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biocore / gemelli

Gemelli is a tool box for running Robust Aitchison PCA (RPCA), Joint Robust Aitchison PCA (Joint-RPCA), TEMPoral TEnsor Decomposition (TEMPTED), and Compositional Tensor Factorization (CTF) on sparse compositional omics datasets.
BSD 3-Clause "New" or "Revised" License
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Error with Install of Gemelli standalone #102

Open tmdoswald87 opened 1 month ago

tmdoswald87 commented 1 month ago

Greetings, I am having some issues trying to install gemelli as a standalone outside of qiime2. The output states that there is no module named 'numpy' but I have installed. I can see it in my pip list too. Is there anything I can do differently to install this library?

cameronmartino commented 1 month ago

I @tmdoswald87,

Could you please copy/paste the whole error report? That would help me diagnose thee issue.

Thanks!

Cameron

tmdoswald87 commented 1 month ago

install_screenshot

please see the attachment and thank you! -Thomas

cameronmartino commented 1 month ago

Hi @tmdoswald87 ,

I am unable to replicate the error, assuming numpy and Cython are already installed, I can get the same error if they are not.

Could you tell me the result of the commands:

Additionally what operating system (and version) are you using?

That should verify that they are installed and the versions so I can try and replicate.

Thanks,

Cameron

tmdoswald87 commented 1 month ago

install_screenshot_2

I appreciate the time you are giving to assist with this

cameronmartino commented 1 month ago

Thanks, @tmdoswald87. Looping in @wasade because the issue seems to be in the iow install. Could you try installing after changing to cython version < 3 (e.g., cython==0.29.37)?

tmdoswald87 commented 1 month ago

I'm afraid it looks like the same error. install_screenshot_3

cameronmartino commented 1 month ago

Thanks for confirming @tmdoswald87. Can you run pip install iow to make sure that is where things are breaking?

wasade commented 1 month ago

And what happens if numpy is installed explicitly prior?

Note we do not test iow on Windows, and given it is concerned with specific C types, it is more likely to be sensitive to Windows than vanilla Python

tmdoswald87 commented 1 month ago

I am hesitant to install iow on my current device since I don't know that much about it, so I have switched to a different laptop. I am installing this through PyCharm. My python version is 3.11.3 and my pip list can be seen here:

iow_failed_pt3

Trying to install iow:

iow_failed_pt2 iow_failed_pt1

I also tried to follow the instructions given on the iow pypi page and it failed install as well. Found here: https://pypi.org/project/iow/#:~:text=Project%20description.%20Improved%20Octo

wasade commented 1 month ago

What happens if you do pip install --use-pep517 as suggested in the output?

tmdoswald87 commented 1 month ago

iow_pt1 iow_pt2