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docker: new build for new XClim and to get Dask dashboard and Panel server app to work #105

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merged 38 commits into from May 5, 2022

Commits on Apr 7, 2022

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Commits on Apr 8, 2022

  1. docker: get dask dashboard and "panel serve" to work

    Add `jupyter-server-proxy`, `dask-labextension` and enable
    `panel.io.jupyter_server_extension`.
    
    The `jupyter-server-proxy` allows to proxy URL like
    "http://127.0.0.1:8787/status" (dask dashboard URL sample) to
    "https://pavics.ouranos.ca/jupyter/user-redirect/proxy/8787/status"
    which the `dask-labextension` will accept.
    
    http://127.0.0.1:8787/status
    is mapped to
    https://pavics.ouranos.ca/jupyter/user-redirect/proxy/8787/status
    
    For "panel serve", we can do it this way:
    
    `! panel serve --allow-websocket-origin=pavics.ouranos.ca --port 5007 /notebook_dir/writable-workspace/tmp-test/test-panel.ipynb`
    
    2022-04-08 01:33:50,268 Starting Bokeh server version 2.4.2 (running on Tornado 6.1)
    2022-04-08 01:33:50,270 User authentication hooks NOT provided (default user enabled)
    2022-04-08 01:33:50,272 Bokeh app running at: http://localhost:5007/test-panel
    2022-04-08 01:33:50,272 Starting Bokeh server with process id: 2155
    2022-04-08 01:34:06,179 WebSocket connection opened
    2022-04-08 01:34:06,179 ServerConnection created
    
    Then open a new browser tab to https://pavics.ouranos.ca/jupyter, login
    again if it asks, and to go this URL:
    https://pavics.ouranos.ca/jupyter/user-redirect/proxy/5007/test-panel
    
    http://localhost:5007/test-panel
    is mapped to
    https://pavics.ouranos.ca/jupyter/user-redirect/proxy/5007/test-panel
    tlvu committed Apr 8, 2022
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Commits on Apr 12, 2022

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Commits on Apr 14, 2022

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Commits on Apr 22, 2022

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Commits on Apr 26, 2022

  1. binder: commit test notebooks to avoid external dependencies and guar…

    …anty reproducibility
    tlvu committed Apr 26, 2022
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  4. binder: try to fix conda install on cli

    ```
    ! conda install -c pyviz/label/dev jupyter-panel-proxy
    
    Collecting package metadata (current_repodata.json): failed
    
    NotWritableError: The current user does not have write permissions to a
    required path.
      path: /opt/conda/pkgs/cache/37adb69c.json
      uid: 1000
      gid: 1000
    
    If you feel that permissions on this path are set incorrectly, you can
    manually
    change them by executing
    
      $ sudo chown 1000:1000 /opt/conda/pkgs/cache/37adb69c.json
    
    In general, it's not advisable to use 'sudo conda'.
    ```
    tlvu committed Apr 26, 2022
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Commits on Apr 27, 2022

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  2. docker: fix conda install cli permission error

    Fix for this error:
    ```
    ! conda install -c pyviz/label/dev jupyter-panel-proxy
    
    Collecting package metadata (current_repodata.json): failed
    
    NotWritableError: The current user does not have write permissions to a
    required path.
      path: /opt/conda/pkgs/cache/37adb69c.json
      uid: 1000
      gid: 1000
    
    If you feel that permissions on this path are set incorrectly, you can
    manually
    change them by executing
    
      $ sudo chown 1000:1000 /opt/conda/pkgs/cache/37adb69c.json
    
    In general, it's not advisable to use 'sudo conda'.
    ```
    tlvu committed Apr 27, 2022
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  4. docker: fix everything executable under /opt/conda for all, wanted ex…

    …isting executable only
    tlvu committed Apr 27, 2022
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  7. binder: new base image has the steps already integrated

    The conda install step did not work, error below:
    
    ```
    Step 10/13 : RUN conda install -c pyviz/label/dev jupyter-panel-proxy
     ---> Running in 3bf123abf1a8
    Collecting package metadata (current_repodata.json): ...working... done
    Solving environment: ...working... failed with initial frozen solve.
    Retrying with flexible solve.
    Solving environment: ...working... failed with repodata from
    current_repodata.json, will retry with next repodata source.
    Collecting package metadata (repodata.json): ...working... done
    Solving environment: ...working... failed with initial frozen solve.
    Retrying with flexible solve.
    Examining @/linux-64::__linux==5.4.170=0:  17%|█▋        | 1/6
    [00:00<00:00, 3591.01it/Examining @/linux-64::__glibc==2.31=0:  33%|███▎
    | 2/6 [00:00<00:00, 4232.40it/s] Examining
    @/linux-64::__archspec==1=x86_64:  83%|████████▎ | 5/6 [00:00<00:00,
    38.59it/
    Examining conflict for jupyter-panel-proxy python:  17%|█▋        | 1/6
    [00:00<00:00, 9
    Found conflicts! Looking for incompatible packages.
    ```
    tlvu committed Apr 27, 2022
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  8. docker: use devel version of panel to hopefully fix Panel preview pro…

    …blem
    
    See comment holoviz/panel#3440 (comment)
    
    To hopefully fix this error:
    ```
    ServerApp - ERROR - Uncaught exception GET
    /panel-preview/render/workdir/PAVICS-e2e-workflow-tests/binder/test-notebooks/TEST-panel-servable.ipynb
    (10.10.10.7)
    HTTPServerRequest(protocol='http', host='lvu.ouranos.ca:8890',
    method='GET',
    uri='/panel-preview/render/workdir/PAVICS-e2e-workflow-tests/binder/test-notebooks/TEST-panel-servable.ipynb',
    version='HTTP/1.1', remote_ip='10.10.10.7')
    Traceback (most recent call last):
      File
    "/opt/conda/envs/birdy/lib/python3.8/site-packages/tornado/web.py", line
    1704, in _execute
        result = await result
      File
    "/opt/conda/envs/birdy/lib/python3.8/site-packages/panel/io/jupyter_server_extension.py",
    line 116, in get
        page = server_html_page_for_session(
      File
    "/opt/conda/envs/birdy/lib/python3.8/site-packages/bokeh/embed/server.py",
    line 255, in server_html_page_for_session
        bundle = bundle_for_objs_and_resources(None, resources)
      File
    "/opt/conda/envs/birdy/lib/python3.8/site-packages/bokeh/embed/bundle.py",
    line 211, in bundle_for_objs_and_resources
        js_files.extend(js_resources.js_files)
      File
    "/opt/conda/envs/birdy/lib/python3.8/site-packages/panel/io/resources.py",
    line 299, in js_files
        dist_dir = self.dist_dir
      File
    "/opt/conda/envs/birdy/lib/python3.8/site-packages/panel/io/resources.py",
    line 259, in dist_dir
        if self.absolute:
    AttributeError: 'Resources' object has no attribute 'absolute'
    ```
    tlvu committed Apr 27, 2022
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Commits on Apr 28, 2022

  1. docker: unpin cf_xarray for clisops 0.9.0 need cf_xarray >= 0.7.0

    Previous docker build error:
    ```
    Encountered problems while solving:
    - package clisops-0.9.0-pyh6c4a22f_0 requires cf_xarray >=0.7.0, but none of the providers can be installed
    ```
    
    cf_xarray was previously pinned because of climex.ipynb (not
    WPS_example.ipynb, my mistake reading the Jenkins output) performance
    but it was already happening before the pin so cf_xarray might not be
    the real culprit.
    
    See issue about cf_xarray pinning here
    #100
    tlvu committed Apr 28, 2022
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Commits on May 3, 2022

  1. docker: patch Panel for 'Render with Panel' button regression fix

    Remove this patch once a Panel release contain this PR
    holoviz/panel#3469
    tlvu committed May 3, 2022
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Commits on May 4, 2022

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