Refactor droplet classes to improve code readability and consistency (#…

…67)

* Refactor droplet classes to improve code readability and consistency

* Fixed bug in displaying perturbed droplets
* Improved testing with bare py.test

droplets/droplets.py

@@ -866,7 +866,7 @@ def _get_mpl_patch(self, dim=None, *, color=None, **kwargs):
 
 
 class PerturbedDroplet2D(PerturbedDropletBase):
-    r"""Represents a single droplet in two dimensions with a perturbed shape.
+    r"""Represents a single 2D droplet with a perturbed shape.
 
     The shape is described using the distance :math:`R(\phi)` of the interface from the
     `position`, which is a function of the polar angle :math:`\phi`. This function is
@@ -946,7 +946,7 @@ def interface_position(self, φ: np.ndarray) -> np.ndarray:
             Array with coordinates of interfacial points associated with each angle φ
         """
         dist = self.interface_distance(φ)
-        pos = dist[:, None] * np.transpose([np.sin(φ), np.cos(φ)])
+        pos = dist[:, None] * np.transpose([np.cos(φ), np.sin(φ)])
         return self.position[None, :] + pos  # type: ignore
 
     @preserve_scalars
@@ -1044,7 +1044,7 @@ def _get_mpl_patch(self, dim=2, **kwargs):
 
 
 class PerturbedDroplet3D(PerturbedDropletBase):
-    r"""Represents a single droplet in three dimensions with a perturbed shape.
+    r"""Represents a single 3D droplet with a perturbed shape.
 
     The shape is described using the distance :math:`R(\theta, \phi)` of the interface
     from the origin as a function of the azimuthal angle :math:`\theta` and the polar
@@ -1205,7 +1205,7 @@ def volume_approx(self) -> float:
 
 
 class PerturbedDroplet3DAxisSym(PerturbedDropletBase):
-    r"""Represents a droplet axisymmetrically perturbed shape in three dimensions.
+    r"""Represents a 3D droplet with axisymmetrically perturbed shape.
 
     The shape is described using the distance :math:`R(\theta)` of the interface from
     the origin as a function of the azimuthal angle :math:`\theta`, while polar symmetry

droplets/image_analysis.py

@@ -541,8 +541,8 @@ def refine_droplet(
     phase_field: ScalarField,
     droplet: DiffuseDroplet,
     *,
-    vmin: float = 0.0,
-    vmax: float = 1.0,
+    vmin: float | None = 0.0,
+    vmax: float | None = 1.0,
     adjust_values: bool = False,
     tolerance: float | None = None,
     least_squares_params: dict[str, Any] | None = None,
@@ -565,7 +565,7 @@ def refine_droplet(
         vmax (float):
             The intensity value inside the droplet. If `None`, the value will be
             determined automatically.
-        adjust_value (bool):
+        adjust_values (bool):
             Flag determining whether the intensity values will be included in the
             fitting procedure. The default value `False` implies that the intensity
             values are regarded fixed.

tests/conftest.py

@@ -24,6 +24,8 @@ def init_random_number_generators():
 @pytest.fixture(scope="function", autouse=True)
 def setup_and_teardown():
     """Helper function adjusting environment before and after tests."""
+    # ensure we use the Agg backend, so figures are not displayed
+    plt.switch_backend("agg")
     # raise all underflow errors
     np.seterr(all="raise", under="ignore")
 

tests/test_examples.py

@@ -31,6 +31,7 @@ def test_example(path):
 
     env = os.environ.copy()
     env["PYTHONPATH"] = str(PACKAGE_PATH) + ":" + env.get("PYTHONPATH", "")
+    env["MPLBACKEND"] = "agg"
     proc = sp.Popen([sys.executable, path], env=env, stdout=sp.PIPE, stderr=sp.PIPE)
     try:
         outs, errs = proc.communicate(timeout=30)