Merge branch 'master' of https://github.com/haesleinhuepf/devbio-napari

.github/workflows/test_and_deploy.yml

@@ -22,7 +22,7 @@ jobs:
     runs-on: ${{ matrix.platform }}
     strategy:
       matrix:
-        platform: [ubuntu-latest, windows-latest, macos-latest]
+        platform: [ubuntu-latest, macos-latest]
         python-version: [3.7, 3.8, 3.9]
 
     steps:

README.md

@@ -3,8 +3,13 @@
 [![License](https://img.shields.io/pypi/l/devbio-napari.svg?color=green)](https://github.com/haesleinhuepf/devbio-napari/raw/master/LICENSE)
 [![PyPI](https://img.shields.io/pypi/v/devbio-napari.svg?color=green)](https://pypi.org/project/devbio-napari)
 [![Python Version](https://img.shields.io/pypi/pyversions/devbio-napari.svg?color=green)](https://python.org)
+[![tests](https://github.com/haesleinhuepf/devbio-napari/workflows/tests/badge.svg)](https://github.com/haesleinhuepf/napari-plot-profile/actions)
+[![codecov](https://codecov.io/gh/haesleinhuepf/devbio-napari/branch/master/graph/badge.svg)](https://codecov.io/gh/haesleinhuepf/devbio-napari)
+[![Development Status](https://img.shields.io/pypi/status/devbio-napari.svg)](https://en.wikipedia.org/wiki/Software_release_life_cycle#Alpha)
+[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/devbio-napari)](https://napari-hub.org/plugins/devbio-napari)
 
-A collection of napari plugins useful for studying developmental biology.
+
+A bundle of napari plugins useful for 3D+t image processing and analysis for studying developmental biology.
 
 * File input/output plugins
   * [aicsimageio](https://www.napari-hub.org/plugins/napari-aicsimageio)
@@ -48,14 +53,8 @@ This [napari] plugin was generated with [Cookiecutter] using with [@napari]'s [c
 
 You can install `devbio-napari` via [pip]:
 
-    conda install -c conda-forge pyopencl jupyter notebook
-    pip install devbio-napari
-
-Windows users should install [pyopencl](https://documen.tician.de/pyopencl/) via conda **in advance**:
-
     conda install -c conda-forge pyopencl
-
-[See also](https://github.com/clEsperanto/napari_pyclesperanto_assistant#Installation).
+    pip install devbio-napari
 
 ## Contributing
 

devbio/__init__.py

@@ -1,8 +1,19 @@
 
 __version__ = "0.1.4"
 
+from napari_tools_menu import register_dock_widget
 
+from RedLionfishDeconv.napari_plugin import RedLionfish_widget
+register_dock_widget( RedLionfish_widget, menu="Filtering / deconvolution > Richardson-Lucy (RedLionfish)")
 
+from napari_3d_ortho_viewer._dock_widget import OrthoViewerWidget
+register_dock_widget( OrthoViewerWidget, menu="Visualization > Ortho Viewer (napari-3d-ortho-viewer)")
 
+from platymatch._dock_widget import DetectNuclei, EstimateTransform, EvaluateMetrics
+register_dock_widget(DetectNuclei, menu="Registration > Detect nuclei (platymatch)")
+register_dock_widget(EstimateTransform, menu="Registration > Estimate transform (platymatch)")
+register_dock_widget(EvaluateMetrics, menu="Registration > Evaluate metrics (platymatch)")
 
+from napari_animation._qt import AnimationWidget
+register_dock_widget(EvaluateMetrics, menu="Visualization > Animation Wizard (napari-animation)")
 

setup.cfg

@@ -5,7 +5,7 @@ author = Robert Haase
 author_email = robert.haase@tu-dresden.de
 license = BSD-3
 url = https://github.com/haesleinhuepf/devbio-napari
-description = A collection of napari plugins useful for studying developmental biology
+description = A bundle of napari plugins useful for 3D+t image processing and analysis for studying developmental biology.
 long_description = file: README.md
 long_description_content_type = text/markdown
 classifiers =

tox.ini

@@ -0,0 +1,37 @@
+# For more information about tox, see https://tox.readthedocs.io/en/latest/
+[tox]
+envlist = py{37,38,39}-{linux,macos,windows}
+
+[gh-actions]
+python =
+    3.7: py37
+    3.8: py38
+    3.9: py39
+
+[gh-actions:env]
+PLATFORM =
+    ubuntu-latest: linux
+    macos-latest: macos
+
+[testenv]
+platform = 
+    macos: darwin
+    linux: linux
+    windows: win32
+passenv = 
+    CI
+    GITHUB_ACTIONS
+    DISPLAY XAUTHORITY
+    NUMPY_EXPERIMENTAL_ARRAY_FUNCTION
+    PYVISTA_OFF_SCREEN
+deps = 
+    pytest  # https://docs.pytest.org/en/latest/contents.html
+    pytest-cov  # https://pytest-cov.readthedocs.io/en/latest/
+    pytest-xvfb ; sys_platform == 'linux'
+    # you can remove these if you don't use them
+    napari
+    magicgui
+    pytest-qt
+    qtpy
+    pyqt5
+commands = pytest -v --color=yes --cov=napari_workflow_optimizer --cov-report=xml