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‎.copier-answers.yml‎

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# Do not edit - changes here will be overwritten by Copier
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_commit: v1
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_src_path: gh:pydev-guide/pyrepo-copier
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author_email: kevin.yamauchi@gmail.com
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author_name: Kevin Yamauchi
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git_versioning: true
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github_username: kevinyamauchi
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minimum_python: 11
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mode: customize
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module_name: oz_viewer
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project_license: BSD-3-Clause
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project_name: oz-viewer
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project_short_description: A viewer for ome-zarr images.
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test_lowest_pinned_dependencies: false
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test_pre_release: true
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use_mypy: false
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use_pre_commit: true
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use_ruff: true
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‎.github/ISSUE_TEMPLATE.md‎

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* oz-viewer version:
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* Python version:
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* Operating System:
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### Description
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Describe what you were trying to get done.
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Tell us what happened, what went wrong, and what you expected to happen.
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### What I Did
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```
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Paste the command(s) you ran and the output.
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If there was a crash, please include the traceback here.
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```

‎.github/TEST_FAIL_TEMPLATE.md‎

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---
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title: "{{ env.TITLE }}"
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labels: [bug]
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---
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The {{ workflow }} workflow failed on {{ date | date("YYYY-MM-DD HH:mm") }} UTC
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The most recent failing test was on {{ env.PLATFORM }} py{{ env.PYTHON }}
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with commit: {{ sha }}
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Full run: https://github.com/{{ repo }}/actions/runs/{{ env.RUN_ID }}
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(This post will be updated if another test fails, as long as this issue remains open.)

‎.github/dependabot.yml‎

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# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
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version: 2
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updates:
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- package-ecosystem: "github-actions"
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directory: "/"
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schedule:
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interval: "weekly"
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commit-message:
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prefix: "ci(dependabot):"

‎.github/workflows/ci.yml‎

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name: CI
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on:
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push:
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branches: [main]
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tags: [v*]
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pull_request:
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workflow_dispatch:
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schedule:
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# run every week (for --pre release tests)
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- cron: "0 0 * * 0"
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# cancel in-progress runs that use the same workflow and branch
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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check-manifest:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v5
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- run: pipx run check-manifest
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test:
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name: ${{ matrix.platform }} (${{ matrix.python-version }})
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runs-on: ${{ matrix.platform }}
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env:
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UV_PRERELEASE: ${{ github.event_name == 'schedule' && 'allow' || 'if-necessary-or-explicit' }}
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.11", "3.12", "3.13", "3.14"]
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platform: [ubuntu-latest, macos-latest, windows-latest]
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steps:
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- uses: actions/checkout@v5
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- name: 🐍 Set up Python ${{ matrix.python-version }}
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uses: astral-sh/setup-uv@v6
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with:
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python-version: ${{ matrix.python-version }}
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enable-cache: true
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- name: Install Dependencies
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run: uv sync --no-dev --group test
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- name: 🧪 Run Tests
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run: uv run pytest --cov --cov-report=xml --cov-report=term-missing
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# If something goes wrong with --pre tests, we can open an issue in the repo
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- name: 📝 Report --pre Failures
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if: failure() && github.event_name == 'schedule'
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uses: JasonEtco/create-an-issue@v2
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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PLATFORM: ${{ matrix.platform }}
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PYTHON: ${{ matrix.python-version }}
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RUN_ID: ${{ github.run_id }}
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TITLE: "[test-bot] pip install --pre is failing"
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with:
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filename: .github/TEST_FAIL_TEMPLATE.md
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update_existing: true
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- name: Coverage
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uses: codecov/codecov-action@v5
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# with:
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# token: ${{ secrets.CODECOV_TOKEN }}
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build-and-inspect-package:
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name: Build & inspect package.
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needs: test
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v5
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with:
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fetch-depth: 0
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- uses: hynek/build-and-inspect-python-package@v2
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upload-to-pypi:
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name: Upload package to PyPI
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needs: build-and-inspect-package
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if: success() && startsWith(github.ref, 'refs/tags/') && github.event_name != 'schedule'
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runs-on: ubuntu-latest
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permissions:
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# IMPORTANT: this permission is mandatory for trusted publishing on PyPi
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# see https://docs.pypi.org/trusted-publishers/
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id-token: write
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# This permission allows writing releases
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contents: write
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steps:
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- name: Download built artifact to dist/
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uses: actions/download-artifact@v5
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with:
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name: Packages
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path: dist
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- name: 🚢 Publish to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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- uses: softprops/action-gh-release@v2
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with:
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generate_release_notes: true
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files: './dist/*'

‎.gitignore‎

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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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env/
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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.DS_Store
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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.hypothesis/
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.pytest_cache/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# pyenv
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.python-version
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# celery beat schedule file
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celerybeat-schedule
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# SageMath parsed files
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*.sage.py
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# dotenv
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.env
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# virtualenv
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.venv
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venv/
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ENV/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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# ruff
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.ruff_cache/
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# IDE settings
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.vscode/
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.idea/

‎.pre-commit-config.yaml‎

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# enable pre-commit.ci at https://pre-commit.ci/
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# it adds:
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# 1. auto fixing pull requests
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# 2. auto updating the pre-commit configuration
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ci:
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autoupdate_schedule: monthly
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autofix_commit_msg: "style(pre-commit.ci): auto fixes [...]"
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autoupdate_commit_msg: "ci(pre-commit.ci): autoupdate"
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repos:
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- repo: https://github.com/abravalheri/validate-pyproject
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rev: v0.24.1
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hooks:
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- id: validate-pyproject
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- repo: https://github.com/rhysd/actionlint
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rev: v1.7.7
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hooks:
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- id: actionlint
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- repo: https://github.com/adhtruong/mirrors-typos
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rev: v1.36.2
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hooks:
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- id: typos
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args: [--force-exclude] # omitting --write-changes
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.13.0
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hooks:
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- id: ruff-check
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args: [--fix] # may also add '--unsafe-fixes'
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- id: ruff-format

‎LICENSE‎

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BSD 3-Clause License
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Copyright (c) 2023, Kevin Yamauchi
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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1. Redistributions of source code must retain the above copyright notice, this
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list of conditions and the following disclaimer.
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2. Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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3. Neither the name of the copyright holder nor the names of its
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contributors may be used to endorse or promote products derived from
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this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

‎README.md‎

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# oz-viewer
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[![License](https://img.shields.io/pypi/l/oz-viewer.svg?color=green)](https://github.com/kevinyamauchi/oz-viewer/raw/main/LICENSE)
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[![PyPI](https://img.shields.io/pypi/v/oz-viewer.svg?color=green)](https://pypi.org/project/oz-viewer)
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[![Python Version](https://img.shields.io/pypi/pyversions/oz-viewer.svg?color=green)](https://python.org)
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[![CI](https://github.com/kevinyamauchi/oz-viewer/actions/workflows/ci.yml/badge.svg)](https://github.com/kevinyamauchi/oz-viewer/actions/workflows/ci.yml)
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[![codecov](https://codecov.io/gh/kevinyamauchi/oz-viewer/branch/main/graph/badge.svg)](https://codecov.io/gh/kevinyamauchi/oz-viewer)
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A viewer for ome-zarr images.
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## Development
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The easiest way to get started is to use the [github cli](https://cli.github.com)
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and [uv](https://docs.astral.sh/uv/getting-started/installation/):
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```sh
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gh repo fork kevinyamauchi/oz-viewer --clone
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# or just
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# gh repo clone kevinyamauchi/oz-viewer
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cd oz-viewer
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uv sync
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```
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Run tests:
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```sh
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uv run pytest
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```
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Lint files:
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```sh
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uv run pre-commit run --all-files
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```

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