fixed the py-linting and turned off alphabetical sorting of imports due to an...

fixed the py-linting and turned off alphabetical sorting of imports due to an issue with compiler version with which numpy was built

apps/hiopy/configure/configure.py

@@ -29,7 +29,7 @@ def _collect_groups(dataset):
         yield from _collect_groups(g)
 
 
-def add_height(dataset, name, positive_direction: str = "up", values: list[int] = []):
+def add_height(dataset, name, positive_direction: str, values: list[int]):
     for g in _collect_groups(dataset):
         height = g.create_array(name, fill_value=None, dtype=np.int64, shape=(len(values),))
         height[:] = np.asarray(values, dtype=np.int64)

apps/hiopy/configure/create_dataset.py

@@ -23,8 +23,9 @@ def add_coordinates(
 
     Notes
     -----
-    This function creates two new arrays in the dataset: `coord_names[0]` for longitude and `coord_names[1]` for latitude.
-    The `crs` array is also created, with its attributes set to indicate that it's a "point_cloud" coordinate reference system.
+    This function creates two new arrays in the dataset: `coord_names[0]` for longitude and
+    `coord_names[1]` for latitude. The `crs` array is also created, with its attributes set
+    to indicate that it's a "point_cloud" coordinate reference system.
     Example: add_coordinates(dataset, [(10.2, 45.3), (20.4, 50.5)])
     """
 
@@ -54,19 +55,20 @@ def add_coordinates(
 
 def add_healpix_grid(dataset: zarr.Group, order: int):
     """
-        Add a HealPix grid to the specified Zarr dataset.
-
-        Parameters
-        ----------
-        dataset : zarr.Group
-            The Zarr group where the HealPix grid will be added to the crs.
-        order : int
-            The order of the HealPix grid. This corresponds to 2^order for the NSIDE.
-
-        Notes
-        -----
-        The HealPix grid is stored as a single array named "crs" in the dataset, with the healpix_nside and healpix_order attributes set
-    accordingly. No values are added to it
+    Add a HealPix grid to the specified Zarr dataset.
+
+    Parameters
+    ----------
+    dataset : zarr.Group
+        The Zarr group where the HealPix grid will be added to the crs.
+    order : int
+        The order of the HealPix grid. This corresponds to 2^order for the NSIDE.
+
+    Notes
+    -----
+    The HealPix grid is stored as a single array named "crs" in the dataset, with
+    the healpix_nside and healpix_order attributes set accordingly.
+    No values are added to it
     """
     crs = dataset.create_array(name="crs", dtype=np.float32, shape=(1,))
     crs.attrs["_ARRAY_DIMENSIONS"] = ("crs",)
@@ -84,8 +86,9 @@ def add_healpix_hierarchy(
     """
     Add a hierarchical structure to the specified Zarr dataset for a given Healpix order.
 
-    This function creates a group hierarchy with each level representing a specific resolution of the Healpix grid.
-    The `add_healpix_grid` function is used to create the actual grid arrays within each group.
+    This function creates a group hierarchy with each level representing a specific
+    resolution of the Healpix grid. The `add_healpix_grid` function is used to create the
+    actual grid arrays within each group.
 
     Parameters
     ----------
@@ -100,12 +103,15 @@ def add_healpix_hierarchy(
 
     Notes
     -----
-    This function sets up a hierarchical structure with each level representing a specific resolution of the Healpix grid.
-    The `hiopy::parent` attribute is used to link each group to its parent in the hierarchy, allowing for efficient navigation.
+    This function sets up a hierarchical structure with each level representing a
+    specific resolution of the Healpix grid. The `hiopy::parent` attribute is used
+    to link each group to its parent in the hierarchy, allowing for efficient navigation.
     """
     for o in range(order, order - nr_of_coarsenings, -1):
         zg = dataset.create_group(name=f"{prefix}{o}")
         add_healpix_grid(zg, o)
         if o < order:
-            parent_name = f"{dataset.basename}/{prefix}{o+1}" if dataset.basename is not "" else f"{prefix}{o+1}"
+            parent_name = (
+                f"{dataset.basename}/{prefix}{o+1}" if dataset.basename != "" else f"{prefix}{o+1}"
+            )
             zg.attrs["hiopy::parent"] = parent_name

apps/hiopy/worker.py

 #!/usr/bin/env python3
-import zarr
 from coyote import (
     Coyote,
     ensure_enddef,
@@ -17,13 +16,13 @@ from ._grids import def_grid, grid_id
 from ._zarr_utils import get_var_group
 from .loco import LocoServer
 
-import numpy as np
-import json
-import zarr
-import logging
 from argparse import ArgumentParser
 from itertools import chain, groupby
 
+import json
+import logging
+import numpy as np
+import zarr
 
 
 def main():
@@ -200,9 +199,7 @@ def main():
     ensure_enddef()
     if group_comm_rank() == 0:
         for v in data_vars:
-            if "hiopy::yac_source" not in v.attrs:
-                continue
-            else: 
+            if "hiopy::copy_metadata" in v.attrs:
                 comp, grid, field = get_source_triple(v)
                 md_str = get_field_metadata(comp, grid, field)
                 metadata = json.loads(md_str)
@@ -213,7 +210,7 @@ def main():
 
         # re-consolidate the newly updated metadata
         for ds in args.datasets:
-            zarr.consolidate_metadata(ds.store)    
+            zarr.consolidate_metadata(ds.store)
 
     run()
 

pyproject.toml

@@ -43,7 +43,5 @@ lint.select = [
     "B",
     # flake8-simplify
     "SIM",
-    # isort
-    "I",
 ]
 line-length = 100 # accomodate any libc++ motivated requirements of over 80 characters