Update docker image and add nc-time-axis #47
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tlogan2000
approved these changes
Jul 17, 2020
tlvu
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Jul 17, 2020
subsetting.ipynb: fix Jenkins failure since FP upgrade from 1.5.1 to 1.6 Code changed to account for new metalink and removed tar archive. New passing build: http://jenkins.ouranos.ca/job/PAVICS-e2e-workflow-tests/job/update-docker-image-and-add-nc-time-axis/2/console Failure with new Jupyter image (PR Ouranosinc/PAVICS-e2e-workflow-tests#47): ``` 17:03:43 _______ pavics-sdi-master/docs/source/notebooks/subsetting.ipynb::Cell 2 _______ 17:03:43 Notebook cell execution failed 17:03:43 Cell 2: Cell outputs differ 17:03:43 17:03:43 Input: 17:03:43 help(fp.subset_continents) 17:03:43 17:03:43 Traceback: 17:03:43 mismatch 'stdout' 17:03:43 17:03:43 assert reference_output == test_output failed: 17:03:43 17:03:43 'Help on meth... dataset.\n\n' == 'Help on meth... outputs.\n\n' 17:03:43 Skipping 101 identical leading characters in diff, use -v to show 17:03:43 - n='Africa') method of birdy.client.base.WPSClient instance 17:03:43 + n='Africa', mosaic=False) method of birdy.client.base.WPSClient instance 17:03:43 ? ++++++++++++++ 17:03:43 Return the data whose grid cells intersect the selected continents for each input dataset. 17:03:43 17:03:43 Parameters 17:03:43 ---------- 17:03:43 region : {'Africa', 'Asia', 'Australia', 'North America', 'Oceania', 'South America', 'Antarctica', 'Europe'}string 17:03:43 Continent name. 17:03:43 + mosaic : boolean 17:03:43 + If True, selected regions will be merged into a single geometry. 17:03:43 resource : ComplexData:mimetype:`application/x-netcdf`, :mimetype:`application/x-tar`, :mimetype:`application/zip` 17:03:43 NetCDF Files or archive (tar/zip) containing netCDF files. 17:03:43 17:03:43 Returns 17:03:43 ------- 17:03:43 + output : ComplexData:mimetype:`application/x-tar` 17:03:43 + Tar archive of the subsetted netCDF files. 17:03:43 - output : ComplexData:mimetype:`application/x-netcdf` 17:03:43 ? --- 17:03:43 + ncout : ComplexData:mimetype:`application/x-netcdf` 17:03:43 ? ++ 17:03:43 + NetCDF file with subset for one dataset. 17:03:43 - NetCDF output for first resource file. 17:03:43 - metalink : ComplexData:mimetype:`application/metalink+xml; version=4.0` 17:03:43 - Metalink file with links to all NetCDF outputs. 17:03:43 17:03:43 17:03:43 17:03:43 _______ pavics-sdi-master/docs/source/notebooks/subsetting.ipynb::Cell 4 _______ 17:03:43 Notebook cell execution failed 17:03:43 Cell 4: Cell outputs differ 17:03:43 17:03:43 Input: 17:03:43 tar_url, nc_out_url = resp.get() 17:03:43 print("URL: ", nc_out_url) 17:03:43 tar_out, nc_out = resp.get(asobj=True) 17:03:43 nc_out 17:03:43 17:03:43 Traceback: 17:03:43 Missing output fields from running code: {'text/html'} ``` Failure with old Jupyter image: ``` 20:35:36 pavics-sdi-master/docs/source/notebooks/subsetting.ipynb .. 20:35:36 INTERNALERROR> Traceback (most recent call last): 20:35:36 INTERNALERROR> File "/opt/conda/envs/birdy/lib/python3.7/site-packages/_pytest/main.py", line 191, in wrap_session 20:35:36 INTERNALERROR> session.exitstatus = doit(config, session) or 0 20:35:36 INTERNALERROR> File "/opt/conda/envs/birdy/lib/python3.7/site-packages/_pytest/main.py", line 247, in _main 20:35:36 INTERNALERROR> config.hook.pytest_runtestloop(session=session) 20:35:36 INTERNALERROR> File "/opt/conda/envs/birdy/lib/python3.7/site-packages/pluggy/hooks.py", line 286, in __call__ 20:35:36 INTERNALERROR> return self._hookexec(self, self.get_hookimpls(), kwargs) 20:35:36 INTERNALERROR> File "/opt/conda/envs/birdy/lib/python3.7/site-packages/pluggy/manager.py", line 93, in _hookexec 20:35:36 INTERNALERROR> return self._inner_hookexec(hook, methods, kwargs) 20:35:36 INTERNALERROR> File "/opt/conda/envs/birdy/lib/python3.7/site-packages/pluggy/manager.py", line 87, in <lambda> 20:35:36 INTERNALERROR> firstresult=hook.spec.opts.get("firstresult") if hook.spec else False, 20:35:36 INTERNALERROR> File "/opt/conda/envs/birdy/lib/python3.7/site-packages/pluggy/callers.py", line 208, in _multicall 20:35:36 INTERNALERROR> return outcome.get_result() 20:35:36 INTERNALERROR> File "/opt/conda/envs/birdy/lib/python3.7/site-packages/pluggy/callers.py", line 80, in get_result 20:35:36 INTERNALERROR> raise ex[1].with_traceback(ex[2]) 20:35:36 INTERNALERROR> File "/opt/conda/envs/birdy/lib/python3.7/site-packages/pluggy/callers.py", line 187, in _multicall 20:35:36 INTERNALERROR> res = hook_impl.function(*args) 20:35:36 INTERNALERROR> File "/opt/conda/envs/birdy/lib/python3.7/site-packages/_pytest/main.py", line 272, in pytest_runtestloop 20:35:36 INTERNALERROR> item.config.hook.pytest_runtest_protocol(item=item, nextitem=nextitem) 20:35:36 INTERNALERROR> File "/opt/conda/envs/birdy/lib/python3.7/site-packages/pluggy/hooks.py", line 286, in __call__ 20:35:36 INTERNALERROR> return self._hookexec(self, self.get_hookimpls(), kwargs) 20:35:36 INTERNALERROR> File "/opt/conda/envs/birdy/lib/python3.7/site-packages/pluggy/manager.py", line 93, in _hookexec 20:35:36 INTERNALERROR> return self._inner_hookexec(hook, methods, kwargs) 20:35:36 INTERNALERROR> File "/opt/conda/envs/birdy/lib/python3.7/site-packages/pluggy/manager.py", line 87, in <lambda> 20:35:36 INTERNALERROR> firstresult=hook.spec.opts.get("firstresult") if hook.spec else False, 20:35:36 INTERNALERROR> File "/opt/conda/envs/birdy/lib/python3.7/site-packages/pluggy/callers.py", line 208, in _multicall 20:35:36 INTERNALERROR> return outcome.get_result() 20:35:36 INTERNALERROR> File "/opt/conda/envs/birdy/lib/python3.7/site-packages/pluggy/callers.py", line 80, in get_result 20:35:36 INTERNALERROR> raise ex[1].with_traceback(ex[2]) 20:35:36 INTERNALERROR> File "/opt/conda/envs/birdy/lib/python3.7/site-packages/pluggy/callers.py", line 187, in _multicall 20:35:36 INTERNALERROR> res = hook_impl.function(*args) 20:35:36 INTERNALERROR> File "/opt/conda/envs/birdy/lib/python3.7/site-packages/_pytest/runner.py", line 85, in pytest_runtest_protocol 20:35:36 INTERNALERROR> runtestprotocol(item, nextitem=nextitem) 20:35:36 INTERNALERROR> File "/opt/conda/envs/birdy/lib/python3.7/site-packages/_pytest/runner.py", line 100, in runtestprotocol 20:35:36 INTERNALERROR> reports.append(call_and_report(item, "call", log)) 20:35:36 INTERNALERROR> File "/opt/conda/envs/birdy/lib/python3.7/site-packages/_pytest/runner.py", line 188, in call_and_report 20:35:36 INTERNALERROR> report = hook.pytest_runtest_makereport(item=item, call=call) 20:35:36 INTERNALERROR> File "/opt/conda/envs/birdy/lib/python3.7/site-packages/pluggy/hooks.py", line 286, in __call__ 20:35:36 INTERNALERROR> return self._hookexec(self, self.get_hookimpls(), kwargs) 20:35:36 INTERNALERROR> File "/opt/conda/envs/birdy/lib/python3.7/site-packages/pluggy/manager.py", line 93, in _hookexec 20:35:36 INTERNALERROR> return self._inner_hookexec(hook, methods, kwargs) 20:35:36 INTERNALERROR> File "/opt/conda/envs/birdy/lib/python3.7/site-packages/pluggy/manager.py", line 87, in <lambda> 20:35:36 INTERNALERROR> firstresult=hook.spec.opts.get("firstresult") if hook.spec else False, 20:35:36 INTERNALERROR> File "/opt/conda/envs/birdy/lib/python3.7/site-packages/pluggy/callers.py", line 203, in _multicall 20:35:36 INTERNALERROR> gen.send(outcome) 20:35:36 INTERNALERROR> File "/opt/conda/envs/birdy/lib/python3.7/site-packages/dash/testing/plugin.py", line 79, in pytest_runtest_makereport 20:35:36 INTERNALERROR> for name, fixture in item.funcargs.items(): 20:35:36 INTERNALERROR> AttributeError: 'IPyNbCell' object has no attribute 'funcargs' ```
tlvu
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to bird-house/birdhouse-deploy
that referenced
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Jul 17, 2020
Noticeable changes: ```diff < - dask=2.17.2=py_0 > - dask=2.20.0=py_0 > - nc-time-axis=1.2.0=py_1 < - xarray=0.15.1=py_0 > - xarray=0.16.0=py_0 < - xclim==0.17.0 > - xclim==0.18.0 ``` See PR Ouranosinc/PAVICS-e2e-workflow-tests#47 (commit Ouranosinc/PAVICS-e2e-workflow-tests@4e03a67) for more info.
tlvu
added a commit
to bird-house/birdhouse-deploy
that referenced
this pull request
Jul 18, 2020
…-axis jupyter: new build and add nc-time-axis Corresponding change to deploy the new Jupyter env to PAVICS. Noticeable changes: ```diff < - dask=2.17.2=py_0 > - dask=2.20.0=py_0 > - nc-time-axis=1.2.0=py_1 < - xarray=0.15.1=py_0 > - xarray=0.16.0=py_0 < - xclim==0.17.0 > - xclim==0.18.0 ``` See PR Ouranosinc/PAVICS-e2e-workflow-tests#47 (commit Ouranosinc/PAVICS-e2e-workflow-tests@4e03a67) for more info.
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Noticeable changes:
Also fix the weirdo Jenkins build error that appears out of no where without docker image change:
Passing Jenkins build http://jenkins.ouranos.ca/job/PAVICS-e2e-workflow-tests/job/update-docker-image-and-add-nc-time-axis/2/console together with this PR Ouranosinc/pavics-sdi#172 (commit Ouranosinc/pavics-sdi@e06f4dd).
Full conda env export diff:
200605-200716-conda-env-export.diff.txt
Full new conda env export:
200716-conda-env-export.yml.txt