Logging error
ivirshup opened this issue · comments
It looks like logging has been broken by an update to scanpy.
It's pretty straight forward to fix the timing error, now logg.info returns a date time, which you pass to the next logg.info you want to have the elapsed time.
I'm not sure how to replace the end argument. @flying-sheep, any suggestion?
Oh, just saw #14, sorry about the duplicate!
Thanks for letting me know this went live in a release, I'll amend BBKNN accordingly early next week.
Apparently, the most recent scanpy in pip is still 1.4.3. @ivirshup when is this logging change actually going to go live? I don't want to push out an update to make this compatible with a version of scanpy that's not on pip yet.
@ktpolanski scanpy pip version is now 1.4.4
Thanks for the heads up. I'm encountering some trouble with getting the new logging to cooperate (not just BBKNN-side), popped open an issue on the scanpy repo. Depending on the outcome, I'll either push a nice, fully compatible version with deep, or a stand-in with two logging messages to circumvent the functionality not cooperating.
I failed to get a response on my deep-related issues here, and I've waited a week. No point delaying this further, so I'm pushing 1.3.5 to pip. It comes with deep syntax, which is non-operational on my end, but at least it matches how scanpy's neighbour function behaves. As such, maybe it'll be operational somewhere in mysterious ways.
EDIT: deep got fixed in 1.4.4.post1!