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docker: Install xclim using conda to pull new clisops #52

Merged
merged 7 commits into from
Sep 28, 2020
Merged

docker: Install xclim using conda to pull new clisops #52

merged 7 commits into from
Sep 28, 2020

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tlvu
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@tlvu tlvu commented Sep 26, 2020

Relevant changes:

>   - clisops=0.3.1=pyh32f6830_1

<     - xclim==0.19.0
>   - xclim=0.20.0=py_0

<   - xarray=0.16.0py_0
>   - xarray=0.16.1=py_0

<   - dask=2.26.0=py_0
>   - dask=2.27.0=py_0

<   - fiona=1.8.13=py37h0492a4a_1
>   - fiona=1.8.17=py37ha3d844c_0

<   - gdal=3.0.4=py37h4b180d9_10
>   - gdal=3.1.2=py37h518339e_2

<   - jupyter_server=0.1.1=py37_0
>   - jupyter_server=1.0.1=py37hc8dfbb8_0

>     - jupyternotify==0.1.15

>     - pytest-tornasync==0.6.0.post2

Passing Jenkins build: http://jenkins.ouranos.ca/job/PAVICS-e2e-workflow-tests/job/install-xclim-using-conda-to-pull-new-clisops/7/console

Full conda env export diff:
200914.1-200925.1-conda-env-export.diff.txt

New conda env export:
200925.1-conda-env-export.yml.txt

@tlvu
docker: install xclim using conda to pull new clisops automatically
21b707b
@tlvu
release: update to use image pavics/workflow-tests:200918
e4c93e2
@tlvu
release: update to use image pavics/workflow-tests:200920
4387efe
@tlvu
docker: add jupyternotify and jupyterlab-topbar
4140f91
@tlvu
release: update to use image pavics/workflow-tests:200925
2272d9f
@tlvu
docker: add pytest-tornasync for notebooks tests
5f82a41 
Fix following Jenkins notebook test error:

```
  + export PYTHONWARNINGS=ignore:Unverified HTTPS request
  + py.test --nbval notebooks/hummingbird.ipynb pavics-sdi-master/docs/source/notebooks/WCS_example.ipynb pavics-sdi-master/docs/source/notebooks/WFS_example.ipynb pavics-sdi-master/docs/source/notebooks/WMS_example.ipynb pavics-sdi-master/docs/source/notebooks/WPS_example.ipynb pavics-sdi-master/docs/source/notebooks/catalog_search.ipynb pavics-sdi-master/docs/source/notebooks/esgf-dap.ipynb pavics-sdi-master/docs/source/notebooks/opendap.ipynb pavics-sdi-master/docs/source/notebooks/pavics_thredds.ipynb pavics-sdi-master/docs/source/notebooks/rendering.ipynb pavics-sdi-master/docs/source/notebooks/subsetting.ipynb finch-master/docs/source/notebooks/dap_subset.ipynb finch-master/docs/source/notebooks/finch-usage.ipynb --sanitize-with notebooks/output-sanitize.cfg
  Traceback (most recent call last):
    File "/opt/conda/envs/birdy/lib/python3.7/site-packages/_pytest/config/__init__.py", line 689, in import_plugin
      __import__(importspec)
  ModuleNotFoundError: No module named 'pytest_tornasync'

  The above exception was the direct cause of the following exception:

  Traceback (most recent call last):
    File "/opt/conda/envs/birdy/bin/py.test", line 11, in <module>
      sys.exit(main())
    File "/opt/conda/envs/birdy/lib/python3.7/site-packages/_pytest/config/__init__.py", line 136, in main
      config = _prepareconfig(args, plugins)
    File "/opt/conda/envs/birdy/lib/python3.7/site-packages/_pytest/config/__init__.py", line 314, in _prepareconfig
      pluginmanager=pluginmanager, args=args
    File "/opt/conda/envs/birdy/lib/python3.7/site-packages/pluggy/hooks.py", line 286, in __call__
      return self._hookexec(self, self.get_hookimpls(), kwargs)
    File "/opt/conda/envs/birdy/lib/python3.7/site-packages/pluggy/manager.py", line 93, in _hookexec
      return self._inner_hookexec(hook, methods, kwargs)
    File "/opt/conda/envs/birdy/lib/python3.7/site-packages/pluggy/manager.py", line 87, in <lambda>
      firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
    File "/opt/conda/envs/birdy/lib/python3.7/site-packages/pluggy/callers.py", line 203, in _multicall
      gen.send(outcome)
    File "/opt/conda/envs/birdy/lib/python3.7/site-packages/_pytest/helpconfig.py", line 99, in pytest_cmdline_parse
      config = outcome.get_result()  # type: Config
    File "/opt/conda/envs/birdy/lib/python3.7/site-packages/pluggy/callers.py", line 80, in get_result
      raise ex[1].with_traceback(ex[2])
    File "/opt/conda/envs/birdy/lib/python3.7/site-packages/pluggy/callers.py", line 187, in _multicall
      res = hook_impl.function(*args)
    File "/opt/conda/envs/birdy/lib/python3.7/site-packages/_pytest/config/__init__.py", line 932, in pytest_cmdline_parse
      self.parse(args)
    File "/opt/conda/envs/birdy/lib/python3.7/site-packages/_pytest/config/__init__.py", line 1204, in parse
      self._preparse(args, addopts=addopts)
    File "/opt/conda/envs/birdy/lib/python3.7/site-packages/_pytest/config/__init__.py", line 1097, in _preparse
      self.pluginmanager.load_setuptools_entrypoints("pytest11")
    File "/opt/conda/envs/birdy/lib/python3.7/site-packages/pluggy/manager.py", line 300, in load_setuptools_entrypoints
      self.register(plugin, name=ep.name)
    File "/opt/conda/envs/birdy/lib/python3.7/site-packages/_pytest/config/__init__.py", line 431, in register
      self.consider_module(plugin)
    File "/opt/conda/envs/birdy/lib/python3.7/site-packages/_pytest/config/__init__.py", line 656, in consider_module
      self._import_plugin_specs(getattr(mod, "pytest_plugins", []))
    File "/opt/conda/envs/birdy/lib/python3.7/site-packages/_pytest/config/__init__.py", line 663, in _import_plugin_specs
      self.import_plugin(import_spec)
    File "/opt/conda/envs/birdy/lib/python3.7/site-packages/_pytest/config/__init__.py", line 693, in import_plugin
      ).with_traceback(e.__traceback__) from e
    File "/opt/conda/envs/birdy/lib/python3.7/site-packages/_pytest/config/__init__.py", line 689, in import_plugin
      __import__(importspec)
  ImportError: Error importing plugin "pytest_tornasync": No module named 'pytest_tornasync'
  + EXIT_CODE=1
```
@tlvu
release: update to use image pavics/workflow-tests:200925.1
9d6eb15
tlvu added a commit to bird-house/birdhouse-deploy that referenced this pull request Sep 26, 2020
@tlvu
jupyter: new build for new xclim with fix for missing clisops dependency
507cdf6 
Deploy new Jupyter env from PR Ouranosinc/PAVICS-e2e-workflow-tests#52.

Relevant changes:
```diff
>   - clisops=0.3.1=pyh32f6830_1

<     - xclim==0.19.0
>   - xclim=0.20.0=py_0

<   - xarray=0.16.0py_0
>   - xarray=0.16.1=py_0

<   - dask=2.26.0=py_0
>   - dask=2.27.0=py_0

<   - fiona=1.8.13=py37h0492a4a_1
>   - fiona=1.8.17=py37ha3d844c_0

<   - gdal=3.0.4=py37h4b180d9_10
>   - gdal=3.1.2=py37h518339e_2

<   - jupyter_server=0.1.1=py37_0
>   - jupyter_server=1.0.1=py37hc8dfbb8_0

>     - jupyternotify==0.1.15

>     - pytest-tornasync==0.6.0.post2
```

See PR above for full changes.
@tlvu tlvu mentioned this pull request Sep 26, 2020
Merged
@tlvu tlvu merged commit 18c8397 into master Sep 28, 2020
@tlvu tlvu deleted the install-xclim-using-conda-to-pull-new-clisops branch September 28, 2020 13:41
tlvu added a commit to bird-house/birdhouse-deploy that referenced this pull request Sep 28, 2020
@tlvu
Merge pull request #70 from bird-house/new-jupyter-env
7e7e75c 
jupyter: new build for new xclim with fix for missing clisops dependency

Matching PR to deploy new Jupyter env from PR Ouranosinc/PAVICS-e2e-workflow-tests#52 (commit Ouranosinc/PAVICS-e2e-workflow-tests@18c8397).

Deployed to https://medus.ouranos.ca/jupyter/ for testing.

Relevant changes:
```diff
>   - clisops=0.3.1=pyh32f6830_1

<     - xclim==0.19.0
>   - xclim=0.20.0=py_0

<   - xarray=0.16.0py_0
>   - xarray=0.16.1=py_0

<   - dask=2.26.0=py_0
>   - dask=2.27.0=py_0

<   - fiona=1.8.13=py37h0492a4a_1
>   - fiona=1.8.17=py37ha3d844c_0

<   - gdal=3.0.4=py37h4b180d9_10
>   - gdal=3.1.2=py37h518339e_2

<   - jupyter_server=0.1.1=py37_0
>   - jupyter_server=1.0.1=py37hc8dfbb8_0

>     - jupyternotify==0.1.15

>     - pytest-tornasync==0.6.0.post2
```

See PR above for full changes.
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@tlogan2000 tlogan2000 tlogan2000 approved these changes

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@tlvu @tlogan2000