Jupyter docker: new build for xclim, ravenpy, globus personal connect and latest of everything else

Jenkinsfile

@@ -10,7 +10,7 @@ pipeline {
     // https://jenkins.io/doc/book/pipeline/syntax/
     agent {
         docker {
-            image "pavics/workflow-tests:221130"
+            image "pavics/workflow-tests:230217-update230221-1"
             label 'linux && docker'
         }
     }

binder/Dockerfile

@@ -1,4 +1,4 @@
-FROM pavics/workflow-tests:221130
+FROM pavics/workflow-tests:230217-update230221-1
 
 USER root
 

docker/Dockerfile

@@ -101,11 +101,25 @@ RUN wget https://raw.githubusercontent.com/jupyter/docker-stacks/$DOCKER_STACKS_
     mkdir /notebook_dir && chown jenkins /notebook_dir && \
     chmod a+rwX -R /opt/conda/envs/birdy/fonts && \
     chmod a+rwX -R /opt/conda/pkgs/cache && \
-    chown jenkins:jenkins -R /opt/conda/pkgs/cache
+    chown jenkins:jenkins -R /opt/conda/pkgs/cache && \
+    mkdir -p /usr/local/bin && \
+    wget https://downloads.globus.org/globus-connect-personal/linux/stable/globusconnectpersonal-latest.tgz -O /usr/local/bin/globusconnectpersonal-latest.tgz && \
+    tar xzf /usr/local/bin/globusconnectpersonal-latest.tgz -C /usr/local/bin/ && \
+    ln -vs /usr/local/bin/globusconnectpersonal*/globusconnectpersonal /usr/local/bin/globusconnectpersonal && \
+    rm -v /usr/local/bin/globusconnectpersonal-latest.tgz
 
 # For jupyter-panel-proxy launcher.
 ENV BOKEH_ALLOW_WS_ORIGIN "*"
 
+# For import xesmf since esmf-8.4.0, see
+# https://github.com/conda-forge/esmf-feedstock/issues/91
+ENV ESMFMKFILE="/opt/conda/envs/birdy/lib/esmf.mk"
+
+# To avoid error "PROJ: proj_create_from_database: Open of
+# /opt/conda/envs/birdy/share/proj failed"
+# This simulates a real `conda activate birdy`.
+ENV PROJ_DATA="/opt/conda/envs/birdy/share/proj"
+
 # problem running start-notebook.sh when being root
 # the jupyter/base-notebook image also do not default to root user so we do the same here
 USER jenkins

docker/Dockerfile.testing

@@ -1,13 +1,17 @@
 # For testing quickly without having to do a full rebuild.
 
-FROM pavics/workflow-tests:220728
+FROM pavics/workflow-tests:230217
 
-USER root
+ENV ESMFMKFILE="/opt/conda/envs/birdy/lib/esmf.mk"
+
+ENV PROJ_DATA="/opt/conda/envs/birdy/share/proj"
+
+#USER root
 
 # Use 'update' for existing and 'install' for new package.
 # Keep same channel ordering to not revert anything.
-RUN umask 0000 \
-    && mamba install -c conda-forge -c cdat -c bokeh -c plotly -c pyston -c pyviz/label/dev -c defaults -n birdy geopy
+#RUN umask 0000 \
+#    && mamba install -c conda-forge -c cdat -c bokeh -c plotly -c pyston -c pyviz/label/dev -c defaults -n birdy geopy
 #    && pip uninstall -y ravenpy \
 #    && mamba install -c conda-forge -c cdat -c bokeh -c plotly -c defaults -n birdy ravenpy aiohttp
 
@@ -20,4 +24,4 @@ RUN umask 0000 \
 #RUN umask 0000 \
 #    && pip install https://github.com/CSHS-CWRA/RavenPy/archive/refs/heads/master.zip
 
-USER jenkins
+#USER jenkins

docker/environment.yml

@@ -120,6 +120,8 @@ dependencies:
   - memory_profiler
   # for esgf notebooks
   - esgf-compute-api
+  # https://anaconda.org/conda-forge/esgf-pyclient (for pavics-sdi esgf-dap.ipynb)
+  - esgf-pyclient
   - cdms2
   # Disable vcs because it was forcing python downgrade to below 3.9.
   # See https://github.com/CDAT/vcs/issues/457
@@ -192,6 +194,9 @@ dependencies:
   # for pip packages
   - pip
   - pip:
+    # https://pypi.org/project/xncml/
+    # Tools for manipulating and opening NCML (NetCDF Markup) files with/for xarray
+    - xncml
     # visual debugger for Jupyter Notebook, not working with JupyterLab at this moment
     - pixiedust
     # block execution of 'run_all_cells' until user input finished

launchcontainer

@@ -1,7 +1,7 @@
 #!/bin/sh -x
 
 if [ -z "$DOCKER_IMAGE" ]; then
-    DOCKER_IMAGE="pavics/workflow-tests:221130"
+    DOCKER_IMAGE="pavics/workflow-tests:230217-update230221-1"
 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:221130"
+    DOCKER_IMAGE="pavics/workflow-tests:230217-update230221-1"
 fi
 
 if [ -z "$CONTAINER_NAME" ]; then