split off partner deps into own extra

avoids dep conflicts to run tests during local conda build,
because then dev extras do not depend on core themselves

Author: FynnBe

.github/workflows/build.yaml

@@ -82,7 +82,7 @@ jobs:
       - name: Install dependencies
         run: |
           pip install --upgrade pip
-          pip install -e .[dev] numpy==${{matrix.numpy-version}}.*
+          pip install -e .[dev,partners] numpy==${{matrix.numpy-version}}.*
       - name: Pyright
         if: matrix.run-expensive-tests # pyright is not expensive, but we only want to run it once due to otherwise inconsistent typing
         run: |
@@ -165,7 +165,7 @@ jobs:
         with:
           python-version: '3.12'
           cache: 'pip'
-      - run: pip install -e .[dev]
+      - run: pip install -e .[dev,partners]
       - name: Generate developer docs
         run: ./scripts/pdoc/run.sh
       - run: cp README.md ./dist/README.md

pyproject.toml

@@ -43,16 +43,19 @@ Source = "https://github.com/bioimage-io/core-bioimage-io-python"
 onnx = ["onnxruntime"]
 pytorch = ["torch>=1.6,<3", "torchvision>=0.21", "keras>=3.0,<4"]
 tensorflow = ["tensorflow", "keras>=2.15,<4"]
-dev = [
+partners = [
     # "biapy",          # pins core exactly
     "careamics",
-    "cellpose",         # for model testing
+    # "stardist",         # for model testing and stardist postprocessing  # TODO: add updated stardist to partners env
+]
+dev = [
+    "cellpose",          # for model testing
     "crick",
     "httpx",
     "jupyter",
     "keras>=3.0,<4",
     "matplotlib",
-    "monai",            # for model testing
+    "monai",             # for model testing
     "numpy",
     "onnx",
     "onnxruntime",
@@ -63,8 +66,7 @@ dev = [
     "pytest-cov",
     "pytest",
     "python-dotenv",
-    "segment-anything", # for model testing
-    # "stardist",          # for model testing and stardist postprocessing  # TODO: add updated stardist to dev env
+    "segment-anything",  # for model testing
     "tensorflow",
     "timm",              # for model testing
     "torch>=1.6,<3",

tests/test_bioimageio_collection.py

@@ -101,8 +101,8 @@ def depends_on(dep: str) -> bool:
 
         for skip_if_depends_on in (
             "biapy",
-            "git+https://github.com/CAREamics/careamics.git",
-            "careamics",
+            "git+https://github.com/CAREamics/careamics.git",  # TODO: include tests depending on careamics
+            "careamics",  # TODO: include tests depending on careamics
             "inferno",
             "plantseg",
         ):