Merge pull request #11 from Renumics/lint.-format

Lint-format

Author: markus-stoll

docs/examples/aggregate_warpage.py

@@ -2,6 +2,7 @@
 Aggregate Warpage
 ===================
 """
+
 # pylint: disable=pointless-statement
 from pathlib import Path
 import numpy as np

docs/examples/plot_neighbor_distances.py

@@ -3,6 +3,7 @@
 ========================
 This example shows ho to plot the distances of nearby elements to a specific element (d<10)
 """
+
 # pylint: disable=pointless-statement
 from pathlib import Path
 import numpy as np

docs/examples/plot_stress.py

@@ -3,6 +3,7 @@
 ====================
 
 """
+
 # pylint: disable=pointless-statement
 from pathlib import Path
 import numpy as np

docs/examples/quickstart.py

@@ -2,6 +2,7 @@
 Quick Start Example
 ====================
 """
+
 # pylint: disable=pointless-statement
 from pathlib import Path
 import numpy as np

mesh2vec/helpers.py

@@ -1,11 +1,13 @@
 """helper functions"""
+
 from typing import OrderedDict, List, Dict
 from collections import deque
 from abc import ABC, abstractmethod
 
 import numpy as np
 from scipy.sparse import csr_array, coo_array, eye
 
+
 # pylint: disable=invalid-name
 class AbstractAdjacencyStrategy(ABC):
     # pylint: disable=too-few-public-methods

mesh2vec/mesh2vec_base.py

@@ -1,4 +1,5 @@
 """Mesh2VecBase"""
+
 import collections
 from pathlib import Path
 from typing import List, Optional, Callable, OrderedDict, Dict, Union, Iterable

mesh2vec/mesh2vec_cae.py

@@ -1,4 +1,5 @@
 """Mesh2VecCae"""
+
 import json
 import os
 import subprocess
@@ -254,15 +255,18 @@ def from_d3plot_shell(
         return Mesh2VecCae(distance, mesh, element_info, calc_strategy=calc_strategy)
 
     @staticmethod
-    def from_keyfile_shell(distance: int, keyfile: Path, partid="", calc_strategy="bfs") -> "Mesh2VecCae":
+    def from_keyfile_shell(
+        distance: int, keyfile: Path, partid="", calc_strategy="bfs"
+    ) -> "Mesh2VecCae":
         """
         Read the given keyfile and use the shell elements to generate a hypergraph, using mesh
         nodes as hyperedges, and adjacent elements as hypervertices.
 
         Args:
             distance: the maximum distance for neighborhood generation and feature aggregation
             keyfile: path to keyfile
-            partid: part id to use for hypergraph generation (default empty string, use all shell parts)
+            partid: part id to use for hypergraph generation
+                (default empty string, use all shell parts)
             calc_strategy: choose the algorithm to calculate adjacencies
 
                 * "dfs": depth first search (defaultl fast)

mesh2vec/mesh2vec_exceptions.py

@@ -1,4 +1,5 @@
 """Exceptions for mesh2vec"""
+
 from typing import Any, Dict, List
 from loguru import logger
 import numpy as np

mesh2vec/mesh_features.py

@@ -1,4 +1,5 @@
 """calculation of mesh based features"""
+
 from typing import Tuple, List, Any, Optional
 
 import numpy as np
@@ -34,17 +35,21 @@ def _quad_to_tris(element_node_idxs: np.ndarray) -> Tuple[List[bool], np.ndarray
     if len(element_node_idxs.shape) == 3:  # points
         is_quads = [any(element[3] != element[2]) for element in element_node_idxs]
         tri_faces_nested = [
-            [element[:3].tolist(), element[[0, 2, 3]].tolist()]
-            if is_quad
-            else [element[:3].tolist()]
+            (
+                [element[:3].tolist(), element[[0, 2, 3]].tolist()]
+                if is_quad
+                else [element[:3].tolist()]
+            )
             for is_quad, element in zip(is_quads, element_node_idxs)
         ]
     else:
         is_quads = [element[3] != element[2] for element in element_node_idxs]
         tri_faces_nested = [
-            [element[:3].tolist(), element[[0, 2, 3]].tolist()]
-            if is_quad
-            else [element[:3].tolist()]
+            (
+                [element[:3].tolist(), element[[0, 2, 3]].tolist()]
+                if is_quad
+                else [element[:3].tolist()]
+            )
             for is_quad, element in zip(is_quads, element_node_idxs)
         ]
     tri_faces = np.array([tri_face for tri_faces in tri_faces_nested for tri_face in tri_faces])
@@ -125,10 +130,12 @@ def _make_ids_unique(
     cumcounts = pd.DataFrame(array, columns=["ids"]).groupby("ids").cumcount().values
     return np.array(
         [
-            old_id
-            if postfix == 0
-            else f"{old_id}_{point_uid[e[0]]}_{point_uid[e[1]]}_"
-            f"{point_uid[e[2]]}_{point_uid[e[3]]}"
+            (
+                old_id
+                if postfix == 0
+                else f"{old_id}_{point_uid[e[0]]}_{point_uid[e[1]]}_"
+                f"{point_uid[e[2]]}_{point_uid[e[3]]}"
+            )
             for old_id, e, postfix in zip(array, element_node_idxs, cumcounts)
         ]
     )
@@ -252,6 +259,7 @@ def from_keyfile(keyfile: str, partid: str = "") -> "CaeShellMesh":
         (6400, 3)
         """
 
+        # pylint: disable=too-many-branches, too-many-nested-blocks
         def parse_contents(file_contents):
             lines = file_contents.split("\n")
             current_section = ""
@@ -265,34 +273,46 @@ def parse_contents(file_contents):
             for line in lines:
                 if line.startswith("*"):
                     current_section = line.split()[0].upper()
-                    current_section_options = set(current_section.split('_')[1:])
+                    current_section_options = set(current_section.split("_")[1:])
                     current_section_lines_per_entry = 1
                     current_section_lineno = 0
                     continue
                 if line.startswith("$"):  # comment
                     continue
                 if current_section == "*NODE":
                     try:
-                        point_coordinates.append([float(line[8+i*16:8+(i+1)*16]) for i in range(3)])
+                        point_coordinates.append(
+                            [float(line[8 + i * 16 : 8 + (i + 1) * 16]) for i in range(3)]
+                        )
                         pnt_ids.append(line[:8].strip())
-                    except:
+                    except [ValueError, IndexError]:
                         pass
                 elif current_section.startswith("*ELEMENT_SHELL"):
-                    
 
                     if current_section_lineno % current_section_lines_per_entry == 0:
                         if partid == "" or partid == line[8:16].strip():
-                            node_ids = [line[16+i*8:16+(i+1)*8].strip() for i in range(8)]
-                            node_ids = [node_id for node_id in node_ids if len(node_id) > 0 and node_id != "0"]
+                            node_ids = [
+                                line[16 + i * 8 : 16 + (i + 1) * 8].strip() for i in range(8)
+                            ]
+                            node_ids = [
+                                node_id
+                                for node_id in node_ids
+                                if len(node_id) > 0 and node_id != "0"
+                            ]
+                            # pylint: disable=fixme
                             # TODO: Check for unhandled options, e.g. COMPOSITE, DOF
                             if current_section_lineno == 0:
                                 if len(current_section_options & thickcard_options_set) > 0:
-                                    current_section_lines_per_entry += 1 # skip thickness card
+                                    current_section_lines_per_entry += 1  # skip thickness card
                                     if len(node_ids) > 4:
-                                        current_section_lines_per_entry += 1 # skip additional thickness card for mid-side nodes
+                                        current_section_lines_per_entry += (
+                                            1  # skip additional thickness card for mid-side nodes
+                                        )
                                 if "OFFSET" in current_section_options:
-                                        current_section_lines_per_entry += 1 # skip offset card
-                            elem_node_ids.append([node_id for node_id in node_ids if len(node_id) > 0])
+                                    current_section_lines_per_entry += 1  # skip offset card
+                            elem_node_ids.append(
+                                [node_id for node_id in node_ids if len(node_id) > 0]
+                            )
                             if node_ids[0] == 1.0:
                                 print("HERE")
                             elem_ids.append(line[:8].strip())