test

.woodpecker.yml

@@ -1,19 +1,16 @@
 steps:
-  publish-container:
-    image: taywee/woodpecker-buildah:amd64
-    pull: true
-    environment:
-     - CONDA_CUDA_OVERRIDE=11.2
-     - NVIDIA_VISIBLE_DEVICES=all
+  build_and_release:
+    image: maltegrosse/woodpecker-buildah:0.0.12
     settings:
       registry: git.sandbox.iuk.hdm-stuttgart.de
-      repo: specht/woodpecker-test
-      cache: false
-      tag: git.sandbox.iuk.hdm-stuttgart.de/specht/woodpecker-test:test
+      repository: specht/woodpecker-test
+      #tag: 4.0.12c
+      architectures: aarch64 amd64
       context: Dockerfile
+      imagename: jupyterlab-datascience
       username:
         from_secret: docker_username
       password:
         from_secret: docker_password
-    when:
-      - branch: audio
+    when: 
+      branch: main

Dockerfile

@@ -1,183 +1,20 @@
-FROM python:3.10.8-slim-bullseye
-# debian:bullseye-20230109-slim
+ARG LAB_IMAGE=quay.io/jupyter/scipy-notebook:lab-4.0.12
 ARG NB_USER="jovyan"
 ARG NB_UID="1000"
 ARG NB_GID="100"
-
+FROM ${LAB_IMAGE}
+# kaniko issue https://github.com/GoogleContainerTools/kaniko/issues/1087
+SHELL ["/bin/bash", "-o", "pipefail", "-c"]
+USER root
 RUN apt-get update --yes && \
-    # - apt-get upgrade is run to patch known vulnerabilities in apt-get packages as
-    #   the ubuntu base image is rebuilt too seldom sometimes (less than once a month)
-    apt-get upgrade --yes && \
     apt-get install --yes --no-install-recommends \
-    # - bzip2 is necessary to extract the micromamba executable.
-    bzip2 \
-    ca-certificates \
-    ffmpeg  \
-    git \
-    git-lfs \
-    locales \
-    curl \
-    libportaudio2  \
-    dnsutils \
-    sudo \
-    nano \
-    build-essential \
-    tini \
-    wget && \
-    apt-get clean && rm -rf /var/lib/apt/lists/* && \
-    echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
-    locale-gen
-
-
-# Configure environment
-ENV CONDA_DIR=/opt/conda \
-    SHELL=/bin/bash \
-    NB_USER="${NB_USER}" \
-    NB_UID=${NB_UID} \
-    NB_GID=${NB_GID} \
-    LC_ALL=en_US.UTF-8 \
-    LANG=en_US.UTF-8 \
-    LANGUAGE=en_US.UTF-8
-ENV PATH="${CONDA_DIR}/bin:${PATH}" \
-    HOME="/home/${NB_USER}"
-
-# Copy a script that we will use to correct permissions after running certain commands
-COPY fix-permissions /usr/local/bin/fix-permissions
-RUN chmod a+rx /usr/local/bin/fix-permissions
-
-# Enable prompt color in the skeleton .bashrc before creating the default NB_USER
-# hadolint ignore=SC2016
-RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc && \
-   # Add call to conda init script see https://stackoverflow.com/a/58081608/4413446
-   echo 'eval "$(command conda shell.bash hook 2> /dev/null)"' >> /etc/skel/.bashrc
-
-# Create NB_USER with name jovyan user with UID=1000 and in the 'users' group
-# and make sure these dirs are writable by the `users` group.
-RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
-    sed -i.bak -e 's/^%admin/#%admin/' /etc/sudoers && \
-    sed -i.bak -e 's/^%sudo/#%sudo/' /etc/sudoers && \
-    useradd -l -m -s /bin/bash -N -u "${NB_UID}" "${NB_USER}" && \
-    mkdir -p "${CONDA_DIR}" && \
-    chown "${NB_USER}:${NB_GID}" "${CONDA_DIR}" && \
-    chmod g+w /etc/passwd && \
-    fix-permissions "${HOME}" && \
-    fix-permissions "${CONDA_DIR}"
-
+    git-lfs
 USER ${NB_UID}
-
-# Pin python version here, or set it to "default"
-ARG PYTHON_VERSION=3.10
-
-# Setup work directory for backward-compatibility
-RUN mkdir "/home/${NB_USER}/work" && \
-    fix-permissions "/home/${NB_USER}"
-
-COPY --chown="${NB_UID}:${NB_GID}" initial-condarc "${CONDA_DIR}/.condarc"
-WORKDIR /tmp
-RUN set -x && \
-    arch=$(uname -m) && \
-    if [ "${arch}" = "x86_64" ]; then \
-        # Should be simpler, see <https://github.com/mamba-org/mamba/issues/1437>
-        arch="64"; \
-    fi && \
-    wget -qO /tmp/micromamba.tar.bz2 \
-        "https://micromamba.snakepit.net/api/micromamba/linux-${arch}/latest" && \
-    tar -xvjf /tmp/micromamba.tar.bz2 --strip-components=1 bin/micromamba && \
-    rm /tmp/micromamba.tar.bz2 && \
-    PYTHON_SPECIFIER="python=${PYTHON_VERSION}" && \
-    if [[ "${PYTHON_VERSION}" == "default" ]]; then PYTHON_SPECIFIER="python"; fi && \
-    # Install the packages
-    ./micromamba install \
-        --root-prefix="${CONDA_DIR}" \
-        --prefix="${CONDA_DIR}" \
-        --yes \
-        "${PYTHON_SPECIFIER}" \
-        'mamba' \
-        'jupyter_core' && \
-    rm micromamba && \
-    # Pin major.minor version of python
-    mamba list python | grep '^python ' | tr -s ' ' | cut -d ' ' -f 1,2 >> "${CONDA_DIR}/conda-meta/pinned" && \
-    mamba clean --all -f -y && \
-    fix-permissions "${CONDA_DIR}" && \
-    fix-permissions "/home/${NB_USER}"
-
-#RUN conda update --all --yes
-#RUN conda install -c conda-forge tensorflow-gpu=2.11 -y 
-
-#RUN CONDA_CUDA_OVERRIDE="11.2" mamba install --yes -c conda-forge tensorflow==2.10.0=cuda112py310*
-ENV CONDA_CUDA_OVERRIDE="11.2"  
-ENV NUM_GPUS=1
-#RUN mamba install -y tensorflow cudatoolkit>=11.2 -c conda-forge
-#==2.11.0=cuda*
-#RUN mamba install -y -c conda-forge tensorflow-gpu
-RUN CONDA_OVERRIDE_CUDA="11.2" conda install tensorflow-gpu==2.11.0 -c conda-forge
-RUN CONDA_OVERRIDE_CUDA="11.2" conda install -c conda-forge pytorch-gpu
-WORKDIR /tmp
-RUN mamba install --quiet --yes \
-    'notebook==6.4.12' \
-    'jupyterhub==2.3.1' \
-    'mathjax' \
-    'voila==0.3.7' \
-    'jupyterlab-git' \
-    'numba' \
-    'cython' \
-    'matplotlib' \
-    'pandas' \
-    'scipy' \
-    'scikit-image' \
-    'scikit-learn' \
-    'jupyterlab==3.4.3' \
-    'ipywebrtc' && \
-    jupyter notebook --generate-config && \
-    mamba clean --all -f -y && \
-  #  npm cache clean --force && \
-    jupyter lab clean && \
-    rm -rf "/home/${NB_USER}/.cache/yarn" && \
-    fix-permissions "${CONDA_DIR}" && \
-    fix-permissions "/home/${NB_USER}"
-
-ENV JUPYTER_PORT=8888
-EXPOSE $JUPYTER_PORT
-
-
-
-#RUN pip install ipywidgets voila jupyter-collaboration mathjax
-RUN pip install --extra-index-url https://git.sandbox.iuk.hdm-stuttgart.de/api/packages/grosse/pypi/simple jupyterlab-sandbox-theme
+RUN echo "install custom extensions "
+RUN pip install --extra-index-url https://git.sandbox.iuk.hdm-stuttgart.de/api/packages/grosse/pypi/simple jupyterlab-sandbox-theme==0.1.4
+RUN pip install --extra-index-url https://git.sandbox.iuk.hdm-stuttgart.de/api/packages/grosse/pypi/simple jupyterlab-sandbox-announcement==0.1.3
 #RUN pip install --extra-index-url https://git.sandbox.iuk.hdm-stuttgart.de/api/packages/grosse/pypi/simple jupyterlab-data-pool
 #RUN pip install --extra-index-url https://git.sandbox.iuk.hdm-stuttgart.de/api/packages/grosse/pypi/simple jupyterlab-training
 #RUN pip install --extra-index-url https://git.sandbox.iuk.hdm-stuttgart.de/api/packages/grosse/pypi/simple jupyterlab-synthetic-data
-RUN pip install --extra-index-url https://git.sandbox.iuk.hdm-stuttgart.de/api/packages/grosse/pypi/simple jupyterlab-sandbox-announcement
-RUN pip install sounddevice wavio
-RUN pip install torch==1.13.1+cu116 torchvision==0.14.1+cu116 torchaudio==0.13.1 --extra-index-url https://download.pytorch.org/whl/cu116
-RUN pip install opencv-python-headless
-# Configure container startup
-CMD ["start-notebook.sh"]
-
-# Copy local files as late as possible to avoid cache busting
-COPY start-notebook.sh start-singleuser.sh /usr/local/bin/
-# Currently need to have both jupyter_notebook_config and jupyter_server_config to support classic and lab
-COPY jupyter_server_config.py /etc/jupyter/
-
-# Fix permissions on /etc/jupyter as root
-USER root
-
-RUN echo 'export PATH=/opt/conda/bin:$PATH' >> /etc/profile
-#RUN source /etc/profile
-
-# Legacy for Jupyter Notebook Server, see: [#1205](https://github.com/jupyter/docker-stacks/issues/1205)
-RUN sed -re "s/c.ServerApp/c.NotebookApp/g" \
-    /etc/jupyter/jupyter_server_config.py > /etc/jupyter/jupyter_notebook_config.py && \
-    fix-permissions /etc/jupyter/
-
-# HEALTHCHECK documentation: https://docs.docker.com/engine/reference/builder/#healthcheck
-# This healtcheck works well for `lab`, `notebook`, `nbclassic`, `server` and `retro` jupyter commands
-# https://github.com/jupyter/docker-stacks/issues/915#issuecomment-1068528799
-HEALTHCHECK  --interval=5s --timeout=3s --start-period=5s --retries=3 \
-    CMD wget -O- --no-verbose --tries=1 --no-check-certificate \
-    http${GEN_CERT:+s}://localhost:${JUPYTER_PORT}${JUPYTERHUB_SERVICE_PREFIX:-/}api || exit 1
-
-# Switch back to jovyan to avoid accidental container runs as root
-USER ${NB_UID}
-RUN jupyter labextension disable "@jupyterlab/apputils-extension:announcements"
-#USER root
-WORKDIR "${HOME}"
+RUN pip install ipywebrtc==0.6.0 opencv-python-headless==4.9.0.80 voila==0.5.5
+RUN jupyter labextension disable "@jupyterlab/apputils-extension:announcements"

fix-permissions

@@ -1,35 +0,0 @@
-#!/bin/bash
-# set permissions on a directory
-# after any installation, if a directory needs to be (human) user-writable,
-# run this script on it.
-# It will make everything in the directory owned by the group ${NB_GID}
-# and writable by that group.
-# Deployments that want to set a specific user id can preserve permissions
-# by adding the `--group-add users` line to `docker run`.
-
-# uses find to avoid touching files that already have the right permissions,
-# which would cause massive image explosion
-
-# right permissions are:
-# group=${NB_GID}
-# AND permissions include group rwX (directory-execute)
-# AND directories have setuid,setgid bits set
-
-set -e
-
-for d in "$@"; do
-    find "${d}" \
-        ! \( \
-            -group "${NB_GID}" \
-            -a -perm -g+rwX \
-        \) \
-        -exec chgrp "${NB_GID}" {} \; \
-        -exec chmod g+rwX {} \;
-    # setuid, setgid *on directories only*
-    find "${d}" \
-        \( \
-            -type d \
-            -a ! -perm -6000 \
-        \) \
-        -exec chmod +6000 {} \;
-done

initial-condarc

@@ -1,6 +0,0 @@
-# Conda configuration see https://conda.io/projects/conda/en/latest/configuration.html
-
-auto_update_conda: false
-show_channel_urls: true
-channels:
-  - conda-forge

jupyter_server_config.py

@@ -1,57 +0,0 @@
-# Copyright (c) Jupyter Development Team.
-# Distributed under the terms of the Modified BSD License.
-# mypy: ignore-errors
-import os
-import stat
-import subprocess
-
-from jupyter_core.paths import jupyter_data_dir
-
-c = get_config()  # noqa: F821
-c.ServerApp.ip = "0.0.0.0"
-c.ServerApp.port = 8888
-c.ServerApp.open_browser = False
-
-# https://github.com/jupyter/notebook/issues/3130
-c.FileContentsManager.delete_to_trash = False
-
-# Generate a self-signed certificate
-OPENSSL_CONFIG = """\
-[req]
-distinguished_name = req_distinguished_name
-[req_distinguished_name]
-"""
-if "GEN_CERT" in os.environ:
-    dir_name = jupyter_data_dir()
-    pem_file = os.path.join(dir_name, "notebook.pem")
-    os.makedirs(dir_name, exist_ok=True)
-
-    # Generate an openssl.cnf file to set the distinguished name
-    cnf_file = os.path.join(os.getenv("CONDA_DIR", "/usr/lib"), "ssl", "openssl.cnf")
-    if not os.path.isfile(cnf_file):
-        with open(cnf_file, "w") as fh:
-            fh.write(OPENSSL_CONFIG)
-
-    # Generate a certificate if one doesn't exist on disk
-    subprocess.check_call(
-        [
-            "openssl",
-            "req",
-            "-new",
-            "-newkey=rsa:2048",
-            "-days=365",
-            "-nodes",
-            "-x509",
-            "-subj=/C=XX/ST=XX/L=XX/O=generated/CN=generated",
-            f"-keyout={pem_file}",
-            f"-out={pem_file}",
-        ]
-    )
-    # Restrict access to the file
-    os.chmod(pem_file, stat.S_IRUSR | stat.S_IWUSR)
-    c.ServerApp.certfile = pem_file
-
-# Change default umask for all subprocesses of the notebook server if set in
-# the environment
-if "NB_UMASK" in os.environ:
-    os.umask(int(os.environ["NB_UMASK"], 8))

start-notebook.sh

@@ -1,22 +0,0 @@
-#!/bin/bash
-# Copyright (c) Jupyter Development Team.
-# Distributed under the terms of the Modified BSD License.
-
-set -e
-
-# The Jupyter command to launch
-# JupyterLab by default
-DOCKER_STACKS_JUPYTER_CMD="${DOCKER_STACKS_JUPYTER_CMD:=lab}"
-
-if [[ -n "${JUPYTERHUB_API_TOKEN}" ]]; then
-    echo "WARNING: using start-singleuser.sh instead of start-notebook.sh to start a server associated with JupyterHub."
-    exec /usr/local/bin/start-singleuser.sh "$@"
-fi
-
-wrapper=""
-if [[ "${RESTARTABLE}" == "yes" ]]; then
-    wrapper="run-one-constantly"
-fi
-
-# shellcheck disable=SC1091,SC2086
-exec /usr/local/bin/start.sh ${wrapper} jupyter ${DOCKER_STACKS_JUPYTER_CMD} ${NOTEBOOK_ARGS} "$@"

start-singleuser.sh

@@ -1,13 +0,0 @@
-#!/bin/bash
-# Copyright (c) Jupyter Development Team.
-# Distributed under the terms of the Modified BSD License.
-
-set -e
-
-# set default ip to 0.0.0.0
-if [[ "${NOTEBOOK_ARGS} $*" != *"--ip="* ]]; then
-    NOTEBOOK_ARGS="--ip=0.0.0.0 ${NOTEBOOK_ARGS}"
-fi
-
-# shellcheck disable=SC1091,SC2086
-. /usr/local/bin/start.sh jupyterhub-singleuser ${NOTEBOOK_ARGS} "$@"