Merge branch 'main' into labeled_comprehension-channel-axis

Author: jakirkham

.github/workflows/test_and_deploy.yml

@@ -25,8 +25,6 @@ jobs:
       - name: Setup Conda Environment
         uses: conda-incubator/setup-miniconda@v3
         with:
-          miniforge-variant: Mambaforge
-          use-mamba: true
           python-version: ${{ matrix.python-version }}
           environment-file: continuous_integration/environment-${{ matrix.python-version }}.yml
           activate-environment: dask-image-testenv
@@ -44,7 +42,7 @@ jobs:
         run: pytest -v --cov=dask_image --cov-report lcov
 
       - name: Coveralls Parallel
-        uses: coverallsapp/github-action@v2.3.0
+        uses: coverallsapp/github-action@v2.3.6
         with:
           github-token: ${{ secrets.github_token }}
           flag-name: run-${{ matrix.test_number }}
@@ -56,7 +54,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Coveralls Finished
-      uses: coverallsapp/github-action@v2.3.0
+      uses: coverallsapp/github-action@v2.3.6
       with:
         github-token: ${{ secrets.github_token }}
         parallel-finished: true

dask_image/ndinterp/__init__.py

@@ -367,10 +367,11 @@ def rotate(
     if reshape:
         # Compute transformed input bounds
         iy, ix = in_plane_shape
-        out_bounds = rot_matrix @ [[0, 0, iy, iy],
-                                   [0, ix, 0, ix]]
+        in_bounds = np.array([[0, 0, iy, iy],
+                              [0, ix, 0, ix]])
+        out_bounds = rot_matrix @ in_bounds
         # Compute the shape of the transformed input plane
-        out_plane_shape = (out_bounds.ptp(axis=1) + 0.5).astype(int)
+        out_plane_shape = (np.ptp(out_bounds, axis=1) + 0.5).astype(int)
     else:
         out_plane_shape = img_shape[axes]
 

dask_image/ndmeasure/__init__.py

@@ -10,6 +10,7 @@
 import dask.dataframe as dd
 import numpy as np
 from dask import compute, delayed
+import dask.config as dask_config
 
 from . import _utils
 from ._utils import _label
@@ -244,7 +245,9 @@ def find_objects(label_image):
     result = bag.fold(functools.partial(_find_objects, label_image.ndim), split_every=2).to_delayed()
     meta = dd.utils.make_meta([(i, object) for i in range(label_image.ndim)])
     result = delayed(compute)(result)[0]  # avoid the user having to call compute twice on result
-    result = dd.from_delayed(result, meta=meta, prefix="find-objects-", verify_meta=False)
+
+    with dask_config.set({'dataframe.convert-string': False}):
+        result = dd.from_delayed(result, meta=meta, prefix="find-objects-", verify_meta=False)
 
     return result
 

dask_image/ndmeasure/_utils/_find_objects.py

@@ -2,6 +2,7 @@
 import pandas as pd
 from dask.delayed import Delayed
 import dask.dataframe as dd
+import dask.config as dask_config
 
 
 def _array_chunk_location(block_id, chunks):
@@ -67,9 +68,11 @@ def _find_objects(ndim, df1, df2):
     """Main utility function for find_objects."""
     meta = dd.utils.make_meta([(i, object) for i in range(ndim)])
     if isinstance(df1, Delayed):
-        df1 = dd.from_delayed(df1, meta=meta)
+        with dask_config.set({'dataframe.convert-string': False}):
+            df1 = dd.from_delayed(df1, meta=meta)
     if isinstance(df2, Delayed):
-        df2 = dd.from_delayed(df2, meta=meta)
+        with dask_config.set({'dataframe.convert-string': False}):
+            df2 = dd.from_delayed(df2, meta=meta)
     ddf = dd.merge(df1, df2, how="outer", left_index=True, right_index=True)
     result = ddf.apply(_merge_bounding_boxes, ndim=ndim, axis=1, meta=meta)
     return result

docs/conf.py

@@ -120,6 +120,15 @@
 
 # -- Options for HTML output -------------------------------------------
 
+# Set canonical URL from the Read the Docs Domain
+html_baseurl = os.environ.get("READTHEDOCS_CANONICAL_URL", "")
+
+# Tell Jinja2 templates the build is running on Read the Docs
+if os.environ.get("READTHEDOCS", "") == "True":
+    if "html_context" not in globals():
+        html_context = {}
+    html_context["READTHEDOCS"] = True
+
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 html_theme = 'dask_sphinx_theme'

tests/test_dask_image/test_imread/test_core.py

@@ -76,7 +76,8 @@ def test_tiff_imread(tmpdir, seed, nframes, shape, dtype, is_pathlib_Path):  # n
     fn = str(dirpth.join("test.tiff"))
     with tifffile.TiffWriter(fn) as fh:
         for i in range(len(a)):
-            fh.save(a[i], contiguous=True)
+            fh.write(a[i], contiguous=True)
+
     if is_pathlib_Path:
         fn = pathlib.Path(fn)
     d = dask_image.imread.imread(fn, nframes=nframes)