Merge pull request #13 from ilastik/fix-float-warning

Fix float warning

.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/deploy.yml

@@ -0,0 +1,32 @@
+name: deploy
+
+on:
+  push:
+    tags:
+      - '0.*'
+
+jobs:
+  package:
+    runs-on: ubuntu-latest
+    environment: conda-deploy
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          auto-activate-base: true
+          activate-environment: ""
+          channel-priority: strict
+          miniforge-version: latest
+      - name: install build dependencies
+        run: |
+          conda install -n base -c conda-forge boa setuptools_scm anaconda-client -y
+      - name: linux conda build and upload
+        shell: bash -l {0}
+        env:
+          ANACONDA_API_TOKEN: ${{ secrets.CONDA_UPLOAD_TOKEN }}
+        run: |
+          conda config --set anaconda_upload yes
+          conda build conda-forge --user ilastik-forge conda-recipe

.github/workflows/test.yml

@@ -0,0 +1,27 @@
+name: test
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  conda-noarch-build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          auto-activate-base: true
+          activate-environment: ""
+          channel-priority: strict
+          miniforge-version: latest
+      - name: install common conda dependencies
+        run: conda install -n base -q conda-build pip anaconda-client -y
+      - name: linux conda build test
+        shell: bash -l {0}
+        run: conda build -c conda-forge conda-recipe

dev/environment-dev.yaml

@@ -1,14 +1,15 @@
 name: ndstructs-dev
 channels:
-  - defaults
   - conda-forge
+  - nodefaults
 dependencies:
   - black
   - bumpversion
   - numpy
   - scikit-image
   - h5py
   - pre_commit
-  - pytest <5.4
-  - python >=3.7
+  - pytest
+  - python >=3.8
+  - imageio
   - fs

ndstructs/array5D.py

@@ -2,7 +2,7 @@
 from typing import Iterator, Tuple, Iterable, Optional, Union, TypeVar, Type, cast, Sequence
 import numpy as np
 from skimage import measure as skmeasure
-import skimage.io
+import imageio.v3 as iio
 import io
 import os
 import uuid
@@ -72,7 +72,7 @@ def to_json_data(self) -> dict:
 
     @classmethod
     def from_file(cls: Type[Arr], filelike: io.IOBase, location: Point5D = Point5D.zero()) -> Arr:
-        data = skimage.io.imread(filelike)
+        data = iio.imread(filelike)
         return cls(data, "yxc"[: len(data.shape)], location=location)
 
     def __repr__(self) -> str:

ndstructs/datasource/DataSource.py

@@ -8,7 +8,7 @@
 
 import h5py
 import numpy as np
-import skimage.io
+import imageio.v3 as iio
 from fs.base import FS
 from fs.errors import ResourceNotFound
 from fs.osfs import OSFS
@@ -255,7 +255,7 @@ def __init__(
         self, path: Path, *, location: Point5D = Point5D.zero(), filesystem: FS, tile_shape: Optional[Shape5D] = None
     ):
         try:
-            raw_data = skimage.io.imread(filesystem.openbin(path.as_posix()))
+            raw_data = iio.imread(filesystem.openbin(path.as_posix()))
         except ValueError:
             raise UnsupportedUrlException(path)
         axiskeys = "yxc"[: len(raw_data.shape)]

ndstructs/utils/JsonSerializable.py

@@ -90,7 +90,7 @@ def from_json_data(cls, data, *, dereferencer: Optional[Dereferencer] = None, in
         for type_parts in itertools.product(["u", ""], ["int"], ["8", "16", "32", "64"])
     ]
 )
-float_classes = tuple([float] + [np.float, np.float16, np.float32, np.float64])
+float_classes = tuple([float] + [np.float16, np.float32, np.float64])
 
 Referencer = Callable[[Any], Optional["JsonReference"]]
 

pyproject.toml

@@ -1,3 +1,3 @@
 [tool.black]
 line-length = 120
-target-version = ['py37']
+target-version = ['py38', 'py39', 'py310', 'py311']

setup.py

@@ -8,7 +8,7 @@
     license="MIT",
     description="Short description",
     packages=["ndstructs", "ndstructs.utils", "ndstructs.datasource", "ndstructs.datasink", "ndstructs.caching"],
-    python_requires=">=3.7",
-    install_requires=["numpy", "scikit-image", "h5py", "fs", "typing_extensions"],
-    extras_require={"dev": ["pytest<5.4"]},
+    python_requires=">=3.8",
+    install_requires=["numpy", "scikit-image", "h5py", "fs", "typing_extensions", "imageio"],
+    extras_require={"dev": ["pytest"]},
 )

tests/test_datasource.py

@@ -20,7 +20,8 @@
 import h5py
 import json
 import shutil
-import skimage.io
+import imageio.v3 as iio
+
 
 # fmt: off
 raw = np.asarray([
@@ -64,7 +65,7 @@
 
 def create_png(array: Array5D) -> Path:
     png_path = tempfile.mkstemp()[1] + ".png"
-    skimage.io.imsave(png_path, array.raw("yxc"))
+    iio.imwrite(png_path, array.raw("yxc").squeeze())
     return Path(png_path)