Merge pull request #171 from constantinpape/modelzoo2

Use bioimageio.core.build_spec to generate stardist export

.github/workflows/tests.yml

@@ -55,4 +55,10 @@ jobs:
         if: startsWith(matrix.os, 'macos') == false
         run: pip install ".[test]"
 
+      - name: Install bioimage.io dependencies
+        if: |
+          matrix.python-version >= 3.7 &&
+          matrix.tensorflow != 'tensorflow'
+        run: pip install ".[bioimageio]"
+
       - run: pytest -v --durations=50 -m "not gpu"

.github/workflows/tests_cron.yml

@@ -55,4 +55,10 @@ jobs:
       #     pip uninstall -y stardist
       #     pip install --no-cache-dir --only-binary stardist "stardist>0"
 
+      - name: Install bioimage.io dependencies
+        if: |
+          matrix.python-version >= 3.7 &&
+          matrix.tensorflow != 'tensorflow'
+        run: pip install --no-binary stardist "stardist[bioimageio]"
+
       - run: pytest -v --durations=50 -m "not gpu"

setup.py

@@ -62,13 +62,13 @@ def build_extension(self, ext):
 setup(
     name='stardist',
     version=__version__,
-    description='StarDist',
+    description='StarDist - Object Detection with Star-convex Shapes',
     long_description=long_description,
     long_description_content_type='text/markdown',
     url='https://github.com/stardist/stardist',
     author='Uwe Schmidt, Martin Weigert',
     author_email='research@uweschmidt.org, martin.weigert@epfl.ch',
-    license='BSD 3-Clause License',
+    license='BSD-3-Clause',
     packages=find_packages(),
     python_requires='>=3.6',
 
@@ -114,6 +114,7 @@ def build_extension(self, ext):
     extras_require={
         "tf1":  ["csbdeep[tf1]>=0.6.3"],
         "test": ["pytest"],
+        "bioimageio": ["bioimageio.core>=0.5.0","importlib-metadata"],
     },
 
 )

stardist/__init__.py

@@ -18,3 +18,4 @@ def format_warning(message, category, filename, lineno, line=''):
 from .plot.render import render_label, render_label_pred
 from .rays3d import rays_from_json, Rays_Cartesian, Rays_SubDivide, Rays_Tetra, Rays_Octo, Rays_GoldenSpiral, Rays_Explicit
 from .sample_patches import sample_patches
+from .bioimageio_utils import export_bioimageio, import_bioimageio