docker: new build with latest Xclim and RavenPy and latest of everything else

.gitignore

@@ -13,6 +13,7 @@ pavics-sdi-*/
 finch-*/
 raven-*/
 esgf-compute-api-*/
+PAVICS-landing-*/
 
 # files produced by build
 buildout/

Jenkinsfile

@@ -10,7 +10,7 @@ pipeline {
     // https://jenkins.io/doc/book/pipeline/syntax/
     agent {
         docker {
-            image "pavics/workflow-tests:220502"
+            image "pavics/workflow-tests:220728"
             label 'linux && docker'
         }
     }

binder/Dockerfile

@@ -1,4 +1,4 @@
-FROM pavics/workflow-tests:220502
+FROM pavics/workflow-tests:220728
 
 USER root
 

docker/Dockerfile

@@ -3,8 +3,12 @@ FROM continuumio/miniconda3
 # Use mamba for much improved performance over conda.
 # The 'channel_priority strict' did help conda but it was not enough.
 RUN conda update conda -n base && \
-    conda install mamba -n base -c defaults -c conda-forge && \
-    conda config --set channel_priority strict
+    conda install mamba -n base -c conda-forge -c defaults && \
+    conda config --set channel_priority strict && \
+    wget -qO- https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -C /usr/local -xvj bin/micromamba
+
+# Default for micromamba is $HOME/micromamba which is wrong.
+ENV MAMBA_ROOT_PREFIX="/opt/conda"
 
 # to checkout other notebooks and to run pip install
 RUN apt-get update && \
@@ -45,8 +49,7 @@ COPY environment.yml /environment.yml
 # Pin python=3.8 because according to DavidH, xESMF has not been tested with 3.9 yet.
 RUN umask 0000 && \
     mamba create --name birdy --channel conda-forge --channel defaults xclim ravenpy python=3.8 && \
-    mamba env update --name birdy --file /environment.yml && \
-    conda remove mamba -n base
+    mamba env update --name birdy --file /environment.yml
 
 # alternate way to 'source activate birdy'
 ENV PATH="/opt/conda/envs/birdy/bin:$PATH"
@@ -97,7 +100,8 @@ RUN wget https://raw.githubusercontent.com/jupyter/docker-stacks/$DOCKER_STACKS_
     chmod a+r /etc/jupyter/jupyter_notebook_config.py && \
     mkdir /notebook_dir && chown jenkins /notebook_dir && \
     chmod a+rwX -R /opt/conda/envs/birdy/fonts && \
-    chmod a+rwX -R /opt/conda/pkgs/cache
+    chmod a+rwX -R /opt/conda/pkgs/cache && \
+    chown jenkins:jenkins -R /opt/conda/pkgs/cache
 
 # For jupyter-panel-proxy launcher.
 ENV BOKEH_ALLOW_WS_ORIGIN "*"

docker/environment.yml

@@ -5,6 +5,7 @@ channels:
   - cdat
   - bokeh
   - plotly  # for jupyter-dash
+  - pyston
   - pyviz/label/dev  # for jupyter-panel-proxy, panel
   - defaults
 
@@ -16,10 +17,9 @@ dependencies:
   # xclim direct dependencies: https://github.com/conda-forge/xclim-feedstock/blob/master/recipe/meta.yaml
   # ravenpy direct dependencies: https://github.com/conda-forge/ravenpy-feedstock/blob/master/recipe/meta.yaml
 
-  # Pin latest xclim and ravenpy to avoid downgrading during the second install
-  # phase.  Mamba is quicker to solve dependencies than conda but it is less
-  # precise so accidental downgrade happends.
-  - xclim >= 0.32.1
+  # Pin latest xclim and ravenpy to avoid downgrading during the second installation phase.
+  # Mamba is quicker to solve dependencies than conda, but it is less precise so accidental downgrades can happen.
+  - xclim >= 0.38.0
   - ravenpy >= 0.7.8
 
   # Pin dask and distributed for slow PAVICStutorial_ClimateDataAnalysis-3Climate-Indicators.ipynb.
@@ -40,7 +40,7 @@ dependencies:
   - cfgrib
   - pydap
   - cartopy >= 0.20.1
-  - descartes
+  - descartes # Is this really needed???
     # - rasterio  # from ravenpy
     # - gdal  # for osgeo, from ravenpy
     # - geopandas  # from ravenpy
@@ -66,6 +66,9 @@ dependencies:
   # https://github.com/bird-house/birdhouse-deploy/pull/63#issuecomment-668270608
   # pinning hvplot did not solve the problem with violin plot.
   - hvplot
+  # https://streamlit.io/
+  # https://anaconda.org/conda-forge/streamlit
+  - streamlit
   - nc-time-axis
     # - cftime  # from xclim and ravenpy
     # - statsmodels  # for ravenpy
@@ -156,7 +159,7 @@ dependencies:
   - jupytext
   # jupyterlab extension for git
   - jupyterlab-git
-  # Voila turns Jupyter notebooks into standalone web applications
+  # Voilà turns Jupyter notebooks into standalone web applications
   - voila
   - jupyter-archive
   # https://github.com/jtpio/jupyterlab-topbar
@@ -173,7 +176,8 @@ dependencies:
   # https://github.com/dask/dask-labextension
   - dask-labextension
   # https://github.com/holoviz/jupyter-panel-proxy
-  - jupyter-panel-proxy >= 0.2.0a2
+  # DISABLE: seems to interfere with 'panel serve' command
+  #- jupyter-panel-proxy >= 0.2.0a2
   # Force newer nodejs for 'jupyter lab build' issue
   # https://github.com/jupyterlab/jupyterlab/issues/11726#issuecomment-998901247
   # TODO: remove nodejs once all extensions move to prebuilt extensions, see comment
@@ -184,18 +188,20 @@ dependencies:
   - wget
   - nested_dict
   - paramiko
+  - pymetalink  # for Raven notebook Extract_geographical_watershed_properties.ipynb
+  - requests-magpie
   - scp
   - selenium
   - geckodriver
   - xlrd
   - pre-commit
+  # https://github.com/pyston/pyston/
+  - pyston_lite_autoload
   # for pip packages
   - pip
   - pip:
     # visual debugger for Jupyter Notebook, not working with JupyterLab at this moment
     - pixiedust
-    - requests-magpie
-    - pymetalink  # for Raven notebook Extract_geographical_watershed_properties.ipynb
     # block execution of 'run_all_cells' until user input finished
     - ipython_blocking
     # Mimics how one might format their calculation if it were written with a
@@ -209,6 +215,8 @@ dependencies:
     - jupyternotify
     # https://github.com/jupyterlab-contrib/jupyterlab-logout (was from jupyterlab-topbar)
     - jupyterlab-logout
+    # https://github.com/jupytercalpoly/jupyterlab-tabular-data-editor
+    - jupyterlab-tabular-data-editor
     # Needed to run notebook tests.  Missing indirect recursive dependencies
     # somewhere, should not need to manually add it here.
     - pytest-tornasync

launchcontainer

@@ -1,7 +1,7 @@
 #!/bin/sh -x
 
 if [ -z "$DOCKER_IMAGE" ]; then
-    DOCKER_IMAGE="pavics/workflow-tests:220502"
+    DOCKER_IMAGE="pavics/workflow-tests:220728"
 fi
 
 if [ -z "$CONTAINER_NAME" ]; then

launchnotebook

@@ -7,7 +7,7 @@ if [ -z "$PORT" ]; then
 fi
 
 if [ -z "$DOCKER_IMAGE" ]; then
-    DOCKER_IMAGE="pavics/workflow-tests:220502"
+    DOCKER_IMAGE="pavics/workflow-tests:220728"
 fi
 
 if [ -z "$CONTAINER_NAME" ]; then