Error: No such command 'template-gui'.

[Lildev0408]

Hello, I'm trying to get the phy works, but having no lucks. I created conda environment using the environment.yml file. I had an issue with scikit-learn installing. But I fixed it by installing scikit-learn first and the others (replaced order of the packages in the environment file). And I needed to install the 'traitlets' in addition to the provided yml. I'm using latest version of miniconda and python 3.11. In the macOS Ventura version 13 (M1 chip). When I try to run the phy, I keep get the error message of "Error: No such command 'template-gui'" I saw a comment that it should be fixed after PyQt5. But I think at some point, it tries to use PyQt4 which I don't have. I would really appreciate it if someone can help me out!

[zm711]

@Lildev0408 dev0408 what did you exactly type? did you activate your environment? the environment yaml definitely doesn't include python 3.11 so which dependencies did you include. For instance using numpy 1.24+ will fail because of #1193.

My guess is first type

conda activate phy2

Then try typing

phy template-gui params.py

In general template-gui is not a command by itself. It is an argument to be given after the phy command.

[brendonw1]

I have this same issue. I am able to type "phy" and I get this: _brendonw@LNX10027:~/analysis/Brendon/NicoletteEphys_ConcatenatedGroupDats$ phy Usage: phy [OPTIONS] COMMAND [ARGS]...

By default, the phy command does nothing. Add subcommands with plugins using attach_to_cli() and the click library.

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

... so I think I'm able to access phy itself But typing "phy template-gui params.py" (in the right folder, used auto-complete to make sure params. py was in there) gives: _brendonw@LNX10027:~/analysis/Brendon/NicoletteEphys_ConcatenatedGroupDats$ phy template-gui params.py Usage: phy [OPTIONS] COMMAND [ARGS]...

Error: No such command "template-gui"._

??

[zm711]

Did you install in base or a virtual environment? And are you using conda or not? Could you copy the whole output of the error here (straight from the terminal).

[brendonw1]

Thanks so much! Installed in base I think. I had someone do it for us, but I think these were the install commands: [root@LNX10027 ~]# pip install phy traitlets Collecting phy Downloading phy-1.0.9-py2.py3-none-any.whl (204 kB) |████████████████████████████████| 204 kB 2.2 MB/s Collecting traitlets Using cached traitlets-5.9.0-py3-none-any.whl (117 kB) Installing collected packages: phy, traitlets Successfully installed phy-1.0.9 traitlets-5.9.0 [root@LNX10027 python3.8]# sed -i 's/np.float,/float,/; s/np.int,/int,/; s/np.bool/bool/' /usr/local/lib/python3.8/dist-packages/phy/utils/_types.py

no conda or source activate here And shown above is the full terminal output actually

[brendonw1]

Essentially we followed instructions on the front of this github repo webpage but had to compensate for some things not working. including "pre" causing errors for one thing

[zm711]

The official instructions are to install by typing: pip install phy --pre --upgrade (your install is missing the --pre --upgrade). So I would actually start with that.

Is there a reason why you don't want to use a virtual environment? Phy hasn't been updated for a while so it might be safer to keep it isolated from your base python install using a conda env or one of the python virtual envs. (I'm a conda user personally so it's easier for me to give conda recs vs python environment recs).

In that case what error did pre cause?

[brendonw1]

Again, appreciated We just went by the front page instructions here: https://github.com/cortex-lab/phy#installation-instructions

I didn't see anything about environments, but are there better instructions elsewhere? I'm on Ubuntu 20.04 (bc managed by my institution)

Using --pre produces tons of output but ends with the following:

Collecting PyQtWebEngine-Qt5>=5.15.0 Using cached PyQtWebEngine_Qt5-5.15.2-py3-none-manylinux2014_x86_64.whl (67.5 MB) Collecting PyQt5>=5.15.4 Using cached PyQt5-5.15.9.tar.gz (3.2 MB) Installing build dependencies ... done Getting requirements to build wheel ... done Preparing wheel metadata ... error ERROR: Command errored out with exit status 1: command: /usr/bin/python3 /tmp/tmpgm62_bkp prepare_metadata_for_build_wheel /tmp/tmp_z8sfes3 cwd: /tmp/pip-install-_9o80yd1/PyQt5 Complete output (31 lines): Traceback (most recent call last): File "/tmp/tmpgm62_bkp", line 126, in prepare_metadata_for_build_wheel hook = backend.prepare_metadata_for_build_wheel AttributeError: module 'sipbuild.api' has no attribute 'prepare_metadata_for_build_wheel'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/tmpgm62_bkp", line 280, in <module>
    main()
  File "/tmp/tmpgm62_bkp", line 263, in main
    json_out['return_val'] = hook(**hook_input['kwargs'])
  File "/tmp/tmpgm62_bkp", line 130, in prepare_metadata_for_build_wheel
    return _get_wheel_metadata_from_wheel(backend, metadata_directory,
  File "/tmp/tmpgm62_bkp", line 159, in _get_wheel_metadata_from_wheel
    whl_basename = backend.build_wheel(metadata_directory, config_settings)
  File "/tmp/pip-build-env-k7a2g0e3/overlay/lib/python3.8/site-packages/sipbuild/api.py", line 46, in build_wheel
    project = AbstractProject.bootstrap('wheel',
  File "/tmp/pip-build-env-k7a2g0e3/overlay/lib/python3.8/site-packages/sipbuild/abstract_project.py", line 87, in bootstrap
    project.setup(pyproject, tool, tool_description)
  File "/tmp/pip-build-env-k7a2g0e3/overlay/lib/python3.8/site-packages/sipbuild/project.py", line 586, in setup
    self.apply_user_defaults(tool)
  File "/tmp/pip-install-_9o80yd1/PyQt5/project.py", line 68, in apply_user_defaults
    super().apply_user_defaults(tool)
  File "/tmp/pip-build-env-k7a2g0e3/overlay/lib/python3.8/site-packages/pyqtbuild/project.py", line 70, in apply_user_defaults
    super().apply_user_defaults(tool)
  File "/tmp/pip-build-env-k7a2g0e3/overlay/lib/python3.8/site-packages/sipbuild/project.py", line 237, in apply_user_defaults
    self.builder.apply_user_defaults(tool)
  File "/tmp/pip-build-env-k7a2g0e3/overlay/lib/python3.8/site-packages/pyqtbuild/builder.py", line 69, in apply_user_defaults
    raise PyProjectOptionException('qmake',
sipbuild.pyproject.PyProjectOptionException
----------------------------------------

ERROR: Command errored out with exit status 1: /usr/bin/python3 /tmp/tmpgm62_bkp prepare_metadata_for_build_wheel /tmp/tmp_z8sfes3 Check the logs for full command output.

[zm711]

Again, appreciated We just went by the front page instructions here: https://github.com/cortex-lab/phy#installation-instructions

It's more about python best practices. For most python packages it's best to store them in a virtual environment (for example if you have NumPy>=1.24 in your base environment it will break Phy. But if you have a virtual environment you can force that environment to have <1.24 so that you don't break Phy. If you don't want to use conda maybe read up a bit here: https://docs.python.org/3/library/venv.html. They actually use to include instructions on how to put Phy2 into a virtual environment, but I think at some point they figured people would just do it themselves (which is a shame in my opinion).

ERROR: Command errored out with exit status 1: /usr/bin/python3 /tmp/tmpgm62_bkp prepare_metadata_for_build_wheel /tmp/tmp_z8sfes3 Check the logs for full command output.

So this is saying that the metadata isn't correct, so a couple of the packages aren't playing well together (ie the PyQt5 that is being downloaded either isn't happy with your pip, your python, or the 20.04)

You could start by trying to update pip (to make sure it's up-to-date):

pip install --upgrade pip

If updating pip doesn't fix things you'll probably have to read up on your ubuntu version and try to figure out which package is messing things up. To make the virtual env with the "correct" packages they do include the requirements.txt file https://github.com/cortex-lab/phy/blob/master/requirements.txt But unfortunately it doesn't work super well, since they haven't pinned their version numbers (like NumPy that I mentioned above).

Their recommendation for python in the requirements.txt is 3.7 so if changing pip doesn't work you could also try install 3.7 to see if that helps with version numbering between the packages. (again with a venv or conda you can easily specify which python version you want).

[brendonw1]

Thank you. pip install --upgrade pip was successful but didn't fix the problems either with installation or running template-gui :(

I guess we'll keep digging

[zm711]

@brendonw1

Just as an FYI, the package has been updated to allow for python 3.11 and numpy 1.24. You could try reinstalling on your ubuntu system if you wanted. Took a spell, but if you're still trying to work with Phy great chance to try again. You could use the below command to automatically do everything for you (if you use conda)

conda create env -f environment.yml

[brendonw1]

Oh thanks so much. I think we started with a new box and it's working well since then. Much appreciated B

Brendon Watson, MD-PhD Assistant Professor in Psychiatry, Bioinformatics and Biomedical Engineering

Biomedical Sciences Research Building, Room 5059 University of Michigan 109 Zina Pitcher Place Ann Arbor, MI 48109-5720 Lab Website: http://watsonneurolab.org Clinical phone: 734-764-0231

On Sat, Aug 5, 2023 at 12:13 PM Zach McKenzie @.***> wrote:

@brendonw1 https://github.com/brendonw1

Just as an FYI, the package has been updated to allow for python 3.11 and numpy 1.24. You could try reinstalling on your ubuntu system if you wanted. Took a spell, but if you're still trying to work with Phy great chance to try again. You could use the below command to automatically do everything for you (if you use conda)

conda create env -f environment.yml

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