Merge pull request #4 from portugueslab/npe2

from napari-plugin-engine to npe2

.github/workflows/main.yml

@@ -6,9 +6,9 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.8
       - name: Install dependencies
@@ -24,9 +24,9 @@ jobs:
     needs: lint
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.8
       - name: Install dependencies
@@ -46,9 +46,9 @@ jobs:
     runs-on: ubuntu-latest
     if: startsWith(github.ref, 'refs/tags/v')
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v4
         with:
           python-version: "3.x"
       - name: Install dependencies

README.md

@@ -9,7 +9,7 @@
 
 
 
-# hdf5/split-dataset file reader for napari
+# split-dataset/hdf5 file reader for napari
 
 A `napari` plugin for visualising [`SplitDataset`](https://github.com/portugueslab/split_dataset) objects. This package has been developed in the [Portugues lab](http://www.portugueslab.com).
 

napari_split_dataset/__init__.py

@@ -1,6 +1,6 @@
 """hdf5/split-dataset file reader for napari"""
 
 __author__ = """You Wu @portugueslab"""
-__version__ = "0.1.1"
+__version__ = "0.2.0"
 
 from napari_split_dataset.napari_split_dataset import napari_get_reader

napari_split_dataset/napari.yaml

@@ -0,0 +1,10 @@
+name: napari-split-dataset
+contributions:
+  commands:
+  - id: napari-split-dataset.get_reader
+    python_name: napari_split_dataset.napari_split_dataset:napari_get_reader
+    title: Open SplitDataset files
+  readers:
+  - command: napari-split-dataset.get_reader
+    accepts_directories: true
+    filename_patterns: ["*.h5", "*.hdf5"]

napari_split_dataset/napari_split_dataset.py

@@ -3,11 +3,9 @@
 
 import flammkuchen as fl
 import numpy as np
-from napari_plugin_engine import napari_hook_implementation
 from split_dataset import SplitDataset
 
 
-@napari_hook_implementation
 def napari_get_reader(path):
     path = Path(path)
     if path.is_dir():
@@ -40,7 +38,7 @@ def read_directory(path):
         data = data[:, :, :]
         add_kwargs = {}
 
-    layer_type = "image"  # default
+    layer_type = "image"
     return [(data, add_kwargs, layer_type)]
 
 
@@ -61,4 +59,5 @@ def read_hdf5(path):
             return None
 
     add_kwargs = {}
-    return [(data, add_kwargs)]
+    layer_type = "image"
+    return [(data, add_kwargs, layer_type)]

setup.cfg

@@ -1,11 +1,60 @@
+[metadata]
+name = napari-split-dataset
+version = 0.2.0
+url = https://github.com/portugueslab/napari-split-dataset
+author = You Wu @portugueslab
+author_email = [email protected]
+classifiers =
+    Development Status :: 2 - Pre-Alpha
+    Intended Audience :: Developers
+    License :: OSI Approved :: MIT License
+    Natural Language :: English
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
+license = MIT
+description = split-dataset/hdf5 file reader for napari
+long_description = file: README.md
+long_description_content_type = text/markdown
+
+[options]
+zip_safe = False
+# setup_requires = pytest-runner
+install_requires = 
+    numpy
+    flammkuchen
+    split_dataset
+python_requires = >=3.7
+tests_require = pytest>=3
+test_suite = tests
+include_package_data = True
+packages = find_namespace:
+
+[options.extras_require]
+dev = 
+    pytest
+    pytest-cov
+    black
+    flake8
+    isort
+
+[options.entry_points]
+napari.manifest = 
+	napari-split-dataset = napari_split_dataset:napari.yaml
+
+[options.package_data]
+napari_split_dataset = napari.yaml
+
 [bumpversion]
-current_version = 0.1.1
+current_version = 0.2.0
 commit = True
 tag = True
 
-[bumpversion:file:setup.py]
-search = version="{current_version}"
-replace = version="{new_version}"
+[bumpversion:file:setup.cfg]
+search = version = "{current_version}"
+replace = version = "{new_version}"
 
 [bumpversion:file:napari_split_dataset/__init__.py]
 search = __version__ = "{current_version}"

setup.py

@@ -1,58 +1,5 @@
 #!/usr/bin/env python
 
-"""The setup script."""
+from setuptools import setup
 
-from setuptools import find_namespace_packages, setup
-
-with open("README.md") as readme_file:
-    readme = readme_file.read()
-
-with open("requirements.txt") as f:
-    requirements = f.read().splitlines()
-
-with open("requirements_dev.txt") as f:
-    requirements_dev = f.read().splitlines()
-
-setup_requirements = [
-    "pytest-runner",
-]
-
-test_requirements = [
-    "pytest>=3",
-]
-
-setup(
-    author="You Wu @portugueslab",
-    author_email="[email protected]",
-    python_requires=">=3.5",
-    classifiers=[
-        "Development Status :: 2 - Pre-Alpha",
-        "Intended Audience :: Developers",
-        "License :: OSI Approved :: MIT License",
-        "Natural Language :: English",
-        "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.5",
-        "Programming Language :: Python :: 3.6",
-        "Programming Language :: Python :: 3.7",
-        "Programming Language :: Python :: 3.8",
-    ],
-    description="hdf5/split-dataset file reader for napari",
-    long_description=readme,
-    long_description_content_type="text/markdown",
-    extras_require=dict(dev=requirements_dev),
-    entry_points={
-        "napari.plugin": ["split-dataset = napari_split_dataset"],
-    },
-    install_requires=requirements,
-    license="MIT",
-    include_package_data=True,
-    keywords="napari_split_dataset",
-    name="napari_split_dataset",
-    packages=find_namespace_packages(exclude=("docs", "tests*")),
-    setup_requires=setup_requirements,
-    test_suite="tests",
-    tests_require=test_requirements,
-    url="https://github.com/portugueslab/napari_split_dataset",
-    version="0.1.1",
-    zip_safe=False,
-)
+setup()