Nbval default ignore html and javascript output #73
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…ecrease usage of NBVAL_IGNORE_OUTPUT Following https://nbval.readthedocs.io/en/latest/index.html?highlight=skip#Skipping-certain-output-types Error: ``` INTERNALERROR> File "/opt/conda/envs/birdy/lib/python3.7/site-packages/pluggy/callers.py", line 80, in get_result INTERNALERROR> raise ex[1].with_traceback(ex[2]) INTERNALERROR> File "/opt/conda/envs/birdy/lib/python3.7/site-packages/pluggy/callers.py", line 187, in _multicall INTERNALERROR> res = hook_impl.function(*args) INTERNALERROR> File "/repos/PAVICS-e2e-workflow-tests/conftest.py", line 2, in pytest_collectstart INTERNALERROR> collector.skip_compare += 'text/html', 'application/javascript', INTERNALERROR> AttributeError: 'Session' object has no attribute 'skip_compare' ```
…rease usage of NBVAL_IGNORE_OUTPUT Fix the error found in the previous commit 36d2fb4.
matprov
approved these changes
May 18, 2021
tlvu
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May 27, 2021
Also removed `NBVAL_IGNORE_OUTPUT` since Jenkins is configured to by default ignore html changes, see PR Ouranosinc/PAVICS-e2e-workflow-tests#73. To fix this error: ``` _______ pavics-sdi-master/docs/source/notebooks/subsetting.ipynb::Cell 2 _______ Notebook cell execution failed Cell 2: Cell outputs differ Input: help(fp.subset_continents) Traceback: mismatch 'stdout' assert reference_output == test_output failed: 'Help on meth... outputs.\n\n' == 'Help on meth... outputs.\n\n' Skipping 101 identical leading characters in diff, use -v to show - n='Africa') method of birdy.client.base.WPSClient instance + n='Africa', output_formats=None) method of birdy.client.base.WPSClient instance ? +++++++++++++++++++++ Return the data whose grid cells intersect the selected continents for each input dataset. Parameters ---------- region : {'Africa', 'Asia', 'Australia', 'North America', 'Oceania', 'South America', 'Antarctica', 'Europe'}string Continent name. resource : ComplexData:mimetype:`application/x-netcdf`, :mimetype:`application/x-tar`, :mimetype:`application/zip` NetCDF Files or archive (tar/zip) containing netCDF files. Returns ------- output : ComplexData:mimetype:`application/x-netcdf` NetCDF output for first resource file. metalink : ComplexData:mimetype:`application/metalink+xml; version=4.0` Metalink file with links to all NetCDF outputs. ```
tlvu
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to bird-house/finch
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May 27, 2021
Also removed `NBVAL_IGNORE_OUTPUT` since Jenkins is configured to by default ignore html changes, see PR Ouranosinc/PAVICS-e2e-workflow-tests#73. To fix this error: ``` _________ finch-master/docs/source/notebooks/finch-usage.ipynb::Cell 1 _________ Notebook cell execution failed Cell 1: Cell outputs differ Input: help(wps.frost_days) Traceback: mismatch 'stdout' assert reference_output == test_output failed: 'Help on meth...ut files.\n\n' == 'Help on meth...ut files.\n\n' Skipping 201 identical leading characters in diff, use -v to show - iable=None) method of birdy.client.base.WPSClient instance + iable=None, output_formats=None) method of birdy.client.base.WPSClient instance ? +++++++++++++++++++++ Number of days where daily minimum temperatures are below 0. Parameters ---------- tasmin : ComplexData:mimetype:`application/x-netcdf`, :mimetype:`application/x-ogc-dods` NetCDF Files or archive (tar/zip) containing netCDF files. thresh : string Freezing temperature. freq : {'YS', 'MS', 'QS-DEC', 'AS-JUL'}string Resampling frequency. check_missing : {'any', 'wmo', 'pct', 'at_least_n', 'skip', 'from_context'}string Method used to determine which aggregations should be considered missing. missing_options : ComplexData:mimetype:`application/json` JSON representation of dictionary of missing method parameters. cf_compliance : {'log', 'warn', 'raise'}string Whether to log, warn or raise when inputs have non-CF-compliant attributes. data_validation : {'log', 'warn', 'raise'}string Whether to log, warn or raise when inputs fail data validation checks. variable : string Name of the variable in the NetCDF file. Returns ------- output_netcdf : ComplexData:mimetype:`application/x-netcdf` The indicator values computed on the original input grid. output_log : ComplexData:mimetype:`text/plain` Collected logs during process run. ref : ComplexData:mimetype:`application/metalink+xml; version=4.0` Metalink file storing all references to output files. ```
This was referenced May 27, 2021
tlvu
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Jun 15, 2021
…ut-for-jenkins finch-usage.ipynb: update output due to new birdy 0.8.0 New birdy removed `output_formats`. Clarification from DavidH: To clarify, the `output_formats` option still exists, but it's only appearing when the process has a complexoutput supporting more than one data format. bird-house/birdy@2bea46c#diff-ba0f245ac7a3747697d42961f7a19568e294dc5d2b4ad14b62a47d8c240ed12eR230-R238 Also removed `NBVAL_IGNORE_OUTPUT` since Jenkins is configured to by default ignore html changes, see PR Ouranosinc/PAVICS-e2e-workflow-tests#73. Jenkins passing build with upcoming Jupyter env: http://jenkins.ouranos.ca/job/PAVICS-e2e-workflow-tests/job/new-docker-build-for-ravenpy/10/console New Jupyter env PR: Ouranosinc/PAVICS-e2e-workflow-tests#75 To fix this error: ``` _________ finch-master/docs/source/notebooks/finch-usage.ipynb::Cell 1 _________ Notebook cell execution failed Cell 1: Cell outputs differ Input: help(wps.frost_days) Traceback: mismatch 'stdout' assert reference_output == test_output failed: 'Help on meth...ut files.\n\n' == 'Help on meth...ut files.\n\n' Skipping 201 identical leading characters in diff, use -v to show - iable=None) method of birdy.client.base.WPSClient instance + iable=None, output_formats=None) method of birdy.client.base.WPSClient instance ? +++++++++++++++++++++ Number of days where daily minimum temperatures are below 0. Parameters ---------- tasmin : ComplexData:mimetype:`application/x-netcdf`, :mimetype:`application/x-ogc-dods` NetCDF Files or archive (tar/zip) containing netCDF files. thresh : string Freezing temperature. freq : {'YS', 'MS', 'QS-DEC', 'AS-JUL'}string Resampling frequency. check_missing : {'any', 'wmo', 'pct', 'at_least_n', 'skip', 'from_context'}string Method used to determine which aggregations should be considered missing. missing_options : ComplexData:mimetype:`application/json` JSON representation of dictionary of missing method parameters. cf_compliance : {'log', 'warn', 'raise'}string Whether to log, warn or raise when inputs have non-CF-compliant attributes. data_validation : {'log', 'warn', 'raise'}string Whether to log, warn or raise when inputs fail data validation checks. variable : string Name of the variable in the NetCDF file. Returns ------- output_netcdf : ComplexData:mimetype:`application/x-netcdf` The indicator values computed on the original input grid. output_log : ComplexData:mimetype:`text/plain` Collected logs during process run. ref : ComplexData:mimetype:`application/metalink+xml; version=4.0` Metalink file storing all references to output files. ```
tlvu
added a commit
to Ouranosinc/pavics-sdi
that referenced
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Jun 15, 2021
…t-for-jenkins subsetting.ipynb: update output due to new birdy 0.8.0 New birdy removed `output_formats`. Clarification from DavidH: To clarify, the `output_formats` option still exists, but it's only appearing when the process has a complexoutput supporting more than one data format. bird-house/birdy@2bea46c#diff-ba0f245ac7a3747697d42961f7a19568e294dc5d2b4ad14b62a47d8c240ed12eR230-R238 Also removed `NBVAL_IGNORE_OUTPUT` since Jenkins is configured to by default ignore html changes, see PR Ouranosinc/PAVICS-e2e-workflow-tests#73. Jenkins passing build with upcoming Jupyter env: http://jenkins.ouranos.ca/job/PAVICS-e2e-workflow-tests/job/new-docker-build-for-ravenpy/10/console New Jupyter env PR: Ouranosinc/PAVICS-e2e-workflow-tests#75 To fix this error: ``` _______ pavics-sdi-master/docs/source/notebooks/subsetting.ipynb::Cell 2 _______ Notebook cell execution failed Cell 2: Cell outputs differ Input: help(fp.subset_continents) Traceback: mismatch 'stdout' assert reference_output == test_output failed: 'Help on meth... outputs.\n\n' == 'Help on meth... outputs.\n\n' Skipping 101 identical leading characters in diff, use -v to show - n='Africa') method of birdy.client.base.WPSClient instance + n='Africa', output_formats=None) method of birdy.client.base.WPSClient instance ? +++++++++++++++++++++ Return the data whose grid cells intersect the selected continents for each input dataset. Parameters ---------- region : {'Africa', 'Asia', 'Australia', 'North America', 'Oceania', 'South America', 'Antarctica', 'Europe'}string Continent name. resource : ComplexData:mimetype:`application/x-netcdf`, :mimetype:`application/x-tar`, :mimetype:`application/zip` NetCDF Files or archive (tar/zip) containing netCDF files. Returns ------- output : ComplexData:mimetype:`application/x-netcdf` NetCDF output for first resource file. metalink : ComplexData:mimetype:`application/metalink+xml; version=4.0` Metalink file with links to all NetCDF outputs. ```
tlvu
added a commit
to bird-house/finch
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Jun 16, 2021
With PR #188 removing `NBVAL_IGNORE_OUTPUT` since Jenkins is configured by default to ignore html changes (PR Ouranosinc/PAVICS-e2e-workflow-tests#73), test-notebooks target here is broken because it does not have the same `conftest.py` as Jenkins. This change brings the same `conftest.py` from Jenkins here to fix test-notebooks target.
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Overview
Ignore by default html and javascript output to decrease usage of
NBVAL_IGNORE_OUTPUT.Changes
conftest.pyfollowing https://nbval.readthedocs.io/en/latest/index.html?highlight=skip#Skipping-certain-output-typesRelated Issue / Discussion
--nbval-lax.Additional Information
Nbval documentation was not 100% correct: computationalmodelling/nbval#168