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51 changes: 21 additions & 30 deletions Dockerfile
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Expand Up @@ -13,39 +13,30 @@ WORKDIR "${HOME}"
# remove the "work/" directory added in an earlier layer...
RUN rm -rf work


RUN pip install docutils==0.17.1 # Need to pin docutils to an old version for now, due to https://github.com/executablebooks/jupyter-book/issues/2022
RUN pip install referencing
RUN pip install jupyter-book
# Pinning pandas until altair 5.1.2 to avoid future warning https://github.com/altair-viz/altair/issues/3181
RUN pip install numpy jinja2 pandas altair">=5.1.2" "vegafusion[embed]" vl-convert-python">=0.14" click ibis-framework ghp-import jupytext nodejs lxml

# forces scikit-learn to grab latest to avoid bug in 1.3.0 related to checking for c-contiguity breaking figures in classification 2. See https://github.com/scikit-learn/scikit-learn/pull/26772
# TODO: remove this once scikit-learn 1.4.x or beyond releases and is incorporated into jupyter/scipy-notebook
RUN pip install -U git+https://github.com/scikit-learn/scikit-learn.git@main

# install plotly for 3d figures
RUN pip install plotly

# disable warnings that pollute build logs; seems to be related to the update to python 3.11
# https://discourse.jupyter.org/t/debugger-warning-it-seems-that-frozen-modules-are-being-used-python-3-11-0/16544/12
ENV PYDEVD_DISABLE_FILE_VALIDATION=1

## Install various python packages
# commented out for now due to various package version conflicts
# installing via pip instead above
#RUN mamba install --quiet --yes \
# 'numpy' \
# 'jinja2' \
# 'altair_data_server' \
# 'altair_saver' \
# 'click' \
# 'ibis-framework' \
# 'ghp-import' \
# 'jupytext' \
# 'jupyter-book' \
# 'nodejs' \
# && mamba clean --all -f -y \
# && fix-permissions "${CONDA_DIR}" \
# && fix-permissions "/home/${NB_USER}"
RUN mamba install --quiet --yes \
'numpy' \
'pandas>=2.1.3' \
'jinja2' \
'altair>=5.1.2' \
'vl-convert-python>=0.14' \
'vegafusion[embed]' \
'click' \
'ibis-framework' \
'ghp-import' \
'jupytext' \
'jupyter-book' \
'scikit-learn>=1.3.2' \
'nodejs' \
'plotly' \
'lxml' \
'referencing' \
'docutils==0.17.1' \
&& mamba clean --all -f -y \
&& fix-permissions "${CONDA_DIR}" \
&& fix-permissions "/home/${NB_USER}"