Merge pull request #27 from NHPatterson/update-requirements

change requirements for zarr

docs/conf.py

@@ -178,8 +178,8 @@
     (
         master_doc,
         "napari-cookiecutterplugin_name.tex",
-        u"napari-\\{\\{cookiecutter.plugin\\_name\\}\\} Documentation",
-        u"\\{\\{cookiecutter.full\\_name\\}\\}",
+        "napari-\\{\\{cookiecutter.plugin\\_name\\}\\} Documentation",
+        "\\{\\{cookiecutter.full\\_name\\}\\}",
         "manual",
     ),
 ]
@@ -213,7 +213,7 @@
     (
         master_doc,
         "napari-cookiecutterplugin_name",
-        u"napari-imsmicrolink Documentation",
+        "napari-imsmicrolink Documentation",
         [author],
         1,
     )
@@ -232,7 +232,7 @@
     (
         master_doc,
         "napari-cookiecutterplugin_name",
-        u"napari-imsmicrolink Documentation",
+        "napari-imsmicrolink Documentation",
         author,
         "napari-cookiecutterplugin_name",
         "One line description of project.",

napari_imsmicrolink/__init__.py

@@ -1,4 +1,4 @@
 __version__ = "0.1.5.1"
 
 
-from ._dock_widget import napari_experimental_provide_dock_widget
+from ._dock_widget import napari_experimental_provide_dock_widget  # noqa: F401

napari_imsmicrolink/_dock_widget.py

@@ -7,6 +7,7 @@
 import dask.array as da
 import SimpleITK as sitk
 
+
 from napari_plugin_engine import napari_hook_implementation
 import napari
 from napari.qt.threading import thread_worker
@@ -64,7 +65,6 @@ def __init__(self, napari_viewer: napari.Viewer):
         """
         super().__init__()
         self.viewer = napari_viewer
-
         # data classes
         self.ims_pixel_map: Optional[PixelMapIMS] = None
         self.microscopy_image: Optional[MicroRegImage] = None

napari_imsmicrolink/_tests/data_tests/test_image_transform.py

@@ -1,4 +1,3 @@
-import pytest
 import numpy as np
 import SimpleITK as sitk
 from napari_imsmicrolink.data.image_transform import ImageTransform

napari_imsmicrolink/_tests/data_tests/test_microscopy_writer.py

@@ -1,13 +1,13 @@
 import pytest
 from pathlib import Path
-import tempfile
 import numpy as np
 from tifffile import imwrite, imread, TiffFile
 from ome_types import from_xml
 import SimpleITK as sitk
 from napari_imsmicrolink.data.tifffile_reader import TiffFileRegImage
 from napari_imsmicrolink.data.microscopy_writer import OmeTiffWriter
 
+
 @pytest.fixture(scope="session")
 def data_out_dir(tmpdir_factory):
     out_dir = tmpdir_factory.mktemp("output")
@@ -44,6 +44,7 @@ def test_OmeTiffWriter_rgb(data_out_dir):
     assert ome_metadata.images[0].pixels.size_y == 2048
     assert ome_metadata.images[0].pixels.size_x == 2048
 
+
 def test_OmeTiffWriter_mc(data_out_dir):
     out_fp = Path(data_out_dir) / "test_rgb.tiff"
 

napari_imsmicrolink/data/__init__.py

@@ -1,6 +1,6 @@
-from .ims_pixel_map import PixelMapIMS
-from .image_transform import ImageTransform
-from .microscopy_reader import MicroRegImage
-from .czi_reader import CziRegImage
-from .tifffile_reader import TiffFileRegImage, TIFFFILE_EXTS
-from .microscopy_writer import OmeTiffWriter
+from .ims_pixel_map import PixelMapIMS  # noqa: F401
+from .image_transform import ImageTransform  # noqa: F401
+from .microscopy_reader import MicroRegImage  # noqa: F401
+from .czi_reader import CziRegImage  # noqa: F401
+from .tifffile_reader import TiffFileRegImage, TIFFFILE_EXTS  # noqa: F401
+from .microscopy_writer import OmeTiffWriter  # noqa: F401

napari_imsmicrolink/data/ims_pixel_map.py

@@ -368,7 +368,7 @@ def _make_shape_map(
         for region_name, roi in zip(region_names, np.unique(region_indices)):
             try:
                 (region_name, self._approximate_roi(pix_map_arr, roi + 1))
-            except:
+            except:  # noqa: E722
                 break
 
         ims_rois = [

napari_imsmicrolink/data/microscopy_reader.py

@@ -1,15 +1,13 @@
 import os
 
-os.environ[
-    "BIOFORMATS_MEMORY"
-] = "8g"  # need to source before bioformats is initialized
-from typing import Union, List, Dict
-from pathlib import Path
-import numpy as np
-import dask.array as da
-from aicsimageio.readers.bioformats_reader import BioFile
-from ome_types import OME
-from napari_imsmicrolink.utils.image import guess_rgb
+os.environ["BIOFORMATS_MEMORY"] = "8g"  # noqa: E402
+from typing import Union, List, Dict  # noqa: E402
+from pathlib import Path  # noqa: E402
+import numpy as np  # noqa: E402
+import dask.array as da  # noqa: E402
+from aicsimageio.readers.bioformats_reader import BioFile  # noqa: E402
+from ome_types import OME  # noqa: E402
+from napari_imsmicrolink.utils.image import guess_rgb  # noqa: E402
 
 PathLike = Union[str, Path]
 

napari_imsmicrolink/data/microscopy_writer.py

@@ -221,7 +221,7 @@ def get_n_ch_mc(shape):
 
                         yx_shape = rgb_interleaved.shape[:2]
                         ds = 1
-                        while np.min(yx_shape) // 2 ** ds >= 512:
+                        while np.min(yx_shape) // 2**ds >= 512:
                             ds += 1
 
                         # write rgb to ome.tiff file

napari_imsmicrolink/qwidgets/__init__.py

@@ -1,5 +1,5 @@
-from .data_ctl_group import DataControl
-from .ims_ctl_group import IMSControl
-from .save_ctl_group import SaveControl
-from .save_dialog import SavePopUp
-from .tform_ctl_group import TformControl
+from .data_ctl_group import DataControl  # noqa: F401
+from .ims_ctl_group import IMSControl  # noqa: F401
+from .save_ctl_group import SaveControl  # noqa: F401
+from .save_dialog import SavePopUp  # noqa: F401
+from .tform_ctl_group import TformControl  # noqa: F401

napari_imsmicrolink/utils/czi.py

@@ -287,7 +287,7 @@ def zarr_pyramidalize_czi(self, zarr_fp):
         yx_shape = np.array(self.shape[slice(yx_dims[0], yx_dims[1] + 1)])
 
         ds = 1
-        while np.min(yx_shape) // 2 ** ds >= 512:
+        while np.min(yx_shape) // 2**ds >= 512:
             ds += 1
 
         self.sub_asarray(

napari_imsmicrolink/utils/image.py

@@ -4,7 +4,6 @@
 import zarr
 import dask.array as da
 import SimpleITK as sitk
-from dask import array as da
 from tifffile import TiffFile, imread, xml2dict
 
 
@@ -383,10 +382,10 @@ def yield_tiles(z, tile_size, is_rgb):
 
 def compute_sub_res(zarray, ds_factor, tile_size, is_rgb, im_dtype):
     if is_rgb:
-        resampling_axis = {0: 2 ** ds_factor, 1: 2 ** ds_factor, 2: 1}
+        resampling_axis = {0: 2**ds_factor, 1: 2**ds_factor, 2: 1}
         tiling = (tile_size, tile_size, 3)
     else:
-        resampling_axis = {0: 1, 1: 2 ** ds_factor, 2: 2 ** ds_factor}
+        resampling_axis = {0: 1, 1: 2**ds_factor, 2: 2**ds_factor}
         tiling = (1, tile_size, tile_size)
 
     resampled_zarray_subres = da.coarsen(

napari_imsmicrolink/utils/ome.py

@@ -1,5 +1,5 @@
 from ome_types.model import Image, Pixels, Channel, OME
-from ome_types.model.simple_types import UnitsLength, Color
+from ome_types.model.simple_types import UnitsLength
 
 pixel_metadata = {
     "size_c": 1000,

requirements.txt

@@ -2,10 +2,11 @@
 # Requirements of your napari plugin should be listed in setup.cfg
 # See also: https://caremad.io/posts/2013/07/setup-vs-requirement/
 
+napari
 numpy
 tifffile
 dask
-zarr==2.10.3
+zarr>=2.10.3
 qtpy
 aicsimageio[bioformats]
 bioformats_jar

setup.cfg

@@ -34,7 +34,7 @@ install_requires =
 	numpy
 	tifffile
 	dask
-	zarr==2.10.3
+	zarr>=2.10.3
 	qtpy
 	aicsimageio[bioformats]
 	bioformats_jar

tox.ini

@@ -35,3 +35,7 @@ deps =
     qtpy
     pyqt5
 commands = pytest -v --color=yes --cov=napari_imsmicrolink --cov-report=xml
+
+[flake8]
+max-line-length = 88
+extend-ignore = E501, E203