Polaris fails to locate zarr.DirectoryStore with Zarr 3.x installed (installed automatically by conda)

[FabianKruger]

Polaris version

0.7.9

Python Version

3.12.2

Operating System

Linux (Ubuntu 22.04.5 LTS (ARM architecture))

Installation

conda install -c conda-forge polaris

Description

Description:
When installing Polaris via conda, the dependency resolver automatically installs Zarr version 3.0.6. However, running polaris login results in an AttributeError because Polaris tries to access zarr.DirectoryStore, which is no longer available in Zarr 3.x. Also importing polaris in a script does not work. Downgrading to a Zarr 2.x version manually resolves the issue. A proper fix or explicit dependency version requirement would improve the package's user-friendliness.

Steps to reproduce

conda create -n polaris python=3.12
conda activate polaris
conda install -c conda-forge polaris
polaris login

Additional output

AttributeError: module 'zarr' has no attribute 'DirectoryStore'

[jstlaurent]

@FabianKruger : I see that you are running version 0.7.9 of Polaris. The newest version correctly sets the dependency as zarr >=2,<3, which avoids this issue. Try updating the Polaris version to the latest, and let me know if you're still experiencing the issue.

[FabianKruger]

Thanks for the quick answer @jstlaurent !
I tried updating Polaris in my conda environment (linux-aarch64) to the latest version (0.11.10) as suggested. However, conda failed to resolve dependencies because Polaris 0.11.10 now requires the package fastpdb, which doesn’t seem to be available for my platform through conda. Therefore it automatically falls back to version 0.79 (possible the last one without fastpdb). Installing fastpdb via pip did not resolve the issue with conda for me, but I could install the newest version of Polaris via pip.
I have attached the error below in case it is relevant. Feel free to close the issue.

Thanks for your help!

$ conda install -c conda-forge polaris=0.11.10
Channels:

• conda-forge
• defaults
  Platform: linux-aarch64
  Collecting package metadata (repodata.json): done
  Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:

• nothing provides fastpdb needed by polaris-0.11.10-pyhd8ed1ab_0

Could not solve for environment specs
The following package could not be installed
└─ polaris =0.11.10 * is not installable because it requires
└─ fastpdb =* *, which does not exist (perhaps a missing channel).

[jstlaurent]

Interesting... Let me check with folks on the team that know Conda better than I do. We'll figure something out for you.

As a temporary workaround for you, you might be able to define the dependency zarr >=2,<3 in you own project. That should force Conda to resolve it to Zarr 2, which Polaris should happily accept. There might however be some things broken in that older version of the client, unfortunately.

[FabianKruger]

Thanks for looking into it! I was able to get the newest Polaris version via pip, and it’s working fine for me now. Installing it via Conda didn’t work, but that’s not an issue on my end.

[jstlaurent]

For future reference: Given the interwoven nature of FastPDB in the code base, it's unfortunately impossible to make it an optional dependency. We're also not in control of that package's Conda publication strategy. If a similar situation recurs, the workaround will be to install Polaris through Pypi, instead of Conda.