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Make it possible to run HermiT on EMMO #740

Merged
merged 5 commits into from
May 1, 2024
Merged

Make it possible to run HermiT on EMMO #740

merged 5 commits into from
May 1, 2024

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jesper-friis
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Description

Make it possible to run HermiT on EMMO, by:

  • Add support for additional keyword arguments that sync_reasoner() may pass to the save() method.
  • Remove custom datatypes before running HermiT. Readd the removed data properties after HermiT completes.
  • Add --java-executable and --java-memory arguments to ontoconvert to control how to run java.

Type of change

  • Bug fix.
  • New feature.
  • Documentation update.
  • Test update.

Checklist

This checklist can be used as a help for the reviewer.

  • Is the code easy to read and understand?
  • Are comments for humans to read, not computers to disregard?
  • Does a new feature has an accompanying new test (in the CI or unit testing schemes)?
  • Has the documentation been updated as necessary?
  • Does this close the issue?
  • Is the change limited to the issue?
  • Are errors handled for all outcomes?
  • Does the new feature provide new restrictions on dependencies, and if so is this documented?

Comments

@jesper-friis jesper-friis mentioned this pull request Apr 12, 2024
15 tasks
Comment on lines 945 to 947
filepath = os.path.join(
dir, file if isinstance(file, str) else file.name
)
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@francescalb francescalb Apr 15, 2024

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why? If I revert this, tests pass without problem.

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Add fix: isinstance(file, str) -> isinstance(file, (str, Path))

@francescalb
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We should have a test on this. It is important that we wuickly pick up if running sync_reasoner on EMMO does not work.

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codecov bot commented Apr 15, 2024

Codecov Report

Attention: Patch coverage is 66.66667% with 9 lines in your changes are missing coverage. Please review.

Project coverage is 72.14%. Comparing base (a8f5c24) to head (3b7c21b).

Files Patch % Lines
ontopy/ontology.py 66.66% 9 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##           master     #740      +/-   ##
==========================================
- Coverage   72.21%   72.14%   -0.07%     
==========================================
  Files          17       17              
  Lines        3462     3486      +24     
==========================================
+ Hits         2500     2515      +15     
- Misses        962      971       +9     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

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@francescalb francescalb left a comment

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As a general rule I think that untested features should be tested properly before being smerged to master.

Please make an issue that clearly decribes what needs to be tested so that it can be picked up later.

@jesper-friis jesper-friis merged commit f769bcb into master May 1, 2024
10 of 12 checks passed
@jesper-friis jesper-friis deleted the fix_hermit branch May 1, 2024 13:48
francescalb added a commit that referenced this pull request May 8, 2024
# Description
Make it possible to run HermiT on EMMO, by:
* Add support for additional keyword arguments that `sync_reasoner()` may pass to the `save()` method.
* Remove custom datatypes before running HermiT. Readd the removed data properties after HermiT completes.
* Add `--java-executable` and `--java-memory` arguments to ontoconvert to control how to run java.

## Type of change
- [x] Bug fix.
- [ ] New feature.
- [ ] Documentation update.
- [ ] Test update.

Co-authored-by: francescalb <[email protected]>
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2 participants