Initial release

.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:
+      - wheels
+  release:
+    types:
+      - published
+
+jobs:
+  test:
+    name: ${{ matrix.platform }} py${{ matrix.python-version }}
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      matrix:
+        platform: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: [3.9, "3.10", "3.11"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        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
+          if (Test-Path -Path "C:\Windows\system32\opengl32.dll" -PathType Leaf) {Exit 0} else {Exit 1}
+
+      # 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@v1
+        with:
+          run: python -m tox
+        env:
+          PLATFORM: ${{ matrix.platform }}
+
+  deploy:
+    needs: [test]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release' && github.event.action == 'published' # upload to pypi only on release
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        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.PYPI_API_TOKEN }}
+        run: |
+          python -m build .
+          twine upload dist/*

.gitignore

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+*/__pycache__/
+*.py[cod]
+.idea
+
+.DS_Store
+.ipynb_checkpoints
+.pytest_cache
+*.egg-info/
+build/
+dist/
+htmlcov/
+.coverage*
+
+*.npz
+*.tif*
+*.hdf5
+*.h5
+*.zip
+*.so
+*.tfevents.*

.napari/DESCRIPTION.md

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+
+
+<!-- This file is designed to provide you with a starting template for documenting
+the functionality of your plugin. Its content will be rendered on your plugin's
+napari hub page.
+
+The sections below are given as a guide for the flow of information only, and
+are in no way prescriptive. You should feel free to merge, remove, add and 
+rename sections at will to make this document work best for your plugin. 
+
+# Description
+
+This should be a detailed description of the context of your plugin and its 
+intended purpose.
+
+If you have videos or screenshots of your plugin in action, you should include them
+here as well, to make them front and center for new users. 
+
+You should use absolute links to these assets, so that we can easily display them 
+on the hub. The easiest way to include a video is to use a GIF, for example hosted
+on imgur. You can then reference this GIF as an image.
+
+![Example GIF hosted on Imgur](https://i.imgur.com/A5phCX4.gif)
+
+Note that GIFs larger than 5MB won't be rendered by GitHub - we will however,
+render them on the napari hub.
+
+The other alternative, if you prefer to keep a video, is to use GitHub's video
+embedding feature.
+
+1. Push your `DESCRIPTION.md` to GitHub on your repository (this can also be done
+as part of a Pull Request)
+2. Edit `.napari/DESCRIPTION.md` **on GitHub**.
+3. Drag and drop your video into its desired location. It will be uploaded and
+hosted on GitHub for you, but will not be placed in your repository.
+4. We will take the resolved link to the video and render it on the hub.
+
+Here is an example of an mp4 video embedded this way.
+
+https://user-images.githubusercontent.com/17995243/120088305-6c093380-c132-11eb-822d-620e81eb5f0e.mp4
+
+# Intended Audience & Supported Data
+
+This section should describe the target audience for this plugin (any knowledge,
+skills and experience required), as well as a description of the types of data
+supported by this plugin.
+
+Try to make the data description as explicit as possible, so that users know the
+format your plugin expects. This applies both to reader plugins reading file formats
+and to function/dock widget plugins accepting layers and/or layer data.
+For example, if you know your plugin only works with 3D integer data in "tyx" order,
+make sure to mention this.
+
+If you know of researchers, groups or labs using your plugin, or if it has been cited
+anywhere, feel free to also include this information here.
+
+# Quickstart
+
+This section should go through step-by-step examples of how your plugin should be used.
+Where your plugin provides multiple dock widgets or functions, you should split these
+out into separate subsections for easy browsing. Include screenshots and videos
+wherever possible to elucidate your descriptions. 
+
+Ideally, this section should start with minimal examples for those who just want a
+quick overview of the plugin's functionality, but you should definitely link out to
+more complex and in-depth tutorials highlighting any intricacies of your plugin, and
+more detailed documentation if you have it.
+
+# Additional Install Steps (uncommon)
+We will be providing installation instructions on the hub, which will be sufficient
+for the majority of plugins. They will include instructions to pip install, and
+to install via napari itself.
+
+Most plugins can be installed out-of-the-box by just specifying the package requirements
+over in `setup.cfg`. However, if your plugin has any more complex dependencies, or 
+requires any additional preparation before (or after) installation, you should add 
+this information here.
+
+# Getting Help
+
+This section should point users to your preferred support tools, whether this be raising
+an issue on GitHub, asking a question on image.sc, or using some other method of contact.
+If you distinguish between usage support and bug/feature support, you should state that
+here.
+
+# How to Cite
+
+Many plugins may be used in the course of published (or publishable) research, as well as
+during conference talks and other public facing events. If you'd like to be cited in
+a particular format, or have a DOI you'd like used, you should provide that information here. -->
+
+The developer has not yet provided a napari-hub specific description.

.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.254
+    hooks:
+    - id: ruff
+      args: [--fix, --fix-only, --exit-non-zero-on-fix]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+    - id: check-yaml
+    - id: end-of-file-fixer
+    - id: trailing-whitespace
+  - repo: https://github.com/psf/black
+    rev: 22.6.0
+    hooks:
+    - id: black
+  - repo: https://github.com/mwouts/jupytext
+    rev: v1.14.0
+    hooks:
+    - id: jupytext
+      args: [--from, ipynb, --to, "py:percent"]

LICENSE

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+
+Copyright (c) 2023, Albert Dominguez Mantes, Martin Weigert
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of napari-spotiflow nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

MANIFEST.in

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+include LICENSE
+include README.md
+include requirements.txt
+
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]

README.md

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+[![License: BSD-3](https://img.shields.io/badge/License-BSD3-blue.svg)](https://www.gnu.org/licenses/bsd3)
+[![PyPI](https://img.shields.io/pypi/v/napari-spotiflow.svg?color=green)](https://pypi.org/project/napari-spotiflow)
+[![Python Version](https://img.shields.io/pypi/pyversions/napari-spotiflow.svg?color=green)](https://python.org)
+[![tests](https://github.com/weigertlab/napari-spotiflow/workflows/tests/badge.svg)](https://github.com/weigertlab/napari-spotiflow/actions)
+[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-spotiflow)](https://napari-hub.org/plugins/napari-spotiflow)
+
+![Logo](artwork/spotiflow_logo.png)
+---
+
+# napari-spotiflow
+
+Napari plugin for *Spotiflow*, a deep learning-based, threshold-agnostic, and subpixel-accurate spot detection method for fluorescence microscopy. For the main repo, see [here](https://github.com/weigertlab/spotiflow). 
+
+
+https://github.com/weigertlab/napari-spotiflow/assets/11042162/99c09826-bda7-46bc-a9a8-6e0c52b3f9f1
+
+
+----------------------------------
+
+# Usage 
+
+1. Open 2d raw image (or open one of our samples eg `File > Open Sample > napari-spotiflow > HybISS`)
+2. Start Plugin `Plugins > napari-spotiflow`
+3. Select model (pretrained or custom trained) and optionally adjust other parameter
+4. Click `run`
+
+## Supported input formats
+- [x] 2D (YX or YXC)
+- [x] 2D+t (TYX or TYXC)
+
+## Installation
+
+Clone the repo and install it in an environment with `napari` and `spotiflow`.
+
+```
+git clone [email protected]:weigertlab/napari-spotiflow.git
+pip install -e napari-spotiflow
+```

docs/index.md

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+# Welcome to napari-spotiflow
+
+Napari plugin for Spotiflow

mkdocs.yml

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+site_name: napari-spotiflow
+site_description: Napari plugin for Spotiflow
+site_author: Albert Dominguez Mantes, Martin Weigert
+
+theme: readthedocs
+
+
+repo_url: https://github.com/weigertlab/napari-spotiflow
+
+pages:
+- Home: index.md

napari_spotiflow/__init__.py

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+__version__ = "0.0.2"
+
+_point_layer2d_default_kwargs = dict(size=8,
+                                     symbol='ring',
+                                     opacity=1,
+                                     face_color=[1.,.5,.2],
+                                     edge_color=[1.,.5,.2])
+
+
+# def sample_data_2d():
+#     from spotiflow.data import hybiss_data_2d
+#     
+#     return [(hybiss_data_2d(), {"name": "HybISS data (2d)"})]