Dependency and warning fix and compatibility with Scipy 1.12

matsengrp / gctree

GCtree: phylogenetic inference of genotype-collapsed trees

https://matsengrp.github.io/gctree

GNU General Public License v3.0

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Dependency and warning fix and compatibility with Scipy 1.12 #122

Closed willdumm closed 7 months ago

willdumm commented 7 months ago

Fixes #121 (Thanks Jared!)
Fixes a warning about a deprecated method call in historydag
Scipy <1.12 re-exported some numpy modules and functions, which were called in various places. Scipy 1.12 no longer re-exports these names, resulting in import errors. This is fixed, and we now call numpy methods directly when we mean to.

willdumm commented 7 months ago

@WSDeWitt This also removes the deprecated file mode rU in phylip_parse.py::parse_outfile. As far as I understand, this won't cause any issues (and CI tests will show if it does on non-windows machines)

When this is merged I'll release it as v4.1.3. The historydag version requirements of v4.1.2 will remain incorrect in PyPI.