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Dockerfile for EUCP project data & Jupyter server
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‎Dockerfile‎

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# Docker notebook for climate analysis - European Climate Prediction project
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FROM jupyter/datascience-notebook:1386e2046833
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LABEL maintainer="EUCP-NLESC <e.rol@esciencecenter.nl>"
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ENV PCRASTER_DIR=/usr/local/pcraster
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USER root
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RUN apt-get update \
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&& apt-get install -y --no-install-recommends \
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tcsh \
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zsh \
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less \
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htop \
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grads \
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ncl-ncarg \
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cmake \
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libgl1-mesa-dev \
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gcc \
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g++ \
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git \
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gnuplot \
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imagemagick \
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qtbase5-dev \
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libncurses5-dev \
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libqwt-qt5-dev \
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libqt5opengl5-dev \
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libboost-all-dev \
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libgdal-dev \
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python3-numpy \
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python3-docopt \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/*
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RUN mkdir -p $PCRASTER_DIR \
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&& chown $NB_UID $PCRASTER_DIR \
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&& fix-permissions $PCRASTER_DIR
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RUN cd /tmp \
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&& curl -O http://pcraster.geo.uu.nl/pcraster/4.2.1/pcraster-4.2.1.tar.bz2 \
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&& tar -jxvf pcraster-4.2.1.tar.bz2 \
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&& cd pcraster-4.2.1 \
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&& mkdir build \
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&& cd build \
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&& PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin \
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&& cmake -Wno-dev -DPYTHON_EXECUTABLE:FILEPATH=/usr/bin/python3 -DFERN_BUILD_ALGORITHM:BOOL=TRUE -DCMAKE_INSTALL_PREFIX:PATH=$PCRASTER_DIR .. \
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&& cmake --build . \
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&& make install
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RUN rm -r /tmp/pcraster*
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USER $NB_UID
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# Notes:
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# - grads is not available under Conda
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# - installing ncl under Conda messes up the notebook; for example, the R kernel disappears from the menu
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# - Downgrade Matplotlib to 2.2 for Iris
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# - pyngl and pynio have incompatible dependencies with some other packages
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RUN conda install --quiet --yes --channel esmvalgroup --channel conda-forge --channel pcmdi/label/nightly --override-channels \
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'ipyleaflet' \
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'ipywidgets' \
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'iris' \
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'iris-sample-data' \
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'cftime' \
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'nc-time-axis' \
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'h5py' \
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'netcdf4' \
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'pyproj' \
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'cartopy' \
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'dask' \
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'xarray' \
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'boost' \
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'gdal' \
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'cdo' \
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'nco' \
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'cdms2' \
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'eofs' \
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'esmpy' \
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# 'esmvalcore' \
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'cmor' \
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'python=3.7' \
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&& conda clean --all -f -y \
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&& fix-permissions $CONDA_DIR \
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&& fix-permissions /home/$NB_USER
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# For some reason, Conda's cdo does not appear to include the Python
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# interface, so it's installed through pip
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# The installation of cf-plot will install matplotlib 3.1, which is technically
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# different than 2.2; the latter is used by Iris.
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# Note: cfunits is not cf-units: cf(dm/-python/-lplot) uses cfunits,
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# Iris uses cf-units (imported as cf_units)
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RUN pip install \
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cdo==1.5.3 \
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cfdm==1.7.7 \
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cf-python==3.0.1 \
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cf-plot==3.0.5 \
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cfunits==3.1.1 \
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MetPy==0.11.1
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RUN pip install jupyterlab_thredds
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RUN jupyter labextension install @jupyter-widgets/jupyterlab-manager
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RUN jupyter labextension install jupyter-leaflet
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#RUN jupyter labextension install @ewatercycle/jupyterlab_thredds
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ENV PATH=${PATH}:${PCRASTER_DIR}/bin
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ENV PYTHONPATH=${PYTHONPATH}:${PCRASTER_DIR}/python
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# set path explicitly, because otherwise cfunits can't be imported
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ENV UDUNITS2_XML_PATH=/opt/conda/share/udunits/udunits2.xml

‎LICENSE‎

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‎NOTICE‎

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EUCP notebook
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Copyright 2019 Netherlands eScience Center
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Licensed under the Apache License, Version 2.0 (the "License");
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you may not use this file except in compliance with the License.
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You may obtain a copy of the License at
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http://www.apache.org/licenses/LICENSE-2.0
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Unless required by applicable law or agreed to in writing, software
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distributed under the License is distributed on an "AS IS" BASIS,
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WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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See the License for the specific language governing permissions and
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limitations under the License.

‎todo.txt‎

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New base: jupyter/datascience-notebook
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One that contains JupyterLab > 1.0.1
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Python packages:
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- MetPy
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System packages:
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- tsc? [npm]
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