Build created bad version 2.3.2

[matandro]

Describe the bug
The tool crashes if built or installed directly via python requirements. This seems to be related to a Cython update that does not support the "long" type. If you can lock the cython version in your project.toml it might help (we are checking now)

CRITICAL @ Fri, 16 May 2025 17:02:58 (0.5% done):
         Traceback (most recent call last):
  File "/usr/local/lib/python3.12/site-packages/CRISPResso2/CRISPRessoCORE.py", line 1429, in main
    aln_matrix = CRISPResso2Align.read_matrix(aln_matrix_loc)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "CRISPResso2/CRISPResso2Align.pyx", line 43, in CRISPResso2.CRISPResso2Align.read_matrix
  File "CRISPResso2/CRISPResso2Align.pyx", line 51, in CRISPResso2.CRISPResso2Align.read_matrix
NameError: name 'long' is not defined
 

CRITICAL @ Fri, 16 May 2025 17:02:58 (0.5% done):
         Unexpected error, please check your input.

ERROR: name 'long' is not defined 

Expected behavior
Tool to run properly

To reproduce
Install CRISPResso via requirement file CRISPResso2 @git+https://github.com/pinellolab/CRISPResso2.git@v2.3.2 or clone and build
Obviously we run it in a docker container that has fastp

Debug output
Paste the entire output when you run CRISPResso with the flag --debug.

[matandro]

Proposed solution, tested in our production environment

[matandro]

It's probably best to just not use numpy long like other tools

[Colelyman]

Hi @matandro and @rohan-mammothbio,

Thanks for submitting the issue and the associated PR. We ran into the same issue a few days ago and have a fix that is backwards compatible with Cython 3.0.12 and 3.1.0, where we use np.int64 instead of long directly. We would have the preference of supporting more versions of Cython rather than pinning.

I will keep this issue updated when that PR is merged in.

Thanks,
Cole

[matandro]

Yes, we made that comment in the PR that it's not the best way to fix. We needed a quick fix.
Can you close the issue only when it's pushed to release so we know to update our install tag?

[Colelyman]

Thanks @matandro, the PR (#537) has been merged in. @kclem would you be able to close this issue?

[alanorth]

Thanks. I'm deploying this on our cluster with the np.int64 patch on top of v2.3.2 as well. Does it warrant a 2.3.3 release?

[kclem]

@alanorth Yes, we'll do a release and version bump with some more changes early next week.

[kclem]

@alanorth
Done https://github.com/pinellolab/CRISPResso2/releases/tag/v2.3.3