M2 mac – stuck at v2.2.8; ERROR: module 'numpy' has no attribute 'float'

[francoiskroll]

Not quite a bug (unless you can suggest a better solution?) but my experience could probably be useful for someone else.

I'm on a mac with M2 chip.

I created my conda environment as:

conda create --name crispr
source activate crispr
conda config --env --set subdir osx-64

Frustratingly, installation with

conda install -c bioconda crispresso2

gives me crispresso2 2.2.8, not the latest.

Consequently, I get old error #269, which was solved in later versions.

For some reason, I cannot update crispresso2. If I try to force conda with

conda install -c bioconda crispresso2=2.2.14

I get

Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                                                                                        

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versionsThe following specifications were found to be incompatible with your system:

  - feature:/osx-64::__osx==13.4=0
  - feature:|@/osx-64::__osx==13.4=0
  - crispresso2=2.2.14 -> matplotlib-base -> __osx[version='>=10.11']

Your installed version is: 13.4

I do not precisely understand what prevents it. I'm imagining it's lingering compatibility issues with M2 mac, but not sure.

As the error from crispresso2 says:
[...] The aliases was originally deprecated in NumPy 1.20

I installed the last 1.19 numpy with

conda install -c anaconda numpy=1.19.5

And now everything is finally collaborating!

Obviously I'd prefer having the last version of everything – is there a solution I'm missing?

But for the time being, I hope someone can save an hour or so looking for the same solution...

[Colelyman]

Thanks for sharing this! Installing on the Apple Silicon is not ideal, and we are working on making it easier.

We are also unsure what this error means (submitted it to the matplotlib feedstock conda-forge/matplotlib-feedstock#351 (comment)), but happy to hear that you ultimately got a version installed.

Was the version you got installed 2.28 or 2.2.14? One of our team members @mbowcut was recently able to successfully install the latest version on his M2. I'm on an M1 (running OS X Monterey, I haven't updated out of fears of potential incompatibility issues). If you aren't on the latest version, you should be able to clone the repo and pip install . to get the latest version.

Thanks again,
Cole

[francoiskroll]

conda would only give me crispresso2 2.2.8.

Nice one! pip install seems to work to get 2.2.15 without creating conflicts. Who knows why conda would not give me that version then.

If useful to anyone, I did:

git clone https://github.com/pinellolab/CRISPResso2 #(in some folder where you want to keep packages)
cd CRISPResso2/
pip install .

Thanks a lot for the help