some tests failed on macOS about truvari HOT 3 CLOSED

Functional tests off of develop now pass on mac. If you're still seeing a problem, please re-open this ticket.

These changes will be present in v4.1. However It'll be some time before that release is cut as there's at least two more features to add and a lot of user testing happening for a publication tied to the next version.

from truvari.

Thank you for reporting this. I'm sure it wasn't easy to solve. I was able to recreate the issue and confirm that having multiprocessing.set_start_method('fork') before with multiprocessing.Pool.. calls can get tests to pass.

However, I don't think changing the set_start_method is a viable solution. The python docs state:

Changed in version 3.8: On macOS, the spawn start method is now the default. The fork start method should be considered unsafe as it can lead to crashes of the subprocess. See bpo-33725.

Possible solutions:

• Make it clear that some truvari anno commands will fail on macOS
• Make it clear that truvari is designed on/for unix and recommend docker (which is how I run truvari tests on my mac).
• Change design pattern to not depending on 'fork' sharing semantics. Specifically it's the global namespace.

And as I'm digging deeper into bpo-33725 and the issues it references, I'm thinking changing the code might need to be the solution as this non-explicit sharing may become not possible in a future python version.. maybe.

from truvari.

Thanks for your response.

However, I don't think changing the set_start_method is a viable solution.

Yes, I don't think using set_start_method is a good way to fix it.

and thank you for starting the fix as quickly.
Let me know if I can help in any way.

from truvari.