ome-arrow 0.0.2__tar.gz → 0.0.4__tar.gz

{ome_arrow-0.0.2 → ome_arrow-0.0.4}/.github/workflows/publish-docs.yml

@@ -10,26 +10,30 @@ on:
     types:
       - published
 
+permissions:
+  contents: write
+
 jobs:
   build:
     # only build and deploy docs if the actor is not dependabot
     if: ${{ github.actor != 'dependabot[bot]' }}
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
           python-version: "3.11"
       - name: Install the latest version of uv
-        uses: astral-sh/setup-uv@v6
+        uses: astral-sh/setup-uv@v7
       - name: Build documentation
         run: |
           mkdir pages
           touch pages/.nojekyll
           cd docs
+          uv sync --all-extras --all-groups
           uv run --frozen sphinx-build src build
           # remove any doctrees dirs which aren't needed for publishing
           find ./build -type d -name '.doctrees' -exec rm -rf {} +

{ome_arrow-0.0.2 → ome_arrow-0.0.4}/.github/workflows/publish-pypi.yml

@@ -16,17 +16,17 @@ jobs:
       id-token: write
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
       - name: Fetch tags
         run: git fetch --all --tags
       - name: Python setup
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.11"
       - name: Install the latest version of uv
-        uses: astral-sh/setup-uv@v6
+        uses: astral-sh/setup-uv@v7
       - name: uv build distribution content
         run: uv build
       - name: Publish package distributions to PyPI

{ome_arrow-0.0.2 → ome_arrow-0.0.4}/.github/workflows/run-tests.yml

@@ -13,14 +13,14 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       # checks out the repo
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       # run pre-commit
       - name: Python setup
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.11"
       - name: Install the latest version of uv
-        uses: astral-sh/setup-uv@v6
+        uses: astral-sh/setup-uv@v7
       - uses: pre-commit/action@v3.0.1
       # run pre-commit ci lite for automated fixes
       - uses: pre-commit-ci/lite-action@v1.1.0
@@ -35,12 +35,12 @@ jobs:
       OS: ${{ matrix.os }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       - name: Python setup
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python_version }}
       - name: Install the latest version of uv
-        uses: astral-sh/setup-uv@v6
+        uses: astral-sh/setup-uv@v7
       - name: Run pytest
         run: uv run --frozen pytest

{ome_arrow-0.0.2 → ome_arrow-0.0.4}/.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: "v0.14.4"
+    rev: "v0.14.7"
     hooks:
     -   id: ruff-format
     -   id: ruff-check
 -   repo: https://github.com/rhysd/actionlint
-    rev: v1.7.8
+    rev: v1.7.9
     hooks:
     -   id: actionlint
 -   repo: https://gitlab.com/vojko.pribudic.foss/pre-commit-update

ome_arrow-0.0.4/CITATION.cff

@@ -0,0 +1,131 @@
+# 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

ome_arrow-0.0.4/PKG-INFO

@@ -0,0 +1,120 @@
+Metadata-Version: 2.4
+Name: ome-arrow
+Version: 0.0.4
+Summary: Using OME specifications with Apache Arrow for fast, queryable, and language agnostic bioimage data.
+Author: Dave Bunten
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: bioio>=3
+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: matplotlib>=3.10.7
+Requires-Dist: numpy>=2.2.6
+Requires-Dist: pandas>=2.2.3
+Requires-Dist: pillow>=12
+Requires-Dist: pyarrow>=22
+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"
+Dynamic: license-file
+
+<img height="200" 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
+
+OME-Arrow uses [Open Microscopy Environment (OME)](https://github.com/ome) specifications through [Apache Arrow](https://arrow.apache.org/) for fast, queryable, and language agnostic bioimage data.
+
+<img height="200" src="https://raw.githubusercontent.com/wayscience/ome-arrow/main/docs/src/_static/references_to_files.png">
+
+__Images are often left behind from the data model, referenced but excluded from databases.__
+
+<img height="200" src="https://raw.githubusercontent.com/wayscience/ome-arrow/main/docs/src/_static/various_ome_arrow_schema.png">
+
+__OME-Arrow brings images back into the story.__
+
+OME Arrow enables image data to be stored alongside metadata or derived data such as single-cell morphology features.
+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:
+
+```sh
+# install from pypi
+pip install ome-arrow
+
+# install directly from source
+pip install git+https://github.com/wayscience/ome-arrow.git
+```
+
+## Quick start
+
+See below for a quick start guide.
+Please also reference an example notebook: [Learning to fly with OME-Arrow](https://github.com/wayscience/ome-arrow/tree/main/docs/src/examples/learning_to_fly_with_ome-arrow.ipynb).
+
+```python
+from ome_arrow import OMEArrow
+
+# Ingest a tif image through a convenient OME Arrow class
+# We can also ingest OME-Zarr or NumPy arrays.
+oa_image = OMEArrow(
+    data="your_image.tif"
+)
+
+# Access the OME Arrow struct itself
+# (compatible with Arrow-compliant data storage).
+oa_image.data
+
+# Show information about the image.
+oa_image.info()
+
+# Display the image with matplotlib.
+oa_image.view(how="matplotlib")
+
+# Display the image with pyvista
+# (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")
+```
+
+## Contributing, Development, and Testing
+
+Please see our [contributing documentation](https://github.com/wayscience/ome-arrow/tree/main/CONTRIBUTING.md) for more details on contributions, development, and testing.
+
+## Related projects
+
+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 and creating OME Parquet files.
+- [`coSMicQC`](https://github.com/cytomining/coSMicQC): performs quality control on microscopy feature datasets, visualized using CytoDataFrames.

ome_arrow-0.0.4/README.md

@@ -0,0 +1,88 @@
+<img height="200" 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
+
+OME-Arrow uses [Open Microscopy Environment (OME)](https://github.com/ome) specifications through [Apache Arrow](https://arrow.apache.org/) for fast, queryable, and language agnostic bioimage data.
+
+<img height="200" src="https://raw.githubusercontent.com/wayscience/ome-arrow/main/docs/src/_static/references_to_files.png">
+
+__Images are often left behind from the data model, referenced but excluded from databases.__
+
+<img height="200" src="https://raw.githubusercontent.com/wayscience/ome-arrow/main/docs/src/_static/various_ome_arrow_schema.png">
+
+__OME-Arrow brings images back into the story.__
+
+OME Arrow enables image data to be stored alongside metadata or derived data such as single-cell morphology features.
+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:
+
+```sh
+# install from pypi
+pip install ome-arrow
+
+# install directly from source
+pip install git+https://github.com/wayscience/ome-arrow.git
+```
+
+## Quick start
+
+See below for a quick start guide.
+Please also reference an example notebook: [Learning to fly with OME-Arrow](https://github.com/wayscience/ome-arrow/tree/main/docs/src/examples/learning_to_fly_with_ome-arrow.ipynb).
+
+```python
+from ome_arrow import OMEArrow
+
+# Ingest a tif image through a convenient OME Arrow class
+# We can also ingest OME-Zarr or NumPy arrays.
+oa_image = OMEArrow(
+    data="your_image.tif"
+)
+
+# Access the OME Arrow struct itself
+# (compatible with Arrow-compliant data storage).
+oa_image.data
+
+# Show information about the image.
+oa_image.info()
+
+# Display the image with matplotlib.
+oa_image.view(how="matplotlib")
+
+# Display the image with pyvista
+# (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")
+```
+
+## Contributing, Development, and Testing
+
+Please see our [contributing documentation](https://github.com/wayscience/ome-arrow/tree/main/CONTRIBUTING.md) for more details on contributions, development, and testing.
+
+## Related projects
+
+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 and creating OME Parquet files.
+- [`coSMicQC`](https://github.com/cytomining/coSMicQC): performs quality control on microscopy feature datasets, visualized using CytoDataFrames.

{ome_arrow-0.0.2 → ome_arrow-0.0.4}/docs/src/conf.py

@@ -83,3 +83,6 @@ autodoc_preserve_defaults = True
 
 # enable anchor creation
 myst_heading_anchors = 3
+
+# disable notebook execution
+nb_execution_mode = "off"