Joblib compablity/ update enviroment yml

[Einsied]

Hello together,
it seems that joblib has removed the bytes_limit keyword without incrementing the major as semver would suggest.

This breaks set_memory in context.

This would be a good opprotunity to check the enviroment.yml and freeze the dependencies at their current version, to prevent this in the future.

Cheers
Einsied

[ryan-budde]

We fixed this with
pip uninstall joblib
pip install joblib==1.4.2

[Einsied]

Thank you @ryan-budde .

I (mis)posted my temporary solution in the pull request, instead of my issue, for which I am sorry.
I went with conda install joblib=1.4.2, to ensure the dependency management stays within conda.
I think both should work out the same.

[allllex3202]

We fixed this with pip uninstall joblib pip install joblib==1.4.2
Thank you Ryan, I'm able to open phy2 with this change,
but error will showup as :
QMimeDatabase: Error loading internal MIME data
An error has been encountered at line 1 of : Premature end of document.:

Which may clean up the contents in cluster_group.txt, do you have similar issue?

[Einsied]

@allllex3202
Did you stumble over: (https://stackoverflow.com/questions/74469839/qmimedatabase-error-opencv-premature-end-of-document#75878574 ).

Also does the problem persist with anaconda and would you like a frozen env to compare versions and spot potential incompabilities?

Cheers
Einsied

[caroll675]

I have luck with installing dependencies with uv. Here's my pyproject.toml file:

[project]
name = "phy2"
version = "0.1.0"
description = "Environment for phy2 analysis"
readme = "README.md"
requires-python = ">=3.11"
dependencies = [
    "cython",
    "dask",
    "h5py",
    "joblib==1.2.0", #Here
    "matplotlib",
    "numpy",
    "phy",
    "pillow",
    "pip",
    "pyopengl",
    "pyqt5==5.15.7", #Here
    "pyqt5-qt5==5.15.2", #Here
    "pyqtwebengine-qt5==5.15.2", #And Here (these are for windows compatibility)
    "pytest",
    "qtconsole",
    "requests",
    "responses",
    "scikit-learn",
    "scipy",
    "traitlets",
]

[tool.uv.sources]
phy = { git = "https://github.com/cortex-lab/phy.git" }

[allllex3202]

Thank you so much guys, it is the dependencies issue that causes the error, and the uv method by caroll works perfectly for me.

[Einsied]

@caroll675
Is it okay for you if I add the version numbers to my pull request or do you prefer to make your own?

[caroll675]

@Einsied I can add UV support with all the dependencies version number + a short readme section if you prefer :)

On a side note, would you consider publishing the package to uv tool registry? I think if the users can just uvx phy or uv tool install phy to use it locally it would be much simpler for people.

[Einsied]

@caroll675 that would be quite nice.
I cloned to https://github.com/Einsied/phy/tree/hotfix-joblib the changes could be implemented there, before a merge.

I just left the airport and could not read up on uv, but I assume we should keep the package up to date, so I would prefer if the owners of this repository merge the change instead of creating a fork I may not be able to maintain if funding for my current position dries up.

[caroll675]

@Einsied Oh in that case you can just add the requirement in your PR; don't know if the maintainers want to switch package managers. Thanks!

[Einsied]

@caroll675 I tried to contact them, hope they respond next week.

Good I will try to add your handle to the commit message if that is fine with you.

[junQree]

Hi,

I have been struggling for a day now, trying to get the phy2 environment working.
I can't get un sync to work with @caroll675 's pyproject.toml.

x No solution found when resolving dependencies:
`-> Because only phy==2.0b6 is available and phy==2.0b6 depends on joblib==1.4.2, we can conclude that all versions of phy depend on joblib==1.4.2.
And because your project depends on joblib==1.2.0 and phy, we can conclude that your project's requirements are unsatisfiable.

Has anybody found a work around that works?