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Upgrade binder submodule, use fully pinned environment definition #4

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Upgrade binder submodule, use fully pinned environment definition #4

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25 changes: 7 additions & 18 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -2,13 +2,13 @@ FROM jupyter/base-notebook

USER root
RUN apt-get update \
&& apt-get install -yq --no-install-recommends dnsutils libfuse-dev nano fuse vim git build-essential openssh-client \
&& apt-get install -yq --no-install-recommends dnsutils libfuse-dev nano fuse vim git build-essential openssh-client \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*

USER $NB_USER
RUN conda config --set ssl_verify no
COPY binder/environment.yml /tmp/environment.yml
COPY binder/environment-pinned-linux.yml /tmp/environment.yml
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This is the main change, using the fully pinned environment file.


ARG tag
RUN echo "image tag is $tag"
Expand All @@ -17,29 +17,22 @@ ENV IMAGETAG=$tag
RUN echo " ---------------------------------- "
RUN echo "env variable IMAGETAG is ${IMAGETAG}"

# create default scientific Python environment



# create default scientific Python environment

RUN conda config --add channels pyviz/label/dev
RUN conda config --add channels bokeh/label/dev
RUN conda config --add channels intake
RUN conda config --add channels bioconda
RUN conda config --add channels conda-forge
#RUN conda update --yes conda
RUN conda config --set channel_priority strict
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This is also an important change, ensures packages are pulled from conda-forge instead of defaults wherever possible, which results in a more consistent environment.

RUN conda update --yes conda
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I saw this had been commented out, but there have been some improvements in recent conda versions, so thought maybe best to run it?


RUN conda env update --file /tmp/environment.yml --prune
RUN conda env update --file /tmp/environment.yml
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We are installing this into the base environment, is that right?

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I.e., I think the environment name from within the environment file will be ignored.

RUN conda clean -afy
# && find /opt/conda/ -follow -type f -name '*.a' -delete \
# && find /opt/conda/ -follow -type f -name '*.pyc' -delete \
# && find /opt/conda/ -follow -type f -name '*.js.map' -delete
#


RUN /opt/conda/bin/pip install nbserverproxy
RUN conda install nb_conda

RUN conda install nb_conda

RUN jupyter labextension install @jupyter-widgets/jupyterlab-manager
RUN jupyter labextension install @jupyterlab/hub-extension
Expand All @@ -49,9 +42,6 @@ RUN jupyter labextension install dask-labextension

RUN jupyter serverextension enable --py nbserverproxy --sys-prefix




USER root
COPY prepare.sh /usr/bin/prepare.sh
RUN chmod +x /usr/bin/prepare.sh
Expand All @@ -76,4 +66,3 @@ ENV PATH /opt/conda/envs/$(head -1 /tmp/environment.yml | cut -d' ' -f2)/bin:$PA

ENTRYPOINT ["tini", "--", "/usr/bin/prepare.sh"]
CMD ["start.sh jupyter lab"]

2 changes: 1 addition & 1 deletion binder
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Submodule binder updated from aeb86c to 13624d