Stuck on Adding default color schemes to TraceView.

[1HosseinHeydari8]

Hello, I have created the environment using "environment.yml". The data I'm trying to visualize is from Kilosort/docs/tutorials/basic_example.ipynb (ZFM-02370_mini.imec0.ap.bin). I fed that data to the kilosort GUI, and got some results: Running the phy template-gui params.py gives me an error: Downgrading numpy didn't help. So instead, I changed that line of code as suggested in the error. Running the gui again, this time I get this: It has been stuck on the last line.

I appreciate any help.

[zm711]

Downgrading to which numpy and which python version?

[1HosseinHeydari8]

Thank you for the prompt response. The Python version is 3.11.9. I've tried numpy 1.25.0 and 1.26.0. I get this error in both cases: However, when I check the installation, it is actually there (using pip list): Package Version

---

asttokens 2.4.1 bokeh 3.4.1 Brotli 1.1.0 cached-property 1.5.2 certifi 2024.6.2 charset-normalizer 3.3.2 click 8.1.7 cloudpickle 3.0.0 colorama 0.4.6 colorcet 3.1.0 comm 0.2.2 contourpy 1.2.1 cycler 0.12.1 Cython 3.0.10 cytoolz 0.12.3 dask 2024.6.0 dask-expr 1.1.3 debugpy 1.8.1 decorator 5.1.1 distributed 2024.6.0 exceptiongroup 1.2.0 executing 2.0.1 fonttools 4.53.0 fsspec 2024.6.0 ghp-import 2.1.0 h5py 3.11.0 idna 3.7 importlib_metadata 7.1.0 iniconfig 2.0.0 ipykernel 6.29.4 ipython 8.25.0 jedi 0.19.1 Jinja2 3.1.4 joblib 1.4.2 jupyter_client 8.6.2 jupyter_core 5.7.2 kiwisolver 1.4.5 locket 1.0.0 lz4 4.3.3 Markdown 3.6 MarkupSafe 2.1.5 matplotlib 3.8.4 matplotlib-inline 0.1.7 mergedeep 1.3.4 mkdocs 1.6.0 mkdocs-get-deps 0.2.0 msgpack 1.0.8 mtscomp 1.0.2 munkres 1.1.4 nest_asyncio 1.6.0 numpy 1.25.0 packaging 24.1 pandas 2.2.2 parso 0.8.4 partd 1.4.2 pathspec 0.12.1 phy 2.0b6 phylib 2.6.0 pickleshare 0.7.5 pillow 10.3.0 pip 24.0 platformdirs 4.2.2 pluggy 1.5.0 ply 3.11 prompt_toolkit 3.0.47 psutil 5.9.8 pure-eval 0.2.2 pyarrow 16.1.0 pyarrow-hotfix 0.6 Pygments 2.18.0 PyOpenGL 3.1.6 pyparsing 3.1.2 PyQt5 5.15.9 PyQt5-sip 12.12.2 PyQtWebEngine 5.15.4 PySocks 1.7.1 pytest 8.2.2 python-dateutil 2.9.0 pytz 2024.1 pywin32 306 PyYAML 6.0.1 pyyaml_env_tag 0.1 pyzmq 26.0.3 qtconsole 5.5.2 QtPy 2.4.1 requests 2.32.3 responses 0.25.3 scikit-learn 1.5.0 scipy 1.13.1 setuptools 70.1.0 sip 6.7.12 six 1.16.0 sortedcontainers 2.4.0 stack-data 0.6.2 tblib 3.0.0 threadpoolctl 3.5.0 toml 0.10.2 tomli 2.0.1 toolz 0.12.1 tornado 6.4.1 tqdm 4.66.4 traitlets 5.14.3 types-PyYAML 6.0.12.20240311 typing_extensions 4.12.2 tzdata 2024.1 urllib3 2.2.2 watchdog 4.0.1 wcwidth 0.2.13 wheel 0.43.0 win-inet-pton 1.1.0 xyzservices 2024.6.0 zict 3.0.0 zipp 3.19.2

[zm711]

Could you try reinstalling with a numpy limit in the yaml file. I wonder if the pickle and numpy are out of sync because of just downgrading rather than installing at the beginning. Sometimes pip-conda messes these things up.

To be clear: in the file do

name: phy2
channels:
  - conda-forge
  - defaults
dependencies:
  - python=3.11
  - pip
  - git
  - numpy<2.0
  - 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

[1HosseinHeydari8]

Thank you! It is working now:

[zm711]

wonderful. The risks of pip + conda. haha. Have a nice day!