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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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Installation issue #1164

Closed guilhemibos closed 2 years ago

guilhemibos commented 2 years ago

Hi

I don't manage to install Phy, I don't know why. I've first created an environment conda create -n Phy conda activate Phy

I tried to install Phy a first time but had some installation issues (related to spyder which I solved). However, as I tried to launch phy : phy template-gui params.py it seems phy is not installed: Command 'phy' not found, did you mean

So I tried to reinstall it (I've tried by erasing and recreating my environments also, but then every requirements are already satisfied: pip install phy --pre --upgrade Defaulting to user installation because normal site-packages is not writeable Requirement already satisfied: phy in ./.local/lib/python3.6/site-packages (2.0b5) Requirement already satisfied: phylib in ./.local/lib/python3.6/site-packages (from phy) (2.4.1) Requirement already satisfied: mtscomp in ./.local/lib/python3.6/site-packages (from phy) (1.0.2) Requirement already satisfied: numpy in ./.local/lib/python3.6/site-packages (from phy) (1.19.5) Requirement already satisfied: matplotlib in /usr/lib/python3/dist-packages (from phy) (2.1.1) Requirement already satisfied: scipy in ./.local/lib/python3.6/site-packages (from phy) (1.5.4) Requirement already satisfied: h5py in ./.local/lib/python3.6/site-packages (from phy) (3.1.0) Requirement already satisfied: dask in ./.local/lib/python3.6/site-packages (from phy) (2021.3.0) Requirement already satisfied: cython in ./.local/lib/python3.6/site-packages (from phy) (3.0.0a10) Requirement already satisfied: pillow in /usr/lib/python3/dist-packages (from phy) (5.1.0) Requirement already satisfied: colorcet in ./.local/lib/python3.6/site-packages (from phy) (3.0.0) Requirement already satisfied: pyopengl in ./.local/lib/python3.6/site-packages (from phy) (3.1.6) Requirement already satisfied: requests in /usr/lib/python3/dist-packages (from phy) (2.18.4) Requirement already satisfied: qtconsole in ./.local/lib/python3.6/site-packages (from phy) (5.2.2) Requirement already satisfied: tqdm in ./.local/lib/python3.6/site-packages (from phy) (4.64.0) Requirement already satisfied: joblib in ./.local/lib/python3.6/site-packages (from phy) (1.1.0) Requirement already satisfied: click in ./.local/lib/python3.6/site-packages (from phy) (8.0.4) Requirement already satisfied: mkdocs in ./.local/lib/python3.6/site-packages (from phy) (1.3.0) Requirement already satisfied: PyQtWebEngine in ./.local/lib/python3.6/site-packages (from phy) (5.15.5) Requirement already satisfied: importlib-metadata in ./.local/lib/python3.6/site-packages (from click->phy) (4.8.3) Requirement already satisfied: param>=1.7.0 in ./.local/lib/python3.6/site-packages (from colorcet->phy) (1.12.2) Requirement already satisfied: pyct>=0.4.4 in ./.local/lib/python3.6/site-packages (from colorcet->phy) (0.4.8) Requirement already satisfied: pyyaml in /usr/lib/python3/dist-packages (from dask->phy) (3.12) Requirement already satisfied: cached-property in ./.local/lib/python3.6/site-packages (from h5py->phy) (1.5.2) Requirement already satisfied: ghp-import>=1.0 in ./.local/lib/python3.6/site-packages (from mkdocs->phy) (2.1.0) Requirement already satisfied: pyyaml-env-tag>=0.1 in ./.local/lib/python3.6/site-packages (from mkdocs->phy) (0.1) Requirement already satisfied: Jinja2>=2.10.2 in ./.local/lib/python3.6/site-packages (from mkdocs->phy) (3.0.3) Requirement already satisfied: mergedeep>=1.3.4 in ./.local/lib/python3.6/site-packages (from mkdocs->phy) (1.3.4) Requirement already satisfied: watchdog>=2.0 in ./.local/lib/python3.6/site-packages (from mkdocs->phy) (2.1.9) Requirement already satisfied: packaging>=20.5 in ./.local/lib/python3.6/site-packages (from mkdocs->phy) (21.3) Requirement already satisfied: Markdown>=3.2.1 in ./.local/lib/python3.6/site-packages (from mkdocs->phy) (3.3.7) Requirement already satisfied: toolz in ./.local/lib/python3.6/site-packages (from phylib->phy) (0.11.2) Requirement already satisfied: PyQt5>=5.15.4 in ./.local/lib/python3.6/site-packages (from PyQtWebEngine->phy) (5.15.6) Requirement already satisfied: PyQt5-sip<13,>=12.8 in ./.local/lib/python3.6/site-packages (from PyQtWebEngine->phy) (12.9.1) Requirement already satisfied: PyQtWebEngine-Qt5>=5.15.2 in ./.local/lib/python3.6/site-packages (from PyQtWebEngine->phy) (5.15.2) Requirement already satisfied: ipykernel>=4.1 in ./.local/lib/python3.6/site-packages (from qtconsole->phy) (5.5.6) Requirement already satisfied: traitlets in ./.local/lib/python3.6/site-packages (from qtconsole->phy) (4.3.3) Requirement already satisfied: jupyter-client>=4.1 in ./.local/lib/python3.6/site-packages (from qtconsole->phy) (7.1.2) Requirement already satisfied: qtpy in ./.local/lib/python3.6/site-packages (from qtconsole->phy) (2.0.1) Requirement already satisfied: ipython-genutils in ./.local/lib/python3.6/site-packages (from qtconsole->phy) (0.2.0) Requirement already satisfied: pygments in ./.local/lib/python3.6/site-packages (from qtconsole->phy) (2.12.0) Requirement already satisfied: jupyter-core in ./.local/lib/python3.6/site-packages (from qtconsole->phy) (4.9.2) Requirement already satisfied: pyzmq>=17.1 in ./.local/lib/python3.6/site-packages (from qtconsole->phy) (23.2.0) Requirement already satisfied: importlib-resources in ./.local/lib/python3.6/site-packages (from tqdm->phy) (5.4.0) Requirement already satisfied: python-dateutil>=2.8.1 in ./.local/lib/python3.6/site-packages (from ghp-import>=1.0->mkdocs->phy) (2.8.2) Requirement already satisfied: zipp>=0.5 in ./.local/lib/python3.6/site-packages (from importlib-metadata->click->phy) (3.6.0) Requirement already satisfied: typing-extensions>=3.6.4 in ./.local/lib/python3.6/site-packages (from importlib-metadata->click->phy) (4.1.1) Requirement already satisfied: tornado>=4.2 in ./.local/lib/python3.6/site-packages (from ipykernel>=4.1->qtconsole->phy) (6.1) Requirement already satisfied: ipython>=5.0.0 in ./.local/lib/python3.6/site-packages (from ipykernel>=4.1->qtconsole->phy) (7.16.3) Requirement already satisfied: MarkupSafe>=2.0 in ./.local/lib/python3.6/site-packages (from Jinja2>=2.10.2->mkdocs->phy) (2.0.1) Requirement already satisfied: nest-asyncio>=1.5 in ./.local/lib/python3.6/site-packages (from jupyter-client>=4.1->qtconsole->phy) (1.5.5) Requirement already satisfied: entrypoints in ./.local/lib/python3.6/site-packages (from jupyter-client>=4.1->qtconsole->phy) (0.4) Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in /usr/lib/python3/dist-packages (from packaging>=20.5->mkdocs->phy) (2.2.0) Requirement already satisfied: PyQt5-Qt5>=5.15.2 in ./.local/lib/python3.6/site-packages (from PyQt5>=5.15.4->PyQtWebEngine->phy) (5.15.2) Requirement already satisfied: six in /usr/lib/python3/dist-packages (from traitlets->qtconsole->phy) (1.11.0) Requirement already satisfied: decorator in ./.local/lib/python3.6/site-packages (from traitlets->qtconsole->phy) (5.1.1) Requirement already satisfied: prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 in ./.local/lib/python3.6/site-packages (from ipython>=5.0.0->ipykernel>=4.1->qtconsole->phy) (3.0.30) Requirement already satisfied: pickleshare in ./.local/lib/python3.6/site-packages (from ipython>=5.0.0->ipykernel>=4.1->qtconsole->phy) (0.7.5) Requirement already satisfied: pexpect in /usr/lib/python3/dist-packages (from ipython>=5.0.0->ipykernel>=4.1->qtconsole->phy) (4.2.1) Requirement already satisfied: setuptools>=18.5 in /usr/local/lib/python3.6/dist-packages (from ipython>=5.0.0->ipykernel>=4.1->qtconsole->phy) (51.0.0) Requirement already satisfied: backcall in ./.local/lib/python3.6/site-packages (from ipython>=5.0.0->ipykernel>=4.1->qtconsole->phy) (0.2.0) Requirement already satisfied: jedi<=0.17.2,>=0.10 in ./.local/lib/python3.6/site-packages (from ipython>=5.0.0->ipykernel>=4.1->qtconsole->phy) (0.17.2) Requirement already satisfied: parso<0.8.0,>=0.7.0 in ./.local/lib/python3.6/site-packages (from jedi<=0.17.2,>=0.10->ipython>=5.0.0->ipykernel>=4.1->qtconsole->phy) (0.7.1) Requirement already satisfied: wcwidth in ./.local/lib/python3.6/site-packages (from prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0->ipython>=5.0.0->ipykernel>=4.1->qtconsole->phy) (0.2.5)

Any help? Thanks Guilhem

guilhemibos commented 2 years ago

Solved it by completely reinstalling everything from scratch.