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fastlmm / FaST-LMM

Python version of Factored Spectrally Transformed Linear Mixed Models
https://fastlmm.github.io/
Apache License 2.0
47 stars 11 forks source link

Support cbgen>=1.0.1 #32

Closed ofrei closed 6 months ago

ofrei commented 2 years ago

@CarlKCarlK thank you so much for adding support for cbgen==1.0.2 in PySnpTools! I thought while we're on this topic I may also ask for implementing a fix similar to https://github.com/fastlmm/PySnpTools/pull/4 also for FaST-LMM. If that's possible that would be great.

CarlKCarlK commented 2 years ago

Oleksandr,

FaST-LMM 0.6.3 (a new version released on Sunday) should use BGEN >= 1.0.2 on Linux and MacOS on Python 3.8 to 3.10+.

Please let me know if it works as expected.

Yours, Carl

p.s. Thanks for using FaST-LMM.

From: Oleksandr Frei @.> Sent: Tuesday, October 25, 2022 1:41 AM To: fastlmm/FaST-LMM @.> Cc: Carl Kadie @.>; Mention @.> Subject: [fastlmm/FaST-LMM] Support cbgen>=1.0.1 (PR #32) Importance: High

@CarlKCarlKhttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FCarlKCarlK&data=05%7C01%7C%7C79829d837db7461acffe08dab664b2aa%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C638022840860502901%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=4YywLCnc9pQqOAD%2Be%2F0g%2Bww4IY0W9f3XscnrZXjvtDs%3D&reserved=0 thank you so much for adding support for cbgen==1.0.2 in PySnpTools! I thought while we're on this topic I may also ass for implementing a fix similar to fastlmm/PySnpTools#4https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Ffastlmm%2FPySnpTools%2Fpull%2F4&data=05%7C01%7C%7C79829d837db7461acffe08dab664b2aa%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C638022840860502901%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ykev9u2XhFOhxyIHS8Qz4q0Br2Ccn93pewqtjz1K9Ls%3D&reserved=0 also for FaST-LMM. If that's possible that would be great.

You can view, comment on, or merge this pull request online at:

https://github.com/fastlmm/FaST-LMM/pull/32https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Ffastlmm%2FFaST-LMM%2Fpull%2F32&data=05%7C01%7C%7C79829d837db7461acffe08dab664b2aa%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C638022840860502901%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=vzW5iMB%2BPz7ThoWkJQAGM06ky2s8KZnRHYOcAE8VkBE%3D&reserved=0

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ofrei commented 2 years ago

@CarlKCarlK I briefly tested FaST-LMM 0.6.3 today and it worked without any problems - also when I installed cbgen==1.0.2 as a dependency. So everything works fine. But I saw cbgen==1.0.1 in https://github.com/fastlmm/FaST-LMM/blob/master/requirements.txt , also in the latest master branch - and that was somewhat confusing...

CarlKCarlK commented 2 years ago

Great! I'm very glad it's working.

Thanks for catching the error in requirements.txt! It will be fixed.

From: Oleksandr Frei @.> Sent: Tuesday, October 25, 2022 12:59 PM To: fastlmm/FaST-LMM @.> Cc: Carl Kadie @.>; Mention @.> Subject: Re: [fastlmm/FaST-LMM] Support cbgen>=1.0.1 (PR #32) Importance: High

@CarlKCarlKhttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FCarlKCarlK&data=05%7C01%7C%7C810b0b4a71dd44802bdf08dab6c35525%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C638023247304648240%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=c%2BnzvAWNFb4veLS6%2BLBMGsV8vZuZ5tx3FyEf0Nxqs5g%3D&reserved=0 I briefly tested FaST-LMM 0.6.3 today and it worked without any problems - also when I installed cbgen==1.0.2 as a dependency. So everything works fine. But I saw cbgen==1.0.1 in https://github.com/fastlmm/FaST-LMM/blob/master/requirements.txthttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Ffastlmm%2FFaST-LMM%2Fblob%2Fmaster%2Frequirements.txt&data=05%7C01%7C%7C810b0b4a71dd44802bdf08dab6c35525%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C638023247304648240%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=EylrOkrN3cNBfQC0%2FBM0rYqJ2cSX0T17XQ7ffZ9RqxE%3D&reserved=0 , also in the latest master branch - and that was somewhat confusing...

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CarlKCarlK commented 2 years ago

The requirements.txt bug is fixed in the new 0.6.4. Thanks for reporting the bug and thanks for using FaST-LMM.

From: Carl K Sent: Tuesday, October 25, 2022 1:04 PM To: fastlmm/FaST-LMM @.>; fastlmm/FaST-LMM @.> Cc: Mention @.***> Subject: RE: [fastlmm/FaST-LMM] Support cbgen>=1.0.1 (PR #32)

Great! I'm very glad it's working.

Thanks for catching the error in requirements.txt! It will be fixed.

From: Oleksandr Frei @.**@.>> Sent: Tuesday, October 25, 2022 12:59 PM To: fastlmm/FaST-LMM @.**@.>> Cc: Carl Kadie @.**@.>>; Mention @.**@.>> Subject: Re: [fastlmm/FaST-LMM] Support cbgen>=1.0.1 (PR #32) Importance: High

@CarlKCarlKhttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FCarlKCarlK&data=05%7C01%7C%7C810b0b4a71dd44802bdf08dab6c35525%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C638023247304648240%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=c%2BnzvAWNFb4veLS6%2BLBMGsV8vZuZ5tx3FyEf0Nxqs5g%3D&reserved=0 I briefly tested FaST-LMM 0.6.3 today and it worked without any problems - also when I installed cbgen==1.0.2 as a dependency. So everything works fine. But I saw cbgen==1.0.1 in https://github.com/fastlmm/FaST-LMM/blob/master/requirements.txthttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Ffastlmm%2FFaST-LMM%2Fblob%2Fmaster%2Frequirements.txt&data=05%7C01%7C%7C810b0b4a71dd44802bdf08dab6c35525%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C638023247304648240%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=EylrOkrN3cNBfQC0%2FBM0rYqJ2cSX0T17XQ7ffZ9RqxE%3D&reserved=0 , also in the latest master branch - and that was somewhat confusing...

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