ome-arrow 0.0.4__tar.gz → 0.0.6__tar.gz

{ome_arrow-0.0.4 → ome_arrow-0.0.6}/.github/dependabot.yml

@@ -14,6 +14,10 @@ updates:
     schedule:
       # Check for updates to GitHub Actions every week
       interval: "weekly"
+    groups:
+      github-actions:
+        patterns:
+          - "*"
 
   # Perform checks and updates for python uv environment.
   # This depends on changes to dependabot via:
@@ -25,3 +29,7 @@ updates:
     schedule:
       # Check for updates to uv environment files every week
       interval: "weekly"
+    groups:
+      uv:
+        patterns:
+          - "*"

{ome_arrow-0.0.4 → ome_arrow-0.0.6}/.github/workflows/run-tests.yml

@@ -42,5 +42,7 @@ jobs:
           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-0.0.4 → ome_arrow-0.0.6}/.pre-commit-config.yaml

@@ -9,7 +9,7 @@ repos:
     -   id: check-yaml
     -   id: detect-private-key
 -   repo: https://github.com/tox-dev/pyproject-fmt
-    rev: "v2.11.1"
+    rev: "v2.12.1"
     hooks:
     -   id: pyproject-fmt
 -   repo: https://github.com/citation-file-format/cffconvert
@@ -34,17 +34,17 @@ repos:
         additional_dependencies:
         -   mdformat-gfm
 -   repo: https://github.com/adrienverge/yamllint
-    rev: v1.37.1
+    rev: v1.38.0
     hooks:
     -   id: yamllint
         exclude: pre-commit-config.yaml
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.14.7"
+    rev: "v0.15.0"
     hooks:
     -   id: ruff-format
     -   id: ruff-check
 -   repo: https://github.com/rhysd/actionlint
-    rev: v1.7.9
+    rev: v1.7.10
     hooks:
     -   id: actionlint
 -   repo: https://gitlab.com/vojko.pribudic.foss/pre-commit-update

{ome_arrow-0.0.4 → ome_arrow-0.0.6}/CITATION.cff

@@ -129,3 +129,29 @@ references:
       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-0.0.4/src/ome_arrow.egg-info → ome_arrow-0.0.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ome-arrow
-Version: 0.0.4
+Version: 0.0.6
 Summary: Using OME specifications with Apache Arrow for fast, queryable, and language agnostic bioimage data.
 Author: Dave Bunten
 Classifier: Programming Language :: Python :: 3 :: Only
@@ -28,9 +28,11 @@ 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)
@@ -104,6 +106,9 @@ 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

{ome_arrow-0.0.4 → ome_arrow-0.0.6}/README.md

@@ -1,4 +1,4 @@
-<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)
@@ -72,6 +72,9 @@ 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