Use pangeo/pangeo-notebook as base image

Curated upstream image! But it doesn't have R, so we add it. Our environment.yml file only adds packages that aren't in the base image. Ref #3
2i2c-org · Nov 12, 2020 · f070c29 · f070c29
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commit f070c29
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diff --git a/deployments/ohw/image/Dockerfile b/deployments/ohw/image/Dockerfile
@@ -1,62 +1,21 @@
-FROM buildpack-deps:focal-scm
+FROM pangeo/pangeo-notebook:6b2df38
 
-ENV LC_ALL en_US.UTF-8
-ENV LANG en_US.UTF-8
-ENV LANGUAGE en_US.UTF-8
+USER root
 ENV DEBIAN_FRONTEND=noninteractive
-ENV NB_USER jovyan
-ENV NB_UID 1000
-
-ENV CONDA_DIR /opt/conda
 ENV R_LIBS_USER /opt/r
 
-ENV PATH ${CONDA_DIR}/bin:$PATH
-
-RUN adduser --disabled-password --gecos "Default Jupyter user" ${NB_USER}
-#
 # Create user owned R libs dir
 # This lets users temporarily install packages
 RUN mkdir -p ${R_LIBS_USER} && chown ${NB_USER}:${NB_USER} ${R_LIBS_USER}
-
-# Install these without 'recommended' packages to keep image smaller.
-# Useful utils that folks sort of take for granted
-RUN apt-get update -qq --yes && \
-    apt-get install --yes --no-install-recommends -qq \
-        htop \
-        less \
-        man \
-        nano \
-        screen \
-        tar \
-        tmux \
-        wget \
-        vim \
-        locales > /dev/null
-
-RUN echo "${LC_ALL} UTF-8" > /etc/locale.gen && \
-    locale-gen
-
-# for nbconvert & notebook-to-pdf
-RUN apt-get update -qq --yes && \
-    apt-get install --yes -qq \
-        pandoc \
-        texlive-xetex \
-        texlive-fonts-recommended \
-        > /dev/null
-
-WORKDIR /home/jovyan
-
-COPY install-miniforge.bash /tmp/install-miniforge.bash
-RUN /tmp/install-miniforge.bash
-
 # Install R packages
 RUN apt-get update -qq --yes > /dev/null && \
     apt-get install --yes -qq \
+    curl \
     r-base \
     r-base-dev \
     r-recommended \
-    r-cran-littler > /dev/null
-#
+    r-cran-littler
+
 # Needed by many R libraries
 # Picked up from https://github.com/rocker-org/rocker/blob/9dc3e458d4e92a8f41ccd75687cd7e316e657cc0/r-rspm/focal/Dockerfile
 # Our pre-built R packages from rspm are built against system libs in focal
@@ -104,9 +63,6 @@ COPY rsession.conf /etc/rstudio/rsession.conf
 
 USER ${NB_USER}
 
-# FIXME: Split this into two files
-# We can then install things that require python / jupyter separate
-# from scientific python libs - speeding up image build times a lot
 COPY environment.yml /tmp/
 
 RUN conda env update -p ${CONDA_DIR} -f /tmp/environment.yml

diff --git a/deployments/ohw/image/environment.yml b/deployments/ohw/image/environment.yml
@@ -1,73 +1,33 @@
+# Environment we need *on top* of base PANGEO stack
+# Get list of pangeo packages from https://github.com/pangeo-data/pangeo-docker-images/blob/master/pangeo-notebook/packages.txt
+# BUT REMEMBER TO PICK THE HASH THAT CORRESPONDS TO OUR BASE IMAGE
 channels:
   - conda-forge
 
 dependencies:
-  # language runtimes
-  - python=3.8.*
-  - nodejs=14.8.*
-
-  - beautifulsoup4
-  - boto3
-  - botocore
-  - bottleneck
-  - cartopy
   - cdsapi
   - cmip6_preprocessing
-  - esmf
-  - ffmpeg
-  - fsspec
-  - gcsfs
-  - h5py
   - iris
-  - lxml
-  - matplotlib
-  - metpy
-  - netcdf4
-  - numpy
-  # - opendrift
-  - pandas
   - pvlib-python
-  - s3fs
-  - satpy
-  - scikit-learn
-  - scipy
   - seaborn
   - seawater
   - siphon
   - pytables
-  - xarray
   - xesmf
-  - zarr
-  - geopandas
-  - descartes
-  - rioxarray
-  - nc-time-axis
-  # Let's make sure that dask-versions match between here & dask gateway
-  - dask==2.27.0
-  - distributed==2.27.0
-  - dask-gateway==0.8.0
-  - dask-kubernetes==0.10.1
 
   - pip
 
   - pip:
     # Infrastructure things
-    - jupyterlab==2.*
     - voila==0.1.23
-    - nbgitpuller==0.9.*
     - nbresuse==0.3.6
     - nbinteract==0.2.5
     - jupytext==1.6.*
     - RISE==5.6.1
     - jupyter_contrib_nbextensions==0.5.1
     - jupyter-desktop-server==0.1.3
-    - notebook==6.1.4
-    - jupyterhub==1.1.0
-    - jupyter-server-proxy==1.5.0
     - jupyter-rsession-proxy==1.2
     - jupyter-tree-download==1.0.1
-    - ipywidgets==7.5.1
-    - dask-labextension==3.0.0
 
     # Science things. Prefer conda for these if possible
     - git+https://github.com/trondkr/xESMF.git@27952e1ab2f1b7b23c443953b9d1e079376efb08

diff --git a/deployments/ohw/image/install-jupyter-extensions.bash b/deployments/ohw/image/install-jupyter-extensions.bash
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/bash -l
 
 jupyter labextension install --debug \
     @jupyter-widgets/jupyterlab-manager@2 \