duck-work

dascore/core/attrs.py

@@ -10,7 +10,6 @@
 from pydantic import ConfigDict, Field, PlainValidator, model_validator
 from typing_extensions import Self
 
-import dascore as dc
 from dascore.constants import (
     VALID_DATA_CATEGORIES,
     VALID_DATA_TYPES,
@@ -23,12 +22,11 @@
     to_str,
 )
 from dascore.utils.models import (
-    StrTupleStrSerialized,
-    IntTupleStrSerialized,
     DascoreBaseModel,
+    IntTupleStrSerialized,
+    StrTupleStrSerialized,
     UnitQuantity,
     frozen_dict_serializer,
-    frozen_dict_validator,
 )
 
 str_validator = PlainValidator(to_str)
@@ -46,7 +44,7 @@ def _to_coord_summary(coord_dict) -> FrozenDict[str, CoordSummary]:
     for i, v in coord_dict.items():
         if hasattr(v, "to_summary"):
             v = v.to_summary()
-        elif isinstance(v,CoordSummary):
+        elif isinstance(v, CoordSummary):
             pass
         else:
             v = CoordSummary(**v)
@@ -133,7 +131,6 @@ class PatchAttrs(DascoreBaseModel):
         frozen_dict_serializer,
     ] = Field(default_factory=dict)
 
-
     @model_validator(mode="before")
     @classmethod
     def _get_dims(cls, data: Any) -> Any:
@@ -144,8 +141,8 @@ def _get_dims(cls, data: Any) -> Any:
             coords = data.get("coords", {})
             dims = getattr(coords, "dims", None)
             if dims is None and isinstance(coords, dict):
-                dims = coords.get('dims', ())
-            data['dims'] = dims
+                dims = coords.get("dims", ())
+            data["dims"] = dims
         return data
 
     def __getitem__(self, item):

dascore/core/coordmanager.py

@@ -289,7 +289,9 @@ def _divide_kwargs(kwargs):
     update_coords = update
 
     def update_from_attrs(
-        self, attrs: Mapping | dc.PatchAttrs, data=None,
+        self,
+        attrs: Mapping | dc.PatchAttrs,
+        data=None,
     ) -> tuple[Self, dc.PatchAttrs]:
         """
         Update coordinates from attrs.

dascore/core/coords.py

@@ -47,9 +47,9 @@
 from dascore.utils.models import (
     ArrayLike,
     DascoreBaseModel,
-    UnitQuantity,
     IntTupleStrSerialized,
     StrTupleStrSerialized,
+    UnitQuantity,
 )
 from dascore.utils.time import dtype_time_like, is_datetime64, is_timedelta64, to_float
 
@@ -104,7 +104,7 @@ class CoordSummary(DascoreBaseModel):
     step: step_type | None = None
     units: UnitQuantity | None = None
     dims: StrTupleStrSerialized = ()
-    name: str = ''
+    name: str = ""
 
     @model_serializer(when_used="json")
     def ser_model(self) -> dict[str, str]:
@@ -710,15 +710,15 @@ def get_attrs_dict(self, name):
             out[f"{name}_units"] = self.units
         return out
 
-    def to_summary(self, dims=(), name='') -> CoordSummary:
+    def to_summary(self, dims=(), name="") -> CoordSummary:
         """Get the summary info about the coord."""
         return CoordSummary(
             min=self.min(),
             max=self.max(),
             step=self.step,
             dtype=self.dtype,
             units=self.units,
-            shape = self.shape,
+            shape=self.shape,
             dims=dims,
             name=name,
         )
@@ -979,7 +979,7 @@ def change_length(self, length: int) -> Self:
         assert self.ndim == 1, "change_length only works on 1D coords."
         return get_coord(shape=(length,))
 
-    def to_summary(self, dims=(), name='') -> CoordSummary:
+    def to_summary(self, dims=(), name="") -> CoordSummary:
         """Get the summary info about the coord."""
         return CoordSummary(
             min=np.nan,

dascore/core/patch.py

@@ -60,6 +60,7 @@ class Patch:
     if there is a conflict between information contained in both, the coords
     will be recalculated.
     """
+
     data: ArrayLike
     coords: CoordManager
     dims: tuple[str, ...]

dascore/examples.py

@@ -84,7 +84,7 @@ def random_patch(
         time_coord = dc.get_coord(
             data=time_array,
             step=time_step if time_array.size <= 1 else None,
-            units='s',
+            units="s",
         )
     else:
         time_coord = dascore.core.get_coord(

dascore/io/core.py

@@ -40,9 +40,9 @@
 from dascore.utils.mapping import FrozenDict
 from dascore.utils.misc import _iter_filesystem, cached_method, iterate, warn_or_raise
 from dascore.utils.models import (
-    StrTupleStrSerialized,
     DascoreBaseModel,
     DateTime64,
+    StrTupleStrSerialized,
     TimeDelta64,
 )
 from dascore.utils.pd import _model_list_to_df

dascore/io/dasdae/core.py

@@ -134,5 +134,5 @@ def scan(self, resource: H5Reader, **kwargs):
             A path to the file.
         """
         file_format = self.name
-        version = resource.attrs['__DASDAE_version__']
+        version = resource.attrs["__DASDAE_version__"]
         return _get_contents_from_patch_groups(resource, version, file_format)

dascore/io/dasdae/utils.py

@@ -2,20 +2,16 @@
 
 from __future__ import annotations
 
-import pickle
-from contextlib import suppress
-
 import numpy as np
 from tables import NodeError
 
 import dascore as dc
 from dascore.core.attrs import PatchAttrs
 from dascore.core.coordmanager import get_coord_manager
 from dascore.core.coords import get_coord
-from dascore.utils.misc import suppress_warnings
-from dascore.utils.time import to_int
-from dascore.utils.misc import unbyte
 from dascore.utils.hdf5 import Empty
+from dascore.utils.misc import suppress_warnings, unbyte
+from dascore.utils.time import to_int
 
 # --- Functions for writing DASDAE format
 
@@ -33,7 +29,7 @@ def _santize_pytables(some_dict):
             continue
         # Get rid of empty enum.
         if isinstance(val, Empty):
-            val = ''
+            val = ""
         out[i] = val
     return out
 
@@ -90,15 +86,12 @@ def _save_array(data, name, group, h5):
     return array_node
 
 
-
-
 def _save_coords(patch, patch_group, h5):
     """Save coordinates."""
     cm = patch.coords
     for name, coord in cm.coord_map.items():
-        summary = (
-            coord.to_summary(name=name, dims=cm.dims[name])
-            .model_dump(exclude_defaults=True)
+        summary = coord.to_summary(name=name, dims=cm.dims[name]).model_dump(
+            exclude_defaults=True
         )
         breakpoint()
         # First save coordinate arrays
@@ -108,9 +101,6 @@ def _save_coords(patch, patch_group, h5):
         dataset.attrs.update(summary)
 
 
-
-
-
 def _save_patch(patch, wave_group, h5, name):
     """Save the patch to disk."""
     patch_group = _create_or_get_group(h5, wave_group, name)
@@ -229,22 +219,23 @@ def _get_coord_info(info, group):
         attrs = _santize_pytables(dict(ds.attrs))
         # Need to get old dimensions from c_dims in attrs.
         if "dims" not in attrs:
-            attrs['dims'] = info.get(f"_cdims_{name}", name)
+            attrs["dims"] = info.get(f"_cdims_{name}", name)
         # The summary info is not stored in attrs; need to read coord array.
         c_info = {}
-        if 'min' not in attrs:
+        if "min" not in attrs:
             c_summary = (
                 dc.core.get_coord(data=ds[:])
                 .to_summary()
                 .model_dump(exclude_unset=True, exclude_defaults=True)
             )
             c_info.update(c_summary)
 
-        c_info.update({
-            "dtype": ds.dtype.str,
-            'shape': ds.shape,
-            "name": name,
-        }
+        c_info.update(
+            {
+                "dtype": ds.dtype.str,
+                "shape": ds.shape,
+                "name": name,
+            }
         )
         coords[name] = c_info
     return coords
@@ -261,10 +252,10 @@ def _get_patch_content_from_group(group):
             value = np.atleast_1d(value)[0]
         out[new_key] = value
     # Add coord info.
-    out['coords'] = _get_coord_info(out, group)
+    out["coords"] = _get_coord_info(out, group)
     # Add data info.
-    out['shape'] = group['data'].shape
-    out['dtype'] = group['data'].dtype.str
+    out["shape"] = group["data"].shape
+    out["dtype"] = group["data"].dtype.str
     # rename dims
     out["dims"] = out.pop("_dims")
     return out

dascore/io/h5simple/core.py

@@ -41,9 +41,7 @@ def read(self, resource: H5Reader, snap=True, **kwargs) -> SpoolType:
         patch = dc.Patch(coords=new_cm, data=new_data[:], attrs=attrs)
         return dc.spool([patch])
 
-    def scan(
-        self, resource: H5Reader, snap=True, **kwargs
-    ) -> list[dc.PatchAttrs]:
+    def scan(self, resource: H5Reader, snap=True, **kwargs) -> list[dc.PatchAttrs]:
         """Get the attributes of a h5simple file."""
         attrs, cm, data = _get_attrs_coords_and_data(resource, snap, self)
         attrs["coords"] = cm.to_summary_dict()

dascore/utils/duck.py

@@ -1,5 +1,3 @@
 """
 Utilities for working with DuckDB.
 """
-
-

dascore/utils/hdf5.py

@@ -19,7 +19,6 @@
 import pandas as pd
 import tables
 from h5py import File as H5pyFile
-from h5py import Empty
 from packaging.version import parse as get_version
 from pandas.io.common import stringify_path
 from tables import ClosedNodeError
@@ -44,7 +43,6 @@
 )
 from dascore.utils.time import get_max_min_times, to_datetime64, to_int, to_timedelta64
 
-
 HDF5ExtError = tables.HDF5ExtError
 NoSuchNodeError = tables.NoSuchNodeError
 NodeError = tables.NodeError

dascore/utils/models.py

@@ -27,9 +27,10 @@
 def _str_to_int_tuple(value):
     """Convert a string of ints to a tuple."""
     if isinstance(value, str):
-        return tuple(int(x) for x in value.split(','))
+        return tuple(int(x) for x in value.split(","))
     return value
 
+
 # A datetime64
 DateTime64 = Annotated[
     np.datetime64,
@@ -70,7 +71,7 @@ def _str_to_int_tuple(value):
 IntTupleStrSerialized = Annotated[
     tuple[int, ...],
     PlainValidator(_str_to_int_tuple),
-    PlainSerializer(lambda x: ",".join((str(y) for y in x))),
+    PlainSerializer(lambda x: ",".join(str(y) for y in x)),
 ]
 
 FrozenDictType = Annotated[

dascore/utils/pd.py

@@ -2,13 +2,11 @@
 
 from __future__ import annotations
 
-
 import fnmatch
 import os
 from collections import defaultdict
-from collections.abc import Collection, Mapping, Sequence
+from collections.abc import Collection, Iterable, Mapping, Sequence
 from functools import cache
-from typing import Iterable
 
 import numpy as np
 import pandas as pd
@@ -559,7 +557,7 @@ def rolling_df(df, window, step=None, axis=0, center=False):
 
 
 def get_attrs_coords_patch_table(
-        patch_or_attrs: Iterable[dc.PatchAttrs | dc.Patch | dc.BaseSpool],
+    patch_or_attrs: Iterable[dc.PatchAttrs | dc.Patch | dc.BaseSpool],
 ) -> tuple(pd.DataFrame, pd.DataFrame, pd.DataFrame):
     """
     Get seperated attributes, coordinates, and patch tables from attrs.
@@ -569,11 +567,12 @@ def get_attrs_coords_patch_table(
     patch_or_attrs
         An iterable with patch content.
     """
+
     def get_coord_dict(attr, num):
         """Get the coordinate information from the attrs."""
         out = []
         for coord in attr.values():
-            coord['id'] = num
+            coord["id"] = num
             out.append(coord)
         return out
 
@@ -588,11 +587,3 @@ def get_coord_dict(attr, num):
         breakpoint()
         coord_info.extend(get_coord_dict(attr.pop("coords", {}), num))
         breakpoint()
-
-
-
-
-
-
-
-

tests/test_core/test_attrs.py

@@ -37,7 +37,10 @@ def attrs_coords_2() -> PatchAttrs:
     """Add non-standard coords to attrs."""
     coords = {"depth": {"min": 10.0, "max": 12.0, "dtype": "<f8", "shape": (12,)}}
     attrs = {
-        "coords": coords, "another_name": "FooBar", "dtype": "<i4", "shape": (12,22)
+        "coords": coords,
+        "another_name": "FooBar",
+        "dtype": "<i4",
+        "shape": (12, 22),
     }
     return PatchAttrs(**attrs)
 
@@ -131,9 +134,7 @@ def test_extra_attrs_not_in_dump_random_attrs(self, random_attrs):
     def test_supports_extra_attrs(self, random_attrs):
         """The attr dict should allow extra attributes."""
         model_dump = random_attrs.model_dump()
-        out = PatchAttrs(
-            bob="doesnt", bill_min=12, bob_max="2012-01-12", **model_dump
-        )
+        out = PatchAttrs(bob="doesnt", bill_min=12, bob_max="2012-01-12", **model_dump)
         assert out.bob == "doesnt"
         assert out.bill_min == 12
 
@@ -173,7 +174,7 @@ def test_coords_to_coord_summary(self):
             "dims": ("time", "distance"),
         }
         attr = dc.PatchAttrs(**out)
-        assert attr.dims == out['dims']
+        assert attr.dims == out["dims"]
         for name, coord in attr.coords.items():
             assert isinstance(coord, CoordSummary)
 

tests/test_utils/test_hdf_utils.py

@@ -163,7 +163,6 @@ def test_metadata_created(self, tmp_path_factory):
         assert meta is not None
 
 
-
 class TestH5MatchesStructure:
     """Tests for the h5 matches structure function."""