ngio 0.3.3__py3-none-any.whl → 0.3.5__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (8) hide show
  1. ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py +3 -12
  2. ngio/tables/backends/__init__.py +2 -1
  3. ngio/tables/backends/_anndata.py +9 -0
  4. ngio/tables/backends/_table_backends.py +3 -2
  5. {ngio-0.3.3.dist-info → ngio-0.3.5.dist-info}/METADATA +10 -10
  6. {ngio-0.3.3.dist-info → ngio-0.3.5.dist-info}/RECORD +8 -8
  7. {ngio-0.3.3.dist-info → ngio-0.3.5.dist-info}/WHEEL +0 -0
  8. {ngio-0.3.3.dist-info → ngio-0.3.5.dist-info}/licenses/LICENSE +0 -0
ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py CHANGED
@@ -21,21 +21,12 @@ from ngio.utils import NgioValueError, ngio_logger
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  def path_in_well_validation(path: str) -> str:
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  """Validate the path in the well."""
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- if path.find("_") != -1:
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- # Remove underscores from the path
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- # This is a custom serialization step
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- old_value = path
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- path = path.replace("_", "")
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- ngio_logger.warning(
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- f"Underscores in well-paths are not allowed. "
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- f"Path '{old_value}' was changed to '{path}'"
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- f" to comply with the specification."
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- )
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  # Check if the value contains only alphanumeric characters
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  if not path.isalnum():
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- raise NgioValueError(
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+ ngio_logger.warning(
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  f"Path '{path}' contains non-alphanumeric characters. "
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- f"Only alphanumeric characters are allowed."
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+ "This may cause issues with some tools. "
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+ "Consider using only alphanumeric characters in the path."
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  )
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  return path
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ngio/tables/backends/__init__.py CHANGED
@@ -1,7 +1,7 @@
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  """Ngio Tables backend implementations."""
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  from ngio.tables.backends._abstract_backend import AbstractTableBackend, BackendMeta
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- from ngio.tables.backends._anndata import AnnDataBackend
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+ from ngio.tables.backends._anndata import AnnDataBackend, AnnDataBackendV1
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  from ngio.tables.backends._csv import CsvTableBackend
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  from ngio.tables.backends._json import JsonTableBackend
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  from ngio.tables.backends._parquet import ParquetTableBackend
@@ -31,6 +31,7 @@ from ngio.tables.backends._utils import (
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  __all__ = [
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  "AbstractTableBackend",
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  "AnnDataBackend",
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+ "AnnDataBackendV1",
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  "BackendMeta",
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  "CsvTableBackend",
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  "DefaultTableBackend",
ngio/tables/backends/_anndata.py CHANGED
@@ -75,3 +75,12 @@ class AnnDataBackend(AbstractTableBackend):
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  index_key=self.index_key,
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  )
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  self.write_from_anndata(anndata)
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+
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+
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+ class AnnDataBackendV1(AnnDataBackend):
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+ """A wrapper for the AnnData backend that for backwards compatibility."""
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+
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+ @staticmethod
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+ def backend_name() -> str:
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+ """Return the name of the backend."""
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+ return "anndata_v1"
ngio/tables/backends/_table_backends.py CHANGED
@@ -7,7 +7,7 @@ from pandas import DataFrame
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  from polars import DataFrame as PolarsDataFrame
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  from polars import LazyFrame
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- from ngio.tables.backends._anndata import AnnDataBackend
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+ from ngio.tables.backends._anndata import AnnDataBackend, AnnDataBackendV1
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  from ngio.tables.backends._csv import CsvTableBackend
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  from ngio.tables.backends._json import JsonTableBackend
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  from ngio.tables.backends._parquet import ParquetTableBackend
@@ -213,7 +213,8 @@ class ImplementedTableBackends:
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  )
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- ImplementedTableBackends().add_backend(AnnDataBackend, aliases=["anndata_v1"])
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+ ImplementedTableBackends().add_backend(AnnDataBackend)
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+ ImplementedTableBackends().add_backend(AnnDataBackendV1)
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  ImplementedTableBackends().add_backend(
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  JsonTableBackend, aliases=["experimental_json_v1"]
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  )
{ngio-0.3.3.dist-info → ngio-0.3.5.dist-info}/METADATA RENAMED
@@ -1,9 +1,9 @@
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  Metadata-Version: 2.4
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  Name: ngio
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- Version: 0.3.3
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+ Version: 0.3.5
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  Summary: Next Generation file format IO
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- Project-URL: homepage, https://github.com/fractal-analytics-platform/ngio
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- Project-URL: repository, https://github.com/fractal-analytics-platform/ngio
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+ Project-URL: homepage, https://github.com/BioVisionCenter/ngio
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+ Project-URL: repository, https://github.com/BioVisionCenter/ngio
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  Author-email: Lorenzo Cerrone <lorenzo.cerrone@uzh.ch>
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  License: BSD-3-Clause
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  License-File: LICENSE
@@ -16,7 +16,7 @@ Classifier: Programming Language :: Python :: 3.13
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  Classifier: Typing :: Typed
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  Requires-Python: <3.14,>=3.11
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  Requires-Dist: aiohttp
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- Requires-Dist: anndata>=0.8.0
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+ Requires-Dist: anndata<0.11.4,>=0.8.0
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  Requires-Dist: dask[array]
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  Requires-Dist: dask[distributed]
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  Requires-Dist: filelock
@@ -65,11 +65,11 @@ Description-Content-Type: text/markdown
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  # Ngio - Next Generation file format IO
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- [![License](https://img.shields.io/pypi/l/ngio.svg?color=green)](https://github.com/lorenzocerrone/ngio/raw/main/LICENSE)
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+ [![License](https://img.shields.io/pypi/l/ngio.svg?color=green)](https://github.com/BioVisionCenter/ngio/raw/main/LICENSE)
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  [![PyPI](https://img.shields.io/pypi/v/ngio.svg?color=green)](https://pypi.org/project/ngio)
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  [![Python Version](https://img.shields.io/pypi/pyversions/ngio.svg?color=green)](https://python.org)
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- [![CI](https://github.com/fractal-analytics-platform/ngio/actions/workflows/ci.yml/badge.svg)](https://github.com/fractal-analytics-platform/ngio/actions/workflows/ci.yml)
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- [![codecov](https://codecov.io/gh/fractal-analytics-platform/ngio/graph/badge.svg?token=FkmF26FZki)](https://codecov.io/gh/fractal-analytics-platform/ngio)
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+ [![CI](https://github.com/BioVisionCenter/ngio/actions/workflows/ci.yml/badge.svg)](https://github.com/BioVisionCenter/ngio/actions/workflows/ci.yml)
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+ [![codecov](https://codecov.io/gh/BioVisionCenter/ngio/graph/badge.svg?token=FkmF26FZki)](https://codecov.io/gh/BioVisionCenter/ngio)
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  ngio is a Python library designed to simplify bioimage analysis workflows, offering an intuitive interface for working with OME-Zarr files.
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@@ -89,7 +89,7 @@ Ngio's mission is to streamline working with OME-Zarr files by providing a simpl
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  ### 🔍 Rich Tables and Regions of Interest (ROI) Support
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  - Extract and analyze specific regions of interest
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- - Tight integration with [Tabular Data](https://fractal-analytics-platform.github.io/ngio/stable/table_specs/overview/)
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+ - Tight integration with [Tabular Data](https://BioVisionCenter.github.io/ngio/stable/table_specs/overview/)
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  ### 🔄 Scalable Data Processing (Coming Soon)
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@@ -104,7 +104,7 @@ You can install ngio via pip:
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  pip install ngio
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  ```
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- To get started check out the [Quickstart Guide](https://fractal-analytics-platform.github.io/ngio/stable/getting_started/0_quickstart/).
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+ To get started check out the [Quickstart Guide](https://BioVisionCenter.github.io/ngio/stable/getting_started/0_quickstart/).
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  ## Supported OME-Zarr versions
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@@ -136,4 +136,4 @@ Ngio is developed at the [BioVisionCenter](https://www.biovisioncenter.uzh.ch/en
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  ## License
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- Ngio is released under the BSD-3-Clause License. See [LICENSE](https://github.com/fractal-analytics-platform/ngio/blob/main/LICENSE) for details.
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+ Ngio is released under the BSD-3-Clause License. See [LICENSE](https://github.com/BioVisionCenter/ngio/blob/main/LICENSE) for details.
{ngio-0.3.3.dist-info → ngio-0.3.5.dist-info}/RECORD RENAMED
@@ -25,7 +25,7 @@ ngio/ome_zarr_meta/ngio_specs/__init__.py,sha256=05NQukZG0nNvjzf8AKWGu7PhjhQcImG
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  ngio/ome_zarr_meta/ngio_specs/_axes.py,sha256=tHtx6NfBgDcCgDk9CosjIjw1KZJ2qi0i_eoLgrdiEWw,16681
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  ngio/ome_zarr_meta/ngio_specs/_channels.py,sha256=Jwys1yYC8q6_gIaJ52KcKcTP7hzqVjBE-VlVQvJurCs,15394
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  ngio/ome_zarr_meta/ngio_specs/_dataset.py,sha256=hY8ogPPxvCgVg6k02t3zUr24lasYrvnxBd1iPEigdG4,5892
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- ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py,sha256=uh345KQmEQtslIyMmLK9sB-NbjPYxi0Y9FuYIFhd3Rc,17465
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+ ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py,sha256=R8F7Wkhpo1YqG2gWWwGUJflILo6gsowJg8eVXYdMxdw,17146
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  ngio/ome_zarr_meta/ngio_specs/_ngio_image.py,sha256=8E38Mgw-l0Ff1nkmCJIzo64G_paAVhM8xktUS_V5egY,17960
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  ngio/ome_zarr_meta/ngio_specs/_pixel_size.py,sha256=5TT8250XdCKUnk3OwZeyXIMNFKOg_jx4NnoCo9RLsXI,4079
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  ngio/ome_zarr_meta/v04/__init__.py,sha256=dJRzzxyYc81kf-0Hip_bqvbdManaM8XTdQX2meWyCSs,583
@@ -34,15 +34,15 @@ ngio/ome_zarr_meta/v04/_v04_spec_utils.py,sha256=05tEr2eEP_XVIfBMOAWLT7lzJV4KS5e
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  ngio/tables/__init__.py,sha256=_BV3sclNMLITu_J8_3DkkUrCB6Kro0HzeWLDCD1ivKM,877
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  ngio/tables/_abstract_table.py,sha256=rwGa47TzbFmosucBWVfFq6JEXtgGvOdUVtU9DIelV88,8204
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  ngio/tables/_tables_container.py,sha256=3xmpREaN671l40MPprnl1BD-VoOb6xfjECb5mNoMW0w,12173
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- ngio/tables/backends/__init__.py,sha256=nQZVazwTL1IHU08gL-BZcFZd7Cehhbc_AsJ3t3XSps0,1577
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+ ngio/tables/backends/__init__.py,sha256=MwSRXNF1rWQBFOTDA_vT3oGoNZpviVgytsL5Txnu08I,1619
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  ngio/tables/backends/_abstract_backend.py,sha256=tsbHzSPTX88fiCbVc8khXv5aN68ck6HKG8r5OHkY3S8,7457
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- ngio/tables/backends/_anndata.py,sha256=8RX2NO15CLxys3p6gw54Nd-_0WATU4WBlNndX06wvzI,2587
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+ ngio/tables/backends/_anndata.py,sha256=0r6zOP9Nm9VVpKLB1-xZTId-e7VFJ6EGYhFSoAIylik,2831
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  ngio/tables/backends/_anndata_utils.py,sha256=DBWIcR0btnH-DIvDvzlcnMXoYhhtXc9DstryiOP0Qsg,3122
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  ngio/tables/backends/_csv.py,sha256=Ev61D-AUKo4LIhXRmWPJgYbHI7eQdxiajQR574DevEM,932
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  ngio/tables/backends/_json.py,sha256=1ZsEuXDJm1rOZV_KjFm8CB0qhv7L1W7L2EGWPf4q_p0,3137
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  ngio/tables/backends/_non_zarr_backends.py,sha256=SvPPhT6n5TrKUOyV1mNcdHQK49huZ5lwR8EVe9MdydM,7254
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  ngio/tables/backends/_parquet.py,sha256=ic-p86h8lce8q9luBJGRzy6vxlWyJvA0-2l5cUD6OqY,1398
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- ngio/tables/backends/_table_backends.py,sha256=QUS59VU395966AEul2SNJQAzklSitvISL0wnZTKWZa0,7267
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+ ngio/tables/backends/_table_backends.py,sha256=56lMLrkmRS8-NTwNF0wkMzrRwTmOFLk1g_LBDA2i6wg,7318
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  ngio/tables/backends/_utils.py,sha256=tJBSWN6OhO_1ybxl4vT2l3ImB028Fb6h0vaitPRcr8A,19668
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  ngio/tables/v1/__init__.py,sha256=Wr1_9RZFpaN8FYMTnxT9Yjkw4AS7y9FMWailmB_uj5g,617
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  ngio/tables/v1/_condition_table.py,sha256=T0Uq5BKkmMoEspt_Rx0U99Ow6S9GAMZDHqvUO5obCAM,1780
@@ -55,7 +55,7 @@ ngio/utils/_errors.py,sha256=pKQ12LUjQLYE1nUawemA5h7HsgznjaSvV1n2PQU33N0,759
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  ngio/utils/_fractal_fsspec_store.py,sha256=RdcCFOgHexRKX9zZvJV5RI-5OPc7VOPS6q_IeRxm24I,1548
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  ngio/utils/_logger.py,sha256=HIuqD_2ShfFGDswBddcouStbKfL0Vz_ah8cAIFGhbS8,888
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  ngio/utils/_zarr_utils.py,sha256=qOI-HL2HsfFLCj_yxsTR-aq4oHpSqS9KR13aEIvhGDY,13593
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- ngio-0.3.3.dist-info/METADATA,sha256=R88An5Xll3DjctQyVOwJKH7Z0DaNpefeehYOqH79FoE,5868
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- ngio-0.3.3.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
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- ngio-0.3.3.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
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- ngio-0.3.3.dist-info/RECORD,,
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+ ngio-0.3.5.dist-info/METADATA,sha256=hOkz1FyqV41g-YgwZrtgDSZ18HxApONqsl1aoSxrZGM,5778
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+ ngio-0.3.5.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
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+ ngio-0.3.5.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
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+ ngio-0.3.5.dist-info/RECORD,,
{ngio-0.3.3.dist-info → ngio-0.3.5.dist-info}/WHEEL RENAMED
File without changes