Npe2 plugin

.github/workflows/test_and_deploy.yml

@@ -12,6 +12,14 @@ on:
   workflow_dispatch:
 
 jobs:
+  check-manifest:
+    name: Check Manifest
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
+      - run: pip install check-manifest && check-manifest
+
   # Won't work without GPU
 
   # test:
@@ -54,25 +62,36 @@ jobs:
   # - name: Coverage
   #   uses: codecov/codecov-action@v1
 
+
   deploy:
-    # needs: test
+    name: Deploy
+    needs: check-manifest
+    if: "success() && startsWith(github.ref, 'refs/tags/')"
     runs-on: ubuntu-latest
-    if: ${{ github.repository == 'tlambert03/pycudadecon' && contains(github.ref, 'tags') }}
+
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
         with:
           python-version: "3.x"
-      - name: Install dependencies
+
+      - name: install
         run: |
-          python -m pip install --upgrade pip
-          pip install -U setuptools wheel twine
+          git tag
+          pip install -U pip
+          pip install -U build twine
+          python -m build
+          twine check dist/*
+          ls -lh dist
+
       - name: Build and publish
+        run: twine upload dist/*
         env:
           TWINE_USERNAME: __token__
           TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
-        run: |
-          git tag
-          python setup.py sdist bdist_wheel
-          twine upload dist/*
+
+      - uses: softprops/action-gh-release@v1
+        with:
+          generate_release_notes: true

pycudadecon/__init__.py

@@ -1,4 +1,13 @@
-__version__ = "0.2.0"
+try:
+    from importlib.metadata import PackageNotFoundError, version
+except ImportError:
+    from importlib_metadata import PackageNotFoundError, version
+
+try:
+    __version__ = version("pycudadecon")
+except PackageNotFoundError:
+    __version__ = "uninstalled"
+
 from typing import Any
 
 lib: Any

pycudadecon/napari.py

@@ -1,28 +1,44 @@
-"""
-This module is an example of a barebones QWidget plugin for napari
+from typing import TYPE_CHECKING
 
-It implements the ``napari_experimental_provide_dock_widget`` hook specification.
-see: https://napari.org/docs/dev/plugins/hook_specifications.html
+if TYPE_CHECKING:
+    import napari.types
 
-Replace code below according to your needs.
-"""
-from magicgui import magic_factory
-from napari_plugin_engine import napari_hook_implementation
 
-from napari.types import ImageData
-from pycudadecon.deconvolution import decon
-
-
-@magic_factory(call_button="Deconvolve")
 def deconvolve(
-    image: ImageData,
-    psf: ImageData,
+    image: "napari.types.ImageData",
+    psf: "napari.types.ImageData",
     image_pixel_size=0.1,
     image_zstep=0.5,
     psf_pixel_size=0.1,
     psf_zstep=0.1,
     iterations=10,
-) -> ImageData:
+) -> "napari.types.ImageData":
+    """Deconvolve `image` using `psf`.
+
+    Parameters
+    ----------
+    image : ImageData
+        image array
+    psf : ImageData
+        psf array
+    image_pixel_size : float, optional
+        image pixel size in microns, by default 0.1
+    image_zstep : float, optional
+        image z step in microns, by default 0.5
+    psf_pixel_size : float, optional
+        psf pixel size in microns, by default 0.1
+    psf_zstep : float, optional
+        psf z step size in microns, by default 0.1
+    iterations : int, optional
+        number of iterations, by default 10
+
+    Returns
+    -------
+    ImageData
+        deconvolved image.
+    """
+    from pycudadecon.deconvolution import decon
+
     return decon(
         image,
         psf,
@@ -32,9 +48,3 @@ def deconvolve(
         dzpsf=psf_zstep,
         n_iters=iterations,
     )
-
-
-@napari_hook_implementation
-def napari_experimental_provide_dock_widget():
-    # you can return either a single widget, or a sequence of widgets
-    return deconvolve, {"name": "CUDA-Deconvolution"}

pycudadecon/napari.yaml

@@ -0,0 +1,11 @@
+name: pycudadecon
+display_name: pyCUDAdecon
+contributions:
+  commands:
+    - id: pycudadecon.deconvolve
+      python_name: pycudadecon.napari:deconvolve
+      title: Deconvolve
+  widgets:
+    - command: pycudadecon.deconvolve
+      display_name: CUDA-Deconvolution
+      autogenerate: True

pyproject.toml

@@ -0,0 +1,14 @@
+[build-system]
+requires = ["setuptools>=45", "wheel", "setuptools-scm>=6.2"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
+
+[tool.check-manifest]
+ignore = [
+  ".pre-commit-config.yaml",
+  "test/**/*",
+  "docs/**/*",
+  "examples/**/*",
+  "CHANGELOG.md",
+]

setup.cfg

@@ -1,6 +1,5 @@
 [metadata]
 name = pycudadecon
-version = 0.2.0
 description = Python wrapper for CUDA-accelerated 3D deconvolution
 long_description = file: README.md
 long_description_content_type = text/markdown
@@ -35,15 +34,21 @@ project_urls =
 
 [options]
 packages = find:
+include_package_data = True
 install_requires =
     numpy
     tifffile
     typing_extensions
+    importlib-metadata;python_version<'3.8'
 python_requires = >=3.6
 
 [options.entry_points]
-napari.plugin =
-    pycudadecon = pycudadecon.napari
+napari.manifest =
+    pycudadecon = pycudadecon:napari.yaml
+
+[options.package_data]
+* = *.yaml
+
 
 [options.extras_require]
 dev =