Can't open a read-only dataset

[hyanwong]

I'm getting errors with this:

sc2ts/sc2ts/dataset.py", line 261, in init
  self.store = zarr.ZipStore(path)

According to chatGPT:

zarr.ZipStore is trying to open the ZIP file in a mode that requires write access.
Your plain open(...) succeeds because the default mode for open() is read-only ("r"). But zarr.ZipStore(...)defaults to append/update mode > (mode="a"), which requires write permission on the file.

[jeromekelleher]

None of this should have changed if we're using the pinned software from the pipeline. I don't understand what's happening here.

[jeromekelleher]

Is sc2ts pulling in Zarr v3 now instead of v2?

[hyanwong]

 conda activate sc2ts
(sc2ts) [sbk774@cloudcomp100 ~]$ python
Python 3.12.11 | packaged by conda-forge | (main, Jun  4 2025, 14:45:31) [GCC 13.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import zarr
zarr.__version>>> zarr.__version__
'2.18.7'

But possibly you were previously running it where you had write access to viridian_mafft_2024-10-14_v1.vcz.zip? I'm running it within Shing's folder, and I only have read access to that file.

[jeromekelleher]

Ah I see - I didn't get that detail. Yeah, we should be opening the ZipStore in mode="r".