Merge pull request #727 from bioimage-io/dev

minor improvements

Author: FynnBe

.github/workflows/build.yaml

@@ -147,6 +147,29 @@ jobs:
           branch: ${{ steps.get_branch.outputs.branch }}
           folder: dist
 
+  build:
+    needs: test
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v6
+        with:
+          python-version: '3.10'
+          cache: 'pip'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip --version
+          pip install --upgrade build
+          pip install .
+      - name: Build package
+        run: |
+          python -m build
+      - uses: actions/upload-artifact@v4
+        with:
+          path: dist/
+          name: dist
+
   conda-build:
     needs: test
     runs-on: ubuntu-latest
@@ -186,9 +209,8 @@ jobs:
   #      with:
   #        recipe-path: conda-recipe/recipe.yaml
 
-  pip-build:
-    name: Build and publish to PyPI
-    needs: [deploy, conda-build]
+  publish:
+    needs: [build, conda-build]
     runs-on: ubuntu-latest
     environment:
       name: release
@@ -200,17 +222,6 @@ jobs:
         uses: actions/checkout@v4
         with:
           fetch-depth: 2
-      - name: Set up Python
-        uses: actions/setup-python@v6
-        with:
-          python-version: '3.10'
-          cache: 'pip'
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip --version
-          pip install --upgrade build
-          pip install .
       - name: Check if there is a parent commit
         id: check-parent-commit
         run: |
@@ -231,11 +242,10 @@ jobs:
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           custom_tag: ${{ steps.check-version.outputs.current-version }}
-
-      - name: Build package
-        run: |
-          python -m build
-
+      - uses: actions/download-artifact@v4
+        if: github.ref == 'refs/heads/main' && steps.tag-version.outputs.new_tag
+        with:
+          name: dist
       - name: Publish package on PyPI
         if: github.ref == 'refs/heads/main' && steps.tag-version.outputs.new_tag
         uses: pypa/gh-action-pypi-publish@release/v1

example_descriptions/models/unet2d_multi_tensor/bioimageio.yaml

@@ -143,7 +143,7 @@ weights:
         in_channels: 2
         initial_features: 16
         out_channels: 2
-      sha256: 89204f8f3513b3c227127a8137bedaec9eafe49925f7734c73c6650ec135b34e
+      sha256: 74b6d27cd17b40560e70fde4d57b5675614979ffab4f1e0328a6c3a3f64a1ff2
       source: multi_tensor_unet.py
     pytorch_version: 1.6
     sha256: c498522b3f2b02429b41fe9dbcb722ce0d7ad4cae7fcf8059cee27857ae49b00

example_descriptions/models/unet2d_multi_tensor/multi_tensor_unet.py

@@ -1,4 +1,6 @@
 # type: ignore
+from typing import List, Optional
+
 import torch
 import torch.nn as nn
 
@@ -75,11 +77,16 @@ def _apply_default(self, x):
 
         return x
 
-    def forward(self, *x):
-        assert isinstance(x, (list, tuple)), type(x)
-        # fix issue in onnx export
-        if isinstance(x[0], list) and len(x) == 1:
-            x = x[0]
+    def forward(
+        self,
+        x0: torch.Tensor,
+        x1: Optional[torch.Tensor] = None,
+        x2: Optional[torch.Tensor] = None,
+        x3: Optional[torch.Tensor] = None,
+        x4: Optional[torch.Tensor] = None,
+        /,
+    ) -> List[torch.Tensor]:
+        x = [x for x in [x0, x1, x2, x3, x4] if x is not None]
         assert len(x) == self.in_channels, f"{len(x)}, {self.in_channels}"
         x = torch.cat(x, dim=1)
         out = self._apply_default(x)

src/bioimageio/spec/model/v0_5.py

@@ -66,6 +66,7 @@
     FileSource,
     WithSuffix,
     YamlValue,
+    extract_file_name,
     get_reader,
     wo_special_file_name,
 )
@@ -2376,6 +2377,19 @@ class OnnxWeightsDescr(WeightsEntryDescrBase):
     """Source of the external ONNX data file holding the weights.
     (If present **source** holds the ONNX architecture without weights)."""
 
+    @model_validator(mode="after")
+    def _validate_external_data_unique_file_name(self) -> Self:
+        if self.external_data is not None and (
+            extract_file_name(self.source)
+            == extract_file_name(self.external_data.source)
+        ):
+            raise ValueError(
+                f"ONNX `external_data` file name '{extract_file_name(self.external_data.source)}'"
+                + " must be different from ONNX `source` file name."
+            )
+
+        return self
+
 
 class PytorchStateDictWeightsDescr(WeightsEntryDescrBase):
     type = "pytorch_state_dict"

tests/conftest.py

@@ -5,6 +5,7 @@
 
 import pytest
 from dotenv import load_dotenv
+from loguru import logger
 
 from bioimageio.spec._internal.constants import (
     KNOWN_GITHUB_USERS,
@@ -18,6 +19,8 @@
 
 _ = load_dotenv()
 
+logger.enable("bioimageio")
+
 EXAMPLE_DESCRIPTIONS = Path(__file__).parent / "../example_descriptions/"
 UNET2D_ROOT = EXAMPLE_DESCRIPTIONS / "models/unet2d_nuclei_broad"