Merge pull request #259 from bioimage-io/update_for_resolved_paths

Update for resolved paths

Author: FynnBe

dev/environment-base.yaml

@@ -15,6 +15,6 @@ dependencies:
   - pytorch
   - onnxruntime
   - tensorflow >=1.12,<2.0
-  - tifffile
+  - tifffile <=2022.4.8  # pin fixes Syntax error; see https://github.com/bioimage-io/core-bioimage-io-python/pull/259
   - pip:
     - keras==1.2.2

dev/environment-tf.yaml

@@ -13,5 +13,5 @@ dependencies:
   - python >=3.7,<3.8  # this environment is only available for python 3.7
   - xarray
   - tensorflow >1.14,<2.0
-  - tifffile
+  - tifffile <=2022.4.8  # pin fixes Syntax error; see https://github.com/bioimage-io/core-bioimage-io-python/pull/259
   - keras

dev/environment-torch.yaml

@@ -14,4 +14,5 @@ dependencies:
   - xarray
   - pytorch
   - onnxruntime
-  - tifffile
+  - tifffile <=2022.4.8  # pin fixes Syntax error; see https://github.com/bioimage-io/core-bioimage-io-python/pull/259
+

setup.py

@@ -25,7 +25,15 @@
         "Programming Language :: Python :: 3.8",
     ],
     packages=find_namespace_packages(exclude=["tests"]),  # Required
-    install_requires=["bioimageio.spec>=0.4.5", "imageio>=2.5", "numpy", "ruamel.yaml", "tqdm", "xarray"],
+    install_requires=[
+        "bioimageio.spec>=0.4.5",
+        "imageio>=2.5",
+        "numpy",
+        "ruamel.yaml",
+        "tqdm",
+        "xarray",
+        "tifffile<=2022.4.8",  # fixes Syntax error; see https://github.com/bioimage-io/core-bioimage-io-python/pull/259
+    ],
     include_package_data=True,
     extras_require={
         "test": ["pytest", "black", "mypy"],

tests/build_spec/test_build_spec.py

@@ -1,10 +1,10 @@
-import os
+from marshmallow import missing
+
 import bioimageio.spec as spec
 from bioimageio.core import load_raw_resource_description, load_resource_description
 from bioimageio.core.resource_io import nodes
 from bioimageio.core.resource_io.utils import resolve_source
 from bioimageio.core.resource_tests import test_model as _test_model
-from marshmallow import missing
 
 
 def _test_build_spec(
@@ -16,7 +16,6 @@ def _test_build_spec(
     use_implicit_output_shape=False,
     add_deepimagej_config=False,
     use_original_covers=False,
-    use_absoloute_arch_path=False,
     training_data=None,
     parent=None,
 ):
@@ -44,11 +43,6 @@ def _test_build_spec(
     if weight_type == "pytorch_state_dict":
         model_kwargs = None if weight_spec.kwargs is missing else weight_spec.kwargs
         architecture = str(weight_spec.architecture)
-        if use_absoloute_arch_path:
-            arch_path, cls_name = architecture.split(":")
-            arch_path = os.path.abspath(os.path.join(root, arch_path))
-            assert os.path.exists(arch_path)
-            architecture = f"{arch_path}:{cls_name}"
         weight_type_ = None  # the weight type can be auto-detected
     elif weight_type == "torchscript":
         architecture = None
@@ -233,10 +227,3 @@ def test_build_spec_deepimagej_keras(unet2d_keras, tmp_path):
 # test with original covers
 def test_build_spec_with_original_covers(unet2d_nuclei_broad_model, tmp_path):
     _test_build_spec(unet2d_nuclei_broad_model, tmp_path / "model.zip", "torchscript", use_original_covers=True)
-
-
-# test with absolute path for the architecture file
-def test_build_spec_abs_arch_path(unet2d_nuclei_broad_model, tmp_path):
-    _test_build_spec(
-        unet2d_nuclei_broad_model, tmp_path / "model.zip", "pytorch_state_dict", use_absoloute_arch_path=True
-    )

tests/prediction_pipeline/test_processing.py

@@ -0,0 +1,39 @@
+import dataclasses
+
+import pytest
+
+from bioimageio.core.prediction_pipeline._processing import KNOWN_PROCESSING
+from bioimageio.core.prediction_pipeline._utils import FIXED
+
+try:
+    from typing import get_args
+except ImportError:
+    from typing_extensions import get_args  # type: ignore
+
+
+@pytest.mark.parametrize(
+    "proc",
+    list(KNOWN_PROCESSING["pre"].values()) + list(KNOWN_PROCESSING["post"].values()),
+)
+def test_no_req_measures_for_mode_fixed(proc):
+    # check if mode=fixed is valid for this proc
+    for f in dataclasses.fields(proc):
+        if f.name == "mode":
+            break
+    else:
+        raise AttributeError("Processing is missing mode attribute")
+    # mode is always annotated as literals (or literals of literals)
+    valid_modes = get_args(f.type)
+    for inner in get_args(f.type):
+        valid_modes += get_args(inner)
+
+    if FIXED not in valid_modes:
+        return
+
+    # we might be missing required kwargs. These have marshmallow.missing value as default
+    # and raise a TypeError is in __post_init__()
+    proc.__post_init__ = lambda self: None  # ignore missing kwargs
+
+    proc_instance = proc(tensor_name="tensor_name", mode=FIXED)
+    req_measures = proc_instance.get_required_measures()
+    assert not req_measures

tests/test_export_package.py

@@ -37,6 +37,7 @@ def test_package_with_folder(unet2d_nuclei_broad_model):
         # alter package to have its documentation in a nested folder
         doc = model.documentation
         assert doc is not missing
+        doc = doc.relative_to(model.root_path)
         assert not doc.is_absolute()
         new_doc = Path("nested") / "folder" / doc
         (package_folder / new_doc).parent.mkdir(parents=True)
@@ -55,5 +56,5 @@ def test_package_with_folder(unet2d_nuclei_broad_model):
         # load altered package
         reloaded_model = load_raw_resource_description(altered_package_folder / "rdf.yaml")
         assert isinstance(reloaded_model, raw_nodes.Model)
-        assert reloaded_model.documentation == new_doc
-        assert (altered_package_folder / reloaded_model.documentation).exists()
+        assert reloaded_model.documentation.as_posix().endswith(new_doc.as_posix())
+        assert reloaded_model.documentation.exists()