fixing code to python standards

doc_template/source/conf.py

@@ -1,12 +1,15 @@
 """Configuration file for the Sphinx documentation builder."""
+
 #
 # For the full list of built-in configuration values, see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
+from datetime import date
+
 # -- Path Setup --------------------------------------------------------------
-from os.path import dirname, abspath
+from os.path import abspath, dirname
 from pathlib import Path
-from datetime import date
+
 from aind_smartspim_data_transformation import __version__ as package_version
 
 INSTITUTE_NAME = "Allen Institute for Neural Dynamics"

src/aind_smartspim_data_transformation/compress/__init__.py

@@ -1,3 +1,3 @@
 """
-Init internal package
+Init SmartSPIM data transformation package
 """

src/aind_smartspim_data_transformation/compress/dask_utils.py

@@ -39,9 +39,9 @@ def log_dashboard_address(
         client: the Client instance
         login_node_address: the address of the cluster login node
     """
-    host = client.run_on_scheduler(socket.gethostname)
-    port = client.scheduler_info()["services"]["dashboard"]
-    user = os.getenv("USER")
+    host = client.run_on_scheduler(socket.gethostname)  # noqa: F841
+    port = client.scheduler_info()["services"]["dashboard"]  # noqa: F841
+    user = os.getenv("USER")  # noqa: F841
     LOGGER.info(
         f"To access the dashboard, run the following in "
         "a terminal: ssh -L {port}:{host}:{port} {user}@"

src/aind_smartspim_data_transformation/compress/png_to_zarr.py

@@ -15,8 +15,6 @@
 
 import dask
 import dask.array as da
-
-# import matplotlib.pyplot as plt
 import numpy as np
 import pims
 import xarray_multiscale
@@ -33,7 +31,11 @@
 from ome_zarr.writer import write_multiscales_metadata
 from skimage.io import imread as sk_imread
 
-from aind_smartspim_data_transformation.compress.zarr_utilities import *
+from aind_smartspim_data_transformation.compress.zarr_utilities import (
+    ArrayLike,
+    PathLike,
+    pad_array_n_d,
+)
 from aind_smartspim_data_transformation.compress.zarr_writer import (
     BlockedArrayWriter,
 )
@@ -144,16 +146,20 @@ def _compute_scales(
     data_shape: Tuple[int, int, int, int, int],
     translation: Optional[List[float]] = None,
 ) -> Tuple[List, List]:
-    """Generate the list of coordinate transformations and associated chunk options.
+    """
+    Generate the list of coordinate transformations
+    and associated chunk options.
 
     Parameters
     ----------
     scale_num_levels: the number of downsampling levels
     scale_factor: a tuple of scale factors in each spatial dimension (Z, Y, X)
     pixelsizes: a list of pixel sizes in each spatial dimension (Z, Y, X)
-    chunks: a 5D tuple of integers with size of each chunk dimension (T, C, Z, Y, X)
+    chunks: a 5D tuple of integers with size of each
+    chunk dimension (T, C, Z, Y, X)
     data_shape: a 5D tuple of the full resolution image's shape
-    translation: a 5 element list specifying the offset in physical units in each dimension
+    translation: a 5 element list specifying the offset
+    in physical units in each dimension
 
     Returns
     -------
@@ -364,7 +370,7 @@ def _get_pyramid_metadata():
     """
     return {
         "metadata": {
-            "description": "Downscaling implementation based on the windowed mean of the original array",
+            "description": "Downscaling using the windowed mean",
             "method": "xarray_multiscale.reducers.windowed_mean",
             "version": str(xarray_multiscale.__version__),
             "args": "[false]",
@@ -438,7 +444,8 @@ def wavelength_to_hex(wavelength: int) -> int:
     """
     # Each wavelength key is the upper bound to a wavelgnth band.
     # Wavelengths range from 380-750nm.
-    # Color map wavelength/hex pairs are generated by sampling along a CIE diagram arc.
+    # Color map wavelength/hex pairs are generated
+    # by sampling along a CIE diagram arc.
     color_map = {
         460: 0x690AFE,  # Purple
         470: 0x3F2EFE,  # Blue-Purple
@@ -657,6 +664,7 @@ def smartspim_channel_zarr_writer(
         # Formatting to 5D block shape
         block_shape = ([1] * (5 - len(block_shape))) + block_shape
         written_pyramid = []
+        pyramid_group = None
 
         # Writing multiple levels
         for level in range(n_lvls):

src/aind_smartspim_data_transformation/io/_io.py

@@ -262,7 +262,8 @@ def metadata(self) -> Dict:
 
         zattrs_metadata = ""
         zarray_metadata = ""
-        # Checking inside and outside of folder due to dimension separator "." or "/"
+        # Checking inside and outside of folder
+        # due to dimension separator "." or "/"
         for path in [data_path, data_path.parent]:
             if path.joinpath(".zattrs").exists():
                 zattrs_metadata = path.joinpath(".zattrs")