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cortex-lab / phy

phy: interactive visualization and manual spike sorting of large-scale ephys data
BSD 3-Clause "New" or "Revised" License
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"zsh: segmentation fault phy template-gui params.py" #1244

Closed syedtamim4nov closed 1 month ago

syedtamim4nov commented 6 months ago

The following error occurs when I run the line ' phy template-gui params.py' in terminal. I am an undergraduate trying to learn and master Phy and any help would be highly appreciated.

zm711 commented 5 months ago

@syedtamim4nov

zsh is the base shell for Macs. Since Phy relies heavily on openGL, it isn't super friendly with Macs any more.

Could you let us know your OS and copy the contents of a:

conda list

inside your environment (if you're using conda--if using a python virtual env then the equivalent.

syedtamim4nov commented 5 months ago

The MacOS is Sonoma 14.1

packages in environment at /Users/syedtamimahmad/anaconda3/envs/phy2:

#

Name Version Build Channel

abseil-cpp 20230802.0 h313beb8_2
appnope 0.1.2 py311hca03da5_1001
arrow-cpp 11.0.0 hc7aafb3_2
asttokens 2.0.5 pyhd3eb1b0_0
aws-c-common 0.6.8 h80987f9_1
aws-c-event-stream 0.1.6 h313beb8_6
aws-checksums 0.1.11 h80987f9_2
aws-sdk-cpp 1.8.185 ha71a6ea_1
backcall 0.2.0 pyhd3eb1b0_0
blas 1.0 openblas
bokeh 3.3.0 py311hb6e6a13_0
boost-cpp 1.82.0 h48ca7d4_2
bottleneck 1.3.5 py311ha0d4635_0
brotli 1.0.9 h1a28f6b_7
brotli-bin 1.0.9 h1a28f6b_7
brotli-python 1.0.9 py311h313beb8_7
bzip2 1.0.8 h620ffc9_4
c-ares 1.19.1 h80987f9_0
ca-certificates 2023.12.12 hca03da5_0
certifi 2023.11.17 py311hca03da5_0
cffi 1.16.0 py311h80987f9_0
charset-normalizer 2.0.4 pyhd3eb1b0_0
click 8.1.7 py311hca03da5_0
cloudpickle 2.2.1 py311hca03da5_0
colorcet 3.0.1 pypi_0 pypi comm 0.1.2 py311hca03da5_0
contourpy 1.2.0 py311h48ca7d4_0
cryptography 41.0.7 py311hd4332d6_0
cycler 0.11.0 pyhd3eb1b0_0
cyrus-sasl 2.1.28 h9131b1a_1
cython 3.0.6 py311h80987f9_0
cytoolz 0.12.2 py311h80987f9_0
dask 2023.11.0 py311hca03da5_0
dask-core 2023.11.0 py311hca03da5_0
debugpy 1.6.7 py311h313beb8_0
decorator 5.1.1 pyhd3eb1b0_0
distributed 2023.11.0 py311hca03da5_0
executing 0.8.3 pyhd3eb1b0_0
fonttools 4.25.0 pyhd3eb1b0_0
freetype 2.12.1 h1192e45_0
fsspec 2023.10.0 py311hca03da5_0
gettext 0.21.0 h13f89a0_1
gflags 2.2.2 hc377ac9_0
ghp-import 2.1.0 pypi_0 pypi giflib 5.2.1 h80987f9_3
glib 2.69.1 h514c7bf_2
glog 0.5.0 hc377ac9_0
grpc-cpp 1.48.2 hc60591f_4
gst-plugins-base 1.14.1 h313beb8_1
gstreamer 1.14.1 h80987f9_1
gtest 1.14.0 h48ca7d4_0
h5py 3.9.0 py311hba6ad2f_0
hdf5 1.12.1 h05c076b_3
heapdict 1.0.1 pyhd3eb1b0_0
icu 73.1 h313beb8_0
idna 3.4 py311hca03da5_0
importlib-metadata 6.0.0 py311hca03da5_0
iniconfig 1.1.1 pyhd3eb1b0_0
ipykernel 6.25.0 py311hb6e6a13_0
ipython 8.15.0 py311hca03da5_0
jedi 0.18.1 py311hca03da5_1
jinja2 3.1.2 py311hca03da5_0
joblib 1.2.0 py311hca03da5_0
jpeg 9e h80987f9_1
jupyter_client 8.6.0 py311hca03da5_0
jupyter_core 5.5.0 py311hca03da5_0
kiwisolver 1.4.4 py311h313beb8_0
klusta 3.0.16 pypi_0 pypi klustakwik2 0.2.6 pypi_0 pypi krb5 1.20.1 hf3e1bf2_1
lcms2 2.12 hba8e193_0
lerc 3.0 hc377ac9_0
libboost 1.82.0 h0bc93f9_2
libbrotlicommon 1.0.9 h1a28f6b_7
libbrotlidec 1.0.9 h1a28f6b_7
libbrotlienc 1.0.9 h1a28f6b_7
libclang 14.0.6 default_h1b80db6_1
libclang13 14.0.6 default_h24352ff_1
libcurl 8.4.0 h3e2b118_1
libcxx 14.0.6 h848a8c0_0
libdeflate 1.17 h80987f9_1
libedit 3.1.20230828 h80987f9_0
libev 4.33 h1a28f6b_1
libevent 2.1.12 h02f6b3c_1
libffi 3.4.4 hca03da5_0
libgfortran 5.0.0 11_3_0_hca03da5_28
libgfortran5 11.3.0 h009349e_28
libiconv 1.16 h1a28f6b_2
libllvm14 14.0.6 h7ec7a93_3
libnghttp2 1.57.0 h62f6fdd_0
libopenblas 0.3.21 h269037a_0
libpng 1.6.39 h80987f9_0
libpq 12.15 h02f6b3c_1
libprotobuf 3.20.3 h514c7bf_0
libsodium 1.0.18 h1a28f6b_0
libssh2 1.10.0 h02f6b3c_2
libthrift 0.15.0 h73c2103_2
libtiff 4.5.1 h313beb8_0
libwebp 1.3.2 ha3663a8_0
libwebp-base 1.3.2 h80987f9_0
libxml2 2.10.4 h0dcf63f_1
llvm-openmp 14.0.6 hc6e5704_0
locket 1.0.0 py311hca03da5_0
lz4 4.3.2 py311h80987f9_0
lz4-c 1.9.4 h313beb8_0
markdown 3.5.1 pypi_0 pypi markupsafe 2.1.1 py311h80987f9_0
matplotlib 3.8.0 py311hca03da5_0
matplotlib-base 3.8.0 py311h7aedaa7_0
matplotlib-inline 0.1.6 py311hca03da5_0
mergedeep 1.3.4 pypi_0 pypi mkdocs 1.5.3 pypi_0 pypi msgpack-python 1.0.3 py311h48ca7d4_0
mtscomp 1.0.2 pypi_0 pypi munkres 1.1.4 py_0
mysql 5.7.24 ha71a6ea_2
ncurses 6.4 h313beb8_0
nest-asyncio 1.5.6 py311hca03da5_0
numexpr 2.8.7 py311h6dc990b_0
numpy 1.26.2 py311he598dae_0
numpy-base 1.26.2 py311hfbfe69c_0
openjpeg 2.3.0 h7a6adac_2
openssl 3.0.12 h1a28f6b_0
orc 1.7.4 hdca1487_1
packaging 23.1 py311hca03da5_0
pandas 2.1.4 py311h7aedaa7_0
param 2.0.1 pypi_0 pypi parso 0.8.3 pyhd3eb1b0_0
partd 1.4.1 py311hca03da5_0
pathspec 0.12.1 pypi_0 pypi pcre 8.45 hc377ac9_0
pexpect 4.8.0 pyhd3eb1b0_3
phy 2.0b5 pypi_0 pypi phylib 2.4.3 pypi_0 pypi pickleshare 0.7.5 pyhd3eb1b0_1003
pillow 10.0.1 py311h3b245a6_0
pip 23.3.1 py311hca03da5_0
platformdirs 3.10.0 py311hca03da5_0
pluggy 1.0.0 py311hca03da5_1
ply 3.11 py311hca03da5_0
prompt-toolkit 3.0.36 py311hca03da5_0
psutil 5.9.0 py311h80987f9_0
ptyprocess 0.7.0 pyhd3eb1b0_2
pure_eval 0.2.2 pyhd3eb1b0_0
pyarrow 11.0.0 py311h7575258_1
pycparser 2.21 pyhd3eb1b0_0
pyct 0.5.0 pypi_0 pypi pygments 2.15.1 py311hca03da5_1
pyopengl 3.1.1a1 py311hca03da5_0
pyopenssl 23.2.0 py311hca03da5_0
pyparsing 3.0.9 py311hca03da5_0
pyqt 5.15.10 py311h313beb8_0
pyqt5-sip 12.13.0 py311h80987f9_0
pyqtwebengine 5.15.10 py311h313beb8_0
pysocks 1.7.1 py311hca03da5_0
pytest 7.4.0 py311hca03da5_0
python 3.11.5 hb885b13_0
python-dateutil 2.8.2 pyhd3eb1b0_0
python-lmdb 1.4.1 py311h313beb8_0
python-tzdata 2023.3 pyhd3eb1b0_0
pytz 2023.3.post1 py311hca03da5_0
pyyaml 6.0.1 py311h80987f9_0
pyyaml-env-tag 0.1 pypi_0 pypi pyzmq 25.1.0 py311h313beb8_0
qt-main 5.15.2 h0917680_10
qt-webengine 5.15.9 h2903aaf_7
qtconsole 5.5.0 py311hca03da5_0
qtpy 2.4.1 py311hca03da5_0
re2 2022.04.01 hc377ac9_0
readline 8.2 h1a28f6b_0
requests 2.31.0 py311hca03da5_0
responses 0.13.3 pyhd3eb1b0_0
scikit-learn 1.2.2 py311h313beb8_1
scipy 1.11.4 py311hc76d9b0_0
setuptools 68.2.2 py311hca03da5_0
sip 6.7.12 py311h313beb8_0
six 1.16.0 pyhd3eb1b0_1
snappy 1.1.10 h313beb8_1
sortedcontainers 2.4.0 pyhd3eb1b0_0
sqlite 3.41.2 h80987f9_0
stack_data 0.2.0 pyhd3eb1b0_0
tblib 1.7.0 pyhd3eb1b0_0
threadpoolctl 2.2.0 pyh0d69192_0
tk 8.6.12 hb8d0fd4_0
toolz 0.12.0 py311hca03da5_0
tornado 6.3.3 py311h80987f9_0
tqdm 4.66.1 pypi_0 pypi traitlets 5.7.1 py311hca03da5_0
tzdata 2023c h04d1e81_0
urllib3 1.26.18 py311hca03da5_0
utf8proc 2.6.1 h1a28f6b_0
watchdog 3.0.0 pypi_0 pypi wcwidth 0.2.5 pyhd3eb1b0_0
wheel 0.41.2 py311hca03da5_0
xyzservices 2022.9.0 py311hca03da5_1
xz 5.4.5 h80987f9_0
yaml 0.2.5 h1a28f6b_0
zeromq 4.3.4 hc377ac9_0
zict 3.0.0 py311hca03da5_0
zipp 3.11.0 py311hca03da5_0
zlib 1.2.13 h5a0b063_0
zstd 1.5.5 hd90d995_0

zm711 commented 5 months ago

So as I said unfortunately the current version of MacOS isn't really compatible with Phy any more and since phy isn't being actively developed at the moment it likely won't work. Your best bet is to use a Linux or Windows computer for this analysis.

syedtamim4nov commented 5 months ago

@zm711

I am using VS Code on MacOs Sonoma 14.1....... is there any way to rectify the issue? Thanks a lot for the input!

syedtamim4nov commented 5 months ago

@zm711 Thanks a lot!

zm711 commented 5 months ago

Of course. If you run into any install issue on a different computer just let me know--happy to help.