Bypass punning in ontodoc. #532
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Also added a test to check that ontodoc actually runs with non-punned individuals and punned individuals
ontopy/ontodoc.py
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| except TypeError: | ||
| warnings.warn( |
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Very good warning message. Are we sure that there are not other TypeErrors what will be catched by this except statement?
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No, I am not sure that there are not others. But I think it is only punning that will be caught by this because we ask for an indivudal, and then we iterate of the concepts that the individual is an instance of. But I think this is a good point. If there is punning I know that is_instance_of returns 'property' and not a list of concepts, so I changed it to be a positive test for that. Better?
…EMMOntoPy into flb/bypass_punning_in_ontodoc
Pushed with no verify as the pylint errors are due to pylint upgrade which finds errors in other parts of the core. This is addressed in another PR.
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Yes, this looks very good.
I have not tested it locally which I normally would do if I had my linux machine at hand, but I see you have a good test.
As far as I can see, PR #535 fixes the issue with failing tests. Please merge that into this branch before merging to master.
Note, only the ontodoc tests have been updated, so all other tool tests will fail.
This reverts commit a80a96e.
…_ontodoc Fix fixtures for Python3.7.
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## master #532 +/- ##
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+ Coverage 65.59% 65.84% +0.24%
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Files 16 16
Lines 3090 3095 +5
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+ Hits 2027 2038 +11
+ Misses 1063 1057 -6
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Description:
Closes #506.
Ontodoc fails when punned individuals are included in the ontology.
After discussions with various people (see #507) we have agreed to not support punning for now.
This might be changed in the future if we see the need.
Tests have been added to see that ontodoc runs for ontologies with an individual, and that it runs with a warning
when the individual is a punned individual. Pytest is set to ignore that particualr warning so that this test
will continue to pass if pytest is set to fail on warnings as well in the future.
Type of change:
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