Commit 516d7d66 authored by Nicolas M. Thiéry's avatar Nicolas M. Thiéry
Browse files

Dockerfile refactorisation

- extract environment.yml for base software stack
- add some software for data analysis (notably for ParcoursSup)
- cleanup
parent 5df790be
Pipeline #65451 canceled with stage
in 3 minutes and 7 seconds
#FROM jupyter/minimal-notebook
FROM jupyter/scipy-notebook FROM jupyter/scipy-notebook
#FROM jupyter/minimal-notebook
# Use apt to install rsync, ssh, less, tree # Install system utilities with apt
USER root USER root
RUN apt-get update && \ RUN apt-get update && \
apt-get install -y --no-install-recommends openssh-client rsync unison less tree curl gdb imagemagick && \ apt-get install -y --no-install-recommends openssh-client rsync unison less tree curl gdb imagemagick && \
...@@ -10,13 +10,14 @@ RUN apt-get update && \ ...@@ -10,13 +10,14 @@ RUN apt-get update && \
RUN echo 'export PS1=`echo $JUPYTERHUB_USER| sed s/-at-u-psud.fr//`"@jupyterhub \w \$ "' > /root/.bash_profile RUN echo 'export PS1=`echo $JUPYTERHUB_USER| sed s/-at-u-psud.fr//`"@jupyterhub \w \$ "' > /root/.bash_profile
# Use conda to install the software stack from the relevant repositories # Install conda software stack
USER $NB_UID USER $NB_UID
RUN conda update -n base -c conda-forge --update-all RUN conda update -n base -c conda-forge --update-all
RUN conda install -n base -c conda-forge mamba
# Install the base software stack
RUN conda env update -n base -f environment.yml
# Install the software stack for each of the following repositories
RUN for REPO in \ RUN for REPO in \
https://gitlab.u-psud.fr/MethNum/scripts.git \ https://gitlab.u-psud.fr/MethNum/scripts.git \
https://gitlab.u-psud.fr/Info111/outbound.git \ https://gitlab.u-psud.fr/Info111/outbound.git \
...@@ -30,13 +31,10 @@ RUN for REPO in \ ...@@ -30,13 +31,10 @@ RUN for REPO in \
echo $REPO ;\ echo $REPO ;\
echo =================================================;\ echo =================================================;\
git clone $REPO repo && \ git clone $REPO repo && \
(cd repo; test -d binder && cd binder; conda env update -n base -f environment.yml) && \ (cd repo; test -d binder && cd binder; mamba env update -n base -f environment.yml) && \
rm -rf repo || \ rm -rf repo || \
break 0; \ break 0; \
done done
# R: potential users at STAPS # Install unpackaged jupyterlab extensions and force jupyterlab rebuild
# FactoMineR package: used by Albane Saintenoy and students for PCA / clustering
# in the course "Traitement de données hydrologiques" of M2 HSS
RUN mamba install -c conda-forge r r-essentials r-factominer
RUN jupyter labextension install @wallneradam/run_all_buttons RUN jupyter labextension install @wallneradam/run_all_buttons
# Software installed by default on Paris-Saclay JupyterHub's server
name: jupyterhub-paris-saclay
channels:
- conda-forge
dependencies:
- mamba
- notebook
- jupyterlab
- jupyter_contrib_nbextensions
- ipywidgets
- rise
- pip
- pip:
- nbdime
# Some additional packages that don't have a specific repo yet
# Visualisation
- matplotlib
- cycler # missing matplotlib dependecy: https://stackoverflow.com/questions/44419333/matplotlib-cant-find-cycler
# Data analysis
- pandas # for managing grades
- xlrd # Excel file import / export
- pivottablejs
- qgrid
# R: potential users at STAPS
- r
- r-essentials
# FactoMineR package: used by Albane Saintenoy and students for PCA / clustering
# in the course "Traitement de données hydrologiques" of M2 HSS
- r-factominer
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