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Cleaned Dockerfile for Lipari23 #148

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Jul 4, 2023
Merged

Cleaned Dockerfile for Lipari23 #148

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103 changes: 4 additions & 99 deletions single-user-sobigdata-lipari23/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -7,109 +7,14 @@
# __/ |
# |___/

FROM jupyter/datascience-notebook:59c973d16bca
ARG BASE_IMAGE=eginotebooks/d4science-base:latest

USER root

RUN apt-get update \
&& apt-get install --no-install-recommends -y \
nco \
cdo \
cmake \
g++ \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
FROM $BASE_IMAGE

USER $NB_UID

ARG SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL=True

RUN mamba install -y --quiet \
basemap \
beakerx \
xgboost \
lightgbm \
catboost \
netcdf4 \
aiohttp \
graph-tool \
scikit-learn \
scikit-mobility \
dask-jobqueue \
fs \
rasterio \
contextily \
nb_conda_kernels \
nb_conda \
&& conda clean -tipsy

# Pinned networkx to 2.6.3 as 2.7 makes networksns fail
RUN pip install --no-cache-dir \
bicm \
rdp \
sentinelhub \
import_ipynb \
nbresuse \
ndlib \
motuclient \
panel==0.9.* \
cython \
node_conformity \
git+https://github.com/geopython/OWSLib.git \
git+https://github.com/guglielmocola/RetweetCascade.git \
fast-forward-indexes \
NEMtropy \
folium==0.11.0 \
geopy==2.0.0 \
hvplot==0.6.0 \
intake==0.6.0 \
intake-esm==2020.8.15 \
hda \
seaborn==0.11.0 \
zarr==2.5.0 \
holoviews \
networkx==2.6.3 \
networksns \
eventclf \
XAI-Library \
convrewriting \
git+https://github.com/guglielmocola/TwitterMonitorLib_v2.git \
pygm \
structify-net

# -------------------------------
# SoBigData ++ specific libraries
# -------------------------------
RUN mamba install -y --quiet \
pyspark \
pyfim \
pyclustering \
transformers \
rtree \
geopandas \
nltk \
pydotplus \
plotly \
graphviz \
keras \
selenium \
tweepy \
openjdk=8 \
&& conda clean --all

RUN mamba install -y pytorch==1.6.0 torchtext torchvision -c pytorch \
&& conda clean --all

RUN pip install --no-cache-dir \
import_ipynb \
opencv-python \
simpletransformers \
shuffle-graph \
privlib \
ash_model \
cdlib==0.3.0 \
bayanpy \
dynetx==0.3.2

# -------------------------------
# SoBigData Lipari Summer School 2023 (https://sobigdata23.liparischool.it)
Expand Down Expand Up @@ -143,5 +48,5 @@ RUN pip install --no-cache-dir \

# -------------------------------

#RUN jupyter labextension install jupyterlab-topbar-extension jupyterlab-system-monitor
#RUN jupyter labextension disable @jupyterlab/filebrowser-extension:share-file
RUN jupyter labextension install jupyterlab-topbar-extension jupyterlab-system-monitor
RUN jupyter labextension disable @jupyterlab/filebrowser-extension:share-file