Temporarily commenting phenotype tests in `tests/integration/test_ag3.py`

[jonbrenas]

Following #1161, the error handling in phenotypes.py has been greatly improved but it is now at odds with some integration tests in test_ag3.py. The phenotypic data doesn't really exist yet so I will handle that at a later date once the data becomes more available.

For now, the tests have been commented, most of them should still be fine, the issue is with the checks that required a specific warning or error that have been modified.

[Kaustubh2k5]

any reasons as to why this is marked as wont fix?

[jonbrenas]

Hi @Kaustubh2k5. I have not decided yet what I want to do with respect to the phenotypic data, how it is handled, ... I won't create and fix the tests until I have come to a decision.

[Kaustubh2k5]

hmm, what kind of PRs would you like to see contributors making? do you want bug fixes/ features. any core APIs you want people to focus on ?

[khushthecoder]

Hi @jonbrenas, I came across this issue and wanted to offer help if it would be useful.

I've been looking through the phenotype tests in test_ag3.py, and they're already well-structured — covering phenotype_data, phenotype_binary, phenotype_sample_sets, and the SNP/haplotype integration methods.

Once the direction for phenotype data availability is finalized, I'd be happy to help with:

• updating the commented tests to align with the final data format and checks
• replacing them with proper pytest.skip guards so they're self-documenting and automatically activate when data is available
• improving error handling in phenotypes.py for clearer missing-data behavior

No rush at all — just wanted to mention that I'm available whenever it's the right time.