Hi @jonbrenas and @ahernank,

I’ve opened PR #933 to expand the documentation for sample_metadata().
I’d appreciate your feedback when you have time.
Also, the workflows are awaiting maintainer approval for CI to run.

Thank you!

Hi @jonbrenas ,
All checks are now passing for this PR. Could you please review it when convenient?
Happy to make any changes if needed.
Thank you!

Hi @jonbrenas, I've removed the parameters section as requested — only summary and returns remain. Could you please take another look when convenient? Thank you!

Thanks @Tanisha127. When I run len(ag3.sample_metadata(sample_sets='3.0').columns), I get 58. How did you choose which columns to list? Why not all of them?

Thanks @jonbrenas! I chose those columns because they seemed like the most commonly used ones for a typical analysis — sample identity, collection metadata, QC, and species assignment. However, I can see that only listing 18 out of 58 columns could be misleading or incomplete for users who need the full picture.
I can update the returns section to either:
List all 58 columns with descriptions
Group them by category (e.g. general metadata, QC, AIM, cohorts) with a note that the exact columns vary by sample set
Which approach would you prefer?

Hi @Tanisha127. I thinking grouping columns by category would be very convenient.

Hi @jonbrenas, I've updated the returns section to group all columns by category. All checks are now passing. Could you please take another look when convenient? Thank you!

Thanks @Tanisha127. Why did you choose to make 'Surveillance flags' its own category? Are there cases (I am thinking about the AIMs columns, for example) where it is possible to be more precise on whether a column will be present or not?

Hi , Could you please take another look when convenient? Thank you!

Thanks @Tanisha127, it is great! Is there a reason why 'quarter' is the only one with the details of what the value is when the data is missing?

Hi @jonbrenas, I've removed the missing value detail from the quarter field to keep the documentation consistent with all other columns. I've also resolved the merge conflict with master. Could you please take another look when convenient? Thank you!