ome-arrow 0.0.2__tar.gz

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!

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.

ome_arrow-0.0.2/.github/dependabot.yml

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+# GitHub Dependabot configuration
+# Note: there is no interaction between this
+# configuration and dependabot security updates.
+# See here for more information:
+# https://docs.github.com/en/code-security/dependabot/dependabot-security-updates/about-dependabot-security-updates#about-dependabot-security-updates
+
+version: 2
+updates:
+  # GitHub Actions checks
+  # See here for more information:
+  # https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuring-dependabot-version-updates
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"
+
+  # Perform checks and updates for python uv environment.
+  # This depends on changes to dependabot via:
+  # https://github.com/dependabot/dependabot-core/pull/10040
+  # See here for more information:
+  # https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file#pip-and-pip-compile
+  - package-ecosystem: "uv"
+    directory: "/"
+    schedule:
+      # Check for updates to uv environment files every week
+      interval: "weekly"

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

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 }}

ome_arrow-0.0.2/.github/workflows/publish-docs.yml

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+---
+# used for publishing documentation on push to main or published release
+name: publish docs
+
+on:
+  push:
+    branches:
+      - main
+  release:
+    types:
+      - published
+
+jobs:
+  build:
+    # only build and deploy docs if the actor is not dependabot
+    if: ${{ github.actor != 'dependabot[bot]' }}
+    runs-on: ubuntu-22.04
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v6
+      - name: Build documentation
+        run: |
+          mkdir pages
+          touch pages/.nojekyll
+          cd docs
+          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 {} +
+          cp -r build/* ../pages/
+      - name: Deploy documentation
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          branch: pages
+          folder: pages

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@v4
+        with:
+          fetch-depth: 0
+      - name: Fetch tags
+        run: git fetch --all --tags
+      - name: Python setup
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v6
+      - name: uv build distribution content
+        run: uv build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

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@v4
+      # run pre-commit
+      - name: Python setup
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v6
+      - 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: ["3.10", "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@v4
+      - name: Python setup
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python_version }}
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v6
+      - name: Run pytest
+        run: uv run --frozen pytest

ome_arrow-0.0.2/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# 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/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py.cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+#poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+#pdm.lock
+#pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+#pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.envrc
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer,
+#  you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+_version.py
+
+*.tiff
+*.tif
+*.zarr
+*.parquet

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: "v0.14.4"
+    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

ome_arrow-0.0.2/.python-version

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+3.11

ome_arrow-0.0.2/CITATION.cff

@@ -0,0 +1,59 @@
+# 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: 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"