Image Update - March 2026

.github/workflows/docker-testing.yml

@@ -40,4 +40,4 @@ jobs:
             set -e
             echo "Running tests in Docker container"
             # Run the test script inside the Docker container
-            conda run -n birdy mamba list
+            micromamba run -n birdy micromamba list

Jenkinsfile

@@ -10,8 +10,9 @@ pipeline {
     // https://jenkins.io/doc/book/pipeline/syntax/
     agent {
         docker {
-            image "pavics/workflow-tests:py311-250423-update250730"
+            image "pavics/workflow-tests:py312-260320"
             label 'linux && docker'
+            args "-e ENV_NAME='birdy'"
         }
     }
 

binder/Dockerfile

@@ -1,4 +1,4 @@
-FROM pavics/workflow-tests:py311-250423-update250730
+FROM pavics/workflow-tests:py312-260320
 
 USER root
 

docker/Dockerfile

@@ -1,89 +1,67 @@
-FROM continuumio/miniconda3
-
-# Use mamba for much improved performance over conda.
-# The 'channel_priority strict' did help conda but it was not enough.
-RUN conda config --prepend channels nodefaults || true && \
-    conda config --remove channels defaults || true && \
-    conda update conda -n base && \
-    conda install mamba conda-pack -n base -c conda-forge && \
-    conda clean --all --yes && \
-    conda config --set channel_priority strict && \
-    wget -qO- https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -C /usr/local -xvj bin/micromamba
-
-# Default for micromamba is $HOME/micromamba which is wrong.
-ENV MAMBA_ROOT_PREFIX="/opt/conda"
-
-# to checkout other notebooks and to run pip install
+# Use micromamba for improved speed and reduced image size
+FROM mambaorg/micromamba
+# No interactive apt calls
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Install all jupyter and docker build dependencies in base
+COPY environment-base.yml /tmp/environment-base.yml
+RUN micromamba install --yes --name base --file /tmp/environment-base.yml && \
+    micromamba clean --all --yes
+
+# Rename mambauser to jenkins for our Jenkins e2e notebooks test suite.
+ARG NEW_MAMBA_USER=jenkins
+ARG NEW_MAMBA_USER_ID=1000
+ARG NEW_MAMBA_USER_GID=1000
+
+USER root
+# Rename mambauser to jenkins; copied from mambaorg/micromamba documentation
+RUN if grep -q '^ID=alpine$' /etc/os-release; then \
+      # alpine does not have usermod/groupmod
+      apk add --no-cache --virtual temp-packages shadow; \
+    fi && \
+    usermod "--login=${NEW_MAMBA_USER}" "--home=/home/${NEW_MAMBA_USER}" \
+        --move-home "-u ${NEW_MAMBA_USER_ID}" "${MAMBA_USER}" && \
+    groupmod "--new-name=${NEW_MAMBA_USER}" \
+        "-g ${NEW_MAMBA_USER_GID}" "${MAMBA_USER}" && \
+    if grep -q '^ID=alpine$' /etc/os-release; then \
+      # remove the packages that were only needed for usermod/groupmod
+      apk del temp-packages; \
+    fi && \
+    # Update the expected value of MAMBA_USER for the
+    # _entrypoint.sh consistency check.
+    echo "${NEW_MAMBA_USER}" > "/etc/arg_mamba_user" && \
+    :
+ENV MAMBA_USER=$NEW_MAMBA_USER
+
+# Alias UID and GID for use with docker-stacks
+ENV NB_USER=${MAMBA_USER}
+ARG NB_GID="${NEW_MAMBA_USER_GID}"
+
+# Copy environment file
+COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /tmp/environment.yml
+
+# Add additional fonts and x11-utils for matplotlib and firefox support
 RUN apt-get update && \
-    DEBIAN_FRONTEND=noninteractive apt-get install -y \
-    git mercurial gcc unzip patch fonts-humor-sans firefox-esr x11-utils && \
+    apt-get install --yes fonts-humor-sans x11-utils && \
     apt-get clean
 
-# Create user jenkins for our Jenkins e2e notebooks test suite.
-# Change /opt/conda folder permissions for jupyter-conda extension.
-RUN groupadd --gid 1000 jenkins && \
-    useradd --uid 1000 --gid jenkins --shell /bin/bash --create-home jenkins && \
-    chmod -R a+rwX /opt/conda
-
-COPY environment.yml /environment.yml
-
-# create env "birdy"
+# Create "birdy" environment
 # use umask 0000 so that the files for the new environment are usable by user 'jenkins' for the jupyter-conda-extension
-#
-# Perform 2 stages install because one single 'conda env create -f
-# /environment.yml' was taking forever to complete, same with mamba.
-# Had to do this 2 stages install.  2 stages install was also taking forever
-# with conda so had to switch to mamba.
-#
-# One single 'conda env create -f /environment.yml' takes forever because we
-# removed all direct dependencies of xclim and ravenpy in /environment.yml for
-# dependencies pinning by xclim and ravenpy to take effect.  This results in
-# conda having a lot more packages to "solve" and it seems the solver
-# performance dropped exponentially with the number of packages to solve.
-#
-# Conda was stuck at this step:
-# DEBUG conda.common._logic:_run_sat(607): Invoking SAT with clause count: 2500273
-#
 RUN umask 0000 && \
-    mamba create --name birdy --channel conda-forge python=3.11 clisops figanos ravenpy xclim xscen xsdba --yes && \
-    (conda env export --name birdy 2>&1 | tee /conda-env-export-phase1.yml) && \
-    (du -sh /opt/conda 2>&1 | tee /conda-envs-size-phase1.txt) && \
-    mamba env update --name birdy --file /environment.yml && \
-    mamba clean --all --yes
-
-# alternate way to 'source activate birdy'
-ENV PATH="/opt/conda/envs/birdy/bin:$PATH"
-
-# our notebooks are hardcoded to lookup for kernel named 'birdy'
-# this python is from the birdy env above
-RUN python -m ipykernel install --name birdy && \
-    (conda env export --name birdy 2>&1 | tee /conda-env-export-final.yml) && \
-    (diff --unified /conda-env-export-phase1.yml /conda-env-export-final.yml 2>&1 | tee /conda-env-export.diff) && \
-    (du -sh /opt/conda 2>&1 | tee /conda-envs-size-final.txt) && \
-    diff /conda-envs-size-phase1.txt /conda-envs-size-final.txt || true
-
-# install using same channel preferences as birdy original env to not downgrade anything accidentally
-# this is for debug only, all dependencies should be specified in environment.yml above
-# RUN mamba install -c conda-forge -c cdat -c bokeh -c fortiers -n birdy nbdime
-
-# build jupyterlab extensions installed by conda, see `jupyter labextension list`
-# Supposedly not needed with jupyterlab v3 anymore but see
-# https://github.com/jupyterlab/jupyterlab/issues/11726#issuecomment-998901247
-# TODO: remove 'jupyter lab build' step once all extensions move to prebuilt extensions,
-# see comment https://github.com/jupyterlab/jupyterlab/issues/11726#issuecomment-998917305
-# Currently jupyter-dash is holding back this step, see
-# https://github.com/plotly/jupyter-dash/issues/49
-RUN jupyter lab build
-
-RUN jupyter serverextension enable voila --sys-prefix && \
-    jupyter serverextension enable panel.io.jupyter_server_extension --sys-prefix && \
-    jupyter serverextension list
-#   jupyter labextension install jupyterlab-clipboard
-
-# This should be "master" but commit
-# https://github.com/jupyter/docker-stacks/commit/c772e98ac794173d6ed83a08ec249038b27ca3be
-# is breaking with us since we do not have user jovyan.
-ENV DOCKER_STACKS_COMMIT=709206ac8788475728cc9c992c25fb5f1501bc29
+    micromamba create --name birdy --file /tmp/environment.yml "python>=3.12,<3.13" --yes && \
+    micromamba clean --all --yes
+
+# Notebooks are hardcoded to lookup for kernel named 'birdy' created in the previous code block
+RUN umask 0000 && \
+    micromamba run --name birdy python -m ipykernel install --name birdy && \
+    micromamba env export --name birdy | tee /conda-env-export-final.yml && \
+    du -sh "${MAMBA_ROOT_PREFIX}" | tee /conda-envs-size-final.txt
+
+# Docker-stacks commit from last time base-notebook was modified (2025/05/24)
+ENV DOCKER_STACKS_COMMIT=e73d308ba06fd5bcc75a4ee8417711743860c964
+
+# Activate base environment
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
 
 # /notebook_dir for Pavics-landing notebooks to re-create Jupyter env layout:
 # /notebook_dir/writable-workspace, /notebook_dir/pavics-homepage.
@@ -92,48 +70,67 @@ ENV DOCKER_STACKS_COMMIT=709206ac8788475728cc9c992c25fb5f1501bc29
 # hardcoded so users can copy the nb to writable-workspace/ dir and still be able
 # to run them seemlessly from the Jupyter env (without having to also copy
 # those *.geojson files with the notebooks).
-RUN wget https://raw.githubusercontent.com/jupyter/docker-stacks/$DOCKER_STACKS_COMMIT/base-notebook/start.sh --output-document /usr/local/bin/start.sh && \
-    wget https://raw.githubusercontent.com/jupyter/docker-stacks/$DOCKER_STACKS_COMMIT/base-notebook/start-singleuser.sh --output-document /usr/local/bin/start-singleuser.sh && \
-    wget https://raw.githubusercontent.com/jupyter/docker-stacks/$DOCKER_STACKS_COMMIT/base-notebook/start-notebook.sh --output-document /usr/local/bin/start-notebook.sh && \
-    wget https://raw.githubusercontent.com/jupyter/docker-stacks/$DOCKER_STACKS_COMMIT/base-notebook/fix-permissions --output-document /usr/local/bin/fix-permissions && \
+RUN wget https://raw.githubusercontent.com/jupyter/docker-stacks/$DOCKER_STACKS_COMMIT/images/base-notebook/start-singleuser.py --output-document /usr/local/bin/start-singleuser.py && \
+    wget https://raw.githubusercontent.com/jupyter/docker-stacks/$DOCKER_STACKS_COMMIT/images/base-notebook/start-notebook.py --output-document /usr/local/bin/start-notebook.py && \
     mkdir /etc/jupyter && \
-    wget https://raw.githubusercontent.com/jupyter/docker-stacks/$DOCKER_STACKS_COMMIT/base-notebook/jupyter_notebook_config.py --output-document /etc/jupyter/jupyter_notebook_config.py && \
-    chmod a+rx /usr/local/bin/start.sh /usr/local/bin/start-singleuser.sh /usr/local/bin/start-notebook.sh /usr/local/bin/fix-permissions && \
-    chmod a+r /etc/jupyter/jupyter_notebook_config.py && \
+    wget https://raw.githubusercontent.com/jupyter/docker-stacks/$DOCKER_STACKS_COMMIT/images/base-notebook/jupyter_server_config.py --output-document /etc/jupyter/jupyter_server_config.py && \
+    wget https://raw.githubusercontent.com/jupyter/docker-stacks/$DOCKER_STACKS_COMMIT/images/base-notebook/docker_healthcheck.py --output-document /etc/jupyter/docker_healthcheck.py && \
+    chmod a+rx /usr/local/bin/start-singleuser.py /usr/local/bin/start-notebook.py /etc/jupyter/docker_healthcheck.py && \
+    chmod a+r /etc/jupyter/jupyter_server_config.py && \
     mkdir -p /notebook_dir/writable-workspace && \
-    chown jenkins /notebook_dir/writable-workspace && \
+    chown "${MAMBA_USER}" /notebook_dir/writable-workspace && \
     mkdir -p /notebook_dir/pavics-homepage && \
-    chown jenkins /notebook_dir/pavics-homepage && \
+    chown "${MAMBA_USER}" /notebook_dir/pavics-homepage && \
     chown root:root /notebook_dir && \
     chmod a-w /notebook_dir && \
-    chmod a+rwX -R /opt/conda/envs/birdy/fonts && \
-    mkdir /opt/conda/pkgs/cache && \
-    chown jenkins:jenkins -R /opt/conda/pkgs/cache && \
+    mkdir -p "${MAMBA_ROOT_PREFIX}/envs/birdy/fonts" && \
+    chmod a+rwX -R "${MAMBA_ROOT_PREFIX}/envs/birdy/fonts" && \
+    mkdir -p "${MAMBA_ROOT_PREFIX}/pkgs/cache" && \
+    chown "${MAMBA_USER}":"${MAMBA_USER}" -R "${MAMBA_ROOT_PREFIX}/pkgs/cache" && \
+    touch "${MAMBA_ROOT_PREFIX}/pkgs/pkgs.lock" && \
+    chown "${MAMBA_USER}":"${MAMBA_USER}" "${MAMBA_ROOT_PREFIX}/pkgs/pkgs.lock" && \
     mkdir -p /usr/local/bin && \
     wget https://downloads.globus.org/globus-connect-personal/linux/stable/globusconnectpersonal-latest.tgz -O /usr/local/bin/globusconnectpersonal-latest.tgz && \
     tar xzf /usr/local/bin/globusconnectpersonal-latest.tgz -C /usr/local/bin/ && \
     ln -vs /usr/local/bin/globusconnectpersonal*/globusconnectpersonal /usr/local/bin/globusconnectpersonal && \
     rm -v /usr/local/bin/globusconnectpersonal-latest.tgz
 
+# Set birdy as the default kernel
+RUN echo "c.MultiKernelManager.default_kernel_name = 'birdy'" >> /etc/jupyter/jupyter_server_config.py
+
 # For jupyter-panel-proxy launcher.
 ENV BOKEH_ALLOW_WS_ORIGIN="*"
 
+# To supply the location of the RavenHydroFramework binary
+# FIXME: This location should be provided via the raven-hydro package which would help with the discovery logic in RavenPy
+ENV RAVENPY_RAVEN_BINARY_PATH="${MAMBA_ROOT_PREFIX}/envs/birdy/bin/raven"
+
 # For import xesmf since esmf-8.4.0, see: https://github.com/conda-forge/esmf-feedstock/issues/91
-ENV ESMFMKFILE="/opt/conda/envs/birdy/lib/esmf.mk"
+ENV ESMFMKFILE="${MAMBA_ROOT_PREFIX}/envs/birdy/lib/esmf.mk"
 
-# To avoid error "PROJ: proj_create_from_database: Open of /opt/conda/envs/birdy/share/proj failed"
+# To avoid error "PROJ: proj_create_from_database: Open of ${MAMBA_ROOT_PREFIX}/envs/birdy/share/proj failed"
 # This simulates a real `conda activate birdy`.
-ENV PROJ_DATA="/opt/conda/envs/birdy/share/proj"
+ENV PROJ_DATA="${MAMBA_ROOT_PREFIX}/envs/birdy/share/proj"
 
 # To expose conda-installed compilers so that users can make use of them
 ENV gcc=x86_64-conda-linux-gnu-gcc
 ENV g++=x86_64-conda-linux-gnu-g++
 ENV gfortran=x86_64-conda-linux-gnu-gfortran
 
-# problem running start-notebook.sh when being root
+# JupyterLab cannot write to hidden folders by design
+ENV XDG_CACHE_HOME="/home/${MAMBA_USER}/cache"
+
+# Healthcheck - Requires NB_USER variable (copied from Docker-stacks)
+HEALTHCHECK --interval=3s --timeout=1s --start-period=3s --retries=3 CMD /etc/jupyter/docker_healthcheck.py || exit 1
+
+# Problem running start-notebook.sh when being root
 # the jupyter/base-notebook image also do not default to root user so we do the same here
-USER jenkins
+USER $MAMBA_USER
+# Activate birdy environment
+ENV ENV_NAME=birdy
+# Set entrypoint for jenkins to root directory
+WORKDIR /
 
 # follow jupyter/base-notebook image so config in jupyterhub is simpler
 # start notebook in conda environment to have working jupyter extensions
-CMD ["conda", "run", "-n", "birdy", "/usr/local/bin/start-notebook.sh"]
+CMD ["/usr/local/bin/_entrypoint.sh", "run", "-n", "base", "/usr/local/bin/start-notebook.py"]

docker/environment-base.yml

@@ -0,0 +1,94 @@
+# conda env create -f environment-base.yml
+name: base
+channels:
+  - conda-forge
+dependencies:
+  # UTILITIES
+
+  # conda: a cross-platform, language-agnostic binary package manager
+  # NOTE: Included as a requirement for gator
+  # https://github.com/conda/conda
+  - conda >= 4.7.12
+  # git: fast, scalable, distributed revision control system
+  # NOTES: Included as a requirement for jupyterlab-git
+  - git
+  # mamba: a reimplementation of the conda package manager in C++
+  # NOTE: Included as a requirement for gator
+  # https://github.com/mamba-org/mamba
+  - mamba >= 2.0
+  # wget: command-line utility for downloading files from the web
+  - wget
+
+  # JUPYTER LIBRARIES
+
+  # Jupyter conda metapackage: Install all the Jupyter components in one go.
+  # https://anaconda.org/conda-forge/jupyter
+  - jupyter
+  # notebook: A web-based notebook environment for interactive computing.
+  # to be launched by image jupyterhub/jupyterhub
+  # https://github.com/jupyter/notebook
+  - notebook
+  # jupyterlab: An extensible environment for interactive and reproducible computing
+  # https://github.com/jupyterlab/jupyterlab
+  - jupyterlab >= 4.0
+  # JupyterHub: A multi-user server for Jupyter notebooks
+  # https://github.com/jupyterhub/jupyterhub
+  - jupyterhub
+  # ipywidgets: Interactive HTML Widgets
+  # https://github.com/jupyter-widgets/ipywidgets
+  # https://ipywidgets.readthedocs.io/en/latest/user_install.html
+  - ipywidgets
+  # ipyleaflet: A Jupyter / Leaflet bridge enabling interactive maps in the Jupyter notebook.
+  # https://github.com/jupyter-widgets/ipyleaflet
+  - ipyleaflet
+  # gator: The Mamba Navigator, a Web UI for managing conda environments
+  # https://github.com/mamba-org/gator
+  - mamba_gator
+  # nbdime: Jupyter Notebook Diff and Merge tools
+  # https://github.com/jupyter/nbdime
+  - nbdime
+  # jupyter_bokeh: An extension for rendering Bokeh content in JupyterLab notebooks
+  # https://github.com/bokeh/jupyter_bokeh
+  - jupyter_bokeh
+  # jupytext: extension to produce .py files from notebook .ipynb files
+  # https://github.com/mwouts/jupytext
+  - jupytext
+  # jupyterlab-git: A JupyterLab extension for version control using Git
+  # https://github.com/jupyterlab/jupyterlab-git
+  - jupyterlab-git >= 0.44.0
+  # voila: Voilà turns Jupyter notebooks into standalone web applications
+  # https://github.com/voila-dashboards/voila
+  - voila
+  # jupyterlab-archive: A Jupyter extension to make, download and extract archive files.
+  # https://github.com/jupyterlab-contrib/jupyter-archive
+  - jupyter-archive
+  # jupyter-resource-usage: Jupyter Extension to show resource usage
+  # https://github.com/jupyter-server/jupyter-resource-usage
+  # migrated from https://github.com/jtpio/jupyterlab-system-monitor and originally from jupyterlab-topbar
+  - jupyter-resource-usage
+  # xeus-python: back-end kernel implementing the Jupyter Debug Protocol
+  # https://github.com/jupyter-xeus/xeus-python
+  - xeus-python
+  # jupyter-server-proxy: run arbitrary external processes alongside your notebook server
+  # https://github.com/jupyterhub/jupyter-server-proxy
+  - jupyter-server-proxy
+  # dask-labextension: A JupyterLab extension for Dask.
+  # https://github.com/dask/dask-labextension
+  - dask-labextension
+  # jupyterlab-geojson: JupyterLab extension for rendering GeoJSON
+  # https://github.com/jupyterlab/jupyter-renderers/tree/main/packages/geojson-extension
+  - jupyterlab-geojson
+  # jupyterlab-topbar: JupyterLab Top Bar Extensions
+  # https://github.com/jtpio/jupyterlab-topbar
+  - pip:
+    - jupyterlab-logout >= 1.1.0
+    - jupyterlab-theme-toggler >= 1.1.0
+
+  # BROWSER SUPPORT
+
+  # firefox: The one and only
+  # https://github.com/mozilla-firefox/firefox
+  - firefox
+  # selenium: Python library for automating web browser interaction
+  # https://github.com/SeleniumHQ/Selenium
+  - selenium