diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml index ffc047b..aaaf4de 100644 --- a/.github/workflows/test_and_deploy.yml +++ b/.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: diff --git a/README.md b/README.md index 3d1dda3..30c6b8c 100644 --- a/README.md +++ b/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) @@ -44,14 +49,8 @@ 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 diff --git a/devbio/__init__.py b/devbio/__init__.py index 9933ac1..5a721f8 100644 --- a/devbio/__init__.py +++ b/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)") diff --git a/setup.cfg b/setup.cfg index d9ade4f..62145f9 100644 --- a/setup.cfg +++ b/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 = diff --git a/tox.ini b/tox.ini new file mode 100644 index 0000000..fe9c5eb --- /dev/null +++ b/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