Demo zarr does not work
maweigert opened this issue · 7 comments
Hi,
It appears that in the current versions (0.5.0 and main) the opening of the demo url does not work anymore:
napari "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.3/9836842.zarr/"
yields
napari.errors.reader_errors.NoAvailableReaderError: No plugin found capable of reading https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.3/9836842.zarr/
versions:
napari : 0.4.16
zarr : 2.11.3
napari_ome_zarr : 0.5.1.dev4+g4e506d
Thanks @maweigert, we also noticed that the napari-ome-zarr plugin is currently broken with the latest and recent versions of napari - see #55 (comment). We are still unsure where this regression comes from
Also tried to downgrade to former version of the plugin and/or napari but the plugin is still not registered by the plugin engine
(napari) sbesson@Sebastiens-MacBook-Pro ~ % napari --version
/Users/sbesson/miniconda3/envs/napari/lib/python3.10/site-packages/napari/__main__.py:423: UserWarning: pythonw executable not found.
To unfreeze the menubar on macOS, click away from napari to another app, then reactivate napari. To avoid this problem, please install python.app in conda using:
conda install -c conda-forge python.app
warnings.warn(msg)
napari version 0.4.12
(napari) sbesson@Sebastiens-MacBook-Pro ~ % pip freeze | grep napari
napari @ file:///home/conda/feedstock_root/build_artifacts/napari_1634857948574/work
napari-console @ file:///home/conda/feedstock_root/build_artifacts/napari-console_1644771676323/work
napari-ome-zarr==0.4.0
napari-plugin-engine @ file:///home/conda/feedstock_root/build_artifacts/napari-plugin-engine_1637358573066/work
napari-svg @ file:///home/conda/feedstock_root/build_artifacts/napari-svg_1652348013801/work
(napari) sbesson@Sebastiens-MacBook-Pro ~ % napari --plugin-info
/Users/sbesson/miniconda3/envs/napari/lib/python3.10/site-packages/napari/__main__.py:423: UserWarning: pythonw executable not found.
To unfreeze the menubar on macOS, click away from napari to another app, then reactivate napari. To avoid this problem, please install python.app in conda using:
conda install -c conda-forge python.app
warnings.warn(msg)
PluginManager for "napari"
(12 hook specs and 4 plugins)
---------------------------------------------
builtins v0.4.12 6 hooks
- napari_get_reader
- napari_get_writer
- napari_write_image
- napari_write_labels
- napari_write_points
- napari_write_shapes
console v0.0.4 0 hooks
scikit-image v0.4.12 1 hooks
- napari_provide_sample_data
svg v0.1.6 6 hooks
- napari_get_writer
- napari_write_image
- napari_write_labels
- napari_write_points
- napari_write_shapes
- napari_write_vectors
Blocked Plugins:
----------------
napari-svg
napari-ome-zarr
napari
(napari) sbesson@Sebastiens-MacBook-Pro ~ % cat napari.yml
name: napari
channels:
- conda-forge
- defaults
dependencies:
- "napari<0.4.13"
- pip
- pip:
- "napari-ome-zarr<0.5"
Hi team, reproducing my response from this comment here for visibility:
The URL does not open because it does not match the provided filename_pattern due to the trailing /. Essentially, running napari "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.3/9836842.zarr" (note no trailing slash) works as expected. To remedy this, you could update your example to remove the trailing slash, or update your napari.yaml to add a dedicated pattern for remote URLs e.g.
name: napari-ome-zarr
schema_version: 0.1.0
contributions:
commands:
- id: napari-ome-zarr.get_reader
title: Get Reader
python_name: napari_ome_zarr._reader:napari_get_reader
readers:
- command: napari-ome-zarr.get_reader
filename_patterns:
- "*.zarr"
- "https://*.zarr/"
accepts_directories: true
PS - What a gorgeous example 😍
@maweigert can you confirm removing the trailing slash fixes your issue? #55 should also add support for URIs with trailing slash in the upcoming release of the napari-ome-zarr plugin
Hi All,
thanks for looking into this!
@maweigert can you confirm removing the trailing slash fixes your issue
Yes, that was it! it does work without the trailing slash. Thanks!
Additionally, when using the branch in PR #55 it does work again with the trailing slash. As I assume this will be merged, I am closing now :)
Thanks for the feedback, @maweigert!