Fresh installation using Bioconda yields numpy error

[dmitrisvetlov]

Describe the bug An attempted installation of CRISPResso2 via Bioconda used the latest numpy, as one would expect without version restrictions in the environment file. This yielded an incompatibility error, which you will see below.

Note that I was able to fix it via conda update numpy=1.19, so that could be a temporary workaround until the code can be updated to reflect the deprecation of np.float.

I think that this has some overlap with #519, but the platform is different in my case (Linux on AMD Milan).

Expected behavior

Successful completion of the plot-making step.

To reproduce

Your NHEJ example in the documentation.

Debug output

INFO @ Sun, 27 Apr 2025 02:33:14: Making Plots...

CRITICAL @ Sun, 27 Apr 2025 02:33:15: Unexpected error, please check your input.

ERROR: module 'numpy' has no attribute 'float'. np.float was a deprecated alias for the builtin float. To avoid this error in existing code, use float by itself. Doing this will not modify any behavior an d is safe. If you specifically wanted the numpy scalar type, use np.float64 here. The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

[Colelyman]

Hi @dmitrisvetlov,

Thanks for using CRISPResso and sorry that you have had installation troubles. Would you be able to confirm that conda is indeed installing the latest version of CRISPResso (v2.3.2)? This numpy bug was fixed a few previous versions ago, in this PR https://github.com/pinellolab/CRISPResso2/commit/104866e1080c973bb025d1a5ba59b19dca1658af

Please let us know if you need any additional help!

Thanks, Cole

[dmitrisvetlov]

Hi @Colelyman,

Bioconda, at least, is not using the latest version. Here is the relevant entry in my output of conda list:

crispresso2 2.2.7 py38h5094d80_1 bioconda

- Dmitri

[kclem]

@dmitrisvetlov I believe this issue should be resolved. Please reopen or respond if you continue to have problems.