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Mappy Python3.9 - pip installation error #719
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I don't know what is the cause. Python 3.9 in Travis compiles mappy without problems. |
The
mappy.c has been generated by an older version of Cython that is not fully compatible with Python 3.9. It's unclear whether that means @vepain needs to update Cython on their machine or that the problem is that mappy.c was generated elsewhere and just needs to be regenerated locally. |
Thank you two for your answer, In fact, I can install correctly However, for $: python3.9 -m pip freeze | grep 'Cython'
Cython==0.29.21 |
From the python issue linked above, it appears that the issue is not with cython, but with the python version used to compile the mappy cython found in pypi. The released mappy package in pypi appears to use the most recent cython version (0.29 from the files header), but was probably compiled with an older version of python (not listed in the cython header that I can find). I suspect the pypi package will have to be submitted from a python3.9 compiled distribution in order to resolve this issue. This could create backwards compatibility issues with older versions of python and may have to be tested. |
I have just merged @marcus1487's #723. With this PR, |
Hi @lh3,
I really like your work on minimap2 and I currently work on a new long reads assembly method for my PhD which use your aligner, so thank you!
I use
python3.9
for all my code until I meet time or memory complexity issues.That's why I used
python3.9 -m pip install mappy
but it returns an exit status 1.It seems to be due to
error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’
(see https://bugs.python.org/issue39361) and some depreciated PyUnicode[...] objects perhaps.You can see the complete compilation error print below:
Thank you for your help and your time,
Best regards
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