napari-copick 1.1.0__tar.gz

napari_copick-1.1.0/.github/workflows/conventional-commits.yml

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+# Validates PR title follows conventional commits
+name: conventional-commits
+on:
+  pull_request:
+    branches: [main]
+    types:
+      - edited
+      - opened
+      - synchronize
+      - reopened
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  conventional_commit_title:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: chanzuckerberg/github-actions/.github/actions/conventional-commits@v6.4.0

napari_copick-1.1.0/.github/workflows/py-formatting.yml

@@ -0,0 +1,23 @@
+name: Python Linting
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre_commit_checks:
+    name: pre-commit checks
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.12.5"
+      - name: Install action-validator with asdf
+        uses: asdf-vm/actions/install@v3
+        with:
+          tool_versions: |
+            action-validator 0.6.0
+      - name: check linting
+        uses: pre-commit/action@v3.0.1

napari_copick-1.1.0/.github/workflows/release-please.yml

@@ -0,0 +1,64 @@
+name: Create Release PRs
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+
+permissions:
+  contents: write
+  issues: write
+  pull-requests: write
+
+jobs:
+  release-please:
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}
+      cancel-in-progress: true
+
+    runs-on: ubuntu-latest
+    steps:
+      - name: release please
+        uses: googleapis/release-please-action@v4
+        id: release
+        with:
+          manifest-file: ".release-please.manifest.json"
+          config-file: "release-please.config.json"
+          target-branch: "main"
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+    outputs:
+      paths_released: ${{ steps.release.outputs.paths_released }}
+
+  publish-pypi-package:
+    name: Build and publish Python package to PyPI
+    runs-on: ubuntu-latest
+    needs: release-please
+    if: contains(needs.release-please.outputs.paths_released, '.')
+    environment:
+      name: pypi
+      url: https://pypi.org/p/napari-copick
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+    steps:
+      - name: Checkout ref branch
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.ref }}
+          fetch-depth: 0
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          version: "0.7.13"
+          python-version: "3.12"
+
+      - name: build
+        run: |
+          uv build
+
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist

napari_copick-1.1.0/.github/workflows/test.yml

@@ -0,0 +1,60 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: tests
+
+on:
+  push:
+    branches:
+      - main
+      - npe2
+    tags:
+      - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
+  pull_request:
+    branches:
+      - main
+      - npe2
+  workflow_dispatch:
+
+jobs:
+  test:
+    name: ${{ matrix.platform }} py${{ matrix.python-version }}
+    runs-on: ${{ matrix.platform }}
+    timeout-minutes: 30
+    strategy:
+      matrix:
+        platform: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ['3.9', '3.10']
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          version: "0.7.13"
+          python-version: ${{ matrix.python-version }}
+
+      # these libraries enable testing on Qt on linux
+      - uses: tlambert03/setup-qt-libs@v1
+
+      # strategy borrowed from vispy for installing opengl libs on windows
+      - name: Install Windows OpenGL
+        if: runner.os == 'Windows'
+        run: |
+          git clone --depth 1 https://github.com/pyvista/gl-ci-helpers.git
+          powershell gl-ci-helpers/appveyor/install_opengl.ps1
+
+      - name: Install napari-copick
+        run: uv sync --locked --extra testing --extra dev
+
+      # this runs the platform-specific tests declared in tox.ini
+      - name: Test with tox
+        uses: aganders3/headless-gui@v1
+        with:
+          run: uv run tox
+        env:
+          PLATFORM: ${{ matrix.platform }}
+
+      - name: Coverage
+        uses: codecov/codecov-action@v3

napari_copick-1.1.0/.gitignore

@@ -0,0 +1,84 @@
+# 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_copick-1.1.0/.napari-hub/DESCRIPTION.md

@@ -0,0 +1,9 @@
+<!-- This file is a placeholder for customizing description of your plugin 
+on the napari hub if you wish. The readme file will be used by default if
+you wish not to do any customization for the napari hub listing.
+
+If you need some help writing a good description, check out our 
+[guide](https://github.com/chanzuckerberg/napari-hub/wiki/Writing-the-Perfect-Description-for-your-Plugin)
+-->
+
+The developer has not yet provided a napari-hub specific description.

napari_copick-1.1.0/.pre-commit-config.yaml

@@ -0,0 +1,29 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: check-docstring-first
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+        exclude: ^\.napari-hub/.*
+      - id: check-yaml # checks for correct yaml syntax for github actions ex.
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.4
+    hooks:
+      - id: ruff
+        args:
+          - --fix
+  - repo: https://github.com/psf/black
+    rev: 24.3.0
+    hooks:
+      - id: black
+  - repo: https://github.com/tlambert03/napari-plugin-checks
+    rev: v0.3.0
+    hooks:
+      - id: napari-plugin-checks
+  # https://mypy.readthedocs.io/en/stable/
+  # you may wish to add this as well!
+  # - repo: https://github.com/pre-commit/mirrors-mypy
+  #   rev: v1.9.0
+  #   hooks:
+  #     - id: mypy

napari_copick-1.1.0/.release-please.manifest.json

@@ -0,0 +1,3 @@
+{
+  ".": "1.1.0"
+}

napari_copick-1.1.0/CHANGELOG.md

@@ -0,0 +1,42 @@
+# Changelog
+
+## [1.1.0](https://github.com/copick/napari-copick/compare/napari-copick-v1.0.1...napari-copick-v1.1.0) (2025-11-07)
+
+
+### ✨ Features
+
+* Add segmentation storage options ([#16](https://github.com/copick/napari-copick/issues/16)) ([df34dec](https://github.com/copick/napari-copick/commit/df34dec4451dfd2924ab2f7ed4ea41ea5269460e))
+
+
+### 🐞 Bug Fixes
+
+* Save copick config after updating objects in UI. ([#17](https://github.com/copick/napari-copick/issues/17)) ([f0b4690](https://github.com/copick/napari-copick/commit/f0b4690e787ea707b622870a1f64c3cf64d517a1))
+
+## [1.0.1](https://github.com/copick/napari-copick/compare/napari-copick-v1.0.0...napari-copick-v1.0.1) (2025-07-27)
+
+
+### 🐞 Bug Fixes
+
+* fix screenshot link for pypi ([cadb6fb](https://github.com/copick/napari-copick/commit/cadb6fba40e3b904e3a52508a15283beff158aa9))
+
+## [1.0.0](https://github.com/copick/napari-copick/compare/napari-copick-v0.0.1...napari-copick-v1.0.0) (2025-07-27)
+
+
+### ⚠ BREAKING CHANGES
+
+* Add shared components to the napari-copick UI ([#11](https://github.com/copick/napari-copick/issues/11))
+* Separate the widget code from the execution code.  ([#7](https://github.com/copick/napari-copick/issues/7))
+
+### ✨ Features
+
+* Add shared components to the napari-copick UI ([#11](https://github.com/copick/napari-copick/issues/11)) ([c5d4c4c](https://github.com/copick/napari-copick/commit/c5d4c4cf63febb937214234303397d74792742d7))
+* Load Tree contents and images async ([#10](https://github.com/copick/napari-copick/issues/10)) ([3905d15](https://github.com/copick/napari-copick/commit/3905d159be1db15942649df423c64724421ac591))
+* Save buttons, Make Tree more human-readable, Refactor widget code for readability ([#12](https://github.com/copick/napari-copick/issues/12)) ([5d0f684](https://github.com/copick/napari-copick/commit/5d0f6842102e5213c8799a52dace70e42b620011))
+* Separate the widget code from the execution code.  ([#7](https://github.com/copick/napari-copick/issues/7)) ([f2244fc](https://github.com/copick/napari-copick/commit/f2244fc6db5bd52e7c391fd04b6c5d09cb3ef1cc))
+
+
+### 🧹 Miscellaneous Chores
+
+* FInal fixes before 1.0.0 ([#14](https://github.com/copick/napari-copick/issues/14)) ([b0efbeb](https://github.com/copick/napari-copick/commit/b0efbeb2efb68ccdf290c5395f98a780e69b4477))
+* Fix test workflow by switching to uv ([#8](https://github.com/copick/napari-copick/issues/8)) ([3493276](https://github.com/copick/napari-copick/commit/3493276a86b6c91259f267a91477bbec338739a0))
+* Set up CI for napari-copick ([#6](https://github.com/copick/napari-copick/issues/6)) ([b97f55b](https://github.com/copick/napari-copick/commit/b97f55b6c0e316bd57c5f8fb54a807a5512fc868))

napari_copick-1.1.0/LICENSE

@@ -0,0 +1,22 @@
+
+The MIT License (MIT)
+
+Copyright (c) 2024 Kyle Harrington
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

napari_copick-1.1.0/MANIFEST.in

@@ -0,0 +1,5 @@
+include LICENSE
+include README.md
+
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]

napari_copick-1.1.0/PKG-INFO

@@ -0,0 +1,187 @@
+Metadata-Version: 2.4
+Name: napari-copick
+Version: 1.1.0
+Summary: A plugin for collaborative annotation in cryoET using copick
+Project-URL: Repository, https://github.com/kephale/napari-copick
+Project-URL: Issues, https://github.com/kephale/napari-copick/issues
+Project-URL: Documentation, https://github.com/kephale/napari-copick#README.md
+Project-URL: Bug Tracker, https://github.com/kephale/napari-copick/issues
+Project-URL: Source Code, https://github.com/kephale/napari-copick
+Project-URL: User Support, https://github.com/kephale/napari-copick/issues
+Author-email: Kyle Harrington <czi@kyleharrington.com>, "Utz H. Ermel" <utz.ermel@czii.org>
+License: 
+        The MIT License (MIT)
+        
+        Copyright (c) 2024 Kyle Harrington
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in
+        all copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+        THE SOFTWARE.
+License-File: LICENSE
+Keywords: annotation,copick,cryo-et,cryoet,napari,plugin,tomography
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Framework :: napari
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Programming Language :: Python :: Implementation :: PyPy
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: >=3.9
+Requires-Dist: click
+Requires-Dist: copick-shared-ui==0.2.0
+Requires-Dist: copick>=1.6.0
+Requires-Dist: fsspec
+Requires-Dist: magicgui
+Requires-Dist: napari
+Requires-Dist: napari-ome-zarr
+Requires-Dist: numpy
+Requires-Dist: pydantic>=2
+Requires-Dist: qtpy
+Requires-Dist: scikit-image
+Requires-Dist: trimesh
+Requires-Dist: zarr
+Provides-Extra: dev
+Requires-Dist: black>=25.1.0; extra == 'dev'
+Requires-Dist: hatch-vcs>=0.4.0; extra == 'dev'
+Requires-Dist: hatchling>=1.25.0; extra == 'dev'
+Requires-Dist: pre-commit>=4.2.0; extra == 'dev'
+Requires-Dist: ruff>=0.12.0; extra == 'dev'
+Provides-Extra: testing
+Requires-Dist: napari; extra == 'testing'
+Requires-Dist: pyqt6; extra == 'testing'
+Requires-Dist: pytest; extra == 'testing'
+Requires-Dist: pytest-cov; extra == 'testing'
+Requires-Dist: pytest-qt; extra == 'testing'
+Requires-Dist: tox; extra == 'testing'
+Requires-Dist: tox-gh-actions; extra == 'testing'
+Requires-Dist: tox-uv; extra == 'testing'
+Description-Content-Type: text/markdown
+
+# napari-copick
+
+[![License MIT](https://img.shields.io/pypi/l/napari-copick.svg?color=green)](https://github.com/kephale/napari-copick/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/napari-copick.svg?color=green)](https://pypi.org/project/napari-copick)
+[![Python Version](https://img.shields.io/pypi/pyversions/napari-copick.svg?color=green)](https://python.org)
+[![tests](https://github.com/kephale/napari-copick/workflows/tests/badge.svg)](https://github.com/kephale/napari-copick/actions)
+[![codecov](https://codecov.io/gh/kephale/napari-copick/branch/main/graph/badge.svg)](https://codecov.io/gh/kephale/napari-copick)
+[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-copick)](https://napari-hub.org/plugins/napari-copick)
+
+A plugin for collaborative annotation in cryoET using copick
+
+![interface.png](https://github.com/copick/napari-copick/raw/main/docs/assets/interface.png)
+
+----------------------------------
+
+This [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.
+
+<!--
+Don't miss the full getting started guide to set up your new package:
+https://github.com/napari/cookiecutter-napari-plugin#getting-started
+
+and review the napari docs for plugin developers:
+https://napari.org/stable/plugins/index.html
+-->
+
+## Installation
+
+You can install `napari-copick` via [pip]:
+
+    pip install napari-copick
+
+To install latest development version:
+
+    pip install git+https://github.com/copick/napari-copick.git
+
+## Usage
+
+### Using a copick config file
+
+```bash
+napari-copick run --config path/to/copick_config.json
+```
+
+### Using dataset IDs from CZ cryoET Data Portal
+
+```bash
+napari-copick run --dataset-ids 10440 10441 --overlay-root /path/to/overlay_root
+```
+
+You can specify multiple dataset IDs separated by spaces.
+
+### GUI Usage
+
+The plugin provides an intuitive interface with two loading options:
+
+1. **Load Config File**: Opens a file dialog to select a copick configuration JSON file
+2. **Load from Dataset IDs**: Opens a dialog to enter CZ cryoET Data Portal dataset IDs and overlay root path
+
+After loading, you'll see a hierarchical tree of the project structure that you can navigate to access tomograms, segmentations, and picks.
+
+### Tomogram Handling
+
+napari-copick now handles multiscale zarr arrays directly:
+
+- Automatically detects and loads all available resolution levels
+- Creates a proper multiscale image stack using napari's native multiscale API
+- Uses dask for efficient lazy loading of large tomogram data
+- Applies appropriate scaling factors based on the voxel size metadata
+
+This direct zarr handling provides better performance and more flexibility compared to relying on external plugins.
+
+## Contributing
+
+Contributions are very welcome. Tests can be run with [tox], please ensure
+the coverage at least stays the same before you submit a pull request.
+
+## License
+
+Distributed under the terms of the [MIT] license,
+"napari-copick" is free and open source software
+
+## Issues
+
+If you encounter any problems, please [file an issue] along with a detailed description.
+
+[napari]: https://github.com/napari/napari
+[Cookiecutter]: https://github.com/audreyr/cookiecutter
+[@napari]: https://github.com/napari
+[MIT]: http://opensource.org/licenses/MIT
+[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
+
+[file an issue]: https://github.com/kephale/napari-copick/issues
+
+[napari]: https://github.com/napari/napari
+[tox]: https://tox.readthedocs.io/en/latest/
+[pip]: https://pypi.org/project/pip/
+[PyPI]: https://pypi.org/
+
+## Code of Conduct
+
+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).
+
+## Reporting Security Issues
+
+If you believe you have found a security issue, please responsibly disclose by contacting us at [security@chanzuckerberg.com](mailto:security@chanzuckerberg.com).

napari_copick-1.1.0/README.md

@@ -0,0 +1,105 @@
+# napari-copick
+
+[![License MIT](https://img.shields.io/pypi/l/napari-copick.svg?color=green)](https://github.com/kephale/napari-copick/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/napari-copick.svg?color=green)](https://pypi.org/project/napari-copick)
+[![Python Version](https://img.shields.io/pypi/pyversions/napari-copick.svg?color=green)](https://python.org)
+[![tests](https://github.com/kephale/napari-copick/workflows/tests/badge.svg)](https://github.com/kephale/napari-copick/actions)
+[![codecov](https://codecov.io/gh/kephale/napari-copick/branch/main/graph/badge.svg)](https://codecov.io/gh/kephale/napari-copick)
+[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-copick)](https://napari-hub.org/plugins/napari-copick)
+
+A plugin for collaborative annotation in cryoET using copick
+
+![interface.png](https://github.com/copick/napari-copick/raw/main/docs/assets/interface.png)
+
+----------------------------------
+
+This [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.
+
+<!--
+Don't miss the full getting started guide to set up your new package:
+https://github.com/napari/cookiecutter-napari-plugin#getting-started
+
+and review the napari docs for plugin developers:
+https://napari.org/stable/plugins/index.html
+-->
+
+## Installation
+
+You can install `napari-copick` via [pip]:
+
+    pip install napari-copick
+
+To install latest development version:
+
+    pip install git+https://github.com/copick/napari-copick.git
+
+## Usage
+
+### Using a copick config file
+
+```bash
+napari-copick run --config path/to/copick_config.json
+```
+
+### Using dataset IDs from CZ cryoET Data Portal
+
+```bash
+napari-copick run --dataset-ids 10440 10441 --overlay-root /path/to/overlay_root
+```
+
+You can specify multiple dataset IDs separated by spaces.
+
+### GUI Usage
+
+The plugin provides an intuitive interface with two loading options:
+
+1. **Load Config File**: Opens a file dialog to select a copick configuration JSON file
+2. **Load from Dataset IDs**: Opens a dialog to enter CZ cryoET Data Portal dataset IDs and overlay root path
+
+After loading, you'll see a hierarchical tree of the project structure that you can navigate to access tomograms, segmentations, and picks.
+
+### Tomogram Handling
+
+napari-copick now handles multiscale zarr arrays directly:
+
+- Automatically detects and loads all available resolution levels
+- Creates a proper multiscale image stack using napari's native multiscale API
+- Uses dask for efficient lazy loading of large tomogram data
+- Applies appropriate scaling factors based on the voxel size metadata
+
+This direct zarr handling provides better performance and more flexibility compared to relying on external plugins.
+
+## Contributing
+
+Contributions are very welcome. Tests can be run with [tox], please ensure
+the coverage at least stays the same before you submit a pull request.
+
+## License
+
+Distributed under the terms of the [MIT] license,
+"napari-copick" is free and open source software
+
+## Issues
+
+If you encounter any problems, please [file an issue] along with a detailed description.
+
+[napari]: https://github.com/napari/napari
+[Cookiecutter]: https://github.com/audreyr/cookiecutter
+[@napari]: https://github.com/napari
+[MIT]: http://opensource.org/licenses/MIT
+[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
+
+[file an issue]: https://github.com/kephale/napari-copick/issues
+
+[napari]: https://github.com/napari/napari
+[tox]: https://tox.readthedocs.io/en/latest/
+[pip]: https://pypi.org/project/pip/
+[PyPI]: https://pypi.org/
+
+## Code of Conduct
+
+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).
+
+## Reporting Security Issues
+
+If you believe you have found a security issue, please responsibly disclose by contacting us at [security@chanzuckerberg.com](mailto:security@chanzuckerberg.com).

napari_copick-1.1.0/SECURITY.md

@@ -0,0 +1,3 @@
+## Reporting Security Issues
+
+If you believe you have found a security issue, please responsibly disclose by contacting us at [security@chanzuckerberg.com](mailto:security@chanzuckerberg.com).