The archs4py from maayanlab

archs4py does not install in python 3.12

I tried to use the archs4py for easier handling of the archs4 dataset. However, when I tried installing it in my conda envrionment via pip3 install archs4py I got the following error during numpy 1.24.3 building:

      Traceback (most recent call last):
        File "/users/daniel.malzl/.conda/envs/scllm/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
          main()
        File "/users/daniel.malzl/.conda/envs/scllm/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
                                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/users/daniel.malzl/.conda/envs/scllm/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 112, in get_requires_for_build_wheel
          backend = _build_backend()
                    ^^^^^^^^^^^^^^^^
        File "/users/daniel.malzl/.conda/envs/scllm/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 77, in _build_backend
          obj = import_module(mod_path)
                ^^^^^^^^^^^^^^^^^^^^^^^
        File "/users/daniel.malzl/.conda/envs/scllm/lib/python3.12/importlib/__init__.py", line 90, in import_module
          return _bootstrap._gcd_import(name[level:], package, level)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "<frozen importlib._bootstrap>", line 1381, in _gcd_import
        File "<frozen importlib._bootstrap>", line 1354, in _find_and_load
        File "<frozen importlib._bootstrap>", line 1304, in _find_and_load_unlocked
        File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed
        File "<frozen importlib._bootstrap>", line 1381, in _gcd_import
        File "<frozen importlib._bootstrap>", line 1354, in _find_and_load
        File "<frozen importlib._bootstrap>", line 1325, in _find_and_load_unlocked
        File "<frozen importlib._bootstrap>", line 929, in _load_unlocked
        File "<frozen importlib._bootstrap_external>", line 994, in exec_module
        File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed
        File "/tmp/pip-build-env-1dnxzgn8/overlay/lib/python3.12/site-packages/setuptools/__init__.py", line 16, in <module>
          import setuptools.version
        File "/tmp/pip-build-env-1dnxzgn8/overlay/lib/python3.12/site-packages/setuptools/version.py", line 1, in <module>
          import pkg_resources
        File "/tmp/pip-build-env-1dnxzgn8/overlay/lib/python3.12/site-packages/pkg_resources/__init__.py", line 2172, in <module>
          register_finder(pkgutil.ImpImporter, find_on_path)
                          ^^^^^^^^^^^^^^^^^^^
      AttributeError: module 'pkgutil' has no attribute 'ImpImporter'. Did you mean: 'zipimporter'?

A quick google search implied that this might be an issue with the newest Python version 3.12 which I am also running. Newer numpy versions installed fine (I currently have 1.26.2 installed which is the latest). I guess this can be fixed by simply relaxing the requirement from numpy==1.24.3 to numpy>=1.24.3 or something.

Greek characters are not decoded correctly

To proceed with my work I quickly just copied the relevant code from your package and adapted it where needed for my problem. In the course of this I noticed that there seems to be a problem with the character encoding in the ARCHS5 file. I basically decode the metadata similar to you by using

[x.decode('utf-8') for x in table[key][:]]

However, some characters are not decoded correctly, specifically this seems to affect greek letters as the examples I encountered until now are the letter mu and the letter beta (but might not be limited to them). I tried several other encodings but was not able to decode it properly. Could you have a look or at least tell me the right encoding?

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archs4py does not install in python 3.12

Greek characters are not decoded correctly

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