module 'pysam.libcalignedsegment' has no attribute 'CMATCH'

[Adamtaranto]

I'm getting a strange pysam error that only seems to occur when I am running with Python 3.8 on on MacOS latest in this github action. Error does not occur on ubuntu.

When importing pysam I get this error:

/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/pysam/__init__.py:21: in <module>
    from pysam.libcalignedsegment import *
E   AttributeError: module 'pysam.libcalignedsegment' has no attribute 'CMATCH'

Versions:

• Python version: 3.8.10 (v3.8.10:3d8993a744, May 3 2021, 09:09:08)
• [Clang 12.0.5 (clang-1205.0.22.9)]
• Pysam: pysam-0.23.0-cp38-cp38-macosx_11_0_universal2.whl

Here is the log of the github action where this is failing: https://github.com/tanghaibao/jcvi/actions/runs/14951392044/job/42001281341

I don't see how libcalignedsegment could be missing that attribute.

Maybe similar to #1055 ?

[jmarshall]

The first version of Python to support Apple Silicon natively was 3.9. Pysam does not provide a 3.8 wheel on ARM macOS — you will see that this particular job has built pysam from source whereas your other GH Actions jobs were able to download a wheel.

So this problem is likely due to some architecture confusion in the wheel that your GitHub Actions job has built. Perhaps related to #1231.

Python 3.8 is EOL and the pysam maintainers do not support 3.8 wheels on ARM macOS. I would suggest you do the same.

[Adamtaranto]

Thanks. We will ditch 3.8.

[MoLuLuMo]

I have the same issue here

/python3.10/site-packages/pysam/__init__.py#line=20)
     19 from pysam.libcalignmentfile import *
     20 import pysam.libcalignedsegment as libcalignedsegment
---> 21 from pysam.libcalignedsegment import *
     22 import pysam.libcvcf as libcvcf
     23 from pysam.libcvcf import *

AttributeError: module 'pysam.libcalignedsegment' has no attribute 'CMATCH'

[ajw2329]

I just encountered the same issue when installing 0.23.0 for python 3.10 via pip on CentOS 7.

[jmarshall]

@MoLuLuMo: What platform is this? What version of pysam?

@ajw2329: Please show the logs.

[andyb3]

We've started getting the same error with pysam 0.22.1 installed on the latest python 3.11 aws lambda image (public.ecr.aws/lambda/python:3.11)

We first noticed it on Friday.

  File "/var/lang/lib/python3.11/site-packages/pysam/__init__.py", line 21, in <module>
    from pysam.libcalignedsegment import *
AttributeError: module 'pysam.libcalignedsegment' has no attribute 'CMATCH'

[MoLuLuMo]

@jmarshall

I'm running Python 3.10.17 (packaged by conda-forge, GCC 13.3.0) on Linux, with pysam version 0.23.0.

[jmarshall]

Thanks for all the reports; I have now been able to reproduce this. In all these cases, you are building wheels from scratch via pip rather than being able to use the pre-built wheels (which were built at the time of the last release back in February).

This problem started happening last week due to the release of Cython 3.1, which included this change: cython/cython#4571:

Named cpdef enums no longer copy their item names into the global module namespace. This was considered unhelpful for named enums which already live in their own class namespace.

So we will work around this in some way, either via the workaround suggested, by declaring these enums properly in the .pxd file if that makes a difference, or by adjusting our use of these enumerators accordingly (which could be just removing them from __all__!).

In the meantime, you can work around this by adding Cython<3.1 to your requirements as appropriate.

[Adamtaranto]

I've set cython<3.1 here tanghaibao/jcvi#779 and am still getting the same issue.

[jmarshall]

@Adamtaranto — Flipping between Cython 3.0.12 and 3.1.0 flips the build between working and no CMATCH in my testing.

I suspect if you add appropriate verbosity flags to pip you'll see that Cython<3.1 is being applied for the jcvi build but when pip creates an ephemeral virtual environment to do the pysam build, it uses pysam's requirements and populates this environment using Cython>=0.29.12,<4 and chooses 3.1.0.

[Adamtaranto]

If that is the case, is there a way to force a specific cython version?