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More installation updates

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This commit is contained in:
Ayaz Salikhov
2021-05-25 14:34:02 +03:00
parent 7942cb1c2b
commit ccebe16e6e
9 changed files with 60 additions and 36 deletions
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4
all-spark-notebook/Dockerfile
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@@ -8,8 +8,8 @@ LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
USER root
# RSpark config
ENV R_LIBS_USER $SPARK_HOME/R/lib
RUN fix-permissions $R_LIBS_USER
ENV R_LIBS_USER "${SPARK_HOME}/R/lib"
RUN fix-permissions "${R_LIBS_USER}"
# R pre-requisites
RUN apt-get update --yes && \

14
base-notebook/Dockerfile
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@@ -90,15 +90,15 @@ RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
mkdir -p $CONDA_DIR && \
chown $NB_USER:$NB_GID $CONDA_DIR && \
chmod g+w /etc/passwd && \
fix-permissions $HOME && \
fix-permissions $CONDA_DIR
fix-permissions "${HOME}" && \
fix-permissions "${CONDA_DIR}"
USER $NB_UID
ARG PYTHON_VERSION=default
# Setup work directory for backward-compatibility
RUN mkdir "/home/$NB_USER/work" && \
fix-permissions "/home/$NB_USER"
fix-permissions "/home/${NB_USER}"
# Install conda as jovyan and check the sha256 sum provided on the download site
WORKDIR /tmp
@@ -120,8 +120,8 @@ RUN wget --quiet "https://github.com/conda-forge/miniforge/releases/download/${m
conda update --all --quiet --yes && \
conda clean --all -f -y && \
rm -rf /home/$NB_USER/.cache/yarn && \
fix-permissions $CONDA_DIR && \
fix-permissions /home/$NB_USER
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"
# Install Jupyter Notebook, Lab, and Hub
# Generate a notebook server config
@@ -138,8 +138,8 @@ RUN conda install --quiet --yes \
jupyter notebook --generate-config && \
jupyter lab clean && \
rm -rf /home/$NB_USER/.cache/yarn && \
fix-permissions $CONDA_DIR && \
fix-permissions /home/$NB_USER
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"
EXPOSE 8888

2
docs/using/common.md
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@@ -137,7 +137,7 @@ conda install --channel defaults humanize
conda config --system --prepend channels defaults
# install a package
conda install --quiet --yes humanize && \
mamba clean --all -f -y && \
conda clean --all -f -y && \
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"
```

61
docs/using/recipes.md
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@@ -32,7 +32,9 @@ Create a new Dockerfile like the one shown below.
# Start from a core stack version
FROM jupyter/datascience-notebook:33add21fab64
# Install in the default python3 environment
RUN pip install 'ggplot==0.6.8'
RUN pip install --quiet --no-cache-dir 'flake8==3.9.2' && \
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"
```
Then build a new image.
@@ -49,9 +51,9 @@ packages desired. Next, create a new Dockerfile like the one shown below.
FROM jupyter/datascience-notebook:33add21fab64
# Install from requirements.txt file
COPY --chown=${NB_UID}:${NB_GID} requirements.txt /tmp/
RUN pip install --requirement /tmp/requirements.txt && \
fix-permissions $CONDA_DIR && \
fix-permissions /home/$NB_USER
RUN pip install --quiet --no-cache-dir --requirement /tmp/requirements.txt && \
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"
```
For conda, the Dockerfile is similar:
@@ -62,8 +64,9 @@ FROM jupyter/datascience-notebook:33add21fab64
# Install from requirements.txt file
COPY --chown=${NB_UID}:${NB_GID} requirements.txt /tmp/
RUN conda install --yes --file /tmp/requirements.txt && \
fix-permissions $CONDA_DIR && \
fix-permissions /home/$NB_USER
conda clean --all -f -y && \
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"
```
Ref: [docker-stacks/commit/79169618d571506304934a7b29039085e77db78c](https://github.com/jupyter/docker-stacks/commit/79169618d571506304934a7b29039085e77db78c#commitcomment-15960081)
@@ -124,8 +127,8 @@ RUN conda create --quiet --yes -p $CONDA_DIR/envs/$conda_env python=$py_ver ipyt
# create Python 3.x environment and link it to jupyter
RUN $CONDA_DIR/envs/${conda_env}/bin/python -m ipykernel install --user --name=${conda_env} && \
fix-permissions $CONDA_DIR && \
fix-permissions /home/$NB_USER
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"
# any additional pip installs can be added by uncommenting the following line
# RUN $CONDA_DIR/envs/${conda_env}/bin/pip install
@@ -154,7 +157,9 @@ Run jupyterlab using a command such as
FROM jupyter/scipy-notebook:latest
# Install the Dask dashboard
RUN pip install dask-labextension
RUN pip install --quiet --no-cache-dir dask-labextension && \
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"
# Dask Scheduler & Bokeh ports
EXPOSE 8787
@@ -192,7 +197,10 @@ notebooks, with no conversion, adding javascript Reveal.js:
```bash
# Add Live slideshows with RISE
RUN conda install -c damianavila82 rise
RUN conda install --quiet --yes -c damianavila82 rise && \
conda clean --all -f -y && \
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"
```
Credit: [Paolo D.](https://github.com/pdonorio) based on
@@ -204,11 +212,16 @@ You need to install conda's gcc for Python xgboost to work properly. Otherwise,
exception about libgomp.so.1 missing GOMP_4.0.
```bash
%%bash
conda install -y gcc
pip install xgboost
conda install --quiet --yes gcc && \
conda clean --all -f -y && \
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"
import xgboost
pip install --quiet --no-cache-dir xgboost && \
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"
# run "import xgboost" in python
```
## Running behind a nginx proxy
@@ -308,7 +321,9 @@ version in the Hub itself.
```dockerfile
FROM jupyter/base-notebook:33add21fab64
RUN pip install jupyterhub==0.8.0b1
RUN pip install --quiet --no-cache-dir jupyterhub==1.4.1 && \
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"
```
Credit: [MinRK](https://github.com/jupyter/docker-stacks/issues/423#issuecomment-322767742)
@@ -444,9 +459,11 @@ USER $NB_USER
# - Dashboards
# - PyDoop
# - PyHive
RUN pip install jupyter_dashboards faker && \
RUN pip install --quiet --no-cache-dir jupyter_dashboards faker && \
jupyter dashboards quick-setup --sys-prefix && \
pip2 install pyhive pydoop thrift sasl thrift_sasl faker
pip2 install --quiet --no-cache-dir pyhive pydoop thrift sasl thrift_sasl faker && \
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"
USER root
# Ensure we overwrite the kernel config so that toree connects to cluster
@@ -488,10 +505,12 @@ FROM jupyter/minimal-notebook:latest
USER $NB_USER
RUN pip install jupyter_contrib_nbextensions && \
RUN pip install --quiet --no-cache-dir jupyter_contrib_nbextensions && \
jupyter contrib nbextension install --user && \
# can modify or enable additional extensions here
jupyter nbextension enable spellchecker/main --user
jupyter nbextension enable spellchecker/main --user && \
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"
```
Ref: <https://github.com/jupyter/docker-stacks/issues/675>
@@ -513,7 +532,9 @@ RUN apt-get update --yes && \
USER $NB_UID
RUN pip install --quiet --no-cache-dir auto-sklearn
RUN pip install --quiet --no-cache-dir auto-sklearn && \
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"
```
## Enable Delta Lake in Spark notebooks

2
examples/docker-compose/notebook/Dockerfile
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@@ -13,4 +13,4 @@ USER $NB_UID
# Switch back to jovyan to avoid accidental container runs as root
# Add permanent pip/conda installs, data files, other user libs here
# e.g., RUN pip install jupyter_dashboards
# e.g., RUN pip install --quiet --no-cache-dir flake8

2
examples/make-deploy/Dockerfile
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@@ -13,4 +13,4 @@ USER $NB_UID
# Switch back to jovyan to avoid accidental container runs as root
# Add permanent pip/conda installs, data files, other user libs here
# e.g., RUN pip install jupyter_dashboards
# e.g., RUN pip install --quiet --no-cache-dir flake8

4
examples/source-to-image/README.md
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@@ -102,8 +102,8 @@ This means that so long as a set of notebook files provides one of these files l
A final step is:
```bash
fix-permissions $CONDA_DIR
fix-permissions /home/$NB_USER
fix-permissions "${CONDA_DIR}"
fix-permissions "/home/${NB_USER}"
```
This fixes up permissions on any new files created by the build. This is necessary to ensure that when the image is run, you can still install additional files. This is important for when an image is run in `sudo` mode, or it is hosted in a more secure container platform such as Kubernetes/OpenShift where it will be run as a set user ID that isn't known in advance.

5
r-notebook/Dockerfile
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@@ -49,4 +49,7 @@ RUN conda install --quiet --yes \
fix-permissions "/home/${NB_USER}"
# Install e1071 R package (dependency of the caret R package)
RUN conda install --quiet --yes r-e1071
RUN conda install --quiet --yes r-e1071 && \
conda clean --all -f -y && \
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"

2
tensorflow-notebook/Dockerfile
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@@ -8,6 +8,6 @@ LABEL maintainer="Jupyter Project <jupyter@googlegroups.com>"
# Install Tensorflow
RUN mamba install --quiet --yes \
'tensorflow=2.4.1' && \
conda clean --all -f -y && \
mamba clean --all -f -y && \
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"