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Package versions in .yml file #74

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lefterov opened this issue Sep 7, 2021 · 10 comments
Closed

Package versions in .yml file #74

lefterov opened this issue Sep 7, 2021 · 10 comments

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@lefterov
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lefterov commented Sep 7, 2021

It is rather a question, not an issue:

in the .yml file some of the packages are listed with older than most recent versions:

  • python>=3.5, <3.7
  • cmake>=3.9, <3.11

the most recent and installed are:
-python=3.9.7
-cmake=3.21.2

there should not be a problem, right?

nice day,

Iliya

@LuckyMD
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LuckyMD commented Sep 7, 2021

Hey!

I can't imagine there would be a problem with cmake updates. For python, I'm not sure... but I don't think there should be backwards compatibility issues there either. Sorry I can't give you a more detailed answer.

@lefterov
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lefterov commented Sep 7, 2021 via email

@LuckyMD LuckyMD closed this as completed Sep 8, 2021
@lefterov
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lefterov commented Sep 8, 2021

at this time I have no problem with the newest versions. I don't know if it is worth changing the content of the .yml file. for more experienced users, such a question would not have existed.

@LuckyMD
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LuckyMD commented Sep 8, 2021

I'm trying to stick to the docker rather than the yaml file for the moment. But could you add this as a comment on the PR #58 ? Then I can try to add it there when i get around to it.

@lefterov
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lefterov commented Sep 8, 2021 via email

@LuckyMD
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LuckyMD commented Sep 8, 2021

Thanks. I'm usually quite responsive on github as well ;).

@theislab theislab deleted a comment from lefterov Sep 10, 2021
@dturaev
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dturaev commented Sep 18, 2021

Here is some additional information:

  • with the original yml file, conda was stuck at "Solving environment" for many hours, so I aborted
  • removing the version restrictions from python>=3.5, <3.7 and cmake>=3.9, <3.11 to python and cmake allowed for solving the environment, however the installation (creating the Makefile for fa2) failed with the error message was "CMake Error: Unknown argument --" (cmake 3.21.2), which seems to be related to https://gitlab.kitware.com/cmake/cmake/-/issues/22060
  • after adding cmake <=3.19, the installation (building the wheel for fa2) failed with error messages like error: 'PyTypeObject' {aka 'struct _typeobject'} has no member named 'tp_print', which seems to be related to changes in Python 3.9
  • after adding python=3.8, the installation completed successfully. So, the versions that worked for me were python=3.8 and cmake <=3.19

@lefterov
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lefterov commented Sep 19, 2021 via email

@LuckyMD
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LuckyMD commented Dec 17, 2021

@dturaev Thanks so much for that! This is really useful!

@lefterov
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@LuckyMD: We have finally moved to diffxpy and are trying to move faster...

quick question: to compare two groups (each comprised of 2 biological replicates), is it sufficient to supply the h5ad files written after we ranked the genes using Wilcoxon method?

Thanks in advance.

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