Merge pull request #296 from boutproject/ruff-fixes

Fix linting errors

.github/workflows/master.yml

@@ -68,22 +68,3 @@ jobs:
     - name: Test with pytest
       run: |
         pytest -vv --long --cov
-
-
-  # Need to tidy up the things that flake8 finds before we activate this
-  #flake8:
-
-  #  runs-on: ubuntu-latest
-  #  if: always()
-
-  #  steps:
-  #  - uses: actions/checkout@v2
-  #  - name: Set up Python
-  #    uses: actions/setup-python@v1
-  #  - name: Install dependencies
-  #    run: |
-  #      python -m pip install --upgrade pip
-  #  - name: Lint with flake8
-  #    run: |
-  #      pip install flake8
-  #      flake8

.github/workflows/pythonpackage.yml

@@ -68,21 +68,3 @@ jobs:
     - name: Test with pytest
       run: |
         pytest -vv --long --cov
-
-  # Need to tidy up the things that flake8 finds before we activate this
-  #flake8:
-
-  #  runs-on: ubuntu-latest
-  #  if: always()
-
-  #  steps:
-  #  - uses: actions/checkout@v2
-  #  - name: Set up Python
-  #    uses: actions/setup-python@v1
-  #  - name: Install dependencies
-  #    run: |
-  #      python -m pip install --upgrade pip
-  #  - name: Lint with flake8
-  #    run: |
-  #      pip install flake8
-  #      flake8

.github/workflows/ruff.yaml

@@ -0,0 +1,15 @@
+name: Linting
+on: [pull_request]
+
+jobs:
+  dependency-review:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.x'
+      - name: Install ruff
+        run: pip install ruff
+      - name: Run ruff
+        run: ruff xbout

examples/boutmodules/tests/test_stormdataset.py

@@ -2,7 +2,6 @@
 
 from xarray import concat
 from xbout import open_boutdataset
-from xbout.tests.test_load import bout_xyt_example_files
 
 
 @pytest.mark.skip

pyproject.toml

@@ -78,3 +78,6 @@ write_to = "xbout/_version.py"
 
 [tool.setuptools]
 packages = ["xbout"]
+
+[tool.ruff]
+ignore = ["E501"]

xbout/__init__.py

@@ -11,13 +11,25 @@
 
 from .fastoutput import open_fastoutput
 
-try:
-    from importlib.metadata import version, PackageNotFoundError
-except ModuleNotFoundError:
-    from importlib_metadata import version, PackageNotFoundError
+from importlib.metadata import version, PackageNotFoundError
+
 try:
     __version__ = version(__name__)
 except PackageNotFoundError:
     from setuptools_scm import get_version
 
     __version__ = get_version(root="..", relative_to=__file__)
+
+__all__ = [
+    "open_boutdataset",
+    "collect",
+    "geometries",
+    "register_geometry",
+    "REGISTERED_GEOMETRIES",
+    "BoutDataArrayAccessor",
+    "BoutDatasetAccessor",
+    "animate_pcolormesh",
+    "animate_poloidal",
+    "plot_separatrix",
+    "open_fastoutput",
+]

xbout/boutdataarray.py

@@ -306,7 +306,6 @@ def interpolate_parallel(
         # Select a particular 'region' and interpolate to higher parallel resolution
         da = self.data
         region = da.bout._regions[region]
-        tcoord = da.metadata["bout_tdim"]
         xcoord = da.metadata["bout_xdim"]
         ycoord = da.metadata["bout_ydim"]
         zcoord = da.metadata["bout_zdim"]
@@ -385,9 +384,6 @@ def interpolate_parallel(
 
         return da
 
-    def add_cartesian_coordinates(self):
-        return _add_cartesian_coordinates(self.data)
-
     def add_cartesian_coordinates(self):
         """
         Add Cartesian (X,Y,Z) coordinates.
@@ -950,7 +946,6 @@ def interpolate_from_unstructured(
             method = "linear"
 
         # extend input coordinates to cover all dims, so we can flatten them
-        input_coords = []
         for coord in kwargs:
             data = da[coord]
             missing_dims = tuple(set(dims) - set(data.dims))

xbout/boutdataset.py

@@ -266,9 +266,6 @@ def find_with_dims(first_var, dims):
 
         return ds
 
-    def add_cartesian_coordinates(self):
-        return _add_cartesian_coordinates(self.data)
-
     def integrate_midpoints(self, variable, *, dims=None, cumulative_t=False):
         """
         Integrate using the midpoint rule for spatial dimensions, and trapezium rule for
@@ -619,7 +616,6 @@ def interpolate_to_cartesian(
 
         from scipy.interpolate import (
             RegularGridInterpolator,
-            griddata,
         )
 
         # Create Cylindrical coordinates for intermediate grid
@@ -681,9 +677,6 @@ def interp_single_time(da):
             # just use da.min().item() here (to get a scalar value instead of a
             # zero-size array) because .item() doesn't work for dask arrays (yet!).
 
-            datamin = float_type(da.min().values)
-            datamax = float_type(da.max().values)
-
             if tdim in da.dims:
                 data_cartesian = np.zeros((nt, nX, nY, nZ), dtype=float_type)
                 for tind in range(nt):

xbout/calc/__init__.py

@@ -1 +1,3 @@
 from .turbulence import rms
+
+__all__ = ["rms"]

xbout/geometries.py

@@ -4,7 +4,7 @@
 import xarray as xr
 import numpy as np
 
-from .region import Region, _create_regions_toroidal, _create_single_region
+from .region import _create_regions_toroidal, _create_single_region
 from .utils import (
     _add_attrs_to_var,
     _set_attrs_on_all_vars,
@@ -156,7 +156,6 @@ def apply_geometry(ds, geometry_name, *, coordinates=None, grid=None):
         _add_attrs_to_var(updated_ds, xcoord)
 
     if ycoord not in updated_ds.coords:
-        ny = updated_ds.dims[ycoord]
         # dy should always be constant in x, so it is safe to convert to a 1d
         # coordinate.  [The y-coordinate has to be a 1d coordinate that labels x-z
         # slices of the grid (similarly x-coordinate is 1d coordinate that labels y-z
@@ -206,7 +205,7 @@ def apply_geometry(ds, geometry_name, *, coordinates=None, grid=None):
             if bout_v5:
                 if not np.all(updated_ds["dz"].min() == updated_ds["dz"].max()):
                     raise ValueError(
-                        f"Spacing is not constant. Cannot create z coordinate"
+                        "Spacing is not constant. Cannot create z coordinate"
                     )
 
                 dz = updated_ds["dz"].min()

xbout/plotting/plotfuncs.py

@@ -13,7 +13,6 @@
     _decompose_regions,
     _is_core_only,
     _k3d_plot_isel,
-    _make_structured_triangulation,
     plot_separatrices,
     plot_targets,
 )
@@ -48,7 +47,7 @@ def plot_regions(da, ax=None, **kwargs):
     da_regions = _decompose_regions(da)
 
     colored_regions = [
-        xr.full_like(da_region, fill_value=num / len(regions))
+        xr.full_like(da_region, fill_value=num / len(da_regions))
         for num, da_region in enumerate(da_regions.values())
     ]
 
@@ -311,11 +310,11 @@ def plot2d_wrapper(
 
         for x, y in zip(x_regions, y_regions):
             if (
-                not da.metadata["bout_xdim"] in x.dims
-                and not da.metadata["bout_ydim"] in x.dims
+                da.metadata["bout_xdim"] not in x.dims
+                and da.metadata["bout_ydim"] not in x.dims
             ) or (
-                not da.metadata["bout_xdim"] in y.dims
-                and not da.metadata["bout_ydim"] in y.dims
+                da.metadata["bout_xdim"] not in y.dims
+                and da.metadata["bout_ydim"] not in y.dims
             ):
                 # Small regions around X-point do not have segments in x- or y-directions,
                 # so skip
@@ -545,7 +544,6 @@ def plot3d(
                 from scipy.interpolate import (
                     RegularGridInterpolator,
                     griddata,
-                    LinearNDInterpolator,
                 )
 
                 print("start interpolating")
@@ -801,7 +799,7 @@ def create_or_update_plot(plot_objects=None, tind=None, this_save_as=None):
                         # First create png files in the temporary directory
                         temp_path = Path(d)
                         temp_save_as = str(temp_path.joinpath("temp.png"))
-                        print(f"tind=0")
+                        print("tind=0")
                         plot_objects = create_or_update_plot(
                             tind=0, this_save_as=temp_save_as
                         )

xbout/plotting/utils.py

@@ -129,7 +129,6 @@ def plot_targets(da, ax, *, x="R", y="Z", hatching=True):
 
     da0 = list(da_regions.values())[0]
 
-    xcoord = da0.metadata["bout_xdim"]
     ycoord = da0.metadata["bout_ydim"]
 
     if da0.metadata["keep_yboundaries"]:

xbout/region.py

@@ -1,4 +1,4 @@
-from copy import copy, deepcopy
+from copy import deepcopy
 import numpy as np
 import xarray as xr
 from .utils import _set_attrs_on_all_vars
@@ -145,9 +145,6 @@ def __repr__(self):
             result += f"\t{attr}\t{val}\n"
         return result
 
-    def __eq__(self, other):
-        return vars(self) == vars(other)
-
     def get_slices(self, mxg=0, myg=0):
         """
         Return x- and y-dimension slices that select this region from the global
@@ -1229,11 +1226,6 @@ def _create_single_region(ds, periodic_y=True):
     nx = ds.metadata["nx"]
     ny = ds.metadata["ny"]
 
-    mxg = ds.metadata["MXG"]
-    myg = ds.metadata["MYG"]
-    # keep_yboundaries is 1 if there are y-boundaries and 0 if there are not
-    ybndry = ds.metadata["keep_yboundaries"] * myg
-
     connection = "all" if periodic_y else None
 
     regions = {