phy: numpy broken and empty interface on Linux

Linux Ubuntu-like with KDE

<ws>:~/.local/apps$ python --version
Python 3.10.6
<ws>:~/.local/apps$ qmake --version
QMake version 3.1
Using Qt version 5.15.3 in /usr/lib/x86_64-linux-gnu

Virtual environment

<ws>:~/.local/apps$ python -m venv phy
<ws>:~/.local/apps$ source phy/bin/activate
(phy) <ws>:~/.local/apps$ pip install phy --pre --upgrade
Collecting phy
  Using cached phy-2.0b5-py2.py3-none-any.whl
Collecting requests
  Using cached requests-2.29.0-py3-none-any.whl (62 kB)
Collecting scipy
  Using cached scipy-1.10.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (34.4 MB)
Collecting click
  Using cached click-8.1.3-py3-none-any.whl (96 kB)
Collecting qtconsole
  Using cached qtconsole-5.4.2-py3-none-any.whl (121 kB)
Collecting mtscomp
  Using cached mtscomp-1.0.2-py2.py3-none-any.whl (16 kB)
Collecting PyQtWebEngine
  Using cached PyQtWebEngine-5.15.6-cp37-abi3-manylinux1_x86_64.whl (230 kB)
Collecting matplotlib
  Using cached matplotlib-3.7.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.6 MB)
Collecting dask
  Using cached dask-2023.4.1-py3-none-any.whl (1.2 MB)
Collecting PyQt5
  Using cached PyQt5-5.15.9-cp37-abi3-manylinux_2_17_x86_64.whl (8.4 MB)
Collecting pillow
  Using cached Pillow-9.5.0-cp310-cp310-manylinux_2_28_x86_64.whl (3.4 MB)
Collecting tqdm
  Using cached tqdm-4.65.0-py3-none-any.whl (77 kB)
Collecting h5py
  Using cached h5py-3.8.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.6 MB)
Collecting numpy
  Using cached numpy-1.24.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.3 MB)
Collecting colorcet
  Using cached colorcet-3.0.1-py2.py3-none-any.whl (1.7 MB)
Collecting joblib
  Using cached joblib-1.2.0-py3-none-any.whl (297 kB)
Collecting pyopengl
  Using cached PyOpenGL-3.1.6-py3-none-any.whl (2.4 MB)
Collecting mkdocs
  Using cached mkdocs-1.4.2-py3-none-any.whl (3.7 MB)
Collecting phylib
  Using cached phylib-2.4.3-py2.py3-none-any.whl (80 kB)
Collecting cython
  Using cached Cython-3.0.0b2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.6 MB)
Collecting pyct>=0.4.4
  Using cached pyct-0.5.0-py2.py3-none-any.whl (15 kB)
Collecting toolz>=0.10.0
  Using cached toolz-0.12.0-py3-none-any.whl (55 kB)
Collecting packaging>=20.0
  Using cached packaging-23.1-py3-none-any.whl (48 kB)
Collecting partd>=1.2.0
  Using cached partd-1.4.0-py3-none-any.whl (18 kB)
Collecting pyyaml>=5.3.1
  Using cached PyYAML-6.0-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (682 kB)
Collecting importlib-metadata>=4.13.0
  Using cached importlib_metadata-6.6.0-py3-none-any.whl (22 kB)
Collecting cloudpickle>=1.5.0
  Using cached cloudpickle-2.2.1-py3-none-any.whl (25 kB)
Collecting fsspec>=2021.09.0
  Using cached fsspec-2023.4.0-py3-none-any.whl (153 kB)
Collecting contourpy>=1.0.1
  Using cached contourpy-1.0.7-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (300 kB)
Collecting pyparsing>=2.3.1
  Using cached pyparsing-3.1.0b1-py3-none-any.whl (102 kB)
Collecting kiwisolver>=1.0.1
  Using cached kiwisolver-1.4.4-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.6 MB)
Collecting python-dateutil>=2.7
  Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
Collecting cycler>=0.10
  Using cached cycler-0.11.0-py3-none-any.whl (6.4 kB)
Collecting fonttools>=4.22.0
  Using cached fonttools-4.39.3-py3-none-any.whl (1.0 MB)
Collecting markdown<3.4,>=3.2.1
  Using cached Markdown-3.3.7-py3-none-any.whl (97 kB)
Collecting ghp-import>=1.0
  Using cached ghp_import-2.1.0-py3-none-any.whl (11 kB)
Collecting mergedeep>=1.3.4
  Using cached mergedeep-1.3.4-py3-none-any.whl (6.4 kB)
Collecting jinja2>=2.11.1
  Using cached Jinja2-3.1.2-py3-none-any.whl (133 kB)
Collecting pyyaml-env-tag>=0.1
  Using cached pyyaml_env_tag-0.1-py3-none-any.whl (3.9 kB)
Collecting watchdog>=2.0
  Using cached watchdog-3.0.0-py3-none-manylinux2014_x86_64.whl (82 kB)
Collecting PyQt5-sip<13,>=12.11
  Using cached PyQt5_sip-12.12.1-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.whl (360 kB)
Collecting PyQt5-Qt5>=5.15.2
  Using cached PyQt5_Qt5-5.15.2-py3-none-manylinux2014_xphy template-gui params.py 
15:45:39.332 [W] model:603            Unreferenced clusters found in templates (generally not a problem)
15:45:39.333 [W] model:625            Unreferenced clusters found in spike_clusters (generally not a problem)
15:45:39.337 [W] model:667            Skipping spike waveforms that do not exist, they will be extracted on the fly from the raw data as needed.
15:45:39.338 [W] model:55             133/4489 values are nan in /home/rth/Rhythm_FPGA-100.0-ks2.5/similar_templates.npy, replacing by zero.

86_64.whl (59.9 MB)
Collecting PyQtWebEngine-Qt5>=5.15.0
  Using cached PyQtWebEngine_Qt5-5.15.2-py3-none-manylinux2014_x86_64.whl (67.5 MB)
Collecting jupyter-core
  Using cached jupyter_core-5.3.0-py3-none-any.whl (93 kB)
Collecting jupyter-client>=4.1
  Using cached jupyter_client-8.2.0-py3-none-any.whl (103 kB)
Collecting ipython-genutils
  Using cached ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB)
Collecting pygments
  Using cached Pygments-2.15.1-py3-none-any.whl (1.1 MB)
Collecting qtpy>=2.0.1
  Using cached QtPy-2.3.1-py3-none-any.whl (84 kB)
Collecting traitlets!=5.2.1,!=5.2.2
  Using cached traitlets-5.9.0-py3-none-any.whl (117 kB)
Collecting ipykernel>=4.1
  Using cached ipykernel-6.22.0-py3-none-any.whl (149 kB)
Collecting pyzmq>=17.1
  Using cached pyzmq-25.0.2-cp310-cp310-manylinux_2_28_x86_64.whl (1.1 MB)
Collecting idna<4,>=2.5
  Using cached idna-3.4-py3-none-any.whl (61 kB)
Collecting urllib3<1.27,>=1.21.1
  Using cached urllib3-1.26.15-py2.py3-none-any.whl (140 kB)
Collecting charset-normalizer<4,>=2
  Using cached charset_normalizer-3.1.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (199 kB)
Collecting certifi>=2017.4.17
  Using cached certifi-2022.12.7-py3-none-any.whl (155 kB)
Collecting zipp>=0.5
  Using cached zipp-3.15.0-py3-none-any.whl (6.8 kB)
Collecting debugpy>=1.6.5
  Using cached debugpy-1.6.7-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.0 MB)
Collecting comm>=0.1.1
  Using cached comm-0.1.3-py3-none-any.whl (6.6 kB)
Collecting tornado>=6.1
  Using cached tornado-6.3.1-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (426 kB)
Collecting psutil
  Using cached psutil-5.9.5-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (282 kB)
Collecting ipython>=7.23.1
  Using cached ipython-8.13.1-py3-none-any.whl (797 kB)
Collecting matplotlib-inline>=0.1
  Using cached matplotlib_inline-0.1.6-py3-none-any.whl (9.4 kB)
Collecting nest-asyncio
  Using cached nest_asyncio-1.5.6-py3-none-any.whl (5.2 kB)
Collecting MarkupSafe>=2.0
  Using cached MarkupSafe-2.1.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB)
Collecting platformdirs>=2.5
  Using cached platformdirs-3.5.0-py3-none-any.whl (15 kB)
Collecting locket
  Using cached locket-1.0.0-py2.py3-none-any.whl (4.4 kB)
Collecting param>=1.7.0
  Using cached param-1.13.0-py2.py3-none-any.whl (87 kB)
Collecting six>=1.5
  Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting backcall
  Using cached backcall-0.2.0-py2.py3-none-any.whl (11 kB)
Collecting prompt-toolkit!=3.0.37,<3.1.0,>=3.0.30
  Using cached prompt_toolkit-3.0.38-py3-none-any.whl (385 kB)
Collecting pickleshare
  Using cached pickleshare-0.7.5-py2.py3-none-any.whl (6.9 kB)
Collecting stack-data
  Using cached stack_data-0.6.2-py3-none-any.whl (24 kB)
Collecting pexpect>4.3
  Using cached pexpect-4.8.0-py2.py3-none-any.whl (59 kB)
Collecting decorator
  Using cached decorator-5.1.1-py3-none-any.whl (9.1 kB)
Collecting jedi>=0.16
  Using cached jedi-0.18.2-py2.py3-none-any.whl (1.6 MB)
Collecting parso<0.9.0,>=0.8.0
  Using cached parso-0.8.3-py2.py3-none-any.whl (100 kB)
Collecting ptyprocess>=0.5
  Using cached ptyprocess-0.7.0-py2.py3-none-any.whl (13 kB)
Collecting wcwidth
  Using cached wcwidth-0.2.6-py2.py3-none-any.whl (29 kB)
Collecting executing>=1.2.0
  Using cached executing-1.2.0-py2.py3-none-any.whl (24 kB)
Collecting pure-eval
  Using cached pure_eval-0.2.2-py3-none-any.whl (11 kB)
Collecting asttokens>=2.1.0
  Using cached asttokens-2.2.1-py2.py3-none-any.whl (26 kB)
Installing collected packages: wcwidth, PyQtWebEngine-Qt5, PyQt5-Qt5, pyopengl, pure-eval, ptyprocess, pickleshare, mtscomp, ipython-genutils, executing, backcall, zipp, watchdog, urllib3, traitlets, tqdm, tornado, toolz, six, pyzmq, pyyaml, PyQt5-sip, pyparsing, pygments, psutil, prompt-toolkit, platformdirs, pillow, pexpect, parso, param, packaging, numpy, nest-asyncio, mergedeep, MarkupSafe, markdown, locket, kiwisolver, joblib, idna, fsspec, fonttools, decorator, debugpy, cython, cycler, cloudpickle, click, charset-normalizer, certifi, scipy, requests, qtpy, pyyaml-env-tag, python-dateutil, PyQt5, pyct, partd, matplotlib-inline, jupyter-core, jinja2, jedi, importlib-metadata, h5py, contourpy, comm, asttokens, stack-data, PyQtWebEngine, matplotlib, jupyter-client, ghp-import, dask, colorcet, phylib, mkdocs, ipython, ipykernel, qtconsole, phy
Successfully installed MarkupSafe-2.1.2 PyQt5-5.15.9 PyQt5-Qt5-5.15.2 PyQt5-sip-12.12.1 PyQtWebEngine-5.15.6 PyQtWebEngine-Qt5-5.15.2 asttokens-2.2.1 backcall-0.2.0 certifi-2022.12.7 charset-normalizer-3.1.0 click-8.1.3 cloudpickle-2.2.1 colorcet-3.0.1 comm-0.1.3 contourpy-1.0.7 cycler-0.11.0 cython-3.0.0b2 dask-2023.4.1 debugpy-1.6.7 decorator-5.1.1 executing-1.2.0 fonttools-4.39.3 fsspec-2023.4.0 ghp-import-2.1.0 h5py-3.8.0 idna-3.4 importlib-metadata-6.6.0 ipykernel-6.22.0 ipython-8.13.1 ipython-genutils-0.2.0 jedi-0.18.2 jinja2-3.1.2 joblib-1.2.0 jupyter-client-8.2.0 jupyter-core-5.3.0 kiwisolver-1.4.4 locket-1.0.0 markdown-3.3.7 matplotlib-3.7.1 matplotlib-inline-0.1.6 mergedeep-1.3.4 mkdocs-1.4.2 mtscomp-1.0.2 nest-asyncio-1.5.6 numpy-1.24.3 packaging-23.1 param-1.13.0 parso-0.8.3 partd-1.4.0 pexpect-4.8.0 phy-2.0b5 phylib-2.4.3 pickleshare-0.7.5 pillow-9.5.0 platformdirs-3.5.0 prompt-toolkit-3.0.38 psutil-5.9.5 ptyprocess-0.7.0 pure-eval-0.2.2 pyct-0.5.0 pygments-2.15.1 pyopengl-3.1.6 pyparsing-3.1.0b1 python-dateutil-2.8.2 pyyaml-6.0 pyyaml-env-tag-0.1 pyzmq-25.0.2 qtconsole-5.4.2 qtpy-2.3.1 requests-2.29.0 scipy-1.10.1 six-1.16.0 stack-data-0.6.2 toolz-0.12.0 tornado-6.3.1 tqdm-4.65.0 traitlets-5.9.0 urllib3-1.26.15 watchdog-3.0.0 wcwidth-0.2.6 zipp-3.15.0

phy crashes because of fresh numpy

(phy) <ws>:~/.local/apps$ phy -h
/home/rth/.local/apps/phy/lib/python3.10/site-packages/phy/plot/gloo/variable.py:86: FutureWarning: In the future `np.bool` will be defined as the corresponding NumPy scalar.
  gl.GL_BOOL: (1, gl.GL_BOOL, np.bool),
Traceback (most recent call last):
  File "/home/rth/.local/apps/phy/bin/phy", line 5, in <module>
    from phy.apps import phycli
  File "/home/rth/.local/apps/phy/lib/python3.10/site-packages/phy/apps/__init__.py", line 25, in <module>
    from .base import (  # noqa
  File "/home/rth/.local/apps/phy/lib/python3.10/site-packages/phy/apps/base.py", line 26, in <module>
    from phy.cluster._utils import RotatingProperty
  File "/home/rth/.local/apps/phy/lib/python3.10/site-packages/phy/cluster/__init__.py", line 9, in <module>
    from .views import *  # noqa
  File "/home/rth/.local/apps/phy/lib/python3.10/site-packages/phy/cluster/views/__init__.py", line 10, in <module>
    from .base import ManualClusteringView  # noqa
  File "/home/rth/.local/apps/phy/lib/python3.10/site-packages/phy/cluster/views/base.py", line 21, in <module>
    from phy.plot import PlotCanvas, NDC, extend_bounds
  File "/home/rth/.local/apps/phy/lib/python3.10/site-packages/phy/plot/__init__.py", line 17, in <module>
    from .base import BaseVisual, GLSLInserter, BaseCanvas, BaseLayout
  File "/home/rth/.local/apps/phy/lib/python3.10/site-packages/phy/plot/base.py", line 20, in <module>
    from . import gloo
  File "/home/rth/.local/apps/phy/lib/python3.10/site-packages/phy/plot/gloo/__init__.py", line 10, in <module>
    from .program import Program
  File "/home/rth/.local/apps/phy/lib/python3.10/site-packages/phy/plot/gloo/program.py", line 18, in <module>
    from .variable import Uniform, Attribute
  File "/home/rth/.local/apps/phy/lib/python3.10/site-packages/phy/plot/gloo/variable.py", line 86, in <module>
    gl.GL_BOOL: (1, gl.GL_BOOL, np.bool),
  File "/home/rth/.local/apps/phy/lib/python3.10/site-packages/numpy/__init__.py", line 305, in __getattr__
    raise AttributeError(__former_attrs__[attr])
AttributeError: module 'numpy' has no attribute 'bool'.
`np.bool` was a deprecated alias for the builtin `bool`. To avoid this error in existing code, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
    https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations. Did you mean: 'bool_'?

FIX for the numpy problem

(phy) <ws>:~/.local/apps$ pip install numpy==1.23.5
Collecting numpy==1.23.5
  Using cached numpy-1.23.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.1 MB)
Installing collected packages: numpy
  Attempting uninstall: numpy
    Found existing installation: numpy 1.24.3
    Uninstalling numpy-1.24.3:
      Successfully uninstalled numpy-1.24.3
Successfully installed numpy-1.23.5
(phy) <ws>:~/.local/apps$ phy -h
Usage: phy [OPTIONS] COMMAND [ARGS]...

  Interactive visualization and manual spike sorting of large-scale ephys
  data.

Options:
  --version   Show the version and exit.
  -h, --help  Show this message and exit.

Commands:
  alf-convert        Convert an ephys dataset into ALF.
  extract-waveforms  Extract spike waveforms.
  kwik-describe      Describe a Kwik file.
  kwik-gui           Launch the Kwik GUI on a Kwik file.
  template-describe  Describe a template file.
  template-gui       Launch the template GUI on a params.py file.
  trace-gui          Launch the trace GUI on a raw data file.

Trying KS 2.5 phy export

(phy) <ws>:~/.local/apps$ cd ~/Rhythm_FPGA-100.0-ks2.5/
(phy) <ws>:~/Rhythm_FPGA-100.0-ks2.5$ phy template-describe params.py 
15:44:42.226 [W] model:603            Unreferenced clusters found in templates (generally not a problem)
15:44:42.228 [W] model:625            Unreferenced clusters found in spike_clusters (generally not a problem)
15:44:42.232 [W] model:667            Skipping spike waveforms that do not exist, they will be extracted on the fly from the raw data as needed.
15:44:42.233 [W] model:55             133/4489 values are nan in /home/rth/Rhythm_FPGA-100.0-ks2.5/similar_templates.npy, replacing by zero.
Data files              /home/rth/Rhythm_FPGA-100.0-ks2.5/temp_wh.dat
Directory               /home/rth/Rhythm_FPGA-100.0-ks2.5
Duration                1014.6s
Sample rate             30.0 kHz
Data type               int16
# of channels           128
# of channels (raw)     128
# of templates          67
# of spikes             46,850
(phy) <ws>:~/Rhythm_FPGA-100.0-ks2.5$ phy template-gui params.py 
15:45:39.332 [W] model:603            Unreferenced clusters found in templates (generally not a problem)
15:45:39.333 [W] model:625            Unreferenced clusters found in spike_clusters (generally not a problem)
15:45:39.337 [W] model:667            Skipping spike waveforms that do not exist, they will be extracted on the fly from the raw data as needed.
15:45:39.338 [W] model:55             133/4489 values are nan in /home/rth/Rhythm_FPGA-100.0-ks2.5/similar_templates.npy, replacing by zero.

Then try to close