opencobra / memote

memote – the genome-scale metabolic model test suite
https://memote.readthedocs.io/
Apache License 2.0
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Update RegEx patterns for annotation IDs #751

Open WalkerKnapp opened 1 year ago

WalkerKnapp commented 1 year ago

This fix is related to issue #315, but it is a band-aid solution for the current state of database IDs, not an automatic solution as suggested in the issue.

The Regex patterns which are used to match against annotation IDs in test_*_annotation_wrong_ids tests have gone out of date since they were last updated. This PR replaces out-of-date ID patterns with the latest versions retrieved from https://registry.identifiers.org/registry.

I first noticed this problem when evaluating a model which uses a refseq id in the format WP_*, which is now a valid ID. While updating this pattern, I noticed that others have gone out of date as well and have updated them too.

All previous tests in tests/test_for_support/test_for_annotation.py still apply and pass, and no additional functionality which would require tests has been introduced.

codecov[bot] commented 1 year ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Comparison is base (12338a6) 74.85% compared to head (8358d2a) 74.85%.

:exclamation: Current head 8358d2a differs from pull request most recent head 0666f99. Consider uploading reports for the commit 0666f99 to get more accurate results

Additional details and impacted files ```diff @@ Coverage Diff @@ ## develop #751 +/- ## ======================================== Coverage 74.85% 74.85% ======================================== Files 50 50 Lines 2955 2955 Branches 669 669 ======================================== Hits 2212 2212 Misses 649 649 Partials 94 94 ``` | [Files](https://app.codecov.io/gh/opencobra/memote/pull/751?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=opencobra) | Coverage Δ | | |---|---|---| | [src/memote/support/annotation.py](https://app.codecov.io/gh/opencobra/memote/pull/751?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=opencobra#diff-c3JjL21lbW90ZS9zdXBwb3J0L2Fubm90YXRpb24ucHk=) | `100.00% <ø> (ø)` | |

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