merge

Author: yrkim98

.github/workflows/plugin_preview.yml

@@ -12,7 +12,7 @@ jobs:
     strategy:
       matrix:
         platform: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: [3.8, 3.9]
+        python-version: [3.9]
 
     steps:
       - uses: actions/checkout@v2

.github/workflows/test_and_lint.yml

@@ -3,8 +3,6 @@
 except ImportError:
     __version__ = "unknown"
 
-from ._dock_widget import napari_experimental_provide_dock_widget  # noqa: F401
-
 # Do not edit this string manually, always use bumpversion
 # Details in CONTRIBUTING.md
 __version__ = "2.1.12"

napari_allencell_segmenter/__init__.py

@@ -1,8 +1,6 @@
-# Hook specifications: https://napari.org/docs/dev/plugins/hook_specifications.html
 import napari
 
 from napari_allencell_segmenter.core.application import Application
-from napari_plugin_engine import napari_hook_implementation
 from qtpy.QtWidgets import QWidget, QVBoxLayout, QSizePolicy
 
 """
@@ -28,8 +26,3 @@ def __init__(self, napari_viewer: napari.Viewer):
         self.setLayout(QVBoxLayout())
         self._application = Application(napari_viewer, self.layout())
         self._application.router.batch_processing()  # Initialize first screen
-
-
-@napari_hook_implementation
-def napari_experimental_provide_dock_widget():  # pragma: no-cover
-    return [(WorkflowEditorWidget, {"name": "Workflow editor"}), (BatchProcessingWidget, {"name": "Batch processing"})]

napari_allencell_segmenter/_dock_widget.py

@@ -0,0 +1,20 @@
+name: napari-allencell-segmenter
+display_name: Allen Cell Segmenter
+contributions:
+  commands:
+    - id: napari-allencell-segmenter.workflow_editor
+      title: Workflow editor
+      python_name: napari_allencell_segmenter._dock_widget:WorkflowEditorWidget
+
+    - id: napari-allencell-segmenter.batch_processing
+      title: Batch processing
+      python_name: napari_allencell_segmenter._dock_widget:BatchProcessingWidget
+  readers:
+  writers:
+  sample_data:
+  widgets:
+    - command: napari-allencell-segmenter.workflow_editor
+      display_name: Workflow editor
+
+    - command: napari-allencell-segmenter.batch_processing
+      display_name: Batch processing

napari_allencell_segmenter/napari.yaml

@@ -19,7 +19,6 @@
 
 
 class WorkflowThumbnails(QWidget):
-
     """
     A widget containing thumbnail images for workflows.
 

napari_allencell_segmenter/widgets/workflow_thumbnails.py

@@ -1,2 +1,94 @@
 [tool.black]
 line-length = 120
+
+[build-system]
+requires = ["setuptools>=61", "setuptools_scm>=7"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "napari-allencell-segmenter"
+version = "2.1.12-dev0"  # setuptools_scm will override if tags exist
+description = "A plugin that enables 3D image segmentation provided by Allen Institute for Cell Science"
+readme = "README.md"
+license = { text = "BSD-3" }
+requires-python = ">=3.9"
+authors = [
+  { name = "Allen Institute for Cell Science" }
+]
+classifiers = [
+  "Development Status :: 5 - Production/Stable",
+  "Intended Audience :: Science/Research",
+  "Framework :: napari",
+  "Topic :: Scientific/Engineering",
+  "Topic :: Scientific/Engineering :: Visualization",
+  "Topic :: Scientific/Engineering :: Information Analysis",
+  "Topic :: Scientific/Engineering :: Bio-Informatics",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.9",
+  "Operating System :: OS Independent",
+  "License :: OSI Approved :: BSD License",
+]
+
+dependencies = [
+  "napari>=0.4.9,<0.6.2",
+  "napari-plugin-engine>=0.1.4",
+  "numpy<2.0.0",
+  "aicssegmentation >= 0.5.3",
+  "magicgui >= 0.2.9",
+  "aicsimageio ~= 4.0.5",
+  "opencv-python-headless>=4.5.1",
+  "importlib-metadata==4.11.4",
+  "npe2",
+  # the following changes were made to get ci working on 3.9
+  "itk-core>=5.3,<5.4",
+  "itkwidgets==0.27.0",
+  "itk-meshtopolydata==0.10.0",
+  "pydantic==1.10.12",
+]
+
+[project.optional-dependencies]
+test = [
+  "black>=19.10b0",
+  "codecov>=2.0.22",
+  "docutils>=0.10,<0.16",
+  "flake8>=3.7.7",
+  "psutil>=5.7.0",
+  "pytest>=4.3.0",
+  "pytest-cov==2.6.1",
+  "pytest-raises>=0.10",
+  "pytest-qt>=3.3.0",
+  "quilt3>=3.1.12",
+]
+dev = [
+  "bumpversion>=0.5.3",
+  "coverage>=5.0a4",
+  "gitchangelog>=3.0.4",
+  "ipython>=7.5.0",
+  "m2r>=0.2.1",
+  "pytest-runner>=4.4",
+  "Sphinx>=2.0.0b1,<3",
+  "sphinx_rtd_theme>=0.1.2",
+  "tox==3.25.0",
+  "twine>=1.13.0",
+  "wheel>=0.33.1",
+]
+setup = ["pytest-runner"]
+
+[project.entry-points."napari.manifest"]
+napari-allencell-segmenter = "napari_allencell_segmenter:napari.yaml"
+
+[tool.setuptools_scm]
+write_to = "napari_allencell_segmenter/_version.py"
+
+[tool.setuptools.packages.find]
+include = ["napari_allencell_segmenter*"]
+
+[project.urls]
+"Bug Tracker" = "https://github.com/AllenCell/napari-allencell-segmenter/issues"
+"Documentation" = "https://github.com/AllenCell/napari-allencell-segmenter#README.md"
+"Source Code" = "https://github.com/AllenCell/napari-allencell-segmenter"
+"User Support" = "https://github.com/AllenCell/napari-allencell-segmenter/issues"
+
+# allow pytest testing on pyqt5
+[tool.pytest]
+qt_api="pyqt5"

pyproject.toml

@@ -51,9 +51,5 @@ omit =
 	*/_tests/*
 	**/__init__.py
 
-[options.entry_points]
-napari.manifest = 
-	example-plugin = napari_allencell_segmenter:napari.yaml
-
 [options.package_data]
 example-plugin = napari.yaml

setup.cfg

@@ -1,11 +1,9 @@
 # For more information about tox, see https://tox.readthedocs.io/en/latest/
 [tox]
-envlist = py{37,38,39}-{linux,macos,windows}
+envlist = py{39}-{linux,macos,windows}
 
 [gh-actions]
 python =
-    3.7: py37
-    3.8: py38
     3.9: py39
 
 [gh-actions:env]
@@ -35,4 +33,10 @@ deps =
     qtpy
     pyqt5
     opencv-python-headless
+    scikit-build
+    itk-core>=5.3,<5.4
+    itkwidgets==0.27.0
+    itk-meshtopolydata==0.10.0
+    pydantic==1.10.12
+
 commands = pytest -v --color=yes --cov=napari_allencell_segmenter --cov-report=xml