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Description

Added Pytest for OMOP ID, fixed formatting of some unit tests

Addressed issue #13 re indices

Fixes #13 #13

Type of change

Please delete options that are not relevant.

  • Bug fix (non-breaking change which fixes an issue)
  • New feature (non-breaking change which adds functionality)
  • Breaking change (fix or feature that would cause existing functionality to not work as expected)
  • Requires a documentation revision

Testing

Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration

  • test_omop_output.py

Test Configuration

  • Library version: 1.0.3
  • OS: Ubuntu
  • Toolchain: Pycharm

Checklist

  • [X ] My PR is for one issue, rather than for multiple unrelated fixes.
  • [X ] My code follows the style guidelines of this project. I have applied a Linter (recommended: Pycharm's code formatter) to make my whitespace consistent with the rest of the project.
  • I have performed a self-review of my own code
  • I have commented my code, particularly in hard-to-understand areas
  • I have made corresponding changes to the documentation
  • My changes generate no new warnings
  • I have added tests that prove my fix is effective or that my feature works
  • New and existing unit tests pass locally with my changes
  • Any dependent changes have been merged and published in downstream modules
  • I have checked my code and corrected any misspellings
  • The Harmony API is not broken by my change to the Harmony Python library
  • I add third party dependencies only when necessary. If I changed the requirements, it changes in pyproject.toml
  • If I introduced a new feature, I documented it ideally in the README examples so that people will know how to use it.

@woodthom2 woodthom2 merged commit 7b00fd9 into main Mar 28, 2025
1 check passed
@woodthom2 woodthom2 deleted the fix_indices_and_tests branch March 28, 2025 11:51
jaydugad pushed a commit to jaydugad/drug_named_entity_recognition that referenced this pull request Apr 10, 2025
…s_and_tests

Fix indices and tests, update version
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Successfully merging this pull request may close these issues.

Question: why are the token_idx equal for exact matches in the output of find_drugs?

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