From 8ed9823295117b12b4124fd4a57af31fb82bae5c Mon Sep 17 00:00:00 2001
From: Anne Fouilloux <annefou@geo.uio.no>
Date: Wed, 27 Nov 2019 09:27:02 +0100
Subject: [PATCH] create a separate conda env for esmvaltool

---
 Dockerfile                 | 22 +++++++++++++---------
 jupyterhub_environment.yml | 27 +++++++++++----------------
 2 files changed, 24 insertions(+), 25 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index fcfe816..9c31e5c 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -9,16 +9,20 @@ RUN apt-get update && apt-get install -y vim
 # Install requirements for Python 3
 ADD jupyterhub_environment.yml jupyterhub_environment.yml
 
-RUN conda env update -f jupyterhub_environment.yml
+RUN conda env create -f jupyterhub_environment.yml
 
-RUN /opt/conda/bin/jupyter labextension install @jupyterlab/hub-extension @jupyter-widgets/jupyterlab-manager
-RUN /opt/conda/bin/nbdime extensions --enable
-RUN /opt/conda/bin/jupyter labextension install jupyterlab-datawidgets nbdime-jupyterlab dask-labextension
-RUN /opt/conda/bin/jupyter labextension install @jupyter-widgets/jupyterlab-sidecar
-RUN /opt/conda/bin/jupyter serverextension enable jupytext
-RUN /opt/conda/bin/jupyter nbextension install --py jupytext
-RUN /opt/conda/bin/jupyter nbextension enable --py jupytext
-RUN /opt/conda/bin/jupyter labextension install @pyviz/jupyterlab_pyviz jupyter-leaflet
+RUN source activate esmvaltool && \
+    /opt/conda/bin/ipython kernel install --user --name esmvaltool && \
+    /opt/conda/bin/python -m ipykernel install --user --name=esmvaltool && \
+    /opt/conda/bin/jupyter labextension install @jupyterlab/hub-extension \
+                           @jupyter-widgets/jupyterlab-manager && \
+    /opt/conda/bin/jupyter labextension install jupyterlab-datawidgets && \
+    /opt/conda/bin/jupyter labextension install @jupyter-widgets/jupyterlab-sidecar && \
+    /opt/conda/bin/jupyter labextension install @pyviz/jupyterlab_pyviz \
+                           jupyter-leaflet
+
+# Fix hub failure
+RUN fix-permissions $HOME
 
 # Install other packages
 USER notebook
diff --git a/jupyterhub_environment.yml b/jupyterhub_environment.yml
index d95d3ac..8383b95 100644
--- a/jupyterhub_environment.yml
+++ b/jupyterhub_environment.yml
@@ -1,20 +1,19 @@
-name: base
+name: esmvaltool
 
 channels:
-  - esmvalgroup 
+  - esmvalgroup
   - conda-forge
-  - bioconda
   - defaults
 
 dependencies:
   - numpy
   - xarray
   - pandas
-  - cartopy 
-  - matplotlib 
-  - seaborn 
+  - cartopy
+  - matplotlib
+  - seaborn
   - basemap
-  - geopy 
+  - geopy
   - netcdf4
   - cis
   - metpy
@@ -29,21 +28,17 @@ dependencies:
   - pillow
   - branca
   - geopandas
-  - psyplot
-  - psy-maps 
-  - psyplot-gui 
-  - psy-reg 
-  - cdsapi 
-  - folium
+  - cdsapi
+  - folium  
+  - esmvaltool
   - basemap-data-hires
   - rasterstats
   - cfgrib
   - cdo
   - nco
-  - jupytext
-  - rise
   - papermill
-  - esmvaltool
+  - jupytext
+  - pip
   - pip:
       - dask_labextension
       - ipydatawidgets