doc: change reference section style

src/dipcoatimage/finitedepth/polysubstrate.py

@@ -54,8 +54,8 @@ class PolySubstrateBase(
 ):
     """Abstract base class for substrate whose cross section is a simple polygon.
 
-    A simple polygon does not have intersection nor hole [#simple-polygon]_.
-    Smooth corners are allowed.
+    A simple polygon does not have intersection nor hole. Smooth corners are
+    allowed.
 
     The following substrate images are not supported:
 
@@ -76,7 +76,7 @@ class PolySubstrateBase(
         draw_options
 
     References:
-        .. [#simple-polygon] https://en.wikipedia.org/wiki/Simple_polygon
+        * https://en.wikipedia.org/wiki/Simple_polygon
     """
 
     SidesNum: int
@@ -103,22 +103,22 @@ def contour(self) -> npt.NDArray[np.int32]:
     def vertices(self) -> npt.NDArray[np.int32]:
         """Find vertices of the polygon from its contour.
 
-        A vertex is a point where two sides of a polygon meet[#vertex-geom]_.
+        A vertex is a point where two sides of a polygon meet.
         The sides can be curves, where the vertices can be defined as local
-        extrema of curvature [#vertex-curve]_.
+        extrema of curvature.
 
         Returns:
             Indices of the vertex points in :meth:`contour`.
             The number of the vertices is defined by :attr:`SidesNum`.
 
         Note:
-            Contour is Gaussian-filtered to reduce noise[#so-curvature]_.
+            Contour is Gaussian-filtered to reduce noise.
             Sigma value of the kernel is determined from :attr:`parameters`.
 
         References:
-            .. [#vertex-geom] https://en.wikipedia.org/wiki/Vertex_(geometry)
-            .. [#vertex-curve] https://en.wikipedia.org/wiki/Vertex_(curve)
-            .. [#so-curvature] https://stackoverflow.com/q/32629806
+            * https://en.wikipedia.org/wiki/Vertex_(geometry)
+            * https://en.wikipedia.org/wiki/Vertex_(curve)
+            * https://stackoverflow.com/q/32629806
         """
         cnt = self.contour().astype(np.float64)
 
@@ -171,14 +171,14 @@ def sides(self) -> Tuple[npt.NDArray[np.int32], ...]:
     def sidelines(self) -> npt.NDArray[np.float32]:
         r"""Find linear model of polygon sides.
 
-        This method finds straight sidelines [#extended-side]_ using
-        Hough line transformation. Radian and angle resolutions are determined
-        by :attr:`parameters`.
+        This method finds straight sidelines using Hough line transformation.
+        Radian and angle resolutions are determined by :attr:`parameters`.
 
         Returns:
             Vector of line parameters in :math:`(\rho, \theta)`.
             :math:`\rho` is the distance from the coordinate origin.
-            :math:`\theta` is the angle of normal vector from the origin to the line.
+            :math:`\theta` is the angle of normal vector from the origin
+            to the line.
 
         Note:
             Range of angle is
@@ -187,7 +187,7 @@ def sidelines(self) -> npt.NDArray[np.float32]:
             :math:`\theta + \frac{\pi}{2}`.
 
         References:
-            .. [#extended-side] https://en.wikipedia.org/wiki/Extended_side
+            * https://en.wikipedia.org/wiki/Extended_side
         """
         # Do not find the line from smoothed contour. Noise is removed anyway
         # without smoothing by Hough transformation. In fact, smoothing

src/dipcoatimage/finitedepth/rectcoatinglayer.py

@@ -491,8 +491,8 @@ def surface(self) -> Tuple[np.int64, np.int64]:
     def uniform_layer(self) -> Tuple[np.float64, npt.NDArray[np.float64]]:
         """Imaginary uniform layer.
 
-        Uniform layer is a parallel curve[#parallel]_ of substrate surface, having
-        same cross-sectional area as the actual coating layer.
+        Uniform layer is a parallel curve of substrate surface, having same
+        cross-sectional area as the actual coating layer.
 
         Returns:
             Thickness and points of the uniform layer.
@@ -506,7 +506,7 @@ def uniform_layer(self) -> Tuple[np.float64, npt.NDArray[np.float64]]:
             :func:`polyline_parallel_area`.
 
         References:
-            .. [#parallel] https://en.wikipedia.org/wiki/Parallel_curve
+            * https://en.wikipedia.org/wiki/Parallel_curve
         """
         if not self.interfaces():
             return (np.float64(0), np.empty((0, 1, 2), np.float64))
@@ -823,7 +823,7 @@ def equidistant_interpolate(points, n) -> npt.NDArray[np.float64]:
 
 
 def polyline_parallel_area(line: npt.NDArray, t: float) -> np.float64:
-    """Calculate the area between convex polyline[#polyline]_ and its parallel curve.
+    """Calculate the area between convex polyline and its parallel curve.
 
     Arguments:
         line: Vertices of a polyline.
@@ -835,7 +835,7 @@ def polyline_parallel_area(line: npt.NDArray, t: float) -> np.float64:
         area: Area between the polyline and its parallel curve.
 
     References:
-        .. [#polyline] https://en.wikipedia.org/wiki/Polygonal_chain
+        * https://en.wikipedia.org/wiki/Polygonal_chain
     """
     vec = np.diff(line, axis=0)
     d_l = np.linalg.norm(vec, axis=-1)
@@ -847,8 +847,6 @@ def polyline_parallel_area(line: npt.NDArray, t: float) -> np.float64:
 def acm(cm: npt.NDArray[np.float64]) -> npt.NDArray[np.float64]:
     """Compute accumulated cost matrix from local cost matrix.
 
-    Implements the algorithm from [#dtw1]_, with modification from [#dtw2]_.
-
     Arguments:
         cm: Local cost matrix.
 
@@ -858,10 +856,10 @@ def acm(cm: npt.NDArray[np.float64]) -> npt.NDArray[np.float64]:
             If *cm* is empty, return value is an empty array.
 
     References:
-        .. [#dtw1] Senin, Pavel. "Dynamic time warping algorithm review."
-           Information and Computer Science Department University of Hawaii at
-           Manoa Honolulu, USA 855.1-23 (2008): 40.
-        .. [#dtw2] https://pypi.org/project/similaritymeasures/
+        * Senin, Pavel. "Dynamic time warping algorithm review."
+          Information and Computer Science Department University of Hawaii at
+          Manoa Honolulu, USA 855.1-23 (2008): 40.
+        * https://pypi.org/project/similaritymeasures/
     """
     p, q = cm.shape
     ret = np.zeros((p, q), dtype=np.float64)
@@ -892,6 +890,12 @@ def owp(acm: npt.NDArray[np.float64]) -> npt.NDArray[np.int32]:
 
     Returns:
         Indices for the two series to get the optimal warping path.
+
+    References:
+        * Senin, Pavel. "Dynamic time warping algorithm review."
+          Information and Computer Science Department University of Hawaii at
+          Manoa Honolulu, USA 855.1-23 (2008): 40.
+        * https://pypi.org/project/similaritymeasures/
     """
     p, q = acm.shape
     if p == 0 or q == 0: