Open gilgameshjw opened 1 year ago
I guess this one needs a patch too:
https://github.com/FoxoTech/methylprep/blob/master/requirements.txt
@marcmaxson @notmaurox could you look into this free bug fix/patch? Clean installs are breaking due to dependency problems w/ pandas
Hi @yhoogstrate - I appreciate your contribution. I unfortunately do not have write access and cannot merge. I know @marcmaxson is not at foxo anymore. I recommend reaching out to FOXO directly to see if they can assign someone new to maintain the repo.
Hi @notmaurox ,
Please acknowledge @gilgameshjw for the patch and not me. I contacted you because you were top committer, my apologies if that was not appropriate. I have reached out to FOXO, to see how they envision this. Let's wait a few days to enlist the options.
@gilgameshjw I pushed you a change in setup.py
and requirements.txt
so they are always in sync and explicitly depending on pandas 2.*
.
kind regards,
Youri
@gilgameshjw @notmaurox FOXO did not even respond. I'm afraid this PR will not get accepted under this repo, so forking and version bumping would be my suggestion, but will come with the burden of maintenance... I think also the project's name should be renamed to get pip
access
@gilgameshjw @notmaurox FOXO did not even respond. I'm afraid this PR will not get accepted under this repo, so forking and version bumping would be my suggestion, but will come with the burden of maintenance... I think also the project's name should be renamed to get
pip
access
So what is currently the best way to fit pandas 2.0 if we need to use methylprep
Patch it yourself I'm afraid ...
I had to do this for a project for myself too: https://github.com/yhoogstrate/pymetharray/tree/api_restructure - you can look at the changes, probably the branch itself won't work for you because I had to restructure the API considerably for the use case(s), which probably breaks with other code
Then install your pulled project folder through pip (pip install -e ...
) with virtual environment
Are you still using methylprep after the Pandas 2.0 update? If so, have you patched it yourselves?
Alternatively, has anyone found a good solution to methylation data (.idat) pre-processing? Most of the python libraries that I found for this purpose also suffer from lack of maintenance/support and have outdated dependencies.
Are you still using methylprep after the Pandas 2.0 update? If so, have you patched it yourselves?
Alternatively, has anyone found a good solution to methylation data (.idat) pre-processing? Most of the python libraries that I found for this purpose also suffer from lack of maintenance/support and have outdated dependencies.
Here, the first answer using pip install for right version of Methylprep works out : https://stackoverflow.com/questions/78668908/how-to-use-a-specific-version-of-methylprep-in-jupyter-notebook/78712454?noredirect=1#comment138783762_78712454
Because DataFrame.append is deprecated and replaced by concat
1) file methylprep/files/sample_sheets.py adjusted 2) file methylprep/processing/infer_channel_switch.py adjusted
There might be others .append in the code that need replacement, but these two are the changes I needed to get my job done.