Merge pull request #471 from bioimage-io/dev

Stability improvements

Author: FynnBe

.github/workflows/build.yaml

@@ -2,9 +2,9 @@ name: Test and Deploy bioimageio.core
 
 on:
   push:
-    branches: [ main ]
+    branches: [main]
   pull_request:
-    branches: [ "**" ]
+    branches: ['**']
 
 defaults:
   run:
@@ -58,81 +58,69 @@ jobs:
       matrix:
         include:
           - python-version: '3.9'
-            conda-env: dev
-            spec: conda
             numpy-version: 1
           - python-version: '3.9'
-            conda-env: dev
-            spec: main
             numpy-version: 2
           - python-version: '3.10'
-            conda-env: full
             run-expensive-tests: true
             report-coverage: true
             save-cache: true
-            spec: conda
             numpy-version: 1
           - python-version: '3.11'
-            conda-env: dev
-            spec: main
             numpy-version: 2
           - python-version: '3.12'
-            conda-env: dev
-            spec: conda
             numpy-version: 1
           # - python-version: '3.13'
-          #   conda-env: '313'
-          #   spec: main
           #   numpy-version: 2
 
     steps:
-    - uses: actions/checkout@v4
-    - uses: actions/setup-python@v6
-      with:
-        python-version: ${{matrix.python-version}}
-        cache: 'pip'
-    - name: Install dependencies
-      run: |
-        pip install --upgrade pip
-        pip install -e .[dev] numpy==${{matrix.numpy-version}}.*
-    - name: Pyright
-      if: matrix.run-expensive-tests
-      run: |
-        pyright --version
-        pyright -p pyproject.toml --pythonversion ${{ matrix.python-version }}
-    - name: Restore bioimageio cache ${{needs.populate-cache.outputs.cache-key}}
-      uses: actions/cache/restore@v4
-      with:
-        path: bioimageio_cache
-        key: ${{needs.populate-cache.outputs.cache-key}}
-    - name: pytest
-      run: pytest --cov bioimageio --cov-report xml --cov-append --capture no --disable-pytest-warnings
-      env:
-        BIOIMAGEIO_CACHE_PATH: bioimageio_cache
-        RUN_EXPENSIVE_TESTS: ${{ matrix.run-expensive-tests && 'true' || 'false' }}
-    - name: Save bioimageio cache ${{needs.populate-cache.outputs.cache-key}}
-      if: matrix.save-cache
-      uses: actions/cache/save@v4
-      with:
-        path: bioimageio_cache
-        key: ${{needs.populate-cache.outputs.cache-key}}
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v6
+        with:
+          python-version: ${{matrix.python-version}}
+          cache: 'pip'
+      - name: Install dependencies
+        run: |
+          pip install --upgrade pip
+          pip install -e .[dev] numpy==${{matrix.numpy-version}}.*
+      - name: Pyright
+        if: matrix.run-expensive-tests # pyright is not expensive, but we only want to run it once due to otherwise inconsistent typing
+        run: |
+          pyright --version
+          pyright -p pyproject.toml --pythonversion ${{ matrix.python-version }}
+      - name: Restore bioimageio cache ${{needs.populate-cache.outputs.cache-key}}
+        uses: actions/cache/restore@v4
+        with:
+          path: bioimageio_cache
+          key: ${{needs.populate-cache.outputs.cache-key}}
+      - name: pytest
+        run: pytest --cov bioimageio --cov-report xml --cov-append --capture no --disable-pytest-warnings
+        env:
+          BIOIMAGEIO_CACHE_PATH: bioimageio_cache
+          RUN_EXPENSIVE_TESTS: ${{ matrix.run-expensive-tests && 'true' || 'false' }}
+      - name: Save bioimageio cache ${{needs.populate-cache.outputs.cache-key}}
+        if: matrix.save-cache
+        uses: actions/cache/save@v4
+        with:
+          path: bioimageio_cache
+          key: ${{needs.populate-cache.outputs.cache-key}}
 
-    - if: matrix.report-coverage && github.event_name == 'pull_request'
-      uses: orgoro/[email protected]
-      with:
-        coverageFile: coverage.xml
-        token: ${{secrets.GITHUB_TOKEN}}
-    - 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.report-coverage && github.ref == 'refs/heads/main'
-      uses: actions/upload-artifact@v4
-      with:
-        name: coverage
-        retention-days: 1
-        path: dist
+      - if: matrix.report-coverage && github.event_name == 'pull_request'
+        uses: orgoro/[email protected]
+        with:
+          coverageFile: coverage.xml
+          token: ${{secrets.GITHUB_TOKEN}}
+      - 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.report-coverage && github.ref == 'refs/heads/main'
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage
+          retention-days: 1
+          path: dist
 
   conda-build:
     needs: test
@@ -145,7 +133,7 @@ jobs:
         with:
           auto-update-conda: true
           auto-activate-base: true
-          activate-environment: ""
+          activate-environment: ''
           channel-priority: strict
           miniforge-version: latest
           conda-solver: libmamba
@@ -242,14 +230,14 @@ jobs:
         uses: pypa/gh-action-pypi-publish@release/v1.12
         with:
           user: __token__
-          password: "${{ secrets.PYPI_TOKEN }}"
+          password: '${{ secrets.PYPI_TOKEN }}'
           packages-dir: dist/
           verbose: true
       - name: Publish the release notes
         if: github.ref == 'refs/heads/main'
         uses: release-drafter/[email protected]
         with:
           publish: "${{ steps.tag-version.outputs.new_tag != '' }}"
-          tag: "${{ steps.tag-version.outputs.new_tag }}"
+          tag: '${{ steps.tag-version.outputs.new_tag }}'
         env:
-          GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
+          GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}'

.pre-commit-config.yaml

@@ -1,8 +1,4 @@
 repos:
-  - repo: https://github.com/ambv/black
-    rev: 25.1.0
-    hooks:
-      - id: black-jupyter
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.12.8
     hooks:

README.md

@@ -364,9 +364,16 @@ may be controlled with the `LOGURU_LEVEL` environment variable.
 
 ## Changelog
 
+### 0.9.3
+
+- bump bioimageio.spec library version to 0.5.5.5
+- more robust test model reporting
+- improved user input axis intepretation
+- fixed conda subprocess calls
+
 ### 0.9.2
 
-fix model inference tolerance reporting
+- fix model inference tolerance reporting
 
 ### 0.9.1
 

example/dataset_statistics_demo.ipynb

@@ -329,12 +329,14 @@
    "source": [
     "# compute dataset statistics on all samples\n",
     "# (in this case we should really use the non-overlapping tiles as samples in dataset_for_initial_statistics)\n",
-    "with create_prediction_pipeline(\n",
-    "    bioimageio_model=model_resource,\n",
-    "    dataset_for_initial_statistics=dataset,\n",
-    "    update_dataset_stats_for_n_samples=0,  # if you call the prediciton pipeline more then len(dataset)\n",
-    "    # times you might want to set this to zero to avoid further updates to the dataset statistics\n",
-    ") as pp:\n",
+    "with (\n",
+    "    create_prediction_pipeline(\n",
+    "        bioimageio_model=model_resource,\n",
+    "        dataset_for_initial_statistics=dataset,\n",
+    "        update_dataset_stats_for_n_samples=0,  # if you call the prediciton pipeline more then len(dataset)\n",
+    "        # times you might want to set this to zero to avoid further updates to the dataset statistics\n",
+    "    ) as pp\n",
+    "):\n",
     "    only_init_dataset_stats = process_dataset(pp, dataset)"
    ]
   },

example/model_usage.ipynb

@@ -111,7 +111,6 @@
     "        Mapping[str, NDArray[Any]], Mapping[TensorId, Union[Tensor, NDArray[Any]]]\n",
     "    ],\n",
     ") -> None:\n",
-    "\n",
     "    for title, image in images.items():\n",
     "        if isinstance(image, Tensor):\n",
     "            input_array = image.data.data\n",

pyproject.toml

@@ -6,7 +6,7 @@ requires-python = ">=3.9"
 readme = "README.md"
 dynamic = ["version"]
 dependencies = [
-    "bioimageio.spec ==0.5.5.4",
+    "bioimageio.spec ==0.5.5.5",
     "h5py",
     "imagecodecs",
     "imageio>=2.10",
@@ -44,15 +44,14 @@ onnx = ["onnxruntime"]
 pytorch = ["torch>=1.6,<3", "torchvision>=0.21", "keras>=3.0,<4"]
 tensorflow = ["tensorflow", "keras>=2.15,<4"]
 dev = [
-    "black",
     "cellpose",          # for model testing
     "crick",
     "httpx",
-    "jupyter-black",
     "jupyter",
     "keras>=3.0,<4",
     "matplotlib",
     "monai",             # for model testing
+    "numpy",
     "onnx",
     "onnxruntime",
     "packaging>=17.0",
@@ -79,12 +78,6 @@ where = ["src/"]
 [tool.setuptools.dynamic]
 version = { attr = "bioimageio.core.__version__" }
 
-[tool.black]
-line-length = 88
-extend-exclude = "/presentations/"
-target-version = ["py39", "py310", "py311", "py312"]
-preview = true
-
 [tool.pyright]
 exclude = [
     "**/__pycache__",

src/bioimageio/core/__init__.py

@@ -3,7 +3,7 @@
 """
 # ruff: noqa: E402
 
-__version__ = "0.9.2"
+__version__ = "0.9.3"
 from loguru import logger
 
 logger.disable("bioimageio.core")

src/bioimageio/core/_magic_tensor_ops.py

@@ -71,12 +71,14 @@ def __ge__(self, other: _Compatible) -> Self:
 
     def __eq__(self, other: _Compatible) -> Self:  # type: ignore[override]
         return self._binary_op(
-            other, nputils.array_eq  # pyright: ignore[reportUnknownArgumentType]
+            other,
+            nputils.array_eq,  # pyright: ignore[reportUnknownArgumentType]
         )
 
     def __ne__(self, other: _Compatible) -> Self:  # type: ignore[override]
         return self._binary_op(
-            other, nputils.array_ne  # pyright: ignore[reportUnknownArgumentType]
+            other,
+            nputils.array_ne,  # pyright: ignore[reportUnknownArgumentType]
         )
 
     # When __eq__ is defined but __hash__ is not, then an object is unhashable,
@@ -171,22 +173,30 @@ def __invert__(self) -> Self:
 
     def round(self, *args: Any, **kwargs: Any) -> Self:
         return self._unary_op(
-            ops.round_, *args, **kwargs  # pyright: ignore[reportUnknownArgumentType]
+            ops.round_,  # pyright: ignore[reportUnknownArgumentType]
+            *args,
+            **kwargs,
         )
 
     def argsort(self, *args: Any, **kwargs: Any) -> Self:
         return self._unary_op(
-            ops.argsort, *args, **kwargs  # pyright: ignore[reportUnknownArgumentType]
+            ops.argsort,  # pyright: ignore[reportUnknownArgumentType]
+            *args,
+            **kwargs,
         )
 
     def conj(self, *args: Any, **kwargs: Any) -> Self:
         return self._unary_op(
-            ops.conj, *args, **kwargs  # pyright: ignore[reportUnknownArgumentType]
+            ops.conj,  # pyright: ignore[reportUnknownArgumentType]
+            *args,
+            **kwargs,
         )
 
     def conjugate(self, *args: Any, **kwargs: Any) -> Self:
         return self._unary_op(
-            ops.conjugate, *args, **kwargs  # pyright: ignore[reportUnknownArgumentType]
+            ops.conjugate,  # pyright: ignore[reportUnknownArgumentType]
+            *args,
+            **kwargs,
         )
 
     __add__.__doc__ = operator.add.__doc__