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numpy 1.24.1 and plastid 0.6.1 appear to have an issue due to dropping of support for numpy.int by numpy. #55

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cjhull opened this issue Dec 31, 2022 · 6 comments
Open

numpy 1.24.1 and plastid 0.6.1 appear to have an issue due to dropping of support for numpy.int by numpy. #55

cjhull opened this issue Dec 31, 2022 · 6 comments

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@cjhull
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cjhull commented Dec 31, 2022 •
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Hello,

In installing a conda environment with plastid for a customer (python 3.9.15, plastid 0.6.1, numpy 1.24.1) my customer found that their test "metagene generate -h" failed with "AttributeError: module 'numpy' has no attribute 'int'".

From searching online copycode.org indicates that as of numpy 1.24 support for numpy.float and numpy.int were removed. I've downgraded the conda numpy to 1.23.5 and am waiting to hear back from my customer whether their test is successful with the downgraded version.

I'm not a developer, but I'm guessing it might warrant setting a requirement for plastid/0.6.1 for numpy to be <= 1.23.5.

Thank you.
@mnapolitano89
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Hello, this is actually an issue with the bioconda recipe not restricting the np version like requirements.txt does, if I figure out how to submit a change to their setup I will make sure that it restricts to under 1.24.

@mnapolitano89 mnapolitano89 mentioned this issue Jan 4, 2023
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@cjhull
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cjhull commented Jan 4, 2023 via email

@mnapolitano89
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This should be fixed in bioconda now

@cjhull
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cjhull commented Jan 6, 2023 via email

@joshuagryphon
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Thank you @mnapolitano89 for the bioconda fix!

Keeping this issue open because we'll need to adjust here for future proofing

@cwilling
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I'm not sure if this is related but seems to concern numpy dropping support for some numeric types. Building plastid fails with numpy-1.26.0 (previously OK with 1.24.4) with error:

running build_ext
Could not find .c files. Regenerating via recythonize.
Cythonizing
running recythonize
running clean

Error compiling Cython file:
------------------------------------------------------------
...
LONG   = np.long

ctypedef np.int_t    INT_t
ctypedef np.float_t  FLOAT_t
ctypedef np.double_t DOUBLE_t
ctypedef np.long_t   LONG_t
        ^
------------------------------------------------------------

plastid/genomics/map_factories.pyx:154:9: 'long_t' is not a type identifier

The discussion above points to limiting numpy to 1.24.x - is that the only possibility?

willysr pushed a commit to SlackBuildsOrg/slackbuilds that referenced this issue Jun 15, 2024
@aclemons @willysr
libraries/plastid: Build against python3-numpy-legacy.
708fd48 
This package is incompatible with later version of numpy. See
upstream ticket:

joshuagryphon/plastid#55

Signed-off-by: Andrew Clemons <[email protected]>

Signed-off-by: Willy Sudiarto Raharjo <[email protected]>
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@cwilling @mnapolitano89 @joshuagryphon @cjhull