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Fix NetworkX transitive dependency problem in Python 3.9 #614

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merged 1 commit into from
May 11, 2021

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tskir
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@tskir tskir commented May 9, 2021

Fixes #606. Adds a temporary specification of networkx >= 2.4, actually a transitive dependency of pomegranate, to ensure correct installation and operation under Python 3.9.

Reported to pomegranate developers in jmschrei/pomegranate#909.

Fixes #606. Adds a temporary specification of `networkx >= 2.4`,
actually a transitive dependency of `pomegranate`, to ensure correct
installation and operation under Python 3.9.
@tskir tskir added the bug label May 9, 2021
@tskir tskir requested a review from etal May 9, 2021 16:01
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tskir commented May 9, 2021

(The original suggestion was to bump to 2.5, but my investigations showed that the minimal version to bump up to is 2.4, which already resolves the issue.)

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Thanks, I agree with this. I'll roll another CNVkit release sometime after this lands (and any other outstanding PRs / bug fixes) to ensure users have access to this solution independently of pomegranate's release schedule.

@etal etal merged commit 6d70f05 into master May 11, 2021
@etal etal deleted the 606-transitive-networkx-dependency-fix branch May 11, 2021 17:16
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Bump networkx dependency to 2.5
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