Comments (5)
yger
commented on June 10, 2024
Dear Sara
Indeed, the code is written for python 2, but it is compatible with python
3 when installed (using the 2to3 converter). So despite the fact that
individual files in the source branch may not comply with python 3 syntax,
everything should work properly.
Do you have trouble running it ?
Best
Pierre
Le jeu. 15 févr. 2018 à 01:50, Elliott Sales de Andrade <
[email protected]> a écrit :
… I see that Travis and AppVeyor test out Python 3 and the FAQ claims Python
3 support, but it seems that circus.shared is not really tested as it
contains many bits of Python 2 specific code.
For example, circus/shared/__init__.py uses:
import filesimport parserimport algorithmsimport plotimport utils
These relative imports don't work any more and must be made absolute.
There's also imports of cPickle in many places.
cc @SaraMahallati <https://github.com/saramahallati>
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SaraMati
commented on June 10, 2024
Hi Pierre,
yes, I'm getting errors.
I installed the package through conda, but I have first forked the repo. does that mean that the installation didn't overwrite it? I fixed those lines manually but I'm getting a new error. probably similar issue. I'll email you the last one.
Do you recommend a new installation?
Sara
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yger
commented on June 10, 2024
Be sure you don't have several install... to be sure remove everything by
doing
> pip uninstall spyking-circus
As many times as needed. As said, if you install from the repo, you should
not have the hdf5 error (fixed). With conda, you may have it, and if so
just downgrade hdf5
Best
Pierre
Le jeu. 15 févr. 2018 à 02:55, Sara Mahallati <[email protected]> a
écrit :
… Hi Pierre,
yes, I'm getting errors.
I installed the package through conda, but I have first forked the repo.
does that mean that the installation didn't overwrite it? I fixed those
lines manually but I'm getting a new error. probably similar issue. I'll
email you the last one.
Do you recommend a new installation?
Sara
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QuLogic
commented on June 10, 2024
Ah, sorry, I completely forgot about 2to3 because it's a very outdated method of providing support for both versions. It's not even mentioned in the Python 3 porting guide any more. I'd recommend using futurize to convert to a shared codebase. It is much easier to work with a shared codebase since you don't need to run that 2to3 conversion on every install.
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yger
commented on June 10, 2024
Dear Elliott
Thanks again for the hint. We are currently working on a real-time
rewriting of the software, to perform sorting online and on the fly, and
this is currently our main priority. This code will be more pythonic,
object oriented and python3 compatible. It should be available as a beta
soon.
But as soon as this will be done, we should clearly refactor a bit the
offline version, as 2to3 is indeed not the best solution
Pierre
Le jeu. 15 févr. 2018 à 04:02, Elliott Sales de Andrade <
[email protected]> a écrit :
… Ah, sorry, I completely forgot about 2to3 because it's a very outdated
method of providing support for both versions. It's not even mentioned in
the Python 3 porting guide
<https://docs.python.org/3/howto/pyporting.html> any more. I'd recommend
using futurize to convert to a shared codebase. It is much easier to work
with a shared codebase since you don't need to run that 2to3 conversion on
every install.
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Related Issues (20)
- Run `spyking-circus` without probe file HOT 2
- Problems using raster plot option in SortingGUI HOT 1
- Circus Parser requires non-existant file HOT 1
- Spyking circus MSMPI installation issue. HOT 6
- Preview mode issue when filtering and overwrite=FALSE
- Polarity of neuralynx data is not used analyses / preview / results mode
- Spike sort in Docker containers with spiking-circus HOT 4
- Suggestion : spyking-circus to Klusters
- Converting step fails HOT 3
- Plotting template waveform
- Trigger File
- Problem on launching the PhyGUI and MatlabGUI through Spyking-circus command
- Use both cpu and gpu for sorting?
- RPV Contamination and Split Bursting Cell
- Installation hanging HOT 1
- 'Failed to create process' error after install [Windows 11] HOT 3
- spyking-circus standard way of parsing results from multiple files? HOT 1
- Unable to run spyking-circus without error HOT 2
- Question about probe file
- error with multi-node mpi
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