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galizia-lab / pyview

GUI + API for processing and visualizing Calcium imaging data. Largely based on the IDL software "VIEW" developed by Giovanni Galizia. Implemented in Python by Ajayrama Kumaraswamy
BSD 3-Clause "New" or "Revised" License
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Installation instructions for Apple Silicon #18

Closed adamltyson closed 1 year ago

adamltyson commented 2 years ago

Hi :wave:,

I'm reviewing the PyView JOSS paper.

I'm having trouble installing PyView on my machine which I assume is partially due to Apple Silicon M1 chip. It fails very early (e.g. Python 3.7 is not available for M1 on conda forge).

Could you add instructions for installing the package on newer macs, or better yet, an environment file?

Thanks!

galizia commented 2 years ago

Hi!

Thanks for the question - I am trying to install conda right now, since yesterday I have an M2 mac, and it does not work yet. Maybe in a few days I will be able to help you. Mac has really changed many things, Anaconda is impossible to install, conda seems to work from the comand line:

https://repo.anaconda.com/archive/Anaconda3-2022.10-MacOSX-arm64.sh https://repo.anaconda.com/archive/Anaconda3-2022.10-MacOSX-arm64.sh

There is an environment file that can be used in conda, and works well with my previous mac. I did not yet have the time to test it with the M2 mac - sorry about that. I will try to do that asap, but I am travelling at the moment and cannot promise how fast I’ll be.

I’m copying Ajayrama Kumaraswamy: he is the computer scientist in our team (I am the biologist), but he does not run a mac, so he might be helpful or might not.

Best Giovanni

Prof. Dr. Giovanni Galizia Direktor Zukunftskolleg Lehrstuhl Neurobiologie Permanent Fellow Wissenschaftskolleg zu Berlin

@.*** http://neuro.uni.kn

On 16. Nov 2022, at 19:02, Adam Tyson @.***> wrote:

Hi 👋,

I'm reviewing the PyView JOSS paper https://github.com/openjournals/joss-reviews/issues/4936.

I'm having trouble installing PyView on my machine which I assume is partially due to Apple Silicon M1 chip. It fails very early (e.g. Python 3.7 is not available for M1 on conda forge).

Could you add instructions for installing the package on newer macs, or better yet, an environment file?

Thanks!

— Reply to this email directly, view it on GitHub https://github.com/galizia-lab/pyview/issues/18, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACRMY4VRQXBS3R2VULRXNGDWIUOU7ANCNFSM6AAAAAASCQK3VQ. You are receiving this because you are subscribed to this thread.

adamltyson commented 2 years ago

Thanks @galizia. Let me know if I can be of any help. We have quite a bit of Python/PyQt5 software that was troublesome to get working on macOS with Apple Silicone, but it is possible.

galizia commented 2 years ago

Hi again!

I have now replicated the python=3.7 problem, python=3.8 seems to work, could you try that? (I cannot check that yet, because I am having problems installing ffmpeg right now - as soon as I solved that, I will tell you. Therefore, if you prefer to wait until I have done that, no problem) (Python=3.10 will need a few adjustments, since scipy has changed quite a bit).

Thanks, Giovanni

Prof. Dr. Giovanni Galizia Direktor Zukunftskolleg Lehrstuhl Neurobiologie Permanent Fellow Wissenschaftskolleg zu Berlin

@.*** http://neuro.uni.kn

On 16. Nov 2022, at 19:02, Adam Tyson @.***> wrote:

Hi 👋,

I'm reviewing the PyView JOSS paper https://github.com/openjournals/joss-reviews/issues/4936.

I'm having trouble installing PyView on my machine which I assume is partially due to Apple Silicon M1 chip. It fails very early (e.g. Python 3.7 is not available for M1 on conda forge).

Could you add instructions for installing the package on newer macs, or better yet, an environment file?

Thanks!

— Reply to this email directly, view it on GitHub https://github.com/galizia-lab/pyview/issues/18, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACRMY4VRQXBS3R2VULRXNGDWIUOU7ANCNFSM6AAAAAASCQK3VQ. You are receiving this because you are subscribed to this thread.

galizia commented 2 years ago

Hi there!

Thanks for your patience!

We have now upgraded the code to python 3.10. You will find a new conda_env_development_py310.yml file to create a conda environment. On my silicon M2 it works fine!

Please let me know if you need any more information.

Best, Giovanni

Prof. Dr. Giovanni Galizia Direktor Zukunftskolleg Lehrstuhl Neurobiologie Permanent Fellow Wissenschaftskolleg zu Berlin

@.*** http://neuro.uni.kn

On 16. Nov 2022, at 19:02, Adam Tyson @.***> wrote:

Hi 👋,

I'm reviewing the PyView JOSS paper https://github.com/openjournals/joss-reviews/issues/4936.

I'm having trouble installing PyView on my machine which I assume is partially due to Apple Silicon M1 chip. It fails very early (e.g. Python 3.7 is not available for M1 on conda forge).

Could you add instructions for installing the package on newer macs, or better yet, an environment file?

Thanks!

— Reply to this email directly, view it on GitHub https://github.com/galizia-lab/pyview/issues/18, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACRMY4VRQXBS3R2VULRXNGDWIUOU7ANCNFSM6AAAAAASCQK3VQ. You are receiving this because you are subscribed to this thread.

ajkswamy commented 2 years ago

Hi @adamltyson :wave:

Thanks for raising the issue. I have made a new release (v1.2) incorporating all the changes mentioned above by @galizia . Please try installing this version. We are available if you have questions or issues.

Thanks!