Merge pull request #337 from bioimage-io/fix-tests

Fix tests

Author: FynnBe

.github/workflows/build.yml

@@ -22,7 +22,7 @@ jobs:
         with:
           tool_name: blackfmt
 
-  test-base-bioimage-spec-conda:
+  test-spec-conda:
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -33,18 +33,18 @@ jobs:
       uses: mamba-org/provision-with-micromamba@main
       with:
         cache-downloads: true
-        cache-env: true
+        cache-env: false  # debugging: torch does not detect onnxruntime
         environment-file: dev/environment-torch.yaml
         extra-specs: |
           python=${{ matrix.python-version }}
     - name: additional setup
       shell: bash -l {0}
       run: pip install --no-deps -e .
-    - name: pytest-base-bioimage-spec-conda
+    - name: pytest-spec-conda
       shell: bash -l {0}
       run: pytest --disable-pytest-warnings
 
-  test-base-bioimage-spec-main:
+  test-spec-main:
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -55,7 +55,7 @@ jobs:
       uses: mamba-org/provision-with-micromamba@main
       with:
         cache-downloads: true
-        cache-env: true
+        cache-env: false  # todo: detect env cache hit and adapt(skip?) additional setup (conda remove?)
         environment-file: dev/environment-torch.yaml
         extra-specs: |
           python=${{ matrix.python-version }}
@@ -65,11 +65,11 @@ jobs:
         conda remove --yes --force bioimageio.spec
         pip install --no-deps git+https://github.com/bioimage-io/spec-bioimage-io
         pip install --no-deps -e .
-    - name: pytest-base-bioimage-spec-main
+    - name: pytest-spec-main
       shell: bash -l {0}
       run: pytest --disable-pytest-warnings
-  
-  test-base-bioimage-spec-tf:
+
+  test-spec-tf:
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -80,7 +80,7 @@ jobs:
       uses: mamba-org/provision-with-micromamba@main
       with:
         cache-downloads: true
-        cache-env: true
+        cache-env: false  # todo: detect env cache hit and adapt(skip?) additional setup (conda remove?)
         environment-file: dev/environment-tf.yaml
         channel-priority: flexible
         extra-specs: |
@@ -91,11 +91,11 @@ jobs:
         conda remove --yes --force bioimageio.spec
         pip install --no-deps git+https://github.com/bioimage-io/spec-bioimage-io
         pip install --no-deps -e .
-    - name: pytest-base-bioimage-spec-tf
+    - name: pytest-spec-tf
       shell: bash -l {0}
       run: pytest --disable-pytest-warnings
 
-  test-base-bioimage-spec-tf-legacy:
+  test-spec-tf-legacy:
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -106,7 +106,7 @@ jobs:
       uses: mamba-org/provision-with-micromamba@main
       with:
         cache-downloads: true
-        cache-env: true
+        cache-env: false  # todo: detect env cache hit and adapt(skip?) additional setup (conda remove?)
         environment-file: dev/environment-tf-legacy.yaml
         channel-priority: flexible
         extra-specs: |
@@ -117,13 +117,13 @@ jobs:
         conda remove --yes --force bioimageio.spec
         pip install --no-deps git+https://github.com/bioimage-io/spec-bioimage-io
         pip install --no-deps -e .
-    - name: pytest-base-bioimage-spec-tf-legacy
+    - name: pytest-spec-tf-legacy
       shell: bash -l {0}
       run: pytest --disable-pytest-warnings
 
   conda-build:
     runs-on: ubuntu-latest
-    needs: test-base-bioimage-spec-conda
+    needs: test-spec-conda
     steps:
     - name: checkout
       uses: actions/checkout@v3

bioimageio/core/build_spec/build_model.py

@@ -279,7 +279,6 @@ def _get_dependencies(dependencies, root):
 
 
 def _get_deepimagej_macro(name, kwargs, export_folder):
-
     # macros available in deepimagej
     macro_names = ("binarize", "scale_linear", "scale_range", "zero_mean_unit_variance")
     if name == "scale_linear":
@@ -536,7 +535,7 @@ def grid_im(im0, im1):
 
         n, m = im_shape
         x, y = ims_per_row * n, n_rows * m
-        out = np.zeros((3, y, x))
+        out = np.zeros((3, y, x), dtype=im0.dtype)
         images = [im0] + [np.repeat(im1[i : i + 1], 3, axis=0) for i in range(n_chan)]
 
         i, j = 0, 0

dev/environment-base.yaml

@@ -14,6 +14,7 @@ dependencies:
   - python >=3.7,<3.8  # this environment is only available for python 3.7
   - xarray
   - pytorch
+  - onnx
   - onnxruntime
   - tensorflow >=1.12,<2.0
   - tifffile <=2022.4.8  # pin fixes Syntax error; see https://github.com/bioimage-io/core-bioimage-io-python/pull/259

dev/environment-torch.yaml

@@ -13,6 +13,7 @@ dependencies:
   - python >=3.7
   - xarray
   - pytorch
+  - onnx
   - onnxruntime
   - tifffile <=2022.4.8  # pin fixes Syntax error; see https://github.com/bioimage-io/core-bioimage-io-python/pull/259
 

tests/conftest.py

@@ -200,8 +200,8 @@ def unet2d_fixed_shape_or_not(request):
     return pytest.model_packages[request.param]
 
 
-@pytest.fixture(params=[] if skip_torch else ["unet2d_nuclei_broad_model", "unet2d_multi_tensor"])
-def unet2d_multi_tensor_or_not(request):
+@pytest.fixture(params=[] if skip_onnx or skip_torch else ["unet2d_nuclei_broad_model", "unet2d_multi_tensor"])
+def convert_to_onnx(request):
     return pytest.model_packages[request.param]
 
 

tests/weight_converter/torch/test_onnx.py

@@ -3,11 +3,11 @@
 
 
 # todo: test with 'any_torch_model'
-def test_onnx_converter(unet2d_multi_tensor_or_not, tmp_path):
+def test_onnx_converter(convert_to_onnx, tmp_path):
     from bioimageio.core.weight_converter.torch.onnx import convert_weights_to_onnx
 
     out_path = tmp_path / "weights.onnx"
-    ret_val = convert_weights_to_onnx(unet2d_multi_tensor_or_not, out_path, test_decimal=3)
+    ret_val = convert_weights_to_onnx(convert_to_onnx, out_path, test_decimal=3)
     assert os.path.exists(out_path)
     if not pytest.skip_onnx:
         assert ret_val == 0  # check for correctness is done in converter and returns 0 if it passes