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add khmer 2.x compat functions back in #1861

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ctb opened this issue May 5, 2018 · 4 comments
Open

add khmer 2.x compat functions back in #1861

ctb opened this issue May 5, 2018 · 4 comments

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@ctb
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ctb commented May 5, 2018

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?

@luizirber
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luizirber commented May 7, 2018

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)

@standage
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standage commented May 8, 2018

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.

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

@luizirber
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We got around this issue in sourmash with sourmash-bio/sourmash#508

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