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daducci / COMMIT

Linear framework to combine tractography and tissue micro-structure estimation with diffusion MRI
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Commit is not compatible with Dipy 1.0 #61

Closed jchoude closed 3 years ago

jchoude commented 4 years ago

This is the same issue as in AMICO (https://github.com/daducci/AMICO/pull/89). Dipy 1.0 drops support for python 2, and therefore removes the dipy.utils.six module and functions.

The same fixes should be applied as in AMICO.

daducci commented 4 years ago

This should be fixed now, isn't it?

jchoude commented 4 years ago

Following your PRs, I think so.

I don't know if it's exactly related, but if I create a simple virtual environment, then install the basic dependencies (numpy, scipy, nibabel, dipy, amico), then do as said in the doc:

pip install .

when I try to import commit, I get a

ModuleNotFoundError: No module named 'commit.core

Not sure if it's my setup, it worked at some point before.

Do you know what could be happening?

daducci commented 4 years ago

Usually that means that the cython compilation failed..

MarioOcampo commented 3 years ago

Hello, Check that the terminal is not in the installation folder.

MarkNelson86 commented 3 years ago

Hi Mario,

Now import commit works, but none of the commit modules work:

AttributeError: module 'commit' has no attribute 'core' AttributeError: module 'commit' has no attribute 'Evaluation'

From: Mario Ocampo notifications@github.com Sent: Tuesday, March 2, 2021 8:41 PM To: daducci/COMMIT COMMIT@noreply.github.com Cc: Mark Nelson mark.nelson3@mail.mcgill.ca; Comment comment@noreply.github.com Subject: Re: [daducci/COMMIT] Commit is not compatible with Dipy 1.0 (#61)

Hello, Check that the terminal is not in the installation folder.

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MarioOcampo commented 3 years ago

Hello Mark, Looks like there is a problem with the installation. did you try pip install dmri-commit Or do you get any messages after the installation? are you using an environment?

MarkNelson86 commented 3 years ago

Good morning,

I re-installed everything from scratch again this morning and it worked this time. Not sure what I did wrong before. Thanks for your help.

Mark

From: Mario Ocampo notifications@github.com Sent: Tuesday, March 2, 2021 9:48 PM To: daducci/COMMIT COMMIT@noreply.github.com Cc: Mark Nelson mark.nelson3@mail.mcgill.ca; Comment comment@noreply.github.com Subject: Re: [daducci/COMMIT] Commit is not compatible with Dipy 1.0 (#61)

Hello Mark, Looks like there is a problem with the installation. did you try pip install dmri-commit Or do you get any messages after the installation? are you using an environment?

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/daducci/COMMIT/issues/61#issuecomment-789204857, or unsubscribehttps://github.com/notifications/unsubscribe-auth/APRIQ633QDODEIAPW25HWCDTBVFIPANCNFSM4ILUZFTQ.

MarioOcampo commented 3 years ago

Hello Mark,

good to know that the program is working properly, thank you for telling us about the problem. Please let us know if you have any other problems with the software.

Best. Mario

daducci commented 3 years ago

Are you sure you didn't download the code from github and, then you installed COMMIT via pip install dmri-commit but the open the python shell from there? If so, then when you issue the command import commit, the system will try to import from the current folder (which is not compiled). Not sure if this was the case, though..

MarkNelson86 commented 3 years ago

Hi Alessandro,

Thanks for your tip. I used a venv to straighten things out. I also realized that I didn't need to append path/to/COMMIT_clone to PYTHONPATH. I did this initially (I am used to Matlab), and it caused problems.

Everything is working fine now. I'm excited to see what this can do!

Thanks, Mark

From: Alessandro Daducci notifications@github.com Sent: Wednesday, March 3, 2021 4:43 PM To: daducci/COMMIT COMMIT@noreply.github.com Cc: Mark Nelson mark.nelson3@mail.mcgill.ca; Comment comment@noreply.github.com Subject: Re: [daducci/COMMIT] Commit is not compatible with Dipy 1.0 (#61)

Are you sure you didn't download the code from github and, then you installed COMMIT via pip install dmri-commit but the open the python shell from there? If so, then when you issue the command import commit, the system will try to import from the current folder (which is not compiled). Not sure if this was the case, though..

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/daducci/COMMIT/issues/61#issuecomment-789809470, or unsubscribehttps://github.com/notifications/unsubscribe-auth/APRIQ67TBWS2F4IZ4HFABKTTBZKLZANCNFSM4ILUZFTQ.