Fix all pre-commit hooks

.github/workflows/ci.yml

@@ -13,7 +13,7 @@ jobs:
     defaults:
       run:
         shell: bash -l {0}
-    
+
     strategy:
       fail-fast: false
       max-parallel: 5

.github/workflows/publish.yml

@@ -17,7 +17,7 @@ jobs:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
- 
+
       - uses: actions/setup-python@v4
         name: Install Python
         with:
@@ -114,4 +114,4 @@ jobs:
         with:
           user: __token__
           password: ${{ secrets.PYPI_TOKEN }}
-          verbose: true
+          verbose: true

docs/api.rst

@@ -297,4 +297,4 @@ GIS methods
    gis_utils.cut_pieces
    gis_utils.check_gpd_attributes
    gis_utils.update_data_columns_attributes_based_on_filter
-   gis_utils.get_gdf_from_branches
+   gis_utils.get_gdf_from_branches

docs/changelog.rst

@@ -28,9 +28,9 @@ Added
 
 Changed
 -------
-- Upgraded meshkernel dependency to version 3.0.0. (PR#109) 
-- Upgraded xugrid dependency to version 0.7.1. (PR#109) 
-- Upgraded hydrolib-core dependency to version 0.6.0. (PR#109) 
+- Upgraded meshkernel dependency to version 3.0.0. (PR#109)
+- Upgraded xugrid dependency to version 0.7.1. (PR#109)
+- Upgraded hydrolib-core dependency to version 0.6.0. (PR#109)
 - Support multiple structures at the same location. (PR#113)
 
 v0.1.2 (20 October 2023)
@@ -43,16 +43,16 @@ Added
 
 Changed
 -------
-- Upgraded hydromt dependency to version 0.9.0. (PR#100) 
+- Upgraded hydromt dependency to version 0.9.0. (PR#100)
 - Updated documentation. (PR #97)
 
 v0.1.1 (13 October 2023)
 ========================
-Dependencies upgrade. 
+Dependencies upgrade.
 
 Changed
 -------
-- Upgraded meshkernel dependency to version 2.1.0. (PR#94) 
+- Upgraded meshkernel dependency to version 2.1.0. (PR#94)
 
 v0.1.0 (22 September 2023)
 ==========================

docs/getting_started/faq.rst

@@ -19,7 +19,7 @@ Updating a dflowfm model
  | **Q**: Can I select a specific dflowfm MDU config file when updating my model ?
 
 It is possible. In that case, you need to start your HydroMT configuration with a **global** section
-where you can specify which MDU file to use using the *config_fn* argument. 
+where you can specify which MDU file to use using the *config_fn* argument.
 Use relative path to the current working directory;.
 
 Others

hydromt_delft3dfm/gis_utils.py

@@ -1,8 +1,6 @@
-# -*- coding: utf-8 -*-
+"""Utilities GIS functions for Delft3D-FM model."""
 
-import configparser
 import logging
-import pathlib
 
 import geopandas as gpd
 import numpy as np
@@ -40,7 +38,8 @@ def cut_pieces(line, distances):
 
 
 def cut(line, distance):
-    """Cuts a line in two at a distance from its starting point
+    """Cut a line in two at a distance from its starting point.
+
     ref: https://shapely.readthedocs.io/en/stable/manual.html.
     """
     if distance <= 0.0 or distance >= line.length:
@@ -118,11 +117,13 @@ def check_gpd_attributes(
     if not (set(required_columns).issubset(gdf.columns)):
         if raise_error:
             raise ValueError(
-                f"GeoDataFrame do not contains all required attributes: {required_columns}."
+                "GeoDataFrame does not contain all required attributes:"
+                f"{required_columns}."
             )
         else:
             logger.warning(
-                f"GeoDataFrame do not contains all required attributes: {required_columns}."
+                "GeoDataFrame does not contain all required attributes:"
+                f"{required_columns}."
             )
         return False
     return True
@@ -135,16 +136,18 @@ def update_data_columns_attributes_based_on_filter(
     filter_value: str = None,
 ):
     """
-    Add or update columns in the geodataframe based on column and values in attributes dataframe.
+    Add or update columns in gdf based on column and values in df.
 
-    If filter_column and filter_value is set, only update the attributes of the filtered geodataframe.
+    If filter_column and filter_value is set, only update the attributes of the filtered
+    geodataframe.
 
     Parameters
     ----------
     gdf : gpd.GeoDataFrame
         geodataframe containing user input
     df : attribute DataFrame
-        a pd.DataFrame with attribute columns and values (e.g. width =  1) per filter_value in the filter_column (e.g. branch_type = pipe)
+        a pd.DataFrame with attribute columns and values (e.g. width =  1) per
+        filter_value in the filter_column (e.g. branch_type = pipe)
     filter_column : str
         Name of the column linking df to gdf.
     filter_value: str
@@ -191,6 +194,7 @@ def get_gdf_from_branches(
     branches: gpd.GeoDataFrame, df: pd.DataFrame
 ) -> gpd.GeoDataFrame:
     """Get geodataframe from dataframe.
+
     Based on interpolation of branches, using columns ["branchid", "chainage" in df].
 
     Parameters
@@ -213,7 +217,7 @@ def get_gdf_from_branches(
 
     df["geometry"] = None
 
-    # Iterate over each point and interpolate a point along the corresponding line feature
+    # Iterate over each point and interpolate a point along the corresponding line
     for i, row in df.iterrows():
         line_geometry = branches.loc[row.branchid, "geometry"]
         new_point_geometry = line_geometry.interpolate(row.chainage)

hydromt_delft3dfm/graph_utils.py

@@ -1,4 +1,4 @@
-# -*- coding: utf-8 -*-
+"""Utilities graph functions for Delft3D-FM model."""
 
 import logging
 
@@ -14,7 +14,10 @@
 
 
 def gpd_to_digraph(data: gpd.GeoDataFrame) -> nx.DiGraph():
-    """Convert a `gpd.GeoDataFrame` to a `nx.DiGraph` by taking the first and last coordinate in a row as source and target, respectively.
+    """Convert a `gpd.GeoDataFrame` to a `nx.DiGraph`.
+
+    This is done by taking the first and last coordinate in a row as source and target,
+    respectively.
 
     Parameters
     ----------
@@ -49,13 +52,13 @@ def get_endnodes_from_lines(
     ----------
     where : {'both', 'upstream', 'downstream'}
         Where at the branches should the boundaries be derived.
-        An upstream end node is defined as a node which has 0 incoming branches and 1 outgoing branch.
-        A downstream end node is defined as a node which has 1 incoming branch and 0 outgoing branches.
+        An upstream end node: 0 incoming branches and 1 outgoing branch.
+        A downstream end node: 1 incoming branch and 0 outgoing branches.
 
     Returns
     -------
     gpd.GeoDataFrame
-        A data frame containing all the upstream and downstream end nodes of the branches
+        A dataframe containing all the upstream and downstream end nodes of the branches
     """
     # convert branches to graph
     G = gpd_to_digraph(lines)

hydromt_delft3dfm/mesh_utils.py

@@ -1,4 +1,4 @@
-# -*- coding: utf-8 -*-
+"""Utilities mesh functions for Delft3D-FM model."""
 
 import logging
 from typing import Tuple
@@ -26,7 +26,7 @@ def hydrolib_network_from_mesh(
     mesh: xu.UgridDataset,
 ) -> Network:
     """
-    Converts from xugrid mesh to hydrolib-core network object.
+    Convert from xugrid mesh to hydrolib-core network object.
 
     Parameters
     ----------
@@ -83,7 +83,7 @@ def mesh1d_network1d_from_hydrolib_network(
     crs: CRS,
 ) -> Tuple[xu.UgridDataset, xu.UgridDataset]:
     """
-    Creates xugrid mesh1d and network1d UgridDataset from hydrolib-core network object.
+    Create xugrid mesh1d and network1d UgridDataset from hydrolib-core network object.
 
     Parameters
     ----------
@@ -130,10 +130,11 @@ def mesh1d_network1d_from_hydrolib_network(
         uds_mesh1d = xu.UgridDataset(ds, grids=grid_mesh1d)
 
         # derive network1d
-        # The 1D network topology serves as the coordinate space in which a 1D mesh discretization
-        # will later be defined. The network is largely based on the UGRID conventions for its topology
-        # (i.e., nodes and edges) and additionally uses an optional edge_geometry to define the
-        # precise network branch geometries (more about this in the next Section).
+        # The 1D network topology serves as the coordinate space in which a 1D mesh
+        # discretization will later be defined. The network is largely based on the
+        # UGRID conventions for its topology (i.e., nodes and edges) and additionally
+        # uses an optional edge_geometry to define the precise network branch geometries
+        # (more about this in the next Section).
 
         grid_network1d = xu.Ugrid1d(
             node_x=mesh1d.network1d_node_x,
@@ -184,7 +185,8 @@ def mesh1d_network1d_from_hydrolib_network(
             network_edge_dim,
             mesh1d.network1d_branch_order,
         )
-        # might be supported in the future https://github.com/Deltares/HYDROLIB-core/issues/561
+        # might be supported in the future
+        # https://github.com/Deltares/HYDROLIB-core/issues/561
         # ds["network1d_branch_type"] = (
         #     edge_dim,
         #     mesh1d.network1d_branch_type,
@@ -238,7 +240,7 @@ def mesh2d_from_hydrolib_network(
     crs: CRS,
 ) -> xu.UgridDataset:
     """
-    Creates xugrid mesh2d UgridDataset from hydrolib-core network object.
+    Create xugrid mesh2d UgridDataset from hydrolib-core network object.
 
     Parameters
     ----------
@@ -276,7 +278,7 @@ def mesh_from_hydrolib_network(
     crs: CRS,
 ) -> xu.UgridDataset:
     """
-    Creates xugrid mesh from hydrolib-core network object.
+    Create xugrid mesh from hydrolib-core network object.
 
     Parameters
     ----------
@@ -339,7 +341,7 @@ def mesh1d_nodes_geodataframe(
     branches: gpd.GeoDataFrame,
 ) -> gpd.GeoDataFrame:
     """
-    Returns the nodes of mesh 1D as geodataframe.
+    Return the nodes of mesh 1D as geodataframe.
 
     Parameters
     ----------