Enable Code Formatting Checks

.github/workflows/python-package.yml

@@ -30,10 +30,10 @@ jobs:
         python -m pip install --upgrade pip
         python -m pip install pytest yapf toml
         python -m pip install .
-    # - name: Lint with yapf
-    #   working-directory: ./${{ matrix.package-name }}
-    #   run: |
-    #     yapf -r --diff .
+    - name: Lint with yapf
+      working-directory: ./${{ matrix.package-name }}
+      run: |
+        yapf -r --diff . --style ../.style.yapf
     # - name: Test with pytest
     #   working-directory: ./${{ matrix.package-name }}
     #   run: |

.style.yapf

@@ -0,0 +1,5 @@
+[style]
+based_on_style = pep8
+spaces_before_comment = 4
+split_before_logical_operator = true
+column_limit = 120

docs/conf.py

@@ -18,17 +18,11 @@
 
 # Add python modules to be documented
 python_root = '..'
-python_modules = ('geosx_mesh_tools_package',
-                  'geosx_xml_tools_package',
-                  'geosx_mesh_doctor',
-                  'geos_ats_package',
-                  'hdf5_wrapper_package',
-                  'pygeosx_tools_package',
-                  'timehistory_package')
+python_modules = ('geosx_mesh_tools_package', 'geosx_xml_tools_package', 'geosx_mesh_doctor', 'geos_ats_package',
+                  'hdf5_wrapper_package', 'pygeosx_tools_package', 'timehistory_package')
 for m in python_modules:
     sys.path.insert(0, os.path.abspath(os.path.join(python_root, m)))
 
-
 # -- Project information -----------------------------------------------------
 
 project = u'GEOS Python Packages'
@@ -40,7 +34,6 @@
 # The full version, including alpha/beta/rc tags
 release = u''
 
-
 # -- General configuration ---------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -51,17 +44,10 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx_design',
-    'sphinx.ext.todo',
-    'sphinx.ext.autodoc',
-    'sphinx.ext.doctest',
-    'sphinx.ext.imgmath',
-    'sphinxarg.ext',
-    'sphinx.ext.napoleon',
-    'sphinxcontrib.programoutput'
+    'sphinx_design', 'sphinx.ext.todo', 'sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.imgmath',
+    'sphinxarg.ext', 'sphinx.ext.napoleon', 'sphinxcontrib.programoutput'
 ]
 
-
 autodoc_mock_imports = ["pygeosx", "pylvarray", "meshio", "lxml", "mpi4py", "h5py", "ats", "scipy"]
 
 # The suffix(es) of source filenames.
@@ -90,27 +76,21 @@
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
 
-
 # -- Theme options ----------------------------------------------
 extensions += [
     'sphinx_rtd_theme',
 ]
 
 html_theme = "sphinx_rtd_theme"
 
-html_theme_options = {
-    'navigation_depth': -1,
-    'collapse_navigation': False
-}
+html_theme_options = {'navigation_depth': -1, 'collapse_navigation': False}
 
 html_static_path = ['./_static']
 
 html_css_files = [
     'theme_overrides.css',
 ]
 
-
 # -- Options for HTMLHelp output ---------------------------------------------
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'geosPythonPackagesDoc'
-

geosx_mesh_doctor/checks/check_fractures.py

@@ -18,17 +18,13 @@
     vtkCell,
 )
 from vtkmodules.vtkCommonCore import (
-    vtkPoints,
-)
+    vtkPoints, )
 from vtkmodules.vtkIOXML import (
-    vtkXMLMultiBlockDataReader,
-)
+    vtkXMLMultiBlockDataReader, )
 from vtkmodules.util.numpy_support import (
-    vtk_to_numpy,
-)
+    vtk_to_numpy, )
 from vtk_utils import (
-    vtk_iter,
-)
+    vtk_iter, )
 
 
 @dataclass(frozen=True)
@@ -47,7 +43,8 @@ class Result:
     errors: Sequence[tuple[int, int, int]]
 
 
-def __read_multiblock(vtk_input_file: str, matrix_name: str, fracture_name: str) -> Tuple[vtkUnstructuredGrid, vtkUnstructuredGrid]:
+def __read_multiblock(vtk_input_file: str, matrix_name: str,
+                      fracture_name: str) -> Tuple[vtkUnstructuredGrid, vtkUnstructuredGrid]:
     reader = vtkXMLMultiBlockDataReader()
     reader.SetFileName(vtk_input_file)
     reader.Update()
@@ -75,10 +72,10 @@ def format_collocated_nodes(fracture_mesh: vtkUnstructuredGrid) -> Sequence[Iter
     return tuple(generator)
 
 
-def __check_collocated_nodes_positions(matrix_points: Sequence[Tuple[float, float, float]],
-                                       fracture_points: Sequence[Tuple[float, float, float]],
-                                       g2l: Sequence[int],
-                                       collocated_nodes: Iterable[Iterable[int]]) -> Collection[Tuple[int, Iterable[int], Iterable[Tuple[float, float, float]]]]:
+def __check_collocated_nodes_positions(
+    matrix_points: Sequence[Tuple[float, float, float]], fracture_points: Sequence[Tuple[float, float, float]],
+    g2l: Sequence[int], collocated_nodes: Iterable[Iterable[int]]
+) -> Collection[Tuple[int, Iterable[int], Iterable[Tuple[float, float, float]]]]:
     issues = []
     for li, bucket in enumerate(collocated_nodes):
         matrix_nodes = (fracture_points[li], ) + tuple(map(lambda gi: matrix_points[g2l[gi]], bucket))
@@ -99,9 +96,7 @@ def my_iter(ccc):
             yield (i, )
 
 
-def __check_neighbors(matrix: vtkUnstructuredGrid,
-                      fracture: vtkUnstructuredGrid,
-                      g2l: Sequence[int],
+def __check_neighbors(matrix: vtkUnstructuredGrid, fracture: vtkUnstructuredGrid, g2l: Sequence[int],
                       collocated_nodes: Sequence[Iterable[int]]):
     fracture_nodes: Set[int] = set()
     for bucket in collocated_nodes:
@@ -121,7 +116,7 @@ def __check_neighbors(matrix: vtkUnstructuredGrid,
     # Finding the cells
     for c in tqdm(range(fracture.GetNumberOfCells()), desc="Finding neighbor cell pairs"):
         cell: vtkCell = fracture.GetCell(c)
-        cns: Set[FrozenSet[int]] = set()  # subset of collocated_nodes
+        cns: Set[FrozenSet[int]] = set()    # subset of collocated_nodes
         point_ids = frozenset(vtk_iter(cell.GetPointIds()))
         for point_id in point_ids:
             bucket = collocated_nodes[point_id]
@@ -134,7 +129,9 @@ def __check_neighbors(matrix: vtkUnstructuredGrid,
             if f in fracture_faces:
                 found += 1
         if found != 2:
-            logging.warning(f"Something went wrong since we should have found 2 fractures faces (we found {found}) for collocated nodes {cns}.")
+            logging.warning(
+                f"Something went wrong since we should have found 2 fractures faces (we found {found}) for collocated nodes {cns}."
+            )
 
 
 def __check(vtk_input_file: str, options: Options) -> Result:
@@ -153,9 +150,7 @@ def __check(vtk_input_file: str, options: Options) -> Result:
     g2l.flags.writeable = False
 
     issues = __check_collocated_nodes_positions(vtk_to_numpy(matrix.GetPoints().GetData()),
-                                                vtk_to_numpy(fracture.GetPoints().GetData()),
-                                                g2l,
-                                                collocated_nodes)
+                                                vtk_to_numpy(fracture.GetPoints().GetData()), g2l, collocated_nodes)
     assert len(issues) == 0
 
     __check_neighbors(matrix, fracture, g2l, collocated_nodes)

geosx_mesh_doctor/checks/collocated_nodes.py

@@ -24,8 +24,8 @@ class Options:
 
 @dataclass(frozen=True)
 class Result:
-    nodes_buckets: Iterable[Iterable[int]]  # Each bucket contains the duplicated node indices.
-    wrong_support_elements: Collection[int]  # Element indices with support node indices appearing more than once.
+    nodes_buckets: Iterable[Iterable[int]]    # Each bucket contains the duplicated node indices.
+    wrong_support_elements: Collection[int]    # Element indices with support node indices appearing more than once.
 
 
 def __check(mesh, options: Options) -> Result:
@@ -69,8 +69,7 @@ def __check(mesh, options: Options) -> Result:
         if len({cell.GetPointId(i) for i in range(num_points_per_cell)}) != num_points_per_cell:
             wrong_support_elements.append(c)
 
-    return Result(nodes_buckets=tmp,
-                  wrong_support_elements=wrong_support_elements)
+    return Result(nodes_buckets=tmp, wrong_support_elements=wrong_support_elements)
 
 
 def check(vtk_input_file: str, options: Options) -> Result:

geosx_mesh_doctor/checks/element_volumes.py

@@ -14,9 +14,7 @@
     vtkMeshQuality,
 )
 from vtkmodules.util.numpy_support import (
-    vtk_to_numpy,
-)
-
+    vtk_to_numpy, )
 
 from . import vtk_utils
 
@@ -39,7 +37,7 @@ def __check(mesh, options: Options) -> Result:
     cs.ComputeSumOff()
     cs.ComputeVertexCountOff()
     cs.ComputeVolumeOn()
-    volume_array_name = "__MESH_DOCTOR_VOLUME-" + str(uuid.uuid4())  # Making the name unique
+    volume_array_name = "__MESH_DOCTOR_VOLUME-" + str(uuid.uuid4())    # Making the name unique
     cs.SetVolumeArrayName(volume_array_name)
 
     cs.SetInputData(mesh)
@@ -50,19 +48,21 @@ def __check(mesh, options: Options) -> Result:
 
     mq.SetTetQualityMeasureToVolume()
     mq.SetHexQualityMeasureToVolume()
-    if hasattr(mq, "SetPyramidQualityMeasureToVolume"):  # This feature is quite recent
+    if hasattr(mq, "SetPyramidQualityMeasureToVolume"):    # This feature is quite recent
         mq.SetPyramidQualityMeasureToVolume()
         SUPPORTED_TYPES.append(VTK_PYRAMID)
         mq.SetWedgeQualityMeasureToVolume()
         SUPPORTED_TYPES.append(VTK_WEDGE)
     else:
-        logging.warning("Your \"pyvtk\" version does not bring pyramid nor wedge support with vtkMeshQuality. Using the fallback solution.")
+        logging.warning(
+            "Your \"pyvtk\" version does not bring pyramid nor wedge support with vtkMeshQuality. Using the fallback solution."
+        )
 
     mq.SetInputData(mesh)
     mq.Update()
 
     volume = cs.GetOutput().GetCellData().GetArray(volume_array_name)
-    quality = mq.GetOutput().GetCellData().GetArray("Quality")  # Name is imposed by vtk.
+    quality = mq.GetOutput().GetCellData().GetArray("Quality")    # Name is imposed by vtk.
 
     assert volume is not None
     assert quality is not None

geosx_mesh_doctor/checks/fix_elements_orderings.py

@@ -8,8 +8,7 @@
 )
 
 from vtkmodules.vtkCommonCore import (
-    vtkIdList,
-)
+    vtkIdList, )
 
 from . import vtk_utils
 from .vtk_utils import (
@@ -34,7 +33,7 @@ def __check(mesh, options: Options) -> Result:
     # The vtk cell type is an int and will be the key of the following mapping,
     # that will point to the relevant permutation.
     cell_type_to_ordering: Dict[int, List[int]] = options.cell_type_to_ordering
-    unchanged_cell_types: Set[int] = set()  # For logging purpose
+    unchanged_cell_types: Set[int] = set()    # For logging purpose
 
     # Preparing the output mesh by first keeping the same instance type.
     output_mesh = mesh.NewInstance()

geosx_mesh_doctor/checks/generate_cube.py

@@ -5,8 +5,7 @@
 import numpy
 
 from vtkmodules.vtkCommonCore import (
-    vtkPoints,
-)
+    vtkPoints, )
 from vtkmodules.vtkCommonDataModel import (
     VTK_HEXAHEDRON,
     vtkCellArray,
@@ -15,13 +14,11 @@
     vtkUnstructuredGrid,
 )
 from vtkmodules.util.numpy_support import (
-    numpy_to_vtk,
-)
+    numpy_to_vtk, )
 
 from . import vtk_utils
 from .vtk_utils import (
-    VtkOutput,
-)
+    VtkOutput, )
 
 from .generate_global_ids import __build_global_ids
 
@@ -87,7 +84,7 @@ def build_rectilinear_blocks_mesh(xyzs: Iterable[XYZ]) -> vtkUnstructuredGrid:
     cells = vtkCellArray()
     cells.AllocateExact(num_cells, num_cells * 8)
 
-    m = (0, 1, 3, 2, 4, 5, 7, 6)  # VTK_VOXEL and VTK_HEXAHEDRON do not share the same ordering.
+    m = (0, 1, 3, 2, 4, 5, 7, 6)    # VTK_VOXEL and VTK_HEXAHEDRON do not share the same ordering.
     offset = 0
     for rg in rgs:
         for i in range(rg.GetNumberOfCells()):
@@ -121,6 +118,7 @@ def __add_fields(mesh: vtkUnstructuredGrid, fields: Iterable[FieldInfo]) -> vtkU
 
 
 def __build(options: Options):
+
     def build_coordinates(positions, num_elements):
         result = []
         it = zip(zip(positions, positions[1:]), num_elements)
@@ -129,18 +127,19 @@ def build_coordinates(positions, num_elements):
             while True:
                 start, stop = coords
                 end_point = False
-                tmp = numpy.linspace(start=start, stop=stop, num=n+end_point, endpoint=end_point)
+                tmp = numpy.linspace(start=start, stop=stop, num=n + end_point, endpoint=end_point)
                 coords, n = next(it)
                 result.append(tmp)
         except StopIteration:
             end_point = True
-            tmp = numpy.linspace(start=start, stop=stop, num=n+end_point, endpoint=end_point)
+            tmp = numpy.linspace(start=start, stop=stop, num=n + end_point, endpoint=end_point)
             result.append(tmp)
         return numpy.concatenate(result)
+
     x = build_coordinates(options.xs, options.nxs)
     y = build_coordinates(options.ys, options.nys)
     z = build_coordinates(options.zs, options.nzs)
-    cube = build_rectilinear_blocks_mesh((XYZ(x, y, z),))
+    cube = build_rectilinear_blocks_mesh((XYZ(x, y, z), ))
     cube = __add_fields(cube, options.fields)
     __build_global_ids(cube, options.generate_cells_global_ids, options.generate_points_global_ids)
     return cube