Add labextensios for code quality

.zenodo.json

@@ -9,6 +9,11 @@
             "affiliation": "Netherlands eScience Center",
             "name": "Kalverla, Peter",
             "orcid": "0000-0002-5025-7862"
+        },
+        {
+            "affiliation": "Netherlands eScience Center",
+            "name": "Camphuijsen, Jaro",
+            "orcid": "0000-0002-8928-7831"
         }
     ],
     "description": "This software specifies the Jupyter Lab environment set up for the Horizon 2020 project \"European Climate Prediction\" (EUCP).",

CITATION.cff

@@ -1,7 +1,7 @@
 # YAML 1.2
 ---
 abstract: "This software specifies the Jupyter Lab environment set up for the Horizon 2020 project \"European Climate Prediction\" (EUCP)."
-authors: 
+authors:
   -
     affiliation: "Netherlands eScience Center"
     family-names: Rol
@@ -12,6 +12,12 @@ authors:
     family-names: Kalverla
     given-names: Peter
     orcid: "https://orcid.org/0000-0002-5025-7862"
+  -
+    affiliation: "Netherlands eScience Center"
+    family-names: Camphuijsen
+    given-names: Jaro
+    orcid: "https://orcid.org/0000-0002-8928-7831"
+
 cff-version: "1.1.0"
 date-released: 2020-05-20
 doi: "10.5281/zenodo.3835951"

Dockerfile

@@ -1,13 +1,9 @@
 # Docker notebook for climate analysis - European Climate Prediction project
 
-FROM jupyter/datascience-notebook:1386e2046833
-
+FROM jupyter/datascience-notebook:3b1f4f5e6cc1
 
 LABEL maintainer="EUCP-NLESC <e.rol@esciencecenter.nl>"
 
-
-ENV PCRASTER_DIR=/usr/local/pcraster
-
 USER root
 
 RUN apt-get update \
@@ -36,71 +32,62 @@ RUN apt-get update \
  && apt-get clean \
  && rm -rf /var/lib/apt/lists/*
 
-RUN mkdir -p $PCRASTER_DIR \
- && chown $NB_UID $PCRASTER_DIR \
- && fix-permissions $PCRASTER_DIR
-
-
 USER $NB_UID
 
 # Notes:
 # - grads is not available under Conda
 # - installing ncl under Conda messes up the notebook; for example, the R kernel disappears from the menu
-# - Downgrade Matplotlib to 2.2 for Iris
 # - pyngl and pynio have incompatible dependencies with some other packages
-RUN conda install --quiet --yes --channel esmvalgroup --channel conda-forge --channel pcmdi/label/nightly --override-channels \
-    'python=3.7.6' \
+# - cfunits is not cf-units: cf(dm/-python/-lplot) uses cfunits, iris uses cf-units (imported as cf_units)
+
+RUN conda install --quiet --yes --channel esmvalgroup --channel pcmdi/label/nightly --channel ncas \
+    # Ensure backwards compatibility:
     'boost=1.72.0'\
-    'cartopy=0.17.0' \
+    'cartopy=0.18.0' \
     'cdms2=3.1.3' \
-    # 'cdo=1.5.3' \
-    'cftime=1.1.1.2' \
+    'cf-plot=3.0.20' \
+    'cf-python=3.1.0' \
+    'cfdm=1.7.11' \
     'cmor=2019.05.16.master.numpy' \
-    'dask=2.2.0' \
     'eofs=1.4.0' \
-    'esmpy=8.0.0' \
-    'gdal=3.0.4' \
-    'h5py=2.10.0' \
+    'esmvalcore=2.0.0b9' \
+    'esmvaltool-python=2.0.0b4' \
     'imod=0.9.0' \
-    'ipyleaflet=0.12.4' \
-    'ipywidgets=7.5.1' \
-    'iris=2.4.0' \
+    'ipyleaflet=0.12.6' \
     'iris-sample-data=2.2.0' \
+    'iris=2.4.0' \
+    'matplotlib=3.2.1' \
+    'metpy=0.12.1' \
     'nc-time-axis=1.2.0' \
-    'nco=4.9.1' \
-    'netcdf4=1.5.3' \
+    'nco=4.9.2' \
     'pcraster=4.3.0' \
-    'pyproj=2.6.0' \
-    'rasterio=1.1.3' \
+    'python-cdo=1.5.3' \
+    'python=3.7.6' \
     'xarray=0.15.1' \
     'zarr=2.4.0' \
-#    'esmvalcore' \
  && conda clean --all -f -y \
  && fix-permissions $CONDA_DIR \
  && fix-permissions /home/$NB_USER
 
-# For some reason, Conda's cdo does not appear to include the Python
-# interface, so it's installed through pip
-# The installation of cf-plot will install matplotlib 3.1, which is technically
-# different than 2.2; the latter is used by Iris.
-# Note: cfunits is not cf-units: cf(dm/-python/-lplot) uses cfunits,
-# Iris uses cf-units (imported as cf_units)
 RUN pip install \
-  cdo==1.5.3 \
-  cfdm==1.7.7 \
-  cf-python==3.0.1 \
-  cf-plot==3.0.5 \
-  cfunits==3.1.1 \
-  MetPy==0.11.1
+  flake8 \
+  black \
+  yapf \
+  autopep8 \
+  isort \
+  flake8-nb \
+  jupyterlab_code_formatter==1.3.1
 
-
-RUN pip install jupyterlab_thredds
-RUN jupyter labextension install @jupyter-widgets/jupyterlab-manager
 RUN jupyter labextension install jupyter-leaflet
-#RUN jupyter labextension install @ewatercycle/jupyterlab_thredds
-
-
-ENV PATH=${PATH}:${PCRASTER_DIR}/bin
-ENV PYTHONPATH=${PYTHONPATH}:${PCRASTER_DIR}/python
-# set path explicitly, because otherwise cfunits can't be imported
-ENV UDUNITS2_XML_PATH=/opt/conda/share/udunits/udunits2.xml
+RUN jupyter labextension install jupyterlab-flake8
+RUN jupyter labextension install @ryantam626/jupyterlab_code_formatter@1.3.1
+RUN jupyter serverextension enable --py jupyterlab_code_formatter
+
+# Try to enable thredds browser extension (see https://github.com/eWaterCycle/jupyterlab_thredds)
+# This doesn't actually seem to work in the notebook, so I'm disabling it for now.
+# RUN pip install jupyterlab_thredds && jupyter labextension install @ewatercycle/jupyterlab_thredds
+
+# These paths are set in the conda 'base' env, but that isn't activated by default on a local build.
+# to test: import cfunits in notebook, esmvaltool -h in a shell.
+# ENV UDUNITS2_XML_PATH=/opt/conda/share/udunits/udunits2.xml
+# ENV PROJ_LIB=/opt/conda/share/proj

README.md

@@ -5,17 +5,21 @@
 ![Docker Cloud Build Status](https://img.shields.io/docker/cloud/build/eucp/notebook)
 
 # EUCP Jupyterlab environment specification
+
 Dockerfile for the EUCP project - based on the Jupyter datascience notebook\
 [View on dockerhub](https://hub.docker.com/repository/docker/eucp/notebook/general)
 
 ## Branches
+
 - master: for regular development and updates. Merging via approved pull requests. Linked to 'latest' tag on dockerhub.
 - feature branches: make a separate branch for each PR/feature that you want to add.
 
 ## Releases
+
 - We'll configure the login environment such that you can select which release you want to use for your compute environment.
 
 ## Update process
+
 1. Checkout, build and run the docker image locally
 1. Make desired changes to the environment
 1. Build and run updated docker image locally for testing
@@ -28,10 +32,24 @@ Dockerfile for the EUCP project - based on the Jupyter datascience notebook\
 ## Changelog
 
 May 20, 2020:
+
+- Inherit from newer jupyter/datascience-notebook
+- Updated jupyter hub & jupyter lab versions
+- Added explicit dependency of matplotlib
+- Removed some packages as they are now part of base- or scipy-nb
+- Removed some packages as they were installed as dependencies of others
+- Moved all pip-installs to conda
+- Add esmvalcore and esmvaltool-python
+- Upgrade several packages to newer versions
+- Disable not-working jupyter-thredds plugin
+
+May 19, 2020:
+
 - Pin versions to current environment configuration
 - Add `package_list_for_change_diffs.txt` for keeping track of environment changes.
 
 May 18, 2020:
+
 - Start changelog
 - Enable autobuild on dockerhub
 - Create master and stable branches