napari-ome-arrow 0.0.2__tar.gz

napari_ome_arrow-0.0.2/.github/ISSUE_TEMPLATE/issue.yml

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+# GitHub Issue template for bug reports
+name: Open a GitHub issue
+description: >
+  Please use this form to send along new ideas for content or
+  changes that might be helpful!
+
+body:
+  - type: checkboxes
+    attributes:
+      label: Is this a duplicate of an existing idea for this project?
+      description: >
+        Please make sure to search the existing issues first
+        to see whether the same issue was reported already.
+        If you find an existing issue, please don't hesitate to comment
+        on it or add a reaction to existing content!
+      options:
+        - label: >
+            I found no existing covering this topic.
+          required: true
+
+  - type: textarea
+    id: description
+    attributes:
+      label: What is your idea?
+      description: >
+        Please provide a specific description of what you'd like to see
+        including the context and what the result might look like.
+      placeholder: >
+        For example: "When x happens I see y.
+        The following might be a good way to address this ..."
+    validations:
+      required: true
+
+  - type: checkboxes
+    attributes:
+      label: Would you like to work on a solution for this?
+      description: >
+        This is a community-driven project and we
+        love new contributors (including through opening or adding to issues)!
+        This is an optional check to help us understand your interest to be
+        involved (especially if you already have a good understanding
+        of how to implement it).
+        We are happy to guide you in the contribution process and please
+        don't hesitate to reach out for help along the way.
+      options:
+        - label: Yes I am willing to submit a PR for this!

napari_ome_arrow-0.0.2/.github/PULL_REQUEST_TEMPLATE.md

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+<!-- _modified from [EmbeddedArtistry](https://embeddedartistry.com/blog/2017/08/04/a-github-pull-request-template-for-your-projects/)_
+_referenced with modifications from [pycytominer](https://github.com/cytomining/pycytominer/blob/master/.github/PULL_REQUEST_TEMPLATE.md)_ -->
+
+# Description
+
+<!--
+Thank you so much for your contribution to this project!
+
+Please _succinctly_ summarize your proposed change.
+Namely, consider addressing the following questions:
+
+- What motivated you to open this pull request?
+- Were there any special adjustments you had to make to complete the work?
+- Are there any issues which are related to this pull request (you may used a `#<digit>` to reference GitHub issues as links within this description)?
+
+Also, if you haven't already, please use `pre-commit run --all-files` to help check your files using this project's pre-commit configuration.
+Pre-commit checks will automatically run as part of opening this pull request and we seek to ensure all checks pass before merging changes.
+-->
+
+## What kind of change(s) are included?
+
+- [ ] Documentation (changes docs or other related content)
+- [ ] Bug fix (fixes an issue).
+- [ ] Enhancement (adds functionality).
+- [ ] Breaking change (these changes would cause existing functionality to not work as expected).
+
+# Checklist
+
+Please ensure that all boxes are checked before indicating that this pull request is ready for review.
+
+- [ ] I have read and followed the [CONTRIBUTING.md](CONTRIBUTING.md) guidelines.
+- [ ] I have searched for existing content to ensure this is not a duplicate.
+- [ ] I have performed a self-review of these additions (including spelling, grammar, and related).
+- [ ] These changes pass all pre-commit checks.
+- [ ] I have added comments to my code to help provide understanding
+- [ ] I have added a test which covers the code changes found within this PR
+- [ ] I have deleted all non-relevant text in this pull request template.

napari_ome_arrow-0.0.2/.github/dependabot.yml

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+# Dependabot configuration
+# https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuring-dependabot-version-updates#enabling-github-dependabot-version-updates
+# https://til.simonwillison.net/github/dependabot-python-setup
+
+version: 2
+updates:
+  # Monitor uv dependencies
+  - package-ecosystem: uv
+    directory: "/"
+    schedule:
+      interval: monthly
+    groups:
+      python-packages:
+        patterns:
+          - "*"
+
+  # Monitor GitHub Actions and propose updates for security and maintenance
+  - package-ecosystem: github-actions
+    directory: "/"
+    schedule:
+      interval: monthly
+    groups:
+      github-actions:
+        patterns:
+          - "*"

napari_ome_arrow-0.0.2/.github/release-drafter.yml

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+---
+# template configuration for release-drafter
+# see: https://github.com/release-drafter/release-drafter
+name-template: 'v$RESOLVED_VERSION'
+tag-template: 'v$RESOLVED_VERSION'
+version-resolver:
+  major:
+    labels:
+      - 'release-major'
+  minor:
+    labels:
+      - 'release-minor'
+  patch:
+    labels:
+      - 'release-patch'
+  default: patch
+change-template: '- $TITLE (@$AUTHOR via #$NUMBER)'
+template: |
+  ## Changes
+
+  $CHANGES

napari_ome_arrow-0.0.2/.github/workflows/draft-release.yml

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+---
+# workflow for drafting releases on GitHub
+# see: https://github.com/release-drafter/release-drafter
+name: release drafter
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  draft_release:
+    permissions:
+      # write permission is required to create a github release
+      contents: write
+      # write permission is required for autolabeler
+      # otherwise, read permission is required at least
+      pull-requests: write
+    runs-on: ubuntu-latest
+    steps:
+      - uses: release-drafter/release-drafter@v6
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

napari_ome_arrow-0.0.2/.github/workflows/publish-pypi.yml

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+---
+# used for publishing packages to pypi on release
+name: publish pypi release
+
+on:
+  release:
+    types:
+      - published
+
+jobs:
+  publish_pypi:
+    runs-on: ubuntu-latest
+    environment: release
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+        with:
+          fetch-depth: 0
+      - name: Fetch tags
+        run: git fetch --all --tags
+      - name: Python setup
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v7
+      - name: uv build distribution content
+        run: uv build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

napari_ome_arrow-0.0.2/.github/workflows/run-tests.yml

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+---
+# used for running tests
+name: tests
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  pre_commit_checks:
+    runs-on: ubuntu-24.04
+    steps:
+      # checks out the repo
+      - uses: actions/checkout@v5
+      # run pre-commit
+      - name: Python setup
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v7
+      - name: Install Windows OpenGL
+        uses: pyvista/setup-headless-display-action@v4.2
+        with:
+          qt: true
+          wm: herbstluftwm
+      - uses: pre-commit/action@v3.0.1
+      # run pre-commit ci lite for automated fixes
+      - uses: pre-commit-ci/lite-action@v1.1.0
+        if: ${{ !cancelled() }}
+  run_tests:
+    strategy:
+      matrix:
+        python_version: ["3.11", "3.12", "3.13"]
+        os: [ubuntu-24.04, macos-14]
+    runs-on: ${{ matrix.os }}
+    env:
+      OS: ${{ matrix.os }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+      - 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: Install Windows OpenGL
+        uses: pyvista/setup-headless-display-action@v4.2
+        with:
+          qt: true
+          wm: herbstluftwm
+      - name: Run pytest
+        run: uv run --python ${{ matrix.python_version }} --frozen pytest

napari_ome_arrow-0.0.2/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+.napari_cache
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask instance folder
+instance/
+
+# Sphinx documentation
+docs/_build/
+
+# MkDocs documentation
+/site/
+
+# PyBuilder
+target/
+
+# Pycharm and VSCode
+.idea/
+venv/
+.vscode/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# OS
+.DS_Store
+
+# written by setuptools_scm
+**/_version.py

napari_ome_arrow-0.0.2/.napari-hub/config.yml

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+# .napari-hub/config.yml
+
+# How this plugin appears on napari hub
+display_name: napari-ome-arrow
+name: napari-ome-arrow
+
+# Use DESCRIPTION.md (plugin-focused) instead of README.md for the hub page
+readme: README.md
+
+# Short one-line summary shown in lists/search results
+summary: >
+  Reader for OME-Arrow-backed OME-TIFF, OME-Zarr,
+  OME-Parquet, and stack patterns, with explicit
+  image/labels selection and automatic 3D for z-stacks.
+
+# Optional: keywords to help people find it
+labels:
+  - reader
+  - ome-tiff
+  - ome-zarr
+  - ome-parquet
+  - bioimaging
+  - microscopy
+  - z-stack
+  - segmentation
+  - labels
+
+# Optional tags (similar to labels; hub treats them slightly differently)
+tags:
+  - data-io
+  - bioimage-analysis
+  - visualization
+
+# License identifier (adjust to match pyproject.toml)
+license: BSD-3-Clause
+
+# Links (replace with your actual URLs)
+code_repository: https://github.com/wayscience/napari-ome-arrow
+documentation: https://github.com/wayscience/napari-ome-arrow#readme
+support:
+  issues: https://github.com/wayscience/napari-ome-arrow/issues

napari_ome_arrow-0.0.2/.pre-commit-config.yaml

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+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: detect-private-key
+-   repo: https://github.com/tox-dev/pyproject-fmt
+    rev: "v2.11.1"
+    hooks:
+    -   id: pyproject-fmt
+-   repo: https://github.com/citation-file-format/cffconvert
+    rev: 5295f87c0e261da61a7b919fc754e3a77edd98a7
+    hooks:
+    -   id: validate-cff
+-   repo: https://github.com/codespell-project/codespell
+    rev: v2.4.1
+    hooks:
+    -   id: codespell
+        exclude: |
+          (?x)^(
+              .*\.lock |
+              .*\.csv |
+              .*\.cff |
+              .*\.ipynb
+          )$
+-   repo: https://github.com/executablebooks/mdformat
+    rev: 0.7.21
+    hooks:
+    -   id: mdformat
+        additional_dependencies:
+        -   mdformat-gfm
+-   repo: https://github.com/adrienverge/yamllint
+    rev: v1.37.1
+    hooks:
+    -   id: yamllint
+        exclude: pre-commit-config.yaml
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.14.5"
+    hooks:
+    -   id: ruff-format
+    -   id: ruff-check
+-   repo: https://github.com/rhysd/actionlint
+    rev: v1.7.8
+    hooks:
+    -   id: actionlint
+-   repo: https://gitlab.com/vojko.pribudic.foss/pre-commit-update
+    rev: v0.6.0
+    hooks:
+    -   id: pre-commit-update
+        args: ["--keep", "mdformat", "--keep", "pre-commit-update", "--keep", "cffconvert"]
+-   repo: https://github.com/jendrikseipp/vulture
+    rev: 'v2.14'
+    hooks:
+    -   id: vulture
+-   repo: https://github.com/tlambert03/napari-plugin-checks
+    rev: v0.3.0
+    hooks:
+    -   id: napari-plugin-checks

napari_ome_arrow-0.0.2/CITATION.cff

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+# 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
+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"

napari_ome_arrow-0.0.2/CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socioeconomic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+- Demonstrating empathy and kindness toward other people
+- Being respectful of differing opinions, viewpoints, and experiences
+- Giving and gracefully accepting constructive feedback
+- Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+- Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+- The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+- Trolling, insulting or derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+- Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official email address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to community leaders responsible for enforcement.
+Please reach out to the maintainers of this repository by using their GitHub profile email address contact information to privately notify us of any incidents of this nature.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][mozilla coc].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][faq]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[faq]: https://www.contributor-covenant.org/faq
+[homepage]: https://www.contributor-covenant.org
+[mozilla coc]: https://github.com/mozilla/diversity
+[translations]: https://www.contributor-covenant.org/translations
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html