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refactor read_zarr #982
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refactor read_zarr #982
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Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## zarrv3 #982 +/- ##
==========================================
+ Coverage 92.10% 92.12% +0.01%
==========================================
Files 48 48
Lines 7489 7467 -22
==========================================
- Hits 6898 6879 -19
+ Misses 591 588 -3
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LucaMarconato
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Sep 23, 2025
* changed pyproject to zarr>=3 * adjust dependencies * wip * more fixes * update ome-zarr dep * Add zarr v3 formats * refactoring formats * wip replace parse_url() with _open_zarr_store() * update way of writing transforms, update typehints * attempt fix consolidated metadata, fix channel names write * fix partial read tests * fix path * access name in group directly * fix read in consolidated metadata * initial ugly fix groups and consolidated metadata when deleting * fix reading back table * open group without using consolidated metadata when writing * revert adding labels * fix read / write issues with consolidated metadata * use_consolidated False when writing transforms * add ome_format arg * check valid element formats in container format * uncomment code arrayNotFoundError * remove future annotations import * update workflow mac version * drop python 3.10 version is not supported by zarr v3.0.8 * change target python version and readthedocs python version * minor updates * update Self import * fix ome errors * add windows workflow * prevent consolidation labels group when deleting element * add shapes test * fix shape conversion * update dask dependency because of zarr v3 * fix multipoly * fix invalid read name test * use UPath * fix paths * resolve paths * refactor overwrite transformations * refactor * further refactor, add docstrings * refactor io_raster * several refactors io * war on warnings * checks backward compatibility * correct test * further reduce warnings * remove log with no useful info * remove log as it is stated in doc string * move log to info in docstring * remove deprecated warning * get rid of categorical and str casting warnings * below 1000 warnings * further reduction of warnings * remove deprecated code * correct location for storing transforms * consistent naming * update according to ome-zarr-py * correct docstring * update docstring * remove todo * remove unassigned function call * refactor new _open_zarr_store to _resolve_zarr_store * silence zarr parquet warnings * change overwriting warning, silence in tests * silence overwriting warnings * silence chunk warning * remove argument from docstring, update typehint * update typehint * small fixes * fail if not root does not exist * write out function name * small fixes * initial replacement parse_url * alter docstring * adjust argument docstring * remove overwrite warnings * fix test * replace parse_url * change version * remove type hints from docstrings * refactor to one function * change typehint * remove typehints from docstring * remove type hint return in docstring * remove comment * ensure comment added back * fix channel metadata * get rid of TableValidateMixin * code fixes * fix * remove format without effect * remove unnecessary catch warnings * add todo * fixes * remove unnecessary .get('ome') * add clarifying comment * wip tests readwrite across formats * return None instead of AnnData * remove TODO * remove invalid characters from test * remove unused fixture and commented code * almost completed extending readwrite tests to all container versions * add OSError * partial fix writing empty spatialdata * fix type * fix overwrite when no zarr store * fix write element to empty directory location * correct no zarr store write test * remove unnecessary code * fix write_element * delete group isntead of .zattrs * remove parse_url * removed logger.ingo() and most of remaining warnings from tests * addressing review comments * addressed consolidate metadata comment * make full coverage of _validate_can_safely_write_to_path() easier to understand * restore partial read/write tests * minor changes in test_partial_read(); code review finished * support ome-zarr-py master * fix docs * ensure multiscales written correctly * refactor read_zarr (#982) * refactor read_zarr * remove unneccesary checks * Refactor zarrv3 (#986) * refactor read_zarr * remove unneccesary checks * emit warning with old spatialdata storage version detected * simplify code for writing (code review changes) * finished addressing review --------- Co-authored-by: Luca Marconato <[email protected]>
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This refactors the
read_zarr
function.