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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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ModuleNotFoundError: No module named 'numpy._core' on Ubuntu 22.04 #1292

Open Idavr opened 4 days ago

Idavr commented 4 days ago

I have downloaded phy according to all instructions (tried both directly with git and by environment.yml files) and gone over multiple tweaks on other opened and closed issues (like installing with different versions of python and numpy) but to no avail. The data I am trying to look at has been spike sorted with Kilosort 4 through their terminal commands (no GUI). No matter what I do I still get this error:

(phy2) idavalik@ida-HP-Z4-G5-Workstation:~/Kilosort/test_data/kilosort4$ phy template-gui params.py 13:54:26.548 [W] model:667 Skipping spike waveforms that do not exist, they will be extracted on the fly from the raw data as needed. 13:54:26.755 [E] init:62 An error has occurred (ModuleNotFoundError): No module named 'numpy._core' Traceback (most recent call last): File "/home/idavalik/anaconda3/envs/phy2/bin/phy", line 8, in sys.exit(phycli()) ^^^^^^^^ File "/home/idavalik/anaconda3/envs/phy2/lib/python3.11/site-packages/click/core.py", line 1157, in call return self.main(args, kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/idavalik/anaconda3/envs/phy2/lib/python3.11/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) ^^^^^^^^^^^^^^^^ File "/home/idavalik/anaconda3/envs/phy2/lib/python3.11/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/idavalik/anaconda3/envs/phy2/lib/python3.11/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, ctx.params) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/idavalik/anaconda3/envs/phy2/lib/python3.11/site-packages/click/core.py", line 783, in invoke return __callback(args, kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/idavalik/anaconda3/envs/phy2/lib/python3.11/site-packages/click/decorators.py", line 33, in new_func return f(get_current_context(), *args, kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/idavalik/anaconda3/envs/phy2/lib/python3.11/site-packages/phy/apps/init.py", line 159, in cli_template_gui template_gui(params_path, kwargs) File "/home/idavalik/anaconda3/envs/phy2/lib/python3.11/site-packages/phy/apps/template/gui.py", line 217, in template_gui controller = TemplateController(model=model, dir_path=dir_path, *kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/idavalik/anaconda3/envs/phy2/lib/python3.11/site-packages/phy/apps/base.py", line 470, in init super(TemplateMixin, self).init(args, kwargs) File "/home/idavalik/anaconda3/envs/phy2/lib/python3.11/site-packages/phy/apps/base.py", line 926, in init self._set_supervisor() File "/home/idavalik/anaconda3/envs/phy2/lib/python3.11/site-packages/phy/apps/template/gui.py", line 95, in _set_supervisor super(TemplateController, self)._set_supervisor() File "/home/idavalik/anaconda3/envs/phy2/lib/python3.11/site-packages/phy/apps/base.py", line 1010, in _set_supervisor supervisor = Supervisor( ^^^^^^^^^^^ File "/home/idavalik/anaconda3/envs/phy2/lib/python3.11/site-packages/phy/cluster/supervisor.py", line 637, in init spc = context.load('spikes_per_cluster') if context else None ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/idavalik/anaconda3/envs/phy2/lib/python3.11/site-packages/phy/utils/context.py", line 208, in load return load_pickle(path) ^^^^^^^^^^^^^^^^^ File "/home/idavalik/anaconda3/envs/phy2/lib/python3.11/site-packages/phylib/utils/_misc.py", line 144, in load_pickle return load(path) ^^^^^^^^^^ File "/home/idavalik/anaconda3/envs/phy2/lib/python3.11/site-packages/joblib/numpy_pickle.py", line 658, in load obj = _unpickle(fobj, filename, mmap_mode) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/idavalik/anaconda3/envs/phy2/lib/python3.11/site-packages/joblib/numpy_pickle.py", line 577, in _unpickle obj = unpickler.load() ^^^^^^^^^^^^^^^^ File "/home/idavalik/anaconda3/envs/phy2/lib/python3.11/pickle.py", line 1213, in load dispatchkey[0] File "/home/idavalik/anaconda3/envs/phy2/lib/python3.11/pickle.py", line 1538, in load_stack_global self.append(self.find_class(module, name)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/idavalik/anaconda3/envs/phy2/lib/python3.11/pickle.py", line 1580, in find_class import(module, level=0) ModuleNotFoundError: No module named 'numpy._core'

This is my conda package list:

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge alsa-lib 1.2.12 h4ab18f5_0 conda-forge asttokens 2.4.1 pyhd8ed1ab_0 conda-forge attr 2.5.1 h166bdaf_1 conda-forge aws-c-auth 0.7.22 h9137712_5 conda-forge aws-c-cal 0.6.15 h88a6e22_0 conda-forge aws-c-common 0.9.19 h4ab18f5_0 conda-forge aws-c-compression 0.2.18 h83b837d_6 conda-forge aws-c-event-stream 0.4.2 h0cbf018_13 conda-forge aws-c-http 0.8.2 h360477d_2 conda-forge aws-c-io 0.14.9 h2d549f9_2 conda-forge aws-c-mqtt 0.10.4 hf85b563_6 conda-forge aws-c-s3 0.5.10 h679ed35_3 conda-forge aws-c-sdkutils 0.1.16 h83b837d_2 conda-forge aws-checksums 0.1.18 h83b837d_6 conda-forge aws-crt-cpp 0.26.12 h8bc9c4d_0 conda-forge aws-sdk-cpp 1.11.329 hf74b5d1_5 conda-forge azure-core-cpp 1.12.0 h830ed8b_0 conda-forge azure-identity-cpp 1.8.0 hdb0d106_1 conda-forge azure-storage-blobs-cpp 12.11.0 ha67cba7_1 conda-forge azure-storage-common-cpp 12.6.0 he3f277c_1 conda-forge azure-storage-files-datalake-cpp 12.10.0 h29b5301_1 conda-forge bokeh 3.4.1 pyhd8ed1ab_0 conda-forge brotli 1.1.0 hd590300_1 conda-forge brotli-bin 1.1.0 hd590300_1 conda-forge brotli-python 1.1.0 py311hb755f60_1 conda-forge bzip2 1.0.8 hd590300_5 conda-forge c-ares 1.28.1 hd590300_0 conda-forge ca-certificates 2024.6.2 hbcca054_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cairo 1.18.0 h3faef2a_0 conda-forge certifi 2024.6.2 pyhd8ed1ab_0 conda-forge cffi 1.16.0 py311hb3a22ac_0 conda-forge charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge click 8.1.7 unix_pyh707e725_0 conda-forge cloudpickle 3.0.0 pyhd8ed1ab_0 conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge colorcet 3.1.0 pyhd8ed1ab_0 conda-forge comm 0.2.2 pyhd8ed1ab_0 conda-forge contourpy 1.2.1 py311h9547e67_0 conda-forge cycler 0.12.1 pyhd8ed1ab_0 conda-forge cython 3.0.10 py311hb755f60_0 conda-forge cytoolz 0.12.3 py311h459d7ec_0 conda-forge dask 2024.6.0 pyhd8ed1ab_0 conda-forge dask-core 2024.6.0 pyhd8ed1ab_0 conda-forge dask-expr 1.1.3 pyhd8ed1ab_0 conda-forge dbus 1.13.6 h5008d03_3 conda-forge debugpy 1.8.1 py311hb755f60_0 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge distributed 2024.6.0 pyhd8ed1ab_0 conda-forge exceptiongroup 1.2.0 pyhd8ed1ab_2 conda-forge executing 2.0.1 pyhd8ed1ab_0 conda-forge expat 2.6.2 h59595ed_0 conda-forge font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 h77eed37_2 conda-forge fontconfig 2.14.2 h14ed4e7_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge fonttools 4.53.0 py311h331c9d8_0 conda-forge freetype 2.12.1 h267a509_2 conda-forge fsspec 2024.6.0 pyhff2d567_0 conda-forge gettext 0.22.5 h59595ed_2 conda-forge gettext-tools 0.22.5 h59595ed_2 conda-forge gflags 2.2.2 he1b5a44_1004 conda-forge ghp-import 2.1.0 pyhd8ed1ab_0 conda-forge giflib 5.2.2 hd590300_0 conda-forge git 2.45.2 pl5321ha099dd3_1 conda-forge glib 2.80.2 h8a4344b_1 conda-forge glib-tools 2.80.2 h73ef956_1 conda-forge glog 0.7.1 hbabe93e_0 conda-forge graphite2 1.3.13 h59595ed_1003 conda-forge gst-plugins-base 1.22.9 hfa15dee_1 conda-forge gstreamer 1.22.9 h98fc4e7_1 conda-forge h2 4.1.0 pyhd8ed1ab_0 conda-forge h5py 3.11.0 nompi_py311h439e445_102 conda-forge harfbuzz 8.5.0 hfac3d4d_0 conda-forge hdf5 1.14.3 nompi_hdf9ad27_105 conda-forge hpack 4.0.0 pyh9f0ad1d_0 conda-forge hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge icu 73.2 h59595ed_0 conda-forge idna 3.7 pyhd8ed1ab_0 conda-forge importlib-metadata 7.1.0 pyha770c72_0 conda-forge importlib_metadata 7.1.0 hd8ed1ab_0 conda-forge iniconfig 2.0.0 pyhd8ed1ab_0 conda-forge ipykernel 6.29.4 pyh3099207_0 conda-forge ipython 8.25.0 pyh707e725_0 conda-forge jedi 0.19.1 pyhd8ed1ab_0 conda-forge jinja2 3.1.4 pyhd8ed1ab_0 conda-forge joblib 1.4.2 pyhd8ed1ab_0 conda-forge jupyter_client 8.6.2 pyhd8ed1ab_0 conda-forge jupyter_core 5.7.2 py311h38be061_0 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.5 py311h9547e67_1 conda-forge krb5 1.21.2 h659d440_0 conda-forge lame 3.100 h166bdaf_1003 conda-forge lcms2 2.16 hb7c19ff_0 conda-forge ld_impl_linux-64 2.40 hf3520f5_7 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libabseil 20240116.2 cxx17_h59595ed_0 conda-forge libaec 1.1.3 h59595ed_0 conda-forge libarrow 16.1.0 h4a673ee_10_cpu conda-forge libarrow-acero 16.1.0 hac33072_10_cpu conda-forge libarrow-dataset 16.1.0 hac33072_10_cpu conda-forge libarrow-substrait 16.1.0 h7e0c224_10_cpu conda-forge libasprintf 0.22.5 h661eb56_2 conda-forge libasprintf-devel 0.22.5 h661eb56_2 conda-forge libblas 3.9.0 22_linux64_openblas conda-forge libbrotlicommon 1.1.0 hd590300_1 conda-forge libbrotlidec 1.1.0 hd590300_1 conda-forge libbrotlienc 1.1.0 hd590300_1 conda-forge libcap 2.69 h0f662aa_0 conda-forge libcblas 3.9.0 22_linux64_openblas conda-forge libclang-cpp15 15.0.7 default_h127d8a8_5 conda-forge libclang13 18.1.7 default_h087397f_0 conda-forge libcrc32c 1.1.2 h9c3ff4c_0 conda-forge libcups 2.3.3 h4637d8d_4 conda-forge libcurl 8.8.0 hca28451_0 conda-forge libdeflate 1.20 hd590300_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 hd590300_2 conda-forge libevent 2.1.12 hf998b51_1 conda-forge libexpat 2.6.2 h59595ed_0 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libflac 1.4.3 h59595ed_0 conda-forge libgcc-ng 13.2.0 h77fa898_13 conda-forge libgcrypt 1.10.3 hd590300_0 conda-forge libgettextpo 0.22.5 h59595ed_2 conda-forge libgettextpo-devel 0.22.5 h59595ed_2 conda-forge libgfortran-ng 13.2.0 h69a702a_13 conda-forge libgfortran5 13.2.0 h3d2ce59_13 conda-forge libglib 2.80.2 h8a4344b_1 conda-forge libgomp 13.2.0 h77fa898_13 conda-forge libgoogle-cloud 2.25.0 h2736e30_0 conda-forge libgoogle-cloud-storage 2.25.0 h3d9a0c8_0 conda-forge libgpg-error 1.49 h4f305b6_0 conda-forge libgrpc 1.62.2 h15f2491_0 conda-forge libiconv 1.17 hd590300_2 conda-forge libjpeg-turbo 3.0.0 hd590300_1 conda-forge liblapack 3.9.0 22_linux64_openblas conda-forge libllvm15 15.0.7 hb3ce162_4 conda-forge libllvm18 18.1.7 hc9dba70_1 conda-forge libnghttp2 1.58.0 h47da74e_1 conda-forge libnsl 2.0.1 hd590300_0 conda-forge libogg 1.3.4 h7f98852_1 conda-forge libopenblas 0.3.27 pthreads_h413a1c8_0 conda-forge libopus 1.3.1 h7f98852_1 conda-forge libparquet 16.1.0 h6a7eafb_10_cpu conda-forge libpng 1.6.43 h2797004_0 conda-forge libpq 16.3 ha72fbe1_0 conda-forge libprotobuf 4.25.3 h08a7969_0 conda-forge libre2-11 2023.09.01 h5a48ba9_2 conda-forge libsndfile 1.2.2 hc60ed4a_1 conda-forge libsodium 1.0.18 h36c2ea0_1 conda-forge libsqlite 3.46.0 hde9e2c9_0 conda-forge libssh2 1.11.0 h0841786_0 conda-forge libstdcxx-ng 13.2.0 hc0a3c3a_13 conda-forge libsystemd0 255 h3516f8a_1 conda-forge libthrift 0.19.0 hb90f79a_1 conda-forge libtiff 4.6.0 h1dd3fc0_3 conda-forge libutf8proc 2.8.0 h166bdaf_0 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libvorbis 1.3.7 h9c3ff4c_0 conda-forge libwebp 1.4.0 h2c329e2_0 conda-forge libwebp-base 1.4.0 hd590300_0 conda-forge libxcb 1.15 h0b41bf4_0 conda-forge libxcrypt 4.4.36 hd590300_1 conda-forge libxkbcommon 1.7.0 h662e7e4_0 conda-forge libxml2 2.12.7 hc051c1a_1 conda-forge libzlib 1.3.1 h4ab18f5_1 conda-forge locket 1.0.0 pyhd8ed1ab_0 conda-forge lz4 4.3.3 py311h38e4bf4_0 conda-forge lz4-c 1.9.4 hcb278e6_0 conda-forge markdown 3.6 pyhd8ed1ab_0 conda-forge markupsafe 2.1.5 py311h459d7ec_0 conda-forge matplotlib 3.8.4 py311h38be061_2 conda-forge matplotlib-base 3.8.4 py311ha4ca890_2 conda-forge matplotlib-inline 0.1.7 pyhd8ed1ab_0 conda-forge mergedeep 1.3.4 pyhd8ed1ab_0 conda-forge mkdocs 1.6.0 pyhd8ed1ab_0 conda-forge mkdocs-get-deps 0.2.0 pyhd8ed1ab_0 conda-forge mpg123 1.32.6 h59595ed_0 conda-forge msgpack-python 1.0.8 py311h52f7536_0 conda-forge mtscomp 1.0.2 pypi_0 pypi munkres 1.1.4 pyh9f0ad1d_0 conda-forge mysql-common 8.3.0 hf1915f5_4 conda-forge mysql-libs 8.3.0 hca2cd23_4 conda-forge ncurses 6.5 h59595ed_0 conda-forge nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge nspr 4.35 h27087fc_0 conda-forge nss 3.101 h593d115_0 conda-forge numpy 1.24.1 py311h8e6699e_0 conda-forge openjpeg 2.5.2 h488ebb8_0 conda-forge openssl 3.3.1 h4ab18f5_1 conda-forge orc 2.0.1 h17fec99_1 conda-forge packaging 24.1 pyhd8ed1ab_0 conda-forge pandas 2.2.2 py311h14de704_1 conda-forge parso 0.8.4 pyhd8ed1ab_0 conda-forge partd 1.4.2 pyhd8ed1ab_0 conda-forge pathspec 0.12.1 pyhd8ed1ab_0 conda-forge pcre2 10.44 h0f59acf_0 conda-forge perl 5.32.1 7_hd590300_perl5 conda-forge pexpect 4.9.0 pyhd8ed1ab_0 conda-forge phy 2.0b6 pypi_0 pypi phylib 2.6.0 pypi_0 pypi pickleshare 0.7.5 py_1003 conda-forge pillow 10.3.0 py311h18e6fac_0 conda-forge pip 24.0 pyhd8ed1ab_0 conda-forge pixman 0.43.2 h59595ed_0 conda-forge platformdirs 4.2.2 pyhd8ed1ab_0 conda-forge pluggy 1.5.0 pyhd8ed1ab_0 conda-forge ply 3.11 pyhd8ed1ab_2 conda-forge prompt-toolkit 3.0.47 pyha770c72_0 conda-forge psutil 5.9.8 py311h459d7ec_0 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge pulseaudio-client 17.0 hb77b528_0 conda-forge pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge pyarrow 16.1.0 py311hbd00459_4 conda-forge pyarrow-core 16.1.0 py311h8c3dac4_4_cpu conda-forge pyarrow-hotfix 0.6 pyhd8ed1ab_0 conda-forge pycparser 2.22 pyhd8ed1ab_0 conda-forge pygments 2.18.0 pyhd8ed1ab_0 conda-forge pyopengl 3.1.6 pyhd8ed1ab_1 conda-forge pyparsing 3.1.2 pyhd8ed1ab_0 conda-forge pyqt 5.15.9 py311hf0fb5b6_5 conda-forge pyqt5-sip 12.12.2 py311hb755f60_5 conda-forge pyqtwebengine 5.15.9 py311hd529140_5 conda-forge pysocks 1.7.1 pyha2e5f31_6 conda-forge pytest 8.2.2 pyhd8ed1ab_0 conda-forge python 3.11.9 hb806964_0_cpython conda-forge python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge python_abi 3.11 4_cp311 conda-forge pytz 2024.1 pyhd8ed1ab_0 conda-forge pyyaml 6.0.1 py311h459d7ec_1 conda-forge pyyaml-env-tag 0.1 pyhd8ed1ab_0 conda-forge pyzmq 26.0.3 py311h08a0b41_0 conda-forge qt-main 5.15.8 h112747c_20 conda-forge qt-webengine 5.15.8 h3e791b3_6 conda-forge qtconsole 5.5.2 pyhd8ed1ab_0 conda-forge qtconsole-base 5.5.2 pyha770c72_0 conda-forge qtpy 2.4.1 pyhd8ed1ab_0 conda-forge re2 2023.09.01 h7f4b329_2 conda-forge readline 8.2 h8228510_1 conda-forge requests 2.32.3 pyhd8ed1ab_0 conda-forge responses 0.25.3 pyhd8ed1ab_0 conda-forge s2n 1.4.16 he19d79f_0 conda-forge scikit-learn 1.5.0 py311he08f58d_1 conda-forge scipy 1.13.1 py311h517d4fd_0 conda-forge setuptools 70.0.0 pyhd8ed1ab_0 conda-forge sip 6.7.12 py311hb755f60_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge snappy 1.2.0 hdb0a2a9_1 conda-forge sortedcontainers 2.4.0 pyhd8ed1ab_0 conda-forge stack_data 0.6.2 pyhd8ed1ab_0 conda-forge tblib 3.0.0 pyhd8ed1ab_0 conda-forge threadpoolctl 3.5.0 pyhc1e730c_0 conda-forge tk 8.6.13 noxft_h4845f30_101 conda-forge toml 0.10.2 pyhd8ed1ab_0 conda-forge tomli 2.0.1 pyhd8ed1ab_0 conda-forge toolz 0.12.1 pyhd8ed1ab_0 conda-forge tornado 6.4.1 py311h331c9d8_0 conda-forge tqdm 4.66.4 pyhd8ed1ab_0 conda-forge traitlets 5.14.3 pyhd8ed1ab_0 conda-forge types-pyyaml 6.0.12.20240311 pyhd8ed1ab_0 conda-forge typing_extensions 4.12.2 pyha770c72_0 conda-forge tzdata 2024a h0c530f3_0 conda-forge urllib3 2.2.2 pyhd8ed1ab_1 conda-forge watchdog 4.0.1 py311h38be061_0 conda-forge wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge wheel 0.43.0 pyhd8ed1ab_1 conda-forge xcb-util 0.4.0 hd590300_1 conda-forge xcb-util-image 0.4.0 h8ee46fc_1 conda-forge xcb-util-keysyms 0.4.0 h8ee46fc_1 conda-forge xcb-util-renderutil 0.3.9 hd590300_1 conda-forge xcb-util-wm 0.4.1 h8ee46fc_1 conda-forge xkeyboard-config 2.42 h4ab18f5_0 conda-forge xorg-compositeproto 0.4.2 h7f98852_1001 conda-forge xorg-damageproto 1.2.1 h7f98852_1002 conda-forge xorg-fixesproto 5.0 h7f98852_1002 conda-forge xorg-inputproto 2.3.2 h7f98852_1002 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.1.1 hd590300_0 conda-forge xorg-libsm 1.2.4 h7391055_0 conda-forge xorg-libx11 1.8.9 h8ee46fc_0 conda-forge xorg-libxau 1.0.11 hd590300_0 conda-forge xorg-libxcomposite 0.4.6 h0b41bf4_1 conda-forge xorg-libxdamage 1.1.5 h7f98852_1 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge xorg-libxi 1.7.10 h7f98852_0 conda-forge xorg-libxrandr 1.5.2 h7f98852_1 conda-forge xorg-libxrender 0.9.11 hd590300_0 conda-forge xorg-libxtst 1.2.3 h7f98852_1002 conda-forge xorg-randrproto 1.5.0 h7f98852_1001 conda-forge xorg-recordproto 1.14.2 h7f98852_1002 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-util-macros 1.19.3 h7f98852_0 conda-forge xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge xorg-xf86vidmodeproto 2.3.1 h7f98852_1002 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xyzservices 2024.6.0 pyhd8ed1ab_0 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yaml 0.2.5 h7f98852_2 conda-forge zeromq 4.3.5 h75354e8_4 conda-forge zict 3.0.0 pyhd8ed1ab_0 conda-forge zipp 3.19.2 pyhd8ed1ab_0 conda-forge zlib 1.3.1 h4ab18f5_1 conda-forge zstandard 0.22.0 py311hb6f056b_1 conda-forge zstd 1.5.6 ha6fb4c9_0 conda-forge

As mentioned in the title, I am running on an Ubuntu 22.04.

Any help, insights, further steps for troubleshooting are all welcome!

zm711 commented 4 days ago

Typically this has been due to mixing conda + pip which means the packages aren't quite playing well together. Could you try:

first clone the repo with git (or download the zip if not using git). Then edit the requirements.txt file such that numpy<2.0

conda create -n phy2_test python=3.11
cd phy
pip install -e .

And let me know if that works. We may need to add in a step where we also update phylib.

Idavr commented 4 days ago

I see! I tried following your instructions and now I got a different error:

14:15:27.361 [W] model:667 Skipping spike waveforms that do not exist, they will be extracted on the fly from the raw data as needed. WebEngineContext used before QtWebEngine::initialize() or OpenGL context creation failed. QGLXContext: Failed to create dummy context 14:15:30.331 [W] gui:671 Could not create view TemplateFeatureView. Failed to create OpenGL context for format QSurfaceFormat(version 2.0, options QFlags(), depthBufferSize 24, redBufferSize -1, greenBufferSize -1, blueBufferSize -1, alphaBufferSize -1, stencilBufferSize 8, samples 0, swapBehavior QSurfaceFormat::DefaultSwapBehavior, swapInterval 1, colorSpace QSurfaceFormat::DefaultColorSpace, profile QSurfaceFormat::NoProfile) Aborted (core dumped)

zm711 commented 4 days ago

So two things to try. One user on Ubuntu just had to restart their computer and things started working after that when they were having qt errors. So worth a try. I think there is some sort of cache that doesn't play well together between the OS and qt/opengl. So I would try that. Then if that doesn't work I would do a full dev install:

conda create -n phy2_full
git clone git@github.com:cortex-lab/phy.git
cd phy
pip install -r requirements.txt
pip install -r requirements-dev.txt
pip install -e .
cd ..
git clone git@github.com:cortex-lab/phylib.git
cd phylib
pip install -e . --upgrade

Again if doing the dev install you need the edited requirements.txt with numpy<2.0.

Idavr commented 3 days ago

The restart worked! Thank you so much!