StephenThornquist
commented
1 week ago This is explored in issue #1047 -- suite2p is not compatible with Python >=3.11 as far as I can tell due to a single line that is not compatible with the builtin dataclasses, and can't even be imported to test whether anything is broken until they fix this bug (which appears not to be a priority?). I've been using it (in a fairly limited way) in Python 3.10 but I'll echo that it would be nice to see this fixed.
GiangTranHU
Describe the issue:
Dear Marius and suite2p administrative team, I am Giang Tran, from Japan. I am using your program suite2p for my research. Unfortunately, when I tried to install it, I got the following errors, I hope you can give me advice to resolve the problem. When I installed it from anaconda, I got the following error after typing "python -m suite2p"
Traceback (most recent call last): File "", line 189, in _run_module_as_main
File "", line 148, in _get_module_details
File "", line 112, in _get_module_details
File "C:\Users\gtran\anaconda3\envs\suite2p\Lib\site-packages\suite2p__init__.py", line 6, in
from .run_s2p import run_s2p, run_plane, pipeline
File "C:\Users\gtran\anaconda3\envs\suite2p\Lib\site-packages\suite2p\run_s2p.py", line 15, in
from . import extraction, io, registration, detection, classification, default_ops
File "C:\Users\gtran\anaconda3\envs\suite2p\Lib\site-packages\suite2p\extraction__init.py", line 5, in
from .extract import create_masks_and_extract, enhanced_mean_image, extract_traces_from_masks, extraction_wrapper
File "C:\Users\gtran\anaconda3\envs\suite2p\Lib\site-packages\suite2p\extraction\extract.py", line 11, in
from .masks import create_masks
File "C:\Users\gtran\anaconda3\envs\suite2p\Lib\site-packages\suite2p\extraction\masks.py", line 9, in
from ..detection.sparsedetect import extendROI
File "C:\Users\gtran\anaconda3\envs\suite2p\Lib\site-packages\suite2p\detection\ init__.py", line 4, in
from .detect import detect, detection_wrapper, bin_movie
File "C:\Users\gtran\anaconda3\envs\suite2p\Lib\site-packages\suite2p\detection\detect.py", line 9, in
from . import sourcery, sparsedetect, chan2detect, utils
File "C:\Users\gtran\anaconda3\envs\suite2p\Lib\site-packages\suite2p\detection\sourcery.py", line 12, in
from .stats import fitMVGaus
File "C:\Users\gtran\anaconda3\envs\suite2p\Lib\site-packages\suite2p\detection\stats.py", line 52, in
@dataclass(frozen=True)
^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\gtran\anaconda3\envs\suite2p\Lib\dataclasses.py", line 1220, in wrap
return _process_class(cls, init, repr, eq, order, unsafe_hash,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\gtran\anaconda3\envs\suite2p\Lib\dataclasses.py", line 958, in _process_class
cls_fields.append(_get_field(cls, name, type, kw_only))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\gtran\anaconda3\envs\suite2p\Lib\dataclasses.py", line 815, in _get_field
raise ValueError(f'mutable default {type(f.default)} for field '
ValueError: mutable default <class 'numpy.ndarray'> for field rsort is not allowed: use default_factory.
I am using python 3.11.7.
I also tried to install using the instruction " Clone the repository with git and cd suite2p Run pip install -e . in that folder " Then, I tried the jupyter notebook "run_suite2p_colab_2023" at the cell " ops = suite2p.default_ops() ops['batch_size'] = 200 # we will decrease the batch_size in case low RAM on computer ops['threshold_scaling'] = 2.0 # we are increasing the threshold for finding ROIs to limit the number of non-cell ROIs found (sometimes useful in gcamp injections) ops['fs'] = 13 # sampling rate of recording, determines binning for cell detection ops['tau'] = 1.25 # timescale of gcamp to use for deconvolution print(ops) " I also got an error "
TypeError Traceback (most recent call last) Cell In[19], line 3 1 #print(suite2p.version) 2 #from suite2p import default_ops ----> 3 ops = suite2p.default_ops() 4 ops['batch_size'] = 200 # we will decrease the batch_size in case low RAM on computer 5 ops['threshold_scaling'] = 2.0 # we are increasing the threshold for finding ROIs to limit the number of non-cell ROIs found (sometimes useful in gcamp injections)
TypeError: 'module' object is not callable "
Would you please give me advice on how to solve the problems? Thank you very much and I am looking forward to hearing from you! Best, Giang Tran
Provide environment info:
active environment : suite2p active env location : C:\Users\gtran\anaconda3\envs\suite2p shell level : 2 user config file : C:\Users\gtran.condarc populated config files : C:\Users\gtran.condarc conda version : 24.4.0 conda-build version : 24.1.2 python version : 3.11.7.final.0 solver : libmamba (default) virtual packages : archspec=1=x86_64_v4 conda=24.4.0=0 cuda=12.3=0 win=0=0 base environment : C:\Users\gtran\anaconda3 (writable) conda av data dir : C:\Users\gtran\anaconda3\etc\conda conda av metadata url : None channel URLs : https://repo.anaconda.com/pkgs/main/win-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/win-64 https://repo.anaconda.com/pkgs/r/noarch https://repo.anaconda.com/pkgs/msys2/win-64 https://repo.anaconda.com/pkgs/msys2/noarch package cache : C:\Users\gtran\anaconda3\pkgs C:\Users\gtran.conda\pkgs C:\Users\gtran\AppData\Local\conda\conda\pkgs envs directories : C:\Users\gtran\anaconda3\envs C:\Users\gtran.conda\envs C:\Users\gtran\AppData\Local\conda\conda\envs platform : win-64 user-agent : conda/24.4.0 requests/2.31.0 CPython/3.11.7 Windows/10 Windows/10.0.22631 solver/libmamba conda-libmamba-solver/24.1.0 libmambapy/1.5.6 aau/0.4.3 c/kG-aFcIWoPdrzB3QmON-aQ s/9Mi_-x20V1u2hkqmK45u8w e/kPgv2tDRiRGO7hI7D-X34w administrator : False netrc file : None offline mode : False