ome-arrow 0.0.3__tar.gz → 0.0.5__tar.gz

{ome_arrow-0.0.3 → ome_arrow-0.0.5}/.github/workflows/publish-docs.yml

@@ -20,7 +20,7 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
       - uses: actions/setup-python@v6

{ome_arrow-0.0.3 → ome_arrow-0.0.5}/.github/workflows/publish-pypi.yml

@@ -16,7 +16,7 @@ jobs:
       id-token: write
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
       - name: Fetch tags

{ome_arrow-0.0.3 → ome_arrow-0.0.5}/.github/workflows/run-tests.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       # checks out the repo
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
       # run pre-commit
       - name: Python setup
         uses: actions/setup-python@v6
@@ -35,12 +35,14 @@ jobs:
       OS: ${{ matrix.os }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
       - name: Python setup
         uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python_version }}
       - name: Install the latest version of uv
         uses: astral-sh/setup-uv@v7
+      - name: Sync dependencies (with viz extra)
+        run: uv sync --frozen --extra viz
       - name: Run pytest
         run: uv run --frozen pytest

{ome_arrow-0.0.3 → ome_arrow-0.0.5}/.pre-commit-config.yaml

@@ -39,12 +39,12 @@ repos:
     -   id: yamllint
         exclude: pre-commit-config.yaml
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.14.5"
+    rev: "v0.14.10"
     hooks:
     -   id: ruff-format
     -   id: ruff-check
 -   repo: https://github.com/rhysd/actionlint
-    rev: v1.7.8
+    rev: v1.7.10
     hooks:
     -   id: actionlint
 -   repo: https://gitlab.com/vojko.pribudic.foss/pre-commit-update

ome_arrow-0.0.5/CITATION.cff

@@ -0,0 +1,157 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+---
+cff-version: 1.2.0
+title: ome_arrow
+message: >-
+  If you use this software, please cite it using the
+  metadata from the CITATION.cff file.
+type: software
+authors:
+  - given-names: Dave
+    family-names: Bunten
+    orcid: "https://orcid.org/0000-0001-6041-3665"
+  - given-names: Jenna
+    family-names: Tomkinson
+    orcid: 'https://orcid.org/0000-0003-2676-5813'
+  - given-names: Michael
+    family-names: Lippincott
+    orcid: 'https://orcid.org/0000-0002-8637-1448'
+  - given-names: Cameron
+    family-names: Mattson
+    orcid: 'https://orcid.org/0009-0008-4969-779X'
+  - given-names: Gregory
+    family-names: Way
+    orcid: 'https://orcid.org/0000-0002-0503-9348'
+repository-code: "https://github.com/wayscience/ome-arrow"
+abstract: >-
+  Using OME specifications with Apache Arrow for fast, queryable, and language agnostic bioimage data.
+keywords:
+  - python
+license: BSD-3-Clause
+identifiers:
+  - description: Zenodo software DOI
+    type: doi
+    value: 10.5281/zenodo.17664969
+references:
+  - authors:
+      - name: "ExampleHuman CellProfiler Data Team"
+    date-accessed: "2022-09-01"
+    title: ExampleHuman CellProfiler Data
+    type: data
+    repository-code: "https://github.com/CellProfiler/examples/tree/master/ExampleHuman"
+    url: "https://cellprofiler.org/examples"
+    scope: "ExampleHuman"
+    notes: >-
+      ExampleHuman CellProfiler data is used to help validate expected results.
+    identifiers:
+      - description: "README.md with Citation Information"
+        type: url
+        value: "https://github.com/CellProfiler/examples/blob/master/ExampleHuman/README.md"
+  - authors:
+      - name: "Open Microscopy Environment (OME) Team"
+    date-accessed: "2025-11-07"
+    title: OME-TIFF Sample Data
+    type: data
+    repository-code: "https://github.com/ome/ome-model"
+    url: "https://ome-model.readthedocs.io/en/stable/ome-tiff/data.html"
+    scope: "OME-TIFF Example Datasets"
+    notes: >-
+      The OME-TIFF sample datasets illustrate the structure and metadata conventions
+      used in the OME-TIFF format, including images for testing readers, writers,
+      and visualization tools.
+    identifiers:
+      - description: "OME Model Documentation — OME-TIFF Sample Data"
+        type: url
+        value: "https://ome-model.readthedocs.io/en/stable/ome-tiff/data.html"
+  - authors:
+      - family-names: Chandrasekaran
+        given-names: Srinivas Niranj
+      - family-names: Cimini
+        given-names: Beth A.
+      - family-names: Goodale
+        given-names: Amy
+      - family-names: Miller
+        given-names: Lisa
+      - family-names: Kost-Alimova
+        given-names: Maria
+      - family-names: Jamali
+        given-names: Nasim
+      - family-names: Doench
+        given-names: John G.
+      - family-names: Fritchman
+        given-names: Briana
+      - family-names: Skepner
+        given-names: Adam
+      - family-names: Melanson
+        given-names: Michelle
+      - family-names: Kalinin
+        given-names: Alexandr A.
+      - family-names: Arevalo
+        given-names: John
+      - family-names: Haghighi
+        given-names: Marzieh
+      - family-names: Caicedo
+        given-names: Juan C.
+      - family-names: Kuhn
+        given-names: Daniel
+      - family-names: Hernandez
+        given-names: Desiree
+      - family-names: Berstler
+        given-names: James
+      - family-names: Shafqat-Abbasi
+        given-names: Hamdah
+      - family-names: Root
+        given-names: David E.
+      - family-names: Swalley
+        given-names: Susanne E.
+      - family-names: Garg
+        given-names: Sakshi
+      - family-names: Singh
+        given-names: Shantanu
+      - family-names: Carpenter
+        given-names: Anne E.
+    date-accessed: "2024-08-21"
+    title: >-
+      Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations
+    type: article
+    issn: 1548-7105
+    issue: 6
+    journal: Nature Methods
+    pages: 1114-1121
+    volume: 21
+    url: https://doi.org/10.1038/s41592-024-02241-6
+    date-published: "2024-06-01"
+    identifiers:
+      - type: doi
+        value: 10.1038/s41592-024-02241-6
+    notes: >-
+      JUMP (cpg0000-jump-pilot) was used to help demonstrate CytoDataFrame performance
+      with large data. See here for more information:
+      https://github.com/broadinstitute/cellpainting-gallery
+  - type: article
+    authors:
+      - family-names: Blin
+        given-names: Guillaume
+      - family-names: Sadurska
+        given-names: Dominika
+      - family-names: Portero Migueles
+        given-names: Rafael
+      - family-names: Chen
+        given-names: Ni
+      - family-names: Watson
+        given-names: James A.
+      - family-names: Lowell
+        given-names: Sally
+    title: "Nessys: A new set of tools for the automated detection of nuclei within intact tissues and dense 3D cultures"
+    journal: PLoS Biology
+    volume: "17"
+    issue: "8"
+    pages: e3000388
+    year: 2019
+    doi: "10.1371/journal.pbio.3000388"
+    url: "https://doi.org/10.1371/journal.pbio.3000388"
+    notes: >
+      This work used the file "6001240_labels.zarr" from the DISCEPTS imaging
+      dataset, available through the Image Data Resource (IDR) under accession
+      number idr0062.

{ome_arrow-0.0.3/src/ome_arrow.egg-info → ome_arrow-0.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ome-arrow
-Version: 0.0.3
+Version: 0.0.5
 Summary: Using OME specifications with Apache Arrow for fast, queryable, and language agnostic bioimage data.
 Author: Dave Bunten
 Classifier: Programming Language :: Python :: 3 :: Only
@@ -16,25 +16,29 @@ Requires-Dist: bioio-ome-tiff>=1.4
 Requires-Dist: bioio-ome-zarr>=3.0.3
 Requires-Dist: bioio-tifffile>=1.3
 Requires-Dist: fire>=0.7
-Requires-Dist: ipywidgets>=8.1.8
-Requires-Dist: jupyterlab-widgets>=3.0.16
 Requires-Dist: matplotlib>=3.10.7
 Requires-Dist: numpy>=2.2.6
 Requires-Dist: pandas>=2.2.3
 Requires-Dist: pillow>=12
 Requires-Dist: pyarrow>=22
-Requires-Dist: pyvista>=0.46.4
-Requires-Dist: trame>=3.12
-Requires-Dist: trame-vtk>=2.10
-Requires-Dist: trame-vuetify>=3.1
+Provides-Extra: viz
+Requires-Dist: ipywidgets>=8.1.8; extra == "viz"
+Requires-Dist: jupyterlab-widgets>=3.0.16; extra == "viz"
+Requires-Dist: pyvista>=0.46.4; extra == "viz"
+Requires-Dist: trame>=3.12; extra == "viz"
+Requires-Dist: trame-vtk>=2.10; extra == "viz"
+Requires-Dist: trame-vuetify>=3.1; extra == "viz"
+Provides-Extra: vortex
+Requires-Dist: vortex-data>=0.56; extra == "vortex"
 Dynamic: license-file
 
-<img height="200" src="https://raw.githubusercontent.com/wayscience/ome-arrow/main/docs/src/_static/logo.png?raw=true">
+<img width="600" src="https://raw.githubusercontent.com/wayscience/ome-arrow/main/docs/src/_static/logo.png?raw=true">
 
 ![PyPI - Version](https://img.shields.io/pypi/v/ome-arrow)
 [![Build Status](https://github.com/wayscience/ome-arrow/actions/workflows/run-tests.yml/badge.svg?branch=main)](https://github.com/wayscience/ome-arrow/actions/workflows/run-tests.yml?query=branch%3Amain)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://github.com/astral-sh/uv)
+[![Software DOI badge](https://zenodo.org/badge/DOI/10.5281/zenodo.17664969.svg)](https://doi.org/10.5281/zenodo.17664969)
 
 # Open, interoperable, and queryable microscopy images with OME Arrow
 
@@ -52,6 +56,13 @@ OME Arrow enables image data to be stored alongside metadata or derived data suc
 Images in OME Arrow are composed of mutlilayer [structs](https://arrow.apache.org/docs/python/generated/pyarrow.struct.html) so they may be stored as values within tables.
 This means you can store, query, and build relationships on data from the same location using any system which is compatible with Apache Arrow (including Parquet) through common data interfaces (such as SQL and DuckDB).
 
+## Project focus
+
+This package is intentionally dedicated to work at a per-image level and not large batch handling (though it may be used for those purposes by users or in other projects).
+
+- For visualizing OME Arrow and OME Parquet data in Napari, please see the [`napari-ome-arrow`](https://github.com/WayScience/napari-ome-arrow) Napari plugin.
+- For more comprehensive handling of many images and features in the context of the OME Parquet format please see the [`CytoDataFrame`](https://github.com/cytomining/CytoDataFrame) project (and relevant [example notebook](https://github.com/cytomining/CytoDataFrame/blob/main/docs/src/examples/cytodataframe_at_a_glance.ipynb)).
+
 ## Installation
 
 Install OME Arrow from PyPI or from source:
@@ -89,12 +100,15 @@ oa_image.info()
 oa_image.view(how="matplotlib")
 
 # Display the image with pyvista
-# (great for ZYX 3D images).
+# (great for ZYX 3D images; install extras: `pip install 'ome-arrow[viz]'`).
 oa_image.view(how="pyvista")
 
 # Export to OME-Parquet.
 # We can also export OME-TIFF, OME-Zarr or NumPy arrays.
 oa_image.export(how="ome-parquet", out="your_image.ome.parquet")
+
+# Export to Vortex (install extras: `pip install 'ome-arrow[vortex]'`).
+oa_image.export(how="vortex", out="your_image.vortex")
 ```
 
 ## Contributing, Development, and Testing
@@ -107,5 +121,5 @@ OME Arrow is used or inspired by the following projects, check them out!
 
 - [`napari-ome-arrow`](https://github.com/WayScience/napari-ome-arrow): enables you to view OME Arrow and related images.
 - [`nViz`](https://github.com/WayScience/nViz): focuses on ingesting and visualizing various 3D image data.
-- [`CytoDataFrame`](https://github.com/cytomining/CytoDataFrame): provides a DataFrame-like experience for viewing feature and microscopy image data within Jupyter notebook interfaces.
+- [`CytoDataFrame`](https://github.com/cytomining/CytoDataFrame): provides a DataFrame-like experience for viewing feature and microscopy image data within Jupyter notebook interfaces and creating OME Parquet files.
 - [`coSMicQC`](https://github.com/cytomining/coSMicQC): performs quality control on microscopy feature datasets, visualized using CytoDataFrames.

{ome_arrow-0.0.3 → ome_arrow-0.0.5}/README.md

@@ -1,9 +1,10 @@
-<img height="200" src="https://raw.githubusercontent.com/wayscience/ome-arrow/main/docs/src/_static/logo.png?raw=true">
+<img width="600" src="https://raw.githubusercontent.com/wayscience/ome-arrow/main/docs/src/_static/logo.png?raw=true">
 
 ![PyPI - Version](https://img.shields.io/pypi/v/ome-arrow)
 [![Build Status](https://github.com/wayscience/ome-arrow/actions/workflows/run-tests.yml/badge.svg?branch=main)](https://github.com/wayscience/ome-arrow/actions/workflows/run-tests.yml?query=branch%3Amain)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://github.com/astral-sh/uv)
+[![Software DOI badge](https://zenodo.org/badge/DOI/10.5281/zenodo.17664969.svg)](https://doi.org/10.5281/zenodo.17664969)
 
 # Open, interoperable, and queryable microscopy images with OME Arrow
 
@@ -21,6 +22,13 @@ OME Arrow enables image data to be stored alongside metadata or derived data suc
 Images in OME Arrow are composed of mutlilayer [structs](https://arrow.apache.org/docs/python/generated/pyarrow.struct.html) so they may be stored as values within tables.
 This means you can store, query, and build relationships on data from the same location using any system which is compatible with Apache Arrow (including Parquet) through common data interfaces (such as SQL and DuckDB).
 
+## Project focus
+
+This package is intentionally dedicated to work at a per-image level and not large batch handling (though it may be used for those purposes by users or in other projects).
+
+- For visualizing OME Arrow and OME Parquet data in Napari, please see the [`napari-ome-arrow`](https://github.com/WayScience/napari-ome-arrow) Napari plugin.
+- For more comprehensive handling of many images and features in the context of the OME Parquet format please see the [`CytoDataFrame`](https://github.com/cytomining/CytoDataFrame) project (and relevant [example notebook](https://github.com/cytomining/CytoDataFrame/blob/main/docs/src/examples/cytodataframe_at_a_glance.ipynb)).
+
 ## Installation
 
 Install OME Arrow from PyPI or from source:
@@ -58,12 +66,15 @@ oa_image.info()
 oa_image.view(how="matplotlib")
 
 # Display the image with pyvista
-# (great for ZYX 3D images).
+# (great for ZYX 3D images; install extras: `pip install 'ome-arrow[viz]'`).
 oa_image.view(how="pyvista")
 
 # Export to OME-Parquet.
 # We can also export OME-TIFF, OME-Zarr or NumPy arrays.
 oa_image.export(how="ome-parquet", out="your_image.ome.parquet")
+
+# Export to Vortex (install extras: `pip install 'ome-arrow[vortex]'`).
+oa_image.export(how="vortex", out="your_image.vortex")
 ```
 
 ## Contributing, Development, and Testing
@@ -76,5 +87,5 @@ OME Arrow is used or inspired by the following projects, check them out!
 
 - [`napari-ome-arrow`](https://github.com/WayScience/napari-ome-arrow): enables you to view OME Arrow and related images.
 - [`nViz`](https://github.com/WayScience/nViz): focuses on ingesting and visualizing various 3D image data.
-- [`CytoDataFrame`](https://github.com/cytomining/CytoDataFrame): provides a DataFrame-like experience for viewing feature and microscopy image data within Jupyter notebook interfaces.
+- [`CytoDataFrame`](https://github.com/cytomining/CytoDataFrame): provides a DataFrame-like experience for viewing feature and microscopy image data within Jupyter notebook interfaces and creating OME Parquet files.
 - [`coSMicQC`](https://github.com/cytomining/coSMicQC): performs quality control on microscopy feature datasets, visualized using CytoDataFrames.