Update and improve test environments

.github/workflows/test_and_deploy.yml

@@ -16,7 +16,7 @@ jobs:
       fail-fast: true
       matrix:
         os: ["windows-latest", "ubuntu-latest", "macos-latest"]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
 
     steps:
       - name: Checkout source
@@ -34,7 +34,7 @@ jobs:
         shell: bash -l {0}
         run: |
           conda activate dask-image-testenv
-          python -m pip install -e .
+          python -m pip install -e .[dataframe]
           conda list
 
       - name: Run tests
@@ -49,6 +49,56 @@ jobs:
           parallel: true
           path-to-lcov: coverage.lcov
 
+  test-minimal:
+    # Verify dask-image works without the optional `dataframe` extras
+    # (i.e. without pandas and dask[dataframe]).
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: true
+      matrix:
+        os: ["windows-latest", "ubuntu-latest", "macos-latest"]
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v5
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+
+      - name: Install dask-image without dataframe extras
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e .[test]
+
+      - name: Run tests (find_objects tests are skipped automatically)
+        run: pytest -v
+
+  test-latest-all-extras:
+    # Verify dask-image works with the latest unfixed dependencies, including
+    # optional `dataframe` extras so find_objects is also tested.
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: true
+      matrix:
+        os: ["windows-latest", "ubuntu-latest", "macos-latest"]
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v5
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.13"
+
+      - name: Install dask-image with all extras
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e .[dataframe,test]
+
+      - name: Run tests
+        run: pytest -v
+
   coveralls:
     needs: test
     runs-on: ubuntu-latest

continuous_integration/environment-3.13.yml

@@ -0,0 +1,24 @@
+name: dask-image-testenv
+
+channels:
+  - conda-forge
+
+dependencies:
+  - python=3.13.*
+  - pip==24.3.1
+  - coverage==7.6.1
+  - flake8==7.1.1
+  - pytest==8.3.4
+  - pytest-cov==6.0.0
+  - pytest-flake8==1.3.0
+  - pytest-timeout >=2.3.1
+  - dask==2025.1.0
+  - numpy==2.2.0
+  - scipy==1.15.0
+  - scikit-image==0.25.0
+  - pims==0.6.1
+  - slicerator==1.1.0
+  - pandas==2.2.3
+  - twine==6.0.1
+  - pip:
+    - build==1.2.2

continuous_integration/environment-3.14.yml

@@ -0,0 +1,24 @@
+name: dask-image-testenv
+
+channels:
+  - conda-forge
+
+dependencies:
+  - python=3.14.*
+  - pip==25.0.1
+  - coverage==7.6.1
+  - flake8==7.1.1
+  - pytest==8.3.4
+  - pytest-cov==6.0.0
+  - pytest-flake8==1.3.0
+  - pytest-timeout >=2.3.1
+  - dask==2025.1.0
+  - numpy==2.2.0
+  - scipy==1.15.0
+  - scikit-image==0.25.0
+  - pims==0.6.1
+  - slicerator==1.1.0
+  - pandas==2.2.3
+  - twine==6.0.1
+  - pip:
+    - build==1.2.2

dask_image/ndmeasure/__init__.py

@@ -9,7 +9,6 @@
 
 import dask.array as da
 import dask.bag as db
-import dask.dataframe as dd
 import numpy as np
 
 from . import _utils
@@ -228,9 +227,21 @@ def find_objects(label_image):
 
     Notes
     -----
-    You must have the optional dependency ``dask[dataframe]`` installed
-    to use the ``find_objects`` function.
+    You must have the optional dependencies ``dask[dataframe]`` and
+    ``pandas`` installed to use the ``find_objects`` function. They can
+    be installed together via the ``dataframe`` extras group:
+    ``pip install dask-image[dataframe]``.
     """
+    try:
+        import pandas  # noqa: F401  # used by the private helpers below
+        import dask.dataframe as dd
+    except ImportError as e:
+        raise ImportError(
+            "dask_image.ndmeasure.find_objects requires the optional "
+            "dependencies `dask[dataframe]` and `pandas`. Install them "
+            "with `pip install dask-image[dataframe]`."
+        ) from e
+
     if label_image.dtype.char not in np.typecodes['AllInteger']:
         raise ValueError("find_objects only accepts integer dtype arrays")
 

dask_image/ndmeasure/_utils/_find_objects.py

@@ -1,7 +1,5 @@
 import numpy as np
-import pandas as pd
 from dask.delayed import Delayed
-import dask.dataframe as dd
 import dask.config as dask_config
 
 
@@ -24,6 +22,8 @@ def _find_bounding_boxes(x, array_location):
     This alternative function returns a pandas dataframe,
     with one row per object found in the image chunk.
     """
+    import pandas as pd
+
     unique_vals = np.unique(x)
     unique_vals = unique_vals[unique_vals != 0]
     result = {}
@@ -53,6 +53,8 @@ def _combine_slices(slices):
 
 def _merge_bounding_boxes(x, ndim):
     "Merge the bounding boxes describing objects over multiple image chunks."
+    import pandas as pd
+
     x = x.dropna()
     data = {}
     # For each dimension in the array,
@@ -72,6 +74,9 @@ def _merge_bounding_boxes(x, ndim):
 
 def _find_objects(ndim, df1, df2):
     """Main utility function for find_objects."""
+    import pandas as pd
+    import dask.dataframe as dd
+
     meta = dd.utils.make_meta([(i, object) for i in range(ndim)])
     if isinstance(df1, Delayed):
         with dask_config.set({'dataframe.convert-string': False}):

pyproject.toml

@@ -10,29 +10,33 @@ keywords = ["dask-image", "dask", "image"]
 readme = "README.rst"
 license = { text = "BSD-3-Clause" }
 dynamic = ["version"]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 classifiers = [
     "Development Status :: 2 - Pre-Alpha",
     "Intended Audience :: Developers",
     "License :: OSI Approved :: BSD License",
     "Natural Language :: English",
     "Operating System :: OS Independent",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
 ]
 dependencies = [
-    "dask[array,dataframe] >=2024.4.1",
+    "dask[array] >=2024.4.1",
     "numpy >=1.18",
     "scipy >=1.7.0",
-    "pandas >=2.0.0",
     "pims >=0.4.1",
     "tifffile >=2020.10.1",
 ]
 
 [project.optional-dependencies]
+dataframe = [
+    "dask[dataframe] >=2024.4.1",
+    "pandas >=2.0.0",
+]
 test = [
     "build >=1.2.1",
     "coverage >=7.2.1",
@@ -72,3 +76,6 @@ include = [
 [tool.pytest.ini_options]
 addopts = "--flake8"
 markers = "cupy"
+
+[tool.flake8]
+exclude = ["dask_image/_version.py"]

tests/test_dask_image/test_ndfilters/test__generic.py

@@ -70,9 +70,9 @@ def test_generic_filter_shape_type(da_func):
 @pytest.mark.parametrize(
     "function, size, footprint",
     [
-        (lambda x: x, 1, None),
-        (lambda x: x, (1, 1), None),
-        (lambda x: x, None, np.ones((1, 1))),
+        (lambda x: x[0], 1, None),
+        (lambda x: x[0], (1, 1), None),
+        (lambda x: x[0], None, np.ones((1, 1))),
     ],
 )
 def test_generic_filter_identity(sp_func, da_func, function, size, footprint):
@@ -94,7 +94,7 @@ def test_generic_filter_identity(sp_func, da_func, function, size, footprint):
     ],
 )
 def test_generic_filter_comprehensions(da_func):
-    da_wfunc = lambda arr: da_func(arr, lambda x: x, 1)  # noqa: E731
+    da_wfunc = lambda arr: da_func(arr, lambda x: x[0], 1)  # noqa: E731
 
     np.random.seed(0)
 

tests/test_dask_image/test_ndmeasure/test_find_objects.py

@@ -1,10 +1,12 @@
-import dask.array as da
-import dask.dataframe as dd
-import numpy as np
-import pandas as pd
 import pytest
 
-import dask_image.ndmeasure
+pd = pytest.importorskip("pandas")
+dd = pytest.importorskip("dask.dataframe")
+
+import dask.array as da  # noqa: E402
+import numpy as np  # noqa: E402
+
+import dask_image.ndmeasure  # noqa: E402
 
 
 @pytest.fixture