Merge branch 'small_tweaks' into 'main'

Small tweaks

See merge request ogs/tools/ogstools!113

ogstools/meshplotlib/animation.py

-import time
 import warnings
 from collections.abc import Sequence
 from functools import partial
@@ -79,7 +78,6 @@ def save_animation(anim: FuncAnimation, filename: str, fps: int) -> bool:
     :param filename:    the name of the resulting file
     :param fps:         the number of frames per second
     """
-    start_time = time.time()
     print("Start saving animation...")
     codec_args = (
         "-crf 28 -preset ultrafast -pix_fmt yuv420p "
@@ -102,8 +100,7 @@ def save_animation(anim: FuncAnimation, filename: str, fps: int) -> bool:
             )
     try:
         anim.save(filename, writer=writer)
-        print("\ndone!")
-        print(f"Elapsed time: {(time.time() - start_time):.2f}")
+        print("Successful!")
         return True
     except Exception as err:
         print("\nSaving Animation failed with the following error:")

ogstools/meshplotlib/levels.py

@@ -51,7 +51,10 @@ def get_levels(lower: float, upper: float, n_ticks: int) -> np.ndarray:
     The length of the arrays will be close to n_ticks.
     At the boundaries the tickspacing may differ from the remaining array.
     """
-    if np.abs(upper - lower) <= 1e-6:
-        return lower + np.array([0.0, 1e-6])
+    n_digits = 6
+    if lower * (1 - 10**-n_digits) <= upper <= lower * (1 + 10**-n_digits):
+        return lower + np.array([0.0, 10**-n_digits])
     levels = nice_range(lower, upper, n_ticks)
-    return np.append(np.append(lower, adaptive_rounding(levels, 6)), upper)
+    return np.unique(
+        np.append(np.append(lower, adaptive_rounding(levels, n_digits)), upper)
+    )

ogstools/meshplotlib/plot_features.py

@@ -31,7 +31,7 @@ def plot_layer_boundaries(
             x_b, y_b = setup.length.strip_units(
                 edges.points[edges.lines % edges.n_points].T[[x_id, y_id]]
             )
-            lw = 0.5 * setup.rcParams_scaled["lines.linewidth"]
+            lw = setup.rcParams_scaled["lines.linewidth"]
             ax.plot(x_b, y_b, "-k", lw=lw)
         x_pos = 0.01 if mat_id % 2 == 0 else 0.99
         ha = "left" if mat_id % 2 == 0 else "right"

ogstools/propertylib/property.py

@@ -9,18 +9,12 @@ from dataclasses import dataclass, replace
 from typing import Any, Callable, Union
 
 import numpy as np
-from pint import UnitRegistry
 from pint.facets.plain import PlainQuantity
 
+from .unit_registry import u_reg
 from .utils import identity, sym_tensor_to_mat
 from .vector2scalar import trace
 
-u_reg: UnitRegistry = UnitRegistry(
-    preprocessors=[lambda s: s.replace("%", "percent")]
-)
-u_reg.default_format = "~.12g"
-u_reg.setup_matplotlib(True)
-
 
 # TODO: rename to BaseProperty?? / GenericProperty
 @dataclass

ogstools/propertylib/unit_registry.py

+from pint import UnitRegistry
+
+u_reg: UnitRegistry = UnitRegistry(
+    preprocessors=[lambda s: s.replace("%", "percent")]
+)
+u_reg.default_format = "~.12g"
+u_reg.setup_matplotlib(True)

tests/test_meshplotlib.py

@@ -34,6 +34,8 @@ class MeshplotlibTest(unittest.TestCase):
         equality(get_levels(1e-3, 1.2, 5), [1e-3, *np.arange(0.2, 1.4, 0.2)])
         equality(get_levels(1e5, 9e6, 20), [1e5, *np.arange(5e5, 9.5e6, 5e5)])
         equality(get_levels(1, 40, 20), [1, *range(2, 42, 2)])
+        equality(get_levels(0.0, 0.0, 10), [0.0, 1e-6])
+        equality(get_levels(1e9, 1e9, 10), [1e9, 1e9 + 1e-6])
 
     def test_missing_data(self):
         """Test missing data in mesh."""

tests/test_msh2vtu.py

@@ -11,7 +11,8 @@ from unittest.mock import patch
 
 import meshio
 
-from ogstools import meshlib, msh2vtu
+from ogstools.meshlib import gmsh_meshing
+from ogstools.msh2vtu import msh2vtu
 from ogstools.msh2vtu._cli import cli
 
 
@@ -24,14 +25,14 @@ def test_rect(tmp_path: Path):
     msh_file = Path(tmp_path, "rect.msh")
     permutations = product([1.0, 2.0], [1, 2], [True, False], [1, 2])
     for edge_length, n_edge_cells, structured, order in permutations:
-        meshlib.gmsh_meshing.rect(
+        gmsh_meshing.rect(
             lengths=edge_length,
             n_edge_cells=n_edge_cells,
             structured_grid=structured,
             order=order,
             out_name=msh_file,
         )
-        assert msh2vtu.msh2vtu(msh_file, tmp_path, output_prefix="rect") == 0
+        assert msh2vtu(msh_file, tmp_path, output_prefix="rect") == 0
 
 
 def test_cuboid(tmp_path: Path):
@@ -39,14 +40,14 @@ def test_cuboid(tmp_path: Path):
     msh_file = Path(tmp_path, "cuboid.msh")
     permutations = product([1.0, 2.0], [1, 2], [True, False], [1, 2])
     for edge_length, n_edge_cells, structured, order in permutations:
-        meshlib.gmsh_meshing.cuboid(
+        gmsh_meshing.cuboid(
             lengths=edge_length,
             n_edge_cells=n_edge_cells,
             structured_grid=structured,
             order=order,
             out_name=msh_file,
         )
-        assert msh2vtu.msh2vtu(msh_file, tmp_path, output_prefix="cuboid") == 0
+        assert msh2vtu(msh_file, tmp_path, output_prefix="cuboid") == 0
 
 
 def test_gmsh(tmp_path: Path):
@@ -60,7 +61,7 @@ def test_gmsh(tmp_path: Path):
         runpy.run_module(f"ogstools.msh2vtu.examples.gmsh.{Path(script).stem}")
         prefix = str(Path(script).stem)
         msh_file = Path(tmp_path, prefix + ".msh")
-        assert msh2vtu.msh2vtu(msh_file, tmp_path, output_prefix=prefix) == 0
+        assert msh2vtu(msh_file, tmp_path, output_prefix=prefix) == 0
     testargs = ["msh2vtu", str(msh_file), "-o", str(tmp_path), "-p", prefix]
     with patch.object(sys, "argv", testargs):
         cli()

tests/test_studies_convergence.py

@@ -8,7 +8,9 @@ from tempfile import mkdtemp
 import numpy as np
 from ogs6py import ogs
 
-from ogstools import meshlib, msh2vtu, propertylib
+from ogstools.meshlib import MeshSeries, gmsh_meshing
+from ogstools.msh2vtu import msh2vtu
+from ogstools.propertylib import Scalar
 from ogstools.studies import convergence
 from ogstools.studies.convergence.examples import (
     steady_state_diffusion_analytical_solution,
@@ -24,12 +26,12 @@ class ConvergenceTest(unittest.TestCase):
         edge_cells = [2**i for i in range(3, 6)]
         for n_edge_cells in edge_cells:
             msh_path = temp_dir / "square.msh"
-            meshlib.gmsh_meshing.rect(
+            gmsh_meshing.rect(
                 n_edge_cells=n_edge_cells,
                 structured_grid=True,
                 out_name=msh_path,
             )
-            msh2vtu.msh2vtu(
+            msh2vtu(
                 input_filename=msh_path, output_path=temp_dir, log_level="ERROR"
             )
             model = ogs.OGS(
@@ -42,13 +44,13 @@ class ConvergenceTest(unittest.TestCase):
             ogs_args = f"-m {temp_dir} -o {temp_dir}"
             model.run_model(write_logs=False, args=ogs_args)
             sim_results += [
-                meshlib.MeshSeries(str(temp_dir / (prefix + ".pvd"))).read(-1)
+                MeshSeries(str(temp_dir / (prefix + ".pvd"))).read(-1)
             ]
 
         topology = sim_results[-3]
         spacing = convergence.add_grid_spacing(topology)["grid_spacing"]
         np.testing.assert_array_less(0.0, spacing)
-        mesh_property = propertylib.Scalar("pressure", "m", "m")
+        mesh_property = Scalar("pressure", "m", "m")
         conv = convergence.grid_convergence(
             sim_results, mesh_property, topology, refinement_ratio=2.0
         )