webknossos-libs

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Expose squeue polling interval to SlurmExecutor parameter and allow setting via env variable

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Hi, we regularly run into problems with our SLURM cluster while running (very) large downsampling jobs on webknossos datasets either via CLI or chunk-wise processing of large datasets via the...

erjel

I cannot read datasets created with version 0.14.25 onward with version 0.14.24. Error message: ``` >>> import webknossos as wk >>> wk.Dataset.open('my_newer_dataset') + Exception Group Traceback (most recent call last):...

erjel

### Description: - Add a CLI for copy_dataset ### Todos: Make sure to delete unnecessary points or to check all before merging: - [x] Updated Changelog - [x] Updated Documentation...

normanrz

`RemoteDataset.explore_and_add_remote` seems to be not working

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## Context - Affected library: webknossos With the current version of wklibs I cannot add a remote dataset via `RemoteDataset.explore_and_add_remote` as this leads to a crash. The reason for the...

MichaelBuessemeyer

### Description: - Deprecates `chunks_per_shard` in favor of `shard_shape` - Deprecates `dtype_per_layer` in favor of `dtype_per_channel` ### Todos: Make sure to delete unnecessary points or to check all before merging:...

normanrz

Make Zarr3 default and deprecations

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### Description: - Makes Zarr3 the default data format - Removes deprecated functions, properties, arguments - Changes the writing behavior to include a `allow_resize` and `allow_unaligned` argument to make it...

normanrz

Add regression test for fix of PR #1256. This needs to be done in a separate pr as I cannot get the test working and it is important to merge...

MichaelBuessemeyer

Saw exception in Dataset.from_images called with a tif file. Stack trace: ``` Traceback (most recent call last): File "/usr/local/lib/python3.11/concurrent/futures/process.py", line 261, in _process_worker r = call_item.fn(*call_item.args, **call_item.kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "site-packages/cluster_tools/executors/multiprocessing_.py",...

fm3

Major version

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We are aiming for the next major release of the `webknossos` and `cluster_tools` packages. Since, the cluster_tools already use 1.x packages, we should jump to 2.x directly. TODO (tbd): -...

normanrz

### Description: - This PR collects all deprecations and changes for the release of version 2.0 ### Issues: - fixes #1200 ### Todos: - [x] Deprecations for cluster tools -...

markbader