phy

[joschaschmiedt]

https://github.com/cortex-lab/phy

https://github.com/cortex-lab/phy/blob/master/environment.yml:

name: phy2
channels:
  - conda-forge
  - defaults
dependencies:
  - python
  - pip
  - git
  - numpy
  - matplotlib
  - scipy
  - h5py
  - pyqt
  - pyopengl
  - pyqtwebengine
  - pytest
  - qtconsole
  - requests
  - responses
  - traitlets
  - dask
  - cython
  - pillow
  - scikit-learn
  - joblib
  - pip:
    - git+https://github.com/cortex-lab/phy.git

[joschaschmiedt]

After installing phy2 from the Git repo, actually starting it on Windows causes a good old Qt error:

(neuro-conda-2024a) PS C:\Users\schmiedt\Downloads\phy-data-master\phy-data-master\template> phy template-gui .\params.py
09:47:59.461 [W] model:603            Unreferenced clusters found in templates (generally not a problem)
09:47:59.462 [W] model:625            Unreferenced clusters found in spike_clusters (generally not a problem)
09:47:59.466 [W] model:667            Skipping spike waveforms that do not exist, they will be extracted on the fly from the raw data as needed.
qt.qpa.plugin: Could not find the Qt platform plugin "windows" in ""
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

[joschaschmiedt]

Pure pip installation works with the following dependencies (output of pip freeze) on Windows 11 and Python 3.11

asttokens==2.4.1
certifi==2024.2.2
charset-normalizer==3.3.2
click==8.1.7
cloudpickle==3.0.0
colorama==0.4.6
colorcet==3.0.1
comm==0.2.1
contourpy==1.2.0
cycler==0.12.1
Cython==3.0.8
dask==2024.2.0
debugpy==1.8.1
decorator==5.1.1
executing==2.0.1
fonttools==4.49.0
fsspec==2024.2.0
ghp-import==2.1.0
h5py==3.10.0
idna==3.6
importlib-metadata==7.0.1
iniconfig==2.0.0
ipykernel==6.29.2
ipython==8.21.0
jedi==0.19.1
Jinja2==3.1.3
joblib==1.3.2
jupyter_client==8.6.0
jupyter_core==5.7.1
kiwisolver==1.4.5
locket==1.0.0
Markdown==3.5.2
MarkupSafe==2.1.5
matplotlib==3.8.3
matplotlib-inline==0.1.6
mergedeep==1.3.4
mkdocs==1.5.3
mtscomp==1.0.2
nest-asyncio==1.6.0
numpy==1.26.4
packaging==23.2
param==2.0.2
parso==0.8.3
partd==1.4.1
pathspec==0.12.1
phy @ git+https://github.com/cortex-lab/phy.git@8bf8cf751fcbd44210b3c5bbdba8c34a7b2cb1ce
phylib==2.4.3
pillow==10.2.0
platformdirs==4.2.0
pluggy==1.4.0
prompt-toolkit==3.0.43
psutil==5.9.8
pure-eval==0.2.2
pyct==0.5.0
Pygments==2.17.2
PyOpenGL==3.1.7
pyparsing==3.1.1
PyQt5==5.15.10
PyQt5-Qt5==5.15.2
PyQt5-sip==12.13.0
PyQt6-WebEngine-Qt6==6.6.2
pyqtgraph==0.13.3
PyQtWebEngine==5.15.6
PyQtWebEngine-Qt5==5.15.2
PySide6==6.6.2
PySide6_Addons==6.6.2
PySide6_Essentials==6.6.2
pytest==8.0.1
python-dateutil==2.8.2
pywin32==306
PyYAML==6.0.1
pyyaml_env_tag==0.1
pyzmq==25.1.2
qtconsole==5.5.1
QtPy==2.4.1
requests==2.31.0
responses==0.25.0
scikit-learn==1.4.1.post1
scipy==1.12.0
shiboken6==6.6.2
six==1.16.0
stack-data==0.6.3
threadpoolctl==3.3.0
toolz==0.12.1
tornado==6.4
tqdm==4.66.2
traitlets==5.14.1
urllib3==2.2.1
watchdog==4.0.0
wcwidth==0.2.13
zipp==3.17.0

[joschaschmiedt]

There is an open pull request updating the requirements.txt: cortex-lab/phy#1230