From b419ade77d5e98cf03ef1da5c019a6e60b5a1965 Mon Sep 17 00:00:00 2001
From: FZill <florian.zill@ufz.de>
Date: Thu, 21 Mar 2024 12:45:26 +0100
Subject: [PATCH] [all] many type fixes
also ignore jupyter notebooks in main folder
---
.gitignore | 5 +-
ogstools/meshlib/boundary.py | 10 +--
ogstools/meshlib/boundary_set.py | 18 ++---
ogstools/meshlib/boundary_subset.py | 10 ++-
ogstools/meshlib/gmsh_meshing.py | 8 +--
ogstools/meshlib/mesh_series.py | 7 +-
ogstools/meshlib/region/region.py | 7 +-
ogstools/meshlib/xdmf_reader.py | 11 +--
ogstools/meshplotlib/animation.py | 16 +++--
ogstools/meshplotlib/core.py | 69 +++++++++++--------
ogstools/meshplotlib/plot_features.py | 15 ++--
ogstools/meshplotlib/plot_setup.py | 14 ++--
ogstools/meshplotlib/utils.py | 5 +-
ogstools/msh2vtu/__init__.py | 18 ++---
ogstools/propertylib/property.py | 14 ++--
ogstools/studies/convergence/convergence.py | 6 +-
.../examples/steady_state_diffusion.py | 6 +-
17 files changed, 134 insertions(+), 105 deletions(-)
diff --git a/.gitignore b/.gitignore
index f0aa73237..3e4a20641 100644
--- a/.gitignore
+++ b/.gitignore
@@ -162,6 +162,9 @@ cython_debug/
# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
# and can be added to the global gitignore or merged into this file. For a more nuclear
# option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+#.idea/S
/docs/auto_examples/
+
+# ignore jupyter notebooks in main folder (useful for testing, annoying for git)
+/**.ipynb
diff --git a/ogstools/meshlib/boundary.py b/ogstools/meshlib/boundary.py
index d298cc7e6..030e3fb95 100644
--- a/ogstools/meshlib/boundary.py
+++ b/ogstools/meshlib/boundary.py
@@ -21,7 +21,7 @@ class Boundary(ABC):
"""
@abstractmethod
- def dim(self):
+ def dim(self) -> int:
"""
Get the dimension of the boundary.
@@ -29,7 +29,7 @@ class Boundary(ABC):
int: The dimension of the boundary. For example, the dimension of a boundary
of a cube (3D) is 2.
"""
- return
+ return 0
@dataclass(frozen=True)
@@ -47,7 +47,7 @@ class Layer(Boundary):
of the layer in the GIS system.
"""
- def __post_init__(self):
+ def __post_init__(self) -> None:
if not self.material_id:
object.__setattr__(self, "material_id", self.bottom._material_id)
@@ -89,7 +89,7 @@ class Layer(Boundary):
rasters.append(bottom_raster)
return rasters
- def dim(self):
+ def dim(self) -> int:
return 3
@@ -100,7 +100,7 @@ class LocationFrame:
ymin: float
ymax: float
- def as_gml(self, filename: Path):
+ def as_gml(self, filename: Path) -> None:
"""
Generate GML representation of the location frame.
diff --git a/ogstools/meshlib/boundary_set.py b/ogstools/meshlib/boundary_set.py
index 17dd54b92..22de2ef82 100644
--- a/ogstools/meshlib/boundary_set.py
+++ b/ogstools/meshlib/boundary_set.py
@@ -20,12 +20,12 @@ class BoundarySet(ABC):
"""
@abstractmethod
- def bounds(self):
- return
+ def bounds(self) -> list:
+ return []
@abstractmethod
- def filenames(self):
- return
+ def filenames(self) -> list[Path]:
+ return []
class LayerSet(BoundarySet):
@@ -49,16 +49,16 @@ class LayerSet(BoundarySet):
raise ValueError(msg)
self.layers = layers
- def bounds(self):
+ def bounds(self) -> list:
return list(self.layers[0].top.mesh.bounds)
- def filenames(self):
+ def filenames(self) -> list[Path]:
layer_filenames = [layer.bottom.filename for layer in self.layers]
layer_filenames.insert(0, self.layers[0].top.filename) # file interface
return layer_filenames
@classmethod
- def from_pandas(cls, df: pd.DataFrame):
+ def from_pandas(cls, df: pd.DataFrame) -> "LayerSet":
"""Create a LayerSet from a Pandas DataFrame."""
Row = namedtuple("Row", ["material_id", "mesh", "resolution"])
surfaces = [
@@ -79,7 +79,7 @@ class LayerSet(BoundarySet):
]
return cls(layers=base_layer)
- def create_raster(self, resolution):
+ def create_raster(self, resolution: float) -> tuple[Path, Path]:
"""
Create raster representations for the LayerSet.
@@ -103,7 +103,7 @@ class LayerSet(BoundarySet):
file.write("\n".join(str(item) for item in raster_set))
return raster_vtu, rastered_layers_txt
- def create_rasters(self, resolution: int) -> list[Path]:
+ def create_rasters(self, resolution: float) -> list[Path]:
"""
For each surface a (temporary) raster file with given resolution is created.
"""
diff --git a/ogstools/meshlib/boundary_subset.py b/ogstools/meshlib/boundary_subset.py
index d297b4fc7..ef74fc93e 100644
--- a/ogstools/meshlib/boundary_subset.py
+++ b/ogstools/meshlib/boundary_subset.py
@@ -21,9 +21,7 @@ class Surface:
return self._material_id
@typechecked
- def __init__(
- self, input: Union[Path, pv.UnstructuredGrid], material_id: int
- ):
+ def __init__(self, input: Union[Path, pv.DataObject], material_id: int):
"""Initialize a surface mesh. Either from pyvista or from a file."""
self._material_id = material_id
@@ -33,7 +31,7 @@ class Surface:
msg = f"{self.filename} does not exist."
raise ValueError(msg)
self.mesh = pv.get_reader(self.filename).read()
- elif isinstance(input, pv.UnstructuredGrid):
+ elif isinstance(input, pv.DataObject):
self.mesh = input
self.filename = Path(tempfile.mkstemp(".vtu", "surface")[1])
pv.save_meshio(self.filename, self.mesh, file_format="vtu")
@@ -42,7 +40,7 @@ class Surface:
np.ones(self.mesh.n_cells) * self.material_id
).astype(np.int32)
- def __eq__(self, other):
+ def __eq__(self, other: object) -> bool:
return self.__dict__ == other.__dict__
def create_raster_file(self, resolution: float) -> Path:
@@ -76,7 +74,7 @@ def Gaussian2D(
spread: float,
height_offset: float,
n: int,
-):
+) -> pv.DataSet:
"""
Generate a 2D Gaussian-like surface using the provided parameters.
diff --git a/ogstools/meshlib/gmsh_meshing.py b/ogstools/meshlib/gmsh_meshing.py
index c58cb076d..c985a5000 100644
--- a/ogstools/meshlib/gmsh_meshing.py
+++ b/ogstools/meshlib/gmsh_meshing.py
@@ -9,7 +9,7 @@ def _geo_square(
lengths: Union[float, list[float]],
n_edge_cells: Union[int, list[int]],
structured: bool,
-):
+) -> None:
_lengths = lengths if isinstance(lengths, list) else [lengths] * 2
_n = n_edge_cells if isinstance(n_edge_cells, list) else [n_edge_cells] * 2
geo.addPoint(0, 0, 0, tag=1)
@@ -41,7 +41,7 @@ def rect(
structured_grid: bool = True,
order: int = 1,
out_name: Path = Path("unit_square.msh"),
-):
+) -> None:
gmsh.initialize()
gmsh.option.set_number("General.Verbosity", 0)
gmsh.model.add("unit_square")
@@ -75,7 +75,7 @@ def cuboid(
structured_grid: bool = True,
order: int = 1,
out_name: Path = Path("unit_cube.msh"),
-):
+) -> None:
gmsh.initialize()
gmsh.option.set_number("General.Verbosity", 0)
gmsh.model.add("unit_cube")
@@ -118,7 +118,7 @@ def bhe_mesh(
bhe_depth: float = 20,
order: int = 1,
out_name: Path = Path("bhe_mesh.msh"),
-):
+) -> None:
gmsh.initialize()
model, geo = (gmsh.model, gmsh.model.geo)
model.add(Path(out_name).stem)
diff --git a/ogstools/meshlib/mesh_series.py b/ogstools/meshlib/mesh_series.py
index 7021fed53..c7dd4a5d9 100644
--- a/ogstools/meshlib/mesh_series.py
+++ b/ogstools/meshlib/mesh_series.py
@@ -7,6 +7,7 @@ import meshio
import numpy as np
import pyvista as pv
import vtuIO
+from h5py import File
from scipy.interpolate import LinearNDInterpolator, NearestNDInterpolator
from tqdm.auto import tqdm
@@ -55,7 +56,7 @@ class MeshSeries:
raise TypeError(msg)
@property
- def hdf5(self):
+ def hdf5(self) -> File:
# We assume there is only one h5 file
return next(iter(self._xdmf_reader.hdf5_files.values()))
@@ -225,7 +226,7 @@ class MeshSeries:
data_name: str,
interp_method: Optional[Literal["nearest", "probefilter"]] = None,
interp_backend: Optional[Literal["vtk", "scipy"]] = None,
- ):
+ ) -> np.ndarray:
obs_pts_dict = {f"pt{j}": point for j, point in enumerate(points)}
dim = self.read(0).get_cell(0).dimension
pvd_path = self.filepath
@@ -242,7 +243,7 @@ class MeshSeries:
points: np.ndarray,
data_name: str,
interp_method: Optional[Literal["nearest", "linear"]] = None,
- ):
+ ) -> np.ndarray:
values = self.hdf5["meshes"][self.hdf5_bulk_name][data_name][:]
geom = self.hdf5["meshes"][self.hdf5_bulk_name]["geometry"][0]
values = np.swapaxes(values, 0, 1)
diff --git a/ogstools/meshlib/region/region.py b/ogstools/meshlib/region/region.py
index dd308bd62..ac6e4b8dc 100644
--- a/ogstools/meshlib/region/region.py
+++ b/ogstools/meshlib/region/region.py
@@ -7,7 +7,7 @@ import numpy as np
import pyvista as pv
from ogs import cli
-from ..boundary_set import LayerSet
+from ..boundary_set import Layer, LayerSet
class RegionSet:
@@ -26,7 +26,7 @@ class RegionSet:
self.filename = Path(tempfile.mkstemp(".vtu", "region_set")[1])
self.mesh = input
- def box_boundaries(self):
+ def box_boundaries(self) -> tuple[pv.UnstructuredGrid, ...]:
"""
Retrieve the boundaries of the mesh in local coordinate system (u, v, w).
@@ -46,6 +46,7 @@ class RegionSet:
mesh = ...
u_min, u_max, v_min, v_max, w_min, w_max = mesh.box_boundaries()
"""
+ assert isinstance(self.mesh, pv.UnstructuredGrid)
surface = self.mesh.extract_surface()
u_max = to_boundary(surface, lambda normals: normals[:, 0] > 0.5)
u_min = to_boundary(surface, lambda normals: normals[:, 0] < -0.5)
@@ -152,7 +153,7 @@ def to_region_prism(layer_set: LayerSet, resolution: float) -> RegionSet:
def layer_to_simplified_mesh(
- layer, resolution: float, rank: int, bounds: list[float]
+ layer: Layer, resolution: float, rank: int, bounds: list[float]
) -> pv.UnstructuredGrid:
"""Convert a geological layer to a simplified mesh.
diff --git a/ogstools/meshlib/xdmf_reader.py b/ogstools/meshlib/xdmf_reader.py
index 6f1b49b57..c82d49041 100644
--- a/ogstools/meshlib/xdmf_reader.py
+++ b/ogstools/meshlib/xdmf_reader.py
@@ -15,6 +15,8 @@ to be read like::
"""
+from xml.etree.ElementTree import Element
+
import meshio
import numpy as np
from meshio.xdmf.time_series import (
@@ -25,10 +27,10 @@ from meshio.xdmf.time_series import (
class XDMFReader(meshio.xdmf.TimeSeriesReader):
- def __init__(self, filename):
+ def __init__(self, filename: str):
super().__init__(filename)
- def read_data(self, k: int):
+ def read_data(self, k: int) -> tuple[float, dict, dict, dict]:
point_data = {}
cell_data_raw = {}
other_data = {}
@@ -67,8 +69,8 @@ class XDMFReader(meshio.xdmf.TimeSeriesReader):
return t, point_data, cell_data, other_data
- def _read_data_item(self, data_item):
- dims = [int(d) for d in data_item.get("Dimensions").split()]
+ def _read_data_item(self, data_item: Element) -> np.ndarray:
+ dims = [int(d) for d in data_item.get("Dimensions", "").split()]
# Actually, `NumberType` is XDMF2 and `DataType` XDMF3, but many files out there
# use both keys interchangeably.
@@ -92,6 +94,7 @@ class XDMFReader(meshio.xdmf.TimeSeriesReader):
data_format = data_item.attrib["Format"]
+ assert isinstance(data_item.text, str)
if data_format == "XML":
return np.fromstring(
data_item.text,
diff --git a/ogstools/meshplotlib/animation.py b/ogstools/meshplotlib/animation.py
index d21069933..e05db2f6a 100644
--- a/ogstools/meshplotlib/animation.py
+++ b/ogstools/meshplotlib/animation.py
@@ -44,7 +44,7 @@ def animate(
index = np.argmin(np.abs(np.asarray(ts) - i))
fig.axes[-1].remove() # remove colorbar
- for ax in np.ravel(fig.axes):
+ for ax in np.ravel(np.asarray(fig.axes)):
ax.clear()
if titles is not None:
setup.title_center = titles[index]
@@ -54,18 +54,20 @@ def animate(
mesh = mesh_series.read_interp(i, True)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
- fig = _draw_plot(mesh, property, fig=fig)
+ fig = _draw_plot(
+ mesh, property, fig=fig
+ ) # type: ignore[assignment]
_func = partial(animate_func, fig=fig)
return FuncAnimation(
- fig,
- _func,
+ fig, # type: ignore[arg-type]
+ _func, # type: ignore[arg-type]
frames=tqdm(ts),
blit=False,
interval=50,
repeat=False,
- init_func=init,
+ init_func=init, # type: ignore[arg-type]
)
@@ -83,7 +85,7 @@ def save_animation(anim: FuncAnimation, filename: str, fps: int) -> bool:
"-vf pad=ceil(iw/2)*2:ceil(ih/2)*2"
).split(" ")
- writer = None
+ writer: Optional[Union[FFMpegWriter, ImageMagickWriter]] = None
if FFMpegWriter.isAvailable():
writer = FFMpegWriter(fps=fps, codec="libx265", extra_args=codec_args)
filename += ".mp4"
@@ -91,7 +93,7 @@ def save_animation(anim: FuncAnimation, filename: str, fps: int) -> bool:
print("\nffmpeg not available. It is recommended for saving animation.")
filename += ".gif"
if ImageMagickWriter.isAvailable():
- writer = "imagemagick"
+ writer = ImageMagickWriter()
else:
print(
"ImageMagick also not available. Falling back to"
diff --git a/ogstools/meshplotlib/core.py b/ogstools/meshplotlib/core.py
index ca139bbfa..8fe6ac039 100644
--- a/ogstools/meshplotlib/core.py
+++ b/ogstools/meshplotlib/core.py
@@ -2,7 +2,7 @@
import warnings
from math import nextafter
-from typing import Literal, Optional, Union
+from typing import Any, Literal, Optional, Union
import numpy as np
import pyvista as pv
@@ -28,13 +28,13 @@ from .utils import get_style_cycler
# TODO: define default data_name for regions in setup
-def _q_zero_line(mesh_property: Property, levels: np.ndarray):
+def _q_zero_line(mesh_property: Property, levels: np.ndarray) -> bool:
return mesh_property.bilinear_cmap or (
mesh_property.data_name == "temperature" and levels[0] < 0 < levels[-1]
)
-def get_level_boundaries(levels: np.ndarray):
+def get_level_boundaries(levels: np.ndarray) -> np.ndarray:
return np.array(
[
levels[0] - 0.5 * (levels[1] - levels[0]),
@@ -57,6 +57,7 @@ def get_cmap_norm(
continuous_cmap = colormaps[mesh_property.cmap]
else:
continuous_cmap = mesh_property.cmap
+ conti_norm: Union[mcolors.TwoSlopeNorm, mcolors.Normalize]
if mesh_property.bilinear_cmap:
if vmin <= 0.0 <= vmax:
vcenter = 0.0
@@ -258,9 +259,13 @@ def subplot(
cmap, norm = get_cmap_norm(levels, mesh_property)
if mesh_property.data_name in mesh.point_data:
- ax.tricontourf(x, y, tri, values, levels=levels, cmap=cmap, norm=norm)
+ ax.tricontourf( # type: ignore[call-overload]
+ x, y, tri, values, levels=levels, cmap=cmap, norm=norm
+ )
if _q_zero_line(mesh_property, levels):
- ax.tricontour(x, y, tri, values, levels=[0], colors="w")
+ ax.tricontour( # type: ignore[call-overload]
+ x, y, tri, values, levels=[0], colors="w"
+ )
else:
ax.tripcolor(x, y, tri, facecolors=values, cmap=cmap, norm=norm)
if mesh_property.is_mask():
@@ -299,7 +304,9 @@ def subplot(
sec_labels += [""]
# TODO: use a function to make this short
secax = ax.secondary_xaxis("top")
- secax.xaxis.set_major_locator(mticker.FixedLocator(ax.get_xticks()))
+ secax.xaxis.set_major_locator(
+ mticker.FixedLocator(list(ax.get_xticks()))
+ )
secax.set_xticklabels(sec_labels)
secax.set_xlabel(f'{"xyz"[projection]} / {setup.length.output_unit}')
@@ -419,21 +426,21 @@ def _draw_plot(
meshes: Union[list[pv.UnstructuredGrid], np.ndarray, pv.UnstructuredGrid],
mesh_property: Property,
fig: Optional[mfigure.Figure] = None,
- ax: Optional[plt.Axes] = None,
-) -> mfigure.Figure:
+ axes: Optional[plt.Axes] = None,
+) -> Optional[mfigure.Figure]:
"""
Plot the property field of meshes on existing figure.
:param meshes: Singular mesh of 2D numpy array of meshes
:param property: the property field to be visualized on all meshes
- :param fig: Matplotlib Figure object to use for plotting (optional)
- :param ax: Matplotlib Axis object to use for plotting (optional)
+ :param fig: Matplotlib figure to use for plotting (optional)
+ :param axes: Matplotlib Axes to use for plotting (optional)
"""
shape = _get_rows_cols(meshes)
np_meshes = np.reshape(meshes, shape)
- if fig is not None and ax is not None:
- np_axs = np.reshape(np.array(ax), shape)
- elif fig is not None and ax is None:
+ if fig is not None and axes is not None:
+ np_axs = np.reshape(np.array(axes), shape)
+ elif fig is not None and axes is None:
# Only Fig is given
# Multiple meshes should be accepted
warnings.warn(
@@ -441,14 +448,14 @@ def _draw_plot(
Warning,
stacklevel=4,
)
- np_axs = np.reshape(fig.axes, shape)
- elif fig is None and ax is not None:
+ np_axs = np.reshape(np.asarray(fig.axes), shape)
+ elif fig is None and axes is not None:
# Only ax is given
# Only one mesh should be accepted
if shape != (1, 1):
msg = "You have provided only one Axis object but multiple meshes. Provide only one mesh per Axis object, or provide Figure object instead."
raise ValueError(msg)
- np_axs = np.reshape(np.array(ax), (1, 1))
+ np_axs = np.reshape(np.array(axes), (1, 1))
else:
msg = "Neither Figure nor Axis object was provided."
raise TypeError(msg)
@@ -459,14 +466,14 @@ def _draw_plot(
_levels = (
combined_levels
if setup.combined_colorbar
- else get_combined_levels([np_meshes[i, j]], mesh_property)
+ else get_combined_levels(np_meshes[i, j, None], mesh_property)
)
subplot(np_meshes[i, j], mesh_property, np_axs[i, j], _levels)
x_id, y_id = get_projection(
np_meshes[0, 0]
) # One mesh is sufficient, it should be the same for all of them
- np_axs = label_spatial_axes(np_axs, np.array([x_id, y_id]))
+ label_spatial_axes(np_axs, "xyz"[x_id], "xyz"[y_id])
np_axs[0, 0].set_title(setup.title_center, loc="center", y=1.02)
np_axs[0, 0].set_title(setup.title_left, loc="left", y=1.02)
np_axs[0, 0].set_title(setup.title_right, loc="right", y=1.02)
@@ -481,7 +488,7 @@ def _draw_plot(
stacklevel=4,
)
else:
- cb_axs = np.ravel(fig.axes).tolist()
+ cb_axs = np.ravel(np.asarray(fig.axes)).tolist()
add_colorbars(
fig, cb_axs, mesh_property, combined_levels, pad=0.05 / shape[1]
)
@@ -497,7 +504,7 @@ def _draw_plot(
for i in range(shape[0]):
for j in range(shape[1]):
_levels = get_combined_levels(
- [np_meshes[i, j]], mesh_property
+ np_meshes[i, j, None], mesh_property
)
add_colorbars(fig, np_axs[i, j], mesh_property, _levels)
return fig
@@ -532,10 +539,14 @@ def update_font_sizes(
subax_xlim = subax.get_xlim()
subax_ylim = subax.get_ylim()
subax.set_xticks(
- subax.get_xticks(), subax.get_xticklabels(), fontsize=fontsize
+ subax.get_xticks(),
+ [label.get_text() for label in subax.get_xticklabels()],
+ fontsize=fontsize,
)
subax.set_yticks(
- subax.get_yticks(), subax.get_yticklabels(), fontsize=fontsize
+ subax.get_yticks(),
+ [label.get_text() for label in subax.get_yticklabels()],
+ fontsize=fontsize,
)
subax.set_xlim(subax_xlim)
subax.set_ylim(subax_ylim)
@@ -549,7 +560,7 @@ def plot(
mesh_property: Union[Property, str],
fig: Optional[mfigure.Figure] = None,
ax: Optional[plt.Axes] = None,
-) -> mfigure.Figure:
+) -> Optional[mfigure.Figure]:
"""
Plot the property field of meshes with default settings.
@@ -576,18 +587,20 @@ def plot(
n_axs = shape[0] * shape[1]
if ax is None and fig is None:
_fig, _ax = _fig_init(rows=shape[0], cols=shape[1], aspect=fig_aspect)
- fig = _draw_plot(meshes, mesh_property, fig=_fig, ax=_ax)
+ fig = _draw_plot(meshes, mesh_property, fig=_fig, axes=_ax)
+ assert isinstance(fig, plt.Figure)
for ax, aspect in zip(fig.axes[: n_axs + 1], ax_aspects):
ax.set_aspect(1.0 / aspect)
elif ax is not None and fig is None:
- _draw_plot(meshes, mesh_property, ax=ax)
+ _draw_plot(meshes, mesh_property, axes=ax)
ax.set_aspect(1.0 / ax_aspects[0])
elif ax is None and fig is not None:
fig = _draw_plot(meshes, mesh_property, fig=fig)
+ assert isinstance(fig, plt.Figure)
for ax, aspect in zip(fig.axes[: n_axs + 1], ax_aspects):
ax.set_aspect(1.0 / aspect)
elif ax is not None and fig is not None:
- _draw_plot(meshes, mesh_property, fig=fig, ax=ax)
+ _draw_plot(meshes, mesh_property, fig=fig, axes=ax)
for ax, aspect in zip(fig.axes[: n_axs + 1], ax_aspects):
ax.set_aspect(1.0 / aspect)
return fig
@@ -606,8 +619,8 @@ def plot_probe(
linestyles: Optional[list] = None,
ax: Optional[plt.Axes] = None,
fill_between: bool = False,
- **kwargs,
-) -> mfigure.Figure:
+ **kwargs: Any,
+) -> Optional[mfigure.Figure]:
"""
Plot the transient property on the observation points in the MeshSeries.
diff --git a/ogstools/meshplotlib/plot_features.py b/ogstools/meshplotlib/plot_features.py
index 5b358b30c..9a5ee911c 100644
--- a/ogstools/meshplotlib/plot_features.py
+++ b/ogstools/meshplotlib/plot_features.py
@@ -74,7 +74,9 @@ def plot_element_edges(ax: plt.Axes, surf: pv.DataSet, projection: int) -> None:
]
verts = setup.length.transform(np.delete(cell_pts, projection, -1))
lw = 0.5 * setup.rcParams_scaled["lines.linewidth"]
- pc = PolyCollection(verts, fc="None", ec="black", lw=lw)
+ pc = PolyCollection(
+ verts, fc="None", ec="black", lw=lw # type: ignore[arg-type]
+ )
ax.add_collection(pc)
@@ -131,9 +133,9 @@ def plot_streamlines(
lw = 2.5 * val_norm / max(1e-16, np.max(val_norm))
lw *= setup.rcParams_scaled["lines.linewidth"]
x_g, y_g = setup.length.transform(np.meshgrid(x, y))
- plot_args = [x_g, y_g, val[..., 0], val[..., 1]]
if plot_type == "streamlines":
- ax.streamplot(*plot_args, color="k", linewidth=lw, density=1.5)
+ ax.streamplot(x_g, y_g, val[..., 0], val[..., 1],
+ color="k", linewidth=lw, density=1.5) # fmt: skip
else:
line_args = (
dict( # noqa: C408
@@ -142,7 +144,8 @@ def plot_streamlines(
if plot_type == "lines"
else {}
)
- ax.quiver(*plot_args, **line_args, scale=1 / 0.03)
+ scale = 1.0 / 0.03
+ ax.quiver(x_g, y_g, val[..., 0], val[..., 1], **line_args, scale=scale)
def plot_on_top(
@@ -161,7 +164,7 @@ def plot_on_top(
x_vals = df_pts.groupby("x")["x"].agg(np.mean).to_numpy()
y_vals = df_pts.groupby("x")["y"].agg(np.max).to_numpy()
contour_vals = [y + scaling * contour(x) for y, x in zip(y_vals, x_vals)]
- ax.set_ylim(top=setup.length.transform(np.max(contour_vals)))
+ ax.set_ylim(top=float(setup.length.transform(np.max(contour_vals))))
ax.fill_between(
setup.length.transform(x_vals),
setup.length.transform(y_vals),
@@ -172,7 +175,7 @@ def plot_on_top(
def plot_contour(
ax: plt.Axes, mesh: pv.DataSet, style: str, lw: int, projection: int = 2
-):
+) -> None:
contour = mesh.extract_surface().strip(join=True)
x_id, y_id = np.delete([0, 1, 2], projection)
x, y = 1e-3 * contour.points[contour.lines[1:]].T[[x_id, y_id]]
diff --git a/ogstools/meshplotlib/plot_setup.py b/ogstools/meshplotlib/plot_setup.py
index d36e7f327..6c933c6b7 100644
--- a/ogstools/meshplotlib/plot_setup.py
+++ b/ogstools/meshplotlib/plot_setup.py
@@ -1,7 +1,7 @@
"""Plot configuration setup."""
from dataclasses import dataclass
-from typing import Union
+from typing import Optional, Union
from ogstools.propertylib.property import Scalar
@@ -23,9 +23,9 @@ class PlotSetup:
"The resolution (dots per inch) for the figure."
fig_scale: float
"A scaling factor for the figure."
- min_ax_aspect: float
+ min_ax_aspect: Optional[float]
"Minimum aspect ratio of subplots."
- max_ax_aspect: float
+ max_ax_aspect: Optional[float]
"Maximum aspect ratio of subplots."
invert_colorbar: bool
"A boolean indicating whether to invert the colorbar."
@@ -38,11 +38,11 @@ class PlotSetup:
num_levels: int
"""The aimed number of levels / bins of the colorbar. See
:obj:`ogstools.meshplotlib.levels`"""
- num_streamline_interp_pts: int
+ num_streamline_interp_pts: Optional[int]
"The number of interpolation points for streamlines."
- p_max: float
+ p_max: Optional[float]
"The fixed upper limit for the current scale."
- p_min: float
+ p_min: Optional[float]
"The fixed lower limit for the current scale."
rcParams: dict
"""Matplotlib runtime configuration. See
@@ -78,7 +78,7 @@ class PlotSetup:
return params
@classmethod
- def from_dict(cls: type["PlotSetup"], obj: dict):
+ def from_dict(cls: type["PlotSetup"], obj: dict) -> "PlotSetup":
"""Create a PlotSetup instance from a dictionary."""
return cls(
fig_scale=obj["fig_scale"],
diff --git a/ogstools/meshplotlib/utils.py b/ogstools/meshplotlib/utils.py
index e31ce760c..8cdc448c9 100644
--- a/ogstools/meshplotlib/utils.py
+++ b/ogstools/meshplotlib/utils.py
@@ -2,12 +2,13 @@ from typing import Optional
import matplotlib.pyplot as plt
import numpy as np
+from cycler import Cycler
def justified_labels(points: np.ndarray) -> list[str]:
"Formats an array of points to a list of aligned str."
- def fmt(val: float):
+ def fmt(val: float) -> str:
return f"{val:.2f}".rstrip("0").rstrip(".")
col_lens = np.max(
@@ -24,7 +25,7 @@ def get_style_cycler(
min_number_of_styles: int,
colors: Optional[Optional[list]] = None,
linestyles: Optional[list] = None,
-) -> plt.cycler:
+) -> Cycler:
if colors is None:
colors = plt.rcParams["axes.prop_cycle"].by_key()["color"]
if linestyles is None:
diff --git a/ogstools/msh2vtu/__init__.py b/ogstools/msh2vtu/__init__.py
index ac2a24d6e..251124ed3 100644
--- a/ogstools/msh2vtu/__init__.py
+++ b/ogstools/msh2vtu/__init__.py
@@ -1,7 +1,7 @@
# Author: Dominik Kern (TU Bergakademie Freiberg)
import logging
from pathlib import Path
-from typing import Union
+from typing import Any, Union
import meshio
import numpy as np
@@ -18,7 +18,7 @@ __all__ = [
]
-def my_remove_orphaned_nodes(my_mesh: meshio.Mesh):
+def my_remove_orphaned_nodes(my_mesh: meshio.Mesh) -> None:
"""Auxiliary function to remove points not belonging to any cell"""
# find connected points and derive mapping from all points to them
@@ -51,11 +51,9 @@ def my_remove_orphaned_nodes(my_mesh: meshio.Mesh):
# cell data are not affected by point changes
my_mesh.cells = output_cell_blocks # update cells
- return
-
# print info for mesh: statistics and data field names
-def print_info(mesh: meshio.Mesh):
+def print_info(mesh: meshio.Mesh) -> None:
N, D = mesh.points.shape
logging.info("%d points in %d dimensions", N, D)
cell_info = "cells: "
@@ -70,13 +68,15 @@ def print_info(mesh: meshio.Mesh):
# function to create node connectivity list, i.e. store for each node (point) to
# which element (cell) it belongs
-def find_cells_at_nodes(cells, node_count, cell_start_index):
+def find_cells_at_nodes(
+ cells: Any, node_count: int, cell_start_index: int
+) -> list[set]:
# depending on the numbering of mixed meshes in OGS one may think of an
# object-oriented way to add elements (of different type) to node
# connectivity
# initialize list of sets
- node_connectivity = [set() for _ in range(node_count)]
+ node_connectivity: list[set] = [set() for _ in range(node_count)]
cell_index = cell_start_index
for cell in cells:
for node in cell:
@@ -95,7 +95,7 @@ def find_cells_at_nodes(cells, node_count, cell_start_index):
# function to find out to which domain elements a boundary element belongs
def find_connected_domain_cells(
- boundary_cells_values, domain_cells_at_node
+ boundary_cells_values: Any, domain_cells_at_node: list[set[int]]
) -> tuple[np.ndarray, np.ndarray]:
warned_gt1 = False # to avoid flood of warnings
warned_lt1 = False # to avoid flood of warnings
@@ -160,7 +160,7 @@ def msh2vtu(
keep_ids: bool = False,
ascii: bool = False,
log_level: Union[int, str] = "DEBUG",
-):
+) -> int:
"""
Convert a gmsh mesh (.msh) to an unstructured grid file (.vtu).
diff --git a/ogstools/propertylib/property.py b/ogstools/propertylib/property.py
index 26a2381ba..0ee376e00 100644
--- a/ogstools/propertylib/property.py
+++ b/ogstools/propertylib/property.py
@@ -7,7 +7,7 @@ via pint.
from collections.abc import Sequence
from dataclasses import dataclass, replace
-from typing import Callable, Union
+from typing import Any, Callable, Union
import numpy as np
import pyvista as pv
@@ -46,15 +46,15 @@ class Property:
categoric: bool = False
"""Does this property only have categoric values?"""
- def __post_init__(self):
+ def __post_init__(self) -> None:
if not self.output_name:
self.output_name = self.data_name
@property
- def type_name(self):
+ def type_name(self) -> str:
return type(self).__name__
- def replace(self, **changes):
+ def replace(self: "Property", **changes: Any) -> "Property":
"""
Create a new Property object with modified attributes.
@@ -68,7 +68,9 @@ class Property:
return replace(self, **changes)
@classmethod
- def from_property(cls, new_property: "Property", **changes):
+ def from_property( # type: ignore[no-untyped-def]
+ cls, new_property: "Property", **changes: Any
+ ):
"Create a new Property object with modified attributes."
return cls(
data_name=new_property.data_name,
@@ -151,7 +153,7 @@ class Property:
"""
return self.data_name == self.mask
- def get_mask(self):
+ def get_mask(self) -> "Property":
"""
:returns: A property representing this properties mask.
"""
diff --git a/ogstools/studies/convergence/convergence.py b/ogstools/studies/convergence/convergence.py
index 9cc39ac75..c5282ecfa 100644
--- a/ogstools/studies/convergence/convergence.py
+++ b/ogstools/studies/convergence/convergence.py
@@ -148,7 +148,7 @@ def convergence_metrics(
:returns: A pandas Dataframe containing all metrics.
"""
- def _data(m: pv.UnstructuredGrid):
+ def _data(m: pv.UnstructuredGrid) -> np.ndarray:
return mesh_property.magnitude.transform(
m.point_data[mesh_property.data_name]
)
@@ -304,7 +304,9 @@ def convergence_metrics_evolution(
.to(units[1])
.magnitude
)
- p_metrics_per_t = np.concatenate(([time_vals], p_metrics_per_t.T)).T
+ p_metrics_per_t = np.concatenate(
+ (np.asarray([time_vals]), p_metrics_per_t.T)
+ ).T
columns = ["timevalue"] + [
f"{t} ({x})"
for t in ["abs. error", "rel. error", "p"]
diff --git a/ogstools/studies/convergence/examples/steady_state_diffusion.py b/ogstools/studies/convergence/examples/steady_state_diffusion.py
index 88be208ea..aba217301 100644
--- a/ogstools/studies/convergence/examples/steady_state_diffusion.py
+++ b/ogstools/studies/convergence/examples/steady_state_diffusion.py
@@ -6,15 +6,15 @@ import numpy as np
import pyvista as pv
-def _c_k(k):
+def _c_k(k: float) -> float:
return 0.5 * (2 * k - 1) * np.pi
-def _a_k(k):
+def _a_k(k: float) -> float:
return 2 / (_c_k(k) ** 2 * np.cosh(_c_k(k)))
-def _h(points):
+def _h(points: np.ndarray) -> np.ndarray:
result = np.ones(len(points))
for k in np.arange(1, 100):
c_k_val = _c_k(k)
--
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