napari-piscis 0.1.21__tar.gz

napari_piscis-0.1.21/.github/ISSUE_TEMPLATE/bug_report.yml

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+name: "Bug Report"
+description: Report a bug encountered while using piscis-ufish
+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: "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: "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: "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: "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: "Additional Context"
+        description: "Please provide any additional information or context regarding the problem here."
+        placeholder: "Add any other context about the problem here."

napari_piscis-0.1.21/.github/ISSUE_TEMPLATE/documentation.md

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

napari_piscis-0.1.21/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: "Feature Request"
+about: Submit a proposal/request for a new piscis-ufish 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_piscis-0.1.21/.github/ISSUE_TEMPLATE/task.md

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+---
+name: "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_piscis-0.1.21/.github/PULL_REQUEST_TEMPLATE.md

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+# 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_piscis-0.1.21/.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_piscis-0.1.21/.github/workflows/test_and_deploy.yml

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+# 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"]
+
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - 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: ${{ matrix.platform }}
+
+      - name: Coverage
+        uses: codecov/codecov-action@v5
+
+  build-and-inspect-package:
+    name: Build & inspect package.
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+      - name: Install setuptools_scm for debugging
+        run: python -m pip install setuptools_scm
+      - name: Debug Git and Setuptools_SCM
+        run: |
+          echo "--- Git Status ---"
+          git status
+          echo "--- Git Log (last 10 commits) ---"
+          git log --oneline -n 10
+          echo "--- Git Tags ---"
+          git tag -l
+          echo "--- Setuptools_SCM Version ---"
+          python -c "from setuptools_scm import get_version; print(get_version())"
+      - uses: hynek/build-and-inspect-python-package@v2
+
+  deploy:
+    needs: [test, build-and-inspect-package]
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags/v')
+    permissions:
+      id-token: write
+    steps:
+      - name: Check out code
+        uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install build backend + setuptools_scm
+        run: python -m pip install --upgrade build setuptools setuptools_scm
+
+      - name: Extract version from tag
+        id: version
+        run: echo "version=${GITHUB_REF#refs/tags/v}" >> "$GITHUB_OUTPUT"
+
+      - name: Show version we will use
+        run: echo "Using version ${{ steps.version.outputs.version }}"
+
+      - name: Build package
+        env:
+          SETUPTOOLS_SCM_PRETEND_VERSION: ${{ steps.version.outputs.version }}
+        run: python -m build
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

napari_piscis-0.1.21/.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_piscis-0.1.21/.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_piscis-0.1.21/.napari-hub/config.yml

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+# 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_piscis-0.1.21/.pre-commit-config.yaml

@@ -0,0 +1,27 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    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: v0.14.6
+    hooks:
+      - id: ruff
+  - repo: https://github.com/psf/black
+    rev: 25.11.0
+    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_piscis-0.1.21/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2023-2024 William Niu
+
+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_piscis-0.1.21/MANIFEST.in

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

napari_piscis-0.1.21/PKG-INFO

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+Metadata-Version: 2.4
+Name: napari-piscis
+Version: 0.1.21
+Summary: Unofficial plugin for Piscis, a deep learning algorithm for spot detection.
+Author-email: Michael Blodgett <michaelablodgett@gmail.com>
+License: MIT License
+        
+        Copyright (c) 2023-2024 William Niu
+        
+        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: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: <3.14,>=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: napari>=0.4.19
+Requires-Dist: magicgui>=0.8
+Requires-Dist: numpy
+Requires-Dist: scikit-image
+Requires-Dist: piscis>=0.2.7
+Requires-Dist: jax<=0.4.30
+Requires-Dist: loguru
+Provides-Extra: all
+Requires-Dist: napari[all]; extra == "all"
+Dynamic: license-file
+
+# napari-piscis
+
+[![License MIT](https://img.shields.io/pypi/l/napari-piscis.svg?color=green)](https://github.com/p5ithurism/napari-piscis/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/napari-piscis.svg?color=green)](https://pypi.org/project/napari-piscis)
+[![Python Version](https://img.shields.io/pypi/pyversions/napari-piscis.svg?color=green)](https://python.org)
+[![tests](https://github.com/p5ithurism/napari-piscis/workflows/tests/badge.svg)](https://github.com/p5ithurism/napari-piscis/actions)
+[![codecov](https://codecov.io/gh/p5ithurism/napari-piscis/branch/main/graph/badge.svg)](https://codecov.io/gh/p5ithurism/napari-piscis)
+[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-piscis)](https://napari-hub.org/plugins/napari-piscis)
+[![npe2](https://img.shields.io/badge/plugin-npe2-blue?link=https://napari.org/stable/plugins/index.html)](https://napari.org/stable/plugins/index.html)
+
+Unofficial [napari] plugin for [Piscis](https://github.com/zjniu/Piscis), a deep learning algorithm for spot detection.
+
+## Installation
+
+You can install `napari-piscis` via [pip]:
+
+```
+pip install napari-piscis
+```
+Or within the napari GUI via the Plugin Manager.
+
+To install latest development version:
+```
+pip install git+https://github.com/p5ithurism/napari-piscis.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.
+
+## Issues
+
+If you encounter any problems, please [file an issue](https://github.com/p5ithurism/napari-piscis/issues/new/choose) along with a detailed description.
+
+## License
+
+Distributed under the terms of the [MIT] license, "napari-piscis" is free and open source software
+
+[napari]: https://github.com/napari/napari
+[@napari]: https://github.com/napari
+[MIT]: http://opensource.org/licenses/MIT
+[napari-plugin-template]: https://github.com/napari/napari-plugin-template
+
+[tox]: https://tox.readthedocs.io/en/latest/
+[pip]: https://pypi.org/project/pip/
+[PyPI]: https://pypi.org/

napari_piscis-0.1.21/README.md

@@ -0,0 +1,46 @@
+# napari-piscis
+
+[![License MIT](https://img.shields.io/pypi/l/napari-piscis.svg?color=green)](https://github.com/p5ithurism/napari-piscis/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/napari-piscis.svg?color=green)](https://pypi.org/project/napari-piscis)
+[![Python Version](https://img.shields.io/pypi/pyversions/napari-piscis.svg?color=green)](https://python.org)
+[![tests](https://github.com/p5ithurism/napari-piscis/workflows/tests/badge.svg)](https://github.com/p5ithurism/napari-piscis/actions)
+[![codecov](https://codecov.io/gh/p5ithurism/napari-piscis/branch/main/graph/badge.svg)](https://codecov.io/gh/p5ithurism/napari-piscis)
+[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-piscis)](https://napari-hub.org/plugins/napari-piscis)
+[![npe2](https://img.shields.io/badge/plugin-npe2-blue?link=https://napari.org/stable/plugins/index.html)](https://napari.org/stable/plugins/index.html)
+
+Unofficial [napari] plugin for [Piscis](https://github.com/zjniu/Piscis), a deep learning algorithm for spot detection.
+
+## Installation
+
+You can install `napari-piscis` via [pip]:
+
+```
+pip install napari-piscis
+```
+Or within the napari GUI via the Plugin Manager.
+
+To install latest development version:
+```
+pip install git+https://github.com/p5ithurism/napari-piscis.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.
+
+## Issues
+
+If you encounter any problems, please [file an issue](https://github.com/p5ithurism/napari-piscis/issues/new/choose) along with a detailed description.
+
+## License
+
+Distributed under the terms of the [MIT] license, "napari-piscis" is free and open source software
+
+[napari]: https://github.com/napari/napari
+[@napari]: https://github.com/napari
+[MIT]: http://opensource.org/licenses/MIT
+[napari-plugin-template]: https://github.com/napari/napari-plugin-template
+
+[tox]: https://tox.readthedocs.io/en/latest/
+[pip]: https://pypi.org/project/pip/
+[PyPI]: https://pypi.org/