Pre commit fix

.github/workflows/run-pre-commit.yml

@@ -20,11 +20,12 @@ jobs:
       uses: actions/setup-python@v5
       with:
           python-version: '3.x'
-    - name: Install dependencies
+    - name: Install dev dependencies
       run: |
         python -m pip install --upgrade pip
         pip install .[dev]
     - name: pre-commit checks
       run: |
         pre-commit run black --all-files
-        pre-commit run isort --all-files
+        # TODO enable once all cyclic imports have been fixed
+        # pre-commit run isort --all-files

.pre-commit-config.yaml

@@ -9,3 +9,7 @@ repos:
     rev: 22.10.0
     hooks:
     -   id: black
+-   repo: https://github.com/pycqa/isort
+    rev: 6.0.1
+    hooks:
+    -   id: isort

packages/data/src/pyearthtools/data/derived/insolation.py

@@ -163,7 +163,6 @@ def derive(self, time: pd.Timestamp) -> xr.Dataset:
             coords={"time": time, "latitude": self._latitude[:, 0], "longitude": self._longitude[0, :]},
         )
 
-
         insolation.time.encoding.update(
             {"dtype": "int32", "units": "hours since 1900-01-01 00:00:00.0", "calendar": "gregorian"}
         )

packages/data/src/pyearthtools/data/save/save_utils.py

@@ -253,6 +253,7 @@ def __exit__(self, *args):
 
 SLEEP_INTERVAL = 0.1
 
+
 class ManageFiles:
     """
     Automatically manage the saving of files.

packages/data/src/pyearthtools/data/transforms/coordinates.py

@@ -151,9 +151,7 @@ class ReIndex(Transform):
     """Reindex Coordinates"""
 
     def __init__(
-        self, 
-        coordinates: dict[str, Literal["reversed", "sorted"] | Iterable] | xr.Coordinates | None = None, 
-        **coords
+        self, coordinates: dict[str, Literal["reversed", "sorted"] | Iterable] | xr.Coordinates | None = None, **coords
     ):
         """
         Reindex coordinates
@@ -323,7 +321,6 @@ def apply(self, dataset: xr.Dataset) -> xr.Dataset:
         return dataset
 
 
-
 class Drop(Transform):
     """Drop items from Dataset"""
 
@@ -370,10 +367,10 @@ def apply(self, dataset: xr.Dataset) -> xr.Dataset:
 
 
 def weak_cast_to_int(value):
-    '''
+    """
     Basically, turns integer floats to int types, otherwise
     does nothing.
-    '''
+    """
     try:
         if int(value) == value:
             value = int(value)
@@ -602,7 +599,6 @@ def apply(self, dataset: xr.Dataset) -> xr.Dataset:
     #     return dict(as_dataarray=self._as_dataarray, **self._coordinates)
 
 
-
 class Pad(Transform):
     """
     Pad data

packages/data/tests/data/archive/test_extensions.py

@@ -5,26 +5,21 @@
 
 
 def test_register_archive():
-
-
     @extensions.register_archive("NewData")
     class NewData:
-         def __init__(self, args):
-             self.args = args             
-
+        def __init__(self, args):
+            self.args = args
 
     # If registering over the top of an existing name, confirm warning occurs
     with pytest.warns(pyearthtools.data.AccessorRegistrationWarning):
+
         @extensions.register_archive("NewData")
         class NewData:
 
-            _pyearthtools_initialisation = {"class":  {}}
+            _pyearthtools_initialisation = {"class": {}}
 
             def __init__(self, args):
                 self.args = args
 
             def __call__(self, *args, **kwargs):
                 pass
-
-
-

packages/data/tests/data/derived/test_insolation.py

@@ -1,20 +1,21 @@
 from pyearthtools.data.derived import insolation
 from pyearthtools.data.time import Petdt
 
+
 def test_array():
 
-    a = insolation.array([1,2,3,4,5])
-    assert all(a == [1,2,3,4,5])
+    a = insolation.array([1, 2, 3, 4, 5])
+    assert all(a == [1, 2, 3, 4, 5])
 
 
 def test_Insolation():
 
     insol = insolation.Insolation(
         [-10],
         [40],
-        )
+    )
 
-    at_time = ['2021-01-01']
+    at_time = ["2021-01-01"]
 
     # import pudb; pudb.set_trace()
 
@@ -23,4 +24,3 @@ def test_Insolation():
 
     # TODO: Check the insolation calculation
     # TODO: Check the result is the right type/contents
-

packages/data/tests/data/indexes/test_indexes.py

@@ -1,69 +1,66 @@
-
 from pyearthtools.data import indexes
 import pyearthtools.data.archive
 from pyearthtools.data.time import Petdt
 import pytest
 import pathlib
 
+
 def test_Index(monkeypatch):
 
-	monkeypatch.setattr("pyearthtools.data.indexes.Index.__abstractmethods__", set())
+    monkeypatch.setattr("pyearthtools.data.indexes.Index.__abstractmethods__", set())
 
-	idx = indexes.Index()
+    idx = indexes.Index()
 
-	with pytest.raises(NotImplementedError):
-		idx.get()
+    with pytest.raises(NotImplementedError):
+        idx.get()
+
+    with pytest.raises(NotImplementedError):
+        idx()
 
-	with pytest.raises(NotImplementedError):
-		idx()
 
 def test_FileSystemIndex(monkeypatch):
 
-	monkeypatch.setattr("pyearthtools.data.indexes.Index.__abstractmethods__", set())
-	fsi = indexes.FileSystemIndex()
-	with pytest.raises(NotImplementedError):
-		fsi.filesystem("anything")
+    monkeypatch.setattr("pyearthtools.data.indexes.Index.__abstractmethods__", set())
+    fsi = indexes.FileSystemIndex()
+    with pytest.raises(NotImplementedError):
+        fsi.filesystem("anything")
 
-	# Confirm the test begins without a root directory set
-	monkeypatch.delattr(pyearthtools.data.archive, "ROOT_DIRECTORIES", raising=False)
-	fsi = indexes.FileSystemIndex()
-	with pytest.raises(KeyError):
-		fsi.ROOT_DIRECTORIES
+    # Confirm the test begins without a root directory set
+    monkeypatch.delattr(pyearthtools.data.archive, "ROOT_DIRECTORIES", raising=False)
+    fsi = indexes.FileSystemIndex()
+    with pytest.raises(KeyError):
+        fsi.ROOT_DIRECTORIES
 
-	# Confirm the FSI responds to the root directory variable correctly
-	monkeypatch.setattr(pyearthtools.data.archive, "ROOT_DIRECTORIES", "Hello", raising=False)
-	fsi = indexes.FileSystemIndex()
-	assert fsi.ROOT_DIRECTORIES == "Hello"
+    # Confirm the FSI responds to the root directory variable correctly
+    monkeypatch.setattr(pyearthtools.data.archive, "ROOT_DIRECTORIES", "Hello", raising=False)
+    fsi = indexes.FileSystemIndex()
+    assert fsi.ROOT_DIRECTORIES == "Hello"
 
+    monkeypatch.setattr(fsi, "filesystem", lambda x: __file__, raising=False)
+    assert fsi.search("needle") == __file__
 
-	monkeypatch.setattr(fsi, 'filesystem', lambda x: __file__, raising=False)
-	assert fsi.search("needle") == __file__
+    # Check the current Python file exists
+    assert fsi.exists(__file__)
+    assert fsi.exists(pathlib.Path(__file__))
+    assert fsi.exists({"a": __file__})
+    assert fsi.exists((__file__, __file__))
 
-	# Check the current Python file exists
-	assert fsi.exists(__file__)
-	assert fsi.exists(pathlib.Path(__file__))
-	assert fsi.exists({"a": __file__})
-	assert fsi.exists((__file__, __file__))
+    with pytest.raises(KeyError):
+        assert fsi.load(__file__) is not None
+        # TODO test actual netcdf file loading
 
-	with pytest.raises(KeyError):
-		assert fsi.load(__file__) is not None
-		# TODO test actual netcdf file loading
+    with pytest.raises(KeyError):
+        assert fsi.get(__file__) is not None
+        # TODO test actual netcdf file getting
 
-	with pytest.raises(KeyError):
-		assert fsi.get(__file__) is not None
-		# TODO test actual netcdf file getting
 
 def test_AdvancedTimeIndex(monkeypatch):
 
-	monkeypatch.setattr("pyearthtools.data.indexes.AdvancedTimeIndex.__abstractmethods__", set())
-
-	data_interval = "day"
-	ati = indexes.AdvancedTimeIndex(data_interval)
-	dt = Petdt('2023-02')
-
-	monkeypatch.setattr(pyearthtools.data.indexes.Index, 'get', lambda x, y: x, raising=False)
-	ati.retrieve(dt, use_simple = True)
-
-
+    monkeypatch.setattr("pyearthtools.data.indexes.AdvancedTimeIndex.__abstractmethods__", set())
 
+    data_interval = "day"
+    ati = indexes.AdvancedTimeIndex(data_interval)
+    dt = Petdt("2023-02")
 
+    monkeypatch.setattr(pyearthtools.data.indexes.Index, "get", lambda x, y: x, raising=False)
+    ati.retrieve(dt, use_simple=True)