From bd0bcfc9d8c08ab1ade602cca4c1f72949b75188 Mon Sep 17 00:00:00 2001 From: LucaMarconato <2664412+LucaMarconato@users.noreply.github.com> Date: Mon, 10 Feb 2025 17:33:56 +0100 Subject: [PATCH 1/7] Update pyproject.toml --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index 03b7e06..3381a22 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -37,6 +37,7 @@ dependencies = [ "python-dateutil", "spatial_image>=0.2.1", "xarray>=2024.10.0", + "xarray-dataclasses>=1.8.0", "zarr", ] From 5a0b451a04993653708fcb156b1b90486fa31c2a Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Tue, 11 Feb 2025 12:42:01 -0500 Subject: [PATCH 2/7] Remove home-page from pyproject.toml Invalid field. --- pyproject.toml | 1 - 1 file changed, 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 3381a22..5bf0770 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -8,7 +8,6 @@ description = "Generate a multiscale, chunked, multi-dimensional spatial image d authors = [{name = "Matt McCormick", email = "matt@mmmccormick.com"}] readme = "README.md" license.file = "LICENSE" -home-page = "https://github.com/spatial-image/multiscale-spatial-image" classifiers = [ "License :: OSI Approved :: Apache Software License", "Programming Language :: Python", From 54519926a910cb679244344c237b44b7ab1acee3 Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Tue, 11 Feb 2025 12:42:42 -0500 Subject: [PATCH 3/7] Update pixi.lock pixi install -a with pixi 0.40.2. --- pixi.lock | 3476 ++++++++++++++--------------------------------------- 1 file changed, 878 insertions(+), 2598 deletions(-) diff --git a/pixi.lock b/pixi.lock index 0850030..960167a 100644 --- a/pixi.lock +++ b/pixi.lock @@ -1,4 +1,4 @@ -version: 5 +version: 6 environments: data: channels: @@ -1827,25 +1827,15 @@ environments: - 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store: Union[MutableMapping, str, Path, BaseStore], + store: StoreLike, mode: str = "w", encoding=None, **kwargs, @@ -43,7 +49,7 @@ def to_zarr( Metadata is added according the OME-NGFF standard. - store : MutableMapping, str or Path, or zarr.storage.BaseStore + store : StoreLike Store or path to directory in file system mode : {{"w", "w-", "a", "r+", None}, default: "w" Persistence mode: “w” means create (overwrite if exists); “w-” means create (fail if exists); From fabcf2fe6420cd9d752e778c87e1cb519f8411ab Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Tue, 11 Feb 2025 14:04:53 -0500 Subject: [PATCH 5/7] COMP: Use LocalStore for Zarr Python 3 Replaces DirectoryStore. --- README.md | 8 ------- test/_data.py | 65 +++++++++++++++++++++++++++++++++++++-------------- 2 files changed, 47 insertions(+), 26 deletions(-) diff --git a/README.md b/README.md index bea4bdd..2c53e3b 100644 --- a/README.md +++ b/README.md @@ -153,14 +153,6 @@ method and `assign_coords`, equivalent to `xr.Dataset` `assign_coords` method. Store as an Open Microscopy Environment-Next Generation File Format ([OME-NGFF]) / [netCDF] [Zarr] store. -It is highly recommended to use `dimension_separator='/'` in the construction of -the Zarr stores. - -```python -store = zarr.storage.DirectoryStore('multiscale.zarr', dimension_separator='/') -multiscale.to_zarr(store) -``` - **Note**: The API is under development, and it may change until 1.0.0 is released. We mean it :-). diff --git a/test/_data.py b/test/_data.py index ff69a81..9247c4c 100644 --- a/test/_data.py +++ b/test/_data.py @@ -2,7 +2,6 @@ import pytest import pooch -from zarr.storage import DirectoryStore import xarray as xr test_data_ipfs_cid = "bafybeiaskr5fxg6rbcwlxl6ibzqhubdleacenrpbnymc6oblwoi7ceqzta" @@ -29,23 +28,41 @@ def input_images(): test_data.fetch("data.tar.gz", processor=untar) result = {} - store = DirectoryStore( - test_data_dir / "input" / "cthead1.zarr", dimension_separator="/" - ) + store_path = test_data_dir / "input" / "cthead1.zarr" + try: + from zarr.storage import DirectoryStore + + store = DirectoryStore(store_path, dimension_separator="/") + except ImportError: + from zarr.storage import LocalStore + + store = LocalStore(store_path) image_ds = xr.open_zarr(store) image_da = image_ds.cthead1 result["cthead1"] = image_da - store = DirectoryStore( - test_data_dir / "input" / "small_head.zarr", dimension_separator="/" - ) + store_path = test_data_dir / "input" / "small_head.zarr" + try: + from zarr.storage import DirectoryStore + + store = DirectoryStore(store_path, dimension_separator="/") + except ImportError: + from zarr.storage import LocalStore + + store = LocalStore(store_path) image_ds = xr.open_zarr(store) image_da = image_ds.small_head result["small_head"] = image_da - store = DirectoryStore( - test_data_dir / "input" / "2th_cthead1.zarr", - ) + store_path = test_data_dir / "input" / "2th_cthead1.zarr" + try: + from zarr.storage import DirectoryStore + + store = DirectoryStore(store_path, dimension_separator="/") + except ImportError: + from zarr.storage import LocalStore + + store = LocalStore(store_path) image_ds = xr.open_zarr(store) image_da = image_ds["2th_cthead1"] result["2th_cthead1"] = image_da @@ -54,10 +71,15 @@ def input_images(): def verify_against_baseline(dataset_name, baseline_name, multiscale): - store = DirectoryStore( - test_data_dir / f"baseline/{dataset_name}/{baseline_name}", - dimension_separator="/", - ) + store_path = test_data_dir / f"baseline/{dataset_name}/{baseline_name}" + try: + from zarr.storage import DirectoryStore + + store = DirectoryStore(store_path, dimension_separator="/") + except ImportError: + from zarr.storage import LocalStore + + store = LocalStore(store_path) dt = xr.open_datatree(store, engine="zarr", mode="r") xr.testing.assert_equal(dt.ds, multiscale.ds) for scale in multiscale.children: @@ -68,8 +90,15 @@ def store_new_image(dataset_name, baseline_name, multiscale_image): """Helper method for writing output results to disk for later upload as test baseline""" path = test_data_dir / f"baseline/{dataset_name}/{baseline_name}" - store = DirectoryStore( - str(path), - dimension_separator="/", - ) + try: + from zarr.storage import DirectoryStore + + store = DirectoryStore( + str(path), + dimension_separator="/", + ) + except ImportError: + from zarr.storage import LocalStore + + store = LocalStore(str(path)) multiscale_image.to_zarr(store, mode="w") From f2adcb6188a5b5716d39e9164a88baab082337f5 Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Tue, 11 Feb 2025 14:11:21 -0500 Subject: [PATCH 6/7] COMP: Remove dimension_deparator arg to MemoryStore Not available in Zarr Python 3. --- test/test_ngff_validation.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/test_ngff_validation.py b/test/test_ngff_validation.py index 0bc3e4c..73f7069 100644 --- a/test/test_ngff_validation.py +++ b/test/test_ngff_validation.py @@ -29,7 +29,7 @@ def load_schema(version: str = "0.4", strict: bool = False) -> Dict: def check_valid_ngff(multiscale: DataTree): - store = zarr.storage.MemoryStore(dimension_separator="/") + store = zarr.storage.MemoryStore() assert isinstance(multiscale.msi, MultiscaleSpatialImage) multiscale.msi.to_zarr(store, compute=True) zarr.convenience.consolidate_metadata(store) From 4e71dd4e05e8a5bac4a4eb0d6eb2e6c4a6d88ab8 Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Tue, 11 Feb 2025 14:19:49 -0500 Subject: [PATCH 7/7] Revert "Update pyproject.toml" This reverts commit bd0bcfc9d8c08ab1ade602cca4c1f72949b75188. --- pixi.lock | 12 +++++++++--- pyproject.toml | 1 - 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