ngio 0.3.3__tar.gz → 0.3.5__tar.gz

{ngio-0.3.3 → ngio-0.3.5}/.pre-commit-config.yaml

@@ -14,7 +14,7 @@ repos:
       - id: validate-pyproject
 
   - repo: https://github.com/crate-ci/typos
-    rev: typos-dict-v0.11.20
+    rev: v1
     hooks:
       - id: typos
         #args: [--force-exclude]  # omitting --write-changes

ngio-0.3.5/CHANGELOG.md

@@ -0,0 +1,26 @@
+# Changelog
+
+## [v0.3.5]
+
+- Remove path normalization for images in wells. While the spec requires paths to be alphanumeric, this patch removes the normalization to allow for arbitrary image paths.
+
+## [v0.3.4]
+
+- allow to write as `anndata_v1` for backward compatibility with older ngio versions.
+
+## [v0.3.3]
+
+### Chores
+
+- improve dataset download process and streamline the CI workflows
+
+## [v0.3.2]
+
+### API Changes
+
+- change table backend default to `anndata_v1` for backward compatibility. This will be chaanged again when ngio `v0.2.x` is no longer supported.
+
+### Bug Fixes
+
+- fix [#13](https://github.com/BioVisionCenter/fractal-converters-tools/issues/13) (converters tools)
+- fix [#88](https://github.com/BioVisionCenter/ngio/issues/88)

{ngio-0.3.3 → ngio-0.3.5}/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.3.3
+Version: 0.3.5
 Summary: Next Generation file format IO
-Project-URL: homepage, https://github.com/fractal-analytics-platform/ngio
-Project-URL: repository, https://github.com/fractal-analytics-platform/ngio
+Project-URL: homepage, https://github.com/BioVisionCenter/ngio
+Project-URL: repository, https://github.com/BioVisionCenter/ngio
 Author-email: Lorenzo Cerrone <lorenzo.cerrone@uzh.ch>
 License: BSD-3-Clause
 License-File: LICENSE
@@ -16,7 +16,7 @@ Classifier: Programming Language :: Python :: 3.13
 Classifier: Typing :: Typed
 Requires-Python: <3.14,>=3.11
 Requires-Dist: aiohttp
-Requires-Dist: anndata>=0.8.0
+Requires-Dist: anndata<0.11.4,>=0.8.0
 Requires-Dist: dask[array]
 Requires-Dist: dask[distributed]
 Requires-Dist: filelock
@@ -65,11 +65,11 @@ Description-Content-Type: text/markdown
 
 # Ngio - Next Generation file format IO
 
-[![License](https://img.shields.io/pypi/l/ngio.svg?color=green)](https://github.com/lorenzocerrone/ngio/raw/main/LICENSE)
+[![License](https://img.shields.io/pypi/l/ngio.svg?color=green)](https://github.com/BioVisionCenter/ngio/raw/main/LICENSE)
 [![PyPI](https://img.shields.io/pypi/v/ngio.svg?color=green)](https://pypi.org/project/ngio)
 [![Python Version](https://img.shields.io/pypi/pyversions/ngio.svg?color=green)](https://python.org)
-[![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)
-[![codecov](https://codecov.io/gh/fractal-analytics-platform/ngio/graph/badge.svg?token=FkmF26FZki)](https://codecov.io/gh/fractal-analytics-platform/ngio)
+[![CI](https://github.com/BioVisionCenter/ngio/actions/workflows/ci.yml/badge.svg)](https://github.com/BioVisionCenter/ngio/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/BioVisionCenter/ngio/graph/badge.svg?token=FkmF26FZki)](https://codecov.io/gh/BioVisionCenter/ngio)
 
 ngio is a Python library designed to simplify bioimage analysis workflows, offering an intuitive interface for working with OME-Zarr files.
 
@@ -89,7 +89,7 @@ Ngio's mission is to streamline working with OME-Zarr files by providing a simpl
 ### 🔍 Rich Tables and Regions of Interest (ROI) Support
 
 - Extract and analyze specific regions of interest
-- Tight integration with [Tabular Data](https://fractal-analytics-platform.github.io/ngio/stable/table_specs/overview/)
+- Tight integration with [Tabular Data](https://BioVisionCenter.github.io/ngio/stable/table_specs/overview/)
 
 ### 🔄 Scalable Data Processing (Coming Soon)
 
@@ -104,7 +104,7 @@ You can install ngio via pip:
 pip install ngio
 ```
 
-To get started check out the [Quickstart Guide](https://fractal-analytics-platform.github.io/ngio/stable/getting_started/0_quickstart/).
+To get started check out the [Quickstart Guide](https://BioVisionCenter.github.io/ngio/stable/getting_started/0_quickstart/).
 
 ## Supported OME-Zarr versions
 
@@ -136,4 +136,4 @@ Ngio is developed at the [BioVisionCenter](https://www.biovisioncenter.uzh.ch/en
 
 ## License
 
-Ngio is released under the BSD-3-Clause License. See [LICENSE](https://github.com/fractal-analytics-platform/ngio/blob/main/LICENSE) for details.
+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 → ngio-0.3.5}/README.md

@@ -1,10 +1,10 @@
 # Ngio - Next Generation file format IO
 
-[![License](https://img.shields.io/pypi/l/ngio.svg?color=green)](https://github.com/lorenzocerrone/ngio/raw/main/LICENSE)
+[![License](https://img.shields.io/pypi/l/ngio.svg?color=green)](https://github.com/BioVisionCenter/ngio/raw/main/LICENSE)
 [![PyPI](https://img.shields.io/pypi/v/ngio.svg?color=green)](https://pypi.org/project/ngio)
 [![Python Version](https://img.shields.io/pypi/pyversions/ngio.svg?color=green)](https://python.org)
-[![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)
-[![codecov](https://codecov.io/gh/fractal-analytics-platform/ngio/graph/badge.svg?token=FkmF26FZki)](https://codecov.io/gh/fractal-analytics-platform/ngio)
+[![CI](https://github.com/BioVisionCenter/ngio/actions/workflows/ci.yml/badge.svg)](https://github.com/BioVisionCenter/ngio/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/BioVisionCenter/ngio/graph/badge.svg?token=FkmF26FZki)](https://codecov.io/gh/BioVisionCenter/ngio)
 
 ngio is a Python library designed to simplify bioimage analysis workflows, offering an intuitive interface for working with OME-Zarr files.
 
@@ -24,7 +24,7 @@ Ngio's mission is to streamline working with OME-Zarr files by providing a simpl
 ### 🔍 Rich Tables and Regions of Interest (ROI) Support
 
 - Extract and analyze specific regions of interest
-- Tight integration with [Tabular Data](https://fractal-analytics-platform.github.io/ngio/stable/table_specs/overview/)
+- Tight integration with [Tabular Data](https://BioVisionCenter.github.io/ngio/stable/table_specs/overview/)
 
 ### 🔄 Scalable Data Processing (Coming Soon)
 
@@ -39,7 +39,7 @@ You can install ngio via pip:
 pip install ngio
 ```
 
-To get started check out the [Quickstart Guide](https://fractal-analytics-platform.github.io/ngio/stable/getting_started/0_quickstart/).
+To get started check out the [Quickstart Guide](https://BioVisionCenter.github.io/ngio/stable/getting_started/0_quickstart/).
 
 ## Supported OME-Zarr versions
 
@@ -71,4 +71,4 @@ Ngio is developed at the [BioVisionCenter](https://www.biovisioncenter.uzh.ch/en
 
 ## License
 
-Ngio is released under the BSD-3-Clause License. See [LICENSE](https://github.com/fractal-analytics-platform/ngio/blob/main/LICENSE) for details.
+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 → ngio-0.3.5}/docs/index.md

@@ -16,7 +16,7 @@ Ngio's mission is to streamline working with OME-Zarr files by providing a simpl
 ### 🔍 Rich Tables and Regions of Interest (ROI) Support
 
 - Extract and analyze specific regions of interest
-- Tight integration with [Fractal's table framework](https://fractal-analytics-platform.github.io/fractal-tasks-core/tables/)
+- Tight integration with [Fractal's table framework](https://BioVisionCenter.github.io/fractal-tasks-core/tables/)
 
 ### 🔄 Scalable Data Processing (Coming Soon)
 
@@ -58,8 +58,8 @@ Ngio is developed at the [BioVisionCenter](https://www.biovisioncenter.uzh.ch/en
 
 ## License
 
-Ngio is released under the BSD-3-Clause License. See [LICENSE](https://github.com/fractal-analytics-platform/ngio/blob/main/LICENSE) for details.
+Ngio is released under the BSD-3-Clause License. See [LICENSE](https://github.com/BioVisionCenter/ngio/blob/main/LICENSE) for details.
 
 ## Repository
 
-Visit our [GitHub repository](https://github.com/fractal-analytics-platform/ngio) for the latest code, issues, and contributions.
+Visit our [GitHub repository](https://github.com/BioVisionCenter/ngio) for the latest code, issues, and contributions.

{ngio-0.3.3 → ngio-0.3.5}/mkdocs.yml

@@ -1,8 +1,8 @@
 site_name: "NGIO: Next Generation File Format I/O"
-site_url: "https://github.com/fractal-analytics-platform/ngio.git"
+site_url: "https://github.com/BioVisionCenter/ngio.git"
 site_description: "A Python library for processing OME-Zarr images"
 repo_name: "ngio"
-repo_url: "https://github.com/fractal-analytics-platform/ngio"
+repo_url: "https://github.com/BioVisionCenter/ngio"
 copyright: "Copyright © 2024-, BioVisionCenter UZH"
 
 theme:
@@ -45,7 +45,7 @@ extra:
     provider: mike
   social:
     - icon: fontawesome/brands/github
-      link: "https://github.com/fractal-analytics-platform/ngio"
+      link: "https://github.com/BioVisionCenter/ngio"
       name: NGIO on GitHub
 
 plugins: 
@@ -71,7 +71,7 @@ plugins:
   - git-revision-date-localized:
       enable_creation_date: true
   - git-committers:
-      repository: fractal-analytics-platform/ngio
+      repository: BioVisionCenter/ngio
       branch: main
   - mkdocs-jupyter:
       execute: true

{ngio-0.3.3 → ngio-0.3.5}/pyproject.toml

@@ -36,7 +36,7 @@ dependencies = [
     "numpy",
     "filelock",
     "zarr<3",
-    "anndata>=0.8.0",
+    "anndata>=0.8.0,<0.11.4", # To be removed when we transition to zarr v3
     "pydantic",
     "pandas>=1.2.0",
     "requests",
@@ -88,8 +88,8 @@ docs = [
 
 
 [project.urls]
-homepage = "https://github.com/fractal-analytics-platform/ngio"
-repository = "https://github.com/fractal-analytics-platform/ngio"
+homepage = "https://github.com/BioVisionCenter/ngio"
+repository = "https://github.com/BioVisionCenter/ngio"
 
 # Entry points
 # https://peps.python.org/pep-0621/#entry-points

{ngio-0.3.3 → ngio-0.3.5}/src/ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py

@@ -21,21 +21,12 @@ from ngio.utils import NgioValueError, ngio_logger
 
 def path_in_well_validation(path: str) -> str:
     """Validate the path in the well."""
-    if path.find("_") != -1:
-        # Remove underscores from the path
-        # This is a custom serialization step
-        old_value = path
-        path = path.replace("_", "")
-        ngio_logger.warning(
-            f"Underscores in well-paths are not allowed. "
-            f"Path '{old_value}' was changed to '{path}'"
-            f" to comply with the specification."
-        )
     # Check if the value contains only alphanumeric characters
     if not path.isalnum():
-        raise NgioValueError(
+        ngio_logger.warning(
             f"Path '{path}' contains non-alphanumeric characters. "
-            f"Only alphanumeric characters are allowed."
+            "This may cause issues with some tools. "
+            "Consider using only alphanumeric characters in the path."
         )
     return path
 

{ngio-0.3.3 → ngio-0.3.5}/src/ngio/tables/backends/__init__.py

@@ -1,7 +1,7 @@
 """Ngio Tables backend implementations."""
 
 from ngio.tables.backends._abstract_backend import AbstractTableBackend, BackendMeta
-from ngio.tables.backends._anndata import AnnDataBackend
+from ngio.tables.backends._anndata import AnnDataBackend, AnnDataBackendV1
 from ngio.tables.backends._csv import CsvTableBackend
 from ngio.tables.backends._json import JsonTableBackend
 from ngio.tables.backends._parquet import ParquetTableBackend
@@ -31,6 +31,7 @@ from ngio.tables.backends._utils import (
 __all__ = [
     "AbstractTableBackend",
     "AnnDataBackend",
+    "AnnDataBackendV1",
     "BackendMeta",
     "CsvTableBackend",
     "DefaultTableBackend",

{ngio-0.3.3 → ngio-0.3.5}/src/ngio/tables/backends/_anndata.py

@@ -75,3 +75,12 @@ class AnnDataBackend(AbstractTableBackend):
             index_key=self.index_key,
         )
         self.write_from_anndata(anndata)
+
+
+class AnnDataBackendV1(AnnDataBackend):
+    """A wrapper for the AnnData backend that for backwards compatibility."""
+
+    @staticmethod
+    def backend_name() -> str:
+        """Return the name of the backend."""
+        return "anndata_v1"

{ngio-0.3.3 → ngio-0.3.5}/src/ngio/tables/backends/_table_backends.py

@@ -7,7 +7,7 @@ from pandas import DataFrame
 from polars import DataFrame as PolarsDataFrame
 from polars import LazyFrame
 
-from ngio.tables.backends._anndata import AnnDataBackend
+from ngio.tables.backends._anndata import AnnDataBackend, AnnDataBackendV1
 from ngio.tables.backends._csv import CsvTableBackend
 from ngio.tables.backends._json import JsonTableBackend
 from ngio.tables.backends._parquet import ParquetTableBackend
@@ -213,7 +213,8 @@ class ImplementedTableBackends:
                 )
 
 
-ImplementedTableBackends().add_backend(AnnDataBackend, aliases=["anndata_v1"])
+ImplementedTableBackends().add_backend(AnnDataBackend)
+ImplementedTableBackends().add_backend(AnnDataBackendV1)
 ImplementedTableBackends().add_backend(
     JsonTableBackend, aliases=["experimental_json_v1"]
 )

{ngio-0.3.3 → ngio-0.3.5}/tests/unit/hcs/test_plate.py

@@ -94,7 +94,7 @@ def test_create_and_edit_plate_path_normalization(tmp_path: Path):
     test_plate.add_image(
         row="B", column="03", image_path="1_illumination_correction", acquisition_id=0
     )
-    assert test_plate.images_paths() == ["B/03/0mip", "B/03/1illuminationcorrection"]
+    assert test_plate.images_paths() == ["B/03/0_mip", "B/03/1_illumination_correction"]
 
 
 def test_derive_plate_from_ome_zarr(cardiomyocyte_tiny_path: Path, tmp_path: Path):

{ngio-0.3.3 → ngio-0.3.5}/tests/unit/ome_zarr_meta/test_unit_v04_utils.py

@@ -69,4 +69,4 @@ def test_well_meta_path_normalization():
     assert isinstance(output_metadata, dict)
 
     images = [image["path"] for image in output_metadata["well"]["images"]]
-    assert images == ["0", "0mip"]
+    assert images == ["0", "0_mip"]

ngio-0.3.3/CHANGELOG.md

@@ -1,18 +0,0 @@
-# Changelog
-
-## [v0.3.3]
-
-### Chores
-
-- improve dataset download process and streamline the CI workflows
-
-## [v0.3.2]
-
-### API Changes
-
-- change table backend default to `anndata_v1` for backward compatibility. This will be chaanged again when ngio `v0.2.x` is no longer supported.
-
-### Bug Fixes
-
-- fix [#13](https://github.com/fractal-analytics-platform/fractal-converters-tools/issues/13) (converters tools)
-- fix [#88](https://github.com/fractal-analytics-platform/ngio/issues/88)