napari-mlarray 0.0.1__tar.gz

napari_mlarray-0.0.1/.copier-answers.yml

@@ -0,0 +1,19 @@
+# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
+_commit: v2.0.1
+_src_path: https://github.com/napari/napari-plugin-template
+display_name: Mlarray
+email: karol.gotkowski@dkfz.de
+full_name: Karol-G
+github_repository_url: provide later
+github_username_or_organization: MIC-DKFZ
+include_reader_plugin: true
+include_sample_data_plugin: false
+include_widget_plugin: true
+include_writer_plugin: true
+install_dependabot: true
+install_precommit: false
+license: MIT
+module_name: napari_mlarray
+plugin_name: napari-mlarray
+short_description: Reader/Writer for MLArray data, an array format specialized for
+    machine learning with Blosc2 backend and standardized metadata

napari_mlarray-0.0.1/.github/ISSUE_TEMPLATE/bug_report.yml

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+name: "\U0001F41B Bug Report"
+description: Report a bug encountered while using napari-mlarray
+labels:
+  - "bug"
+
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for taking the time to report this issue! 🙏🏼
+
+        Please fill out the sections below to help us reproduce the problem.
+
+  - type: textarea
+    id: bug-report
+    attributes:
+      label: "\U0001F41B Bug Report"
+      description: "Please provide a clear and concise description of the bug."
+      placeholder: "What went wrong? What did you expect to happen?"
+    validations:
+      required: true
+
+  - type: textarea
+    id: steps-to-reproduce
+    attributes:
+      label: "\U0001F4A1 Steps to Reproduce"
+      description: "Please provide a minimal code snippet or list of steps to reproduce the bug."
+      placeholder: |
+        1. Go to '...'
+        2. Click on '....'
+        3. Scroll down to '....'
+        4. See error
+    validations:
+      required: true
+
+  - type: textarea
+    id: expected-behavior
+    attributes:
+      label: "\U0001F4A1 Expected Behavior"
+      description: "Please provide a clear and concise description of what you expected to happen."
+      placeholder: "What did you expect to happen?"
+
+  - type: textarea
+    id: environment
+    attributes:
+      label: "\U0001F30E Environment"
+      description: |
+        Please provide detailed information regarding your environment. Please paste the output of `napari --info` here or copy  the information from the "napari info" dialog in the napari Help menu.
+
+        Otherwise, please provide information regarding your operating system (OS), Python version, napari version, Qt backend and version, Qt platform, method of installation, and any other relevant information related to your environment.
+
+
+      placeholder: |
+        napari: 0.5.0
+        Platform: macOS-13.2.1-arm64-arm-64bit
+        System: MacOS 13.2.1
+        Python: 3.11.4 (main, Aug 7 2023, 20:34:01) [Clang 14.0.3 (clang-1403.0.22.14.1)]
+        Qt: 5.15.10
+        PyQt5: 5.15.10
+        NumPy: 1.25.1
+        SciPy: 1.11.1
+        Dask: 2023.7.1
+        VisPy: 0.13.0
+        magicgui: 0.7.2
+        superqt: 0.5.4
+        in-n-out: 0.1.8
+        app-model: 0.2.0
+        npe2: 0.7.2
+
+        OpenGL:
+        - GL version: 2.1 Metal - 83
+        - MAX_TEXTURE_SIZE: 16384
+
+        Screens:
+        - screen 1: resolution 1512x982, scale 2.0
+
+        Settings path:
+        - /Users/.../napari/napari_5c6993c40c104085444cfc0c77fa392cb5cb8f56/settings.yaml
+    validations:
+      required: true
+
+  - type: textarea
+    id: additional-context
+    attributes:
+        label: "\U0001F4A1 Additional Context"
+        description: "Please provide any additional information or context regarding the problem here."
+        placeholder: "Add any other context about the problem here."

napari_mlarray-0.0.1/.github/ISSUE_TEMPLATE/documentation.md

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+---
+name: "\U0001F4DA Documentation"
+about: Report an issue with napari-mlarray documentation
+title: ''
+labels: documentation
+assignees: ''
+
+---
+
+## 📚 Documentation
+<!-- A clear and concise description of the documentation that needs to be created/updated -->

napari_mlarray-0.0.1/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: "\U0001F680 Feature Request"
+about: Submit a proposal/request for a new napari-mlarray feature
+title: ''
+labels: feature
+assignees: ''
+
+---
+
+## 🚀 Feature
+<!-- A clear and concise description of the feature proposal -->
+
+## Motivation
+
+<!-- Please outline the motivation for the proposal. Is your feature request related to a problem? e.g., I'm always frustrated when [...]. If this is related to another GitHub issue, please link here too -->
+
+## Pitch
+
+<!-- A clear and concise description of what you want to happen. -->
+
+## Alternatives
+
+<!-- A clear and concise description of any alternative solutions or features you've considered, if any. -->
+
+## Additional context
+
+<!-- Add any other context or screenshots about the feature request here. -->

napari_mlarray-0.0.1/.github/ISSUE_TEMPLATE/task.md

@@ -0,0 +1,11 @@
+---
+name: "\U0001F9F0 Task"
+about: Maintenance, follow-ups, and other defined to-do items
+title: ''
+labels: task
+assignees: ''
+
+---
+
+## 🧰 Task
+<!-- A clear and concise description of the task -->

napari_mlarray-0.0.1/.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,12 @@
+# References and relevant issues
+<!-- What relevant resources were used in the creation of this PR?
+If this PR addresses an existing issue on the repo,
+please link to that issue here as "Closes #(issue-number)"
+If this PR depends on another PR/issue (even in another repo),
+please link to it with "Depends on #PR-number" or "Depends on org/repo#PR-number"
+-->
+
+# Description
+<!-- What does this pull request (PR) do? Is it a new feature, a bug fix,
+an improvement, or something else? Why is it necessary? If relevant, please add
+a screenshot or a screen capture: "An image is worth a thousand words!" -->

napari_mlarray-0.0.1/.github/dependabot.yml

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

napari_mlarray-0.0.1/.github/workflows/test_and_deploy.yml

@@ -0,0 +1,85 @@
+# 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:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    name: ${{ matrix.platform }} py${{ matrix.python-version }}
+    runs-on: ${{ matrix.platform }}
+    timeout-minutes: 30
+    strategy:
+      fail-fast: false
+      matrix:
+        platform: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Setup python
+        uses: astral-sh/setup-uv@v7
+        with:
+          python-version: ${{ matrix.python-version }}
+          activate-environment: "true"
+      - name: Install Windows OpenGL
+        uses: pyvista/setup-headless-display-action@v4.2
+        with:
+          qt: true
+          wm: herbstluftwm
+
+
+      # note: if you need dependencies from conda, considering using
+      # setup-miniconda: https://github.com/conda-incubator/setup-miniconda
+      # and
+      # tox-conda: https://github.com/tox-dev/tox-conda
+      # this runs the platform-specific tests declared in tox.ini
+      - name: Test with tox
+        run: uvx --with tox-gh-actions tox
+        env:
+          PLATFORM: ${{ matrix.platform }}
+
+      - name: Coverage
+        uses: codecov/codecov-action@v5
+
+  build-and-inspect-package:
+    name: Build & inspect package.
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: hynek/build-and-inspect-python-package@v2
+
+  deploy:
+    # this will run when you have tagged a commit, starting with "v*"
+    # and requires that you have put your twine API key in your
+    # github secrets (see readme for details)
+    needs: [test, build-and-inspect-package]
+    runs-on: ubuntu-latest
+    if: contains(github.ref, 'tags')
+    permissions:
+      id-token: write
+    steps:
+      - name: Download built artifact to dist/
+        uses: actions/download-artifact@v5
+        with:
+          name: Packages
+          path: dist
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

napari_mlarray-0.0.1/.gitignore

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

napari_mlarray-0.0.1/.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_mlarray-0.0.1/.napari-hub/config.yml

@@ -0,0 +1,9 @@
+# You may use this file to customize how your plugin page appears
+# on the napari hub: https://www.napari-hub.org/
+# See their wiki for details https://github.com/chanzuckerberg/napari-hub/wiki
+
+# Please note that this file should only be used IN ADDITION to entering
+# metadata fields (such as summary, description, authors, and various URLS)
+# in your standard python package metadata (e.g. setup.cfg, setup.py, or
+# pyproject.toml), when you would like those fields to be displayed
+# differently on the hub than in the napari application.

napari_mlarray-0.0.1/LICENSE

@@ -0,0 +1,22 @@
+
+The MIT License (MIT)
+
+Copyright (c) 2026 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
+
+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_mlarray-0.0.1/MANIFEST.in

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

napari_mlarray-0.0.1/PKG-INFO

@@ -0,0 +1,119 @@
+Metadata-Version: 2.4
+Name: napari-mlarray
+Version: 0.0.1
+Summary: A reader/writer Napari plugin for MLArray images.
+Author: Karol-G
+Author-email: karol.gotkowski@dkfz.de
+License: 
+        The MIT License (MIT)
+        
+        Copyright (c) 2026 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
+        
+        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.
+        
+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 :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: mlarray
+Provides-Extra: all
+Requires-Dist: napari[all]; extra == "all"
+Dynamic: license-file
+
+# napari-mlarray
+
+[![License MIT](https://img.shields.io/pypi/l/napari-mlarray.svg?color=green)](https://github.com/MIC-DKFZ/napari-mlarray/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/napari-mlarray.svg?color=green)](https://pypi.org/project/napari-mlarray)
+[![Python Version](https://img.shields.io/pypi/pyversions/napari-mlarray.svg?color=green)](https://python.org)
+[![tests](https://github.com/MIC-DKFZ/napari-mlarray/workflows/tests/badge.svg)](https://github.com/MIC-DKFZ/napari-mlarray/actions)
+[![codecov](https://codecov.io/gh/MIC-DKFZ/napari-mlarray/branch/main/graph/badge.svg)](https://codecov.io/gh/MIC-DKFZ/napari-mlarray)
+[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-mlarray)](https://napari-hub.org/plugins/napari-mlarray)
+[![npe2](https://img.shields.io/badge/plugin-npe2-blue?link=https://napari.org/stable/plugins/index.html)](https://napari.org/stable/plugins/index.html)
+[![Copier](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/copier-org/copier/master/img/badge/badge-grayscale-inverted-border-purple.json)](https://github.com/copier-org/copier)
+
+A reader/writer Napari plugin for [MLArray](https://github.com/MIC-DKFZ/mlarray) images. MLArray is an array format specialized for Machine Learning with Blosc2 backend and standardized metadata. 
+
+## Installation
+
+You can install `napari-mlarray` via [pip]:
+
+```
+pip install napari-mlarray
+```
+
+If napari is not already installed, you can install `napari-mlarray` with napari and Qt via:
+
+```
+pip install "napari-mlarray[all]"
+```
+
+
+
+## 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-mlarray" 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
+[copier]: https://copier.readthedocs.io/en/stable/
+[@napari]: https://github.com/napari
+[MIT]: http://opensource.org/licenses/MIT
+[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
+[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
+[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
+[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
+[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
+[napari-plugin-template]: https://github.com/napari/napari-plugin-template
+
+[napari]: https://github.com/napari/napari
+[tox]: https://tox.readthedocs.io/en/latest/
+[pip]: https://pypi.org/project/pip/
+[PyPI]: https://pypi.org/
+
+## Acknowledgments
+
+<p align="left">
+  <img src="https://github.com/MIC-DKFZ/vidata/raw/main/imgs/Logos/HI_Logo.png" width="150"> &nbsp;&nbsp;&nbsp;&nbsp;
+  <img src="https://github.com/MIC-DKFZ/vidata/raw/main/imgs/Logos/DKFZ_Logo.png" width="500">
+</p>
+
+This repository is developed and maintained by the Applied Computer Vision Lab (ACVL)
+of [Helmholtz Imaging](https://www.helmholtz-imaging.de/) and the
+[Division of Medical Image Computing](https://www.dkfz.de/en/medical-image-computing) at DKFZ.

napari_mlarray-0.0.1/README.md

@@ -0,0 +1,69 @@
+# napari-mlarray
+
+[![License MIT](https://img.shields.io/pypi/l/napari-mlarray.svg?color=green)](https://github.com/MIC-DKFZ/napari-mlarray/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/napari-mlarray.svg?color=green)](https://pypi.org/project/napari-mlarray)
+[![Python Version](https://img.shields.io/pypi/pyversions/napari-mlarray.svg?color=green)](https://python.org)
+[![tests](https://github.com/MIC-DKFZ/napari-mlarray/workflows/tests/badge.svg)](https://github.com/MIC-DKFZ/napari-mlarray/actions)
+[![codecov](https://codecov.io/gh/MIC-DKFZ/napari-mlarray/branch/main/graph/badge.svg)](https://codecov.io/gh/MIC-DKFZ/napari-mlarray)
+[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-mlarray)](https://napari-hub.org/plugins/napari-mlarray)
+[![npe2](https://img.shields.io/badge/plugin-npe2-blue?link=https://napari.org/stable/plugins/index.html)](https://napari.org/stable/plugins/index.html)
+[![Copier](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/copier-org/copier/master/img/badge/badge-grayscale-inverted-border-purple.json)](https://github.com/copier-org/copier)
+
+A reader/writer Napari plugin for [MLArray](https://github.com/MIC-DKFZ/mlarray) images. MLArray is an array format specialized for Machine Learning with Blosc2 backend and standardized metadata. 
+
+## Installation
+
+You can install `napari-mlarray` via [pip]:
+
+```
+pip install napari-mlarray
+```
+
+If napari is not already installed, you can install `napari-mlarray` with napari and Qt via:
+
+```
+pip install "napari-mlarray[all]"
+```
+
+
+
+## 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-mlarray" 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
+[copier]: https://copier.readthedocs.io/en/stable/
+[@napari]: https://github.com/napari
+[MIT]: http://opensource.org/licenses/MIT
+[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
+[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
+[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
+[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
+[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
+[napari-plugin-template]: https://github.com/napari/napari-plugin-template
+
+[napari]: https://github.com/napari/napari
+[tox]: https://tox.readthedocs.io/en/latest/
+[pip]: https://pypi.org/project/pip/
+[PyPI]: https://pypi.org/
+
+## Acknowledgments
+
+<p align="left">
+  <img src="https://github.com/MIC-DKFZ/vidata/raw/main/imgs/Logos/HI_Logo.png" width="150"> &nbsp;&nbsp;&nbsp;&nbsp;
+  <img src="https://github.com/MIC-DKFZ/vidata/raw/main/imgs/Logos/DKFZ_Logo.png" width="500">
+</p>
+
+This repository is developed and maintained by the Applied Computer Vision Lab (ACVL)
+of [Helmholtz Imaging](https://www.helmholtz-imaging.de/) and the
+[Division of Medical Image Computing](https://www.dkfz.de/en/medical-image-computing) at DKFZ.

napari_mlarray-0.0.1/pyproject.toml

@@ -0,0 +1,124 @@
+[project]
+name = "napari-mlarray"
+dynamic = ["version"]
+description = "A reader/writer Napari plugin for MLArray images."
+readme = "README.md"
+license = {file = "LICENSE"}
+authors = [
+  {name = "Karol-G"},
+  {email = "karol.gotkowski@dkfz.de"},
+]
+classifiers = [
+    "Development Status :: 2 - Pre-Alpha",
+    "Framework :: napari",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering :: Image Processing",
+]
+requires-python = ">=3.10"
+# napari can be included in dependencies if napari imports are required.
+# However, you should not include napari[all], napari[qt],
+# or any other Qt bindings directly (e.g. PyQt5, PySide2).
+# See best practices: https://napari.org/stable/plugins/building_a_plugin/best_practices.html
+dependencies = [
+    "mlarray"
+]
+
+[project.optional-dependencies]
+# Allow easily installation with the full, default napari installation
+# (including Qt backend) using napari-mlarray[all].
+all = ["napari[all]"]
+
+[dependency-groups]
+dev = [
+    "tox-uv",
+    "pytest",  # https://docs.pytest.org/en/latest/contents.html
+    "pytest-cov",  # https://pytest-cov.readthedocs.io/en/latest/
+    "pytest-qt",  # https://pytest-qt.readthedocs.io/en/latest/
+    "napari[qt]",  # test with napari's default Qt bindings
+]
+
+[project.entry-points."napari.manifest"]
+napari-mlarray = "napari_mlarray:napari.yaml"
+
+
+
+[build-system]
+requires = ["setuptools>=42.0.0", "setuptools_scm"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+"*" = ["*.yaml"]
+
+[tool.setuptools_scm]
+write_to = "src/napari_mlarray/_version.py"
+fallback_version = "0.0.1+nogit"
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"]
+xfail_strict = true
+# filterwarnings = ["error"]  # recommended by PP309; deprecation warnings cause failures so leaving for the user to enable if desired
+log_cli_level = "INFO"
+testpaths = ["tests"]
+
+[tool.black]
+line-length = 79
+target-version = ['py310', 'py311', 'py312', 'py313']
+
+[tool.ruff]
+line-length = 79
+lint.select = [
+    "E", "F", "W", #flake8
+    "UP", # pyupgrade
+    "I", # isort
+    "BLE", # flake8-blind-exception
+    "B", # flake8-bugbear
+    "A", # flake8-builtins
+    "C4", # flake8-comprehensions
+    "ISC", # flake8-implicit-str-concat
+    "G", # flake8-logging-format
+    "PIE", # flake8-pie
+    "SIM", # flake8-simplify
+]
+lint.ignore = [
+    "E501", # line too long. let black handle this
+    "UP006", "UP007", # type annotation. As using magicgui require runtime type annotation then we disable this.
+]
+
+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".mypy_cache",
+    ".pants.d",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "venv",
+    "*vendored*",
+    "*_vendor*",
+]
+fix = true

napari_mlarray-0.0.1/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

napari_mlarray-0.0.1/src/napari_mlarray/__init__.py

@@ -0,0 +1,13 @@
+try:
+    from ._version import version as __version__
+except ImportError:
+    __version__ = "unknown"
+
+
+from ._reader import napari_get_reader
+from ._writer import write_single_image
+
+__all__ = (
+    "napari_get_reader",
+    "write_single_image",
+)

napari_mlarray-0.0.1/src/napari_mlarray/_reader.py

@@ -0,0 +1,77 @@
+"""
+This module is an example of a barebones numpy reader plugin for napari.
+
+It implements the Reader specification, but your plugin may choose to
+implement multiple readers or even other plugin contributions. see:
+https://napari.org/stable/plugins/building_a_plugin/guides.html#readers
+"""
+from mlarray import MLArray
+
+
+def napari_get_reader(path):
+    """A basic implementation of a Reader contribution.
+
+    Parameters
+    ----------
+    path : str or list of str
+        Path to file, or list of paths.
+
+    Returns
+    -------
+    function or None
+        If the path is a recognized format, return a function that accepts the
+        same path or list of paths, and returns a list of layer data tuples.
+    """
+    if isinstance(path, list):
+        # reader plugins may be handed single path, or a list of paths.
+        # if it is a list, it is assumed to be an image stack...
+        # so we are only going to look at the first file.
+        path = path[0]
+
+    # the get_reader function should make as many checks as possible
+    # (without loading the full file) to determine if it can read
+    # the path. Here, we check the dtype of the array by loading
+    # it with memmap, so that we don't actually load the full array into memory.
+    # We pretend that this reader can only read integer arrays.
+    try:
+        if not str(path).endswith(".mla"):
+            return None
+    # napari_get_reader should never raise an exception, because napari
+    # raises its own specific errors depending on what plugins are
+    # available for the given path, so we catch
+    # the OSError that np.load might raise if the file is malformed
+    except OSError:
+        return None
+
+    # otherwise we return the *function* that can read ``path``.
+    return reader_function
+
+
+def reader_function(path):
+    """Take a path or list of paths and return a list of LayerData tuples.
+
+    Readers are expected to return data as a list of tuples, where each tuple
+    is (data, [add_kwargs, [layer_type]]), "add_kwargs" and "layer_type" are
+    both optional.
+
+    Parameters
+    ----------
+    path : str or list of str
+        Path to file, or list of paths.
+
+    Returns
+    -------
+    layer_data : list of tuples
+        A list of LayerData tuples where each tuple in the list contains
+        (data, metadata, layer_type), where data is a numpy array, metadata is
+        a dict of keyword arguments for the corresponding viewer.add_* method
+        in napari, and layer_type is a lower-case string naming the type of
+        layer. Both "meta", and "layer_type" are optional. napari will
+        default to layer_type=="image" if not provided
+    """
+    # handle both a string and a list of strings
+    paths = [path] if isinstance(path, str) else path
+    # load all files into array
+    mlarrays = [MLArray.open(_path) for _path in paths]
+    layer_data = [(mlarray, {"affine": mlarray.affine, "metadata": mlarray.meta.to_dict()}, "labels" if mlarray.meta.is_seg.is_seg == True else "image") for mlarray in mlarrays]
+    return layer_data

napari_mlarray-0.0.1/src/napari_mlarray/_version.py

@@ -0,0 +1,34 @@
+# file generated by setuptools-scm
+# don't change, don't track in version control
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple
+    from typing import Union
+
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+    COMMIT_ID = Union[str, None]
+else:
+    VERSION_TUPLE = object
+    COMMIT_ID = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+commit_id: COMMIT_ID
+__commit_id__: COMMIT_ID
+
+__version__ = version = '0.0.1'
+__version_tuple__ = version_tuple = (0, 0, 1)
+
+__commit_id__ = commit_id = 'g905e69a09'

napari_mlarray-0.0.1/src/napari_mlarray/_widget.py

@@ -0,0 +1,128 @@
+"""
+This module contains four napari widgets declared in
+different ways:
+
+- a pure Python function flagged with `autogenerate: true`
+    in the plugin manifest. Type annotations are used by
+    magicgui to generate widgets for each parameter. Best
+    suited for simple processing tasks - usually taking
+    in and/or returning a layer.
+- a `magic_factory` decorated function. The `magic_factory`
+    decorator allows us to customize aspects of the resulting
+    GUI, including the widgets associated with each parameter.
+    Best used when you have a very simple processing task,
+    but want some control over the autogenerated widgets. If you
+    find yourself needing to define lots of nested functions to achieve
+    your functionality, maybe look at the `Container` widget!
+- a `magicgui.widgets.Container` subclass. This provides lots
+    of flexibility and customization options while still supporting
+    `magicgui` widgets and convenience methods for creating widgets
+    from type annotations. If you want to customize your widgets and
+    connect callbacks, this is the best widget option for you.
+- a `QWidget` subclass. This provides maximal flexibility but requires
+    full specification of widget layouts, callbacks, events, etc.
+
+References:
+- Widget specification: https://napari.org/stable/plugins/building_a_plugin/guides.html#widgets
+- magicgui docs: https://pyapp-kit.github.io/magicgui/
+
+Replace code below according to your needs.
+"""
+from typing import TYPE_CHECKING
+
+from magicgui import magic_factory
+from magicgui.widgets import CheckBox, Container, create_widget
+from qtpy.QtWidgets import QHBoxLayout, QPushButton, QWidget
+from skimage.util import img_as_float
+
+if TYPE_CHECKING:
+    import napari
+
+
+# Uses the `autogenerate: true` flag in the plugin manifest
+# to indicate it should be wrapped as a magicgui to autogenerate
+# a widget.
+def threshold_autogenerate_widget(
+    img: "napari.types.ImageData",
+    threshold: "float",
+) -> "napari.types.LabelsData":
+    return img_as_float(img) > threshold
+
+
+# the magic_factory decorator lets us customize aspects of our widget
+# we specify a widget type for the threshold parameter
+# and use auto_call=True so the function is called whenever
+# the value of a parameter changes
+@magic_factory(
+    threshold={"widget_type": "FloatSlider", "max": 1}, auto_call=True
+)
+def threshold_magic_widget(
+    img_layer: "napari.layers.Image", threshold: "float"
+) -> "napari.types.LabelsData":
+    return img_as_float(img_layer.data) > threshold
+
+
+# if we want even more control over our widget, we can use
+# magicgui `Container`
+class ImageThreshold(Container):
+    def __init__(self, viewer: "napari.viewer.Viewer"):
+        super().__init__()
+        self._viewer = viewer
+        # use create_widget to generate widgets from type annotations
+        self._image_layer_combo = create_widget(
+            label="Image", annotation="napari.layers.Image"
+        )
+        self._threshold_slider = create_widget(
+            label="Threshold", annotation=float, widget_type="FloatSlider"
+        )
+        self._threshold_slider.min = 0
+        self._threshold_slider.max = 1
+        # use magicgui widgets directly
+        self._invert_checkbox = CheckBox(text="Keep pixels below threshold")
+
+        # connect your own callbacks
+        self._threshold_slider.changed.connect(self._threshold_im)
+        self._invert_checkbox.changed.connect(self._threshold_im)
+
+        # append into/extend the container with your widgets
+        self.extend(
+            [
+                self._image_layer_combo,
+                self._threshold_slider,
+                self._invert_checkbox,
+            ]
+        )
+
+    def _threshold_im(self):
+        image_layer = self._image_layer_combo.value
+        if image_layer is None:
+            return
+
+        image = img_as_float(image_layer.data)
+        name = image_layer.name + "_thresholded"
+        threshold = self._threshold_slider.value
+        if self._invert_checkbox.value:
+            thresholded = image < threshold
+        else:
+            thresholded = image > threshold
+        if name in self._viewer.layers:
+            self._viewer.layers[name].data = thresholded
+        else:
+            self._viewer.add_labels(thresholded, name=name)
+
+
+class ExampleQWidget(QWidget):
+    # your QWidget.__init__ can optionally request the napari viewer instance
+    # use a type annotation of 'napari.viewer.Viewer' for any parameter
+    def __init__(self, viewer: "napari.viewer.Viewer"):
+        super().__init__()
+        self.viewer = viewer
+
+        btn = QPushButton("Click me!")
+        btn.clicked.connect(self._on_click)
+
+        self.setLayout(QHBoxLayout())
+        self.layout().addWidget(btn)
+
+    def _on_click(self):
+        print("napari has", len(self.viewer.layers), "layers")

napari_mlarray-0.0.1/src/napari_mlarray/_writer.py

@@ -0,0 +1,41 @@
+"""
+This module is an example of a barebones writer plugin for napari.
+
+It implements the Writer specification.
+see: https://napari.org/stable/plugins/building_a_plugin/guides.html#writers
+
+Replace code below according to your needs.
+"""
+from __future__ import annotations
+
+from collections.abc import Sequence
+from typing import TYPE_CHECKING, Any, Union
+from mlarray import MLArray, Meta
+
+if TYPE_CHECKING:
+    DataType = Union[Any, Sequence[Any]]
+    FullLayerData = tuple[DataType, dict, str]
+
+
+def write_single_image(path: str, data: Any, meta: dict) -> list[str]:
+    """Writes a single image layer.
+
+    Parameters
+    ----------
+    path : str
+        A string path indicating where to save the image file.
+    data : The layer data
+        The `.data` attribute from the napari layer.
+    meta : dict
+        A dictionary containing all other attributes from the napari layer
+        (excluding the `.data` layer attribute).
+
+    Returns
+    -------
+    [path] : A list containing the string path to the saved file.
+    """
+    mlarray = MLArray(data, meta=Meta.from_dict(meta["metadata"]))
+    mlarray.save(path)
+
+    # return path to any file(s) that were successfully written
+    return [path]

napari_mlarray-0.0.1/src/napari_mlarray/napari.yaml

@@ -0,0 +1,22 @@
+name: napari-mlarray
+display_name: Mlarray
+# use 'hidden' to remove plugin from napari hub search results
+visibility: public
+# see https://napari.org/stable/plugins/technical_references/manifest.html#fields for valid categories
+# categories: []
+contributions:
+  commands:
+    - id: napari-mlarray.get_reader
+      python_name: napari_mlarray._reader:napari_get_reader
+      title: Open data with Mlarray
+    - id: napari-mlarray.write_single_image
+      python_name: napari_mlarray._writer:write_single_image
+      title: Save image data with Mlarray
+  readers:
+    - command: napari-mlarray.get_reader
+      accepts_directories: false
+      filename_patterns: ['*.mla']
+  writers:
+    - command: napari-mlarray.write_single_image
+      layer_types: ['image']
+      filename_extensions: ['.mla']

napari_mlarray-0.0.1/src/napari_mlarray.egg-info/PKG-INFO

@@ -0,0 +1,119 @@
+Metadata-Version: 2.4
+Name: napari-mlarray
+Version: 0.0.1
+Summary: A reader/writer Napari plugin for MLArray images.
+Author: Karol-G
+Author-email: karol.gotkowski@dkfz.de
+License: 
+        The MIT License (MIT)
+        
+        Copyright (c) 2026 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
+        
+        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.
+        
+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 :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: mlarray
+Provides-Extra: all
+Requires-Dist: napari[all]; extra == "all"
+Dynamic: license-file
+
+# napari-mlarray
+
+[![License MIT](https://img.shields.io/pypi/l/napari-mlarray.svg?color=green)](https://github.com/MIC-DKFZ/napari-mlarray/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/napari-mlarray.svg?color=green)](https://pypi.org/project/napari-mlarray)
+[![Python Version](https://img.shields.io/pypi/pyversions/napari-mlarray.svg?color=green)](https://python.org)
+[![tests](https://github.com/MIC-DKFZ/napari-mlarray/workflows/tests/badge.svg)](https://github.com/MIC-DKFZ/napari-mlarray/actions)
+[![codecov](https://codecov.io/gh/MIC-DKFZ/napari-mlarray/branch/main/graph/badge.svg)](https://codecov.io/gh/MIC-DKFZ/napari-mlarray)
+[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-mlarray)](https://napari-hub.org/plugins/napari-mlarray)
+[![npe2](https://img.shields.io/badge/plugin-npe2-blue?link=https://napari.org/stable/plugins/index.html)](https://napari.org/stable/plugins/index.html)
+[![Copier](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/copier-org/copier/master/img/badge/badge-grayscale-inverted-border-purple.json)](https://github.com/copier-org/copier)
+
+A reader/writer Napari plugin for [MLArray](https://github.com/MIC-DKFZ/mlarray) images. MLArray is an array format specialized for Machine Learning with Blosc2 backend and standardized metadata. 
+
+## Installation
+
+You can install `napari-mlarray` via [pip]:
+
+```
+pip install napari-mlarray
+```
+
+If napari is not already installed, you can install `napari-mlarray` with napari and Qt via:
+
+```
+pip install "napari-mlarray[all]"
+```
+
+
+
+## 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-mlarray" 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
+[copier]: https://copier.readthedocs.io/en/stable/
+[@napari]: https://github.com/napari
+[MIT]: http://opensource.org/licenses/MIT
+[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
+[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
+[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
+[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
+[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
+[napari-plugin-template]: https://github.com/napari/napari-plugin-template
+
+[napari]: https://github.com/napari/napari
+[tox]: https://tox.readthedocs.io/en/latest/
+[pip]: https://pypi.org/project/pip/
+[PyPI]: https://pypi.org/
+
+## Acknowledgments
+
+<p align="left">
+  <img src="https://github.com/MIC-DKFZ/vidata/raw/main/imgs/Logos/HI_Logo.png" width="150"> &nbsp;&nbsp;&nbsp;&nbsp;
+  <img src="https://github.com/MIC-DKFZ/vidata/raw/main/imgs/Logos/DKFZ_Logo.png" width="500">
+</p>
+
+This repository is developed and maintained by the Applied Computer Vision Lab (ACVL)
+of [Helmholtz Imaging](https://www.helmholtz-imaging.de/) and the
+[Division of Medical Image Computing](https://www.dkfz.de/en/medical-image-computing) at DKFZ.

napari_mlarray-0.0.1/src/napari_mlarray.egg-info/SOURCES.txt

@@ -0,0 +1,30 @@
+.copier-answers.yml
+.gitignore
+LICENSE
+MANIFEST.in
+README.md
+pyproject.toml
+tox.ini
+.github/PULL_REQUEST_TEMPLATE.md
+.github/dependabot.yml
+.github/ISSUE_TEMPLATE/bug_report.yml
+.github/ISSUE_TEMPLATE/documentation.md
+.github/ISSUE_TEMPLATE/feature_request.md
+.github/ISSUE_TEMPLATE/task.md
+.github/workflows/test_and_deploy.yml
+.napari-hub/DESCRIPTION.md
+.napari-hub/config.yml
+src/napari_mlarray/__init__.py
+src/napari_mlarray/_reader.py
+src/napari_mlarray/_version.py
+src/napari_mlarray/_widget.py
+src/napari_mlarray/_writer.py
+src/napari_mlarray/napari.yaml
+src/napari_mlarray.egg-info/PKG-INFO
+src/napari_mlarray.egg-info/SOURCES.txt
+src/napari_mlarray.egg-info/dependency_links.txt
+src/napari_mlarray.egg-info/entry_points.txt
+src/napari_mlarray.egg-info/requires.txt
+src/napari_mlarray.egg-info/top_level.txt
+tests/__init__.py
+tests/test_default.py

napari_mlarray-0.0.1/src/napari_mlarray.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

napari_mlarray-0.0.1/src/napari_mlarray.egg-info/entry_points.txt

@@ -0,0 +1,2 @@
+[napari.manifest]
+napari-mlarray = napari_mlarray:napari.yaml

napari_mlarray-0.0.1/src/napari_mlarray.egg-info/requires.txt

@@ -0,0 +1,4 @@
+mlarray
+
+[all]
+napari[all]

napari_mlarray-0.0.1/src/napari_mlarray.egg-info/top_level.txt

@@ -0,0 +1 @@
+napari_mlarray

napari_mlarray-0.0.1/tests/test_default.py

@@ -0,0 +1,4 @@
+"""Default smoke test to ensure test suite is non-empty."""
+
+def test_default_passes() -> None:
+    assert True

napari_mlarray-0.0.1/tox.ini

@@ -0,0 +1,33 @@
+# For more information about tox, see https://tox.readthedocs.io/en/latest/
+[tox]
+envlist = py{310,311,312,313}-{linux,macos,windows}
+isolated_build=true
+
+[gh-actions]
+python =
+    3.10: py310
+    3.11: py311
+    3.12: py312
+    3.13: py313
+
+[gh-actions:env]
+PLATFORM =
+    ubuntu-latest: linux
+    macos-latest: macos
+    windows-latest: windows
+
+[testenv]
+platform =
+    macos: darwin
+    linux: linux
+    windows: win32
+passenv =
+    CI
+    GITHUB_ACTIONS
+    DISPLAY
+    XAUTHORITY
+    NUMPY_EXPERIMENTAL_ARRAY_FUNCTION
+    PYVISTA_OFF_SCREEN
+dependency_groups =
+    dev
+commands = pytest -v --color=yes --cov=napari_mlarray --cov-report=xml