ngio 0.2.9__py3-none-any.whl → 0.3.0a1__py3-none-any.whl

{ngio-0.2.9.dist-info → ngio-0.3.0a1.dist-info}/METADATA

@@ -1,9 +1,9 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.2.9
+Version: 0.3.0a1
 Summary: Next Generation file format IO
-Project-URL: homepage, https://github.com/lorenzocerrone/ngio
-Project-URL: repository, https://github.com/lorenzocerrone/ngio
+Project-URL: homepage, https://github.com/fractal-analytics-platform/ngio
+Project-URL: repository, https://github.com/fractal-analytics-platform/ngio
 Author-email: Lorenzo Cerrone <lorenzo.cerrone@uzh.ch>
 License: BSD-3-Clause
 License-File: LICENSE
@@ -50,6 +50,7 @@ Requires-Dist: mkdocs; extra == 'docs'
 Requires-Dist: mkdocs-autorefs; extra == 'docs'
 Requires-Dist: mkdocs-git-committers-plugin-2; extra == 'docs'
 Requires-Dist: mkdocs-git-revision-date-localized-plugin; extra == 'docs'
+Requires-Dist: mkdocs-include-markdown-plugin; extra == 'docs'
 Requires-Dist: mkdocs-jupyter; extra == 'docs'
 Requires-Dist: mkdocs-material; extra == 'docs'
 Requires-Dist: mkdocstrings[python]; extra == 'docs'

{ngio-0.2.9.dist-info → ngio-0.3.0a1.dist-info}/RECORD

@@ -1,5 +1,5 @@
 ngio/__init__.py,sha256=zce-RIfRhkiFyfKwO6s7A1-9ZCD3n6RuVuW3GeRj_VA,1309
-ngio/common/__init__.py,sha256=tMKp1eZzGfpdKDkpfHn0iVzSO11dmp-RZARpuxoGGQk,1351
+ngio/common/__init__.py,sha256=BttXCAV2ks6_oXVDfapk1Lvlxp4J0ffX7-FXR3LL1BM,1834
 ngio/common/_array_pipe.py,sha256=we3gZLhgUsiPQwPQqg_XVkyG_9EpQ2xoe0L_nOALDho,7828
 ngio/common/_axes_transforms.py,sha256=kWU0M5erNmgWBXdu5LNv-tLW3jqkT00MMYX7cz-kyHs,2035
 ngio/common/_common_types.py,sha256=OkAYNSNjZkixL1MI-HPBVuXamheFBr862uJ4PvTxmhk,129
@@ -8,20 +8,21 @@ ngio/common/_masking_roi.py,sha256=-o6meGP17iTXEbkO9aGh1VX2drkc2laIcRJvCy_pRRM,4
 ngio/common/_pyramid.py,sha256=SJzPauuduuqcm9B7nFCJhMTzIg6Knjsnp4CY4lN61Is,7411
 ngio/common/_roi.py,sha256=dq1iVT8-G_zWuxcYWJeHfviBSbPgsyKUcDL3Vg6jx6I,5122
 ngio/common/_slicer.py,sha256=AKpwXRncOmF9nhjKYma0C_41WqAgSv860beKGx-aw-0,3075
+ngio/common/_table_ops.py,sha256=oTjCcecBOG_GJoLgJLgag6yl_nznThOKBKANQJow0h8,15493
 ngio/common/_zoom.py,sha256=KsURa5VuixmpbAAY5-6obmuQV8vfiHKZqBxZDXvchpM,5473
 ngio/hcs/__init__.py,sha256=5oAYT_454WGhms97kxo8gS4_rKHtFf_x-9uu8M_VeVM,356
-ngio/hcs/plate.py,sha256=WmUw8qZgWUPBBTqtV8lh_7T0vtRzMkAmduM8b969Ni4,30082
+ngio/hcs/plate.py,sha256=Y_d-ZuV9FmYsSHqwZfcnm_Y024jfdiMd7WlaeNJy73k,43696
 ngio/images/__init__.py,sha256=DYbXAdBgPxyjBRdJrWvU0UnBRI0gUMmx9KaJ-Bucvz4,533
 ngio/images/abstract_image.py,sha256=8PNQPZjiDz-pcTFXSJAVw7nUr4yL_iRwqDEUTKkAnp0,10266
 ngio/images/create.py,sha256=XYn30m_2OSZeHHASYHc3eK9u_gZIYy9wo6mGdRGaq5c,9473
 ngio/images/image.py,sha256=mKLIR2DGQUWtQbf3my2fh0bEPkbbsabUoge_XJPhfWE,17824
 ngio/images/label.py,sha256=qgbBHFPGYpUR2fHf1OiXZh4sn0FgCeeWwH1F4SrOM1c,10460
 ngio/images/masked_image.py,sha256=IBo8x2jHyXBXn7ORo8fSiwBPjV_1JOTb_vatjKNxbJ0,8531
-ngio/images/ome_zarr_container.py,sha256=-9bbzNtsVAjU1X_h78Lr5LOV0JXtOiWVWqmt3DFpXus,28927
+ngio/images/ome_zarr_container.py,sha256=jOodimQzAnaLUSYG1OnBsWqtHeL8_V4wkg_4RSXbwcM,30003
 ngio/ome_zarr_meta/__init__.py,sha256=oZ8PEsWM7U0KwzpsnvVfX9k4UfuTz5sZ8B6B9eY5hyY,1193
-ngio/ome_zarr_meta/_meta_handlers.py,sha256=BLvYt5PONYrWkEb2XgEiAXR_OX9rfeX_C0eEqen0jQA,25549
+ngio/ome_zarr_meta/_meta_handlers.py,sha256=ctknNDT8jxwyvxQf9on5gW31H1tRRsnneO38GT2UXoE,25880
 ngio/ome_zarr_meta/ngio_specs/__init__.py,sha256=05NQukZG0nNvjzf8AKWGu7PhjhQcImGSAOK3D3Bg-Js,1786
-ngio/ome_zarr_meta/ngio_specs/_axes.py,sha256=tHtx6NfBgDcCgDk9CosjIjw1KZJ2qi0i_eoLgrdiEWw,16681
+ngio/ome_zarr_meta/ngio_specs/_axes.py,sha256=Kqe9T7LWa_9o3UWS5uzALyyNluIhXxWhDGxWY4-GIo8,16707
 ngio/ome_zarr_meta/ngio_specs/_channels.py,sha256=2L-HM9K1Xu4qRI2MiXPqgCuHdCBRydEW1StThcqEuvY,15120
 ngio/ome_zarr_meta/ngio_specs/_dataset.py,sha256=hY8ogPPxvCgVg6k02t3zUr24lasYrvnxBd1iPEigdG4,5892
 ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py,sha256=uh345KQmEQtslIyMmLK9sB-NbjPYxi0Y9FuYIFhd3Rc,17465
@@ -30,28 +31,31 @@ ngio/ome_zarr_meta/ngio_specs/_pixel_size.py,sha256=5TT8250XdCKUnk3OwZeyXIMNFKOg
 ngio/ome_zarr_meta/v04/__init__.py,sha256=dJRzzxyYc81kf-0Hip_bqvbdManaM8XTdQX2meWyCSs,583
 ngio/ome_zarr_meta/v04/_custom_models.py,sha256=5GxiDERvLuvq4QvApcA6EiKLS6hLFX1R0R_9rSaa85A,530
 ngio/ome_zarr_meta/v04/_v04_spec_utils.py,sha256=05tEr2eEP_XVIfBMOAWLT7lzJV4KS5eYrpK8l94tn3w,15876
-ngio/tables/__init__.py,sha256=gxvNvAgLePgrngOm06H5qU50Axc6boeIs5iCfrmqTi0,609
-ngio/tables/_validators.py,sha256=7Eqln9j1tWmNakSCnryy2q39SbTuk6V31O2iMByTWWw,3363
-ngio/tables/tables_container.py,sha256=DFlz_6ts5p0lHkm6NMBtKZget30OicCYHrLbiG4xU1s,10188
-ngio/tables/backends/__init__.py,sha256=Y9MIFefwUaSmhhv5FDZFn7jBdYXDML2FovO-uK-vxgI,936
-ngio/tables/backends/_abstract_backend.py,sha256=--4qeVHs4YRo5i5XsREmDm6BxMsQ5tIqc6XZ810GJno,8776
+ngio/tables/__init__.py,sha256=np-XWjUY_HkwMfSy_bIRxh5t5SFZJ9yHEtvtbuaaSgg,824
+ngio/tables/abstract_table.py,sha256=naAeDsPTVjDUOnAxj_57UWXApg_nyWCsWdZ0f7bm740,8169
+ngio/tables/tables_container.py,sha256=c7YnzLy2aaDc0jCH8ih8FTAKpAX8dIAu743nF7EjNTY,11871
+ngio/tables/backends/__init__.py,sha256=tx97ZkK5kF_sAGU2kf_ZI9JxbOXn8GVjE0rUUq9h-QM,1525
+ngio/tables/backends/_abstract_backend.py,sha256=jtai3AqcLNZyxYyK0rernbMtcwxWhWAahCS0fPlMNls,7454
+ngio/tables/backends/_anndata.py,sha256=8RX2NO15CLxys3p6gw54Nd-_0WATU4WBlNndX06wvzI,2587
 ngio/tables/backends/_anndata_utils.py,sha256=DBWIcR0btnH-DIvDvzlcnMXoYhhtXc9DstryiOP0Qsg,3122
-ngio/tables/backends/_anndata_v1.py,sha256=5p_8pWUkYM4rEhm7g-b2yCXt2mmyd6lFisc1ubksAio,2469
-ngio/tables/backends/_csv_v1.py,sha256=o5AGlBH3UQdXx6MP2DtMm7zmXkOwnBBzu5TKk-QgQdI,5847
-ngio/tables/backends/_json_v1.py,sha256=7ALjB2thKTxPBeYOleqn2LNuAy6erp0Nzd-GZ9Xcd4Y,3079
-ngio/tables/backends/_table_backends.py,sha256=NXdH4pxo9XWZ_YxC5RVaw4PTOg-do30c3vlIy8KG4vQ,5831
-ngio/tables/backends/_utils.py,sha256=D0zI8_b6HEBZ2ER-80JvEEh_2-aCC1kpyKJGDPBPHco,14661
-ngio/tables/v1/__init__.py,sha256=XWi6f_KbjbX45Ku-7uymJRSTVWyFAPAAEp_TXDeZV4s,314
-ngio/tables/v1/_feature_table.py,sha256=2pZEENyZAmn_Awezu8VLGq90d-J7aXd6Ry8gNNR0wAQ,6104
-ngio/tables/v1/_generic_table.py,sha256=O2fu8k_TjhWEZtJxlU3Uj7ZTZnc75vLlvjw5lweSnd8,5710
-ngio/tables/v1/_roi_table.py,sha256=zGoISSC5q0UHyc0hcxfm2xpw2W6wUocoYctdi5nMmwg,11460
+ngio/tables/backends/_csv.py,sha256=Ev61D-AUKo4LIhXRmWPJgYbHI7eQdxiajQR574DevEM,932
+ngio/tables/backends/_json.py,sha256=1ZsEuXDJm1rOZV_KjFm8CB0qhv7L1W7L2EGWPf4q_p0,3137
+ngio/tables/backends/_non_zarr_backends.py,sha256=SvPPhT6n5TrKUOyV1mNcdHQK49huZ5lwR8EVe9MdydM,7254
+ngio/tables/backends/_parquet.py,sha256=ic-p86h8lce8q9luBJGRzy6vxlWyJvA0-2l5cUD6OqY,1398
+ngio/tables/backends/_table_backends.py,sha256=9bAwiB93gR8E7NdpH9WMMQhjn34Iz6oW9i_H4upYbW4,6567
+ngio/tables/backends/_utils.py,sha256=tJBSWN6OhO_1ybxl4vT2l3ImB028Fb6h0vaitPRcr8A,19668
+ngio/tables/v1/__init__.py,sha256=Wr1_9RZFpaN8FYMTnxT9Yjkw4AS7y9FMWailmB_uj5g,617
+ngio/tables/v1/_condition_table.py,sha256=LwtmygyhsSgAUoI_XuzF4lsHhTO5SIJqytxNAxqRCFU,1780
+ngio/tables/v1/_feature_table.py,sha256=6QiaHYTxBGwkIkBndA0pIgTpLSnlkJ6b_Nqs_H5g3GI,3819
+ngio/tables/v1/_generic_table.py,sha256=jFpW1vCDurN-TFQtQEyz1Rqnax7sVQoJzdPPBAVopFE,1239
+ngio/tables/v1/_roi_table.py,sha256=VQDLJnXGniups4bhZxn9ga9LRQnEI5PJzWDrQNsjmDM,13455
 ngio/utils/__init__.py,sha256=r3nuLWgp6-cQlS4ODjYSBrfgdTLkCOVke9jKbn1NpkA,1129
 ngio/utils/_datasets.py,sha256=EdYJHIifpRou4f43dIuiKsdxe4K6FaeS4f1_e_EYrcI,1727
 ngio/utils/_errors.py,sha256=pKQ12LUjQLYE1nUawemA5h7HsgznjaSvV1n2PQU33N0,759
-ngio/utils/_fractal_fsspec_store.py,sha256=7qoGLiLi8JQFh9Ej_z5WNwQQuWrujb0f6p9nj8ocsS8,548
+ngio/utils/_fractal_fsspec_store.py,sha256=0PMqPRCw7CYdLPxsNtp_vMLXfiQVwqs5EWrn2YVEuvA,1549
 ngio/utils/_logger.py,sha256=HIuqD_2ShfFGDswBddcouStbKfL0Vz_ah8cAIFGhbS8,888
 ngio/utils/_zarr_utils.py,sha256=qOI-HL2HsfFLCj_yxsTR-aq4oHpSqS9KR13aEIvhGDY,13593
-ngio-0.2.9.dist-info/METADATA,sha256=3hSjDhHlP2G3U8g1HcTNO5bQWGBEB0S1FLSMwDh4RlQ,5215
-ngio-0.2.9.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-ngio-0.2.9.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
-ngio-0.2.9.dist-info/RECORD,,
+ngio-0.3.0a1.dist-info/METADATA,sha256=7yRX4zM74DQkNKw-w5OijTUM7afR7OSks8zLd-1R1ro,5304
+ngio-0.3.0a1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+ngio-0.3.0a1.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
+ngio-0.3.0a1.dist-info/RECORD,,

ngio/tables/_validators.py

@@ -1,108 +0,0 @@
-from collections.abc import Iterable
-from typing import Protocol
-
-import pandas as pd
-
-from ngio.utils import NgioTableValidationError
-
-
-class TableValidator(Protocol):
-    def __call__(self, table: pd.DataFrame) -> pd.DataFrame:
-        """Validate the table DataFrame.
-
-        A Validator is just a simple callable that takes a
-            DataFrame and returns a DataFrame.
-
-        If the DataFrame is valid, the same DataFrame is returned.
-        If the DataFrame is invalid, the Validator can either modify the DataFrame
-            to make it valid or raise a NgioTableValidationError.
-
-        Args:
-            table (pd.DataFrame): The DataFrame to validate.
-
-        Returns:
-            pd.DataFrame: The validated DataFrame.
-
-        """
-        ...
-
-
-def validate_table(
-    table_df: pd.DataFrame,
-    validators: Iterable[TableValidator] | None = None,
-) -> pd.DataFrame:
-    """Validate the table DataFrame.
-
-    Args:
-        table_df (pd.DataFrame): The DataFrame to validate.
-        validators (Collection[Validator] | None): A collection of functions
-            used to validate the table. Default is None.
-
-    Returns:
-        pd.DataFrame: The validated DataFrame.
-    """
-    validators = validators or []
-
-    # Apply all provided validators
-    for validator in validators:
-        table_df = validator(table_df)
-
-    return table_df
-
-
-####################################################################################################
-#
-# Common table validators
-#
-####################################################################################################
-def validate_columns(
-    table_df: pd.DataFrame,
-    required_columns: list[str],
-    optional_columns: list[str] | None = None,
-) -> pd.DataFrame:
-    """Validate the columns headers of the table.
-
-    If a required column is missing, a TableValidationError is raised.
-    If a list of optional columns is provided, only required and optional columns are
-        allowed in the table.
-
-    Args:
-        table_df (pd.DataFrame): The DataFrame to validate.
-        required_columns (list[str]): A list of required columns.
-        optional_columns (list[str] | None): A list of optional columns.
-            Default is None.
-
-    Returns:
-        pd.DataFrame: The validated DataFrame.
-    """
-    table_header = table_df.columns
-    for column in required_columns:
-        if column not in table_header:
-            raise NgioTableValidationError(
-                f"Could not find required column: {column} in the table"
-            )
-
-    if optional_columns is None:
-        return table_df
-
-    possible_columns = [*required_columns, *optional_columns]
-    for column in table_header:
-        if column not in possible_columns:
-            raise NgioTableValidationError(
-                f"Could not find column: {column} in the list of possible columns. ",
-                f"Possible columns are: {possible_columns}",
-            )
-
-    return table_df
-
-
-def validate_unique_index(table_df: pd.DataFrame) -> pd.DataFrame:
-    """Validate that the index of the table is unique."""
-    if table_df.index.is_unique:
-        return table_df
-
-    # Find the duplicates
-    duplicates = table_df.index[table_df.index.duplicated()].tolist()
-    raise NgioTableValidationError(
-        f"Index of the table contains duplicates values. Duplicate: {duplicates}"
-    )