[WIP] Add additional linting to package by yosoyjay · Pull Request #10 · noaa-ocs-modeling/OCSMesh

yosoyjay · 2021-11-19T01:09:09Z

This pull request is to improve the linting for the package in response to issue #105 in ODSSM.

The current PR includes changes resulting the application of isort and black and small change in setup.py to improve the robustness of the version check for the C++ complier (-dumpversion vs. --version) . flake8 compliance is a work in progress. flake8 is currently configured in setup.cfg to ignore E501 (line length), E226 (lack of white space around binary operators), and E503 (line break before binary operator, but other errors remain that I'd like feedback on:

ocsmesh/cmd.py:404:9: F841 local variable 'config_outputs' is assigned to but never used
ocsmesh/cmd.py:442:9: F841 local variable 'opts' is assigned to but never used
ocsmesh/utils.py:1089:5: F841 local variable 'y' is assigned to but never used
ocsmesh/utils.py:1097:5: F841 local variable 'faces_around_vert' is assigned to but never used
ocsmesh/utils.py:1106:5: F841 local variable 'coord' is assigned to but never used
ocsmesh/utils.py:1112:5: F841 local variable 'shared_edges' is assigned to but never used
ocsmesh/raster.py:828:5: F841 local variable 'win_h' is assigned to but never used
ocsmesh/raster.py:829:5: F841 local variable 'win_w' is assigned to but never used
ocsmesh/mesh/mesh.py:795:9: F841 local variable 'coo_to_idx' is assigned to but never used
ocsmesh/features/constraint.py:77:9: F841 local variable 'bound_values' is assigned to but never used
ocsmesh/cli/mesh_upgrader.py:82:9: E266 too many leading '#' for block comment
ocsmesh/cli/mesh_upgrader.py:89:9: E266 too many leading '#' for block comment
ocsmesh/cli/remesh.py:308:9: F841 local variable 'roi_s' is assigned to but never used
ocsmesh/cli/remesh.py:316:9: F841 local variable 'vert_idx_to_refin' is assigned to but never used
ocsmesh/cli/remesh_by_shape_factor.py:236:13: F841 local variable 'vert_in' is assigned to but never used
ocsmesh/geom/collector.py:243:17: F841 local variable 'level0' is assigned to but never used
ocsmesh/geom/collector.py:244:17: F841 local variable 'level1' is assigned to but never used
ocsmesh/ops/__init__.py:4:1: E731 do not assign a lambda expression, use a def
ocsmesh/ops/__init__.py:6:1: E731 do not assign a lambda expression, use a def
ocsmesh/ops/combine_geom.py:438:13: E722 do not use bare 'except'
ocsmesh/hfun/collector.py:125:9: F841 local variable 'srcs' is assigned to but never used
ocsmesh/hfun/mesh.py:143:9: F841 local variable 'coords' is assigned to but never used

Once the flake8 issue is resolved, I'd be in favor of integrating tests for isort, black, and flake8 as part of the Github Action workflow for testing.

yosoyjay · 2021-11-19T01:10:10Z

@SorooshMani-NOAA I'd like your feedback specifically about how to handle the remaining errors and your thoughts about integrating tests for these in the Github Action testing workflow.

SorooshMani-NOAA · 2021-11-19T13:34:41Z

+        #    refine_opts.mesh_top1 = True
+        #    refine_opts.geom_feat = True


Please remove extra spaces between # and the commented code following it now that the lines are shifted

SorooshMani-NOAA · 2021-11-19T13:35:11Z

+        #    if out_crs is not None:
+        #        utils.reproject(jig_remeshed, out_crs)


Same as above, please remove extra spaces

SorooshMani-NOAA · 2021-11-19T13:36:44Z

+            "--contour",
+            action="append",
+            nargs="+",
+            type=float,
+            dest="contours",
+            metavar="CONTOUR_DEFN",
+            default=[],


I think it's too much to spread every argument to a newline. Is there any way to control linter not to do this?

SorooshMani-NOAA · 2021-11-19T13:39:40Z

+from ocsmesh import Geom, Hfun, JigsawDriver, Raster
+from ocsmesh.features.contour import Contour
 from ocsmesh.geom.shapely import MultiPolygonGeom
 from ocsmesh.hfun.mesh import HfunMesh
-from ocsmesh.features.contour import Contour
+from ocsmesh.mesh.mesh import Mesh
 from ocsmesh.mesh.parsers import sms2dm
 from ocsmesh.utils import msh_t_to_2dm


I think it's better if we have a 3rd block of imports specific to the module within this package (ocsmesh) and then organize them separately instead of mixing with other third_party

SorooshMani-NOAA · 2021-11-19T13:46:33Z

+    raster_path,
+    raster_opts,
+    zmin,
+    zmax,
+    join_method,
+    driver,
+    chunk_size,
+    overlap,


I'm not sure how I feel about removing 1 level of indentation here. It looks OK, but I don't know if it causes more confusion or not do to aligning with function body

SorooshMani-NOAA · 2021-11-19T13:47:39Z

+        self,
+        geom: Geom,
+        hfun: Hfun,
+        initial_mesh: bool = False,
+        crs: Union[str, CRS] = None,
+        verbosity: int = 0,


The same issue with indentation aligning with function body

SorooshMani-NOAA · 2021-11-19T13:48:06Z

+        #        if self.opts.hfun_hmin > 0:
+        #            output_mesh = utils.remesh_small_elements(
+        #                self.opts, geom_msh_t, output_mesh, hfun_msh_t)


Please remove extras spaces after # now that the lines are shifted

SorooshMani-NOAA · 2021-11-19T13:49:02Z

+        self,
+        value,
+        upper_bound=np.inf,
+        lower_bound=-np.inf,
+        value_type: str = "min",
+        rate=None,


Same comment!

SorooshMani-NOAA · 2021-11-19T13:49:43Z

+        self,
+        function=lambda i: i / 2.0,
+        upper_bound=np.inf,
+        lower_bound=-np.inf,
+        value_type: str = "min",
+        rate=None,


Just marking as same comment!

SorooshMani-NOAA · 2021-11-19T13:50:19Z

        pass

-#    @abstractmethod
+    #    @abstractmethod


Remove extra spaces after #

SorooshMani-NOAA · 2021-11-19T13:50:42Z

+        self,
+        level0=None,
+        level1=None,
+        sources=[],
+        max_contour_defn: Contour = None,
+        shapefile=None,


Indentation alignment thing!

SorooshMani-NOAA · 2021-11-19T13:50:59Z

+        self,
+        shape: Union[None, MultiPolygon, Polygon] = None,
+        shape_crs: CRS = CRS.from_user_input("EPSG:4326"),
+        shapefile: Union[None, str, Path] = None,


Indentation alignment

SorooshMani-NOAA · 2021-11-19T13:52:49Z

+        self,
+        in_list: Sequence[
+            Union[str, Raster, RasterGeom, MeshGeom, MultiPolygonGeom, PolygonGeom]
+        ],
+        base_mesh: Mesh = None,
+        zmin: float = None,
+        zmax: float = None,
+        nprocs: int = None,
+        chunk_size: int = None,
+        overlap: int = None,
+        verbosity: int = 0,
+        base_shape: Union[Polygon, MultiPolygon] = None,
+        base_shape_crs: Union[str, CRS] = "EPSG:4326",


argument and body indentation alignment

SorooshMani-NOAA · 2021-11-19T13:56:22Z

+        self,
+        shape: Union[MultiPolygon, Polygon] = None,
+        level: Union[Tuple[float, float], float] = None,
+        contour_defn: Union[FilledContour, Contour] = None,
+        patch_defn: Patch = None,
+        shapefile: Union[None, str, Path] = None,


Just marking the same indentation thing since I noticed it!

SorooshMani-NOAA · 2021-11-19T13:58:12Z

+        self,
+        raster: Union[Raster, str, os.PathLike],
+        zmin=None,
+        zmax=None,


Just marking!

SorooshMani-NOAA · 2021-11-19T13:58:47Z


    def get_multipolygon(  # type: ignore[override]
-            self, zmin: float = None, zmax: float = None) -> MultiPolygon:
+        self, zmin: float = None, zmax: float = None


indentation alignment thing again! Maybe I should ignore this?

SorooshMani-NOAA · 2021-11-19T13:59:35Z

+        self,
+        multipolygon: Union[MultiPolygon, Polygon],
+        expansion_rate: float = None,
+        target_size: float = None,
+        nprocs: int = None,


Indentation alignment

SorooshMani-NOAA · 2021-11-19T14:01:47Z

+        #        if self.hmin is not None:
+        #            values[np.where(values < self.hmin)] = self.hmin


extra spaces after #

SorooshMani-NOAA · 2021-11-19T14:05:24Z

+        self,
+        feature: Union[LineString, MultiLineString],
+        expansion_rate: float,
+        target_size: float = None,
+        max_verts=200,
+        *,  # kwarg-only comes after this
+        pool: Pool,


indentation alignement thing again

SorooshMani-NOAA · 2021-11-19T14:05:56Z

+        #        if self.hmin is not None:
+        #            values[np.where(values < self.hmin)] = self.hmin


Extra spaces

SorooshMani-NOAA · 2021-11-19T14:06:54Z

+        self,
+        window: rasterio.windows.Window = None,
+        marche: bool = False,
+        verbosity=None,


Marking for similar comment

SorooshMani-NOAA · 2021-11-19T14:09:32Z

+        self,
+        func=lambda i: i / 2.0,
+        upper_bound=np.inf,
+        lower_bound=-np.inf,
+        value_type: str = "min",
+        rate=0.01,


Indentation alignment

SorooshMani-NOAA · 2021-11-19T14:09:44Z

+        self,
+        multipolygon: Union[MultiPolygon, Polygon],
+        expansion_rate: float = None,
+        target_size: float = None,
+        nprocs: int = None,


Indentation alignment

SorooshMani-NOAA · 2021-11-19T14:10:01Z

+        self,
+        level: Union[List[float], float],
+        expansion_rate: float,
+        target_size: float = None,
+        nprocs: int = None,


Indenatation alignment

SorooshMani-NOAA · 2021-11-19T14:11:52Z

+        self,
+        in_list: Sequence[Union[str, Raster, Mesh, HfunRaster, HfunMesh]],
+        base_mesh: Mesh = None,
+        hmin: float = None,
+        hmax: float = None,
+        nprocs: int = None,
+        verbosity: int = 0,
+        method: str = "exact",
+        base_as_hfun: bool = True,
+        base_shape: Union[Polygon, MultiPolygon] = None,
+        base_shape_crs: Union[str, CRS] = "EPSG:4326",


Indentation alignement

SorooshMani-NOAA · 2021-11-19T14:12:07Z

+        self,
+        value,
+        upper_bound=np.inf,
+        lower_bound=-np.inf,
+        value_type: str = "min",
+        rate=0.01,
+        source_index: Union[List[int], int, None] = None,


Indentation alignement

SorooshMani-NOAA · 2021-11-19T14:12:27Z

+        self,
+        func=lambda i: i / 2.0,
+        upper_bound=np.inf,
+        lower_bound=-np.inf,
+        value_type: str = "min",
+        rate=0.01,
+        source_index: Union[List[int], int, None] = None,


Indentation alignement

SorooshMani-NOAA · 2021-11-19T14:12:40Z

+        self,
+        level: Union[List[float], float] = None,
+        expansion_rate: float = 0.01,
+        target_size: float = None,
+        contour_defn: Contour = None,


Indentation alignment with body

SorooshMani-NOAA · 2021-11-19T14:12:51Z

+        self,
+        level: float = 0,
+        width: float = 1000,  # in meters
+        target_size: float = 200,
+        expansion_rate: float = None,
+        tolerance: Union[None, float] = 50,
+        channel_defn=None,


Indentation alignment

SorooshMani-NOAA · 2021-11-19T14:16:15Z

+        #         self._validate_raster_local(
+        #             Raster(target_path), tmpraster.md5
+        #     os.copyfile()
+        #     tgtraster.save(target_path)


Extra space after #. note not to remove code indentation

SorooshMani-NOAA · 2021-11-19T14:20:09Z

 from ocsmesh.mesh.base import BaseMesh
 from ocsmesh.mesh.parsers import grd, sms2dm
+from ocsmesh.raster import Raster
+from pyproj import CRS, Transformer
+from scipy.interpolate import RectBivariateSpline, RegularGridInterpolator
+from shapely.geometry import LineString, MultiPolygon, Polygon, box
+from shapely.ops import linemerge, polygonize


Separate third party from ocsmesh

SorooshMani-NOAA · 2021-11-19T14:22:24Z

+        self,
+        threshold=0.0,
+        land_ibtype=0,
+        interior_ibtype=1,


body argument alignment

SorooshMani-NOAA · 2021-11-19T14:22:44Z

+            #            ocean_boundaries = utils.sort_edges(ocean_boundary)
+            #            land_boundaries = utils.sort_edges(land_boundary)


Extra spaces

SorooshMani-NOAA · 2021-11-19T14:23:32Z

+        self,
+        path: Union[str, os.PathLike],
+        overwrite: bool = False,
+        format="grd",  # pylint: disable=W0622


body arg alignment

SorooshMani-NOAA · 2021-11-19T14:25:27Z

+        self,
+        dem_files: Union[None, Sequence[Union[str, os.PathLike]]],
+        out_file: Union[str, os.PathLike],
+        out_format: str = "shapefile",
+        mesh_file: Union[str, os.PathLike, None] = None,
+        mesh_multipolygon: Union[MultiPolygon, Polygon] = None,
+        ignore_mesh_final_boundary: bool = False,
+        zmin: Union[float, None] = None,
+        zmax: Union[float, None] = None,
+        chunk_size: Union[int, None] = None,
+        overlap: Union[int, None] = None,
+        nprocs: int = -1,
+        out_crs: Union[str, CRS] = "EPSG:4326",
+        base_crs: Union[str, CRS] = None,


argument body alignment

SorooshMani-NOAA · 2021-11-19T14:25:45Z

+            #            priority_args = []
+            #            for priority, dem_file in zip(priorities, dem_files):
+            #                priority_args.append(
+            #                    (priority, temp_dir, dem_file, chunk_size, overlap))
+            #
+            #            with Pool(processes=nprocs) as p:
+            #                p.starmap(self._process_priority, priority_args)
+            #            p.join()


Remove extra space due to shift

SorooshMani-NOAA · 2021-11-19T14:26:04Z

+        self,
+        path: Union[str, os.PathLike],


alignment thing

SorooshMani-NOAA · 2021-11-19T14:26:14Z

+        self,
+        priority: int,
+        temp_dir: Union[str, os.PathLike],
+        dem_path: Union[str, os.PathLike],
+        chunk_size: Union[int, None] = None,
+        overlap: Union[int, None] = None,


SorooshMani-NOAA · 2021-11-19T14:26:23Z

+        self,
+        base_mesh_path: Union[str, os.PathLike, None],
+        temp_dir: Union[str, os.PathLike],
+        priorities: Sequence[int],
+        dem_files: Sequence[Union[str, os.PathLike]],
+        z_info: dict = {},
+        chunk_size: Union[int, None] = None,
+        overlap: Union[int, None] = None,


SorooshMani-NOAA · 2021-11-19T14:26:48Z

+            #            priority_geodf = gpd.GeoDataFrame(
+            #                    columns=['geometry'],
+            #                    crs=self._calc_crs)
+            #            for p in range(priority):
+            #                higher_pri_path = (
+            #                    pathlib.Path(temp_dir) / f'dem_priority_{p}.feather')
+            #
+            #                if higher_pri_path.is_file():
+            #                    priority_geodf = priority_geodf.append(
+            #                             self._read_to_geodf(higher_pri_path))
+            #
+            #            if len(priority_geodf):
+            #                op_res = priority_geodf.unary_union
+            #                pri_mult_poly = MultiPolygon()
+            #                if isinstance(op_res, MultiPolygon):
+            #                    pri_mult_poly = op_res
+            #                else:
+            #                    pri_mult_poly = MultiPolygon([op_res])
+            #
+            #
+            #                if rast_box.within(pri_mult_poly):
+            #                    _logger.info(
+            #                        f"{dem_path} is ignored due to priority...")
+            #                    continue
+            #
+            #                if rast_box.intersects(pri_mult_poly):
+            #                    _logger.info(
+            #                        f"{dem_path} needs clipping by priority...")
+            #
+            #                    # Clipping raster can cause problem at
+            #                    # boundaries due to difference in pixel size
+            #                    # between high and low resolution rasters
+            #                    # so instead we operate on extracted polygons
+            #                    geom_mult_poly = geom_mult_poly.difference(
+            #                            pri_mult_poly)


extra spaces due to shift

SorooshMani-NOAA · 2021-11-19T14:27:07Z

+        self,
+        base_mesh_path: Union[str, os.PathLike, None],
+        temp_dir: Union[str, os.PathLike],
+        priority: int,
+        dem_file: Union[str, os.PathLike],
+        z_info: dict = {},
+        chunk_size: Union[int, None] = None,
+        overlap: Union[int, None] = None,


SorooshMani-NOAA · 2021-11-19T14:27:49Z

+        self,
+        dem_files: Sequence[Union[str, os.PathLike]],
+        out_file: Union[str, os.PathLike],
+        out_format: str = "shapefile",
+        mesh_file: Union[str, os.PathLike, None] = None,
+        hmin: Union[float, None] = None,
+        hmax: Union[float, None] = None,
+        contours: List[List[float]] = None,
+        constants: List[List[float]] = None,
+        chunk_size: Union[int, None] = None,
+        overlap: Union[int, None] = None,
+        method: str = "exact",
+        nprocs: int = -1,


Arg body alignment

SorooshMani-NOAA · 2021-11-19T14:30:15Z

+        self,
+        path: Union[str, os.PathLike],
+        crs: Union[str, CRS] = None,
+        chunk_size=None,
+        overlap=None,


body arg alignment

SorooshMani-NOAA · 2021-11-19T14:30:30Z

+        self,
+        hmin=None,
+        zmin=None,
+        zmax=None,
+        window=None,
+        overlap=None,
+        band=1,


body arg alignment

SorooshMani-NOAA · 2021-11-19T14:30:41Z

+        self,
+        band=1,
+        window=None,
+        axes=None,
+        vmin=None,
+        vmax=None,
+        cmap="topobathy",
+        levels=None,
+        show=False,
+        title=None,
+        figsize=None,
+        colors=256,
+        cbar_label=None,
+        norm=None,
+        **kwargs,


body arg alignment

SorooshMani-NOAA · 2021-11-19T14:31:05Z

+                #                # Write orignal band
+                #                dst.write_band(i + n_bands_new // 2, outband)


extra spaces due to shift

SorooshMani-NOAA · 2021-11-19T14:31:26Z

+        self,
+        level: float = 0,
+        width: float = 1000,  # in meters
+        tolerance: Union[None, float] = None,


body arg alignment

SorooshMani-NOAA · 2021-11-19T14:34:15Z

+    mesh: jigsaw_msh_t,
+    shape: Union[box, Polygon, MultiPolygon],
+    from_box: bool = False,


body arg alignment

SorooshMani-NOAA · 2021-11-19T14:34:26Z

+    mesh: jigsaw_msh_t,
+    shape: Union[box, Polygon, MultiPolygon],


body arg alignment

SorooshMani-NOAA · 2021-11-19T14:35:14Z

+    mesh: jigsaw_msh_t,
+    shape: Union[box, Polygon, MultiPolygon],
+    use_box_only: bool = False,
+    fit_inside: bool = True,
+    inverse: bool = False,
+    in_place: bool = False,
+    check_cross_edges: bool = False,


argument body alignment

SorooshMani-NOAA · 2021-11-19T14:35:28Z

+    mesh: jigsaw_msh_t,
+    vert_in: Sequence[int],
+    can_use_other_verts: bool = False,
+    inverse: bool = False,
+    in_place: bool = False,


argument body alignment

SorooshMani-NOAA · 2021-11-19T14:36:39Z

+    *mesh_list,
+    out_crs="EPSG:4326",
+    drop_by_bbox=True,
+    can_overlap=True,
+    check_cross_edges=False,


argument body alignment

SorooshMani-NOAA

Hi @yosoyjay, thank you for the changes. It looks much cleaner. I just have a couple of concerns that is vividly visible from my comments on the code:

Some function/method arguments are indented such that the indentation aligns with the body
Some commented lines are shifted and the commented code are not indented properly and there's extra space
Some calls spread the arguments (1 per line) and sometimes it's too much.
Some lines seem to have become very long.

Otherwise I really liked these changes. It would be useful to add it as Github actions so that it's also clear how to run checks locally before submitting the code to repo.

I also have another concern. I made a lot of changes for adding docstring in enhance/docstring branch. I think there would be a lot of conflicts for merging, so I was wondering how much of your changes are manual and how much automatic. In case most things are automatic, we can first merge docstring branch to main and then apply changes to that branch. I'll address your questions in a separate comment.

SorooshMani-NOAA · 2021-11-19T15:39:56Z

For the question of those specific errors (line numbers are based on files in the pull request branch):

ocsmesh/cmd.py:404:9: You can comment the line, I haven't visited this part of the code
ocsmesh/cmd.py:442:9: You can comment the line, I haven't visited this part of the code
ocsmesh/utils.py:1089:5: Please comment the line, I need to revisit later
ocsmesh/utils.py:1097:5: Please comment the line, I need to revisit later
ocsmesh/utils.py:1106:5: Go ahead and remove the unused assignment line
ocsmesh/utils.py:1112:5: Go ahead and remove the unused assignment line
ocsmesh/raster.py:828:5: Remove the assignment but add a comment saying win height is equal to that value
ocsmesh/raster.py:829:5: Remove the assignment but add a comment saying win width is equal to that value
ocsmesh/mesh/mesh.py:795:9: Go ahead and remove it
ocsmesh/features/constraint.py:77:9: Please comment the line, I need to revisit this
ocsmesh/cli/mesh_upgrader.py:82:9: Go ahead and fix the double #
ocsmesh/cli/mesh_upgrader.py:89:9: Go ahead and fix the double #
ocsmesh/cli/remesh.py:308:9: You can remove the unused variable and the other relevant line (307, 308)
ocsmesh/cli/remesh.py:316:9: You can remove the unused variable and the other relevant line (315, 316)
ocsmesh/cli/remesh_by_shape_factor.py:236:13: You can remove the unused variable and the other relevant line (235, 236)
ocsmesh/geom/collector.py:243:17: This is a bug, level1 and level0 must be passed to FilledContour at 251
ocsmesh/geom/collector.py:244:17: This is a bug, level1 and level0 must be passed to FilledContour at 251
ocsmesh/ops/__init__.py:4:1: It's OK to replace with def but I wanted to be compact
ocsmesh/ops/__init__.py:6:1: It's OK to replace with def but I wanted to be compact
ocsmesh/ops/combine_geom.py:438:13: I need to check what errors could occur, can we ignore E722 only for this line?
ocsmesh/hfun/collector.py:125:9: Please comment the srcs line, I need to revisit this
ocsmesh/hfun/mesh.py:143:9: Please go ahead and remove the unused var line

Jesse Lopez added 5 commits November 18, 2021 15:36

apply isort

db0495c

Improve robustness for checking C++ compiler version

36ea149

typo

ae85d9a

add black formatting

853ea3c

flake8 changes

79695a4

SorooshMani-NOAA reviewed Nov 19, 2021

View reviewed changes

SorooshMani-NOAA requested changes Nov 19, 2021

View reviewed changes

		# refine_opts.mesh_top1 = True
		# refine_opts.geom_feat = True

		# if out_crs is not None:
		# utils.reproject(jig_remeshed, out_crs)

		# if self.hmin is not None:
		# values[np.where(values < self.hmin)] = self.hmin

		# ocean_boundaries = utils.sort_edges(ocean_boundary)
		# land_boundaries = utils.sort_edges(land_boundary)

		# # Write orignal band
		# dst.write_band(i + n_bands_new // 2, outband)

		mesh: jigsaw_msh_t,
		shape: Union[box, Polygon, MultiPolygon],

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yosoyjay commented Nov 19, 2021

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yosoyjay commented Nov 19, 2021

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