Merge pull request #472 from bioimage-io/dev

add careamics dev dep and quiet conda output in CI

Author: FynnBe

pyproject.toml

@@ -44,13 +44,15 @@ onnx = ["onnxruntime"]
 pytorch = ["torch>=1.6,<3", "torchvision>=0.21", "keras>=3.0,<4"]
 tensorflow = ["tensorflow", "keras>=2.15,<4"]
 dev = [
-    "cellpose",          # for model testing
+    # "biapy",          # pins core exactly
+    "careamics",
+    "cellpose",         # for model testing
     "crick",
     "httpx",
     "jupyter",
     "keras>=3.0,<4",
     "matplotlib",
-    "monai",             # for model testing
+    "monai",            # for model testing
     "numpy",
     "onnx",
     "onnxruntime",
@@ -61,7 +63,8 @@ dev = [
     "pytest-cov",
     "pytest",
     "python-dotenv",
-    "segment-anything",  # for model testing
+    "segment-anything", # for model testing
+    # "stardist",          # for model testing and stardist postprocessing  # TODO: add updated stardist to dev env
     "tensorflow",
     "timm",              # for model testing
     "torch>=1.6,<3",

src/bioimageio/core/_resource_tests.py

@@ -69,6 +69,7 @@
 from bioimageio.core.io import save_tensor
 
 from ._prediction_pipeline import create_prediction_pipeline
+from ._settings import settings
 from .axis import AxisId, BatchSize
 from .common import MemberId, SupportedWeightsFormat
 from .digest_spec import get_test_input_sample, get_test_output_sample
@@ -394,7 +395,15 @@ def _test_in_env(
             _ = path.write_bytes(encoded_env)
             logger.debug("written conda env to {}", path)
             run_command(
-                [CONDA_CMD, "env", "create", f"--file={path}", f"--name={env_name}"]
+                [
+                    CONDA_CMD,
+                    "env",
+                    "create",
+                    "--yes",
+                    f"--file={path}",
+                    f"--name={env_name}",
+                ]
+                + (["--quiet"] if settings.CI else [])
             )
             run_command([CONDA_CMD, "activate", env_name])
         except Exception as e: