Bacpop-211 - add Streptococcus pyogenes #58
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
absternator
commented
Jan 27, 2025
| assert project_data["status"]["microreact"] == "finished" | ||
| assert project_data["status"]["network"] == "finished" | ||
|
|
||
| def test_run_poppunk_streptococcus_pyogenes(client, qtbot): |
There was a problem hiding this comment.
rest of file is cleanup and extracting common code into functions
EmmaLRussell
approved these changes
Jan 28, 2025
There was a problem hiding this comment.
Looks good, works for me. Could you refactor the integration tests to reduce repetition even more? They're each testing that poppunk goes through the same process - or almost the same? So could have a single function that checks for that, with maybe a couple of parameters for anything that needs to be different e.g. metadata csv file? Up to you though!
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This adds new species Streptococcus pyogenes.
Testing:
For frontend ensure branch is
bacpop-186-v9-dbalso ensure api_branch is pointed tobacpop-211-pyogenes-dev... also you will have to re-run./scripts/download_databasesagain.Run the new sample ive slacked, selecting the Streptococcus pyogenes as the project species