khmer icon indicating copy to clipboard operation
khmer copied to clipboard

Published 20 hours ago • verified publisher icon dib-lab

add khmer 2.x compat functions back in

Open ctb opened this issue 6 years ago • 4 comments

it would be nice to be able to use the next release of khmer with the current version of sourmash, and I think right now sourmash depends on khmer.load_nodegraph which doesn't exist in master. maybe we could put that back into khmer?

ctb avatar May 05 '18 15:05 ctb

we can also do

- self._data = khmer.load_nodegraph(f.name)
+ self._data = khmer.Nodegraph.load(f.name)

(from this PR: https://github.com/dib-lab/sourmash/pull/395/files#diff-0b5baa8c66f625d5b16a6ada6c9aa998R681)

luizirber avatar May 07 '18 18:05 luizirber

Yeah, I think it would be clean and easy to add a clearly marked "backwards compatibility" section to the khmer/__init__.py file with a few such definitions. Let me know if there are any others.

standage avatar May 08 '18 17:05 standage

I'm -1 on this. It should be on external libraries to route around deprecated APIs.

camillescott avatar May 08 '18 21:05 camillescott

We got around this issue in sourmash with https://github.com/dib-lab/sourmash/pull/508

luizirber avatar Jun 27 '18 21:06 luizirber