Merge pull request #191 from mcflugen/mcflugen/add-flake8-simplify

Add linters to deltametrics: flake8-simplify

deltametrics/cube.py

@@ -583,7 +583,7 @@ def show_plan(self, *args, **kwargs):
             stacklevel=2,
         )
         # pass `t` arg to `idx` for legacy
-        if "t" in kwargs.keys():
+        if "t" in kwargs:
             idx = kwargs.pop("t")
             kwargs["idx"] = idx
 
@@ -746,13 +746,10 @@ def __getitem__(self, var):
                 dims=self._view_dimensions,
             )
             _obj = _xrt
-        elif var in self._coords:
+        elif (var in self._coords) or (var in self._variables):
             # ensure coords can be called by cube[var]
             _obj = self._dataio.dataset[var]
 
-        elif var in self._variables:
-            _obj = self._dataio.dataset[var]
-
         else:
             raise AttributeError(
                 f"No variable of {str(self)} named {var}"

deltametrics/io.py

@@ -325,7 +325,7 @@ def write(self):
         raise NotImplementedError
 
     def __getitem__(self, var):
-        if var in self._in_memory_data.keys():
+        if var in self._in_memory_data:
             return self._in_memory_data[var]
         else:
             return self.dataset[var]
@@ -455,7 +455,7 @@ def __getitem__(self, var):
         Returns the variables exactly as they are: either a numpy ndarray or
         xarray.
         """
-        if var in self.dataset.keys():
+        if var in self.dataset:
             return self.dataset[var]
         elif var in self.known_coords:
             return self.dimensions[var]

deltametrics/mask.py

@@ -284,13 +284,12 @@ def _check_deprecated_is_mask(self, is_mask):
             )
 
     def _check_deprecated_3d_input(self, args_0_shape):
-        if self._input_flag == "array":
-            if len(args_0_shape) > 2:
-                raise ValueError(
-                    "Creating a `Mask` with a time dimension is deprecated. "
-                    "Please manage multiple masks manually (e.g., "
-                    "append the masks into a `list`)."
-                )
+        if (self._input_flag == "array") and (len(args_0_shape) > 2):
+            raise ValueError(
+                "Creating a `Mask` with a time dimension is deprecated. "
+                "Please manage multiple masks manually (e.g., "
+                "append the masks into a `list`)."
+            )
 
 
 class ThresholdValueMask(BaseMask, abc.ABC):
@@ -707,18 +706,13 @@ def __init__(self, *args, is_mask=None, **kwargs):
             # do nothing, will need to call ._compute_mask later
             return
 
-        elif self._input_flag == "cube":
+        elif self._input_flag in ("cube", "mask"):
             raise NotImplementedError
             # _tval = kwargs.pop('t', -1)
             # _eta = args[0]['eta'][_tval, :, :]
             # _flow = args[0]['velocity'][_tval, :, :]
             # need to convert these fields to proper masks
 
-        elif self._input_flag == "mask":
-            # this pathway should allow someone to specify a combination of
-            # elevation mask, landmask, and velocity mask to make the new mask.
-            raise NotImplementedError
-
         elif self._input_flag == "array":
             # first make a landmask
             _eta = args[0]
@@ -927,13 +921,7 @@ def __init__(self, *args, **kwargs):
         if self._input_flag is None:
             # do nothing, will need to call ._compute_mask later
             return
-        elif self._input_flag == "cube":
-            raise NotImplementedError
-            # _tval = kwargs.pop('t', -1)
-            # _eta = args[0]['eta'][_tval, :, :]
-        elif self._input_flag == "mask":
-            # this pathway should allow someone to specify a combination of
-            #    landmask, and ocean/elevation mask
+        elif self._input_flag in ("cube", "mask"):
             raise NotImplementedError
         elif self._input_flag == "array":
             _eta = args[0]
@@ -1171,12 +1159,7 @@ def __init__(self, *args, contour_threshold=75, method="OAM", **kwargs):
             # do nothing, will need to call ._compute_mask later
             return
 
-        elif self._input_flag == "cube":
-            raise NotImplementedError
-            # _tval = kwargs.pop('t', -1)
-            # _eta = args[0]['eta'][_tval, :, :]
-
-        elif self._input_flag == "mask":
+        elif self._input_flag in ("cube", "mask"):
             raise NotImplementedError
 
         elif self._input_flag == "array":
@@ -1440,17 +1423,16 @@ def _compute_mask(self, *args, **kwargs):
         from deltametrics.plan import OpeningAnglePlanform
 
         # handle types / input arguments
-        if len(args) <= 2:
-            if len(args) == 1:
-                if isinstance(args[0], OpeningAnglePlanform):
-                    _below_mask = args[0]._below_mask
-                    _opening_angles = args[0]._opening_angles
-                    _method = "OAM"
-                elif isinstance(args[0], MorphologicalPlanform):
-                    _elev_mask = args[0]._elevation_mask
-                    _mean_image = args[0]._mean_image
-                    _method = "MPM"
-        if len(args) >= 3:
+        if len(args) == 1:
+            if isinstance(args[0], OpeningAnglePlanform):
+                _below_mask = args[0]._below_mask
+                _opening_angles = args[0]._opening_angles
+                _method = "OAM"
+            elif isinstance(args[0], MorphologicalPlanform):
+                _elev_mask = args[0]._elevation_mask
+                _mean_image = args[0]._mean_image
+                _method = "MPM"
+        elif len(args) >= 3:
             _method = args[2]
             if _method == "OAM":
                 _below_mask = args[0]
@@ -2020,18 +2002,7 @@ def __init__(self, *args, method="skeletonize", **kwargs):
             # do nothing, will need to call ._compute_mask later
             return
 
-        elif self._input_flag == "cube":
-            raise NotImplementedError
-            # _tval = kwargs.pop('t', -1)
-            # _eta = args[0]['eta'][_tval, :, :]
-            # _flow = args[0]['velocity'][_tval, :, :]
-            # need to convert these fields to proper masks
-
-        elif self._input_flag == "mask":
-            # this pathway should allow someone to specify a combination of
-            # elevation mask, landmask, and velocity mask or channelmask
-            # directly, to make the new mask. This is basically an ambiguous
-            # definition of the static methods.
+        elif self._input_flag in ("cube", "mask"):
             raise NotImplementedError
 
         elif self._input_flag == "array":
@@ -2279,13 +2250,12 @@ def __init__(self, *args, origin=None, **kwargs):
             operation: :obj:`angular`, :obj:`circular`, :obj:`strike`,
             and :obj:`dip`.
         """
-        if len(args) > 0:
-            # most argument are fine, but we need to convert an input tuple
-            # (specific only to GeometricMask type) into an array to be the
-            # basis.
-            if isinstance(args[0], tuple):
-                # args[0] = np.zeros(args[0])
-                args = (np.zeros(args[0]),)
+        # most argument are fine, but we need to convert an input tuple
+        # (specific only to GeometricMask type) into an array to be the
+        # basis.
+        if (len(args) > 0) and isinstance(args[0], tuple):
+            # args[0] = np.zeros(args[0])
+            args = (np.zeros(args[0]),)
 
         super().__init__("geometric", *args, **kwargs)
 
@@ -2687,16 +2657,7 @@ def __init__(self, *args, background_value=0, elevation_tolerance=0.1, **kwargs)
             # do nothing, will need to call ._compute_mask later
             return
 
-        elif self._input_flag == "cube":
-            raise NotImplementedError
-            # _tval = kwargs.pop('t', -1)
-            # _eta = args[0]['eta'][_tval, :, :]
-            # _flow = args[0]['velocity'][_tval, :, :]
-            # need to convert these fields to proper masks
-
-        elif self._input_flag == "mask":
-            # this pathway should allow someone to specify a combination of
-            # elevation mask, landmask, and velocity mask to make the new mask.
+        elif self._input_flag in ("cube", "mask"):
             raise NotImplementedError
 
         elif self._input_flag == "array":

deltametrics/mobility.py

@@ -185,9 +185,11 @@ def check_inputs(chmap, basevalues=None, basevalues_idx=None, window=None,
         raise ValueError('No window or window_idx supplied!')
 
     # check map shapes align
-    if out_maps['landmap'] is not None:
-        if np.shape(out_maps['chmap']) != np.shape(out_maps['landmap']):
-            raise ValueError('Shapes of chmap and landmap do not match.')
+    if (
+        (out_maps['landmap'] is not None)
+        and (np.shape(out_maps['chmap']) != np.shape(out_maps['landmap']))
+    ):
+        raise ValueError('Shapes of chmap and landmap do not match.')
 
     # check that the combined basemap + timewindow does not exceed max t-index
     Kmax = np.max(base_out) + win_out

deltametrics/plan.py

@@ -2047,9 +2047,7 @@ def morphological_closing_method(elevationmask, biggestdisk=None):
         )
 
     # check biggestdisk
-    if biggestdisk is None:
-        biggestdisk = 1
-    elif biggestdisk <= 0:
+    if (biggestdisk is None) or (biggestdisk <= 0):
         biggestdisk = 1
 
     # loop through and do binary closing for each disk size up to biggestdisk

deltametrics/plot.py

@@ -881,9 +881,10 @@ def get_display_arrays(VarInst, data=None):
     elif VarInst.slicetype == "stratigraphy_section":
         # #  StratigraphySection  # #
         data = data or "stratigraphy"
-        if data in VarInst.strat._spacetime_names:
-            VarInst.strat._check_knows_spacetime()  # always False
-        elif data in VarInst.strat._preserved_names:
+        if (
+            (data in VarInst.strat._spacetime_names)
+            or (data in VarInst.strat._preserved_names)
+        ):
             VarInst.strat._check_knows_spacetime()  # always False
         elif data in VarInst.strat._stratigraphy_names:
             _z = VarInst[VarInst.dims[0]]
@@ -968,9 +969,10 @@ def _reshape_long(X):
     elif VarInst.slicetype == "stratigraphy_section":
         # #  StratigraphySection  # #
         data = data or "stratigraphy"
-        if data in VarInst.strat._spacetime_names:
-            VarInst.strat._check_knows_spacetime()  # always False
-        elif data in VarInst.strat._preserved_names:
+        if (
+            (data in VarInst.strat._spacetime_names)
+            or (data in VarInst.strat._preserved_names)
+        ):
             VarInst.strat._check_knows_spacetime()  # always False
         elif data in VarInst.strat._stratigraphy_names:
             raise NotImplementedError  # not sure best implementation
@@ -1034,9 +1036,10 @@ def get_display_limits(VarInst, data=None, factor=1.5):
         # #  StratigraphySection  # #
         data = data or "stratigraphy"
         _S, _Z = np.meshgrid(VarInst["s"], VarInst[VarInst.dims[0]])
-        if data in VarInst.strat._spacetime_names:
-            VarInst.strat._check_knows_spacetime()  # always False
-        elif data in VarInst.strat._preserved_names:
+        if (
+            (data in VarInst.strat._spacetime_names)
+            or (data in VarInst.strat._preserved_names)
+        ):
             VarInst.strat._check_knows_spacetime()  # always False
         elif data in VarInst.strat._stratigraphy_names:
             return np.min(_S), np.max(_S), np.min(_Z), np.max(_Z) * factor
@@ -1593,7 +1596,7 @@ def overlay_sparse_array(
         fig, ax = plt.subplots()
 
     # check this is a tuple or list
-    if isinstance(alpha_clip, tuple) or isinstance(alpha_clip, list):
+    if isinstance(alpha_clip, (tuple, list)):
         if len(alpha_clip) != 2:
             raise ValueError("`alpha_clip` must be tuple or list of length 2.")
     else:  # if it is a tuple, check the length
@@ -1614,8 +1617,6 @@ def overlay_sparse_array(
     if isinstance(cmap, str):
         # cmap = plt.cm.get_cmap(cmap)
         cmap = mpl.colormaps[cmap]
-    else:
-        cmap = cmap
 
     # get the extent to plot
     if "extent" in kwargs:

deltametrics/strat.py

@@ -114,11 +114,11 @@ def _determine_deposit_from_background(sediment_volume, background):
         >>> _ = ax[1, 1].imshow(background2[59], cmap='Greys_r')  # just below initial basin depth
         >>> plt.tight_layout()
     """
-    if (background is None):
+    if background is None:
         deposit = np.ones(sediment_volume.shape, dtype=bool)
-    elif (isinstance(background, float) or isinstance(background, int)):
+    elif isinstance(background, (float, int)):
         deposit = (sediment_volume != background)
-    elif (isinstance(background, np.ndarray)):
+    elif isinstance(background, np.ndarray):
         deposit = ~background.astype(bool)  # ensure boolean
     else:
         raise TypeError('Invalid type for `background`.')

deltametrics/utils.py

@@ -129,9 +129,7 @@ def _attribute_checker(self, checklist):
 def is_ndarray_or_xarray(data):
     """Check that data is numpy array or xarray data.
     """
-    truth = (isinstance(data, xr.core.dataarray.DataArray) or
-             isinstance(data, np.ndarray))
-    return truth
+    return isinstance(data, (xr.core.dataarray.DataArray, np.ndarray))
 
 
 def curve_fit(data, fit='harmonic'):
@@ -518,13 +516,15 @@ def _point_in_polygon(x, y, polygon):
     p1x, p1y = polygon[0]
     for i in range(n+1):
         p2x, p2y = polygon[i % n]
-        if y > min(p1y, p2y):
-            if y <= max(p1y, p2y):
-                if x <= max(p1x, p2x):
-                    if p1y != p2y:
-                        xints = (y-p1y)*(p2x-p1x)/(p2y-p1y)+p1x
-                    if p1x == p2x or x <= xints:
-                        inside = not inside
+        if (
+            (y > min(p1y, p2y))
+            and (y <= max(p1y, p2y))
+            and (x <= max(p1x, p2x))
+        ):
+            if p1y != p2y:
+                xints = (y-p1y)*(p2x-p1x)/(p2y-p1y)+p1x
+            if p1x == p2x or x <= xints:
+                inside = not inside
         p1x, p1y = p2x, p2y
 
     return inside

setup.cfg

@@ -1,11 +1,10 @@
 [flake8]
 exclude = docs/source/pyplots/guides, build, .nox
-ignore =
+extend-ignore =
     C901, E203, E501, W503,
     # These mostly deal with whitespace and will be found and fixed with black
     E121, E125, E126, E127, E226, E241, E261, E275, E302, E305,
     B024, B950,
     W504
 max-line-length = 88
 max-complexity = 18
-select = B,C,E,F,W,T4,B9

tests/cube_test.py

@@ -102,8 +102,8 @@ def test_register_section(self):
         golf.stratigraphy_from("eta", dz=0.1)
         golf.register_section("testsection", StrikeSection(distance_idx=10))
         assert golf.sections is golf.section_set
-        assert len(golf.sections.keys()) == 1
-        assert "testsection" in golf.sections.keys()
+        assert len(golf.sections) == 1
+        assert "testsection" in golf.sections
         with pytest.raises(TypeError, match=r"`SectionInstance` .*"):
             golf.register_section("fail1", "astring")
         with pytest.raises(TypeError, match=r"`SectionInstance` .*"):
@@ -115,7 +115,7 @@ def test_sections_slice_op(self):
         golf = DataCube(golf_path)
         golf.stratigraphy_from("eta", dz=0.1)
         golf.register_section("testsection", StrikeSection(distance_idx=10))
-        assert "testsection" in golf.sections.keys()
+        assert "testsection" in golf.sections
         slc = golf.sections["testsection"]
         assert issubclass(type(slc), BaseSection)
 
@@ -124,8 +124,8 @@ def test_register_planform(self):
         golf.stratigraphy_from("eta", dz=0.1)
         golf.register_planform("testplanform", Planform(idx=10))
         assert golf.planforms is golf.planform_set
-        assert len(golf.planforms.keys()) == 1
-        assert "testplanform" in golf.planforms.keys()
+        assert len(golf.planforms) == 1
+        assert "testplanform" in golf.planforms
         with pytest.raises(TypeError, match=r"`PlanformInstance` .*"):
             golf.register_planform("fail1", "astring")
         with pytest.raises(TypeError, match=r"`PlanformInstance` .*"):
@@ -142,14 +142,14 @@ def test_register_plan_legacy_method(self):
         golf = DataCube(golf_path)
         golf.register_plan("testplanform", Planform(idx=10))
         assert golf.planforms is golf.planform_set
-        assert len(golf.planforms.keys()) == 1
-        assert "testplanform" in golf.planforms.keys()
+        assert len(golf.planforms) == 1
+        assert "testplanform" in golf.planforms
 
     def test_planforms_slice_op(self):
         golf = DataCube(golf_path)
         golf.stratigraphy_from("eta", dz=0.1)
         golf.register_planform("testplanform", Planform(idx=10))
-        assert "testplanform" in golf.planforms.keys()
+        assert "testplanform" in golf.planforms
         slc = golf.planforms["testplanform"]
         assert issubclass(type(slc), BasePlanform)