Try to fix citations

Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>

doc/_static/style.css

@@ -65,6 +65,10 @@ p {
     color: #0366d6;
     text-decoration: underline;
 }
+.rst-content .note a:hover {
+    color: #0366d6;
+    text-decoration: underline;
+}
 .wy-breadcrumbs li a:hover {
     color: #0366d6;
     text-decoration: underline;

doc/bibliography.bib

@@ -34,3 +34,12 @@ @article{jackson2019dictionary
 	year = {2019},
 	doi = {10.1007/s40192-019-00137-4},
 }
+@book{gonzalez2017digital,
+	author = {Gonzalez, Rafael C and Woods, Richard E},
+	edition = {4th},
+	isbn = {978-0133356724},
+	keywords = {image processng, computer vision},
+	publisher = {Pearson Education Limited},
+	title = {{Digital Image Processing}},
+	year = {2017}
+}

doc/bibliography.rst

@@ -3,4 +3,5 @@ Bibliography
 ============
 
 .. bibliography:: bibliography.bib
-   :cited:
+   :all:
+   :style: alpha

doc/pattern_processing.ipynb

@@ -1,5 +1,14 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "nbsphinx": "hidden"
+   },
+   "source": [
+    "This notebook is part of the `kikuchipy` documentation: https://kikuchipy.org."
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -28,16 +37,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "# exchange inline for qt5 for interactive plotting from the pyqt package\n",
     "%matplotlib inline\n",
-    "# exchange inline for qt5 for interactive plotting, from the pyqt package\n",
     "\n",
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
     "import kikuchipy as kp\n",
     "\n",
     "\n",
-    "# s = kp.load(filename=\"/my_data/patterns.h5\")  # To load your own data instead\n",
-    "s = kp.data.nickel_small()"
+    "s = kp.data.nickel_small()  # Use kp.load(\"data.h5\") to load your own data"
    ]
   },
   {
@@ -231,7 +239,8 @@
     "window origin moves from pattern to pattern, computing the sum of products of\n",
     "the window coefficients with the neighbour pattern intensities, defined by the\n",
     "window shape, followed by normalizing by the sum of the window coefficients. For\n",
-    "a symmetrical window of shape $m \\times n$, this becomes [Gonzalez2017]_\n",
+    "a symmetrical window of shape $m \\times n$, this becomes\n",
+    "<cite data-cite=\"gonzalez2017digital\">Gonzalez and Woods (2017)</cite>\n",
     "\n",
     "\\begin{equation}\n",
     "g(n_{\\mathrm{x}}, n_{\\mathrm{y}}) =\n",
@@ -400,8 +409,7 @@
     "Popular uses of filtering of EBSD patterns in the frequency domain include\n",
     "removing large scale variations across the detector with a Gaussian high pass\n",
     "filter, or removing high frequency noise with a Gaussian low pass filter. These\n",
-    "particular functions are readily available via\n",
-    "[Window](reference.rst#kikuchipy.filters.window.Window):"
+    "particular functions are readily available via `Window`:"
    ]
   },
   {
@@ -442,8 +450,8 @@
    "source": [
     "Then, to multiply the FFT of each pattern with this transfer function, and\n",
     "subsequently computing the inverse FFT (IFFT), we use\n",
-    "[fft_filter()](reference.rst#kikuchipy.signals.EBSD.fft_filter), and remember to\n",
-    "shift the zero-frequency components to the centre of the FFT:"
+    "`fft_filter()`, and remember to shift the zero-frequency components to the\n",
+    "centre of the FFT:"
    ]
   },
   {
@@ -517,9 +525,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Note also that [fft_filter()](reference.rst#kikuchipy.signals.EBSD.fft_filter)\n",
-    "performs the filtering on the patterns with data type `np.float32`, and\n",
-    "therefore have to rescale back to the pattern's original data type if necessary."
+    "Note also that `fft_filter()` performs the filtering on the patterns with data\n",
+    "type `np.float32`, and therefore have to rescale back to the pattern's original\n",
+    "data type if necessary."
    ]
   },
   {