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INCATools / ontology-access-kit

Ontology Access Kit: A python library and command line application for working with ontologies
https://incatools.github.io/ontology-access-kit/
Apache License 2.0
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Document instructions for running the obographs-compliance suite #751

Open matentzn opened 4 months ago

matentzn commented 4 months ago

@cmungall can you provide a page docs page on how to use the obographs compliance framework?

We are close to a robot release and we need this merged now:

https://github.com/ontodev/robot/pull/1198

The first in a two stage process towards some important obographs extensions.

cmungall commented 4 months ago

Im unlikely to get to this in the next few days because of the monarch hackathon. But the doc strings are not too bad Claude could do a good first pass. See also the open PR to get a sense of the diffs

On Sun, May 5, 2024 at 6:05 AM Nico Matentzoglu @.***> wrote:

@cmungall https://github.com/cmungall can you provide a page docs page on how to use the obographs compliance framework?

We are close to a robot release and we need this merged now:

ontodev/robot#1198 https://github.com/ontodev/robot/pull/1198

The first in a two stage process towards some important obographs extensions.

— Reply to this email directly, view it on GitHub https://github.com/INCATools/ontology-access-kit/issues/751, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAMMOMX77XXV2MGWMSTAL3ZAYVCTAVCNFSM6AAAAABHHWZTNCVHI2DSMVQWIX3LMV43ASLTON2WKOZSGI3TSNJSGM4DQMI . You are receiving this because you were mentioned.Message ID: @.***>

matentzn commented 4 months ago

But the doc strings are not too bad Claude could do a good first pass. See also the open PR to get a sense of the diffs

Maybe just two bullet points when you have a minute. Like:

  1. Put robot binary on path
  2. Run test suite with poetry run tox -e py
cmungall commented 4 months ago

Unfortunately it's not so simple. You really have to read the full docs right now. There is no established SoT now. The tests involve a bootstrapping component. It looks like there have been some changes since this was first done. For example, as can be seen in #747 the owlapi now injects labels for oio APs. This is a change from the baseline that was previously established. So we need to discuss whether injection of these labels is the new standard and update the obo-syntax docs and regenerate the baseline, or we need to declare the current behavior as in violation

cmungall commented 3 months ago

OK, to keep it simple I have just accepted that it is now the standard that conversion introduces AP label injections.

So the instructions are simple:

  1. Make sure the version of robot you want to test is on the command line
  2. Run the test using pytest or your IDE

If the output doesn't conform, it will fail