Update adapters and converters

.github/workflows/build.yaml

@@ -27,6 +27,9 @@ jobs:
     strategy:
       matrix:
         python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        include:
+          - python-version: '3.12'
+            run-expensive-tests: true
     steps:
     - uses: actions/checkout@v4
     - name: Install Conda environment with Micromamba
@@ -39,6 +42,8 @@ jobs:
         create-args: >-
           python=${{ matrix.python-version }}
         post-cleanup: 'all'
+      env:
+        PIP_NO_DEPS: true
     - name: Install py3.8 environment
       if: matrix.python-version == '3.8'
       uses: mamba-org/setup-micromamba@v1
@@ -47,6 +52,8 @@ jobs:
         cache-environment: true
         environment-file: dev/env-py38.yaml
         post-cleanup: 'all'
+      env:
+        PIP_NO_DEPS: true
     - name: additional setup
       run: pip install --no-deps -e .
     - name: Get Date
@@ -63,6 +70,8 @@ jobs:
       run: pytest --disable-pytest-warnings
       env:
         BIOIMAGEIO_CACHE_PATH: bioimageio_cache
+        RUN_EXPENSIVE_TESTS: ${{ matrix.run-expensive-tests && 'true' || 'false' }}
+
 
   test-spec-main:
     runs-on: ubuntu-latest
@@ -71,7 +80,8 @@ jobs:
         python-version: ['3.8', '3.12']
         include:
           - python-version: '3.12'
-            is-dev-version: true
+            report-coverage: true
+            run-expensive-tests: true
     steps:
     - uses: actions/checkout@v4
     - name: Install Conda environment with Micromamba
@@ -84,6 +94,8 @@ jobs:
         create-args: >-
           python=${{ matrix.python-version }}
         post-cleanup: 'all'
+      env:
+        PIP_NO_DEPS: true
     - name: Install py3.8 environment
       if: matrix.python-version == '3.8'
       uses: mamba-org/setup-micromamba@v1
@@ -92,6 +104,8 @@ jobs:
         cache-environment: true
         environment-file: dev/env-py38.yaml
         post-cleanup: 'all'
+      env:
+        PIP_NO_DEPS: true
     - name: additional setup spec
       run: |
         conda remove --yes --force bioimageio.spec || true  # allow failure for cached env
@@ -112,17 +126,18 @@ jobs:
       run: pytest --disable-pytest-warnings
       env:
         BIOIMAGEIO_CACHE_PATH: bioimageio_cache
-    - if: matrix.is-dev-version && github.event_name == 'pull_request'
+        RUN_EXPENSIVE_TESTS: ${{ matrix.run-expensive-tests && 'true' || 'false' }}
+    - if: matrix.report-coverage && github.event_name == 'pull_request'
       uses: orgoro/[email protected]
       with:
         coverageFile: coverage.xml
         token: ${{ secrets.GITHUB_TOKEN }}
-    - if: matrix.is-dev-version && github.ref == 'refs/heads/main'
+    - if: matrix.report-coverage && github.ref == 'refs/heads/main'
       run: |
         pip install genbadge[coverage]
         genbadge coverage --input-file coverage.xml --output-file ./dist/coverage/coverage-badge.svg
         coverage html -d dist/coverage
-    - if: matrix.is-dev-version && github.ref == 'refs/heads/main'
+    - if: matrix.report-coverage && github.ref == 'refs/heads/main'
       uses: actions/upload-artifact@v4
       with:
         name: coverage
@@ -147,6 +162,8 @@ jobs:
         create-args: >-
           python=${{ matrix.python-version }}
         post-cleanup: 'all'
+      env:
+        PIP_NO_DEPS: true
     - name: additional setup spec
       run: |
         conda remove --yes --force bioimageio.spec || true  # allow failure for cached env
@@ -184,6 +201,8 @@ jobs:
         create-args: >-
           python=${{ matrix.python-version }}
         post-cleanup: 'all'
+      env:
+        PIP_NO_DEPS: true
     - name: additional setup
       run: pip install --no-deps -e .
     - name: Get Date

README.md

@@ -375,6 +375,12 @@ The model specification and its validation tools can be found at <https://github
 
 ## Changelog
 
+### 0.7.1 (to be released)
+
+- New feature: `bioimageio.core.test_description` accepts **runtime_env** and **run_command** to test a resource
+  using the conda environment described by that resource (or another specified conda env)
+- raise validation errors if `ValidationContext.raise_errors is True`
+
 ### 0.7.0
 
 - breaking:

bioimageio/core/__init__.py

@@ -41,6 +41,7 @@
 )
 from ._settings import settings
 from .axis import Axis, AxisId
+from .backends import create_model_adapter
 from .block_meta import BlockMeta
 from .common import MemberId
 from .prediction import predict, predict_many
@@ -73,6 +74,7 @@
     "commands",
     "common",
     "compute_dataset_measures",
+    "create_model_adapter",
     "create_prediction_pipeline",
     "digest_spec",
     "dump_description",

bioimageio/core/_prediction_pipeline.py

@@ -121,19 +121,9 @@ def predict_sample_block(
             self.apply_preprocessing(sample_block)
 
         output_meta = sample_block.get_transformed_meta(self._block_transform)
-        output = output_meta.with_data(
-            {
-                tid: out
-                for tid, out in zip(
-                    self._output_ids,
-                    self._adapter.forward(
-                        *(sample_block.members.get(t) for t in self._input_ids)
-                    ),
-                )
-                if out is not None
-            },
-            stat=sample_block.stat,
-        )
+        local_output = self._adapter.forward(sample_block)
+
+        output = output_meta.with_data(local_output.members, stat=local_output.stat)
         if not skip_postprocessing:
             self.apply_postprocessing(output)
 
@@ -152,20 +142,7 @@ def predict_sample_without_blocking(
         if not skip_preprocessing:
             self.apply_preprocessing(sample)
 
-        output = Sample(
-            members={
-                out_id: out
-                for out_id, out in zip(
-                    self._output_ids,
-                    self._adapter.forward(
-                        *(sample.members.get(in_id) for in_id in self._input_ids)
-                    ),
-                )
-                if out is not None
-            },
-            stat=sample.stat,
-            id=sample.id,
-        )
+        output = self._adapter.forward(sample)
         if not skip_postprocessing:
             self.apply_postprocessing(output)