More ruff & pre-commit rules (#546)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Wei Ji <[email protected]>

.pre-commit-config.yaml

@@ -6,9 +6,17 @@ repos:
       - id: check-yaml
       - id: check-added-large-files
         args: ["--maxkb=5000"]
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: debug-statements
+      - id: name-tests-test
+        args: ["--pytest-test-first"]
       - id: end-of-file-fixer
+      - id: mixed-line-ending
       - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
+      - id: requirements-txt-fixer
 
   - repo: https://github.com/codespell-project/codespell
     rev: v2.3.0

doc/source/conf.py

@@ -19,7 +19,6 @@
 
 import icepyx
 
-
 # -- Project information -----------------------------------------------------
 
 project = "icepyx"
@@ -120,10 +119,9 @@ def setup(app):
 
 # this should possibly be moved to the sphinxext directory as a standalone .py file
 # -- custom style for pybtex output -------------------------------------------
-from pybtex.style.formatting.unsrt import Style as UnsrtStyle
-
 # from pybtex.style.labels.alpha import LabelStyle as AlphaLabelStyle
 from pybtex.plugin import register_plugin
+from pybtex.style.formatting.unsrt import Style as UnsrtStyle
 
 # I seem to be unable to figure out how to control what is used for the label. It would
 # make sense if it were fed into this function, which then just formatted it, but I can't figure out from where

doc/source/tracking/pypistats/get_pypi_stats.py

@@ -1,6 +1,7 @@
 import os
-import pypistats
+
 import pandas as pd
+import pypistats
 
 cwd = os.getcwd()
 

doc/source/tracking/traffic/traffic_data_mgmt.py

@@ -1,5 +1,6 @@
-import matplotlib.pyplot as plt
 import os
+
+import matplotlib.pyplot as plt
 import pandas as pd
 
 cwd = os.getcwd()

icepyx/__init__.py

@@ -1,6 +1,6 @@
-from icepyx.core.query import Query, GenQuery
+from _icepyx_version import version as __version__
+
+from icepyx.core.query import GenQuery, Query
 from icepyx.core.read import Read
-from icepyx.quest.quest import Quest
 from icepyx.core.variables import Variables
-
-from _icepyx_version import version as __version__
+from icepyx.quest.quest import Quest

icepyx/conftest.py

@@ -1,6 +1,7 @@
-import icepyx
 import pytest
 
+import icepyx
+
 
 @pytest.fixture(autouse=True)
 def add_ipx(doctest_namespace):

icepyx/core/APIformatting.py

@@ -2,7 +2,6 @@
 
 import datetime as dt
 
-
 # ----------------------------------------------------------------------
 # parameter-specific formatting for display
 # or input to a set of API parameters (CMR or NSIDC)

icepyx/core/auth.py

@@ -2,6 +2,7 @@
 import datetime
 
 import earthaccess
+
 from icepyx.core.exceptions import DeprecationError
 
 
@@ -10,8 +11,6 @@ class AuthenticationError(Exception):
     Raised when an error is encountered while authenticating Earthdata credentials
     """
 
-    pass
-
 
 class EarthdataAuthMixin:
     """

icepyx/core/exceptions.py

@@ -3,16 +3,12 @@ class DeprecationError(Exception):
     Class raised for use of functionality that is no longer supported by icepyx.
     """
 
-    pass
-
 
 class QueryError(Exception):
     """
     Base class for Query object exceptions
     """
 
-    pass
-
 
 class NsidcQueryError(QueryError):
     """

icepyx/core/granules.py

@@ -1,15 +1,16 @@
 import datetime
-import requests
-import time
 import io
-import re
 import json
-import numpy as np
 import os
 import pprint
+import re
+import time
 from xml.etree import ElementTree as ET
 import zipfile
 
+import numpy as np
+import requests
+
 import icepyx.core.APIformatting as apifmt
 from icepyx.core.auth import EarthdataAuthMixin
 import icepyx.core.exceptions

icepyx/core/is2ref.py

@@ -1,12 +1,11 @@
-import h5py
 import json
-import numpy as np
-import requests
 import warnings
 from xml.etree import ElementTree as ET
 
 import earthaccess
-
+import h5py
+import numpy as np
+import requests
 
 # ICESat-2 specific reference functions
 

icepyx/core/query.py

@@ -1,6 +1,7 @@
+import pprint
+
 import geopandas as gpd
 import matplotlib.pyplot as plt
-import pprint
 
 import icepyx.core.APIformatting as apifmt
 from icepyx.core.auth import EarthdataAuthMixin
@@ -1131,8 +1132,8 @@ def visualize_spatial_extent(
         gdf = self._spatial.extent_as_gdf
 
         try:
-            from shapely.geometry import Polygon  # noqa: F401
             import geoviews as gv
+            from shapely.geometry import Polygon  # noqa: F401
 
             gv.extension("bokeh")
 

icepyx/core/read.py

@@ -432,15 +432,15 @@ def _add_vars_to_ds(is2ds, ds, grp_path, wanted_groups_tiered, wanted_dict):
             ]
 
             # handle delta_times with 1 or more dimensions
-            idx_range = range(0, len(ds.delta_time.data))
+            idx_range = range(len(ds.delta_time.data))
             try:
                 photon_ids = (
                     idx_range
                     + np.full_like(idx_range, np.max(is2ds.photon_idx), dtype="int64")
                     + 1
                 )
             except AttributeError:
-                photon_ids = range(0, len(ds.delta_time.data))
+                photon_ids = range(len(ds.delta_time.data))
 
             hold_delta_times = ds.delta_time.data
             ds = (

icepyx/core/spatial.py

@@ -1,10 +1,10 @@
-import geopandas as gpd
-import numpy as np
 import os
-from shapely.geometry import box, Polygon
-from shapely.geometry.polygon import orient
 import warnings
 
+import geopandas as gpd
+import numpy as np
+from shapely.geometry import Polygon, box
+from shapely.geometry.polygon import orient
 
 # DevGoal: need to update the spatial_extent docstring to describe coordinate order for input
 

icepyx/core/temporal.py

@@ -1,7 +1,6 @@
 import datetime as dt
 import warnings
 
-
 """
 Helper functions for validation of dates
 """

icepyx/core/validate_inputs.py

@@ -1,5 +1,6 @@
 import datetime as dt
 import warnings
+
 import numpy as np
 
 

icepyx/core/variables.py

@@ -1,9 +1,10 @@
-import numpy as np
 import os
 
+import numpy as np
+
 from icepyx.core.auth import EarthdataAuthMixin
-import icepyx.core.is2ref as is2ref
 from icepyx.core.exceptions import DeprecationError
+import icepyx.core.is2ref as is2ref
 import icepyx.core.validate_inputs as val
 
 # DEVGOAL: use h5py to simplify some of these tasks, if possible!

icepyx/core/visualization.py

@@ -10,15 +10,15 @@
 import dask.dataframe as dd
 import datashader as ds
 import holoviews as hv
+from holoviews.operation.datashader import rasterize
 import numpy as np
 import pandas as pd
 import requests
-from holoviews.operation.datashader import rasterize
 from tqdm import tqdm
 
 import icepyx as ipx
-import icepyx.core.is2ref as is2ref
 import icepyx.core.granules as granules
+import icepyx.core.is2ref as is2ref
 
 hv.extension("bokeh")
 

icepyx/quest/quest.py

@@ -1,5 +1,4 @@
 from icepyx.core.query import GenQuery, Query
-
 from icepyx.quest.dataset_scripts.argo import Argo
 
 

icepyx/tests/conftest.py

@@ -1,7 +1,8 @@
 import os
-import pytest
 from unittest import mock
 
+import pytest
+
 
 # PURPOSE: mock environmental variables
 @pytest.fixture(scope="session", autouse=True)

icepyx/tests/test_APIformatting.py

@@ -2,7 +2,6 @@
 
 import icepyx.core.APIformatting as apifmt
 
-
 # DevNote: is this a situation where you'd ideally build a test class,
 # since you're just repeating the test function with different inputs?
 # Especially for the _fmt_spaital, where there's >2 tests?

icepyx/tests/test_Earthdata.py

@@ -1,13 +1,13 @@
-#!/usr/bin/env python
 """
 test icepyx.core.query.Query.earthdata_login function
 """
 
 import netrc
 import os
-import pytest
 import shutil
 
+import pytest
+
 
 # PURPOSE: test different authentication methods
 @pytest.fixture(scope="module", autouse=True)

icepyx/tests/test_auth.py

@@ -1,8 +1,7 @@
+import earthaccess
 import pytest
 import requests
 
-import earthaccess
-
 from icepyx.core.auth import EarthdataAuthMixin
 
 

icepyx/tests/test_behind_NSIDC_API_login.py

@@ -1,11 +1,11 @@
 import json
 import os
+
 import pytest
 
 import icepyx as ipx
 import icepyx.core.is2ref as is2ref
 
-
 # Misc notes and needed tests
 # test avail data and subsetting success for each input type
 # (kml, shp, list of coords, bbox)

icepyx/tests/test_granules.py

@@ -1,11 +1,12 @@
-import pytest
 import re
+
+import pytest
 import responses
 
 import icepyx as ipx
 from icepyx.core import granules as granules
-from icepyx.core.granules import Granules as Granules
 from icepyx.core.exceptions import NsidcQueryError
+from icepyx.core.granules import Granules as Granules
 
 # @pytest.fixture
 # def reg_a():

icepyx/tests/is2class_query.py → icepyx/tests/test_is2class_query.py

@@ -1,5 +1,11 @@
+import pytest
+
 import icepyx as ipx
 
+# Skip the whole module. See:
+# https://docs.pytest.org/en/stable/reference/reference.html#globalvar-pytestmark
+pytestmark = pytest.mark.skip("Legacy tests -- not sure if they ever passed!")
+
 
 def test_CMRparams():
     reg_a = ipx.Query("ATL06", [-64, 66, -55, 72], ["2019-02-22", "2019-02-28"])

icepyx/tests/test_quest_argo.py

@@ -1,7 +1,7 @@
 import os
+import re
 
 import pytest
-import re
 
 from icepyx.quest.quest import Quest
 

icepyx/tests/test_read.py

@@ -29,12 +29,12 @@ def test_parse_source_no_files():
         (  # check list input
             [
                 "./icepyx/core/is2ref.py",
-                "./icepyx/tests/is2class_query.py",
+                "./icepyx/tests/test_is2class_query.py",
             ],
             sorted(
                 [
                     "./icepyx/core/is2ref.py",
-                    "./icepyx/tests/is2class_query.py",
+                    "./icepyx/tests/test_is2class_query.py",
                 ]
             ),
         ),
@@ -45,11 +45,12 @@ def test_parse_source_no_files():
             ],
         ),
         (  # check filename string with glob pattern input
-            "./icepyx/**/is2*.py",
+            "./icepyx/**/*is2*.py",
             sorted(
                 [
                     "./icepyx/core/is2ref.py",
-                    "./icepyx/tests/is2class_query.py",
+                    "./icepyx/tests/test_is2class_query.py",
+                    "./icepyx/tests/test_is2ref.py",
                 ]
             ),
         ),

icepyx/tests/test_spatial.py

@@ -1,13 +1,13 @@
+from pathlib import Path
+import re
+
 import geopandas as gpd
 import numpy as np
-from pathlib import Path
 import pytest
-import re
 from shapely.geometry import Polygon
 
 import icepyx.core.spatial as spat
 
-
 # ######### "Bounding Box" input tests ################################################################################
 # (Note that these ALSO test the @property functions for the class for bounding boxes)