python 3.6 incompatibility

[drneavin]

Hi there,

I am writing to report an incompatability with pythono 3.6 even thought PyPi indicates that solo-sc v1.0 should be compatible with python 3.6 and the PyPi clone + ve instructions still use python 3.6 (git clone [email protected]:calico/solo.git && cd solo && conda create -n solo python=3.6 && conda activate solo && pip install -e .). This is actually due to an incompatibility between scvi-tools and python 3.6 that returns the following error:

Traceback (most recent call last):
  File "/directflow/SCCGGroupShare/projects/DrewNeavin/software/anaconda3/envs/solo_soup_36a/bin/solo", line 33, in <module>
    sys.exit(load_entry_point('solo-sc', 'console_scripts', 'solo')())
  File "/directflow/SCCGGroupShare/projects/DrewNeavin/software/anaconda3/envs/solo_soup_36a/bin/solo", line 25, in importlib_load_entry_point
    return next(matches).load()
  File "/directflow/SCCGGroupShare/projects/DrewNeavin/software/anaconda3/envs/solo_soup_36a/lib/python3.6/site-packages/importlib_metadata/__init__.py", line 105, in load
    module = import_module(match.group('module'))
  File "/directflow/SCCGGroupShare/projects/DrewNeavin/software/anaconda3/envs/solo_soup_36a/lib/python3.6/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 994, in _gcd_import
  File "<frozen importlib._bootstrap>", line 971, in _find_and_load
  File "<frozen importlib._bootstrap>", line 955, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 665, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 678, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/home/drenea/solo/solo/solo.py", line 20, in <module>
    from scvi.external import SOLO
ModuleNotFoundError: No module named 'scvi.external'

This seems to have been resolved in scvi-tools v0.9.1. However, that requires python >= 3.7.

I've been trying to install on 3.6 due to requirements of other softwares I want in the same image. Wanted to post here to ask for update in documents and in case others are facing similar error

[njbernstein]

Hi there,

Thanks for pointing this out. I'll update the documentation now.

[njbernstein]

Ah so the documentation on github is up to date, but not on pypi. Is that where you were seeing this install instruction:

git clone [email protected]:calico/solo.git && cd solo && conda create -n solo python=3.6 && conda activate solo && pip install -e .

[drneavin]

Hi @njbernstein ,

Yes, it seems the github installations instructions both require python 3.7 but PyPi is where I saw python 3.6 in the installation instructions.

Also, on the PyPi page, it indicates the required python version is >= 3.6:
Requires: Python >=3.6

Thanks for updating!

[njbernstein]

My apologies again. Working on getting it updated. Best, Nick

…

On Thu, Oct 14, 2021 at 9:43 PM drneavin ***@***.***> wrote: Hi @njbernstein <https://github.com/njbernstein> , Yes, it seems the github installations instructions both require python 3.7 but PyPi is where I saw python 3.6 in the installation instructions. Also, on the PyPi page, it indicates the required python version is >= 3.6: Requires: Python >=3.6 Thanks for updating! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#69 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUL75QPRK5LRSKS4Q44BXLUG6WOXANCNFSM5GBBBK7A> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[njbernstein]

This is updated. https://pypi.org/project/solo-sc/1.1/

Best,
Nick