docker: new build for new XClim and to get Dask dashboard and Panel server app to work

Jenkinsfile

@@ -10,7 +10,7 @@ pipeline {
     // https://jenkins.io/doc/book/pipeline/syntax/
     agent {
         docker {
-            image "pavics/workflow-tests:220401"
+            image "pavics/workflow-tests:220502"
             label 'linux && docker'
         }
     }

binder/Dockerfile

@@ -1,4 +1,4 @@
-FROM pavics/workflow-tests:220401
+FROM pavics/workflow-tests:220502
 
 USER root
 
@@ -12,6 +12,12 @@ WORKDIR /notebooks
 
 RUN ./downloadrepos; DEPLOY_PAVICS_LANDING_NB=1 ./reorg-notebooks; rm -rfv downloadrepos default_build_params reorg-notebooks; chown -R jenkins:jenkins .
 
-RUN pip install https://github.com/Ouranosinc/xclim/archive/master.tar.gz
+#COPY binder/test-notebooks /notebooks
+
+#RUN mkdir -p subdir1/subdir2; cp TEST-panel-servable.ipynb subdir1/servable1.ipynb; cp TEST-panel-servable.ipynb subdir1/subdir2/servable2.ipynb; cp TEST-panel-servable.ipynb TEST-panel-servable-Copy.ipynb
+
+#RUN chown jenkins:jenkins -R .
+
+# RUN pip install https://github.com/Ouranosinc/xclim/archive/master.tar.gz
 
 USER jenkins

binder/test-notebooks/TEST-panel-binder.ipynb

@@ -0,0 +1,85 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "d79b1053-3144-47d4-824f-49a3666d68e6",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "WARNING:bokeh.server.util:Host wildcard '*' will allow connections originating from multiple (or possibly all) hostnames or IPs. Use non-wildcard values to restrict access explicitly\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Launching server at http://localhost:5007\n"
+     ]
+    }
+   ],
+   "source": [
+    "import panel as pn\n",
+    "srv = pn.panel(\n",
+    "    pn.widgets.FloatInput(name='an input')\n",
+    ").show(port=5007, websocket_origin=\"*\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "8f18de16-80bd-40dc-9438-ca176fc8c169",
+   "metadata": {},
+   "source": [
+    "Your current URL should look something like:\n",
+    "\n",
+    "https://hub.gke2.mybinder.org/user/ouranosinc-pavi--workflow-tests-9jerf8qk/lab/tree/TEST-panel-binder.ipynb\n",
+    "\n",
+    "Open a new browser tab, then to go to something like this URL (replace `lab/tree/TEST-panel-binder.ipynb` with `proxy/5007/`):\n",
+    "\n",
+    "https://hub.gke2.mybinder.org/user/ouranosinc-pavi--workflow-tests-9jerf8qk/proxy/5007/"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2d39a37c-8df6-4f27-9aeb-54181f35c295",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "srv.stop()  # To stop the server."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "fb898f21-f543-40b4-8bf4-b701559b842f",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

binder/test-notebooks/TEST-panel-servable.ipynb

@@ -0,0 +1,36 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7acdd82a-bc2d-443c-8fa8-e432de9cfa30",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import panel as pn\n",
+    "pn.panel('# Ceci est un test').servable()"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

docker/Dockerfile

@@ -17,7 +17,7 @@ RUN apt-get update && \
 # Change /opt/conda folder permissions for jupyter-conda extension.
 RUN groupadd --gid 1000 jenkins \
     && useradd --uid 1000 --gid jenkins --create-home jenkins && \
-    chmod -R a+rwx /opt/conda
+    chmod -R a+rwX /opt/conda
 
 COPY environment.yml /environment.yml
 
@@ -70,7 +70,9 @@ RUN python -m ipykernel install --name birdy
 # https://github.com/plotly/jupyter-dash/issues/49
 RUN jupyter lab build
 
-RUN jupyter serverextension enable voila --sys-prefix
+RUN jupyter serverextension enable voila --sys-prefix \
+    && jupyter serverextension enable panel.io.jupyter_server_extension --sys-prefix \
+    && jupyter serverextension list
 #    && jupyter labextension install jupyterlab-clipboard
 
 # This should be "master" but commit
@@ -94,7 +96,11 @@ RUN wget https://raw.githubusercontent.com/jupyter/docker-stacks/$DOCKER_STACKS_
     chmod a+rx /usr/local/bin/start.sh /usr/local/bin/start-singleuser.sh /usr/local/bin/start-notebook.sh /usr/local/bin/fix-permissions && \
     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/envs/birdy/fonts && \
+    chmod a+rwX -R /opt/conda/pkgs/cache
+
+# For jupyter-panel-proxy launcher.
+ENV BOKEH_ALLOW_WS_ORIGIN "*"
 
 # 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

docker/environment.yml

@@ -5,6 +5,7 @@ channels:
   - cdat
   - bokeh
   - plotly  # for jupyter-dash
+  - pyviz/label/dev  # for jupyter-panel-proxy, panel
   - defaults
 
 dependencies:
@@ -27,9 +28,6 @@ dependencies:
   - dask <= 2022.1.0
   - distributed <= 2022.1.0
 
-  # Pin cf_xarray for slow WPS_example.ipynb.
-  - cf_xarray<=0.6.3
-
   - matplotlib
     # - xarray  # from xclim and ravenpy
     # - numpy  # from xclim and ravenpy
@@ -57,7 +55,7 @@ dependencies:
   - jupyter_bokeh
   - pscript
   - h5netcdf
-  - panel
+  - panel >= 0.13.1a3
   # https://github.com/holoviz/panel
   - pyviz_comms  # (was labextension pyviz/jupyterlab_pyviz in jupyterlab v2)
   - holoviews
@@ -119,7 +117,7 @@ dependencies:
   #     warnings.warn(f'Downloading: {url}', DownloadWarning)
   - shapely <= 1.7.1
   # https://github.com/roocs/clisops
-  - clisops >= 0.8.0
+  - clisops >= 0.9.0
   # Universal Regridder for Geospatial Data
   # https://github.com/pangeo-data/xESMF
   # xesmf-0.6.2 requires clisops>=0.8.0
@@ -170,6 +168,12 @@ dependencies:
   # xeus-python: back-end kernel implementing the Jupyter Debug Protocol
   - xeus-python
   - jupyter-dash
+  # https:://github.com/jupyterhub/jupyter-server-proxy
+  - jupyter-server-proxy
+  # https://github.com/dask/dask-labextension
+  - dask-labextension
+  # https://github.com/holoviz/jupyter-panel-proxy
+  - 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
@@ -197,7 +201,9 @@ dependencies:
     # Mimics how one might format their calculation if it were written with a
     # pencil: write the symbolic formula, followed by numeric substitutions,
     # and then the result.
-    - handcalcs
+    # DISABLE handcalcs, interfere with "Panel preview" button
+    # See comment https://github.com/holoviz/panel/issues/3440#issuecomment-1112182170
+    # - handcalcs
     # https://github.com/ShopRunner/jupyter-notify
     # Jupyter Magic For Browser Notifications of Cell Completion.
     - jupyternotify

launchcontainer

@@ -1,7 +1,7 @@
 #!/bin/sh -x
 
 if [ -z "$DOCKER_IMAGE" ]; then
-    DOCKER_IMAGE="pavics/workflow-tests:220401"
+    DOCKER_IMAGE="pavics/workflow-tests:220502"
 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:220401"
+    DOCKER_IMAGE="pavics/workflow-tests:220502"
 fi
 
 if [ -z "$CONTAINER_NAME" ]; then