phy 2.0 : first alpha release

Cyrille Rossant

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Jun 17, 2019, 7:35:08 AM6/17/19

to phy-...@googlegroups.com, KlustaViewas, spyking-ci...@googlegroups.com

Dear all

I'm pleased to announce the first alpha release of phy 2.0. There are many new features, improvements, bug fixes, several new views, and an improved documentation. The code has been updated to PyQt5, and Python 2 support has been dropped. You'll find the release notes here. The main focus of this release has been the Template GUI, working with KiloSort 1, KiloSort 2, and Spyking Circus datasets.

To try it, you can install the development version on Github, dev branch. Note that the code in phycontrib has been merged into phy, and the phycontrib repository has been deprecated. There is a new little dependency library called phylib that contains I/O code and non-graphical utilities, which should be automatically installed if you follow the installation instructions of phy.

The documentation is available here. This version will be in alpha phase for a while in order to get sufficient user feedback. New features and bug fixes will be continuously pushed to the dev branch as user feedback will be coming in.

If you have written plugins for a past version of phy, please don't hesitate to contact me in order to get help with the update.

I'm looking forward to get your feedback, bug reports, and feature requests!

All the best,

Cyrille

Leandro Aguiar

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Jun 26, 2019, 11:50:50 PM6/26/19

to phy-users

Hi everyone,

After installing phy2, I tried to run kwik-gui on the 'phy kwik-gui g01.kwik' . I got an error: command not found.

Any ideas?

Thanks!

Leandro

Screen Shot 2019-06-27 at 12.48.25 AM.png

Cyrille Rossant

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Jun 27, 2019, 7:56:18 AM6/27/19

to Leandro Aguiar, phy-users

It seems phy was not installed properly for some reason. With the phy2 environment activated, could you do

pip install git+https://github.com/cortex-lab/phy.git@dev

pip install git+https://github.com/cortex-lab/phylib

and try again ?

Cyrille

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Leandro Aguiar

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Jun 27, 2019, 7:09:02 PM6/27/19

to phy-users

Thank you for your help. I did what you suggested.

Now this error appears:

Screen Shot 2019-06-27 at 7.58.37 PM.png

Thanks!

Leandro

Em quinta-feira, 27 de junho de 2019 08:56:18 UTC-3, Cyrille Rossant escreveu:

It seems phy was not installed properly for some reason. With the phy2 environment activated, could you do

pip install git+https://github.com/cortex-lab/phy.git@dev
pip install git+https://github.com/cortex-lab/phylib

and try again ?
Cyrille

Le jeu. 27 juin 2019 à 05:50, Leandro Aguiar <leandr...@biologo.bio.br> a écrit :

Hi everyone,

After installing phy2, I tried to run kwik-gui on the 'phy kwik-gui g01.kwik' . I got an error: command not found.

Any ideas?

Thanks!

Leandro

Em segunda-feira, 17 de junho de 2019 08:35:08 UTC-3, Cyrille Rossant escreveu:
Dear all

I'm pleased to announce the first alpha release of phy 2.0. There are many new features, improvements, bug fixes, several new views, and an improved documentation. The code has been updated to PyQt5, and Python 2 support has been dropped. You'll find the release notes here. The main focus of this release has been the Template GUI, working with KiloSort 1, KiloSort 2, and Spyking Circus datasets.

To try it, you can install the development version on Github, dev branch. Note that the code in phycontrib has been merged into phy, and the phycontrib repository has been deprecated. There is a new little dependency library called phylib that contains I/O code and non-graphical utilities, which should be automatically installed if you follow the installation instructions of phy.

The documentation is available here. This version will be in alpha phase for a while in order to get sufficient user feedback. New features and bug fixes will be continuously pushed to the dev branch as user feedback will be coming in.

If you have written plugins for a past version of phy, please don't hesitate to contact me in order to get help with the update.

I'm looking forward to get your feedback, bug reports, and feature requests!

All the best,
Cyrille

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Cyrille Rossant

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Jun 28, 2019, 3:57:01 AM6/28/19

to Leandro Aguiar, phy-users

Try "pip install klusta" ?

Cyrille

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Leandro Aguiar

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Jul 1, 2019, 9:51:29 AM7/1/19

to phy-users

It worked.

Thank you!

Haixin Liu

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Jul 9, 2019, 9:54:15 PM7/9/19

to phy-users

Dear Cyrille,

I encountered error when installing (following the instruction), see error msg below:

I use windows 10 OS.

Thank you!

Looking forward to your reply!

Best,

Haixin

Cyrille Rossant

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Jul 10, 2019, 10:30:28 AM7/10/19

to Haixin Liu, phy-users

Hi

Could you test the fix explained here? https://github.com/conda/conda/issues/8273#issue-409800067

Cyrille

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Haixin Liu

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Jul 10, 2019, 12:35:47 PM7/10/19

to Cyrille Rossant, phy-users

Thanks Cyrille,

I ended up installing OpenSSL https://slproweb.com/products/Win32OpenSSL.html (I did win64)

then copy

openssl.exe

libcrypto-1_1-x64.dll

libssl-1_1-x64.dll

from OpenSSL-Win64/bin folder

to

miniconda3/DLLs folder

then it worked

--

Haixin Liu, Ph.D.
Postdoctoral Fellow
Tritsch Lab
Neuroscience Institute
NYU Langone Health
Email: haixin.l...@gmail.com or haixi...@nyulangone.org
Address: 435 East 30th St, NYU Science Building, 13th floor, New York, NY 10016
Phone: 646.501.2191 (lab) 646.501.4529 (fax)

Antonin Blot

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Jul 12, 2019, 3:17:48 PM7/12/19

to phy-users

Hi!

I just tried phy2. It seems to work but some of my waveforms are not loaded (completely flat line, see pictures). The corresponding data look fine in the trace view. For all the cluster the same channels are not loaded. The same channels also stay flat if I display the template or the average waveform (cycling with W or pressing M) I tried to remove .phy and restart but that didn't solve the issue.

Basic phy was working fine on that dataset

Any idea on what went wrong?

phy2_flat_waveforms.png

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