Merge pull request #465 from bioimage-io/dev

CLI fixes

Author: FynnBe

.vscode/settings.json

@@ -12,4 +12,11 @@
     ],
     "python.testing.pytestEnabled": true,
     "python.testing.unittestEnabled": false,
+    "python-envs.pythonProjects": [
+        {
+            "path": "",
+            "envManager": "ms-python.python:conda",
+            "packageManager": "ms-python.python:conda"
+        }
+    ],
 }

README.md

@@ -364,6 +364,15 @@ may be controlled with the `LOGURU_LEVEL` environment variable.
 
 ## Changelog
 
+### next release
+
+- fixes:
+  - CLI
+    - improved handling of summary argument to not create a path with brackets when given a list of paths.
+    - improved backward compatibility when runnig tests for models specifying an older bioimageio.core version in their environment.
+    This is relevant when using `runtime_env="as-described"`.
+    It works by simply trying option `--summary` (new option name) and `--summary-path` (outdated option name).
+
 ### 0.9.0
 
 - update to [bioimageio.spec 0.5.4.3](https://github.com/bioimage-io/spec-bioimage-io/blob/main/changelog.md#bioimageiospec-0543)

bioimageio/core/_resource_tests.py

@@ -404,21 +404,50 @@ def _test_in_env(
             )
             return summary
 
-    run_command(
-        [
-            "conda",
-            "run",
-            "-n",
-            env_name,
-            "bioimageio",
-            "test",
-            str(source),
-            f"--summary-path={summary_path}",
-            f"--determinism={determinism}",
-        ]
-        + ([f"--expected-type={expected_type}"] if expected_type else [])
-        + (["--stop-early"] if stop_early else [])
-    )
+    cmd = []
+    for summary_path_arg_name in ("summary", "summary-path"):
+        run_command(
+            cmd := (
+                [
+                    "conda",
+                    "run",
+                    "-n",
+                    env_name,
+                    "bioimageio",
+                    "test",
+                    str(source),
+                    f"--{summary_path_arg_name}={summary_path.as_posix()}",
+                    f"--determinism={determinism}",
+                ]
+                + ([f"--expected-type={expected_type}"] if expected_type else [])
+                + (["--stop-early"] if stop_early else [])
+            )
+        )
+        if summary_path.exists():
+            break
+    else:
+        return ValidationSummary(
+            name="calling bioimageio test command",
+            source_name=str(source),
+            status="failed",
+            type="unknown",
+            format_version="unknown",
+            details=[
+                ValidationDetail(
+                    name="run 'bioimageio test'",
+                    errors=[
+                        ErrorEntry(
+                            loc=(),
+                            type="bioimageio cli",
+                            msg=f"test command '{' '.join(cmd)}' did not produce a summary file at {summary_path}",
+                        )
+                    ],
+                    status="failed",
+                )
+            ],
+            env=set(),
+        )
+
     return ValidationSummary.model_validate_json(summary_path.read_bytes())
 
 

bioimageio/core/cli.py

@@ -46,6 +46,7 @@
 from tqdm import tqdm
 from typing_extensions import assert_never
 
+import bioimageio.spec
 from bioimageio.spec import (
     AnyModelDescr,
     InvalidDescr,
@@ -98,10 +99,8 @@ class ArgMixin(BaseModel, use_attribute_docstrings=True, cli_implicit_flags=True
 
 
 class WithSummaryLogging(ArgMixin):
-    summary: Union[
-        Literal["display"], Path, Sequence[Union[Literal["display"], Path]]
-    ] = Field(
-        "display",
+    summary: Sequence[Union[Literal["display"], Path]] = Field(
+        ("display",),
         examples=[
             "display",
             Path("summary.md"),
@@ -867,7 +866,7 @@ def run(self):
 
 library versions:
   bioimageio.core {VERSION}
-  bioimageio.spec {VERSION}
+  bioimageio.spec {bioimageio.spec.__version__}
 
 spec format versions:
         model RDF {ModelDescr.implemented_format_version}

tests/test_bioimageio_collection.py

@@ -123,6 +123,7 @@ def yield_bioimageio_yaml_urls() -> Iterable[ParameterSet]:
     "mellow-takeout/1": "missing cite",
     "merry-water-buffalo/0.1.0": "requires biapy",
     "mesmerizing-shoe/1.14.1": "missing license",
+    "modest-spider/0.1.1": "non-batch id 'b'",
     "naked-microbe/1": "unknown layer Convolution2D",
     "nice-peacock/1": "invalid id",
     "noisy-ox/1": "batch size is actually limited to 1",
@@ -151,6 +152,7 @@ def yield_bioimageio_yaml_urls() -> Iterable[ParameterSet]:
     ),
     "striking-necktie/1.14.1": "invalid id",
     "stupendous-sheep/1.1": "requires relativ import of attachment",
+    "sympathetic-mosquito/1": "error deserializing VarianceScaling",
     "tempting-pizza/1": "missing license",
     "timeless-running-shirt/1.13.2": "invalid id, missing license",
     "uplifting-backpack/1.14.1": "invalid id, missing license",