napari-nuclephaser 0.0.1__tar.gz

napari_nuclephaser-0.0.1/.github/dependabot.yml

@@ -0,0 +1,14 @@
+# 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:
+- package-ecosystem: pip
+  directory: "/"
+  schedule:
+    interval: monthly
+  groups:
+    python-packages:
+      patterns:
+        - "*"

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

@@ -0,0 +1,91 @@
+# 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: [windows-latest]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          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
+
+      # 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
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install setuptools tox tox-gh-actions
+
+      # this runs the platform-specific tests declared in tox.ini
+      - name: Test with tox
+        uses: aganders3/headless-gui@v2
+        with:
+          run: python -m tox
+        env:
+          PLATFORM: ${{ matrix.platform }}
+
+      - name: Coverage
+        uses: codecov/codecov-action@v3
+
+  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]
+    runs-on: ubuntu-latest
+    if: contains(github.ref, 'tags')
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -U setuptools setuptools_scm wheel twine build
+      - name: Build and publish
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
+        run: |
+          git tag
+          python -m build .
+          twine upload dist/*

napari_nuclephaser-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

napari_nuclephaser-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_nuclephaser-0.0.1/.napari-hub/config.yml

@@ -0,0 +1,11 @@
+# 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.
+
+visibility: hidden

napari_nuclephaser-0.0.1/.pre-commit-config.yaml

@@ -0,0 +1,27 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    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: v0.11.2
+    hooks:
+      - id: ruff
+  - repo: https://github.com/psf/black
+    rev: 25.1.0
+    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_nuclephaser-0.0.1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 nikvo1
+
+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_nuclephaser-0.0.1/MANIFEST.in

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

napari_nuclephaser-0.0.1/PKG-INFO

@@ -0,0 +1,144 @@
+Metadata-Version: 2.4
+Name: napari-nuclephaser
+Version: 0.0.1
+Summary: A Napari plugin to detect and count nuclei on phase contrast images
+Author: Nikita Voloshin
+Author-email: nikita.voloshin.98@gmail.com
+License: MIT License
+        
+        Copyright (c) 2025 nikvo1
+        
+        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.
+        
+Project-URL: Bug Tracker, https://github.com/nikvo1/napari-nuclephaser/issues
+Project-URL: Documentation, https://github.com/nikvo1/napari-nuclephaser#README.md
+Project-URL: Source Code, https://github.com/nikvo1/napari-nuclephaser
+Project-URL: User Support, https://github.com/nikvo1/napari-nuclephaser/issues
+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: setuptools
+Requires-Dist: wheel
+Requires-Dist: napari
+Requires-Dist: ultralytics
+Requires-Dist: yolov5
+Requires-Dist: magicgui
+Requires-Dist: sahi
+Requires-Dist: scikit-image
+Requires-Dist: torch
+Requires-Dist: pathlib
+Requires-Dist: numpy
+Requires-Dist: typing
+Requires-Dist: pandas
+Requires-Dist: openpyxl
+Requires-Dist: seaborn
+Requires-Dist: opencv-python
+Requires-Dist: imagecodecs
+Provides-Extra: testing
+Requires-Dist: tox; extra == "testing"
+Requires-Dist: pytest; extra == "testing"
+Requires-Dist: pytest-cov; extra == "testing"
+Requires-Dist: pytest-qt; extra == "testing"
+Requires-Dist: pytest-mock; extra == "testing"
+Requires-Dist: napari; extra == "testing"
+Requires-Dist: pyqt5; extra == "testing"
+Dynamic: license-file
+
+# napari-nuclephaser
+
+[![License MIT](https://img.shields.io/pypi/l/napari-nuclephaser.svg?color=green)](https://github.com/nikvo1/napari-nuclephaser/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/napari-nuclephaser.svg?color=green)](https://pypi.org/project/napari-nuclephaser)
+[![Python Version](https://img.shields.io/pypi/pyversions/napari-nuclephaser.svg?color=green)](https://python.org)
+[![tests](https://github.com/nikvo1/napari-nuclephaser/workflows/tests/badge.svg)](https://github.com/nikvo1/napari-nuclephaser/actions)
+[![codecov](https://codecov.io/gh/nikvo1/napari-nuclephaser/branch/main/graph/badge.svg)](https://codecov.io/gh/nikvo1/napari-nuclephaser)
+[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-nuclephaser)](https://napari-hub.org/plugins/napari-nuclephaser)
+[![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 Napari plugin to detect and count nuclei on phase contrast images
+
+----------------------------------
+
+This [napari] plugin was generated with [copier] using the [napari-plugin-template].
+
+<!--
+Don't miss the full getting started guide to set up your new package:
+https://github.com/napari/napari-plugin-template#getting-started
+
+and review the napari docs for plugin developers:
+https://napari.org/stable/plugins/index.html
+-->
+
+## Installation
+
+You can install `napari-nuclephaser` via [pip]:
+
+    pip install napari-nuclephaser
+
+
+
+To install latest development version :
+
+    pip install git+https://github.com/nikvo1/napari-nuclephaser.git
+
+
+## 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-nuclephaser" 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
+
+[file an issue]: https://github.com/nikvo1/napari-nuclephaser/issues
+
+[napari]: https://github.com/napari/napari
+[tox]: https://tox.readthedocs.io/en/latest/
+[pip]: https://pypi.org/project/pip/
+[PyPI]: https://pypi.org/

napari_nuclephaser-0.0.1/README.md

@@ -0,0 +1,69 @@
+# napari-nuclephaser
+
+[![License MIT](https://img.shields.io/pypi/l/napari-nuclephaser.svg?color=green)](https://github.com/nikvo1/napari-nuclephaser/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/napari-nuclephaser.svg?color=green)](https://pypi.org/project/napari-nuclephaser)
+[![Python Version](https://img.shields.io/pypi/pyversions/napari-nuclephaser.svg?color=green)](https://python.org)
+[![tests](https://github.com/nikvo1/napari-nuclephaser/workflows/tests/badge.svg)](https://github.com/nikvo1/napari-nuclephaser/actions)
+[![codecov](https://codecov.io/gh/nikvo1/napari-nuclephaser/branch/main/graph/badge.svg)](https://codecov.io/gh/nikvo1/napari-nuclephaser)
+[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-nuclephaser)](https://napari-hub.org/plugins/napari-nuclephaser)
+[![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 Napari plugin to detect and count nuclei on phase contrast images
+
+----------------------------------
+
+This [napari] plugin was generated with [copier] using the [napari-plugin-template].
+
+<!--
+Don't miss the full getting started guide to set up your new package:
+https://github.com/napari/napari-plugin-template#getting-started
+
+and review the napari docs for plugin developers:
+https://napari.org/stable/plugins/index.html
+-->
+
+## Installation
+
+You can install `napari-nuclephaser` via [pip]:
+
+    pip install napari-nuclephaser
+
+
+
+To install latest development version :
+
+    pip install git+https://github.com/nikvo1/napari-nuclephaser.git
+
+
+## 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-nuclephaser" 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
+
+[file an issue]: https://github.com/nikvo1/napari-nuclephaser/issues
+
+[napari]: https://github.com/napari/napari
+[tox]: https://tox.readthedocs.io/en/latest/
+[pip]: https://pypi.org/project/pip/
+[PyPI]: https://pypi.org/

napari_nuclephaser-0.0.1/pyproject.toml

@@ -0,0 +1,131 @@
+[project]
+name = "napari-nuclephaser"
+dynamic = ["version"]
+description = "A Napari plugin to detect and count nuclei on phase contrast images"
+readme = "README.md"
+license = {file = "LICENSE"}
+authors = [
+  {name = "Nikita Voloshin"},
+  {email = "nikita.voloshin.98@gmail.com"},
+]
+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"
+dependencies = ["setuptools",
+		"wheel",
+		"napari",
+		"ultralytics",
+		"yolov5",
+		"magicgui",
+		"sahi",
+		"scikit-image",
+		"torch",
+		"pathlib",
+		"numpy",
+		"typing",
+		"pandas",
+		"openpyxl",
+		"seaborn",
+		"opencv-python",
+		"imagecodecs"]
+
+[project.optional-dependencies]
+testing = [
+    "tox",
+    "pytest",  # https://docs.pytest.org/en/latest/contents.html
+    "pytest-cov",  # https://pytest-cov.readthedocs.io/en/latest/
+    "pytest-qt",
+    "pytest-mock",  # https://pytest-qt.readthedocs.io/en/latest/
+    "napari",
+    "pyqt5",
+]
+
+[project.entry-points."napari.manifest"]
+napari-nuclephaser = "napari_nuclephaser:napari.yaml"
+
+[project.urls]
+"Bug Tracker" = "https://github.com/nikvo1/napari-nuclephaser/issues"
+"Documentation" = "https://github.com/nikvo1/napari-nuclephaser#README.md"
+"Source Code" = "https://github.com/nikvo1/napari-nuclephaser"
+"User Support" = "https://github.com/nikvo1/napari-nuclephaser/issues"
+
+[build-system]
+requires = ["setuptools>=42.0.0", "wheel", "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_nuclephaser/_version.py"
+
+
+[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.
+    "SIM117", # flake8-simplify - some of merged with statements are not looking great with black, reanble after drop python 3.9
+]
+
+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*",
+]
+
+target-version = "py310"
+fix = true

napari_nuclephaser-0.0.1/setup.cfg

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

napari_nuclephaser-0.0.1/src/napari_nuclephaser/__init__.py

@@ -0,0 +1,2 @@
+__version__ = "0.0.1"
+# from .widget import widget_factory