headers \ zlib1g-dev \ - # pip requirements libssl-dev \ libbz2-dev \ libreadline-dev \ libsqlite3-dev \ - llvm \ - libncurses5-dev \ - libncursesw5-dev \ + # replaces libncurses5-dev / libncursesw5-dev, which no longer exist \ + libncurses-dev \ tk-dev \ libffi-dev \ liblzma-dev \ - python3-openssl \ - # install script requirements - sudo \ - locales \ - # for ssh-agent and ssh-add - keychain \ - # openjdk 11 - default-jre \ + libcurl4-openssl-dev \ + # System python3 (3.13 on Ubuntu 26.04) helpers. Users should use the conda env. \ + python3-setuptools \ + python3-snappy \ + python3-tk \ + python3-wheel \ + # RDMA / InfiniBand userspace for multi-GPU networking (only Recommends, so list explicitly) \ + libibverbs1 \ + libnl-3-200 \ + libnl-genl-3-200 \ + libnl-route-3-200 \ + # Java (OpenJDK 25 on Ubuntu 26.04) \ default-jdk \ + # scientific / data libraries \ + libhdf5-dev \ + libnuma-dev \ + libopenblas0 \ + libopenblas0-pthread \ + libsnappy-dev \ + protobuf-compiler \ + # FUSE: libfuse2t64 for legacy fuse2 binaries/AppImages, fuse3 for the userspace tools \ + fuse3 \ + libfuse2t64 \ + # docs / LaTeX for nbconvert PDF export \ + pandoc \ + texlive \ + texlive-fonts-recommended \ + texlive-latex-base \ + texlive-latex-recommended \ + # LuaJITTeX engine (only a Recommends of texlive-binaries) \ + libtexluajit2 \ + # Tk BLT extension \ + blt \ + # misc runtime libraries used by the old deeplearning image \ + libgd3 \ + libjansson4 \ + libsodium23 \ + libuchardet0 \ + m17n-db \ + ########## Removed / redundant on Ubuntu 26.04 ########## + # TensorRT: on CUDA 13.4 libnvinfer11 alone is 2.5GB installed (2.6GB with the plugin and python + # bindings), which takes the image from ~4.5GB to ~7GB. Nothing in this image uses it, and GPU + # frameworks (tensorflow, torch) ship their own TensorRT/CUDA libraries via pip. + # Was libnvinfer8 / libnvinfer-plugin8 on Ubuntu 22.04. + # libnvinfer11 \ + # libnvinfer-plugin11 \ + # python3-libnvinfer \ + # python3-pip: Ubuntu's pip 25.1.1 vendors urllib3 1.26.20 (GHSA-vxq7-64xx-v4gw, GHSA-8988-9cw3-xx77, + # GHSA-qccp-gfcp-xxvc, GHSA-38jv-5279-wg99). PEP 668 blocks it from installing into the system + # python anyway; users get pip from the conda env and uv manages the jupyter server env. + # python3-pip \ + # python3-openssl: it is the only package that pulls in Ubuntu's python3-cryptography 46.0.5 (GHSA-537c-gmf6-5ccf, + # GHSA-jwv3-5hgf-82ww, GHSA-g6cj-pr64-35w5, fixed in 50.0.0). Like python3-pip, nothing uses the system python; + # the conda env has pyopenssl/cryptography for notebooks. + # python3-openssl \ + # python3-distutils / python3-lib2to3: removed from Python in 3.12 / 3.13, no packages on 26.04 \ + # python3-distutils \ + # python3-lib2to3 \ + # libopenblas-base: transitional package dropped after Ubuntu 22.04, libopenblas0 replaces it \ + # libopenblas-base \ + # checkinstall: was only used to build python from source; python now comes from conda/uv \ + # checkinstall \ + # apt-transport-https: empty transitional package, https is built into apt >= 1.5 (26.04 ships apt 3.2) \ + # apt-transport-https \ + # gcc-12 toolchain: 26.04 defaults to gcc-15 via build-essential; gcc-12 was pinned for Ubuntu 22.04 \ + # cpp-12 \ + # gcc-12 \ + # libgcc-12-dev \ + # dkms / kmod / dctrl-tools: build/load kernel modules, which cannot be done from inside a container \ + # dkms \ + # dctrl-tools \ + # kmod \ + # fuse: on 26.04 this is the fuse3 package (3.18), replaced by the explicit fuse3 entry above \ + # fuse \ + # default-jre: pulled in by default-jdk \ + # default-jre \ + # libcmark-gfm*: pandoc 3.x on 26.04 no longer links against the system cmark-gfm \ + # libcmark-gfm-extensions0.29.0.gfm.3 \ + # libcmark-gfm0.29.0.gfm.3 \ + # pulled in by emacs \ + # emacs-bin-common \ + # emacs-common \ + # emacs-gtk \ + # emacsen-common \ + # libgpm2 \ + # libm17n-0 \ + # libotf1 \ + # pulled in by vim \ + # vim-common \ + # vim-runtime \ + # pulled in by pandoc \ + # pandoc-data \ + # pulled in by texlive \ + # texlive-base \ + # texlive-binaries \ + # tex-common \ + # t1utils \ + # fonts-lmodern \ + # libkpathsea6 \ + # libptexenc1 \ + # libsynctex2 \ + # libteckit0 \ + # libtexlua53 \ + # libzzip-0-13 \ + # pulled in by libhdf5-dev (hdf5 1.14.6, soname 310; was 103-1 / 100 / 102 on 22.04) \ + # hdf5-helpers \ + # libaec-dev \ + # libaec0 \ + # libsz2 \ + # libhdf5-103-1 \ + # libhdf5-cpp-103-1 \ + # libhdf5-fortran-102 \ + # libhdf5-hl-100 \ + # libhdf5-hl-cpp-100 \ + # libhdf5-hl-fortran-100 \ + # pulled in by protobuf-compiler (protobuf 3.21.12, libprotobuf32t64; was libprotobuf23 on 22.04) \ + # libprotobuf23 \ + # libprotoc23 \ + # pulled in by libsnappy-dev / libnuma-dev / pciutils / inotify-tools / tmux \ + # libsnappy1v5 \ + # libnuma1 \ + # libpci3 \ + # pci.ids \ + # libinotifytools0 \ + # libevent-core-2.1-7 \ + # pulled in by man-db \ + # groff-base \ + # libpipeline1 \ + # install-info \ + # pulled in by blt \ + # tk8.6-blt2.5 \ + # pulled in by build-essential (gcc-15 sanitizer runtimes) \ + # libasan8 \ + # libtsan2 \ + # pulled in by python3 / python3-tk (libpython3.14 on 26.04) \ + # libpython3.10 \ + # libpopt0: pulled in by rsync \ + # libpopt0 \ + # # Uncomment en_US.UTF-8 for inclusion in generation && sed -i 's/^# *\(en_US.UTF-8\)/\1/' /etc/locale.gen \ # Generate locale && locale-gen \ + # The ubuntu:26.04 base ships Canonical's pebble service manager (/usr/bin/pebble, not owned by any + # package). Nothing here uses it, and it is built with Go 1.26.7 (GO-2026-6601..6613, GO-2026-6617, fixed in 1.26.9). + && rm -rf /usr/bin/pebble /var/lib/pebble \ + # cleanup && apt-get clean \ && rm -rf /var/lib/apt/lists/* -ENV LC_ALL en_US.UTF-8 +# Set only after locale-gen above: setting it earlier makes perl (debconf) warn +# "Setting locale failed" during the apt install, before en_US.UTF-8 exists. +ENV LC_ALL=en_US.UTF-8 -####################### -# Python / Jupyter -####################### +############################## +# Install the Google Cloud CLI +############################## +# Provides gcloud, gsutil and bq. The previous base image +# (gcr.io/deeplearning-platform-release/*) shipped these pre-installed; the +# nvidia/cuda base does not, so install them explicitly (~0.9GB). +# +# The apt package ships its own bundled Python, so it is independent of the +# system interpreter and of both of the image's Python environments. +# Note: it also bundles its own urllib3 copies (in lib/third_party, gsutil and bq) that image +# scanners may flag; those can only be updated by a newer google-cloud-cli release. +# +# google-cloud-cli 589.0.0 also bundles: +# - cryptography 46.0.7 in its python (GHSA-537c-gmf6-5ccf, GHSA-jwv3-5hgf-82ww, GHSA-g6cj-pr64-35w5, fixed in +# 50.0.0). Upgrade it along with pyopenssl, whose 26.0.0 pins cryptography<47 (26.4.0 allows <51). +# - gcloud-crc32c, a Go 1.26.6 binary (GO-2026-6601..6613, GO-2026-6617, fixed in 1.26.9). It is an optional speed-up: +# without it `gcloud storage` hashes with the bundled google_crc32c C extension instead. +# Remove both once a google-cloud-cli release ships the fixed versions. +ENV GCLOUD_PYTHON=/usr/lib/google-cloud-sdk/platform/bundledpythonunix/bin/python3 +RUN curl -fsSL https://packages.cloud.google.com/apt/doc/apt-key.gpg \ + | gpg --dearmor -o /usr/share/keyrings/cloud.google.gpg \ + # "cloud-sdk" is the name of Google's apt repository (it still serves google-cloud-cli), keep it as is + && echo "deb [signed-by=/usr/share/keyrings/cloud.google.gpg] https://packages.cloud.google.com/apt cloud-sdk main" \ + > /etc/apt/sources.list.d/google-cloud-cli.list \ + && apt-get update \ + && apt-get install -yq --no-install-recommends google-cloud-cli \ + && $GCLOUD_PYTHON -m pip install --no-cache-dir --root-user-action=ignore --upgrade "cryptography>=50.0.0" "pyopenssl>=26.4.0" \ + && $GCLOUD_PYTHON -c "import OpenSSL, google_crc32c, cryptography; assert int(cryptography.__version__.split('.')[0]) >= 50" \ + && rm -f /usr/lib/google-cloud-sdk/bin/gcloud-crc32c \ + && gcloud --version \ + && apt-get clean \ + && rm -rf /var/lib/apt/lists/* + +############################## +# Set up Node for Jupyterlab +############################## +# The Google Cloud apt key that terra-base imported here is now installed with google-cloud-cli above. + +# Install Node >18 +# Empty install (no packages listed) in terra-base, it only refreshed the apt index. +# RUN apt-get update && apt-get install -yq --no-install-recommends +# Ubuntu 22.04 shipped a libnode-dev that conflicted with the nodesource nodejs package. +# The 26.04 base image does not include it, so this removal is a no-op. +# RUN dpkg --remove --force-remove-reinstreq libnode-dev +RUN mkdir -p /etc/apt/keyrings \ + && curl -fsSL https://deb.nodesource.com/gpgkey/nodesource-repo.gpg.key | gpg --dearmor -o /etc/apt/keyrings/nodesource.gpg \ + && echo "deb [signed-by=/etc/apt/keyrings/nodesource.gpg] https://deb.nodesource.com/node_$NODE_MAJOR.x nodistro main" > /etc/apt/sources.list.d/nodesource.list \ + && apt-get update \ + && apt-get install -yq --no-install-recommends nodejs \ + && apt-get clean \ + && rm -rf /var/lib/apt/lists/* + +# npm (11.20.0 from nodesource; even the latest, 12.2.0) bundles vulnerable copies of these dependencies. Swap +# each one for the first fixed release in the range npm requires: +# - http-cache-semantics 4.2.0 -> 4.3.0: CVE-2026-93748 / GHSA-ch52-4w7c-c8xp (make-fetch-happen wants ^4.1.1) +# - brace-expansion 5.0.9 -> 5.0.12: GHSA-qhr7-859c-m2p7, GHSA-6j4f-fj2g-mc7p (minimatch wants ^5.0.5; its only +# dependency, balanced-match ^4.0.2, is already bundled at 4.0.4) +# - undici 6.28.0 -> 6.29.1: CVE-2026-19534 / GHSA-rfgv-xxqx-mfg5 (node-gyp wants ^6.25.0). Node's own built-in +# undici (8.11.2) is already fixed. +# Remove an entry once nodesource ships an npm with the fixed version. +# Each package is installed into a scratch prefix and only its own directory is copied over npm's copy. npm extracts +# the tarball itself: GNU tar fails with "Function not implemented" on tarballs with nested directories (e.g. +# brace-expansion's dist/) when the amd64 image is built under emulation on Apple Silicon. +ENV NPM_PATCHES="http-cache-semantics@4.3.0 brace-expansion@5.0.12 undici@6.29.1" +RUN NPM_MODULES=$(npm root -g)/npm/node_modules \ + && for PKG in $NPM_PATCHES; do \ + NAME=${PKG%@*} && VERSION=${PKG##*@} && DEST=$NPM_MODULES/$NAME \ + && test -d $DEST \ + && npm install --silent --no-save --no-package-lock --ignore-scripts --omit=dev --prefix /tmp/npm-patch $PKG \ + && rm -rf $DEST \ + && cp -r /tmp/npm-patch/node_modules/$NAME $DEST \ + && test "$(node -p "require('$DEST/package.json').version")" = "$VERSION" \ + || exit 1; \ + done \ + && rm -rf /tmp/npm-patch \ + && npm cache clean --force \ + && npm --version +########################## +# Create the User's Jupyter User +########################## +# Create the jupyter user and give sudo permission ENV USER=jupyter -RUN usermod -g users jupyter -ENV HOME /home/$USER +# This UID must stay static to be one greater than the welder user (1001) +ENV USER_UID=1002 + +# Create the user home and add to the users group +ENV USER_HOME=/home/$USER +RUN useradd -m -s /bin/bash -d $USER_HOME -N -u $USER_UID $USER \ + && usermod -g users $USER + +# We want to grant the user sudo permissions without password + # so they can install the necessary packages that they want to use on the docker container +RUN echo "$USER ALL=(ALL) NOPASSWD: ALL" > /etc/sudoers.d/$USER \ + && chmod 0440 /etc/sudoers.d/$USER + +############ +# Install R +############ +# add R repo for later R package installation +# software-properties-common (add-apt-repository) is not needed: the CRAN repo (resolute-cran40) +# is written to sources.list.d directly. r-base was also installed twice in terra-base. +# r-base-dev pulls in gfortran. On Ubuntu 26.04 its gfortran.1.gz is a dangling link to +# gfortran-15.1.gz (the page is shipped as x86_64-linux-gnu-gfortran-15.1.gz), which makes +# update-alternatives warn "skip creation of /usr/share/man/man1/f77.1.gz / f95.1.gz" and breaks +# `man gfortran`. Create the missing link first so the f77/f95 man page alternatives are set up. +RUN ln -sf x86_64-linux-gnu-gfortran-15.1.gz /usr/share/man/man1/gfortran-15.1.gz \ + && curl -fsSL https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc -o /usr/share/keyrings/cran.asc \ + && echo "deb [signed-by=/usr/share/keyrings/cran.asc] https://cloud.r-project.org/bin/linux/ubuntu $(. /etc/os-release && echo $VERSION_CODENAME)-cran40/" > /etc/apt/sources.list.d/cran.list \ + && apt-get update \ + && apt-get install -yq --no-install-recommends r-base r-base-dev \ + && apt-get clean \ + && rm -rf /var/lib/apt/lists/* + +############################################ +# Install Miniconda and setup base conda environment +############################################ +## CONDA should not be used by devs to manage package dependencies, +# but is a widely used tool to manage python environments in a runtime + # and we should provide it to users +# download and install conda +ENV CONDA_HOME=/opt/conda +# Don't print Anaconda's "defaults" channel notices (e.g. "Anaconda will stop building new Python 3.10 +# packages") in the build log. They are announcements for all channel users, not about this image, +# which only uses python 3.13. An ARG is only set during the build, so users still see notices. +ARG CONDA_NUMBER_CHANNEL_NOTICES=0 +# ENV PATH="${PATH}:${CONDA_ENV_HOME}/bin:${CONDA_HOME}/bin" +ENV PATH="${PATH}:${CONDA_HOME}/bin" + +# Install, patch, clean and chown in ONE layer. A `conda clean` or `chown -R` in a later RUN does +# not shrink this layer, it writes a second full copy of /opt/conda on top of it (~0.4GB for the +# installer's package cache, ~0.6GB for the chown). +# - conda tos: have to accept the conda terms of service to be able to install packages +# - the Miniconda py313_26.7.1 installer ships these vulnerable packages in the base env: +# - urllib3 2.7.0 (GHSA-vxq7-64xx-v4gw, GHSA-8988-9cw3-xx77, fixed in 2.8.0) +# - anyio 4.12.1 (GHSA-82r6-8w77-94w6, fixed in 4.14.2) +# - pyjwt 2.13.0 (GHSA-ffc3-869f-jxw9, GHSA-w2cx-738m-mc7w, GHSA-r6x4-923q-g947, GHSA-p4g4-x82p-q773, +# GHSA-9v7f-9g4p-ffgj, GHSA-9j54-fg26-wv3r, fixed in 2.14.0) +RUN curl -so $HOME/miniconda.sh $CONDA_INSTALLER \ + && chmod +x $HOME/miniconda.sh \ + && $HOME/miniconda.sh -b -p $CONDA_HOME \ + && rm $HOME/miniconda.sh \ + && conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/main \ + && conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/r \ + && conda install -n base -y "urllib3>=2.8.0" "anyio>=4.14.2" "pyjwt>=2.14.0" "cryptography>=50.0.0" \ + && conda clean -afy \ + && chown -R $USER:users $CONDA_HOME + +# In order to override the default kernel, the conda environment must be named 'python3' +ENV CONDA_ENV_NAME=python3 +# The env must live OUTSIDE /home/jupyter: Leonardo mounts the runtime's persistent disk over the +# notebooks dir (jupyter-docker-compose-gce.yaml: "/mnt/disks/work:${NOTEBOOKS_DIR}", NOTEBOOKS_DIR=/home/jupyter), +# which hides anything the image puts there. With the env at /home/jupyter/.envs/python3 every kernel died +# on Terra with "/home/jupyter/.envs/python3/bin/python: No such file or directory". +# $CONDA_HOME/envs is conda's standard envs dir, so `conda activate python3` also finds it by name. +# ENV CONDA_ENV_HOME=$USER_HOME/.envs/$CONDA_ENV_NAME +ENV CONDA_ENV_HOME=$CONDA_HOME/envs/$CONDA_ENV_NAME +ENV CONDA_FILES=$CONDA_HOME/custom + +# Copy over the conda environment files +COPY --chown=jupyter:users conda/ $CONDA_FILES + +# Set up the path to the user python from conda +ENV BASE_PYTHON_PATH=$CONDA_HOME/bin/python$PYTHON_VERSION +# Tell conda to NOT write bite code (aka these.pyc files) +ENV PYTHONDONTWRITEBYTECODE=true + +# Create the conda environment that will be used by the jupyter user. +# +# Then upgrade urllib3 in it for GHSA-vxq7-64xx-v4gw, GHSA-8988-9cw3-xx77, GHSA-qccp-gfcp-xxvc and +# GHSA-38jv-5279-wg99 (fixed in urllib3 2.8.0, no 1.26.x backport). The env otherwise resolves to +# urllib3 1.26.20 because getm 0.0.5 (a terra-notebook-utils dependency with no newer release) pins +# requests<2.30, and requests<2.30 pins urllib3<1.27. getm and terra-notebook-utils both pass +# Retry(method_whitelist=...), which urllib3 2.x removed; rename it to allowed_methods (available +# since urllib3 1.26) so they import on 2.x. --no-deps skips pip's resolver, so it does not report +# getm's requests<2.30 pin as a conflict; requests' other dependencies (charset-normalizer, idna, +# certifi) are already installed at compatible versions, and the import check below verifies it. +# --root-user-action=ignore: installing into the env as root during the build is intended. +# Remove the patch once getm / terra-notebook-utils publish urllib3 2 compatible releases. +RUN conda env create --prefix $CONDA_ENV_HOME --file $CONDA_FILES/conda-environment.yaml \ + && SITE_PACKAGES=$($CONDA_ENV_HOME/bin/python -c "import sysconfig; print(sysconfig.get_paths()['purelib'])") \ + && sed -i 's/method_whitelist=/allowed_methods=/' \ + $SITE_PACKAGES/getm/http.py \ + $SITE_PACKAGES/terra_notebook_utils/table.py \ + && ! grep -rq "method_whitelist" --include='*.py' $SITE_PACKAGES/getm $SITE_PACKAGES/terra_notebook_utils \ + && $CONDA_ENV_HOME/bin/python -m pip install --no-cache-dir --no-deps --root-user-action=ignore --upgrade "urllib3>=2.8.0" "requests>=2.32.4" \ + && $CONDA_ENV_HOME/bin/python -c "import urllib3, requests, getm.http, terra_notebook_utils.table, firecloud.api; assert int(urllib3.__version__.split('.')[0]) >= 2" \ + # Register the conda env as the 'python3' kernel + && $CONDA_ENV_HOME/bin/python -m ipykernel install --name=$CONDA_ENV_NAME \ + # Remove packages tarballs and python bytecode files from the image + && conda clean -afy \ + && rm $CONDA_FILES/conda-environment.yaml \ + # Make sure the USER owns the env (created as root after /opt/conda was chowned above) + && chown -R $USER:users $CONDA_ENV_HOME + +############################## +# Setup UV Environment for Jupyter +############################## +# Using UV (Universal Virtualenv) to create a virtual environment +# UV is used in place of poetry for speed and simplicity. + +# NOTE: this is for the environment the jupyter server will be running in, +# separate from the jupyter user's conda environment. +COPY uv.lock . +COPY pyproject.toml . + +# Setup UV environment variables +# - tells uv to copy the Python files into the container from the cache mount, +# - tell uv to byte-compile packages for faster application startups, +# - don't seed venv, we need to install separately +# - don't cache to keep the image size small +ENV UV_LINK_MODE=copy \ + UV_COMPILE_BYTECODE=1 \ + UV_VENV_SEED=false \ + UV_NO_CACHE=true + +# Download the latest installer +ADD https://astral.sh/uv/install.sh /uv-installer.sh +RUN sh /uv-installer.sh && rm /uv-installer.sh + +# Add local bin to PATH for uv +ENV PATH="/root/.local/bin/:$PATH" + +ENV JUPYTER_HOME=/etc/jupyter +ENV UNDERSCORE_VERSION=1.13.8 + +# Create a virtual environment and install jupyter packages +# setuptools and wheel are required for some of the jupyter extensions +# chown in the same layer for the same reason as /opt/conda above. +RUN uv venv $JUPYTER_HOME --python $BASE_PYTHON_PATH \ + && source $JUPYTER_HOME/bin/activate \ + && uv pip install wheel \ + && uv pip install setuptools \ + && uv pip install -r pyproject.toml --no-cache --no-build-isolation \ + # GHSA-v638-q856-grg8 / CVE-2023-39663: nbclassic bundles MathJax 2.7.9, and no MathJax 2.x release + # fixes it. Delete it in this layer, so no layer of the image contains it. jupyter_server_config.py + # sets c.NotebookApp.enable_mathjax = False so the classic UI does not request the missing files. + # Notebook 7 and JupyterLab are unaffected: they bundle MathJax 3 (mathjax-full 3.2.2). + && rm -rf $JUPYTER_HOME/lib/python$PYTHON_VERSION/site-packages/nbclassic/static/components/MathJax \ + && ! find $JUPYTER_HOME -name MathJax.js | grep -q . \ + # GHSA-qpx9-hpmf-5gmw: nbclassic 1.3.3 (the latest) bundles underscore 1.13.7, fixed in 1.13.8 (a patch release + # with the same API). Replace the copy in static/components, which is the one with a package.json that scanners + # match. Remove this once nbclassic ships underscore >= 1.13.8. + # Installed with npm rather than extracted with tar, for the reason given at the npm patches above. + && NBC_UNDERSCORE=$JUPYTER_HOME/lib/python$PYTHON_VERSION/site-packages/nbclassic/static/components/underscore \ + && npm install --silent --no-save --no-package-lock --ignore-scripts --prefix /tmp/underscore underscore@$UNDERSCORE_VERSION \ + && rm -rf $NBC_UNDERSCORE && mkdir -p $NBC_UNDERSCORE \ + && cp -r /tmp/underscore/node_modules/underscore/{package.json,README.md,LICENSE,underscore-min.js,underscore-min.js.map,modules} $NBC_UNDERSCORE/ \ + && rm -rf /tmp/underscore && npm cache clean --force \ + && test "$(node -p "require('$NBC_UNDERSCORE/package.json').version")" = "$UNDERSCORE_VERSION" \ + # Remove default jupyter kernel (to force use of the conda python kernel) + && $JUPYTER_HOME/bin/jupyter kernelspec remove python3 -y \ + # Cleanup + && rm uv.lock pyproject.toml \ + && chown -R $USER:users $JUPYTER_HOME + +# add jupyter to path +ENV PATH="${PATH}:${JUPYTER_HOME}/bin" + +# ####################### +# # Terra-specific Utilities +# ####################### \ + +# Copy over utility scripts and config files +ENV JUPYTER_SCRIPTS=$JUPYTER_HOME/scripts +ENV JUPYTER_CUSTOM=$JUPYTER_HOME/custom +ENV JUPYTER_EXTENSIONS=$JUPYTER_SCRIPTS/extension +ENV JUPYTER_KERNEL=$JUPYTER_SCRIPTS/kernel + +COPY --chown=jupyter:users scripts $JUPYTER_HOME/scripts +COPY --chown=jupyter:users custom $JUPYTER_HOME/custom +COPY --chown=jupyter:users jupyter_server_config.py $JUPYTER_HOME +# Settings-free placeholder: Leonardo's init script still runs `sed -i ... /etc/jupyter/jupyter_notebook_config.py` +# and aborts the runtime startup if the file is missing. See the comments in the file. +COPY --chown=jupyter:users jupyter_notebook_config.py $JUPYTER_HOME + +# Put the custom modules on the jupyter server's import path. jupyter_server_config.py +# refers to jupyter_delocalize and jupyter_localize_extension by module name, and neither +# is pip-installed, so without this the server fails at startup with +# "could not be imported". A .pth scopes the path to this venv only, leaving the user's +# conda kernel untouched (which a global PYTHONPATH would not). +# +# Ownership of $JUPYTER_HOME and $CONDA_HOME is set when they are created; terra-base's +# `chown -R $JUPYTER_HOME $CONDA_HOME` here duplicated both trees (~0.9GB) into a new layer. +# Only fix up anything still not owned by the user, and make the scripts executable. +RUN echo "$JUPYTER_CUSTOM" > $JUPYTER_HOME/lib/python$PYTHON_VERSION/site-packages/terra-custom.pth \ + && find $JUPYTER_HOME $CONDA_HOME ! -user $USER -exec chown -h $USER:users {} + \ + && find $JUPYTER_EXTENSIONS $JUPYTER_KERNEL -name '*.sh' -type f -exec chmod +x {} + \ + && chmod +x $JUPYTER_SCRIPTS/run-jupyter.sh + +# Setup the jupyter (python3) kernel. The R kernel is registered by terra-jupyter-r after it installs IRkernel. +ENV JUPYTER_KERNELSPEC_DIR=/usr/local/share/jupyter/ +RUN chown -R $USER:users $JUPYTER_KERNELSPEC_DIR \ + # You can get kernel directory by running `jupyter kernelspec list` + && $JUPYTER_KERNEL/kernelspec.sh $JUPYTER_KERNEL $JUPYTER_KERNELSPEC_DIR/kernels + +# Create the welder user # The welder uid is consistent with the Welder docker definition here: # https://github.com/DataBiosphere/welder/blob/master/project/Settings.scala # Adding welder-user to the Jupyter container isn't strictly required, but it makes welder-added # files display nicer when viewed in a terminal. ENV WELDER_USER=welder-user +# This UID must stay consistent with the UID defined in Welder ENV WELDER_UID=1001 RUN useradd -m -s /bin/bash -N -u $WELDER_UID $WELDER_USER -# ensure this matches c.NotebookApp.port in jupyter_notebook_config.py -ENV JUPYTER_PORT=8000 -ENV JUPYTER_HOME=/etc/jupyter +# Add an empty file to indicate that this is a terra-base image with a separate jupyer server environment +# Need a flag to check in the startup scripts to know whether to use the conda environment jupyter +RUN touch /etc/jupyter/.terra-base-marker -RUN pip3 -V \ - # When we upgraded from jupyter 5.7.8 to 6.1.1, we broke terminal button on terra-ui. - # Hence, make sure to manually test out "launch terminal" button (the button in the green bar next to start and stop buttons) - # to make sure we don't accidentally break it every time we upgrade notebook version until we figure out an automation test for this - && pip3 install python-datauri \ - && pip3 install jupyter_contrib_nbextensions==0.7.0 \ - && pip3 install jupyter_nbextensions_configurator==0.6.3 \ - && pip3 install markupsafe==2.1.2 \ - && pip3 install traitlets==5.9.0 \ - # Avoid broken lower versions: https://github.com/jupyter/nbconvert/pull/1624, pinning to latest known working version on terra - && pip3 install "nbconvert>=7.7.3" \ - # Avoid notebook extension issues - && pip3 install "nbclassic<0.5" \ - # for jupyter_delocalize.py and jupyter_notebook_config.py - # DO NOT CHANGE OR UNPIN NOTEBOOK OR JUPYTERLAB-SERVER! When trying with 6.5.5 and 2.24.0 notebook commands could not find the notebook config file - && pip3 install jupyter_core==5.3.1 \ - && pip3 install jupyter-events==0.7.0 \ - && pip3 install jupyterlab==3.4.8 \ - && pip3 install notebook==6.5.4 \ - && pip3 install jupyter_server==1.24.0 \ - && pip3 install jupyterlab-server==2.23.0 \ - && pip3 install notebook_shim==0.2.3 \ - && pip3 install jupyter_server_proxy==4.0.0 \ - && pip3 install jupyter_server_terminals==0.4.4 \ - && pip3 install jupyterlab_git==0.42.0 \ - && pip3 install jupyterlab-pygments==0.2.2 \ - && pip3 install jupyterlab-widgets==3.0.8 \ - && pip3 install jupytext==1.15.0 \ - && pip3 install requests \ - && pip3 install firecloud \ - && pip3 install terra-notebook-utils==0.13.0 \ - && pip3 install crcmod \ - # For gcloud alpha storage support. - && pip3 install google-crc32c --target /usr/lib/google-cloud-sdk/lib/third_party \ - && pip3 install cromshell==2.0.0 \ - # This plugin is part of the base image and doesn't support our older Jupyter version - && pip3 uninstall -y dataproc_jupyter_plugin - -# to allow file-saving in different formats -# toc2 is not compatible with versions of notebooks over 5.x - deprecated -# RUN jupyter nbextension enable toc2/main - -# tmp hack min-5 -# I'm not installing jupyterlab and I can't update init-actions.sh to not access it -RUN mkdir -p /usr/local/share/jupyter/lab +# Make sure that the jupyter user will have access to the jupyter path in the working directory +EXPOSE $JUPYTER_PORT +WORKDIR $USER_HOME # make pip install to a user directory, instead of a system directory which requires root. # this is useful so `pip install` commands can be run in the context of a notebook. ENV PIP_USER=true -# When using PIP_USER=true packages are installed into Python site.USER_BASE, which is '/home/jupyter' for this system. -# Append '/home/jupyter/.local/bin' to PATH -# pip docs: https://pip.pypa.io/en/stable/reference/pip_install/#cmdoption-user -ENV PATH="${PATH}:${HOME}/.local/bin:${HOME}/packages/bin" - -####################### -# Utilities -####################### - -COPY scripts $JUPYTER_HOME/scripts -COPY custom $JUPYTER_HOME/custom -COPY jupyter_notebook_config.py $JUPYTER_HOME - -# copy workspace_cromwell.py script and make it runnable by all users -# TODO why not move this script into this repo? -RUN curl -o /usr/local/bin/workspace_cromwell.py https://raw.githubusercontent.com/broadinstitute/cromwhelm/1ceedf89587cffd355f37401b179001f029f77ed/scripts/workspace_cromwell.py \ - && chmod +x /usr/local/bin/workspace_cromwell.py - -RUN chown -R $USER:users $JUPYTER_HOME \ - && find $JUPYTER_HOME/scripts -name '*.sh' -type f | xargs chmod +x \ - # You can get kernel directory by running `jupyter kernelspec list` - && $JUPYTER_HOME/scripts/kernel/kernelspec.sh $JUPYTER_HOME/scripts/kernel /opt/conda/share/jupyter/kernels - -# Run a `jupyter lab build` during the Docker image build step so users don't have to do it on their own -# The webpack build during `jupyter lab build` is memory intensive so give it access to more memory as well -RUN NODE_OPTIONS=--max-old-space-size=4096 jupyter lab build --minimize=True - USER $USER -EXPOSE $JUPYTER_PORT -WORKDIR $HOME # Note: this entrypoint is provided for running Jupyter independently of Leonardo. # When Leonardo deploys this image onto a cluster, the entrypoint is overwritten to enable # additional setup inside the container before execution. Jupyter execution occurs when the -# Leonardo init-actions.sh script uses 'docker exec' to call run-jupyter.sh. -ENTRYPOINT ["/opt/conda/bin/jupyter", "notebook"] +# init-actions.sh script uses 'docker exec' to call run-jupyter.sh. +ENTRYPOINT ["/etc/jupyter/bin/jupyter", "notebook"] diff --git a/terra-jupyter-base/README.md b/terra-jupyter-base/README.md index 446559e1..f466b257 100644 --- a/terra-jupyter-base/README.md +++ b/terra-jupyter-base/README.md @@ -3,18 +3,33 @@ This repo contains the terra-jupyter-base image that is compatible with notebook service in [Terra]("https://app.terra.bio/") called Leonardo. For example, use `us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:{version}` in terra. ## Image contents - -The terra-jupyter-base extends the [Ubuntu base image]("https://github.com/tianon/docker-brew-ubuntu-core/blob/9db8c72dd02e8f9fd5dba82ff9266174b088e2e6/bionic/Dockerfile") by including the following: - +- Ubuntu 26.04 (`nvidia/cuda:13.4.2-base-ubuntu26.04`) - OS prerequisites -- google-cloud-sdk -- Python 3.10 -- pip +- google-cloud-cli (gcloud, gsutil, bq) +- Python 3.13 (Miniconda), with three separate environments: + - `/opt/conda/envs/python3` (`$CONDA_ENV_HOME`): the user's conda env, which the `python3` notebook kernel runs + - `/etc/jupyter`: an isolated uv venv for the Jupyter server, from [pyproject.toml](./pyproject.toml) / [uv.lock](./uv.lock) + - `/opt/conda`: conda base + - Ubuntu's own `/usr/bin/python3` is 3.14; it is not used for notebooks +- pip, in the user's conda env (there is no system `pip3`). `PIP_USER=true`, so `pip install` in a notebook installs to `~/.local` - conda -- Jupyter & JupyterLab +- Jupyter Notebook 7, nbclassic & JupyterLab - Leonardo customizations/extensions -- Terra python client library ([FISS](https://github.com/broadinstitute/fiss)) -- OpenJDK 11 +- Terra python client libraries ([FISS](https://github.com/broadinstitute/fiss), [terra-notebook-utils](https://github.com/DataBiosphere/terra-notebook-utils)) +- R and the CRAN apt repository (`r-base`, `r-base-dev`); the R kernel is added by [terra-jupyter-r](../terra-jupyter-r) +- OpenJDK 25 + +## Installing Python packages in images built on this one + +Install into the user's conda env, not with a bare `pip`/`pip3` (that resolves to conda base): + +```dockerfile +RUN $CONDA_ENV_HOME/bin/python -m pip install +# or, from a pyproject.toml +RUN uv pip install --python $CONDA_ENV_HOME/bin/python -r pyproject.toml +``` + +The `python3` kernel is registered in `/usr/local/share/jupyter/kernels`. To see the complete contents of this image please see the [Dockerfile](./Dockerfile). diff --git a/terra-jupyter-base/conda/conda-environment.yaml b/terra-jupyter-base/conda/conda-environment.yaml new file mode 100644 index 00000000..3226fd5d --- /dev/null +++ b/terra-jupyter-base/conda/conda-environment.yaml @@ -0,0 +1,15 @@ +name: python3 +channels: + - defaults +dependencies: + - pip=26.2.1 + - python=3.13 + - ipykernel + # Terra client libraries, for the user's notebook kernel rather than the + # jupyter server env in pyproject.toml. Neither has a conda package, and both + # publish sdists only, so they are compiled here against the build-essential + # and zlib1g-dev installed earlier in the Dockerfile (terra-notebook-utils + # pulls in bgzip, which needs zlib.h and OpenMP). + - pip: + - firecloud==0.16.39 + - terra-notebook-utils==0.16.2 diff --git a/terra-jupyter-base/conda/conda_init.txt b/terra-jupyter-base/conda/conda_init.txt new file mode 100644 index 00000000..59e0cab3 --- /dev/null +++ b/terra-jupyter-base/conda/conda_init.txt @@ -0,0 +1,17 @@ +# >>> conda initialize >>> +# !! Contents within this block are managed by 'conda init' !! +# python3 is the name of the conda environment, must match environment name in environment.yml +# The env is at /opt/conda/envs/python3 (not under /home/jupyter, which Leonardo mounts over); +# conda itself is the base install at /opt/conda. +__conda_setup="$('/opt/conda/bin/conda' 'shell.bash' 'hook' 2> /dev/null)" +if [ $? -eq 0 ]; then +eval "$__conda_setup" +else +if [ -f "/opt/conda/etc/profile.d/conda.sh" ]; then +. "/opt/conda/etc/profile.d/conda.sh" +else +export PATH="/opt/conda/envs/python3/bin:$PATH" +fi +fi +unset __conda_setup +# <<< conda initialize <<< \ No newline at end of file diff --git a/terra-jupyter-base/custom/jupyter_delocalize.py b/terra-jupyter-base/custom/jupyter_delocalize.py index e0e77bc9..ded62c4d 100644 --- a/terra-jupyter-base/custom/jupyter_delocalize.py +++ b/terra-jupyter-base/custom/jupyter_delocalize.py @@ -3,7 +3,7 @@ import os import requests import tornado -from notebook.services.contents.largefilemanager import LargeFileManager +from jupyter_server.services.contents.largefilemanager import LargeFileManager METADATA_TTL = timedelta(minutes=5) diff --git a/terra-jupyter-base/custom/jupyter_localize_extension.py b/terra-jupyter-base/custom/jupyter_localize_extension.py index bd7221ee..9a247f12 100644 --- a/terra-jupyter-base/custom/jupyter_localize_extension.py +++ b/terra-jupyter-base/custom/jupyter_localize_extension.py @@ -5,11 +5,11 @@ import tornado from tornado import gen from tornado.web import HTTPError -from notebook.base.handlers import IPythonHandler -from notebook.utils import url_path_join +from jupyter_server.base.handlers import JupyterHandler +from jupyter_server.utils import url_path_join from datauri import DataURI -class LocalizeHandler(IPythonHandler): +class LocalizeHandler(JupyterHandler): def _sanitize(self, pathstr): """Sanitizes paths. Handles local paths, gs: URIs, and data: URIs.""" # return gs or data uris as is @@ -140,10 +140,14 @@ def post(self): self.set_status(200) self.finish() -def load_jupyter_server_extension(nb_server_app): +def _load_jupyter_server_extension(server_app): """Entrypoint for the Jupyter extension.""" - web_app = nb_server_app.web_app + web_app = server_app.web_app host_pattern = '.*$' route_pattern = url_path_join(web_app.settings['base_url'], '/api/localize') web_app.add_handlers(host_pattern, [(route_pattern, LocalizeHandler)]) - nb_server_app.log.info('initialized jupyter_localize_extension') + server_app.log.info('initialized jupyter_localize_extension') + +# jupyter-server 2.x looks for the underscore-prefixed name; the old name is kept +# as an alias so anything still calling it directly keeps working. +load_jupyter_server_extension = _load_jupyter_server_extension diff --git a/terra-jupyter-base/jupyter_notebook_config.py b/terra-jupyter-base/jupyter_notebook_config.py old mode 100755 new mode 100644 index c9f94268..bbfffbce --- a/terra-jupyter-base/jupyter_notebook_config.py +++ b/terra-jupyter-base/jupyter_notebook_config.py @@ -1,44 +1,13 @@ -# adapted from https://github.com/jupyter/docker-stacks/blob/master/base-notebook/jupyter_notebook_config.py -# Note: this file also lives in the Leonardo repo here: -# https://github.com/DataBiosphere/leonardo/blob/develop/http/src/main/resources/jupyter/jupyter_notebook_config.py -# If you change this please keep the other version consistent as well. - -import os - -c = get_config() - -if os.environ.get('JUPYTER_DEBUG_LOGGING') == 'true': - c.Application.log_level = 'DEBUG' - -c.NotebookApp.ip = '0.0.0.0' -c.NotebookApp.port = 8000 -c.NotebookApp.open_browser = False - -c.NotebookApp.token = '' -c.NotebookApp.disable_check_xsrf = True #see https://github.com/nteract/hydrogen/issues/922 -c.NotebookApp.allow_origin = '*' - -c.NotebookApp.terminado_settings={'shell_command': ['bash']} - -if 'GOOGLE_PROJECT' in os.environ and 'CLUSTER_NAME' in os.environ: - fragment = '/' + os.environ['GOOGLE_PROJECT'] + '/' + os.environ['CLUSTER_NAME'] + '/' -else: - fragment = '/' - -c.NotebookApp.base_url = '/notebooks' + fragment - -# This is also specified in run-jupyter.sh -c.NotebookApp.nbserver_extensions = { - 'jupyter_localize_extension': True -} - -c.NotebookApp.kernel_manager_class = 'notebook.services.kernels.kernelmanager.AsyncMappingKernelManager' - -mgr_class = 'DelocalizingContentsManager' -if os.environ.get('WELDER_ENABLED') == 'true': - mgr_class = 'WelderContentsManager' -c.NotebookApp.contents_manager_class = 'jupyter_delocalize.' + mgr_class - -c.NotebookApp.tornado_settings = { - 'static_url_prefix':'/notebooks' + fragment + 'static/' -} +# Compatibility placeholder for Leonardo. Intentionally contains no settings. +# +# The jupyter configuration for this image lives in jupyter_server_config.py (renamed from this file +# when the image moved to Jupyter Server 2 / Notebook 7, which reads c.ServerApp settings from there). +# +# Leonardo's GCE init script (leonardo: http/src/main/resources/init-resources/gce-init.sh) still runs +# sed -i '/^# to mount there as it effectively deletes existing files on the image/,+5d' /etc/jupyter/jupyter_notebook_config.py +# before starting Jupyter. That sed is a no-op for current images, but it fails with +# "can't read ... No such file or directory" when this file is missing, which aborts the startup script +# before run-jupyter.sh and the runtime times out. Keep this file until Leonardo drops that line. +# +# Notebook 7 also loads jupyter_notebook_config.* files, so do not add settings here; put them in +# jupyter_server_config.py. diff --git a/terra-jupyter-base/jupyter_server_config.py b/terra-jupyter-base/jupyter_server_config.py new file mode 100755 index 00000000..6ee30534 --- /dev/null +++ b/terra-jupyter-base/jupyter_server_config.py @@ -0,0 +1,59 @@ +# adapted from https://github.com/jupyter/docker-stacks/blob/master/base-notebook/jupyter_notebook_config.py +# Note: this file also lives in the Leonardo repo here: +# https://github.com/DataBiosphere/leonardo/blob/develop/http/src/main/resources/jupyter/jupyter_notebook_config.py +# If you change this please keep the other version consistent as well. +# +# Renamed from jupyter_notebook_config.py and ported from c.NotebookApp to c.ServerApp: +# Notebook 7 runs on Jupyter Server, which only reads jupyter_server_config.py and no +# longer defines the NotebookApp traits. Under the old name/class these settings were +# silently dropped and the server came up on a random loopback port with a random token. + +import os + +c = get_config() + +if os.environ.get('JUPYTER_DEBUG_LOGGING') == 'true': + c.Application.log_level = 'DEBUG' + +c.ServerApp.ip = '0.0.0.0' +c.ServerApp.port = 8000 +c.ServerApp.open_browser = False + +# ServerApp.token is deprecated in jupyter-server 2.x in favor of the identity provider +c.IdentityProvider.token = '' +c.ServerApp.disable_check_xsrf = True #see https://github.com/nteract/hydrogen/issues/922 +c.ServerApp.allow_origin = '*' + +c.ServerApp.terminado_settings={'shell_command': ['bash']} + +if 'GOOGLE_PROJECT' in os.environ and 'CLUSTER_NAME' in os.environ: + fragment = '/' + os.environ['GOOGLE_PROJECT'] + '/' + os.environ['CLUSTER_NAME'] + '/' +else: + fragment = '/' + +c.ServerApp.base_url = '/notebooks' + fragment + +# This is also specified in run-jupyter.sh +c.ServerApp.jpserver_extensions = { + 'jupyter_localize_extension': True +} + +# Only override the contents manager when Welder is in play. The old non-Welder +# default, jupyter_delocalize.DelocalizingContentsManager, was removed in #252 and +# naming it here makes jupyter-server fail at startup with +# "'jupyter_delocalize.DelocalizingContentsManager' could not be imported". +# Without Welder, jupyter-server's own AsyncLargeFileManager is the right default. +if os.environ.get('WELDER_ENABLED') == 'true': + c.ServerApp.contents_manager_class = 'jupyter_delocalize.WelderContentsManager' + +c.ServerApp.tornado_settings = { + 'static_url_prefix':'/notebooks' + fragment + 'static/' +} + +# The classic UI (nbclassic, at /nbclassic) is configured through c.NotebookApp, which Notebook 7 no +# longer reads. Its bundled MathJax 2.7.9 is removed from the image (GHSA-v638-q856-grg8), so don't load +# it: LaTeX shows as plain text in the classic UI. Notebook 7 and JupyterLab render math with MathJax 3. +c.NotebookApp.enable_mathjax = False + +# so that the default kernel can be overridden by the conda environment +c.KernelSpecManager.ensure_native_kernel = False diff --git a/terra-jupyter-base/pyproject.toml b/terra-jupyter-base/pyproject.toml new file mode 100644 index 00000000..b555efc6 --- /dev/null +++ b/terra-jupyter-base/pyproject.toml @@ -0,0 +1,49 @@ +[project] +name = "terra-jupyter-base" +version = "1.3.2" +description = "Minimal Jupyter environment for Terra notebooks" +readme = "README.md" +# Note TensorFlow does not support 3.14 +requires-python = ">=3.13, <3.14" +# These are the dependencies of the isolated jupyter *server* environment +# (/etc/jupyter), NOT the jupyter user's conda environment. Notebook packages +# belong in conda/conda-environment.yaml. +dependencies = [ + "ipykernel>=7.4.0", + "jupyter-core==5.9.1", + "jupyter-server==2.21.1", + "jupyter-server-proxy==4.6.0", + "jupyterlab==4.6.4", + "jupyterlab-server==2.28.1", + # Classic Notebook 6 UI alongside Notebook 7, served at /nbclassic (or `jupyter nbclassic`). + # Installing it auto-enables the server extension; see + # https://nbclassic.readthedocs.io/en/latest/nbclassic.html#nbclassicusage + # Its extensions are managed with `jupyter nbclassic-extension`; it does NOT provide + # `jupyter nbextension`, so the scripts in scripts/extension no longer call that. + # nbclassic bundles MathJax 2.7.x (GHSA-v638-q856-grg8 / CVE-2023-39663, ReDoS, no patched 2.x + # release). The Dockerfile deletes it and jupyter_server_config.py disables MathJax in nbclassic. + "nbclassic>=1.3.3", + "nbconvert>=7.17.2", + "nbstripout>=0.9.1", + "notebook==7.6.3", + "python-datauri>=3.0.2", + "requests>=2.34.2", + # distutils left the stdlib in 3.12, so custom/jupyter_localize_extension.py's + # `distutils.util.strtobool` now resolves through the shim that setuptools + # installs via distutils-precedence.pth. Declared here so the shim is locked + # rather than pulled in as a side effect of `uv pip install setuptools`. + "setuptools>=80.9.0", + "tornado>=6.5.10", + "traitlets==5.16.1", +] + +[tool.uv] +# The image is only ever built for linux/amd64; lock for that even when `uv lock` +# runs on an Apple Silicon workstation. +required-environments = ["sys_platform == 'linux' and platform_machine == 'x86_64'"] +# This project only pins an environment, it is never built or installed as a package. +package = false +build-constraint-dependencies = [ + "setuptools>=70.3.0", + "wheel>=0.45.1", +] diff --git a/terra-jupyter-base/scripts/extension/install_jupyter_contrib_nbextensions.sh b/terra-jupyter-base/scripts/extension/install_jupyter_contrib_nbextensions.sh old mode 100644 new mode 100755 index 378f4575..7788ef1b --- a/terra-jupyter-base/scripts/extension/install_jupyter_contrib_nbextensions.sh +++ b/terra-jupyter-base/scripts/extension/install_jupyter_contrib_nbextensions.sh @@ -3,9 +3,15 @@ set -e # installs jupyter_contrib_nbextensions https://github.com/ipython-contrib/jupyter_contrib_nbextensions # also installs the jupyter_nbextensions_configurator https://github.com/Jupyter-contrib/jupyter_nbextensions_configurator -sudo -E -u jupyter /opt/conda/bin/jupyter nbextensions_configurator enable --user -sudo -E -u jupyter /opt/conda/bin/jupyter contrib nbextension install --user -sudo -E -u jupyter /opt/conda/bin/jupyter nbextension enable toc2/main -sudo -E -u jupyter /opt/conda/bin/jupyter nbextension enable codefolding/main -sudo -E -u jupyter /opt/conda/bin/jupyter nbextension enable collapsible_headings/main +# +# Every step below needs `jupyter nbextension`, which does not exist in Notebook 7 (classic nbextensions +# are not supported), and jupyter_contrib_nbextensions / the configurator are not installed in the image. +# Notebook 7 has a built-in table of contents and collapsible headings. Exit 0 so callers don't fail. +echo "install_jupyter_contrib_nbextensions.sh: classic nbextensions are not supported on Notebook 7, skipping" +exit 0 +# sudo -E -u jupyter /etc/jupyter/bin/jupyter nbextensions_configurator enable --sys-prefix +# sudo -E -u jupyter /etc/jupyter/bin/jupyter contrib nbextension install --sys-prefix +# sudo -E -u jupyter /etc/jupyter/bin/jupyter nbextension enable toc2/main --sys-prefix +# sudo -E -u jupyter /etc/jupyter/bin/jupyter nbextension enable codefolding/main --sys-prefix +# sudo -E -u jupyter /etc/jupyter/bin/jupyter nbextension enable collapsible_headings/main --sys-prefix diff --git a/terra-jupyter-base/scripts/extension/jupyter_install_combined_extension.sh b/terra-jupyter-base/scripts/extension/jupyter_install_combined_extension.sh old mode 100644 new mode 100755 index 396a3fea..8a298cd3 --- a/terra-jupyter-base/scripts/extension/jupyter_install_combined_extension.sh +++ b/terra-jupyter-base/scripts/extension/jupyter_install_combined_extension.sh @@ -8,7 +8,8 @@ if [ -n "$1" ]; then mkdir ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} tar -xzf ${JUPYTER_EXTENSION} -C${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} pip3 install -e ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} - sudo -E -u jupyter /opt/conda/bin/jupyter serverextension enable --py ${JUPYTER_EXTENSION_NAME} - sudo -E -u jupyter /opt/conda/bin/jupyter nbextension install --py ${JUPYTER_EXTENSION_NAME} --user - sudo -E -u jupyter /opt/conda/bin/jupyter nbextension enable --py ${JUPYTER_EXTENSION_NAME} + sudo -E -u jupyter /etc/jupyter/bin/jupyter serverextension enable --py ${JUPYTER_EXTENSION_NAME} --sys-prefix + # `jupyter nbextension` does not exist in Notebook 7 (classic nbextensions are not supported). + # sudo -E -u jupyter /etc/jupyter/bin/jupyter nbextension install --py ${JUPYTER_EXTENSION_NAME} --sys-prefix + # sudo -E -u jupyter /etc/jupyter/bin/jupyter nbextension enable --py ${JUPYTER_EXTENSION_NAME} --sys-prefix fi diff --git a/terra-jupyter-base/scripts/extension/jupyter_install_lab_extension.sh b/terra-jupyter-base/scripts/extension/jupyter_install_lab_extension.sh old mode 100644 new mode 100755 diff --git a/terra-jupyter-base/scripts/extension/jupyter_install_notebook_extension.sh b/terra-jupyter-base/scripts/extension/jupyter_install_notebook_extension.sh old mode 100644 new mode 100755 index ef038e2a..abdee378 --- a/terra-jupyter-base/scripts/extension/jupyter_install_notebook_extension.sh +++ b/terra-jupyter-base/scripts/extension/jupyter_install_notebook_extension.sh @@ -1,15 +1,23 @@ #!/bin/bash set -e -if [ -n "$1" ]; then - JUPYTER_EXTENSION=$1 - JUPYTER_EXTENSION_NAME=`basename ${JUPYTER_EXTENSION%%.*}` - mkdir -p ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} - if [[ ${JUPYTER_EXTENSION} == *'.tar.gz' ]]; then - tar -xzf ${JUPYTER_EXTENSION} -C${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} - else - mv ${JUPYTER_EXTENSION} ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME}/main.js - fi - sudo -E -u jupyter /opt/conda/bin/jupyter nbextension install ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME}/ --user - sudo -E -u jupyter /opt/conda/bin/jupyter nbextension enable ${JUPYTER_EXTENSION_NAME}/main -fi +# DISABLED: classic notebook extensions (nbextensions) are not supported by Notebook 7, which has no +# `jupyter nbextension` command. Leonardo calls this script for /etc/jupyter/jupyter-iframe-extension.js +# on every runtime start; failing here aborted Leonardo's startup script before Jupyter was started, +# so the runtime timed out. Exit 0 so startup continues. The nbclassic UI (/nbclassic) is installed, +# but its extensions are managed with `jupyter nbclassic-extension`, not this script. +echo "jupyter_install_notebook_extension.sh: classic nbextensions are not supported on Notebook 7, skipping ${1:-}" +exit 0 + +# if [ -n "$1" ]; then +# JUPYTER_EXTENSION=$1 +# JUPYTER_EXTENSION_NAME=`basename ${JUPYTER_EXTENSION%%.*}` +# mkdir -p ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} +# if [[ ${JUPYTER_EXTENSION} == *'.tar.gz' ]]; then +# tar -xzf ${JUPYTER_EXTENSION} -C${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} +# else +# mv ${JUPYTER_EXTENSION} ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME}/main.js +# fi +# sudo -E -u jupyter /etc/jupyter/bin/jupyter nbextension install ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME}/ --sys-prefix +# sudo -E -u jupyter /etc/jupyter/bin/jupyter nbextension enable ${JUPYTER_EXTENSION_NAME}/main --sys-prefix +# fi diff --git a/terra-jupyter-base/scripts/extension/jupyter_install_server_extension.sh b/terra-jupyter-base/scripts/extension/jupyter_install_server_extension.sh old mode 100644 new mode 100755 index 88816bb9..8a4f0600 --- a/terra-jupyter-base/scripts/extension/jupyter_install_server_extension.sh +++ b/terra-jupyter-base/scripts/extension/jupyter_install_server_extension.sh @@ -8,5 +8,5 @@ if [ -n "$1" ]; then mkdir ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} tar -xzf ${JUPYTER_EXTENSION} -C${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} pip3 install -e ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} - sudo -E -u jupyter jupyter serverextension enable --py ${JUPYTER_EXTENSION_NAME} + sudo -E -u jupyter /etc/jupyter/bin/jupyter serverextension enable --py ${JUPYTER_EXTENSION_NAME} --sys-prefix fi diff --git a/terra-jupyter-base/scripts/extension/jupyter_pip_install_combined_extension.sh b/terra-jupyter-base/scripts/extension/jupyter_pip_install_combined_extension.sh old mode 100644 new mode 100755 index 1054d99f..bbf367c0 --- a/terra-jupyter-base/scripts/extension/jupyter_pip_install_combined_extension.sh +++ b/terra-jupyter-base/scripts/extension/jupyter_pip_install_combined_extension.sh @@ -4,8 +4,9 @@ set -e if [ -n "$1" ]; then JUPYTER_EXTENSION=$1 - pip3 install ${JUPYTER_EXTENSION} - sudo -E -u jupyter jupyter serverextension enable --py ${JUPYTER_EXTENSION} - sudo -E -u jupyter jupyter nbextension install --py ${JUPYTER_EXTENSION} --user - sudo -E -u jupyter jupyter nbextension enable --py ${JUPYTER_EXTENSION} + uv pip install ${JUPYTER_EXTENSION} + sudo -E -u jupyter jupyter serverextension enable --py ${JUPYTER_EXTENSION} --sys-prefix + # `jupyter nbextension` does not exist in Notebook 7 (classic nbextensions are not supported). + # sudo -E -u jupyter jupyter nbextension install --py ${JUPYTER_EXTENSION} --sys-prefix + # sudo -E -u jupyter jupyter nbextension enable --py ${JUPYTER_EXTENSION} --sys-prefix fi diff --git a/terra-jupyter-base/scripts/extension/jupyter_pip_install_notebook_extension.sh b/terra-jupyter-base/scripts/extension/jupyter_pip_install_notebook_extension.sh old mode 100644 new mode 100755 index 5ad45c9a..f873ec74 --- a/terra-jupyter-base/scripts/extension/jupyter_pip_install_notebook_extension.sh +++ b/terra-jupyter-base/scripts/extension/jupyter_pip_install_notebook_extension.sh @@ -3,7 +3,10 @@ set -e if [ -n "$1" ]; then JUPYTER_EXTENSION=$1 - pip3 install ${JUPYTER_EXTENSION} - sudo -E -u jupyter /opt/conda/bin/jupyter nbextension install --py ${JUPYTER_EXTENSION} --user - sudo -E -u jupyter /opt/conda/bin/jupyter nbextension enable --py ${JUPYTER_EXTENSION} + uv pip install ${JUPYTER_EXTENSION} + # `jupyter nbextension` does not exist in Notebook 7 (classic nbextensions are not supported). + # The package is still installed, in case it also ships a JupyterLab / Notebook 7 extension. + # (also fixed the `--sys-prefixr` typo in the install line below) + # sudo -E -u jupyter /etc/jupyter/bin/jupyter nbextension install --py ${JUPYTER_EXTENSION} --sys-prefix + # sudo -E -u jupyter /etc/jupyter/bin/jupyter nbextension enable --py ${JUPYTER_EXTENSION} --sys-prefix fi diff --git a/terra-jupyter-base/scripts/extension/jupyter_pip_install_server_extension.sh b/terra-jupyter-base/scripts/extension/jupyter_pip_install_server_extension.sh old mode 100644 new mode 100755 index c643d9f2..3a87bcc7 --- a/terra-jupyter-base/scripts/extension/jupyter_pip_install_server_extension.sh +++ b/terra-jupyter-base/scripts/extension/jupyter_pip_install_server_extension.sh @@ -4,6 +4,6 @@ set -e if [ -n "$1" ]; then JUPYTER_EXTENSION=$1 - pip3 install ${JUPYTER_EXTENSION} - sudo -E -u jupyter jupyter serverextension enable --py ${JUPYTER_EXTENSION} + uv pip install ${JUPYTER_EXTENSION} + sudo -E -u jupyter /etc/jupyter/bin/jupyter serverextension enable --py ${JUPYTER_EXTENSION} --sys-prefix fi diff --git a/terra-jupyter-base/scripts/kernel/kernel_bootstrap.sh b/terra-jupyter-base/scripts/kernel/kernel_bootstrap.sh old mode 100644 new mode 100755 diff --git a/terra-jupyter-base/scripts/kernel/kernelspec.sh b/terra-jupyter-base/scripts/kernel/kernelspec.sh old mode 100644 new mode 100755 index 59f1cc6f..8954e08e --- a/terra-jupyter-base/scripts/kernel/kernelspec.sh +++ b/terra-jupyter-base/scripts/kernel/kernelspec.sh @@ -3,5 +3,19 @@ TMP_KERNELSPEC_DIR=$1 KERNELSPEC_HOME=$2 -# Replace the contents of the Python kernel scripts -sed -e 's/${PY_VERSION}/3/g' -e 's|${JUPYTER_HOME}|'${JUPYTER_HOME}'|g' ${TMP_KERNELSPEC_DIR}/python_kernelspec.tmpl > ${KERNELSPEC_HOME}/python3/kernel.json +# The R kernel is NOT registered in terra-jupyter-base: IRkernel is not installed here, so an R kernel +# would die on start ("there is no package called 'IRkernel'"). terra-jupyter-r installs IRkernel and +# registers the R kernel (as "ir", the name Terra R notebooks use) after that install. +# mkdir -p ${KERNELSPEC_HOME}/ir + +# Replace the contents of the Python kernel scripts. +# The interpreter must be the absolute path into the user's conda env: a bare "python3" +# resolves against PATH, where /usr/bin comes first and the conda env isn't present at +# all, so the kernel started as /usr/bin/python3 and died with +# "No module named ipykernel_launcher". +sed -e 's/${PY_VERSION}/3/g' \ + -e 's|${JUPYTER_HOME}|'${JUPYTER_HOME}'|g' \ + -e 's|${CONDA_ENV_HOME}|'${CONDA_ENV_HOME}'|g' \ + ${TMP_KERNELSPEC_DIR}/python_kernelspec.tmpl > ${KERNELSPEC_HOME}/python3/kernel.json +# Enable R kernel -- done in terra-jupyter-r, see above +# sed 's|${JUPYTER_HOME}|'${JUPYTER_HOME}'|g' ${TMP_KERNELSPEC_DIR}/r_kernelspec.tmpl > ${KERNELSPEC_HOME}/ir/kernel.json diff --git a/terra-jupyter-base/scripts/kernel/python_kernelspec.tmpl b/terra-jupyter-base/scripts/kernel/python_kernelspec.tmpl index a2b0b66a..b4559d3b 100644 --- a/terra-jupyter-base/scripts/kernel/python_kernelspec.tmpl +++ b/terra-jupyter-base/scripts/kernel/python_kernelspec.tmpl @@ -3,7 +3,7 @@ "display_name": "Python ${PY_VERSION}", "argv": [ "${JUPYTER_HOME}/scripts/kernel/kernel_bootstrap.sh", - "python${PY_VERSION}", + "${CONDA_ENV_HOME}/bin/python", "-m", "ipykernel_launcher", "-f", diff --git a/terra-jupyter-base/scripts/run-jupyter.sh b/terra-jupyter-base/scripts/run-jupyter.sh old mode 100644 new mode 100755 index 2d527695..c0b8d2f8 --- a/terra-jupyter-base/scripts/run-jupyter.sh +++ b/terra-jupyter-base/scripts/run-jupyter.sh @@ -8,9 +8,9 @@ umask 002 # TODO: change default to ${HOME}/notebooks once welder is rolled out to all clusters NOTEBOOKS_DIR=${1:-${HOME}} -# Forces python 3 -JUPYTER_BASE="/opt/conda/bin/python3 /opt/conda/bin/jupyter-notebook" -JUPYTER_CMD="$JUPYTER_BASE --NotebookApp.nbserver_extensions=\"{'jupyter_localize_extension':True}\" &> ${NOTEBOOKS_DIR}/jupyter.log" +# Forces python 3.13 (PYTHON_VERSION in the Dockerfile) +JUPYTER_BASE="/etc/jupyter/bin/python3.13 /etc/jupyter/bin/jupyter-notebook" +JUPYTER_CMD="$JUPYTER_BASE --ServerApp.jpserver_extensions=\"{'jupyter_localize_extension':True}\" &> ${NOTEBOOKS_DIR}/jupyter.log" echo $JUPYTER_CMD diff --git a/terra-jupyter-base/tests/smoke_test.py b/terra-jupyter-base/tests/smoke_test.py index f1461cf7..76281d53 100644 --- a/terra-jupyter-base/tests/smoke_test.py +++ b/terra-jupyter-base/tests/smoke_test.py @@ -8,8 +8,17 @@ """ import os -import pytest +import re +import signal import subprocess +import time +import urllib.request + +import pytest + +JUPYTER_HOME = "/etc/jupyter" +JUPYTER = f"{JUPYTER_HOME}/bin/jupyter" +EXTENSION_SCRIPTS = f"{JUPYTER_HOME}/scripts/extension" def test_firecloud(): import firecloud @@ -30,3 +39,246 @@ def test_terra_notebook_utils(): # if not "collapsible_headings/main" in str(output): # pytest.fail("collapsible_headings not enabled") + + +####################### +# Leonardo startup compatibility +####################### +# Leonardo's startup script runs, for every Jupyter runtime: +# docker exec -u root -e PIP_USER=false jupyter-server \ +# /etc/jupyter/scripts/extension/jupyter_install_notebook_extension.sh /etc/jupyter/jupyter-iframe-extension.js +# and retries it up to 3 times. A non-zero exit aborts the startup script before run-jupyter.sh, +# so Jupyter never starts and the runtime times out. Notebook 7 has no `jupyter nbextension`. + +def _as_root(cmd): + """Run like `docker exec -u root -e PIP_USER=false` (the image's jupyter user has passwordless sudo).""" + prefix = [] if os.geteuid() == 0 else ["sudo", "-E"] + return subprocess.run(prefix + ["env", "PIP_USER=false"] + cmd, capture_output=True, text=True) + +def test_leonardo_iframe_extension_call_exits_0(tmp_path): + extension = tmp_path / "jupyter-iframe-extension.js" + extension.write_text("// placeholder for Leonardo's jupyter-iframe-extension.js\n") + # Twice: Leonardo retries, and the old script was not safe to re-run (it mv'ed the file away) + for attempt in (1, 2): + result = _as_root([f"{EXTENSION_SCRIPTS}/jupyter_install_notebook_extension.sh", str(extension)]) + assert result.returncode == 0, f"attempt {attempt} exited {result.returncode}:\n{result.stdout}\n{result.stderr}" + +def test_leonardo_jupyter_setup_commands_succeed(): + # The image-dependent commands Leonardo's gce-init.sh runs after the extension step and before + # run-jupyter.sh (network steps such as the gitignore download and `pip install nbstripout` are left + # out). Any failure here aborts the startup script and the runtime times out. + # (command, run as root?) -- root ones are `docker exec -u 0` in gce-init.sh + commands = [ + ("sed -i 's/127.0.0.1/welder/g' /etc/jupyter/custom/jupyter_delocalize.py", False), + ("/etc/jupyter/scripts/extension/install_jupyter_contrib_nbextensions.sh" + " && mkdir -p /home/jupyter/.jupyter/custom/" + " && chown -R jupyter:users /home/jupyter/.jupyter" + " && cp /etc/jupyter/custom/google_sign_in.js /home/jupyter/.jupyter/custom/" + " && ls -la /etc/jupyter/custom/extension_entry_jupyter.js" + " && cp /etc/jupyter/custom/extension_entry_jupyter.js /home/jupyter/.jupyter/custom/custom.js" + " && cp /etc/jupyter/custom/safe-mode.js /home/jupyter/.jupyter/custom/" + " && cp /etc/jupyter/custom/edit-mode.js /home/jupyter/.jupyter/custom/" + " && mkdir -p /etc/jupyter/nbconfig", True), + # needs /etc/jupyter/jupyter_notebook_config.py to exist (see the placeholder file in the image) + ("sed -i '/^# to mount there as it effectively deletes existing files on the image/,+5d'" + " /etc/jupyter/jupyter_notebook_config.py", False), + ] + for command, root in commands: + result = _as_root(["bash", "-c", command]) if root else \ + subprocess.run(["bash", "-c", command], capture_output=True, text=True) + assert result.returncode == 0, f"`{command}` exited {result.returncode}:\n{result.stdout}\n{result.stderr}" + +def test_kernels_do_not_depend_on_home_dir(): + # Leonardo mounts the runtime's persistent disk over the notebooks dir (/home/jupyter), hiding whatever + # the image put there. A kernel whose interpreter lives under it dies on Terra with + # "/home/jupyter/.envs/python3/bin/python: No such file or directory". + import glob, json + home = "/home/jupyter" + kernel_files = glob.glob("/usr/local/share/jupyter/kernels/*/kernel.json") + \ + glob.glob(f"{JUPYTER_HOME}/share/jupyter/kernels/*/kernel.json") + assert kernel_files, "no kernelspecs found" + for kernel_file in kernel_files: + argv = json.load(open(kernel_file))["argv"] + for arg in argv: + if arg.startswith("/"): + assert not arg.startswith(home + "/"), f"{kernel_file} uses {arg}, which is hidden by Leonardo's {home} mount" + assert os.path.exists(arg), f"{kernel_file} uses {arg}, which does not exist" + +####################### +# Kernels and the user's conda env +####################### +CONDA_ENV_HOME = os.environ.get("CONDA_ENV_HOME", "/opt/conda/envs/python3") +KERNELSPEC_DIR = "/usr/local/share/jupyter/kernels" + +# Starts a kernel through jupyter_client in the jupyter server's venv, so the kernelspec is resolved +# and launched exactly as the server does it, then runs code in it and prints the output. +_KERNEL_RUNNER = """ +import sys +from jupyter_client.manager import start_new_kernel +kernel_name, code = sys.argv[1], sys.argv[2] +km, kc = start_new_kernel(kernel_name=kernel_name, startup_timeout=120) +out = [] +def hook(msg): + content = msg["content"] + if msg["msg_type"] == "stream": + out.append(content["text"]) + elif msg["msg_type"] in ("execute_result", "display_data"): + out.append(content["data"].get("text/plain", "") + "\\n") + elif msg["msg_type"] == "error": + out.append("\\n".join(content["traceback"])) +try: + reply = kc.execute_interactive(code, timeout=600, output_hook=hook) +finally: + kc.stop_channels() + km.shutdown_kernel(now=True) +sys.stdout.write("".join(out)) +sys.exit(0 if reply["content"]["status"] == "ok" else 1) +""" + +def _emulated_cpu(): + """The CPU vendor when this amd64 container runs under emulation (e.g. Docker Desktop on Apple Silicon), else None.""" + try: + with open("/proc/cpuinfo") as f: + for line in f: + if line.startswith(("vendor_id", "model name")): + for vendor in ("VirtualApple", "QEMU"): + if vendor in line: + return vendor + except OSError: + pass + return None + +# Under amd64 emulation (Rosetta "VirtualApple" / QEMU) every ipykernel starts but never answers +# kernel_info -- it also happens with a plain python:3.14 image -- so the kernel tests can't tell anything +# about the image there. They run normally on real amd64 (CI, Terra VMs). +requires_native_cpu = pytest.mark.skipif( + _emulated_cpu() is not None, + reason=f"jupyter kernels do not respond under {_emulated_cpu()} amd64 emulation; run on native amd64") + +def run_in_kernel(kernel_name, code): + result = subprocess.run([f"{JUPYTER_HOME}/bin/python", "-c", _KERNEL_RUNNER, kernel_name, code], + capture_output=True, text=True, timeout=900) + assert result.returncode == 0, f"{kernel_name} kernel failed:\n{result.stdout}\n{result.stderr}" + return result.stdout + +def kernelspecs(): + import json + output = subprocess.check_output([JUPYTER, "kernelspec", "list", "--json"], text=True) + return json.loads(output)["kernelspecs"] + +def test_python3_kernel_is_registered(): + specs = kernelspecs() + assert "python3" in specs, f"no python3 kernel: {sorted(specs)}" + python3 = specs["python3"] + assert python3["resource_dir"] == f"{KERNELSPEC_DIR}/python3" + argv = python3["spec"]["argv"] + assert argv[0] == f"{JUPYTER_HOME}/scripts/kernel/kernel_bootstrap.sh" + assert argv[1] == f"{CONDA_ENV_HOME}/bin/python", f"python3 kernel does not use the conda env: {argv}" + +@requires_native_cpu +def test_python3_kernel_runs_in_conda_env(): + output = run_in_kernel("python3", "import os, sys; print(sys.executable); print('WORKSPACE_NAME' in os.environ)") + executable, bootstrapped = output.split()[-2:] + assert executable == f"{CONDA_ENV_HOME}/bin/python" + # kernel_bootstrap.sh exports WORKSPACE_NAME, so this shows the kernel was started through it + assert bootstrapped == "True", "kernel was not started through kernel_bootstrap.sh" + +def test_python_versions(): + # conda base, the jupyter server venv and the user's conda env all use PYTHON_VERSION (3.13); + # only Ubuntu's /usr/bin/python3 differs. run-jupyter.sh starts the server with python. + python_version = os.environ["PYTHON_VERSION"] + assert python_version == "3.13" + for python in ["/opt/conda/bin/python", f"{JUPYTER_HOME}/bin/python{python_version}", f"{CONDA_ENV_HOME}/bin/python"]: + output = subprocess.check_output([python, "-c", "import sys; print('%d.%d' % sys.version_info[:2])"], text=True) + assert output.strip() == python_version, f"{python} is Python {output.strip()}" + assert f"{JUPYTER_HOME}/bin/python{python_version} " in open(f"{JUPYTER_HOME}/scripts/run-jupyter.sh").read() + +def test_conda_env_is_registered_with_conda(): + import json + output = subprocess.check_output(["/opt/conda/bin/conda", "env", "list", "--json"], text=True) + assert CONDA_ENV_HOME in json.loads(output)["envs"] + +def test_conda_env_pip(): + output = subprocess.check_output([f"{CONDA_ENV_HOME}/bin/python", "-m", "pip", "--version"], text=True) + assert CONDA_ENV_HOME in output, f"pip does not belong to the conda env: {output}" + +def test_pip_user_install_is_importable_from_conda_env(tmp_path): + # Notebook users run `pip install` with the image's PIP_USER=true, which installs to ~/.local + env = dict(os.environ, HOME=str(tmp_path), PIP_USER="true") + env.pop("PIP_TARGET", None) + install = subprocess.run([f"{CONDA_ENV_HOME}/bin/python", "-m", "pip", "install", "--no-deps", "emoji==2.14.1"], + env=env, capture_output=True, text=True) + assert install.returncode == 0, f"pip install failed:\n{install.stdout}\n{install.stderr}" + location = subprocess.check_output([f"{CONDA_ENV_HOME}/bin/python", "-c", "import emoji; print(emoji.__file__)"], + env=env, text=True).strip() + assert location.startswith(f"{tmp_path}/.local/"), f"emoji was not installed to the user site: {location}" + +def test_extension_scripts_do_not_call_nbextension(): + # `jupyter nbextension` (and contrib/configurator, which wrap it) does not exist in Notebook 7 + pattern = re.compile(r"jupyter\s+(nbextension|contrib\s+nbextension|nbextensions_configurator)\b") + offenders = [] + for name in sorted(os.listdir(EXTENSION_SCRIPTS)): + with open(os.path.join(EXTENSION_SCRIPTS, name)) as f: + for number, line in enumerate(f, 1): + if not line.lstrip().startswith("#") and pattern.search(line): + offenders.append(f"{name}:{number}: {line.strip()}") + assert not offenders, "classic nbextension calls found:\n" + "\n".join(offenders) + +####################### +# Jupyter server: Notebook 7 + nbclassic +####################### +# Start Jupyter the way Leonardo does (scripts/run-jupyter.sh, with jupyter_server_config.py) and +# check that both the Notebook 7 UI (/tree) and the classic UI (/nbclassic/tree) are served. +GOOGLE_PROJECT = "smoke-project" +CLUSTER_NAME = "smoke-cluster" +BASE_URL = f"http://127.0.0.1:8000/notebooks/{GOOGLE_PROJECT}/{CLUSTER_NAME}/" + +def _get(path): + with urllib.request.urlopen(BASE_URL + path, timeout=10) as response: + return response.status, response.read().decode("utf-8", "replace") + +@pytest.fixture(scope="module") +def jupyter_server(tmp_path_factory): + notebooks_dir = tmp_path_factory.mktemp("notebooks") + env = dict(os.environ, GOOGLE_PROJECT=GOOGLE_PROJECT, CLUSTER_NAME=CLUSTER_NAME, HOME=str(notebooks_dir)) + env.pop("WELDER_ENABLED", None) + # run-jupyter.sh writes the server log to /jupyter.log + process = subprocess.Popen([f"{JUPYTER_HOME}/scripts/run-jupyter.sh", str(notebooks_dir)], + env=env, start_new_session=True) + log_file = notebooks_dir / "jupyter.log" + deadline = time.time() + 120 + try: + while True: + if process.poll() is not None: + pytest.fail(f"run-jupyter.sh exited {process.returncode}:\n{log_file.read_text() if log_file.exists() else ''}") + try: + if _get("api/status")[0] == 200: + break + except OSError: + pass + if time.time() > deadline: + pytest.fail(f"Jupyter did not start within 120s:\n{log_file.read_text() if log_file.exists() else ''}") + time.sleep(2) + yield log_file + finally: + os.killpg(process.pid, signal.SIGTERM) + process.wait(timeout=30) + +def test_jupyter_server_versions(): + output = subprocess.check_output([f"{JUPYTER_HOME}/bin/python", "-c", + "import notebook, nbclassic; 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-1,63 +1,47 @@ -FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:1.1.4 +FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:2.0.1 USER root -COPY scripts $JUPYTER_HOME/scripts +# terra-jupyter-base 2.0.1 is built on nvidia/cuda:13.4.2-base-ubuntu26.04 (resolute) and already +# installs r-base / r-base-dev from the CRAN resolute-cran40 repo, so this image only adds the +# system libraries R/Bioconductor packages need, the R packages and the R kernel. +# +# Only the R kernel files are copied. Copying all of scripts/ would replace terra-jupyter-base's +# kernelspec.sh, which registers the python3 kernel against the user's conda env. +COPY --chown=jupyter:users scripts/kernel $JUPYTER_KERNEL # Add env vars to identify binary package installation -ENV TERRA_R_PLATFORM="terra-jupyter-r-2.2.6" -ENV TERRA_R_PLATFORM_BINARY_VERSION=3.21 +ENV TERRA_R_PLATFORM="terra-jupyter-r-3.0.0" +ENV TERRA_R_PLATFORM_BINARY_VERSION=3.23 -# Install protobuf 3.20.3. Note this version comes from base deep learning image. Use `conda list` to see what's installed -RUN cd /tmp \ - && wget https://github.com/protocolbuffers/protobuf/releases/download/v3.20.3/protobuf-all-3.20.3.tar.gz \ - && tar -xvzf protobuf-all-3.20.3.tar.gz \ - && cd protobuf-3.20.3/ \ - && ./configure --disable-dependency-tracking \ - && make \ - && make check \ - && sudo make install \ - && sudo ldconfig \ - && rm -rf /tmp/protobuf-* \ - && cd ~ - -# Add R kernel -RUN find $JUPYTER_HOME/scripts -name '*.sh' -type f | xargs chmod +x \ - && $JUPYTER_HOME/scripts/kernel/kernelspec.sh $JUPYTER_HOME/scripts/kernel /opt/conda/share/jupyter/kernels - -# https://cran.r-project.org/bin/linux/ubuntu/README.html +# Package names verified against Ubuntu 26.04 (resolute). +# Entries that are commented out are kept for reference with the reason they were dropped. +# +# The CRAN repo was set up here with `apt-key adv` and `add-apt-repository`. Neither exists on 26.04 +# (apt-key was removed in apt 2.9, software-properties-common is not installed) and the base image +# already writes /etc/apt/sources.list.d/cran.list, so the repo setup is gone. RUN apt-get update \ - && apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 \ - && add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/' \ - && apt-get install -yq --no-install-recommends apt-transport-https \ - && apt update \ - # Reconfigure dpkg to solve `Sub-process /usr/bin/dpkg returned an error code` when installing below packages - && dpkg --configure -a \ - && apt install -yq --no-install-recommends \ - apt-utils \ + && apt-get install -yq --no-install-recommends \ libssh2-1-dev \ - libssl-dev \ - libcurl4-gnutls-dev \ libgit2-dev \ libxml2-dev \ - r-base-dev \ - r-base-core \ ## This section installs libraries libnetcdf-dev \ - libhdf5-serial-dev \ libfftw3-dev \ libopenbabel-dev \ libopenmpi-dev \ libgdal-dev \ libcairo2-dev \ - libtiff5-dev \ - libgsl0-dev \ + # replaces libtiff5-dev (transitional package on 26.04) \ + libtiff-dev \ + # replaces libgsl0-dev, which no longer exists \ + libgsl-dev \ libgtk2.0-dev \ - libgl1-mesa-dev \ + # replaces libgl1-mesa-dev (transitional package on 26.04) \ + libgl-dev \ libglu1-mesa-dev \ - libgmp3-dev \ - libhdf5-dev \ - libncurses-dev \ + # replaces libgmp3-dev \ + libgmp-dev \ libxpm-dev \ libgtkmm-2.4-dev \ libmpfr-dev \ @@ -71,7 +55,8 @@ RUN apt-get update \ libpoppler-cpp-dev \ libpq-dev \ libperl-dev \ - libgfortran5 \ + # protobuf 3.21.12, the same version as the protobuf-compiler in terra-jupyter-base \ + libprotobuf-dev \ ## software - perl extentions and modules libarchive-extract-perl \ libfile-copy-recursive-perl \ @@ -80,12 +65,12 @@ RUN apt-get update \ libdbd-mysql-perl \ libxml-simple-perl \ ## Databases and other software - sqlite \ + # replaces sqlite (SQLite 2), which no longer exists \ + sqlite3 \ mpi-default-bin \ openmpi-common \ imagemagick \ tabix \ - ggobi \ graphviz \ jags \ ## Additional resources @@ -94,7 +79,6 @@ RUN apt-get update \ biber \ libzmq3-dev \ libsbml5-dev \ - biber \ ## for gpuMagic package ocl-icd-opencl-dev \ ## for ChemmineOB package @@ -105,11 +89,43 @@ RUN apt-get update \ cmake \ ## for archive package libarchive-dev \ - && ln -s /usr/lib/gcc/x86_64-linux-gnu/7/libgfortran.so /usr/lib/x86_64-linux-gnu/libgfortran.so \ - && ln -s /usr/lib/gcc/x86_64-linux-gnu/7/libstdc++.so /usr/lib/x86_64-linux-gnu/libstdc++.so \ + ## for fs (needed by devtools, tidyverse, shiny, ...) \ + libuv1-dev \ + ## for igraph (needed by Seurat, scran) \ + libglpk-dev \ + ## for keyring (gargle / bigrquery / googledrive) \ + libsecret-1-dev \ + ########## Removed / redundant on Ubuntu 26.04 ########## + # installed in terra-jupyter-base \ + # apt-utils \ + # libssl-dev \ + # libhdf5-dev \ + # libncurses-dev \ + # r-base-dev \ + # r-base-core \ + # libcurl4-gnutls-dev: conflicts with libcurl4-openssl-dev, which terra-jupyter-base installs \ + # libcurl4-gnutls-dev \ + # apt-transport-https: empty transitional package, https is built into apt \ + # apt-transport-https \ + # libhdf5-serial-dev: no longer exists, libhdf5-dev (in terra-jupyter-base) replaces it \ + # libhdf5-serial-dev \ + # ggobi: removed from Ubuntu \ + # ggobi \ + # libgfortran5: pulled in by r-base-dev (gfortran) \ + # libgfortran5 \ + # libnode-dev: conflicts with the nodesource nodejs in terra-jupyter-base. The V8 R package + # downloads a static libv8 when it is missing. \ + # libnode-dev \ + # + # The old `ln -s /usr/lib/gcc/x86_64-linux-gnu/7/libgfortran.so|libstdc++.so` links are dropped: gcc-7 + # is not installed (26.04 ships gcc-15), so they were dangling, and gcc finds both libraries itself. && apt-get clean \ && rm -rf /var/lib/apt/lists/* +# protobuf 3.20.3 was built from source here to match the old deeplearning base image's conda +# protobuf. That image is gone, and terra-jupyter-base ships protoc 3.21.12 from apt, so a +# from-source 3.20.3 in /usr/local would only shadow it. libprotobuf-dev above replaces it. + # DEVEL: Add sys env variables to DEVEL image # Variables in Renviron.site are made available inside of R. # Add libsbml CFLAGS @@ -118,15 +134,25 @@ ENV LIBSBML_LIBS="-lsbml" RUN echo 'export LIBSBML_CFLAGS="-I/usr/include"' >> /etc/profile \ && echo 'export LIBSBML_LIBS="-lsbml"' >> /etc/profile +# Extract package tarballs with R's internal untar instead of GNU tar. GNU tar 1.35 on 26.04 fails +# with "Cannot open: Function not implemented" when the amd64 image is built under emulation on +# Apple Silicon (e.g. on GitHub tarballs installed through remotes, such as DataBiosphere/Ronaldo). +# TAR is read by utils::untar() (used by remotes / BiocManager), R_INSTALL_TAR by R CMD INSTALL. +# ARG, so they only apply to the build and users keep the default tar. +ARG TAR=internal +ARG R_INSTALL_TAR=internal + ## set pip3 to run as root, not as jupyter user ENV PIP_USER=false ## Install python packages needed for a few Bioc packages -RUN pip3 -V \ - && pip3 install --upgrade pip \ - && pip3 install cwltool \ - && apt-get clean \ - && rm -rf /var/lib/apt/lists/* +# Ubuntu 26.04 has no system pip (terra-jupyter-base drops python3-pip, and PEP 668 blocks it anyway), +# so install cwltool into the user's conda env and link it onto the default PATH for R to find. +RUN $CONDA_ENV_HOME/bin/python -m pip install --no-cache-dir --root-user-action=ignore cwltool \ + && ln -s $CONDA_ENV_HOME/bin/cwltool /usr/local/bin/cwltool \ + && cwltool --version \ + # chown only what pip added: a chown -R would copy the whole env into this layer + && find $CONDA_ENV_HOME ! -user $USER -exec chown -h $USER:users {} + RUN R -e 'install.packages("BiocManager")' \ ## check version @@ -182,7 +208,12 @@ RUN R -e 'BiocManager::install(c( \ ## pip runs as jupyter user ENV PIP_USER=true +# Register the R kernel ("ir", the name Terra R notebooks use) now that IRkernel is installed. +# installspec() puts the logos and kernel.json in $JUPYTER_KERNELSPEC_DIR/kernels/ir, then +# kernelspec.sh replaces kernel.json with one that starts R through kernel_bootstrap.sh. 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