Merge pull request #3 from portugueslab/drop-dask

dropped transformation of stack in dask

.github/workflows/main.yml

@@ -34,7 +34,13 @@ jobs:
           python -m pip install --upgrade pip
           pip install .[dev]
       - name: Test
-        run: pytest
+        run: pytest --cov
+      - name: Coveralls
+        env:
+            GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+            pip install coveralls
+            coveralls --service=github
   deploy:
     needs: test
     runs-on: ubuntu-latest

README.md

@@ -0,0 +1,15 @@
+[![Python Version](https://img.shields.io/pypi/pyversions/napari-split-dataset.svg)](https://pypi.org/project/napari-split-dataset)
+[![PyPI](https://img.shields.io/pypi/v/napari-split-dataset.svg)](
+    https://pypi.python.org/pypi/napari-split-dataset)
+[![Tests](https://img.shields.io/github/workflow/status/portugueslab/napari-split-dataset/tests)](
+    https://github.com/portugueslab/napari-split-dataset/actions)
+[![Coverage Status](https://coveralls.io/repos/github/portugueslab/napari-split-dataset/badge.svg?branch=master)](https://coveralls.io/github/portugueslab/napari-split-dataset?branch=master)
+[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
+
+
+
+
+# hdf5/split-dataset file reader for napari
+
+A `napari` plugin for visualising [`SplitDataset`](https://github.com/portugueslab/split_dataset) objects. This package has been developed in the [Portugues lab](http://www.portugueslab.com).
+

napari_split_dataset/napari_split_dataset.py

@@ -33,7 +33,6 @@ def read_directory(path):
             np.percentile(partial, 99.9),
         )
 
-        data = data.as_dask()  # read as a dask array
         add_kwargs = {
             "contrast_limits": contrast_limits,
         }

setup.py

@@ -4,7 +4,7 @@
 
 from setuptools import find_namespace_packages, setup
 
-with open("README.rst") as readme_file:
+with open("README.md") as readme_file:
     readme = readme_file.read()
 
 with open("requirements.txt") as f:
@@ -37,6 +37,8 @@
         "Programming Language :: Python :: 3.8",
     ],
     description="hdf5/split-dataset file reader for napari",
+    long_description=readme,
+    long_description_content_type="text/markdown",
     extras_require=dict(dev=requirements_dev),
     entry_points={
         "napari.plugin": ["split-dataset = napari_split_dataset"],

tests/test_napari_split_dataset.py

@@ -5,8 +5,8 @@
 from pathlib import Path
 
 import pytest
-from dask.array.core import Array
 from numpy import ndarray
+from split_dataset import SplitDataset
 
 from napari_split_dataset import napari_split_dataset
 
@@ -37,7 +37,7 @@ def test_reader(path, expected):
     "path, expected",
     [
         (ASSETS_PATH / "sample_3d", ndarray),
-        (ASSETS_PATH / "sample_4d", Array),
+        (ASSETS_PATH / "sample_4d", SplitDataset),
         (ASSETS_PATH / "random", type(None)),
         (ASSETS_PATH / "array.h5", type(None)),
     ],
@@ -56,6 +56,7 @@ def test_dir_reader(path, expected):
         (ASSETS_PATH / "array.h5", ndarray),
         (ASSETS_PATH / "dict_stack.h5", ndarray),
         (ASSETS_PATH / "dict_shift.h5", type(None)),
+        (ASSETS_PATH / "nodict.h5", type(None)),
     ],
 )
 def test_h5_reader(path, expected):