installation issue on Mac

[lhuntneuro]

I've tried to install OSL on a Mac following the installation instructions page, using the osl.yml file to set up a new conda environment.

The conda environment sets up fine, and OSL is downloaded, but when I try to import I get the following issue:

>>> import osl
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/opt/anaconda3/envs/osl/lib/python3.8/site-packages/osl/__init__.py", line 28, in <module>
    from . import utils  # noqa: F401, F403
  File "/opt/anaconda3/envs/osl/lib/python3.8/site-packages/osl/utils/__init__.py", line 15, in <module>
    with open(os.path.join(os.path.dirname(__file__), "README.md"), 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/opt/anaconda3/envs/osl/lib/python3.8/site-packages/osl/utils/README.md'

It looks like when I created the conda environment, all the .py files were correctly installed into /opt/anaconda3/envs/osl/lib/python3.8/site-packages/osl/, but none of the README.md files - which then causes a problem for the import. Is this a known issue, and is there a straightforward workaround?

[cgohil8]

What directory were you in when you launched python? Did do the last step:

pip install -e .

[lhuntneuro]

Thanks Chet, I was just in my home directory but I seem to get the same issue irrespective of where I run it.

I was just installing with the lines:

curl https://raw.githubusercontent.com/OHBA-analysis/osl/main/envs/mac-full.yml > osl.yml
conda env create -f osl.yml
rm osl.yml

using my pre-existing anaconda install - I didn't think from reading https://osl.readthedocs.io/en/latest/install.html that I needed to run

pip install -e . 

unless I was pulling the latest source code?

I imagine if I pull the source code using git clone, it will pull all the readme files and the above issue will disappear - so I'll try that - but just wanted to check I wasn't doing something stupid with the main installation instructions using the osl.yml file

[cgohil8]

What you did is correct and should have been fine (i.e. you shouldn't need to do pip install -e .). The issue's probably on our side. What Mac do you have? In particular, what chip do you have?

[cgohil8]

I've been able to reproduce the error on my M2 Mac. We'll solve this in the next release.

In the meantime maybe it would be worthwhile to clone the repo and install that in your environment:

conda activate osl
git clone https://github.com/OHBA-analysis/osl.git
cd osl
pip install -e .

[lhuntneuro]

OK thanks - mine is a M1 Pro Mac, running Sonoma 14.5.

[cgohil8]

Installing the repo with the above code should work. Otherwise, this has been resolved for the next release (v0.9, which will happen in the next few days).

[cgohil8]

Alright, v0.9.0 has been released and I tested the installation on my Mac. Should work fine now. Thanks for raising the issue.

Please reopen this issue if this has not been resolved for you.