rename

napari_split_dataset/__init__.py

@@ -1,6 +1,6 @@
-"""Top-level package for napari-split-dataset."""
+"""hdf5/split-dataset file reader for napari"""
 
-__author__ = """You Wu"""
+__author__ = """You Wu @portugueslab"""
 __version__ = "0.1.0"
 
-from ._reader import napari_get_reader
+from napari_split_dataset.napari_split_dataset import napari_get_reader

napari_split_dataset/_reader.py → napari_split_dataset/napari_split_dataset.py

@@ -18,7 +18,6 @@ def napari_get_reader(path):
 
 def read_directory(path):
     # read the image stack from a split dataset directory
-
     try:
         data = SplitDataset(path)
     except (IndexError, KeyError, ValueError):
@@ -28,30 +27,26 @@ def read_directory(path):
         # set contrast limits for 4D data.
         # otherwise napari tries to set them after reading everything,
         # which would take too long if the data was large.
-        data_for_contrast = data[
-            min(2, data.shape[0] - 1) : min(7, data.shape[0]), :, :, :
-        ]
+        partial = data[min(2, data.shape[0] - 1) : min(7, data.shape[0]), :, :, :]
         contrast_limits = (
-            np.percentile(data_for_contrast, 0.1),
-            np.percentile(data_for_contrast, 99.9),
+            np.percentile(partial, 0.1),
+            np.percentile(partial, 99.9),
         )
 
         data = data.as_dask()  # read as a dask array
-        # optional kwargs for the corresponding viewer.add_* method
         add_kwargs = {
             "contrast_limits": contrast_limits,
         }
     else:
         data = data[:, :, :]
         add_kwargs = {}
 
-    layer_type = "image"  # optional, default is "image"
+    layer_type = "image"  # default
     return [(data, add_kwargs, layer_type)]
 
 
 def read_hdf5(path):
     # read the image if the h5 file is an array or part of split dataset files
-
     try:
         data = fl.load(path)
     except (OSError, RuntimeError):

setup.py

@@ -7,9 +7,6 @@
 with open("README.rst") as readme_file:
     readme = readme_file.read()
 
-# with open('HISTORY.rst') as history_file:
-#     history = history_file.read()
-
 with open("requirements.txt") as f:
     requirements = f.read().splitlines()
 
@@ -25,13 +22,13 @@
 ]
 
 setup(
-    author="You Wu",
-    author_email="[email protected]",
+    author="You Wu @portugueslab",
+    author_email="[email protected]",
     python_requires=">=3.5",
     classifiers=[
         "Development Status :: 2 - Pre-Alpha",
         "Intended Audience :: Developers",
-        "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+        "License :: OSI Approved :: MIT License",
         "Natural Language :: English",
         "Programming Language :: Python :: 3",
         "Programming Language :: Python :: 3.5",
@@ -42,8 +39,7 @@
     description="hdf5/split-dataset file reader for napari",
     extras_require=dict(dev=requirements_dev),
     install_requires=requirements,
-    license="GNU General Public License v3",
-    # long_description=readme + '\n\n' + history,
+    license="MIT",
     include_package_data=True,
     keywords="napari_split_dataset",
     name="napari_split_dataset",

tests/__init__.py

@@ -1,4 +1 @@
 """Unit test package for napari_split_dataset."""
-from pathlib import Path
-
-ASSETS_PATH = Path(__file__).parent / "assets"

tests/test_napari_split_dataset.py

@@ -2,13 +2,15 @@
 
 """Tests for `napari_split_dataset` package."""
 
+from pathlib import Path
+
 import pytest
 from dask.array.core import Array
 from numpy import ndarray
 
-from napari_split_dataset import _reader
+from napari_split_dataset import napari_split_dataset
 
-from . import ASSETS_PATH
+ASSETS_PATH = Path(__file__).parent / "assets"
 
 
 @pytest.mark.parametrize(
@@ -27,7 +29,7 @@
     ],
 )
 def test_reader(path, expected):
-    reader = _reader.napari_get_reader(path)
+    reader = napari_split_dataset.napari_get_reader(path)
     assert callable(reader) == expected
 
 
@@ -41,7 +43,7 @@ def test_reader(path, expected):
     ],
 )
 def test_dir_reader(path, expected):
-    data = _reader.read_directory(path)
+    data = napari_split_dataset.read_directory(path)
     if isinstance(data, list):
         data = data[0][0]
     assert isinstance(data, expected)
@@ -50,15 +52,14 @@ def test_dir_reader(path, expected):
 @pytest.mark.parametrize(
     "path, expected",
     [
-        (ASSETS_PATH / "sample_4d", type(None)),
-        (ASSETS_PATH / "random", type(None)),
+        (ASSETS_PATH / "sample_3d", type(None)),
         (ASSETS_PATH / "array.h5", ndarray),
         (ASSETS_PATH / "dict_stack.h5", ndarray),
         (ASSETS_PATH / "dict_shift.h5", type(None)),
     ],
 )
 def test_h5_reader(path, expected):
-    data = _reader.read_hdf5(path)
+    data = napari_split_dataset.read_hdf5(path)
     if isinstance(data, list):
         data = data[0][0]
     assert isinstance(data, expected)