Merge pull request #86 from joshmoore/extract-napari

Extract napari to napari-ome-zarr

Author: joshmoore

README.rst

@@ -8,7 +8,7 @@ Experimental support for multi-resolution images stored in Zarr filesets, accord
 Features
 --------
 
-- Use as a image reader plugin for `napari`_. The `napari`_ plugin was generated with `Cookiecutter`_ along with `@napari`_'s `cookiecutter-napari-plugin`_ template.
+- Use as a image reader plugin for `napari`_. See `napari-ome-zarr`_.
 - Simple command-line to read and download conforming Zarr filesets.
 - Helper methods for parsing related metadata.
 
@@ -61,30 +61,6 @@ To download all the resolutions and metadata for an image::
     # Specify output directory
     $ ome_zarr download https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.zarr/ --output image_dir
 
-napari plugin
-=============
-
-Napari will use `ome-zarr` to open images that the plugin recognises as ome-zarr.
-The image metadata from OMERO will be used to set channel names and rendering settings
-in napari::
-
-    $ napari 'https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.zarr/'
-
-    # Also works with local files
-    $ napari 6001240.zarr
-
-OR in python::
-
-    import napari
-    with napari.gui_qt():
-        viewer = napari.Viewer()
-        viewer.open('https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.zarr/')
-
-If single zarray is passed to the plugin, it will be opened without the use of
-the metadata::
-
-    $ napari '/tmp/6001240.zarr/0'
-
 csv to labels
 =============
 
@@ -146,11 +122,10 @@ Distributed under the terms of the `BSD`_ license,
 "ome-zarr-py" is free and open source software
 
 .. _`OME zarr spec`: https://github.com/ome/omero-ms-zarr/blob/master/spec.md
-.. _`Cookiecutter`: https://github.com/audreyr/cookiecutter
 .. _`@napari`: https://github.com/napari
 .. _`BSD`: https://opensource.org/licenses/BSD-2-Clause
 .. _`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
 .. _`napari`: https://github.com/napari/napari
+.. _`napari-ome-zarr`: https://github.com/ome/napari-ome-zarr
 .. _`ome-zarr`: https://pypi.org/project/ome-zarr/

environment.yml

@@ -4,7 +4,6 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - pyqt
   - flake8
   - ipython
   - mypy
@@ -20,8 +19,6 @@ dependencies:
   - xarray
   - zarr >= 2.4.0
   - pip:
-      - napari
       - pre-commit
-      - pytest-qt
 # python.app -- only install on OSX:
 # sys_platform environment marker doesn't work in environment.yml

ome_zarr/napari.py

@@ -48,15 +48,9 @@ def read(fname):
         "Programming Language :: Python :: 3",
         "Operating System :: OS Independent",
         "License :: OSI Approved :: BSD License",
-        "Framework :: napari",
     ],
     entry_points={
         "console_scripts": ["ome_zarr = ome_zarr.cli:main"],
-        "napari.plugin": ["ome_zarr = ome_zarr.napari"],
     },
-    extras_require={
-        "napari:python_version>='3.7'": ["napari"],
-        "napari:python_version<'3.7'": ["napari<0.4.0"],
-    },
-    tests_require=["pytest", "napari"],
+    tests_require=["pytest"],
 )

setup.py

@@ -4,7 +4,6 @@
 import pytest
 
 from ome_zarr.data import astronaut, create_zarr
-from ome_zarr.napari import napari_get_reader
 from ome_zarr.utils import download, info
 
 
@@ -21,31 +20,6 @@ def initdir(self, tmpdir):
         self.path = tmpdir.mkdir("data")
         create_zarr(str(self.path), method=astronaut)
 
-    def test_get_reader_hit(self):
-        reader = napari_get_reader(str(self.path))
-        assert reader is not None
-        assert callable(reader)
-
-    def test_reader(self):
-        reader = napari_get_reader(str(self.path))
-        results = reader(str(self.path))
-        assert len(results) == 2
-        image, label = results
-        assert isinstance(image[0], list)
-        assert isinstance(image[1], dict)
-        assert image[1]["channel_axis"] == 1
-        assert image[1]["name"] == ["Red", "Green", "Blue"]
-
-    def test_get_reader_with_list(self):
-        # a better test here would use real data
-        reader = napari_get_reader([str(self.path)])
-        assert reader is not None
-        assert callable(reader)
-
-    def test_get_reader_pass(self):
-        reader = napari_get_reader("fake.file")
-        assert reader is None
-
     def check_info_stdout(self, out):
         for log in log_strings(0, 1, 3, 1, 1024, 1024, 1, 1, 1, 256, 256, "float64"):
             assert log in out

tests/test_napari.py

@@ -15,8 +15,6 @@ deps =
     PyQt5: PyQt5!=5.15.0
     PySide2: PySide2!=5.15.0
 
-extras = napari
-
 commands =
     pytest {posargs:tests -s}