Initial commit

LICENSE

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+
+The MIT License (MIT)
+
+Copyright (c) 2020 Draga Doncila Pop
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

MANIFEST.in

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+include LICENSE
+include README.md
+include requirements.txt
+
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]

README.md

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+# napari-sentinel-zip
+
+[![License](https://img.shields.io/pypi/l/napari-sentinel-zip.svg?color=green)](https://github.com/napari/napari-sentinel-zip/raw/master/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/napari-sentinel-zip.svg?color=green)](https://pypi.org/project/napari-sentinel-zip)
+[![Python Version](https://img.shields.io/pypi/pyversions/napari-sentinel-zip.svg?color=green)](https://python.org)
+[![tests](https://github.com/DragaDoncila/napari-sentinel-zip/workflows/tests/badge.svg)](https://github.com/DragaDoncila/napari-sentinel-zip/actions)
+[![codecov](https://codecov.io/gh/DragaDoncila/napari-sentinel-zip/branch/master/graph/badge.svg)](https://codecov.io/gh/DragaDoncila/napari-sentinel-zip)
+
+Stacks and opens Sentinel mission zip archives for one tile across different timepoints.
+
+----------------------------------
+
+This [napari] plugin was generated with [Cookiecutter] using with [@napari]'s [cookiecutter-napari-plugin] template.
+
+<!--
+Don't miss the full getting started guide to set up your new package:
+https://github.com/napari/cookiecutter-napari-plugin#getting-started
+
+and review the napari docs for plugin developers:
+https://napari.org/docs/plugins/index.html
+-->
+
+## Installation
+
+You can install `napari-sentinel-zip` via [pip]:
+
+    pip install napari-sentinel-zip
+
+## Contributing
+
+Contributions are very welcome. Tests can be run with [tox], please ensure
+the coverage at least stays the same before you submit a pull request.
+
+## License
+
+Distributed under the terms of the [MIT] license,
+"napari-sentinel-zip" is free and open source software
+
+## Issues
+
+If you encounter any problems, please [file an issue] along with a detailed description.
+
+[napari]: https://github.com/napari/napari
+[Cookiecutter]: https://github.com/audreyr/cookiecutter
+[@napari]: https://github.com/napari
+[MIT]: http://opensource.org/licenses/MIT
+[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
+[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
+[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
+[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
+[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
+[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
+[file an issue]: https://github.com/DragaDoncila/napari-sentinel-zip/issues
+[napari]: https://github.com/napari/napari
+[tox]: https://tox.readthedocs.io/en/latest/
+[pip]: https://pypi.org/project/pip/
+[PyPI]: https://pypi.org/

docs/index.md

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+# Welcome to napari-sentinel-zip
+
+Stacks and opens Sentinel mission zip archives for one tile across different timepoints.

mkdocs.yml

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+site_name: napari-sentinel-zip
+site_description: Stacks and opens Sentinel mission zip archives for one tile across different timepoints.
+site_author: Draga Doncila Pop
+
+theme: readthedocs
+
+repo_url: https://github.com/DragaDoncila/napari-sentinel-zip
+
+pages:
+- Home: index.md

napari_sentinel_zip/__init__.py

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+try:
+    from ._version import version as __version__
+except ImportError:
+    __version__ = "unknown"
+
+# replace the asterisk with named imports
+from .napari_sentinel_zip import napari_get_reader
+
+
+__all__ = ["napari_get_reader"]

napari_sentinel_zip/_tests/test_napari_sentinel_zip.py

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+import numpy as np
+from napari_napari_sentinel_zip import napari_get_reader
+
+
+# tmp_path is a pytest fixture
+def test_reader(tmp_path):
+    """An example of how you might test your plugin."""
+
+    # write some fake data using your supported file format
+    my_test_file = str(tmp_path / "myfile.npy")
+    original_data = np.random.rand(20, 20)
+    np.save(my_test_file, original_data)
+
+    # try to read it back in
+    reader = napari_get_reader(my_test_file)
+    assert callable(reader)
+
+    # make sure we're delivering the right format
+    layer_data_list = reader(my_test_file)
+    assert isinstance(layer_data_list, list) and len(layer_data_list) > 0
+    layer_data_tuple = layer_data_list[0]
+    assert isinstance(layer_data_tuple, tuple) and len(layer_data_tuple) > 0
+
+    # make sure it's the same as it started
+    np.testing.assert_allclose(original_data, layer_data_tuple[0])
+
+
+def test_get_reader_pass():
+    reader = napari_get_reader("fake.file")
+    assert reader is None

napari_sentinel_zip/napari_sentinel_zip.py

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+"""
+This module is an example of a barebones numpy reader plugin for napari.
+
+It implements the ``napari_get_reader`` hook specification, (to create
+a reader plugin) but your plugin may choose to implement any of the hook
+specifications offered by napari.
+see: https://napari.org/docs/plugins/hook_specifications.html
+
+Replace code below accordingly.  For complete documentation see:
+https://napari.org/docs/plugins/for_plugin_developers.html
+"""
+import numpy as np
+from napari_plugin_engine import napari_hook_implementation
+
+
+@napari_hook_implementation
+def napari_get_reader(path):
+    """A basic implementation of the napari_get_reader hook specification.
+
+    Parameters
+    ----------
+    path : str or list of str
+        Path to file, or list of paths.
+
+    Returns
+    -------
+    function or None
+        If the path is a recognized format, return a function that accepts the
+        same path or list of paths, and returns a list of layer data tuples.
+    """
+    if isinstance(path, list):
+        # reader plugins may be handed single path, or a list of paths.
+        # if it is a list, it is assumed to be an image stack...
+        # so we are only going to look at the first file.
+        path = path[0]
+
+    # if we know we cannot read the file, we immediately return None.
+    if not path.endswith(".npy"):
+        return None
+
+    # otherwise we return the *function* that can read ``path``.
+    return reader_function
+
+
+def reader_function(path):
+    """Take a path or list of paths and return a list of LayerData tuples.
+
+    Readers are expected to return data as a list of tuples, where each tuple
+    is (data, [add_kwargs, [layer_type]]), "add_kwargs" and "layer_type" are
+    both optional.
+
+    Parameters
+    ----------
+    path : str or list of str
+        Path to file, or list of paths.
+
+    Returns
+    -------
+    layer_data : list of tuples
+        A list of LayerData tuples where each tuple in the list contains
+        (data, metadata, layer_type), where data is a numpy array, metadata is
+        a dict of keyword arguments for the corresponding viewer.add_* method
+        in napari, and layer_type is a lower-case string naming the type of layer.
+        Both "meta", and "layer_type" are optional. napari will default to
+        layer_type=="image" if not provided
+    """
+    # handle both a string and a list of strings
+    paths = [path] if isinstance(path, str) else path
+    # load all files into array
+    arrays = [np.load(_path) for _path in paths]
+    # stack arrays into single array
+    data = np.squeeze(np.stack(arrays))
+
+    # optional kwargs for the corresponding viewer.add_* method
+    # https://napari.org/docs/api/napari.components.html#module-napari.components.add_layers_mixin
+    add_kwargs = {}
+
+    layer_type = "image"  # optional, default is "image"
+    return [(data, add_kwargs, layer_type)]

requirements.txt

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+napari_plugin_engine>=0.1.4
+numpy

setup.py

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+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import os
+import codecs
+from setuptools import setup, find_packages
+
+
+def read(fname):
+    file_path = os.path.join(os.path.dirname(__file__), fname)
+    return codecs.open(file_path, encoding='utf-8').read()
+
+
+# Add your dependencies in requirements.txt
+# Note: you can add test-specific requirements in tox.ini
+requirements = []
+with open('requirements.txt') as f:
+    for line in f:
+        stripped = line.split("#")[0].strip()
+        if len(stripped) > 0:
+            requirements.append(stripped)
+
+
+# https://github.com/pypa/setuptools_scm
+use_scm = {"write_to": "napari_napari_sentinel_zip/_version.py"}
+
+setup(
+    name='napari-sentinel-zip',
+    author='Draga Doncila Pop',
+    author_email='[email protected]',
+    license='MIT',
+    url='https://github.com/DragaDoncila/napari-sentinel-zip',
+    description='Stacks and opens Sentinel mission zip archives for one tile across different timepoints.',
+    long_description=read('README.md'),
+    long_description_content_type='text/markdown',
+    packages=find_packages(),
+    python_requires='>=3.6',
+    install_requires=requirements,
+    use_scm_version=use_scm,
+    setup_requires=['setuptools_scm'],
+    classifiers=[
+        'Development Status :: 4 - Beta',
+        'Intended Audience :: Developers',
+        'Topic :: Software Development :: Testing',
+        'Programming Language :: Python',
+        'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.6',
+        'Programming Language :: Python :: 3.7',
+        'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: Implementation :: CPython',
+        'Programming Language :: Python :: Implementation :: PyPy',
+        'Operating System :: OS Independent',
+        'License :: OSI Approved :: MIT License',
+    ],
+    entry_points={
+        'napari.plugin': [
+            'sentinel-zip = napari_napari_sentinel_zip',
+        ],
+    },
+)

tox.ini

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+# For more information about tox, see https://tox.readthedocs.io/en/latest/
+[tox]
+envlist = py{36,37,38}-{linux,macos,windows}
+
+[gh-actions]
+python =
+    3.6: py36
+    3.7: py37
+    3.8: py38
+
+[gh-actions:env]
+PLATFORM =
+    ubuntu-latest: linux
+    macos-latest: macos
+    windows-latest: windows
+
+[testenv]
+commands = pytest -v --cov=./ --cov-report=xml
+deps = 
+    pytest-cov  # https://pytest-cov.readthedocs.io/en/latest/
+    pytest  # https://docs.pytest.org/en/latest/contents.html