napari-copick 0.0.1__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- napari_copick-0.0.1/.github/workflows/conventional-commits.yml +19 -0
- napari_copick-0.0.1/.github/workflows/py-formatting.yml +23 -0
- napari_copick-0.0.1/.github/workflows/release-please.yml +64 -0
- napari_copick-0.0.1/.github/workflows/test.yml +60 -0
- napari_copick-0.0.1/.gitignore +84 -0
- napari_copick-0.0.1/.napari-hub/DESCRIPTION.md +9 -0
- napari_copick-0.0.1/.pre-commit-config.yaml +27 -0
- napari_copick-0.0.1/.release-please.manifest.json +3 -0
- napari_copick-0.0.1/LICENSE +22 -0
- napari_copick-0.0.1/MANIFEST.in +5 -0
- napari_copick-0.0.1/PKG-INFO +182 -0
- napari_copick-0.0.1/README.md +103 -0
- napari_copick-0.0.1/SECURITY.md +3 -0
- napari_copick-0.0.1/pyproject.toml +150 -0
- napari_copick-0.0.1/release-please.config.json +29 -0
- napari_copick-0.0.1/src/napari_copick/__init__.py +4 -0
- napari_copick-0.0.1/src/napari_copick/_tests/__init__.py +0 -0
- napari_copick-0.0.1/src/napari_copick/_tests/test_widget.py +5 -0
- napari_copick-0.0.1/src/napari_copick/napari.yaml +12 -0
- napari_copick-0.0.1/src/napari_copick/widget.py +514 -0
- napari_copick-0.0.1/tox.ini +32 -0
- napari_copick-0.0.1/uv.lock +5370 -0
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# Validates PR title follows conventional commits
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name: conventional-commits
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on:
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pull_request:
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branches: [main]
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types:
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- edited
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- opened
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- synchronize
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- reopened
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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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conventional_commit_title:
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runs-on: ubuntu-latest
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steps:
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- uses: chanzuckerberg/github-actions/.github/actions/conventional-commits@v6.4.0
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name: Python Linting
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on:
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pull_request:
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branches: [main]
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jobs:
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pre_commit_checks:
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name: pre-commit checks
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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with:
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python-version: "3.12.5"
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- name: Install action-validator with asdf
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uses: asdf-vm/actions/install@v3
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with:
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tool_versions: |
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action-validator 0.6.0
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uses: pre-commit/action@v3.0.1
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name: Create Release PRs
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workflow_dispatch:
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permissions:
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contents: write
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issues: write
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pull-requests: write
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jobs:
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release-please:
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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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runs-on: ubuntu-latest
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steps:
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uses: googleapis/release-please-action@v4
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id: release
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with:
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manifest-file: ".release-please.manifest.json"
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config-file: "release-please.config.json"
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target-branch: "main"
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token: ${{ secrets.GITHUB_TOKEN }}
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outputs:
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paths_released: ${{ steps.release.outputs.paths_released }}
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publish-pypi-package:
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name: Build and publish Python package to PyPI
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runs-on: ubuntu-latest
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needs: release-please
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if: contains(needs.release-please.outputs.paths_released, '.')
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environment:
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name: pypi
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url: https://pypi.org/p/napari-copick
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permissions:
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id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
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steps:
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- name: Checkout ref branch
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uses: actions/checkout@v4
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with:
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ref: ${{ github.ref }}
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fetch-depth: 0
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- name: Install uv
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uses: astral-sh/setup-uv@v6
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with:
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version: "0.7.13"
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python-version: "3.12"
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run: |
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uv build
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- name: Publish distribution 📦 to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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packages-dir: dist
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# This workflows will upload a Python Package using Twine when a release is created
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# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
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name: tests
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on:
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push:
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- main
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tags:
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- "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
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jobs:
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test:
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name: ${{ matrix.platform }} py${{ matrix.python-version }}
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runs-on: ${{ matrix.platform }}
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timeout-minutes: 30
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strategy:
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matrix:
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platform: [ubuntu-latest, windows-latest, macos-latest]
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python-version: ['3.9', '3.10']
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steps:
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- uses: actions/checkout@v4
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- name: Install uv
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uses: astral-sh/setup-uv@v6
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with:
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version: "0.7.13"
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python-version: ${{ matrix.python-version }}
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# these libraries enable testing on Qt on linux
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- uses: tlambert03/setup-qt-libs@v1
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# strategy borrowed from vispy for installing opengl libs on windows
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- name: Install Windows OpenGL
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if: runner.os == 'Windows'
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run: |
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git clone --depth 1 https://github.com/pyvista/gl-ci-helpers.git
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powershell gl-ci-helpers/appveyor/install_opengl.ps1
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- name: Install napari-copick
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run: uv sync --locked --extra testing --extra dev
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# this runs the platform-specific tests declared in tox.ini
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uses: aganders3/headless-gui@v1
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with:
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run: uv run tox
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env:
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PLATFORM: ${{ matrix.platform }}
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uses: codecov/codecov-action@v3
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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# 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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lib64/
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parts/
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# PyInstaller
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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# Installer logs
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# Unit test / coverage reports
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htmlcov/
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*,cover
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# Translations
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instance/
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target/
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venv/
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<!-- This file is a placeholder for customizing description of your plugin
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on the napari hub if you wish. The readme file will be used by default if
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you wish not to do any customization for the napari hub listing.
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If you need some help writing a good description, check out our
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[guide](https://github.com/chanzuckerberg/napari-hub/wiki/Writing-the-Perfect-Description-for-your-Plugin)
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-->
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The developer has not yet provided a napari-hub specific description.
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.5.0
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hooks:
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- id: check-docstring-first
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- id: end-of-file-fixer
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- id: trailing-whitespace
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exclude: ^\.napari-hub/.*
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- id: check-yaml # checks for correct yaml syntax for github actions ex.
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.3.4
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hooks:
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- id: ruff
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- repo: https://github.com/psf/black
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rev: 24.3.0
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hooks:
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- id: black
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- repo: https://github.com/tlambert03/napari-plugin-checks
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rev: v0.3.0
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hooks:
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# https://mypy.readthedocs.io/en/stable/
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# you may wish to add this as well!
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# - repo: https://github.com/pre-commit/mirrors-mypy
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# rev: v1.9.0
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# hooks:
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# - id: mypy
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The MIT License (MIT)
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Copyright (c) 2024 Kyle Harrington
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in
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all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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THE SOFTWARE.
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Metadata-Version: 2.4
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Name: napari-copick
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Version: 0.0.1
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Summary: A plugin for collaborative annotation in cryoET using copick
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Project-URL: Repository, https://github.com/kephale/napari-copick
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Project-URL: Issues, https://github.com/kephale/napari-copick/issues
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Project-URL: Documentation, https://github.com/kephale/napari-copick#README.md
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Project-URL: Bug Tracker, https://github.com/kephale/napari-copick/issues
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Project-URL: Source Code, https://github.com/kephale/napari-copick
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Project-URL: User Support, https://github.com/kephale/napari-copick/issues
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Author-email: Kyle Harrington <czi@kyleharrington.com>
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License:
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The MIT License (MIT)
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Copyright (c) 2024 Kyle Harrington
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in
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all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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THE SOFTWARE.
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License-File: LICENSE
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Keywords: annotation,copick,cryo-et,cryoet,napari,plugin,tomography
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Classifier: Development Status :: 2 - Pre-Alpha
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Classifier: Framework :: napari
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Classifier: Intended Audience :: Developers
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Classifier: License :: OSI Approved :: MIT License
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Classifier: Operating System :: OS Independent
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Classifier: Programming Language :: Python
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Classifier: Programming Language :: Python :: 3
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Classifier: Programming Language :: Python :: 3 :: Only
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Classifier: Programming Language :: Python :: 3.9
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Classifier: Programming Language :: Python :: 3.10
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Classifier: Programming Language :: Python :: 3.11
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Classifier: Programming Language :: Python :: 3.12
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Classifier: Programming Language :: Python :: 3.13
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Classifier: Programming Language :: Python :: Implementation :: CPython
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Classifier: Programming Language :: Python :: Implementation :: PyPy
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Classifier: Topic :: Scientific/Engineering :: Image Processing
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Requires-Python: >=3.9
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Requires-Dist: copick
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Requires-Dist: fsspec
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Requires-Dist: magicgui
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Requires-Dist: napari-ome-zarr
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Requires-Dist: numpy
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Requires-Dist: pydantic>=2
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Requires-Dist: qtpy
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Requires-Dist: scikit-image
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Requires-Dist: trimesh
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Requires-Dist: zarr
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Provides-Extra: dev
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Requires-Dist: black>=25.1.0; extra == 'dev'
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Requires-Dist: hatch-vcs>=0.4.0; extra == 'dev'
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Requires-Dist: hatchling>=1.25.0; extra == 'dev'
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Requires-Dist: pre-commit>=4.2.0; extra == 'dev'
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Requires-Dist: ruff>=0.12.0; extra == 'dev'
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Provides-Extra: testing
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Requires-Dist: napari; extra == 'testing'
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Requires-Dist: pyqt6; extra == 'testing'
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Requires-Dist: pytest; extra == 'testing'
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Requires-Dist: pytest-qt; extra == 'testing'
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Requires-Dist: tox; extra == 'testing'
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Requires-Dist: tox-gh-actions; extra == 'testing'
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Requires-Dist: tox-uv; extra == 'testing'
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Description-Content-Type: text/markdown
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# napari-copick
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[](https://github.com/kephale/napari-copick/raw/main/LICENSE)
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[](https://pypi.org/project/napari-copick)
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[](https://python.org)
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[](https://github.com/kephale/napari-copick/actions)
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[](https://codecov.io/gh/kephale/napari-copick)
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[](https://napari-hub.org/plugins/napari-copick)
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A plugin for collaborative annotation in cryoET using copick
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----------------------------------
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This [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.
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<!--
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Don't miss the full getting started guide to set up your new package:
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https://github.com/napari/cookiecutter-napari-plugin#getting-started
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and review the napari docs for plugin developers:
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https://napari.org/stable/plugins/index.html
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-->
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## Installation
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You can install `napari-copick` via [pip]:
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pip install napari-copick
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To install latest development version:
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pip install git+https://github.com/kephale/napari-copick.git
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## Usage
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### Using a copick config file
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```bash
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python -m napari_copick.widget --config_path path/to/copick_config.json
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```
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### Using dataset IDs from CZ cryoET Data Portal
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```bash
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python -m napari_copick.widget --dataset_ids 10440 10441 --overlay_root /path/to/overlay_root
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```
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You can specify multiple dataset IDs separated by spaces.
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### GUI Usage
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The plugin provides an intuitive interface with two loading options:
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1. **Load Config File**: Opens a file dialog to select a copick configuration JSON file
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2. **Load from Dataset IDs**: Opens a dialog to enter CZ cryoET Data Portal dataset IDs and overlay root path
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After loading, you'll see a hierarchical tree of the project structure that you can navigate to access tomograms, segmentations, and picks.
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### Tomogram Handling
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napari-copick now handles multiscale zarr arrays directly:
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- Automatically detects and loads all available resolution levels
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- Creates a proper multiscale image stack using napari's native multiscale API
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- Uses dask for efficient lazy loading of large tomogram data
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- Applies appropriate scaling factors based on the voxel size metadata
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This direct zarr handling provides better performance and more flexibility compared to relying on external plugins.
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## Contributing
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Contributions are very welcome. Tests can be run with [tox], please ensure
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the coverage at least stays the same before you submit a pull request.
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## License
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Distributed under the terms of the [MIT] license,
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"napari-copick" is free and open source software
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## Issues
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If you encounter any problems, please [file an issue] along with a detailed description.
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[napari]: https://github.com/napari/napari
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[Cookiecutter]: https://github.com/audreyr/cookiecutter
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[@napari]: https://github.com/napari
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[MIT]: http://opensource.org/licenses/MIT
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[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
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[file an issue]: https://github.com/kephale/napari-copick/issues
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[pip]: https://pypi.org/project/pip/
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[PyPI]: https://pypi.org/
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## Code of Conduct
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This project adheres to the Contributor Covenant [code of conduct](https://github.com/chanzuckerberg/.github/blob/main/CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code. Please report unacceptable behavior to [opensource@chanzuckerberg.com](mailto:opensource@chanzuckerberg.com).
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## Reporting Security Issues
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If you believe you have found a security issue, please responsibly disclose by contacting us at [security@chanzuckerberg.com](mailto:security@chanzuckerberg.com).
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# napari-copick
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[](https://github.com/kephale/napari-copick/raw/main/LICENSE)
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[](https://pypi.org/project/napari-copick)
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[](https://python.org)
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[](https://github.com/kephale/napari-copick/actions)
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[](https://codecov.io/gh/kephale/napari-copick)
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[](https://napari-hub.org/plugins/napari-copick)
|
|
9
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A plugin for collaborative annotation in cryoET using copick
|
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+
|
|
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+
----------------------------------
|
|
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|
+
|
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This [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.
|
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+
|
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+
<!--
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Don't miss the full getting started guide to set up your new package:
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https://github.com/napari/cookiecutter-napari-plugin#getting-started
|
|
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|
+
|
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and review the napari docs for plugin developers:
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https://napari.org/stable/plugins/index.html
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-->
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## Installation
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You can install `napari-copick` via [pip]:
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|
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pip install napari-copick
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To install latest development version:
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pip install git+https://github.com/kephale/napari-copick.git
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## Usage
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### Using a copick config file
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|
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```bash
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python -m napari_copick.widget --config_path path/to/copick_config.json
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```
|
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### Using dataset IDs from CZ cryoET Data Portal
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|
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```bash
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python -m napari_copick.widget --dataset_ids 10440 10441 --overlay_root /path/to/overlay_root
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```
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|
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You can specify multiple dataset IDs separated by spaces.
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### GUI Usage
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The plugin provides an intuitive interface with two loading options:
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|
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1. **Load Config File**: Opens a file dialog to select a copick configuration JSON file
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2. **Load from Dataset IDs**: Opens a dialog to enter CZ cryoET Data Portal dataset IDs and overlay root path
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After loading, you'll see a hierarchical tree of the project structure that you can navigate to access tomograms, segmentations, and picks.
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|
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### Tomogram Handling
|
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+
|
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napari-copick now handles multiscale zarr arrays directly:
|
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62
|
+
|
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- Automatically detects and loads all available resolution levels
|
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- Creates a proper multiscale image stack using napari's native multiscale API
|
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- Uses dask for efficient lazy loading of large tomogram data
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- Applies appropriate scaling factors based on the voxel size metadata
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|
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This direct zarr handling provides better performance and more flexibility compared to relying on external plugins.
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|
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## Contributing
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Contributions are very welcome. Tests can be run with [tox], please ensure
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the coverage at least stays the same before you submit a pull request.
|
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|
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## License
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Distributed under the terms of the [MIT] license,
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"napari-copick" is free and open source software
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## Issues
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If you encounter any problems, please [file an issue] along with a detailed description.
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|
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[napari]: https://github.com/napari/napari
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[Cookiecutter]: https://github.com/audreyr/cookiecutter
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[@napari]: https://github.com/napari
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[MIT]: http://opensource.org/licenses/MIT
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[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
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[file an issue]: https://github.com/kephale/napari-copick/issues
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[napari]: https://github.com/napari/napari
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[tox]: https://tox.readthedocs.io/en/latest/
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[pip]: https://pypi.org/project/pip/
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[PyPI]: https://pypi.org/
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|
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## Code of Conduct
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|
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This project adheres to the Contributor Covenant [code of conduct](https://github.com/chanzuckerberg/.github/blob/main/CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code. Please report unacceptable behavior to [opensource@chanzuckerberg.com](mailto:opensource@chanzuckerberg.com).
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## Reporting Security Issues
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If you believe you have found a security issue, please responsibly disclose by contacting us at [security@chanzuckerberg.com](mailto:security@chanzuckerberg.com).
|