lecture notes update

2020-09-20 23:01:44 +02:00
parent f7fa251939
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@@ -447,9 +447,10 @@
    ":titlesonly:\n",
    "\n",
    "\n",
-    "gettingstarted.ipynb\n",
-    "regression.ipynb\n",
-    "logistic.ipynb\n",
+    "chapter2\n",
+    "chapter3\n",
+    "chapter4\n",
+    "chapter5\n",
    "```\n"
   ]
  }
@@ -436,7 +436,8 @@ society.
 :titlesonly:


-gettingstarted.ipynb
-regression.ipynb
-logistic.ipynb
+chapter2
+chapter3
+chapter4
+chapter5
 ```
@@ -0,0 +1,544 @@
+<!-- dom:TITLE: Data Analysis and Machine Learning: Logistic Regression -->
+# Data Analysis and Machine Learning: Logistic Regression
+<!-- dom:AUTHOR: Morten Hjorth-Jensen at Department of Physics, University of Oslo & Department of Physics and Astronomy and National Superconducting Cyclotron Laboratory, Michigan State University -->
+<!-- Author: -->  
+**Morten Hjorth-Jensen**, Department of Physics, University of Oslo and Department of Physics and Astronomy and National Superconducting Cyclotron Laboratory, Michigan State University
+
+Date: **Oct 17, 2019**
+
+Copyright 1999-2019, Morten Hjorth-Jensen. Released under CC Attribution-NonCommercial 4.0 license
+
+
+
+
+<!-- !split  -->
+## Logistic Regression
+
+In linear regression our main interest was centered on learning the
+coefficients of a functional fit (say a polynomial) in order to be
+able to predict the response of a continuous variable on some unseen
+data. The fit to the continuous variable $y_i$ is based on some
+independent variables $\hat{x}_i$. Linear regression resulted in
+analytical expressions for standard ordinary Least Squares or Ridge
+regression (in terms of matrices to invert) for several quantities,
+ranging from the variance and thereby the confidence intervals of the
+parameters $\hat{\beta}$ to the mean squared error. If we can invert
+the product of the design matrices, linear regression gives then a
+simple recipe for fitting our data.
+
+
+Classification problems, however, are concerned with outcomes taking
+the form of discrete variables (i.e. categories). We may for example,
+on the basis of DNA sequencing for a number of patients, like to find
+out which mutations are important for a certain disease; or based on
+scans of various patients' brains, figure out if there is a tumor or
+not; or given a specific physical system, we'd like to identify its
+state, say whether it is an ordered or disordered system (typical
+situation in solid state physics); or classify the status of a
+patient, whether she/he has a stroke or not and many other similar
+situations.
+
+The most common situation we encounter when we apply logistic
+regression is that of two possible outcomes, normally denoted as a
+binary outcome, true or false, positive or negative, success or
+failure etc.
+
+## Optimization and Deep learning
+
+Logistic regression will also serve as our stepping stone towards
+neural network algorithms and supervised deep learning. For logistic
+learning, the minimization of the cost function leads to a non-linear
+equation in the parameters $\hat{\beta}$. The optimization of the
+problem calls therefore for minimization algorithms. This forms the
+bottle neck of all machine learning algorithms, namely how to find
+reliable minima of a multi-variable function. This leads us to the
+family of gradient descent methods. The latter are the working horses
+of basically all modern machine learning algorithms.
+
+We note also that many of the topics discussed here on logistic 
+regression are also commonly used in modern supervised Deep Learning
+models, as we will see later.
+
+
+<!-- !split  -->
+## Basics
+
+We consider the case where the dependent variables, also called the
+responses or the outcomes, $y_i$ are discrete and only take values
+from $k=0,\dots,K-1$ (i.e. $K$ classes).
+
+The goal is to predict the
+output classes from the design matrix $\hat{X}\in\mathbb{R}^{n\times p}$
+made of $n$ samples, each of which carries $p$ features or predictors. The
+primary goal is to identify the classes to which new unseen samples
+belong.
+
+Let us specialize to the case of two classes only, with outputs
+$y_i=0$ and $y_i=1$. Our outcomes could represent the status of a
+credit card user that could default or not on her/his credit card
+debt. That is
+
+$$
+y_i = \begin{bmatrix} 0 & \mathrm{no}\\  1 & \mathrm{yes} \end{bmatrix}.
+$$
+
+## Linear classifier
+
+Before moving to the logistic model, let us try to use our linear
+regression model to classify these two outcomes. We could for example
+fit a linear model to the default case if $y_i > 0.5$ and the no
+default case $y_i \leq 0.5$.
+
+We would then have our 
+weighted linear combination, namely
+
+<!-- Equation labels as ordinary links -->
+<div id="_auto1"></div>
+
+$$
+\begin{equation}
+\hat{y} = \hat{X}^T\hat{\beta} +  \hat{\epsilon},
+\label{_auto1} \tag{1}
+\end{equation}
+$$
+
+where $\hat{y}$ is a vector representing the possible outcomes, $\hat{X}$ is our
+$n\times p$ design matrix and $\hat{\beta}$ represents our estimators/predictors.
+
+## Some selected properties
+
+The main problem with our function is that it takes values on the
+entire real axis. In the case of logistic regression, however, the
+labels $y_i$ are discrete variables. A typical example is the credit
+card data discussed below here, where we can set the state of
+defaulting the debt to $y_i=1$ and not to $y_i=0$ for one the persons
+in the data set (see the full example below).
+
+One simple way to get a discrete output is to have sign
+functions that map the output of a linear regressor to values $\{0,1\}$,
+$f(s_i)=sign(s_i)=1$ if $s_i\ge 0$ and 0 if otherwise. 
+We will encounter this model in our first demonstration of neural networks. Historically it is called the "perceptron" model in the machine learning
+literature. This model is extremely simple. However, in many cases it is more
+favorable to use a ``soft" classifier that outputs
+the probability of a given category. This leads us to the logistic function.
+
+
+## The logistic function
+
+The perceptron is an example of a ``hard classification" model. We
+will encounter this model when we discuss neural networks as
+well. Each datapoint is deterministically assigned to a category (i.e
+$y_i=0$ or $y_i=1$). In many cases, it is favorable to have a "soft"
+classifier that outputs the probability of a given category rather
+than a single value. For example, given $x_i$, the classifier
+outputs the probability of being in a category $k$.  Logistic regression
+is the most common example of a so-called soft classifier. In logistic
+regression, the probability that a data point $x_i$
+belongs to a category $y_i=\{0,1\}$ is given by the so-called logit function (or Sigmoid) which is meant to represent the likelihood for a given event,
+
+$$
+p(t) = \frac{1}{1+\mathrm \exp{-t}}=\frac{\exp{t}}{1+\mathrm \exp{t}}.
+$$
+
+Note that $1-p(t)= p(-t)$.
+
+## Examples of likelihood functions used in logistic regression and nueral networks
+
+
+The following code plots the logistic function, the step function and other functions we will encounter from here and on.
+
+%matplotlib inline
+
+"""The sigmoid function (or the logistic curve) is a
+function that takes any real number, z, and outputs a number (0,1).
+It is useful in neural networks for assigning weights on a relative scale.
+The value z is the weighted sum of parameters involved in the learning algorithm."""
+
+import numpy
+import matplotlib.pyplot as plt
+import math as mt
+
+z = numpy.arange(-5, 5, .1)
+sigma_fn = numpy.vectorize(lambda z: 1/(1+numpy.exp(-z)))
+sigma = sigma_fn(z)
+
+fig = plt.figure()
+ax = fig.add_subplot(111)
+ax.plot(z, sigma)
+ax.set_ylim([-0.1, 1.1])
+ax.set_xlim([-5,5])
+ax.grid(True)
+ax.set_xlabel('z')
+ax.set_title('sigmoid function')
+
+plt.show()
+
+"""Step Function"""
+z = numpy.arange(-5, 5, .02)
+step_fn = numpy.vectorize(lambda z: 1.0 if z >= 0.0 else 0.0)
+step = step_fn(z)
+
+fig = plt.figure()
+ax = fig.add_subplot(111)
+ax.plot(z, step)
+ax.set_ylim([-0.5, 1.5])
+ax.set_xlim([-5,5])
+ax.grid(True)
+ax.set_xlabel('z')
+ax.set_title('step function')
+
+plt.show()
+
+"""tanh Function"""
+z = numpy.arange(-2*mt.pi, 2*mt.pi, 0.1)
+t = numpy.tanh(z)
+
+fig = plt.figure()
+ax = fig.add_subplot(111)
+ax.plot(z, t)
+ax.set_ylim([-1.0, 1.0])
+ax.set_xlim([-2*mt.pi,2*mt.pi])
+ax.grid(True)
+ax.set_xlabel('z')
+ax.set_title('tanh function')
+
+plt.show()
+
+## Two parameters
+
+We assume now that we have two classes with $y_i$ either $0$ or $1$. Furthermore we assume also that we have only two parameters $\beta$ in our fitting of the Sigmoid function, that is we define probabilities
+
+$$
+\begin{align*}
+p(y_i=1|x_i,\hat{\beta}) &= \frac{\exp{(\beta_0+\beta_1x_i)}}{1+\exp{(\beta_0+\beta_1x_i)}},\nonumber\\
+p(y_i=0|x_i,\hat{\beta}) &= 1 - p(y_i=1|x_i,\hat{\beta}),
+\end{align*}
+$$
+
+where $\hat{\beta}$ are the weights we wish to extract from data, in our case $\beta_0$ and $\beta_1$. 
+
+Note that we used
+
+$$
+p(y_i=0\vert x_i, \hat{\beta}) = 1-p(y_i=1\vert x_i, \hat{\beta}).
+$$
+
+<!-- !split  -->
+## Maximum likelihood
+
+In order to define the total likelihood for all possible outcomes from a  
+dataset $\mathcal{D}=\{(y_i,x_i)\}$, with the binary labels
+$y_i\in\{0,1\}$ and where the data points are drawn independently, we use the so-called [Maximum Likelihood Estimation](https://en.wikipedia.org/wiki/Maximum_likelihood_estimation) (MLE) principle. 
+We aim thus at maximizing 
+the probability of seeing the observed data. We can then approximate the 
+likelihood in terms of the product of the individual probabilities of a specific outcome $y_i$, that is
+
+$$
+\begin{align*}
+P(\mathcal{D}|\hat{\beta})& = \prod_{i=1}^n \left[p(y_i=1|x_i,\hat{\beta})\right]^{y_i}\left[1-p(y_i=1|x_i,\hat{\beta}))\right]^{1-y_i}\nonumber \\
+\end{align*}
+$$
+
+from which we obtain the log-likelihood and our **cost/loss** function
+
+$$
+\mathcal{C}(\hat{\beta}) = \sum_{i=1}^n \left( y_i\log{p(y_i=1|x_i,\hat{\beta})} + (1-y_i)\log\left[1-p(y_i=1|x_i,\hat{\beta}))\right]\right).
+$$
+
+## The cost function rewritten
+
+Reordering the logarithms, we can rewrite the **cost/loss** function as
+
+$$
+\mathcal{C}(\hat{\beta}) = \sum_{i=1}^n  \left(y_i(\beta_0+\beta_1x_i) -\log{(1+\exp{(\beta_0+\beta_1x_i)})}\right).
+$$
+
+The maximum likelihood estimator is defined as the set of parameters that maximize the log-likelihood where we maximize with respect to $\beta$.
+Since the cost (error) function is just the negative log-likelihood, for logistic regression we have that
+
+$$
+\mathcal{C}(\hat{\beta})=-\sum_{i=1}^n  \left(y_i(\beta_0+\beta_1x_i) -\log{(1+\exp{(\beta_0+\beta_1x_i)})}\right).
+$$
+
+This equation is known in statistics as the **cross entropy**. Finally, we note that just as in linear regression, 
+in practice we often supplement the cross-entropy with additional regularization terms, usually $L_1$ and $L_2$ regularization as we did for Ridge and Lasso regression.
+
+## Minimizing the cross entropy
+
+The cross entropy is a convex function of the weights $\hat{\beta}$ and,
+therefore, any local minimizer is a global minimizer. 
+
+
+Minimizing this
+cost function with respect to the two parameters $\beta_0$ and $\beta_1$ we obtain
+
+$$
+\frac{\partial \mathcal{C}(\hat{\beta})}{\partial \beta_0} = -\sum_{i=1}^n  \left(y_i -\frac{\exp{(\beta_0+\beta_1x_i)}}{1+\exp{(\beta_0+\beta_1x_i)}}\right),
+$$
+
+and
+
+$$
+\frac{\partial \mathcal{C}(\hat{\beta})}{\partial \beta_1} = -\sum_{i=1}^n  \left(y_ix_i -x_i\frac{\exp{(\beta_0+\beta_1x_i)}}{1+\exp{(\beta_0+\beta_1x_i)}}\right).
+$$
+
+## A more compact expression
+
+Let us now define a vector $\hat{y}$ with $n$ elements $y_i$, an
+$n\times p$ matrix $\hat{X}$ which contains the $x_i$ values and a
+vector $\hat{p}$ of fitted probabilities $p(y_i\vert x_i,\hat{\beta})$. We can rewrite in a more compact form the first
+derivative of cost function as
+
+$$
+\frac{\partial \mathcal{C}(\hat{\beta})}{\partial \hat{\beta}} = -\hat{X}^T\left(\hat{y}-\hat{p}\right).
+$$
+
+If we in addition define a diagonal matrix $\hat{W}$ with elements 
+$p(y_i\vert x_i,\hat{\beta})(1-p(y_i\vert x_i,\hat{\beta})$, we can obtain a compact expression of the second derivative as
+
+$$
+\frac{\partial^2 \mathcal{C}(\hat{\beta})}{\partial \hat{\beta}\partial \hat{\beta}^T} = \hat{X}^T\hat{W}\hat{X}.
+$$
+
+## Extending to more predictors
+
+Within a binary classification problem, we can easily expand our model to include multiple predictors. Our ratio between likelihoods is then with $p$ predictors
+
+$$
+\log{ \frac{p(\hat{\beta}\hat{x})}{1-p(\hat{\beta}\hat{x})}} = \beta_0+\beta_1x_1+\beta_2x_2+\dots+\beta_px_p.
+$$
+
+Here we defined $\hat{x}=[1,x_1,x_2,\dots,x_p]$ and $\hat{\beta}=[\beta_0, \beta_1, \dots, \beta_p]$ leading to
+
+$$
+p(\hat{\beta}\hat{x})=\frac{ \exp{(\beta_0+\beta_1x_1+\beta_2x_2+\dots+\beta_px_p)}}{1+\exp{(\beta_0+\beta_1x_1+\beta_2x_2+\dots+\beta_px_p)}}.
+$$
+
+## Including more classes
+
+Till now we have mainly focused on two classes, the so-called binary
+system. Suppose we wish to extend to $K$ classes.  Let us for the sake
+of simplicity assume we have only two predictors. We have then
+following model
+
+1
+5
+ 
+<
+<
+<
+!
+!
+M
+A
+T
+H
+_
+B
+L
+O
+C
+K
+
+$$
+\log{\frac{p(C=2\vert x)}{p(K\vert x)}} = \beta_{20}+\beta_{21}x_1,
+$$
+
+and so on till the class $C=K-1$ class
+
+$$
+\log{\frac{p(C=K-1\vert x)}{p(K\vert x)}} = \beta_{(K-1)0}+\beta_{(K-1)1}x_1,
+$$
+
+and the model is specified in term of $K-1$ so-called log-odds or
+**logit** transformations.
+
+
+## More classes
+
+In our discussion of neural networks we will encounter the above again
+in terms of a slightly modified function, the so-called **Softmax** function.
+
+The softmax function is used in various multiclass classification
+methods, such as multinomial logistic regression (also known as
+softmax regression), multiclass linear discriminant analysis, naive
+Bayes classifiers, and artificial neural networks.  Specifically, in
+multinomial logistic regression and linear discriminant analysis, the
+input to the function is the result of $K$ distinct linear functions,
+and the predicted probability for the $k$-th class given a sample
+vector $\hat{x}$ and a weighting vector $\hat{\beta}$ is (with two
+predictors):
+
+$$
+p(C=k\vert \mathbf {x} )=\frac{\exp{(\beta_{k0}+\beta_{k1}x_1)}}{1+\sum_{l=1}^{K-1}\exp{(\beta_{l0}+\beta_{l1}x_1)}}.
+$$
+
+It is easy to extend to more predictors. The final class is
+
+$$
+p(C=K\vert \mathbf {x} )=\frac{1}{1+\sum_{l=1}^{K-1}\exp{(\beta_{l0}+\beta_{l1}x_1)}},
+$$
+
+and they sum to one. Our earlier discussions were all specialized to
+the case with two classes only. It is easy to see from the above that
+what we derived earlier is compatible with these equations.
+
+To find the optimal parameters we would typically use a gradient
+descent method.  Newton's method and gradient descent methods are
+discussed in the material on [optimization
+methods](https://compphysics.github.io/MachineLearning/doc/pub/Splines/html/Splines-bs.html).
+
+
+
+
+## A simple classification problem
+
+import numpy as np
+from sklearn import datasets, linear_model
+import matplotlib.pyplot as plt
+
+
+def generate_data():
+    np.random.seed(0)
+    X, y = datasets.make_moons(200, noise=0.20)
+    return X, y
+
+
+def visualize(X, y, clf):
+    plot_decision_boundary(lambda x: clf.predict(x), X, y)
+
+def plot_decision_boundary(pred_func, X, y):
+    # Set min and max values and give it some padding
+    x_min, x_max = X[:, 0].min() - .5, X[:, 0].max() + .5
+    y_min, y_max = X[:, 1].min() - .5, X[:, 1].max() + .5
+    h = 0.01
+    # Generate a grid of points with distance h between them
+    xx, yy = np.meshgrid(np.arange(x_min, x_max, h), np.arange(y_min, y_max, h))
+    # Predict the function value for the whole gid
+    Z = pred_func(np.c_[xx.ravel(), yy.ravel()])
+    Z = Z.reshape(xx.shape)
+    # Plot the contour and training examples
+    plt.contourf(xx, yy, Z, cmap=plt.cm.Spectral)
+    plt.scatter(X[:, 0], X[:, 1], c=y, cmap=plt.cm.Spectral)
+    plt.show()
+
+
+def classify(X, y):
+    clf = linear_model.LogisticRegressionCV()
+    clf.fit(X, y)
+    return clf
+
+
+def main():
+    X, y = generate_data()
+    # visualize(X, y)
+    clf = classify(X, y)
+    visualize(X, y, clf)
+
+if __name__ == "__main__":
+    main()
+
+## The Credit Card example
+Here we use the the [credit card data](https://archive.ics.uci.edu/ml/datasets/default+of+credit+card+clients). 
+The data are from an extensive database from Taiwan and include more than ten predictors.
+
+For categorical data -Scikit-Learn- provides a so-called **one-hot encoder**.
+This is called one-hot
+encoding, because only one attribute will be equal to 1 (hot), while the others will be 0 (cold).
+**Scikit-Learn** provides a OneHotEncoder encoder to convert integer categorical values into one-hot
+
+from sklearn.preprocessing import OneHotEncoder
+encoder = OneHotEncoder()
+
+## How to read the Credit Card data
+
+import pandas as pd
+import os
+import numpy as np
+
+
+from sklearn.model_selection import train_test_split
+from sklearn.preprocessing import OneHotEncoder
+from sklearn.compose import ColumnTransformer
+from sklearn.preprocessing import StandardScaler, OneHotEncoder
+from sklearn.metrics import confusion_matrix, accuracy_score, roc_auc_score
+
+# Trying to set the seed
+np.random.seed(0)
+import random
+random.seed(0)
+
+# Reading file into data frame
+cwd = os.getcwd()
+filename = cwd + '/default of credit card clients.xls'
+nanDict = {}
+df = pd.read_excel(filename, header=1, skiprows=0, index_col=0, na_values=nanDict)
+
+df.rename(index=str, columns={"default payment next month": "defaultPaymentNextMonth"}, inplace=True)
+
+# Features and targets 
+X = df.loc[:, df.columns != 'defaultPaymentNextMonth'].values
+y = df.loc[:, df.columns == 'defaultPaymentNextMonth'].values
+
+# Categorical variables to one-hot's
+onehotencoder = OneHotEncoder(categories="auto")
+
+X = ColumnTransformer(
+    [("", onehotencoder, [3]),],
+    remainder="passthrough"
+).fit_transform(X)
+
+y.shape
+
+# Train-test split
+trainingShare = 0.5 
+seed  = 1
+XTrain, XTest, yTrain, yTest=train_test_split(X, y, train_size=trainingShare, \
+                                              test_size = 1-trainingShare,
+                                             random_state=seed)
+
+# Input Scaling
+sc = StandardScaler()
+XTrain = sc.fit_transform(XTrain)
+XTest = sc.transform(XTest)
+
+# One-hot's of the target vector
+Y_train_onehot, Y_test_onehot = onehotencoder.fit_transform(yTrain), onehotencoder.fit_transform(yTest)
+
+# Remove instances with zeros only for past bill statements or paid amounts
+'''
+df = df.drop(df[(df.BILL_AMT1 == 0) &
+                (df.BILL_AMT2 == 0) &
+                (df.BILL_AMT3 == 0) &
+                (df.BILL_AMT4 == 0) &
+                (df.BILL_AMT5 == 0) &
+                (df.BILL_AMT6 == 0) &
+                (df.PAY_AMT1 == 0) &
+                (df.PAY_AMT2 == 0) &
+                (df.PAY_AMT3 == 0) &
+                (df.PAY_AMT4 == 0) &
+                (df.PAY_AMT5 == 0) &
+                (df.PAY_AMT6 == 0)].index)
+'''
+df = df.drop(df[(df.BILL_AMT1 == 0) &
+                (df.BILL_AMT2 == 0) &
+                (df.BILL_AMT3 == 0) &
+                (df.BILL_AMT4 == 0) &
+                (df.BILL_AMT5 == 0) &
+                (df.BILL_AMT6 == 0)].index)
+
+df = df.drop(df[(df.PAY_AMT1 == 0) &
+                (df.PAY_AMT2 == 0) &
+                (df.PAY_AMT3 == 0) &
+                (df.PAY_AMT4 == 0) &
+                (df.PAY_AMT5 == 0) &
+                (df.PAY_AMT6 == 0)].index)
+
+from sklearn.linear_model import LogisticRegression
+from sklearn.model_selection import GridSearchCV
+
+lambdas=np.logspace(-5,7,13)
+parameters = [{'C': 1./lambdas, "solver":["lbfgs"]}]#*len(parameters)}]
+scoring = ['accuracy', 'roc_auc']
+logReg = LogisticRegression()
+gridSearch = GridSearchCV(logReg, parameters, cv=5, scoring=scoring, refit='roc_auc')
@@ -1,65 +0,0 @@
-# Content with notebooks
-
-You can also create content with Jupyter Notebooks. This means that you can include
-code blocks and their outputs in your book.
-
-## Markdown + notebooks
-
-As it is markdown, you can embed images, HTML, etc into your posts!
-
-![](https://myst-parser.readthedocs.io/en/latest/_static/logo.png)
-
-You an also $add_{math}$ and
-
-$$
-math^{blocks}
-$$
-
-or
-
-$$
-\begin{aligned}
-\mbox{mean} la_{tex} \\ \\
-math blocks
-\end{aligned}
-$$
-
-But make sure you \$Escape \$your \$dollar signs \$you want to keep!
-
-## MyST markdown
-
-MyST markdown works in Jupyter Notebooks as well. For more information about MyST markdown, check
-out [the MyST guide in Jupyter Book](https://jupyterbook.org/content/myst.html),
-or see [the MyST markdown documentation](https://myst-parser.readthedocs.io/en/latest/).
-
-## Code blocks and outputs
-
-Jupyter Book will also embed your code blocks and output in your book.
-For example, here's some sample Matplotlib code:
-
-from matplotlib import rcParams, cycler
-import matplotlib.pyplot as plt
-import numpy as np
-plt.ion()
-
-# Fixing random state for reproducibility
-np.random.seed(19680801)
-
-N = 10
-data = [np.logspace(0, 1, 100) + np.random.randn(100) + ii for ii in range(N)]
-data = np.array(data).T
-cmap = plt.cm.coolwarm
-rcParams['axes.prop_cycle'] = cycler(color=cmap(np.linspace(0, 1, N)))
-
-
-from matplotlib.lines import Line2D
-custom_lines = [Line2D([0], [0], color=cmap(0.), lw=4),
-                Line2D([0], [0], color=cmap(.5), lw=4),
-                Line2D([0], [0], color=cmap(1.), lw=4)]
-
-fig, ax = plt.subplots(figsize=(10, 5))
-lines = ax.plot(data)
-ax.legend(custom_lines, ['Cold', 'Medium', 'Hot']);
-
-There is a lot more that you can do with outputs (such as including interactive outputs)
-with your book. For more information about this, see [the Jupyter Book documentation](https://jupyterbook.org)
@@ -0,0 +1,101 @@
+;; -*- coding: utf-8; mode: Lisp; -*-
+;; style file for xindy
+;; filename: LICRcyr2utf8.xdy
+;; description: style file for xindy which maps back LaTeX Internal
+;;   Character Representation of Cyrillic to utf-8
+;; usage: for use with pdflatex produced .idx files.
+;; Contributed by the Sphinx team, July 2018.
+(merge-rule "\IeC {\'\CYRG }" "Ѓ" :string)
+(merge-rule "\IeC {\'\CYRK }" "Ќ" :string)
+(merge-rule "\IeC {\'\cyrg }" "ѓ" :string)
+(merge-rule "\IeC {\'\cyrk }" "ќ" :string)
+(merge-rule "\IeC {\CYRA }" "А" :string)
+(merge-rule "\IeC {\CYRB }" "Б" :string)
+(merge-rule "\IeC {\CYRC }" "Ц" :string)
+(merge-rule "\IeC {\CYRCH }" "Ч" :string)
+(merge-rule "\IeC {\CYRD }" "Д" :string)
+(merge-rule "\IeC {\CYRDJE }" "Ђ" :string)
+(merge-rule "\IeC {\CYRDZE }" "Ѕ" :string)
+(merge-rule "\IeC {\CYRDZHE }" "Џ" :string)
+(merge-rule "\IeC {\CYRE }" "Е" :string)
+(merge-rule "\IeC {\CYREREV }" "Э" :string)
+(merge-rule "\IeC {\CYRERY }" "Ы" :string)
+(merge-rule "\IeC {\CYRF }" "Ф" :string)
+(merge-rule "\IeC {\CYRG }" "Г" :string)
+(merge-rule "\IeC {\CYRGUP }" "Ґ" :string)
+(merge-rule "\IeC {\CYRH }" "Х" :string)
+(merge-rule "\IeC {\CYRHRDSN }" "Ъ" :string)
+(merge-rule "\IeC {\CYRI }" "И" :string)
+(merge-rule "\IeC {\CYRIE }" "Є" :string)
+(merge-rule "\IeC {\CYRII }" "І" :string)
+(merge-rule "\IeC {\CYRISHRT }" "Й" :string)
+(merge-rule "\IeC {\CYRJE }" "Ј" :string)
+(merge-rule "\IeC {\CYRK }" "К" :string)
+(merge-rule "\IeC {\CYRL }" "Л" :string)
+(merge-rule "\IeC {\CYRLJE }" "Љ" :string)
+(merge-rule "\IeC {\CYRM }" "М" :string)
+(merge-rule "\IeC {\CYRN }" "Н" :string)
+(merge-rule "\IeC {\CYRNJE }" "Њ" :string)
+(merge-rule "\IeC {\CYRO }" "О" :string)
+(merge-rule "\IeC {\CYRP }" "П" :string)
+(merge-rule "\IeC {\CYRR }" "Р" :string)
+(merge-rule "\IeC {\CYRS }" "С" :string)
+(merge-rule "\IeC {\CYRSFTSN }" "Ь" :string)
+(merge-rule "\IeC {\CYRSH }" "Ш" :string)
+(merge-rule "\IeC {\CYRSHCH }" "Щ" :string)
+(merge-rule "\IeC {\CYRT }" "Т" :string)
+(merge-rule "\IeC {\CYRTSHE }" "Ћ" :string)
+(merge-rule "\IeC {\CYRU }" "У" :string)
+(merge-rule "\IeC {\CYRUSHRT }" "Ў" :string)
+(merge-rule "\IeC {\CYRV }" "В" :string)
+(merge-rule "\IeC {\CYRYA }" "Я" :string)
+(merge-rule "\IeC {\CYRYI }" "Ї" :string)
+(merge-rule "\IeC {\CYRYO }" "Ё" :string)
+(merge-rule "\IeC {\CYRYU }" "Ю" :string)
+(merge-rule "\IeC {\CYRZ }" "З" :string)
+(merge-rule "\IeC {\CYRZH }" "Ж" :string)
+(merge-rule "\IeC {\cyra }" "а" :string)
+(merge-rule "\IeC {\cyrb }" "б" :string)
+(merge-rule "\IeC {\cyrc }" "ц" :string)
+(merge-rule "\IeC {\cyrch }" "ч" :string)
+(merge-rule "\IeC {\cyrd }" "д" :string)
+(merge-rule "\IeC {\cyrdje }" "ђ" :string)
+(merge-rule "\IeC {\cyrdze }" "ѕ" :string)
+(merge-rule "\IeC {\cyrdzhe }" "џ" :string)
+(merge-rule "\IeC {\cyre }" "е" :string)
+(merge-rule "\IeC {\cyrerev }" "э" :string)
+(merge-rule "\IeC {\cyrery }" "ы" :string)
+(merge-rule "\IeC {\cyrf }" "ф" :string)
+(merge-rule "\IeC {\cyrg }" "г" :string)
+(merge-rule "\IeC {\cyrgup }" "ґ" :string)
+(merge-rule "\IeC {\cyrh }" "х" :string)
+(merge-rule "\IeC {\cyrhrdsn }" "ъ" :string)
+(merge-rule "\IeC {\cyri }" "и" :string)
+(merge-rule "\IeC {\cyrie }" "є" :string)
+(merge-rule "\IeC {\cyrii }" "і" :string)
+(merge-rule "\IeC {\cyrishrt }" "й" :string)
+(merge-rule "\IeC {\cyrje }" "ј" :string)
+(merge-rule "\IeC {\cyrk }" "к" :string)
+(merge-rule "\IeC {\cyrl }" "л" :string)
+(merge-rule "\IeC {\cyrlje }" "љ" :string)
+(merge-rule "\IeC {\cyrm }" "м" :string)
+(merge-rule "\IeC {\cyrn }" "н" :string)
+(merge-rule "\IeC {\cyrnje }" "њ" :string)
+(merge-rule "\IeC {\cyro }" "о" :string)
+(merge-rule "\IeC {\cyrp }" "п" :string)
+(merge-rule "\IeC {\cyrr }" "р" :string)
+(merge-rule "\IeC {\cyrs }" "с" :string)
+(merge-rule "\IeC {\cyrsftsn }" "ь" :string)
+(merge-rule "\IeC {\cyrsh }" "ш" :string)
+(merge-rule "\IeC {\cyrshch }" "щ" :string)
+(merge-rule "\IeC {\cyrt }" "т" :string)
+(merge-rule "\IeC {\cyrtshe }" "ћ" :string)
+(merge-rule "\IeC {\cyru }" "у" :string)
+(merge-rule "\IeC {\cyrushrt }" "ў" :string)
+(merge-rule "\IeC {\cyrv }" "в" :string)
+(merge-rule "\IeC {\cyrya }" "я" :string)
+(merge-rule "\IeC {\cyryi }" "ї" :string)
+(merge-rule "\IeC {\cyryo }" "ё" :string)
+(merge-rule "\IeC {\cyryu }" "ю" :string)
+(merge-rule "\IeC {\cyrz }" "з" :string)
+(merge-rule "\IeC {\cyrzh }" "ж" :string)
@@ -0,0 +1,239 @@
+;; style file for xindy
+;; filename: LICRlatin2utf8.xdy
+;; description: style file for xindy which maps back LaTeX Internal
+;;   Character Representation of letters (as arising in .idx index
+;;   file) to UTF-8 encoding for correct sorting by xindy.
+;; usage: for use with the pdflatex engine,
+;;        *not* for use with xelatex or lualatex.
+;;
+;; This is based upon xindy's distributed file tex/inputenc/utf8.xdy.
+;; The modifications include:
+;;
+;; - Updates for compatibility with current LaTeX macro encoding.
+;;
+;; - Systematic usage of the \IeC {...} mark-up, because mark-up in
+;;   tex/inputenc/utf8.xdy was using it on seemingly random basis, and
+;;   Sphinx coercing of xindy usability for both Latin and Cyrillic scripts
+;;   with pdflatex requires its systematic presence here.
+;;
+;; - Support for some extra letters: Ÿ, Ŋ, ŋ, Œ, œ, Ĳ, ĳ, ȷ and ẞ.
+;;
+;;   Indeed Sphinx needs to support for pdflatex engine all Unicode letters
+;;   available in TeX T1 font encoding.  The above letters are found in
+;;   that encoding but not in the Latin1, 2, 3 charsets which are those
+;;   covered by original tex/inputenc/utf8.xdy.
+;;
+;; - There is a problem that ȷ is not supported out-of-the box by LaTeX
+;;   with inputenc, one must add explicitely
+;;       \DeclareUnicodeCharacter{0237}{\j}
+;;   to preamble of LaTeX document.  However this character is not supported
+;;   by the TeX "times" font used by default by Sphinx for pdflatex engine.
+;;
+;;     **Update**: since LaTeX 2018/12/01, the \j as well as \SS, \k{} and
+;;                  \.{} need no extra user declaration anymore.
+;;
+;; - ẞ needs \DeclareUnicodeCharacter{1E9E}{\SS} (but ß needs no extra set-up).
+;;
+;; - U+02DB (˛) and U+02D9 (˙) are also not supported by inputenc
+;;   out of the box and require
+;;       \DeclareUnicodeCharacter{02DB}{\k{}}
+;;       \DeclareUnicodeCharacter{02D9}{\.{}}
+;;   to be added to preamble.
+;;
+;; - U+0127 ħ and U+0126 Ħ are absent from TeX T1+TS1 font encodings.
+;;
+;; - Characters Ŋ and ŋ are not supported by TeX font "times" used by
+;;   default by Sphinx for pdflatex engine but they are supported by
+;;   some TeX fonts, in particular by the default LaTeX font for T1
+;;   encoding.
+;;
+;; - " and ~ must be escaped as ~" and resp. ~~ in xindy merge rules.
+;;
+;; Contributed by the Sphinx team, July 2018.
+;;
+;; See sphinx.xdy for superior figures, as they are escaped by LaTeX writer.
+(merge-rule "\IeC {\textonesuperior }" "¹" :string)
+(merge-rule "\IeC {\texttwosuperior }" "²" :string)
+(merge-rule "\IeC {\textthreesuperior }" "³" :string)
+(merge-rule "\IeC {\'a}" "á" :string)
+(merge-rule "\IeC {\'A}" "Á" :string)
+(merge-rule "\IeC {\`a}" "à" :string)
+(merge-rule "\IeC {\`A}" "À" :string)
+(merge-rule "\IeC {\^a}" "â" :string)
+(merge-rule "\IeC {\^A}" "Â" :string)
+(merge-rule "\IeC {\~"a}" "ä" :string)
+(merge-rule "\IeC {\~"A}" "Ä" :string)
+(merge-rule "\IeC {\~~a}" "ã" :string)
+(merge-rule "\IeC {\~~A}" "Ã" :string)
+(merge-rule "\IeC {\c c}" "ç" :string)
+(merge-rule "\IeC {\c C}" "Ç" :string)
+(merge-rule "\IeC {\'c}" "ć" :string)
+(merge-rule "\IeC {\'C}" "Ć" :string)
+(merge-rule "\IeC {\^c}" "ĉ" :string)
+(merge-rule "\IeC {\^C}" "Ĉ" :string)
+(merge-rule "\IeC {\.c}" "ċ" :string)
+(merge-rule "\IeC {\.C}" "Ċ" :string)
+(merge-rule "\IeC {\c s}" "ş" :string)
+(merge-rule "\IeC {\c S}" "Ş" :string)
+(merge-rule "\IeC {\c t}" "ţ" :string)
+(merge-rule "\IeC {\c T}" "Ţ" :string)
+(merge-rule "\IeC {\-}" "" :string); soft hyphen
+(merge-rule "\IeC {\textdiv }" "÷" :string)
+(merge-rule "\IeC {\'e}" "é" :string)
+(merge-rule "\IeC {\'E}" "É" :string)
+(merge-rule "\IeC {\`e}" "è" :string)
+(merge-rule "\IeC {\`E}" "È" :string)
+(merge-rule "\IeC {\^e}" "ê" :string)
+(merge-rule "\IeC {\^E}" "Ê" :string)
+(merge-rule "\IeC {\~"e}" "ë" :string)
+(merge-rule "\IeC {\~"E}" "Ë" :string)
+(merge-rule "\IeC {\^g}" "ĝ" :string)
+(merge-rule "\IeC {\^G}" "Ĝ" :string)
+(merge-rule "\IeC {\.g}" "ġ" :string)
+(merge-rule "\IeC {\.G}" "Ġ" :string)
+(merge-rule "\IeC {\^h}" "ĥ" :string)
+(merge-rule "\IeC {\^H}" "Ĥ" :string)
+(merge-rule "\IeC {\H o}" "ő" :string)
+(merge-rule "\IeC {\H O}" "Ő" :string)
+(merge-rule "\IeC {\textacutedbl }" "˝" :string)
+(merge-rule "\IeC {\H u}" "ű" :string)
+(merge-rule "\IeC {\H U}" "Ű" :string)
+(merge-rule "\IeC {\ae }" "æ" :string)
+(merge-rule "\IeC {\AE }" "Æ" :string)
+(merge-rule "\IeC {\textcopyright }" "©" :string)
+(merge-rule "\IeC {\c \ }" "¸" :string)
+(merge-rule "\IeC {\dh }" "ð" :string)
+(merge-rule "\IeC {\DH }" "Ð" :string)
+(merge-rule "\IeC {\dj }" "đ" :string)
+(merge-rule "\IeC {\DJ }" "Đ" :string)
+(merge-rule "\IeC {\guillemotleft }" "«" :string)
+(merge-rule "\IeC {\guillemotright }" "»" :string)
+(merge-rule "\IeC {\'\i }" "í" :string)
+(merge-rule "\IeC {\`\i }" "ì" :string)
+(merge-rule "\IeC {\^\i }" "î" :string)
+(merge-rule "\IeC {\~"\i }" "ï" :string)
+(merge-rule "\IeC {\i }" "ı" :string)
+(merge-rule "\IeC {\^\j }" "ĵ" :string)
+(merge-rule "\IeC {\k {}}" "˛" :string)
+(merge-rule "\IeC {\l }" "ł" :string)
+(merge-rule "\IeC {\L }" "Ł" :string)
+(merge-rule "\IeC {\nobreakspace }" " " :string)
+(merge-rule "\IeC {\o }" "ø" :string)
+(merge-rule "\IeC {\O }" "Ø" :string)
+(merge-rule "\IeC {\textsterling }" "£" :string)
+(merge-rule "\IeC {\textparagraph }" "¶" :string)
+(merge-rule "\IeC {\ss }" "ß" :string)
+(merge-rule "\IeC {\textsection }" "§" :string)
+(merge-rule "\IeC {\textbrokenbar }" "¦" :string)
+(merge-rule "\IeC {\textcent }" "¢" :string)
+(merge-rule "\IeC {\textcurrency }" "¤" :string)
+(merge-rule "\IeC {\textdegree }" "°" :string)
+(merge-rule "\IeC {\textexclamdown }" "¡" :string)
+(merge-rule "\IeC {\texthbar }" "ħ" :string)
+(merge-rule "\IeC {\textHbar }" "Ħ" :string)
+(merge-rule "\IeC {\textonehalf }" "½" :string)
+(merge-rule "\IeC {\textonequarter }" "¼" :string)
+(merge-rule "\IeC {\textordfeminine }" "ª" :string)
+(merge-rule "\IeC {\textordmasculine }" "º" :string)
+(merge-rule "\IeC {\textperiodcentered }" "·" :string)
+(merge-rule "\IeC {\textquestiondown }" "¿" :string)
+(merge-rule "\IeC {\textregistered }" "®" :string)
+(merge-rule "\IeC {\textthreequarters }" "¾" :string)
+(merge-rule "\IeC {\textyen }" "¥" :string)
+(merge-rule "\IeC {\th }" "þ" :string)
+(merge-rule "\IeC {\TH }" "Þ" :string)
+(merge-rule "\IeC {\'I}" "Í" :string)
+(merge-rule "\IeC {\`I}" "Ì" :string)
+(merge-rule "\IeC {\^I}" "Î" :string)
+(merge-rule "\IeC {\~"I}" "Ï" :string)
+(merge-rule "\IeC {\.I}" "İ" :string)
+(merge-rule "\IeC {\^J}" "Ĵ" :string)
+(merge-rule "\IeC {\k a}" "ą" :string)
+(merge-rule "\IeC {\k A}" "Ą" :string)
+(merge-rule "\IeC {\k e}" "ę" :string)
+(merge-rule "\IeC {\k E}" "Ę" :string)
+(merge-rule "\IeC {\'l}" "ĺ" :string)
+(merge-rule "\IeC {\'L}" "Ĺ" :string)
+(merge-rule "\IeC {\textlnot }" "¬" :string)
+(merge-rule "\IeC {\textmu }" "µ" :string)
+(merge-rule "\IeC {\'n}" "ń" :string)
+(merge-rule "\IeC {\'N}" "Ń" :string)
+(merge-rule "\IeC {\~~n}" "ñ" :string)
+(merge-rule "\IeC {\~~N}" "Ñ" :string)
+(merge-rule "\IeC {\'o}" "ó" :string)
+(merge-rule "\IeC {\'O}" "Ó" :string)
+(merge-rule "\IeC {\`o}" "ò" :string)
+(merge-rule "\IeC {\`O}" "Ò" :string)
+(merge-rule "\IeC {\^o}" "ô" :string)
+(merge-rule "\IeC {\^O}" "Ô" :string)
+(merge-rule "\IeC {\~"o}" "ö" :string)
+(merge-rule "\IeC {\~"O}" "Ö" :string)
+(merge-rule "\IeC {\~~o}" "õ" :string)
+(merge-rule "\IeC {\~~O}" "Õ" :string)
+(merge-rule "\IeC {\textpm }" "±" :string)
+(merge-rule "\IeC {\r a}" "å" :string)
+(merge-rule "\IeC {\r A}" "Å" :string)
+(merge-rule "\IeC {\'r}" "ŕ" :string)
+(merge-rule "\IeC {\'R}" "Ŕ" :string)
+(merge-rule "\IeC {\r u}" "ů" :string)
+(merge-rule "\IeC {\r U}" "Ů" :string)
+(merge-rule "\IeC {\'s}" "ś" :string)
+(merge-rule "\IeC {\'S}" "Ś" :string)
+(merge-rule "\IeC {\^s}" "ŝ" :string)
+(merge-rule "\IeC {\^S}" "Ŝ" :string)
+(merge-rule "\IeC {\textasciidieresis }" "¨" :string)
+(merge-rule "\IeC {\textasciimacron }" "¯" :string)
+(merge-rule "\IeC {\.{}}" "˙" :string)
+(merge-rule "\IeC {\textasciiacute }" "´" :string)
+(merge-rule "\IeC {\texttimes }" "×" :string)
+(merge-rule "\IeC {\u a}" "ă" :string)
+(merge-rule "\IeC {\u A}" "Ă" :string)
+(merge-rule "\IeC {\u g}" "ğ" :string)
+(merge-rule "\IeC {\u G}" "Ğ" :string)
+(merge-rule "\IeC {\textasciibreve }" "˘" :string)
+(merge-rule "\IeC {\'u}" "ú" :string)
+(merge-rule "\IeC {\'U}" "Ú" :string)
+(merge-rule "\IeC {\`u}" "ù" :string)
+(merge-rule "\IeC {\`U}" "Ù" :string)
+(merge-rule "\IeC {\^u}" "û" :string)
+(merge-rule "\IeC {\^U}" "Û" :string)
+(merge-rule "\IeC {\~"u}" "ü" :string)
+(merge-rule "\IeC {\~"U}" "Ü" :string)
+(merge-rule "\IeC {\u u}" "ŭ" :string)
+(merge-rule "\IeC {\u U}" "Ŭ" :string)
+(merge-rule "\IeC {\v c}" "č" :string)
+(merge-rule "\IeC {\v C}" "Č" :string)
+(merge-rule "\IeC {\v d}" "ď" :string)
+(merge-rule "\IeC {\v D}" "Ď" :string)
+(merge-rule "\IeC {\v e}" "ě" :string)
+(merge-rule "\IeC {\v E}" "Ě" :string)
+(merge-rule "\IeC {\v l}" "ľ" :string)
+(merge-rule "\IeC {\v L}" "Ľ" :string)
+(merge-rule "\IeC {\v n}" "ň" :string)
+(merge-rule "\IeC {\v N}" "Ň" :string)
+(merge-rule "\IeC {\v r}" "ř" :string)
+(merge-rule "\IeC {\v R}" "Ř" :string)
+(merge-rule "\IeC {\v s}" "š" :string)
+(merge-rule "\IeC {\v S}" "Š" :string)
+(merge-rule "\IeC {\textasciicaron }" "ˇ" :string)
+(merge-rule "\IeC {\v t}" "ť" :string)
+(merge-rule "\IeC {\v T}" "Ť" :string)
+(merge-rule "\IeC {\v z}" "ž" :string)
+(merge-rule "\IeC {\v Z}" "Ž" :string)
+(merge-rule "\IeC {\'y}" "ý" :string)
+(merge-rule "\IeC {\'Y}" "Ý" :string)
+(merge-rule "\IeC {\~"y}" "ÿ" :string)
+(merge-rule "\IeC {\'z}" "ź" :string)
+(merge-rule "\IeC {\'Z}" "Ź" :string)
+(merge-rule "\IeC {\.z}" "ż" :string)
+(merge-rule "\IeC {\.Z}" "Ż" :string)
+;; letters not in Latin1, 2, 3 but available in TeX T1 font encoding
+(merge-rule "\IeC {\~"Y}" "Ÿ" :string)
+(merge-rule "\IeC {\NG }" "Ŋ" :string)
+(merge-rule "\IeC {\ng }" "ŋ" :string)
+(merge-rule "\IeC {\OE }" "Œ" :string)
+(merge-rule "\IeC {\oe }" "œ" :string)
+(merge-rule "\IeC {\IJ }" "Ĳ" :string)
+(merge-rule "\IeC {\ij }" "ĳ" :string)
+(merge-rule "\IeC {\j }" "ȷ" :string)
+(merge-rule "\IeC {\SS }" "ẞ" :string)
@@ -0,0 +1,607 @@
+;; style file for xindy
+;; filename: LatinRules.xdy
+;;
+;; It is based upon xindy's files lang/general/utf8.xdy and
+;; lang/general/utf8-lang.xdy which implement
+;; "a general sorting order for Western European languages"
+;;
+;; The aim for Sphinx is to be able to index in a Cyrillic document
+;; also terms using the Latin alphabets, inclusive of letters
+;; with diacritics.  To this effect the xindy rules from lang/general
+;; got manually re-coded to avoid collisions with the encoding
+;; done by xindy for sorting words in Cyrillic languages, which was
+;; observed not to use bytes with octal encoding 0o266 or higher.
+;;
+;; So here we use only 0o266 or higher bytes.
+;; (ÅŠ, Å‹, Ä², and Ä³ are absent from
+;; lang/general/utf8.xdy and not included here)
+;; Contributed by the Sphinx team, 2018.
+
+(define-letter-group "A" :prefixes ("¶"))
+(define-letter-group "B" :after "A" :prefixes ("·"))
+(define-letter-group "C" :after "B" :prefixes ("¸"))
+(define-letter-group "D" :after "C" :prefixes ("¹"))
+(define-letter-group "E" :after "D" :prefixes ("º"))
+(define-letter-group "F" :after "E" :prefixes ("»"))
+(define-letter-group "G" :after "F" :prefixes ("¼"))
+(define-letter-group "H" :after "G" :prefixes ("½"))
+(define-letter-group "I" :after "H" :prefixes ("¾"))
+(define-letter-group "J" :after "I" :prefixes ("¿"))
+(define-letter-group "K" :after "J" :prefixes ("À"))
+(define-letter-group "L" :after "K" :prefixes ("Á"))
+(define-letter-group "M" :after "L" :prefixes ("Â"))
+(define-letter-group "N" :after "M" :prefixes ("Ã"))
+(define-letter-group "O" :after "N" :prefixes ("Ä"))
+(define-letter-group "P" :after "O" :prefixes ("È"))
+(define-letter-group "Q" :after "P" :prefixes ("Ê"))
+(define-letter-group "R" :after "Q" :prefixes ("Ë"))
+(define-letter-group "S" :after "R" :prefixes ("Ð"))
+(define-letter-group "T" :after "S" :prefixes ("Ú"))
+(define-letter-group "U" :after "T" :prefixes ("à"))
+(define-letter-group "V" :after "U" :prefixes ("å"))
+(define-letter-group "W" :after "V" :prefixes ("æ"))
+(define-letter-group "X" :after "W" :prefixes ("ë"))
+(define-letter-group "Y" :after "X" :prefixes ("í"))
+(define-letter-group "Z" :after "Y" :prefixes ("ð"))
+
+(define-rule-set "sphinx-xy-alphabetize"
+
+  :rules  (("Ã€" "¶" :string)
+           ("Ä‚" "¶" :string)
+           ("Ã¢" "¶" :string)
+           ("Ã„" "¶" :string)
+           ("Ã " "¶" :string)
+           ("Ã…" "¶" :string)
+           ("Ãƒ" "¶" :string)
+           ("Ã�" "¶" :string)
+           ("Ã¡" "¶" :string)
+           ("Ã£" "¶" :string)
+           ("Ã‚" "¶" :string)
+           ("Äƒ" "¶" :string)
+           ("Ã¥" "¶" :string)
+           ("Ä…" "¶" :string)
+           ("Ã¤" "¶" :string)
+           ("Ä„" "¶" :string)
+           ("Ã¦" "¶º" :string)
+           ("Ã†" "¶º" :string)
+           ("Ä‡" "¸" :string)
+           ("Ä‰" "¸" :string)
+           ("Ã§" "¸" :string)
+           ("ÄŒ" "¸" :string)
+           ("Ä�" "¸" :string)
+           ("Äˆ" "¸" :string)
+           ("Ã‡" "¸" :string)
+           ("Ä†" "¸" :string)
+           ("Ä�" "¹" :string)
+           ("Ä�" "¹" :string)
+           ("ÄŽ" "¹" :string)
+           ("Ä‘" "¹" :string)
+           ("Ãª" "º" :string)
+           ("Ä˜" "º" :string)
+           ("Äš" "º" :string)
+           ("Ã«" "º" :string)
+           ("Ä›" "º" :string)
+           ("Ã©" "º" :string)
+           ("Ãˆ" "º" :string)
+           ("Ã‹" "º" :string)
+           ("Ã‰" "º" :string)
+           ("Ã¨" "º" :string)
+           ("ÃŠ" "º" :string)
+           ("Ä™" "º" :string)
+           ("Ä�" "¼" :string)
+           ("ÄŸ" "¼" :string)
+           ("Äž" "¼" :string)
+           ("Äœ" "¼" :string)
+           ("Ä¥" "½" :string)
+           ("Ä¤" "½" :string)
+           ("Ã�" "¾" :string)
+           ("Ã�" "¾" :string)
+           ("Ã¯" "¾" :string)
+           ("ÃŽ" "¾" :string)
+           ("Ã®" "¾" :string)
+           ("Ä±" "¾" :string)
+           ("Ä°" "¾" :string)
+           ("Ã" "¾" :string)
+           ("ÃŒ" "¾" :string)
+           ("Ã¬" "¾" :string)
+           ("Ä´" "¿" :string)
+           ("Äµ" "¿" :string)
+           ("Å‚" "Á" :string)
+           ("Å�" "Á" :string)
+           ("Ä¾" "Á" :string)
+           ("Ä½" "Á" :string)
+           ("Å„" "Ã" :string)
+           ("Åƒ" "Ã" :string)
+           ("Ã±" "Ã" :string)
+           ("Åˆ" "Ã" :string)
+           ("Ã‘" "Ã" :string)
+           ("Å‡" "Ã" :string)
+           ("Ã•" "Ä" :string)
+           ("Å�" "Ä" :string)
+           ("Ã³" "Ä" :string)
+           ("Ã¶" "Ä" :string)
+           ("Ã´" "Ä" :string)
+           ("Å‘" "Ä" :string)
+           ("Ã˜" "Ä" :string)
+           ("Ã–" "Ä" :string)
+           ("Ãµ" "Ä" :string)
+           ("Ã”" "Ä" :string)
+           ("Ã¸" "Ä" :string)
+           ("Ã“" "Ä" :string)
+           ("Ã’" "Ä" :string)
+           ("Ã²" "Ä" :string)
+           ("Å“" "Äº" :string)
+           ("Å’" "Äº" :string)
+           ("Å˜" "Ë" :string)
+           ("Å™" "Ë" :string)
+           ("Å”" "Ë" :string)
+           ("Å•" "Ë" :string)
+           ("Å�" "Ð" :string)
+           ("Åš" "Ð" :string)
+           ("È™" "Ð" :string)
+           ("ÅŸ" "Ð" :string)
+           ("Åœ" "Ð" :string)
+           ("Å›" "Ð" :string)
+           ("È˜" "Ð" :string)
+           ("Å¡" "Ð" :string)
+           ("Åž" "Ð" :string)
+           ("Å " "Ð" :string)
+           ("ÃŸ" "ÐÐ" :string)
+           ("Èš" "Ú" :string)
+           ("Å¤" "Ú" :string)
+           ("È›" "Ú" :string)
+           ("Å¥" "Ú" :string)
+           ("Ã»" "à" :string)
+           ("Å" "à" :string)
+           ("Å¯" "à" :string)
+           ("Å±" "à" :string)
+           ("Ã¹" "à" :string)
+           ("Å¬" "à" :string)
+           ("Ã™" "à" :string)
+           ("Å°" "à" :string)
+           ("Ãœ" "à" :string)
+           ("Å®" "à" :string)
+           ("Ãº" "à" :string)
+           ("Ãš" "à" :string)
+           ("Ã›" "à" :string)
+           ("Ã¼" "à" :string)
+           ("Ã¿" "í" :string)
+           ("Ã�" "í" :string)
+           ("Å¸" "í" :string)
+           ("Ã½" "í" :string)
+           ("Å»" "ð" :string)
+           ("Å½" "ð" :string)
+           ("Å¹" "ð" :string)
+           ("Å¾" "ð" :string)
+           ("Å¼" "ð" :string)
+           ("Åº" "ð" :string)
+           ("a" "¶" :string)
+           ("A" "¶" :string)
+           ("b" "·" :string)
+           ("B" "·" :string)
+           ("c" "¸" :string)
+           ("C" "¸" :string)
+           ("d" "¹" :string)
+           ("D" "¹" :string)
+           ("e" "º" :string)
+           ("E" "º" :string)
+           ("F" "»" :string)
+           ("f" "»" :string)
+           ("G" "¼" :string)
+           ("g" "¼" :string)
+           ("H" "½" :string)
+           ("h" "½" :string)
+           ("i" "¾" :string)
+           ("I" "¾" :string)
+           ("J" "¿" :string)
+           ("j" "¿" :string)
+           ("K" "À" :string)
+           ("k" "À" :string)
+           ("L" "Á" :string)
+           ("l" "Á" :string)
+           ("M" "Â" :string)
+           ("m" "Â" :string)
+           ("n" "Ã" :string)
+           ("N" "Ã" :string)
+           ("O" "Ä" :string)
+           ("o" "Ä" :string)
+           ("p" "È" :string)
+           ("P" "È" :string)
+           ("Q" "Ê" :string)
+           ("q" "Ê" :string)
+           ("r" "Ë" :string)
+           ("R" "Ë" :string)
+           ("S" "Ð" :string)
+           ("s" "Ð" :string)
+           ("t" "Ú" :string)
+           ("T" "Ú" :string)
+           ("u" "à" :string)
+           ("U" "à" :string)
+           ("v" "å" :string)
+           ("V" "å" :string)
+           ("W" "æ" :string)
+           ("w" "æ" :string)
+           ("x" "ë" :string)
+           ("X" "ë" :string)
+           ("Y" "í" :string)
+           ("y" "í" :string)
+           ("z" "ð" :string)
+           ("Z" "ð" :string)
+           ))
+
+(define-rule-set "sphinx-xy-resolve-diacritics"
+
+  :rules  (("Ä¤" "£" :string)
+           ("Ã³" "£" :string)
+           ("Ä¾" "£" :string)
+           ("Å˜" "£" :string)
+           ("Ä�" "£" :string)
+           ("Ä�" "£" :string)
+           ("Äš" "£" :string)
+           ("Ä¥" "£" :string)
+           ("ÄŒ" "£" :string)
+           ("Ä´" "£" :string)
+           ("Ä›" "£" :string)
+           ("Å¾" "£" :string)
+           ("ÄŽ" "£" :string)
+           ("Å™" "£" :string)
+           ("Å½" "£" :string)
+           ("Ä±" "£" :string)
+           ("Å¤" "£" :string)
+           ("Ã¡" "£" :string)
+           ("Ä�" "£" :string)
+           ("Ã�" "£" :string)
+           ("Åˆ" "£" :string)
+           ("Å " "£" :string)
+           ("Å‡" "£" :string)
+           ("Äµ" "£" :string)
+           ("Å¥" "£" :string)
+           ("Ã“" "£" :string)
+           ("Ã½" "£" :string)
+           ("Äœ" "£" :string)
+           ("Ãš" "£" :string)
+           ("Ä½" "£" :string)
+           ("Å¡" "£" :string)
+           ("Ã�" "£" :string)
+           ("Ãº" "£" :string)
+           ("Åš" "¤" :string)
+           ("Ä‡" "¤" :string)
+           ("Å�" "¤" :string)
+           ("Å‚" "¤" :string)
+           ("Å„" "¤" :string)
+           ("Ã€" "¤" :string)
+           ("Å¹" "¤" :string)
+           ("Ã " "¤" :string)
+           ("Åƒ" "¤" :string)
+           ("Ä�" "¤" :string)
+           ("Ã¿" "¤" :string)
+           ("Å›" "¤" :string)
+           ("Äž" "¤" :string)
+           ("ÄŸ" "¤" :string)
+           ("Ã™" "¤" :string)
+           ("Ä°" "¤" :string)
+           ("Ä‘" "¤" :string)
+           ("Ã¹" "¤" :string)
+           ("Èš" "¤" :string)
+           ("Ã©" "¤" :string)
+           ("Å•" "¤" :string)
+           ("Ä†" "¤" :string)
+           ("È›" "¤" :string)
+           ("Ã²" "¤" :string)
+           ("Åº" "¤" :string)
+           ("Ã’" "¤" :string)
+           ("Å¸" "¤" :string)
+           ("Å”" "¤" :string)
+           ("Ã‰" "¤" :string)
+           ("Ä‰" "¥" :string)
+           ("Ã´" "¥" :string)
+           ("Ã�" "¥" :string)
+           ("Å�" "¥" :string)
+           ("Å»" "¥" :string)
+           ("Ä‚" "¥" :string)
+           ("Åœ" "¥" :string)
+           ("Ã±" "¥" :string)
+           ("Å" "¥" :string)
+           ("Ã" "¥" :string)
+           ("Ãˆ" "¥" :string)
+           ("Ã”" "¥" :string)
+           ("Å¬" "¥" :string)
+           ("Å¼" "¥" :string)
+           ("Ã‘" "¥" :string)
+           ("Ã¨" "¥" :string)
+           ("Äˆ" "¥" :string)
+           ("Äƒ" "¥" :string)
+           ("Ã¢" "¦" :string)
+           ("Ã»" "¦" :string)
+           ("Ãª" "¦" :string)
+           ("Ã•" "¦" :string)
+           ("Ãµ" "¦" :string)
+           ("È™" "¦" :string)
+           ("Ã§" "¦" :string)
+           ("Ã‚" "¦" :string)
+           ("ÃŠ" "¦" :string)
+           ("Ã›" "¦" :string)
+           ("Ã‡" "¦" :string)
+           ("Ã¬" "¦" :string)
+           ("ÃŒ" "¦" :string)
+           ("È˜" "¦" :string)
+           ("Ã¶" "§" :string)
+           ("Ã–" "§" :string)
+           ("ÅŸ" "§" :string)
+           ("Å¯" "§" :string)
+           ("Ã«" "§" :string)
+           ("Ã£" "§" :string)
+           ("Ã®" "§" :string)
+           ("ÃŽ" "§" :string)
+           ("Ãƒ" "§" :string)
+           ("Åž" "§" :string)
+           ("Å®" "§" :string)
+           ("Ã‹" "§" :string)
+           ("Ã¯" "¨" :string)
+           ("Å�" "¨" :string)
+           ("Ã�" "¨" :string)
+           ("Ä˜" "¨" :string)
+           ("Å‘" "¨" :string)
+           ("Ãœ" "¨" :string)
+           ("Ã…" "¨" :string)
+           ("Ã¼" "¨" :string)
+           ("Ä™" "¨" :string)
+           ("Ã¥" "¨" :string)
+           ("Ã„" "©" :string)
+           ("Å±" "©" :string)
+           ("Ã˜" "©" :string)
+           ("Ã¸" "©" :string)
+           ("Å°" "©" :string)
+           ("Ã¤" "©" :string)
+           ("Ä„" "ª" :string)
+           ("Ä…" "ª" :string)
+           ("Å“" "ÿ" :string)
+           ("ÃŸ" "ÿ" :string)
+           ("Ã†" "ÿ" :string)
+           ("Å’" "ÿ" :string)
+           ("Ã¦" "ÿ" :string)
+           ("e" "¢" :string)
+           ("t" "¢" :string)
+           ("L" "¢" :string)
+           ("Y" "¢" :string)
+           ("J" "¢" :string)
+           ("a" "¢" :string)
+           ("p" "¢" :string)
+           ("u" "¢" :string)
+           ("j" "¢" :string)
+           ("b" "¢" :string)
+           ("G" "¢" :string)
+           ("U" "¢" :string)
+           ("F" "¢" :string)
+           ("H" "¢" :string)
+           ("i" "¢" :string)
+           ("z" "¢" :string)
+           ("c" "¢" :string)
+           ("l" "¢" :string)
+           ("A" "¢" :string)
+           ("Q" "¢" :string)
+           ("w" "¢" :string)
+           ("D" "¢" :string)
+           ("R" "¢" :string)
+           ("d" "¢" :string)
+           ("s" "¢" :string)
+           ("r" "¢" :string)
+           ("k" "¢" :string)
+           ("v" "¢" :string)
+           ("m" "¢" :string)
+           ("P" "¢" :string)
+           ("y" "¢" :string)
+           ("K" "¢" :string)
+           ("q" "¢" :string)
+           ("S" "¢" :string)
+           ("I" "¢" :string)
+           ("C" "¢" :string)
+           ("M" "¢" :string)
+           ("Z" "¢" :string)
+           ("T" "¢" :string)
+           ("W" "¢" :string)
+           ("B" "¢" :string)
+           ("h" "¢" :string)
+           ("x" "¢" :string)
+           ("X" "¢" :string)
+           ("f" "¢" :string)
+           ("E" "¢" :string)
+           ("V" "¢" :string)
+           ("N" "¢" :string)
+           ("O" "¢" :string)
+           ("o" "¢" :string)
+           ("g" "¢" :string)
+           ("n" "¢" :string)
+           ))
+
+(define-rule-set "sphinx-xy-resolve-case"
+
+  :rules  (("Ãš" "8" :string)
+           ("Å¸" "8" :string)
+           ("Ã‡" "8" :string)
+           ("Äˆ" "8" :string)
+           ("Å”" "8" :string)
+           ("Ä½" "8" :string)
+           ("Å®" "8" :string)
+           ("Ã�" "8" :string)
+           ("Ã‰" "8" :string)
+           ("Ã‹" "8" :string)
+           ("È˜" "8" :string)
+           ("ÃŒ" "8" :string)
+           ("ÃŠ" "8" :string)
+           ("Å‡" "8" :string)
+           ("Ä„" "8" :string)
+           ("Å " "8" :string)
+           ("Ã›" "8" :string)
+           ("Åž" "8" :string)
+           ("Ä†" "8" :string)
+           ("Ã’" "8" :string)
+           ("Äœ" "8" :string)
+           ("Ã‘" "8" :string)
+           ("Ã“" "8" :string)
+           ("ÃŽ" "8" :string)
+           ("Ã�" "8" :string)
+           ("Ãƒ" "8" :string)
+           ("Èš" "8" :string)
+           ("Ã…" "8" :string)
+           ("Äž" "8" :string)
+           ("Ãœ" "8" :string)
+           ("Ãˆ" "8" :string)
+           ("Ã”" "8" :string)
+           ("Ä°" "8" :string)
+           ("Å°" "8" :string)
+           ("Ã™" "8" :string)
+           ("Å¬" "8" :string)
+           ("Ã‚" "8" :string)
+           ("Å¤" "8" :string)
+           ("Åƒ" "8" :string)
+           ("ÄŽ" "8" :string)
+           ("Å¹" "8" :string)
+           ("Å½" "8" :string)
+           ("Ä�" "8" :string)
+           ("Åœ" "8" :string)
+           ("ÄŒ" "8" :string)
+           ("Ä´" "8" :string)
+           ("Ã–" "8" :string)
+           ("Ã˜" "8" :string)
+           ("Å»" "8" :string)
+           ("Å�" "8" :string)
+           ("Ä‚" "8" :string)
+           ("Äš" "8" :string)
+           ("Å�" "8" :string)
+           ("Ã•" "8" :string)
+           ("Ä˜" "8" :string)
+           ("Ã�" "8" :string)
+           ("Ã€" "8" :string)
+           ("Ä¤" "8" :string)
+           ("Ã„" "8" :string)
+           ("Åš" "8" :string)
+           ("Å˜" "8" :string)
+           ("Ã�" "8" :string)
+           ("Å’" "89" :string)
+           ("Ã†" "89" :string)
+           ("Ã¬" "9" :string)
+           ("Ã¨" "9" :string)
+           ("Ä…" "9" :string)
+           ("Å¡" "9" :string)
+           ("Ãº" "9" :string)
+           ("Ã¥" "9" :string)
+           ("Äƒ" "9" :string)
+           ("Ä™" "9" :string)
+           ("Ã¼" "9" :string)
+           ("Åº" "9" :string)
+           ("Ã²" "9" :string)
+           ("Å¥" "9" :string)
+           ("È›" "9" :string)
+           ("Äµ" "9" :string)
+           ("Å•" "9" :string)
+           ("Å¼" "9" :string)
+           ("Ã¤" "9" :string)
+           ("Ã½" "9" :string)
+           ("Ã¹" "9" :string)
+           ("Ã¡" "9" :string)
+           ("Ã©" "9" :string)
+           ("Ä�" "9" :string)
+           ("Åˆ" "9" :string)
+           ("Å›" "9" :string)
+           ("Ã¸" "9" :string)
+           ("Ã" "9" :string)
+           ("Ä‘" "9" :string)
+           ("Ä±" "9" :string)
+           ("ÄŸ" "9" :string)
+           ("Ã®" "9" :string)
+           ("Ã£" "9" :string)
+           ("Ã " "9" :string)
+           ("Å™" "9" :string)
+           ("Å‘" "9" :string)
+           ("Å¯" "9" :string)
+           ("È™" "9" :string)
+           ("Ã¿" "9" :string)
+           ("Ã«" "9" :string)
+           ("Å" "9" :string)
+           ("Ã§" "9" :string)
+           ("Å±" "9" :string)
+           ("Ã±" "9" :string)
+           ("Ãµ" "9" :string)
+           ("Ä›" "9" :string)
+           ("ÅŸ" "9" :string)
+           ("Å¾" "9" :string)
+           ("Ä�" "9" :string)
+           ("Å�" "9" :string)
+           ("Å„" "9" :string)
+           ("Ã»" "9" :string)
+           ("Å‚" "9" :string)
+           ("Ä�" "9" :string)
+           ("Ä¥" "9" :string)
+           ("Ãª" "9" :string)
+           ("Ã´" "9" :string)
+           ("Ä‰" "9" :string)
+           ("Ã¢" "9" :string)
+           ("Ä‡" "9" :string)
+           ("Ã¯" "9" :string)
+           ("Ã¶" "9" :string)
+           ("Ä¾" "9" :string)
+           ("Ã³" "9" :string)
+           ("Ã¦" "99" :string)
+           ("ÃŸ" "99" :string)
+           ("Å“" "99" :string)
+           ("N" "8" :string)
+           ("V" "8" :string)
+           ("O" "8" :string)
+           ("X" "8" :string)
+           ("E" "8" :string)
+           ("P" "8" :string)
+           ("K" "8" :string)
+           ("T" "8" :string)
+           ("Z" "8" :string)
+           ("M" "8" :string)
+           ("C" "8" :string)
+           ("I" "8" :string)
+           ("S" "8" :string)
+           ("B" "8" :string)
+           ("W" "8" :string)
+           ("D" "8" :string)
+           ("R" "8" :string)
+           ("H" "8" :string)
+           ("F" "8" :string)
+           ("Q" "8" :string)
+           ("A" "8" :string)
+           ("G" "8" :string)
+           ("U" "8" :string)
+           ("J" "8" :string)
+           ("Y" "8" :string)
+           ("L" "8" :string)
+           ("o" "9" :string)
+           ("n" "9" :string)
+           ("g" "9" :string)
+           ("x" "9" :string)
+           ("f" "9" :string)
+           ("y" "9" :string)
+           ("q" "9" :string)
+           ("h" "9" :string)
+           ("w" "9" :string)
+           ("s" "9" :string)
+           ("d" "9" :string)
+           ("v" "9" :string)
+           ("k" "9" :string)
+           ("r" "9" :string)
+           ("m" "9" :string)
+           ("z" "9" :string)
+           ("c" "9" :string)
+           ("i" "9" :string)
+           ("l" "9" :string)
+           ("b" "9" :string)
+           ("j" "9" :string)
+           ("a" "9" :string)
+           ("p" "9" :string)
+           ("u" "9" :string)
+           ("t" "9" :string)
+           ("e" "9" :string)
+           ))
+
+(use-rule-set :run 0
+	      :rule-set ("sphinx-xy-alphabetize"))
+(use-rule-set :run 1
+	      :rule-set ("sphinx-xy-resolve-diacritics"))
+(use-rule-set :run 2
+	      :rule-set ("sphinx-xy-resolve-case"))
@@ -0,0 +1,64 @@
+# Makefile for Sphinx LaTeX output
+
+ALLDOCS = $(basename $(wildcard *.tex))
+ALLPDF = $(addsuffix .pdf,$(ALLDOCS))
+ALLDVI = $(addsuffix .dvi,$(ALLDOCS))
+ALLXDV =
+ALLPS  = $(addsuffix .ps,$(ALLDOCS))
+
+# Prefix for archive names
+ARCHIVEPREFIX =
+# Additional LaTeX options (passed via variables in latexmkrc/latexmkjarc file)
+export LATEXOPTS ?=
+# Additional latexmk options
+LATEXMKOPTS ?=
+# format: pdf or dvi (used only by archive targets)
+FMT = pdf
+
+LATEX = latexmk -dvi
+PDFLATEX = latexmk -pdf -dvi- -ps-
+
+
+%.dvi: %.tex FORCE_MAKE
+	$(LATEX) $(LATEXMKOPTS) '$<'
+
+%.ps: %.dvi
+	dvips '$<'
+
+%.pdf: %.tex FORCE_MAKE
+	$(PDFLATEX) $(LATEXMKOPTS) '$<'
+
+all: $(ALLPDF)
+
+all-dvi: $(ALLDVI)
+
+all-ps: $(ALLPS)
+
+all-pdf: $(ALLPDF)
+
+zip: all-$(FMT)
+	mkdir $(ARCHIVEPREFIX)docs-$(FMT)
+	cp $(ALLPDF) $(ARCHIVEPREFIX)docs-$(FMT)
+	zip -q -r -9 $(ARCHIVEPREFIX)docs-$(FMT).zip $(ARCHIVEPREFIX)docs-$(FMT)
+	rm -r $(ARCHIVEPREFIX)docs-$(FMT)
+
+tar: all-$(FMT)
+	mkdir $(ARCHIVEPREFIX)docs-$(FMT)
+	cp $(ALLPDF) $(ARCHIVEPREFIX)docs-$(FMT)
+	tar cf $(ARCHIVEPREFIX)docs-$(FMT).tar $(ARCHIVEPREFIX)docs-$(FMT)
+	rm -r $(ARCHIVEPREFIX)docs-$(FMT)
+
+gz: tar
+	gzip -9 < $(ARCHIVEPREFIX)docs-$(FMT).tar > $(ARCHIVEPREFIX)docs-$(FMT).tar.gz
+
+bz2: tar
+	bzip2 -9 -k $(ARCHIVEPREFIX)docs-$(FMT).tar
+
+xz: tar
+	xz -9 -k $(ARCHIVEPREFIX)docs-$(FMT).tar
+
+clean:
+	rm -f *.log *.ind *.aux *.toc *.syn *.idx *.out *.ilg *.pla *.ps *.tar *.tar.gz *.tar.bz2 *.tar.xz $(ALLPDF) $(ALLDVI) $(ALLXDV) *.fls *.fdb_latexmk
+
+.PHONY: all all-pdf all-dvi all-ps clean zip tar gz bz2 xz
+.PHONY: FORCE_MAKE
@@ -0,0 +1,269 @@
+\NeedsTeXFormat{LaTeX2e}
+\ProvidesPackage{footnotehyper-sphinx}%
+ [2017/10/27 v1.7 hyperref aware footnote.sty for sphinx (JFB)]
+%%
+%% Package: footnotehyper-sphinx
+%% Version: based on footnotehyper.sty 2017/03/07 v1.0
+%% as available at https://www.ctan.org/pkg/footnotehyper
+%% License: the one applying to Sphinx
+%%
+%% Refer to the PDF documentation  at https://www.ctan.org/pkg/footnotehyper for
+%% the code comments.
+%%
+%% Differences:
+%% 1. a partial tabulary compatibility layer added (enough for Sphinx mark-up),
+%% 2. use of \spx@opt@BeforeFootnote from sphinx.sty,
+%% 3. use of \sphinxunactivateextrasandspace from sphinx.sty,
+%% 4. macro definition \sphinxfootnotemark,
+%% 5. macro definition \sphinxlongtablepatch
+%% 6. replaced an \undefined by \@undefined
+\DeclareOption*{\PackageWarning{footnotehyper-sphinx}{Option `\CurrentOption' is unknown}}%
+\ProcessOptions\relax
+\newbox\FNH@notes
+\newdimen\FNH@width
+\let\FNH@colwidth\columnwidth
+\newif\ifFNH@savingnotes
+\AtBeginDocument {%
+    \let\FNH@latex@footnote    \footnote
+    \let\FNH@latex@footnotetext\footnotetext
+    \let\FNH@H@@footnotetext   \@footnotetext
+    \newenvironment{savenotes}
+        {\FNH@savenotes\ignorespaces}{\FNH@spewnotes\ignorespacesafterend}%
+    \let\spewnotes      \FNH@spewnotes
+    \let\footnote       \FNH@footnote
+    \let\footnotetext   \FNH@footnotetext
+    \let\endfootnote    \FNH@endfntext
+    \let\endfootnotetext\FNH@endfntext
+    \@ifpackageloaded{hyperref}
+     {\ifHy@hyperfootnotes
+         \let\FNH@H@@footnotetext\H@@footnotetext
+      \else
+         \let\FNH@hyper@fntext\FNH@nohyp@fntext
+      \fi}%
+     {\let\FNH@hyper@fntext\FNH@nohyp@fntext}%
+}%
+\def\FNH@hyper@fntext{\FNH@fntext\FNH@hyper@fntext@i}%
+\def\FNH@nohyp@fntext{\FNH@fntext\FNH@nohyp@fntext@i}%
+\def\FNH@fntext #1{%
+  \ifx\ifmeasuring@\@undefined
+    \expandafter\@secondoftwo\else\expandafter\@firstofone\fi
+% these two lines modified for Sphinx (tabulary compatibility):
+    {\ifmeasuring@\expandafter\@gobbletwo\else\expandafter\@firstofone\fi}%
+    {\ifx\equation$\expandafter\@gobbletwo\fi #1}%$
+}%
+\long\def\FNH@hyper@fntext@i#1{%
+  \global\setbox\FNH@notes\vbox
+  {\unvbox\FNH@notes
+   \FNH@startnote
+   \@makefntext
+    {\rule\z@\footnotesep\ignorespaces
+     \ifHy@nesting\expandafter\ltx@firstoftwo
+             \else\expandafter\ltx@secondoftwo
+     \fi
+     {\expandafter\hyper@@anchor\expandafter{\Hy@footnote@currentHref}{#1}}%
+     {\Hy@raisedlink
+       {\expandafter\hyper@@anchor\expandafter{\Hy@footnote@currentHref}%
+       {\relax}}%
+      \let\@currentHref\Hy@footnote@currentHref
+      \let\@currentlabelname\@empty
+      #1}%
+     \@finalstrut\strutbox
+    }%
+   \FNH@endnote
+  }%
+}%
+\long\def\FNH@nohyp@fntext@i#1{%
+  \global\setbox\FNH@notes\vbox
+  {\unvbox\FNH@notes
+   \FNH@startnote
+   \@makefntext{\rule\z@\footnotesep\ignorespaces#1\@finalstrut\strutbox}%
+   \FNH@endnote
+  }%
+}%
+\def\FNH@startnote{%
+  \hsize\FNH@colwidth
+  \interlinepenalty\interfootnotelinepenalty
+  \reset@font\footnotesize
+  \floatingpenalty\@MM
+  \@parboxrestore
+  \protected@edef\@currentlabel{\csname p@\@mpfn\endcsname\@thefnmark}%
+  \color@begingroup
+}%
+\def\FNH@endnote{\color@endgroup}%
+\def\FNH@savenotes{%
+  \begingroup
+  \ifFNH@savingnotes\else
+    \FNH@savingnotestrue
+    \let\@footnotetext    \FNH@hyper@fntext
+    \let\@mpfootnotetext  \FNH@hyper@fntext
+    \let\H@@mpfootnotetext\FNH@nohyp@fntext
+    \FNH@width\columnwidth
+    \let\FNH@colwidth\FNH@width
+    \global\setbox\FNH@notes\box\voidb@x
+    \let\FNH@thempfn\thempfn
+    \let\FNH@mpfn\@mpfn
+    \ifx\@minipagerestore\relax\let\@minipagerestore\@empty\fi
+    \expandafter\def\expandafter\@minipagerestore\expandafter{%
+      \@minipagerestore
+      \let\thempfn\FNH@thempfn
+      \let\@mpfn\FNH@mpfn
+    }%
+  \fi
+}%
+\def\FNH@spewnotes {%
+  \endgroup
+  \ifFNH@savingnotes\else
+   \ifvoid\FNH@notes\else
+    \begingroup
+     \let\@makefntext\@empty
+     \let\@finalstrut\@gobble
+     \let\rule\@gobbletwo
+     \FNH@H@@footnotetext{\unvbox\FNH@notes}%
+    \endgroup
+   \fi
+  \fi
+}%
+\def\FNH@footnote@envname    {footnote}%
+\def\FNH@footnotetext@envname{footnotetext}%
+\def\FNH@footnote{%
+% this line added for Sphinx:
+    \spx@opt@BeforeFootnote
+    \ifx\@currenvir\FNH@footnote@envname
+        \expandafter\FNH@footnoteenv
+    \else
+        \expandafter\FNH@latex@footnote
+    \fi
+}%
+\def\FNH@footnoteenv{%
+% this line added for Sphinx (footnotes in parsed literal blocks):
+    \catcode13=5 \sphinxunactivateextrasandspace
+    \@ifnextchar[%
+      \FNH@footnoteenv@i %]
+      {\stepcounter\@mpfn
+       \protected@xdef\@thefnmark{\thempfn}%
+       \@footnotemark
+       \def\FNH@endfntext@fntext{\@footnotetext}%
+       \FNH@startfntext}%
+}%
+\def\FNH@footnoteenv@i[#1]{%
+    \begingroup
+     \csname c@\@mpfn\endcsname #1\relax
+     \unrestored@protected@xdef\@thefnmark{\thempfn}%
+    \endgroup
+    \@footnotemark
+    \def\FNH@endfntext@fntext{\@footnotetext}%
+    \FNH@startfntext
+}%
+\def\FNH@footnotetext{%
+    \ifx\@currenvir\FNH@footnotetext@envname
+        \expandafter\FNH@footnotetextenv
+    \else
+        \expandafter\FNH@latex@footnotetext
+    \fi
+}%
+\def\FNH@footnotetextenv{%
+    \@ifnextchar[%
+      \FNH@footnotetextenv@i %]
+      {\protected@xdef\@thefnmark{\thempfn}%
+       \def\FNH@endfntext@fntext{\@footnotetext}%
+       \FNH@startfntext}%
+}%
+\def\FNH@footnotetextenv@i[#1]{%
+    \begingroup
+     \csname c@\@mpfn\endcsname #1\relax
+     \unrestored@protected@xdef\@thefnmark{\thempfn}%
+    \endgroup
+    \ifFNH@savingnotes
+      \def\FNH@endfntext@fntext{\FNH@nohyp@fntext}%
+    \else
+      \def\FNH@endfntext@fntext{\FNH@H@@footnotetext}%
+    \fi
+    \FNH@startfntext
+}%
+\def\FNH@startfntext{%
+  \setbox\z@\vbox\bgroup
+    \FNH@startnote
+    \FNH@prefntext
+    \rule\z@\footnotesep\ignorespaces
+}%
+\def\FNH@endfntext {%
+    \@finalstrut\strutbox
+    \FNH@postfntext
+    \FNH@endnote
+    \egroup
+  \begingroup
+    \let\@makefntext\@empty\let\@finalstrut\@gobble\let\rule\@gobbletwo
+    \FNH@endfntext@fntext {\unvbox\z@}%
+  \endgroup
+}%
+\AtBeginDocument{%
+   \let\FNH@@makefntext\@makefntext
+   \ifx\@makefntextFB\@undefined
+   \expandafter\@gobble\else\expandafter\@firstofone\fi
+   {\ifFBFrenchFootnotes \let\FNH@@makefntext\@makefntextFB \else
+                         \let\FNH@@makefntext\@makefntextORI\fi}%
+   \expandafter\FNH@check@a\FNH@@makefntext{1.2!3?4,}%
+               \FNH@@@1.2!3?4,\FNH@@@\relax
+}%
+\long\def\FNH@check@a #11.2!3?4,#2\FNH@@@#3{%
+    \ifx\relax#3\expandafter\@firstoftwo\else\expandafter\@secondoftwo\fi
+    \FNH@bad@makefntext@alert
+    {\def\FNH@prefntext{#1}\def\FNH@postfntext{#2}\FNH@check@b}%
+}%
+\def\FNH@check@b #1\relax{%
+    \expandafter\expandafter\expandafter\FNH@check@c
+    \expandafter\meaning\expandafter\FNH@prefntext
+    \meaning\FNH@postfntext1.2!3?4,\FNH@check@c\relax
+}%
+\def\FNH@check@c #11.2!3?4,#2#3\relax{%
+    \ifx\FNH@check@c#2\expandafter\@gobble\fi\FNH@bad@makefntext@alert
+}%
+% slight reformulation for Sphinx
+\def\FNH@bad@makefntext@alert{%
+  \PackageWarningNoLine{footnotehyper-sphinx}%
+    {Footnotes will be sub-optimal, sorry. This is due to the document class or^^J
+  some package modifying macro \string\@makefntext.^^J
+  You can try to report this incompatibility at^^J
+  https://github.com/sphinx-doc/sphinx with this info:}%
+    \typeout{\meaning\@makefntext}%
+    \let\FNH@prefntext\@empty\let\FNH@postfntext\@empty
+}%
+% this macro from original footnote.sty is not used anymore by Sphinx
+% but for simplicity sake let's just keep it as is
+\def\makesavenoteenv{\@ifnextchar[\FNH@msne@ii\FNH@msne@i}%]
+\def\FNH@msne@i #1{%
+  \expandafter\let\csname FNH$#1\expandafter\endcsname %$
+                  \csname #1\endcsname
+  \expandafter\let\csname endFNH$#1\expandafter\endcsname %$
+                  \csname end#1\endcsname
+  \FNH@msne@ii[#1]{FNH$#1}%$
+}%
+\def\FNH@msne@ii[#1]#2{%
+  \expandafter\edef\csname#1\endcsname{%
+    \noexpand\savenotes
+    \expandafter\noexpand\csname#2\endcsname
+  }%
+  \expandafter\edef\csname end#1\endcsname{%
+    \expandafter\noexpand\csname end#2\endcsname
+    \noexpand\expandafter
+    \noexpand\spewnotes
+    \noexpand\if@endpe\noexpand\@endpetrue\noexpand\fi
+  }%
+}%
+% end of footnotehyper 2017/02/16 v0.99
+% some extras for Sphinx :
+% \sphinxfootnotemark: usable in section titles and silently removed from TOCs.
+\def\sphinxfootnotemark [#1]%
+   {\ifx\thepage\relax\else\protect\spx@opt@BeforeFootnote
+                             \protect\footnotemark[#1]\fi}%
+\AtBeginDocument{%
+   % let hyperref less complain
+   \pdfstringdefDisableCommands{\def\sphinxfootnotemark [#1]{}}%
+   % to obtain hyperlinked footnotes in longtable environment we must replace
+   % hyperref's patch of longtable's patch of \@footnotetext by our own
+   \let\LT@p@ftntext\FNH@hyper@fntext
+   % this *requires* longtable to be used always wrapped in savenotes environment
+}%
+\endinput
+%%
+%% End of file `footnotehyper-sphinx.sty'.
@@ -0,0 +1,2 @@
+
+<meta http-equiv="Refresh" content="0; url=chapter1.html" />
@@ -0,0 +1,22 @@
+$latex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' -kanji=utf8 %O %S';
+$dvipdf = 'dvipdfmx %O -o %D %S';
+$makeindex = 'internal mendex %S %B %D';
+sub mendex {
+  my ($source, $basename, $destination) = @_;
+  my $dictfile = $basename . ".dic";
+  unlink($destination);
+  system("mendex", "-U", "-f", "-d", $dictfile, "-s", "python.ist", $source);
+  if ($? > 0) {
+    print("mendex exited with error code $? (ignored)\n");
+  }
+  if (!-e $destination) {
+    # create an empty .ind file if nothing
+    open(FH, ">" . $destination);
+    close(FH);
+  }
+  return 0;
+}
+add_cus_dep( "glo", "gls", 0, "makeglo" );
+sub makeglo {
+ return system( "mendex -J -f -s gglo.ist -o '$_[0].gls' '$_[0].glo'" );
+}
@@ -0,0 +1,9 @@
+$latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S';
+$pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S';
+$lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S';
+$xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S';
+$makeindex = 'makeindex -s python.ist %O -o %D %S';
+add_cus_dep( "glo", "gls", 0, "makeglo" );
+sub makeglo {
+ return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" );
+}
@@ -0,0 +1,31 @@
+@ECHO OFF
+
+REM Command file for Sphinx documentation
+
+pushd %~dp0
+
+set PDFLATEX=latexmk -pdf -dvi- -ps-
+
+set "LATEXOPTS= "
+
+if "%1" == "" goto all-pdf
+
+if "%1" == "all-pdf" (
+	:all-pdf
+	for %%i in (*.tex) do (
+		%PDFLATEX% %LATEXMKOPTS% %%i
+	)
+	goto end
+)
+
+if "%1" == "all-pdf-ja" (
+	goto all-pdf
+)
+
+if "%1" == "clean" (
+	del /q /s *.dvi *.log *.ind *.aux *.toc *.syn *.idx *.out *.ilg *.pla *.ps *.tar *.tar.gz *.tar.bz2 *.tar.xz *.fls *.fdb_latexmk
+	goto end
+)
+
+:end
+popd
@@ -0,0 +1,507 @@
+\relax 
+\providecommand\hyper@newdestlabel[2]{}
+\providecommand\HyperFirstAtBeginDocument{\AtBeginDocument}
+\HyperFirstAtBeginDocument{\ifx\hyper@anchor\@undefined
+\global\let\oldcontentsline\contentsline
+\gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}}
+\global\let\oldnewlabel\newlabel
+\gdef\newlabel#1#2{\newlabelxx{#1}#2}
+\gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}}
+\AtEndDocument{\ifx\hyper@anchor\@undefined
+\let\contentsline\oldcontentsline
+\let\newlabel\oldnewlabel
+\fi}
+\fi}
+\global\let\hyper@last\relax 
+\gdef\HyperFirstAtBeginDocument#1{#1}
+\providecommand\HyField@AuxAddToFields[1]{}
+\providecommand\HyField@AuxAddToCoFields[2]{}
+\select@language{english}
+\@writefile{toc}{\select@language{english}}
+\@writefile{lof}{\select@language{english}}
+\@writefile{lot}{\select@language{english}}
+\newlabel{chapter1::doc}{{}{1}{}{section*.2}{}}
+\@writefile{toc}{\contentsline {chapter}{\numberline {1}Introduction}{3}{chapter.1}}
+\@writefile{lof}{\addvspace {10\p@ }}
+\@writefile{lot}{\addvspace {10\p@ }}
+\newlabel{chapter1:introduction}{{1}{3}{Introduction}{chapter.1}{}}
+\@writefile{toc}{\contentsline {chapter}{\numberline {2}Learning outcomes}{5}{chapter.2}}
+\@writefile{lof}{\addvspace {10\p@ }}
+\@writefile{lot}{\addvspace {10\p@ }}
+\newlabel{chapter1:learning-outcomes}{{2}{5}{Learning outcomes}{chapter.2}{}}
+\@writefile{toc}{\contentsline {chapter}{\numberline {3}Machine Learning, a small (and probably biased) introduction}{7}{chapter.3}}
+\@writefile{lof}{\addvspace {10\p@ }}
+\@writefile{lot}{\addvspace {10\p@ }}
+\newlabel{chapter1:machine-learning-a-small-and-probably-biased-introduction}{{3}{7}{Machine Learning, a small (and probably biased) introduction}{chapter.3}{}}
+\@writefile{toc}{\contentsline {chapter}{\numberline {4}Machine Learning, an extremely rich field}{9}{chapter.4}}
+\@writefile{lof}{\addvspace {10\p@ }}
+\@writefile{lot}{\addvspace {10\p@ }}
+\newlabel{chapter1:machine-learning-an-extremely-rich-field}{{4}{9}{Machine Learning, an extremely rich field}{chapter.4}{}}
+\@writefile{toc}{\contentsline {chapter}{\numberline {5}A multidisciplinary approach}{11}{chapter.5}}
+\@writefile{lof}{\addvspace {10\p@ }}
+\@writefile{lot}{\addvspace {10\p@ }}
+\newlabel{chapter1:a-multidisciplinary-approach}{{5}{11}{A multidisciplinary approach}{chapter.5}{}}
+\@writefile{toc}{\contentsline {chapter}{\numberline {6}Types of Machine Learning}{13}{chapter.6}}
+\@writefile{lof}{\addvspace {10\p@ }}
+\@writefile{lot}{\addvspace {10\p@ }}
+\newlabel{chapter1:types-of-machine-learning}{{6}{13}{Types of Machine Learning}{chapter.6}{}}
+\@writefile{toc}{\contentsline {chapter}{\numberline {7}Essential elements of ML}{15}{chapter.7}}
+\@writefile{lof}{\addvspace {10\p@ }}
+\@writefile{lot}{\addvspace {10\p@ }}
+\newlabel{chapter1:essential-elements-of-ml}{{7}{15}{Essential elements of ML}{chapter.7}{}}
+\@writefile{toc}{\contentsline {chapter}{\numberline {8}An optimization/minimization problem}{17}{chapter.8}}
+\@writefile{lof}{\addvspace {10\p@ }}
+\@writefile{lot}{\addvspace {10\p@ }}
+\newlabel{chapter1:an-optimization-minimization-problem}{{8}{17}{An optimization/minimization problem}{chapter.8}{}}
+\@writefile{toc}{\contentsline {chapter}{\numberline {9}A Frequentist approach to data analysis}{19}{chapter.9}}
+\@writefile{lof}{\addvspace {10\p@ }}
+\@writefile{lot}{\addvspace {10\p@ }}
+\newlabel{chapter1:a-frequentist-approach-to-data-analysis}{{9}{19}{A Frequentist approach to data analysis}{chapter.9}{}}
+\@writefile{toc}{\contentsline {chapter}{\numberline {10}What is a good model?}{21}{chapter.10}}
+\@writefile{lof}{\addvspace {10\p@ }}
+\@writefile{lot}{\addvspace {10\p@ }}
+\newlabel{chapter1:what-is-a-good-model}{{10}{21}{What is a good model?}{chapter.10}{}}
+\@writefile{toc}{\contentsline {chapter}{\numberline {11}What is a good model? Can we define it?}{23}{chapter.11}}
+\@writefile{lof}{\addvspace {10\p@ }}
+\@writefile{lot}{\addvspace {10\p@ }}
+\newlabel{chapter1:what-is-a-good-model-can-we-define-it}{{11}{23}{What is a good model? Can we define it?}{chapter.11}{}}
+\@writefile{toc}{\contentsline {chapter}{\numberline {12}Choice of Programming Language}{25}{chapter.12}}
+\@writefile{lof}{\addvspace {10\p@ }}
+\@writefile{lot}{\addvspace {10\p@ }}
+\newlabel{chapter1:choice-of-programming-language}{{12}{25}{Choice of Programming Language}{chapter.12}{}}
+\@writefile{toc}{\contentsline {chapter}{\numberline {13}Data handling, machine learning and ethical aspects}{27}{chapter.13}}
+\@writefile{lof}{\addvspace {10\p@ }}
+\@writefile{lot}{\addvspace {10\p@ }}
+\newlabel{chapter1:data-handling-machine-learning-and-ethical-aspects}{{13}{27}{Data handling, machine learning and ethical aspects}{chapter.13}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {13.1}Data Analysis and Machine Learning: Getting started, our first data and Machine Learning encounters}{28}{section.13.1}}
+\newlabel{chapter2:data-analysis-and-machine-learning-getting-started-our-first-data-and-machine-learning-encounters}{{13.1}{28}{Data Analysis and Machine Learning: Getting started, our first data and Machine Learning encounters}{section.13.1}{}}
+\newlabel{chapter2::doc}{{13.1}{28}{Data Analysis and Machine Learning: Getting started, our first data and Machine Learning encounters}{section.13.1}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {13.1.1}Introduction}{28}{subsection.13.1.1}}
+\newlabel{chapter2:introduction}{{13.1.1}{28}{Introduction}{subsection.13.1.1}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {13.1.2}What is Machine Learning?}{28}{subsection.13.1.2}}
+\newlabel{chapter2:what-is-machine-learning}{{13.1.2}{28}{What is Machine Learning?}{subsection.13.1.2}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {13.1.3}Types of Machine Learning}{29}{subsection.13.1.3}}
+\newlabel{chapter2:types-of-machine-learning}{{13.1.3}{29}{Types of Machine Learning}{subsection.13.1.3}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {13.1.4}Software and needed installations}{30}{subsection.13.1.4}}
+\newlabel{chapter2:software-and-needed-installations}{{13.1.4}{30}{Software and needed installations}{subsection.13.1.4}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {13.1.5}Python installers}{30}{subsection.13.1.5}}
+\newlabel{chapter2:python-installers}{{13.1.5}{30}{Python installers}{subsection.13.1.5}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {13.1.6}Useful Python libraries}{31}{subsection.13.1.6}}
+\newlabel{chapter2:useful-python-libraries}{{13.1.6}{31}{Useful Python libraries}{subsection.13.1.6}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {13.1.7}Installing R, C++, cython or Julia}{31}{subsection.13.1.7}}
+\newlabel{chapter2:installing-r-c-cython-or-julia}{{13.1.7}{31}{Installing R, C++, cython or Julia}{subsection.13.1.7}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {13.1.8}Installing R, C++, cython, Numba etc}{31}{subsection.13.1.8}}
+\newlabel{chapter2:installing-r-c-cython-numba-etc}{{13.1.8}{31}{Installing R, C++, cython, Numba etc}{subsection.13.1.8}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {13.1.9}Numpy examples and Important Matrix and vector handling packages}{32}{subsection.13.1.9}}
+\newlabel{chapter2:numpy-examples-and-important-matrix-and-vector-handling-packages}{{13.1.9}{32}{Numpy examples and Important Matrix and vector handling packages}{subsection.13.1.9}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {13.1.10}Basic Matrix Features}{32}{subsection.13.1.10}}
+\newlabel{chapter2:basic-matrix-features}{{13.1.10}{32}{Basic Matrix Features}{subsection.13.1.10}{}}
+\@writefile{toc}{\contentsline {subsubsection}{Some famous Matrices}{32}{subsubsection*.3}}
+\newlabel{chapter2:some-famous-matrices}{{13.1.10}{32}{Some famous Matrices}{subsubsection*.3}{}}
+\@writefile{toc}{\contentsline {subsubsection}{More Basic Matrix Features}{33}{subsubsection*.4}}
+\newlabel{chapter2:more-basic-matrix-features}{{13.1.10}{33}{More Basic Matrix Features}{subsubsection*.4}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {13.1.11}Numpy and arrays}{33}{subsection.13.1.11}}
+\newlabel{chapter2:numpy-and-arrays}{{13.1.11}{33}{Numpy and arrays}{subsection.13.1.11}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {13.1.12}Matrices in Python}{34}{subsection.13.1.12}}
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@@ -0,0 +1,228 @@
+\select@language {english}
+\contentsline {chapter}{\numberline {1}Introduction}{3}{chapter.1}
+\contentsline {chapter}{\numberline {2}Learning outcomes}{5}{chapter.2}
+\contentsline {chapter}{\numberline {3}Machine Learning, a small (and probably biased) introduction}{7}{chapter.3}
+\contentsline {chapter}{\numberline {4}Machine Learning, an extremely rich field}{9}{chapter.4}
+\contentsline {chapter}{\numberline {5}A multidisciplinary approach}{11}{chapter.5}
+\contentsline {chapter}{\numberline {6}Types of Machine Learning}{13}{chapter.6}
+\contentsline {chapter}{\numberline {7}Essential elements of ML}{15}{chapter.7}
+\contentsline {chapter}{\numberline {8}An optimization/minimization problem}{17}{chapter.8}
+\contentsline {chapter}{\numberline {9}A Frequentist approach to data analysis}{19}{chapter.9}
+\contentsline {chapter}{\numberline {10}What is a good model?}{21}{chapter.10}
+\contentsline {chapter}{\numberline {11}What is a good model? Can we define it?}{23}{chapter.11}
+\contentsline {chapter}{\numberline {12}Choice of Programming Language}{25}{chapter.12}
+\contentsline {chapter}{\numberline {13}Data handling, machine learning and ethical aspects}{27}{chapter.13}
+\contentsline {section}{\numberline {13.1}Data Analysis and Machine Learning: Getting started, our first data and Machine Learning encounters}{28}{section.13.1}
+\contentsline {subsection}{\numberline {13.1.1}Introduction}{28}{subsection.13.1.1}
+\contentsline {subsection}{\numberline {13.1.2}What is Machine Learning?}{28}{subsection.13.1.2}
+\contentsline {subsection}{\numberline {13.1.3}Types of Machine Learning}{29}{subsection.13.1.3}
+\contentsline {subsection}{\numberline {13.1.4}Software and needed installations}{30}{subsection.13.1.4}
+\contentsline {subsection}{\numberline {13.1.5}Python installers}{30}{subsection.13.1.5}
+\contentsline {subsection}{\numberline {13.1.6}Useful Python libraries}{31}{subsection.13.1.6}
+\contentsline {subsection}{\numberline {13.1.7}Installing R, C++, cython or Julia}{31}{subsection.13.1.7}
+\contentsline {subsection}{\numberline {13.1.8}Installing R, C++, cython, Numba etc}{31}{subsection.13.1.8}
+\contentsline {subsection}{\numberline {13.1.9}Numpy examples and Important Matrix and vector handling packages}{32}{subsection.13.1.9}
+\contentsline {subsection}{\numberline {13.1.10}Basic Matrix Features}{32}{subsection.13.1.10}
+\contentsline {subsubsection}{Some famous Matrices}{32}{subsubsection*.3}
+\contentsline {subsubsection}{More Basic Matrix Features}{33}{subsubsection*.4}
+\contentsline {subsection}{\numberline {13.1.11}Numpy and arrays}{33}{subsection.13.1.11}
+\contentsline {subsection}{\numberline {13.1.12}Matrices in Python}{34}{subsection.13.1.12}
+\contentsline {subsection}{\numberline {13.1.13}Meet the Pandas}{38}{subsection.13.1.13}
+\contentsline {subsection}{\numberline {13.1.14}Reading Data and fitting}{43}{subsection.13.1.14}
+\contentsline {subsubsection}{Simple linear regression model using \sphinxstylestrong {scikit\sphinxhyphen {}learn}}{43}{subsubsection*.5}
+\contentsline {subsubsection}{To our real data: nuclear binding energies. Brief reminder on masses and binding energies}{51}{subsubsection*.6}
+\contentsline {subsubsection}{Organizing our data}{52}{subsubsection*.7}
+\contentsline {subsubsection}{Seeing the wood for the trees}{56}{subsubsection*.8}
+\contentsline {subsubsection}{And what about using neural networks?}{58}{subsubsection*.9}
+\contentsline {subsection}{\numberline {13.1.15}A first summary}{62}{subsection.13.1.15}
+\contentsline {section}{\numberline {13.2}Data Analysis and Machine Learning: Elements of Probability Theory and Statistical Data Analysis}{63}{section.13.2}
+\contentsline {subsection}{\numberline {13.2.1}To do list}{63}{subsection.13.2.1}
+\contentsline {subsection}{\numberline {13.2.2}Domains and probabilities}{63}{subsection.13.2.2}
+\contentsline {subsection}{\numberline {13.2.3}Tossing the dice}{63}{subsection.13.2.3}
+\contentsline {subsection}{\numberline {13.2.4}Stochastic variables}{63}{subsection.13.2.4}
+\contentsline {subsection}{\numberline {13.2.5}Stochastic variables and the main concepts, the discrete case}{64}{subsection.13.2.5}
+\contentsline {subsection}{\numberline {13.2.6}Stochastic variables and the main concepts, the continuous case}{64}{subsection.13.2.6}
+\contentsline {subsection}{\numberline {13.2.7}The cumulative probability}{64}{subsection.13.2.7}
+\contentsline {subsection}{\numberline {13.2.8}Properties of PDFs}{64}{subsection.13.2.8}
+\contentsline {subsection}{\numberline {13.2.9}Important distributions, the uniform distribution}{65}{subsection.13.2.9}
+\contentsline {subsection}{\numberline {13.2.10}Gaussian distribution}{65}{subsection.13.2.10}
+\contentsline {subsection}{\numberline {13.2.11}Exponential distribution}{67}{subsection.13.2.11}
+\contentsline {subsection}{\numberline {13.2.12}Expectation values}{67}{subsection.13.2.12}
+\contentsline {subsection}{\numberline {13.2.13}Stochastic variables and the main concepts, mean values}{67}{subsection.13.2.13}
+\contentsline {subsection}{\numberline {13.2.14}Stochastic variables and the main concepts, central moments, the variance}{67}{subsection.13.2.14}
+\contentsline {subsection}{\numberline {13.2.15}Probability Distribution Functions}{68}{subsection.13.2.15}
+\contentsline {subsection}{\numberline {13.2.16}Probability Distribution Functions}{68}{subsection.13.2.16}
+\contentsline {subsection}{\numberline {13.2.17}The three famous Probability Distribution Functions}{68}{subsection.13.2.17}
+\contentsline {subsection}{\numberline {13.2.18}Probability Distribution Functions, the normal distribution}{69}{subsection.13.2.18}
+\contentsline {subsection}{\numberline {13.2.19}Probability Distribution Functions, the normal distribution}{69}{subsection.13.2.19}
+\contentsline {subsection}{\numberline {13.2.20}Probability Distribution Functions, the cumulative distribution}{69}{subsection.13.2.20}
+\contentsline {subsection}{\numberline {13.2.21}Probability Distribution Functions, other important distribution}{70}{subsection.13.2.21}
+\contentsline {subsection}{\numberline {13.2.22}Probability Distribution Functions, the binomial distribution}{70}{subsection.13.2.22}
+\contentsline {subsection}{\numberline {13.2.23}Probability Distribution Functions, Poisson\IeC {\textquoteright }s distribution}{70}{subsection.13.2.23}
+\contentsline {subsection}{\numberline {13.2.24}Probability Distribution Functions, Poisson\IeC {\textquoteright }s distribution}{71}{subsection.13.2.24}
+\contentsline {subsection}{\numberline {13.2.25}Meet the covariance!}{71}{subsection.13.2.25}
+\contentsline {subsection}{\numberline {13.2.26}Meet the covariance in matrix disguise}{71}{subsection.13.2.26}
+\contentsline {subsection}{\numberline {13.2.27}Covariance}{72}{subsection.13.2.27}
+\contentsline {subsection}{\numberline {13.2.28}Meet the covariance, uncorrelated events}{73}{subsection.13.2.28}
+\contentsline {subsection}{\numberline {13.2.29}Numerical experiments and the covariance}{73}{subsection.13.2.29}
+\contentsline {subsection}{\numberline {13.2.30}Numerical experiments and the covariance}{73}{subsection.13.2.30}
+\contentsline {subsection}{\numberline {13.2.31}Numerical experiments and the covariance, actual situations}{73}{subsection.13.2.31}
+\contentsline {subsection}{\numberline {13.2.32}Numerical experiments and the covariance, our observables}{74}{subsection.13.2.32}
+\contentsline {subsection}{\numberline {13.2.33}Numerical experiments and the covariance, the sample variance}{74}{subsection.13.2.33}
+\contentsline {subsection}{\numberline {13.2.34}Numerical experiments and the covariance, central limit theorem}{75}{subsection.13.2.34}
+\contentsline {subsection}{\numberline {13.2.35}Definition of Correlation Functions and Standard Deviation}{75}{subsection.13.2.35}
+\contentsline {subsection}{\numberline {13.2.36}Definition of Correlation Functions and Standard Deviation}{75}{subsection.13.2.36}
+\contentsline {subsection}{\numberline {13.2.37}Definition of Correlation Functions and Standard Deviation}{75}{subsection.13.2.37}
+\contentsline {subsection}{\numberline {13.2.38}Definition of Correlation Functions and Standard Deviation}{76}{subsection.13.2.38}
+\contentsline {subsection}{\numberline {13.2.39}Definition of Correlation Functions and Standard Deviation, sample variance}{76}{subsection.13.2.39}
+\contentsline {subsection}{\numberline {13.2.40}Definition of Correlation Functions and Standard Deviation}{76}{subsection.13.2.40}
+\contentsline {subsection}{\numberline {13.2.41}Code to compute the Covariance matrix and the Covariance}{77}{subsection.13.2.41}
+\contentsline {section}{\numberline {13.3}Random Numbers}{78}{section.13.3}
+\contentsline {section}{\numberline {13.4}Random Numbers, better name: pseudo random numbers}{78}{section.13.4}
+\contentsline {section}{\numberline {13.5}Random number generator RNG}{78}{section.13.5}
+\contentsline {section}{\numberline {13.6}Random number generator RNG and periodic outputs}{78}{section.13.6}
+\contentsline {section}{\numberline {13.7}Random number generator RNG and its period}{79}{section.13.7}
+\contentsline {section}{\numberline {13.8}Random number generator RNG, other examples}{79}{section.13.8}
+\contentsline {section}{\numberline {13.9}Random number generator RNG, other examples}{79}{section.13.9}
+\contentsline {section}{\numberline {13.10}Random number generator RNG, RAN0}{80}{section.13.10}
+\contentsline {section}{\numberline {13.11}Random number generator RNG, RAN0}{80}{section.13.11}
+\contentsline {section}{\numberline {13.12}Random number generator RNG, RAN0}{80}{section.13.12}
+\contentsline {section}{\numberline {13.13}Random number generator RNG, RAN0}{81}{section.13.13}
+\contentsline {section}{\numberline {13.14}Random number generator RNG, RAN0 code}{81}{section.13.14}
+\contentsline {subsection}{\numberline {13.14.1}Properties of Selected Random Number Generators}{82}{subsection.13.14.1}
+\contentsline {subsection}{\numberline {13.14.2}Properties of Selected Random Number Generators}{82}{subsection.13.14.2}
+\contentsline {subsection}{\numberline {13.14.3}Properties of Selected Random Number Generators}{82}{subsection.13.14.3}
+\contentsline {subsection}{\numberline {13.14.4}Simple demonstration of RNGs using python}{82}{subsection.13.14.4}
+\contentsline {subsection}{\numberline {13.14.5}Properties of Selected Random Number Generators}{83}{subsection.13.14.5}
+\contentsline {subsection}{\numberline {13.14.6}Autocorrelation function}{83}{subsection.13.14.6}
+\contentsline {subsection}{\numberline {13.14.7}Correlation function and which random number generators should I use}{85}{subsection.13.14.7}
+\contentsline {section}{\numberline {13.15}Which RNG should I use?}{86}{section.13.15}
+\contentsline {subsection}{\numberline {13.15.1}How to use the Mersenne generator}{86}{subsection.13.15.1}
+\contentsline {subsection}{\numberline {13.15.2}Why blocking?}{86}{subsection.13.15.2}
+\contentsline {subsection}{\numberline {13.15.3}Why blocking?}{87}{subsection.13.15.3}
+\contentsline {subsection}{\numberline {13.15.4}Code to demonstrate the calculation of the autocorrelation function}{87}{subsection.13.15.4}
+\contentsline {subsection}{\numberline {13.15.5}What is blocking?}{89}{subsection.13.15.5}
+\contentsline {subsection}{\numberline {13.15.6}What is blocking?}{89}{subsection.13.15.6}
+\contentsline {subsection}{\numberline {13.15.7}What is blocking?}{89}{subsection.13.15.7}
+\contentsline {subsection}{\numberline {13.15.8}Implementation}{90}{subsection.13.15.8}
+\contentsline {subsection}{\numberline {13.15.9}Actual implementation with code, main function}{90}{subsection.13.15.9}
+\contentsline {subsection}{\numberline {13.15.10}The Bootstrap method}{91}{subsection.13.15.10}
+\contentsline {subsection}{\numberline {13.15.11}Bootstrapping}{91}{subsection.13.15.11}
+\contentsline {subsection}{\numberline {13.15.12}Bootstrapping, recipe}{91}{subsection.13.15.12}
+\contentsline {subsection}{\numberline {13.15.13}Bootstrapping, code}{92}{subsection.13.15.13}
+\contentsline {subsection}{\numberline {13.15.14}Jackknife, code}{92}{subsection.13.15.14}
+\contentsline {section}{\numberline {13.16}Data Analysis and Machine Learning: Linear Regression and more Advanced Regression Analysis}{92}{section.13.16}
+\contentsline {subsection}{\numberline {13.16.1}Why Linear Regression (aka Ordinary Least Squares and family)}{92}{subsection.13.16.1}
+\contentsline {subsection}{\numberline {13.16.2}Regression analysis, overarching aims}{93}{subsection.13.16.2}
+\contentsline {subsection}{\numberline {13.16.3}Regression analysis, overarching aims II}{93}{subsection.13.16.3}
+\contentsline {subsection}{\numberline {13.16.4}Examples}{93}{subsection.13.16.4}
+\contentsline {subsection}{\numberline {13.16.5}General linear models}{94}{subsection.13.16.5}
+\contentsline {subsection}{\numberline {13.16.6}Rewriting the fitting procedure as a linear algebra problem}{94}{subsection.13.16.6}
+\contentsline {subsection}{\numberline {13.16.7}Rewriting the fitting procedure as a linear algebra problem, more details}{94}{subsection.13.16.7}
+\contentsline {subsection}{\numberline {13.16.8}Generalizing the fitting procedure as a linear algebra problem}{95}{subsection.13.16.8}
+\contentsline {subsection}{\numberline {13.16.9}Generalizing the fitting procedure as a linear algebra problem}{95}{subsection.13.16.9}
+\contentsline {subsection}{\numberline {13.16.10}Optimizing our parameters}{95}{subsection.13.16.10}
+\contentsline {subsection}{\numberline {13.16.11}Our model for the nuclear binding energies}{96}{subsection.13.16.11}
+\contentsline {subsection}{\numberline {13.16.12}Optimizing our parameters, more details}{98}{subsection.13.16.12}
+\contentsline {subsection}{\numberline {13.16.13}Interpretations and optimizing our parameters}{98}{subsection.13.16.13}
+\contentsline {subsection}{\numberline {13.16.14}Interpretations and optimizing our parameters}{99}{subsection.13.16.14}
+\contentsline {subsection}{\numberline {13.16.15}Some useful matrix and vector expressions}{99}{subsection.13.16.15}
+\contentsline {subsection}{\numberline {13.16.16}Interpretations and optimizing our parameters}{99}{subsection.13.16.16}
+\contentsline {subsection}{\numberline {13.16.17}Own code for Ordinary Least Squares}{100}{subsection.13.16.17}
+\contentsline {subsection}{\numberline {13.16.18}Adding error analysis and training set up}{101}{subsection.13.16.18}
+\contentsline {subsection}{\numberline {13.16.19}The \(\chi ^2\) function}{101}{subsection.13.16.19}
+\contentsline {subsection}{\numberline {13.16.20}The \(\chi ^2\) function}{102}{subsection.13.16.20}
+\contentsline {subsection}{\numberline {13.16.21}The \(\chi ^2\) function}{102}{subsection.13.16.21}
+\contentsline {subsection}{\numberline {13.16.22}The \(\chi ^2\) function}{102}{subsection.13.16.22}
+\contentsline {subsection}{\numberline {13.16.23}The \(\chi ^2\) function}{103}{subsection.13.16.23}
+\contentsline {subsection}{\numberline {13.16.24}The \(\chi ^2\) function}{103}{subsection.13.16.24}
+\contentsline {subsection}{\numberline {13.16.25}Fitting an Equation of State for Dense Nuclear Matter}{104}{subsection.13.16.25}
+\contentsline {subsection}{\numberline {13.16.26}The code}{104}{subsection.13.16.26}
+\contentsline {subsection}{\numberline {13.16.27}Splitting our Data in Training and Test data}{106}{subsection.13.16.27}
+\contentsline {subsection}{\numberline {13.16.28}The Boston housing data example}{108}{subsection.13.16.28}
+\contentsline {subsection}{\numberline {13.16.29}Housing data, the code}{108}{subsection.13.16.29}
+\contentsline {subsection}{\numberline {13.16.30}Reducing the number of degrees of freedom, overarching view}{114}{subsection.13.16.30}
+\contentsline {subsection}{\numberline {13.16.31}Preprocessing our data}{114}{subsection.13.16.31}
+\contentsline {subsection}{\numberline {13.16.32}More preprocessing}{115}{subsection.13.16.32}
+\contentsline {subsection}{\numberline {13.16.33}Simple preprocessing examples, Franke function and regression}{115}{subsection.13.16.33}
+\contentsline {subsection}{\numberline {13.16.34}The singular value decomposition}{117}{subsection.13.16.34}
+\contentsline {subsection}{\numberline {13.16.35}Linear Regression Problems}{117}{subsection.13.16.35}
+\contentsline {subsection}{\numberline {13.16.36}Fixing the singularity}{118}{subsection.13.16.36}
+\contentsline {subsection}{\numberline {13.16.37}Basic math of the SVD}{118}{subsection.13.16.37}
+\contentsline {subsection}{\numberline {13.16.38}The SVD, a Fantastic Algorithm}{119}{subsection.13.16.38}
+\contentsline {subsection}{\numberline {13.16.39}Economy\sphinxhyphen {}size SVD}{119}{subsection.13.16.39}
+\contentsline {subsection}{\numberline {13.16.40}Codes for the SVD}{120}{subsection.13.16.40}
+\contentsline {subsection}{\numberline {13.16.41}Mathematical Properties}{121}{subsection.13.16.41}
+\contentsline {subsection}{\numberline {13.16.42}Ridge and LASSO Regression}{121}{subsection.13.16.42}
+\contentsline {subsection}{\numberline {13.16.43}More on Ridge Regression}{122}{subsection.13.16.43}
+\contentsline {subsection}{\numberline {13.16.44}Interpreting the Ridge results}{123}{subsection.13.16.44}
+\contentsline {subsection}{\numberline {13.16.45}More interpretations}{123}{subsection.13.16.45}
+\contentsline {subsection}{\numberline {13.16.46}A better understanding of regularization}{123}{subsection.13.16.46}
+\contentsline {subsection}{\numberline {13.16.47}Decomposing the OLS and Ridge expressions}{124}{subsection.13.16.47}
+\contentsline {subsection}{\numberline {13.16.48}Introducing the Covariance and Correlation functions}{124}{subsection.13.16.48}
+\contentsline {subsection}{\numberline {13.16.49}Correlation Function and Design/Feature Matrix}{125}{subsection.13.16.49}
+\contentsline {subsection}{\numberline {13.16.50}Covariance Matrix Examples}{125}{subsection.13.16.50}
+\contentsline {subsection}{\numberline {13.16.51}Correlation Matrix}{126}{subsection.13.16.51}
+\contentsline {subsection}{\numberline {13.16.52}Correlation Matrix with Pandas}{127}{subsection.13.16.52}
+\contentsline {subsection}{\numberline {13.16.53}Correlation Matrix with Pandas and the Franke function}{128}{subsection.13.16.53}
+\contentsline {subsection}{\numberline {13.16.54}Rewriting the Covariance and/or Correlation Matrix}{129}{subsection.13.16.54}
+\contentsline {subsection}{\numberline {13.16.55}Linking with SVD}{130}{subsection.13.16.55}
+\contentsline {subsection}{\numberline {13.16.56}Where are we going?}{130}{subsection.13.16.56}
+\contentsline {subsection}{\numberline {13.16.57}Resampling methods}{130}{subsection.13.16.57}
+\contentsline {subsection}{\numberline {13.16.58}Resampling approaches can be computationally expensive}{130}{subsection.13.16.58}
+\contentsline {subsection}{\numberline {13.16.59}Why resampling methods ?}{131}{subsection.13.16.59}
+\contentsline {subsection}{\numberline {13.16.60}Statistical analysis}{131}{subsection.13.16.60}
+\contentsline {subsection}{\numberline {13.16.61}Linking the regression analysis with a statistical interpretation}{131}{subsection.13.16.61}
+\contentsline {subsection}{\numberline {13.16.62}Assumptions made}{131}{subsection.13.16.62}
+\contentsline {subsection}{\numberline {13.16.63}Expectation value and variance}{132}{subsection.13.16.63}
+\contentsline {subsection}{\numberline {13.16.64}Expectation value and variance for \(\boldsymbol {\beta }\)}{132}{subsection.13.16.64}
+\contentsline {subsection}{\numberline {13.16.65}Resampling methods}{133}{subsection.13.16.65}
+\contentsline {subsection}{\numberline {13.16.66}Resampling methods: Jackknife and Bootstrap}{134}{subsection.13.16.66}
+\contentsline {subsection}{\numberline {13.16.67}Resampling methods: Jackknife}{134}{subsection.13.16.67}
+\contentsline {subsection}{\numberline {13.16.68}Jackknife code example}{134}{subsection.13.16.68}
+\contentsline {subsection}{\numberline {13.16.69}Resampling methods: Bootstrap}{135}{subsection.13.16.69}
+\contentsline {subsection}{\numberline {13.16.70}Resampling methods: Bootstrap background}{135}{subsection.13.16.70}
+\contentsline {subsection}{\numberline {13.16.71}Resampling methods: More Bootstrap background}{135}{subsection.13.16.71}
+\contentsline {subsection}{\numberline {13.16.72}Resampling methods: Bootstrap approach}{136}{subsection.13.16.72}
+\contentsline {subsection}{\numberline {13.16.73}Resampling methods: Bootstrap steps}{136}{subsection.13.16.73}
+\contentsline {subsection}{\numberline {13.16.74}Code example for the Bootstrap method}{136}{subsection.13.16.74}
+\contentsline {subsection}{\numberline {13.16.75}Various steps in cross\sphinxhyphen {}validation}{139}{subsection.13.16.75}
+\contentsline {subsection}{\numberline {13.16.76}How to set up the cross\sphinxhyphen {}validation for Ridge and/or Lasso}{139}{subsection.13.16.76}
+\contentsline {subsection}{\numberline {13.16.77}Cross\sphinxhyphen {}validation in brief}{140}{subsection.13.16.77}
+\contentsline {subsection}{\numberline {13.16.78}Code Example for Cross\sphinxhyphen {}validation and \(k\)\sphinxhyphen {}fold Cross\sphinxhyphen {}validation}{140}{subsection.13.16.78}
+\contentsline {subsection}{\numberline {13.16.79}The bias\sphinxhyphen {}variance tradeoff}{142}{subsection.13.16.79}
+\contentsline {subsection}{\numberline {13.16.80}Example code for Bias\sphinxhyphen {}Variance tradeoff}{143}{subsection.13.16.80}
+\contentsline {subsection}{\numberline {13.16.81}Understanding what happens}{144}{subsection.13.16.81}
+\contentsline {subsection}{\numberline {13.16.82}Summing up}{148}{subsection.13.16.82}
+\contentsline {subsection}{\numberline {13.16.83}Another Example from Scikit\sphinxhyphen {}Learn\IeC {\textquoteright }s Repository}{149}{subsection.13.16.83}
+\contentsline {subsection}{\numberline {13.16.84}More examples on bootstrap and cross\sphinxhyphen {}validation and errors}{150}{subsection.13.16.84}
+\contentsline {subsection}{\numberline {13.16.85}The same example but now with cross\sphinxhyphen {}validation}{151}{subsection.13.16.85}
+\contentsline {subsection}{\numberline {13.16.86}Cross\sphinxhyphen {}validation with Ridge}{153}{subsection.13.16.86}
+\contentsline {subsection}{\numberline {13.16.87}The Ising model}{154}{subsection.13.16.87}
+\contentsline {subsection}{\numberline {13.16.88}Reformulating the problem to suit regression}{154}{subsection.13.16.88}
+\contentsline {subsection}{\numberline {13.16.89}Linear regression}{155}{subsection.13.16.89}
+\contentsline {subsection}{\numberline {13.16.90}Singular Value decomposition}{156}{subsection.13.16.90}
+\contentsline {subsection}{\numberline {13.16.91}The one\sphinxhyphen {}dimensional Ising model}{157}{subsection.13.16.91}
+\contentsline {subsection}{\numberline {13.16.92}Ridge regression}{159}{subsection.13.16.92}
+\contentsline {subsection}{\numberline {13.16.93}LASSO regression}{159}{subsection.13.16.93}
+\contentsline {subsection}{\numberline {13.16.94}Performance as function of the regularization parameter}{160}{subsection.13.16.94}
+\contentsline {subsection}{\numberline {13.16.95}Finding the optimal value of \(\lambda \)}{161}{subsection.13.16.95}
+\contentsline {section}{\numberline {13.17}Data Analysis and Machine Learning: Logistic Regression}{161}{section.13.17}
+\contentsline {subsection}{\numberline {13.17.1}Logistic Regression}{162}{subsection.13.17.1}
+\contentsline {subsection}{\numberline {13.17.2}Optimization and Deep learning}{162}{subsection.13.17.2}
+\contentsline {subsection}{\numberline {13.17.3}Basics}{162}{subsection.13.17.3}
+\contentsline {subsection}{\numberline {13.17.4}Linear classifier}{163}{subsection.13.17.4}
+\contentsline {subsection}{\numberline {13.17.5}Some selected properties}{163}{subsection.13.17.5}
+\contentsline {subsection}{\numberline {13.17.6}The logistic function}{163}{subsection.13.17.6}
+\contentsline {subsection}{\numberline {13.17.7}Examples of likelihood functions used in logistic regression and nueral networks}{164}{subsection.13.17.7}
+\contentsline {subsection}{\numberline {13.17.8}Two parameters}{166}{subsection.13.17.8}
+\contentsline {subsection}{\numberline {13.17.9}Maximum likelihood}{166}{subsection.13.17.9}
+\contentsline {subsection}{\numberline {13.17.10}The cost function rewritten}{167}{subsection.13.17.10}
+\contentsline {subsection}{\numberline {13.17.11}Minimizing the cross entropy}{167}{subsection.13.17.11}
+\contentsline {subsection}{\numberline {13.17.12}A more compact expression}{167}{subsection.13.17.12}
+\contentsline {subsection}{\numberline {13.17.13}Extending to more predictors}{168}{subsection.13.17.13}
+\contentsline {subsection}{\numberline {13.17.14}Including more classes}{168}{subsection.13.17.14}
+\contentsline {subsection}{\numberline {13.17.15}More classes}{168}{subsection.13.17.15}
+\contentsline {subsection}{\numberline {13.17.16}A simple classification problem}{169}{subsection.13.17.16}
+\contentsline {subsection}{\numberline {13.17.17}The Credit Card example}{170}{subsection.13.17.17}
+\contentsline {subsection}{\numberline {13.17.18}How to read the Credit Card data}{170}{subsection.13.17.18}
@@ -0,0 +1,58 @@
+Traceback (most recent call last):
+  File "/Users/hjensen/opt/anaconda3/lib/python3.8/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/Users/hjensen/opt/anaconda3/lib/python3.8/site-packages/nbclient/client.py", line 1082, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/hjensen/opt/anaconda3/lib/python3.8/site-packages/nbclient/util.py", line 74, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/Users/hjensen/opt/anaconda3/lib/python3.8/site-packages/nbclient/util.py", line 53, in just_run
+    return loop.run_until_complete(coro)
+  File "/Users/hjensen/opt/anaconda3/lib/python3.8/asyncio/base_events.py", line 616, in run_until_complete
+    return future.result()
+  File "/Users/hjensen/opt/anaconda3/lib/python3.8/site-packages/nbclient/client.py", line 535, in async_execute
+    await self.async_execute_cell(
+  File "/Users/hjensen/opt/anaconda3/lib/python3.8/site-packages/nbclient/client.py", line 827, in async_execute_cell
+    self._check_raise_for_error(cell, exec_reply)
+  File "/Users/hjensen/opt/anaconda3/lib/python3.8/site-packages/nbclient/client.py", line 735, in _check_raise_for_error
+    raise CellExecutionError.from_cell_and_msg(cell, exec_reply['content'])
+nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
+------------------
+# Blocking
+    @timeFunction
+    def blocking(self, blockSizeMax = 500):
+        blockSizeMin = 1
+
+        self.blockSizes = []
+        self.meanVec = []
+        self.varVec = []
+
+        for i in range(blockSizeMin, blockSizeMax):
+            if(len(self.data) % i != 0):
+                pass#continue
+            blockSize = i
+            meanTempVec = []
+            varTempVec = []
+            startPoint = 0
+            endPoint = blockSize
+
+            while endPoint <= len(self.data):
+                meanTempVec.append(np.average(self.data[startPoint:endPoint]))
+                startPoint = endPoint
+                endPoint += blockSize
+            mean, var = np.average(meanTempVec), np.var(meanTempVec)/len(meanTempVec)
+            self.meanVec.append(mean)
+            self.varVec.append(var)
+            self.blockSizes.append(blockSize)
+
+        self.blockingAvg = np.average(self.meanVec[-200:])
+        self.blockingVar = (np.average(self.varVec[-200:]))
+        self.blockingStd = np.sqrt(self.blockingVar)
+------------------
+
+[0;36m  File [0;32m"<ipython-input-6-2ff97f4bf03b>"[0;36m, line [0;32m2[0m
+[0;31m    @timeFunction[0m
+[0m    ^[0m
+[0;31mIndentationError[0m[0;31m:[0m unexpected indent
+
+IndentationError: unexpected indent (<ipython-input-6-2ff97f4bf03b>, line 2)
+
@@ -0,0 +1,165 @@
+Traceback (most recent call last):
+  File "/Users/hjensen/opt/anaconda3/lib/python3.8/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/Users/hjensen/opt/anaconda3/lib/python3.8/site-packages/nbclient/client.py", line 1082, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/hjensen/opt/anaconda3/lib/python3.8/site-packages/nbclient/util.py", line 74, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/Users/hjensen/opt/anaconda3/lib/python3.8/site-packages/nbclient/util.py", line 53, in just_run
+    return loop.run_until_complete(coro)
+  File "/Users/hjensen/opt/anaconda3/lib/python3.8/asyncio/base_events.py", line 616, in run_until_complete
+    return future.result()
+  File "/Users/hjensen/opt/anaconda3/lib/python3.8/site-packages/nbclient/client.py", line 535, in async_execute
+    await self.async_execute_cell(
+  File "/Users/hjensen/opt/anaconda3/lib/python3.8/site-packages/nbclient/client.py", line 827, in async_execute_cell
+    self._check_raise_for_error(cell, exec_reply)
+  File "/Users/hjensen/opt/anaconda3/lib/python3.8/site-packages/nbclient/client.py", line 735, in _check_raise_for_error
+    raise CellExecutionError.from_cell_and_msg(cell, exec_reply['content'])
+nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
+------------------
+import pandas as pd
+import os
+import numpy as np
+
+
+from sklearn.model_selection import train_test_split
+from sklearn.preprocessing import OneHotEncoder
+from sklearn.compose import ColumnTransformer
+from sklearn.preprocessing import StandardScaler, OneHotEncoder
+from sklearn.metrics import confusion_matrix, accuracy_score, roc_auc_score
+
+# Trying to set the seed
+np.random.seed(0)
+import random
+random.seed(0)
+
+# Reading file into data frame
+cwd = os.getcwd()
+filename = cwd + '/default of credit card clients.xls'
+nanDict = {}
+df = pd.read_excel(filename, header=1, skiprows=0, index_col=0, na_values=nanDict)
+
+df.rename(index=str, columns={"default payment next month": "defaultPaymentNextMonth"}, inplace=True)
+
+# Features and targets 
+X = df.loc[:, df.columns != 'defaultPaymentNextMonth'].values
+y = df.loc[:, df.columns == 'defaultPaymentNextMonth'].values
+
+# Categorical variables to one-hot's
+onehotencoder = OneHotEncoder(categories="auto")
+
+X = ColumnTransformer(
+    [("", onehotencoder, [3]),],
+    remainder="passthrough"
+).fit_transform(X)
+
+y.shape
+
+# Train-test split
+trainingShare = 0.5 
+seed  = 1
+XTrain, XTest, yTrain, yTest=train_test_split(X, y, train_size=trainingShare, \
+                                              test_size = 1-trainingShare,
+                                             random_state=seed)
+
+# Input Scaling
+sc = StandardScaler()
+XTrain = sc.fit_transform(XTrain)
+XTest = sc.transform(XTest)
+
+# One-hot's of the target vector
+Y_train_onehot, Y_test_onehot = onehotencoder.fit_transform(yTrain), onehotencoder.fit_transform(yTest)
+
+# Remove instances with zeros only for past bill statements or paid amounts
+'''
+df = df.drop(df[(df.BILL_AMT1 == 0) &
+                (df.BILL_AMT2 == 0) &
+                (df.BILL_AMT3 == 0) &
+                (df.BILL_AMT4 == 0) &
+                (df.BILL_AMT5 == 0) &
+                (df.BILL_AMT6 == 0) &
+                (df.PAY_AMT1 == 0) &
+                (df.PAY_AMT2 == 0) &
+                (df.PAY_AMT3 == 0) &
+                (df.PAY_AMT4 == 0) &
+                (df.PAY_AMT5 == 0) &
+                (df.PAY_AMT6 == 0)].index)
+'''
+df = df.drop(df[(df.BILL_AMT1 == 0) &
+                (df.BILL_AMT2 == 0) &
+                (df.BILL_AMT3 == 0) &
+                (df.BILL_AMT4 == 0) &
+                (df.BILL_AMT5 == 0) &
+                (df.BILL_AMT6 == 0)].index)
+
+df = df.drop(df[(df.PAY_AMT1 == 0) &
+                (df.PAY_AMT2 == 0) &
+                (df.PAY_AMT3 == 0) &
+                (df.PAY_AMT4 == 0) &
+                (df.PAY_AMT5 == 0) &
+                (df.PAY_AMT6 == 0)].index)
+
+from sklearn.linear_model import LogisticRegression
+from sklearn.model_selection import GridSearchCV
+
+lambdas=np.logspace(-5,7,13)
+parameters = [{'C': 1./lambdas, "solver":["lbfgs"]}]#*len(parameters)}]
+scoring = ['accuracy', 'roc_auc']
+logReg = LogisticRegression()
+gridSearch = GridSearchCV(logReg, parameters, cv=5, scoring=scoring, refit='roc_auc')
+------------------
+
+[0;31m---------------------------------------------------------------------------[0m
+[0;31mFileNotFoundError[0m                         Traceback (most recent call last)
+[0;32m<ipython-input-4-4edad39a9543>[0m in [0;36m<module>[0;34m[0m
+[1;32m     19[0m [0mfilename[0m [0;34m=[0m [0mcwd[0m [0;34m+[0m [0;34m'/default of credit card clients.xls'[0m[0;34m[0m[0;34m[0m[0m
+[1;32m     20[0m [0mnanDict[0m [0;34m=[0m [0;34m{[0m[0;34m}[0m[0;34m[0m[0;34m[0m[0m
+[0;32m---> 21[0;31m [0mdf[0m [0;34m=[0m [0mpd[0m[0;34m.[0m[0mread_excel[0m[0;34m([0m[0mfilename[0m[0;34m,[0m [0mheader[0m[0;34m=[0m[0;36m1[0m[0;34m,[0m [0mskiprows[0m[0;34m=[0m[0;36m0[0m[0;34m,[0m [0mindex_col[0m[0;34m=[0m[0;36m0[0m[0;34m,[0m [0mna_values[0m[0;34m=[0m[0mnanDict[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m
+[0m[1;32m     22[0m [0;34m[0m[0m
+[1;32m     23[0m [0mdf[0m[0;34m.[0m[0mrename[0m[0;34m([0m[0mindex[0m[0;34m=[0m[0mstr[0m[0;34m,[0m [0mcolumns[0m[0;34m=[0m[0;34m{[0m[0;34m"default payment next month"[0m[0;34m:[0m [0;34m"defaultPaymentNextMonth"[0m[0;34m}[0m[0;34m,[0m [0minplace[0m[0;34m=[0m[0;32mTrue[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m
+
+[0;32m~/opt/anaconda3/lib/python3.8/site-packages/pandas/io/excel/_base.py[0m in [0;36mread_excel[0;34m(io, sheet_name, header, names, index_col, usecols, squeeze, dtype, engine, converters, true_values, false_values, skiprows, nrows, na_values, keep_default_na, verbose, parse_dates, date_parser, thousands, comment, skipfooter, convert_float, mangle_dupe_cols, **kwds)[0m
+[1;32m    302[0m [0;34m[0m[0m
+[1;32m    303[0m     [0;32mif[0m [0;32mnot[0m [0misinstance[0m[0;34m([0m[0mio[0m[0;34m,[0m [0mExcelFile[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0;34m[0m[0m
+[0;32m--> 304[0;31m         [0mio[0m [0;34m=[0m [0mExcelFile[0m[0;34m([0m[0mio[0m[0;34m,[0m [0mengine[0m[0;34m=[0m[0mengine[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m
+[0m[1;32m    305[0m     [0;32melif[0m [0mengine[0m [0;32mand[0m [0mengine[0m [0;34m!=[0m [0mio[0m[0;34m.[0m[0mengine[0m[0;34m:[0m[0;34m[0m[0;34m[0m[0m
+[1;32m    306[0m         raise ValueError(
+
+[0;32m~/opt/anaconda3/lib/python3.8/site-packages/pandas/io/excel/_base.py[0m in [0;36m__init__[0;34m(self, io, engine)[0m
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+[1;32m    823[0m [0;34m[0m[0m
+[0;32m--> 824[0;31m         [0mself[0m[0;34m.[0m[0m_reader[0m [0;34m=[0m [0mself[0m[0;34m.[0m[0m_engines[0m[0;34m[[0m[0mengine[0m[0;34m][0m[0;34m([0m[0mself[0m[0;34m.[0m[0m_io[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m
+[0m[1;32m    825[0m [0;34m[0m[0m
+[1;32m    826[0m     [0;32mdef[0m [0m__fspath__[0m[0;34m([0m[0mself[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0;34m[0m[0m
+
+[0;32m~/opt/anaconda3/lib/python3.8/site-packages/pandas/io/excel/_xlrd.py[0m in [0;36m__init__[0;34m(self, filepath_or_buffer)[0m
+[1;32m     19[0m         [0merr_msg[0m [0;34m=[0m [0;34m"Install xlrd >= 1.0.0 for Excel support"[0m[0;34m[0m[0;34m[0m[0m
+[1;32m     20[0m         [0mimport_optional_dependency[0m[0;34m([0m[0;34m"xlrd"[0m[0;34m,[0m [0mextra[0m[0;34m=[0m[0merr_msg[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m
+[0;32m---> 21[0;31m         [0msuper[0m[0;34m([0m[0;34m)[0m[0;34m.[0m[0m__init__[0m[0;34m([0m[0mfilepath_or_buffer[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m
+[0m[1;32m     22[0m [0;34m[0m[0m
+[1;32m     23[0m     [0;34m@[0m[0mproperty[0m[0;34m[0m[0;34m[0m[0m
+
+[0;32m~/opt/anaconda3/lib/python3.8/site-packages/pandas/io/excel/_base.py[0m in [0;36m__init__[0;34m(self, filepath_or_buffer)[0m
+[1;32m    351[0m             [0mself[0m[0;34m.[0m[0mbook[0m [0;34m=[0m [0mself[0m[0;34m.[0m[0mload_workbook[0m[0;34m([0m[0mfilepath_or_buffer[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m
+[1;32m    352[0m         [0;32melif[0m [0misinstance[0m[0;34m([0m[0mfilepath_or_buffer[0m[0;34m,[0m [0mstr[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0;34m[0m[0m
+[0;32m--> 353[0;31m             [0mself[0m[0;34m.[0m[0mbook[0m [0;34m=[0m [0mself[0m[0;34m.[0m[0mload_workbook[0m[0;34m([0m[0mfilepath_or_buffer[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m
+[0m[1;32m    354[0m         [0;32melif[0m [0misinstance[0m[0;34m([0m[0mfilepath_or_buffer[0m[0;34m,[0m [0mbytes[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0;34m[0m[0m
+[1;32m    355[0m             [0mself[0m[0;34m.[0m[0mbook[0m [0;34m=[0m [0mself[0m[0;34m.[0m[0mload_workbook[0m[0;34m([0m[0mBytesIO[0m[0;34m([0m[0mfilepath_or_buffer[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m
+
+[0;32m~/opt/anaconda3/lib/python3.8/site-packages/pandas/io/excel/_xlrd.py[0m in [0;36mload_workbook[0;34m(self, filepath_or_buffer)[0m
+[1;32m     34[0m             [0;32mreturn[0m [0mopen_workbook[0m[0;34m([0m[0mfile_contents[0m[0;34m=[0m[0mdata[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m
+[1;32m     35[0m         [0;32melse[0m[0;34m:[0m[0;34m[0m[0;34m[0m[0m
+[0;32m---> 36[0;31m             [0;32mreturn[0m [0mopen_workbook[0m[0;34m([0m[0mfilepath_or_buffer[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m
+[0m[1;32m     37[0m [0;34m[0m[0m
+[1;32m     38[0m     [0;34m@[0m[0mproperty[0m[0;34m[0m[0;34m[0m[0m
+
+[0;32m~/opt/anaconda3/lib/python3.8/site-packages/xlrd/__init__.py[0m in [0;36mopen_workbook[0;34m(filename, logfile, verbosity, use_mmap, file_contents, encoding_override, formatting_info, on_demand, ragged_rows)[0m
+[1;32m    109[0m     [0;32melse[0m[0;34m:[0m[0;34m[0m[0;34m[0m[0m
+[1;32m    110[0m         [0mfilename[0m [0;34m=[0m [0mos[0m[0;34m.[0m[0mpath[0m[0;34m.[0m[0mexpanduser[0m[0;34m([0m[0mfilename[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m
+[0;32m--> 111[0;31m         [0;32mwith[0m [0mopen[0m[0;34m([0m[0mfilename[0m[0;34m,[0m [0;34m"rb"[0m[0;34m)[0m [0;32mas[0m [0mf[0m[0;34m:[0m[0;34m[0m[0;34m[0m[0m
+[0m[1;32m    112[0m             [0mpeek[0m [0;34m=[0m [0mf[0m[0;34m.[0m[0mread[0m[0;34m([0m[0mpeeksz[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m
+[1;32m    113[0m     [0;32mif[0m [0mpeek[0m [0;34m==[0m [0;34mb"PK\x03\x04"[0m[0;34m:[0m [0;31m# a ZIP file[0m[0;34m[0m[0;34m[0m[0m
+
+[0;31mFileNotFoundError[0m: [Errno 2] No such file or directory: '/Users/hjensen/Teaching/FYS-STK4150/doc/src/LectureNotes/default of credit card clients.xls'
+FileNotFoundError: [Errno 2] No such file or directory: '/Users/hjensen/Teaching/FYS-STK4150/doc/src/LectureNotes/default of credit card clients.xls'
+
@@ -1,82 +0,0 @@
-Traceback (most recent call last):
-<<<<<<< HEAD
-  File "/Users/MortenImac/anaconda3/lib/python3.6/site-packages/jupyter_cache/executors/utils.py", line 56, in single_nb_execution
-    record_timing=False,
-  File "/Users/MortenImac/anaconda3/lib/python3.6/site-packages/nbclient/client.py", line 1082, in execute
-    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
-  File "/Users/MortenImac/anaconda3/lib/python3.6/site-packages/nbclient/util.py", line 74, in wrapped
-    return just_run(coro(*args, **kwargs))
-  File "/Users/MortenImac/anaconda3/lib/python3.6/site-packages/nbclient/util.py", line 53, in just_run
-    return loop.run_until_complete(coro)
-  File "/Users/MortenImac/anaconda3/lib/python3.6/asyncio/base_events.py", line 484, in run_until_complete
-    return future.result()
-  File "/Users/MortenImac/anaconda3/lib/python3.6/site-packages/nbclient/client.py", line 536, in async_execute
-    cell, index, execution_count=self.code_cells_executed + 1
-  File "/Users/MortenImac/anaconda3/lib/python3.6/site-packages/nbclient/client.py", line 827, in async_execute_cell
-    self._check_raise_for_error(cell, exec_reply)
-  File "/Users/MortenImac/anaconda3/lib/python3.6/site-packages/nbclient/client.py", line 735, in _check_raise_for_error
-=======
-  File "/Users/hjensen/opt/anaconda3/lib/python3.8/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
-    executenb(
-  File "/Users/hjensen/opt/anaconda3/lib/python3.8/site-packages/nbclient/client.py", line 1082, in execute
-    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
-  File "/Users/hjensen/opt/anaconda3/lib/python3.8/site-packages/nbclient/util.py", line 74, in wrapped
-    return just_run(coro(*args, **kwargs))
-  File "/Users/hjensen/opt/anaconda3/lib/python3.8/site-packages/nbclient/util.py", line 53, in just_run
-    return loop.run_until_complete(coro)
-  File "/Users/hjensen/opt/anaconda3/lib/python3.8/asyncio/base_events.py", line 616, in run_until_complete
-    return future.result()
-  File "/Users/hjensen/opt/anaconda3/lib/python3.8/site-packages/nbclient/client.py", line 535, in async_execute
-    await self.async_execute_cell(
-  File "/Users/hjensen/opt/anaconda3/lib/python3.8/site-packages/nbclient/client.py", line 827, in async_execute_cell
-    self._check_raise_for_error(cell, exec_reply)
-  File "/Users/hjensen/opt/anaconda3/lib/python3.8/site-packages/nbclient/client.py", line 735, in _check_raise_for_error
->>>>>>> 490fdaaefb7f465badc10b38c531979d063d6c64
-    raise CellExecutionError.from_cell_and_msg(cell, exec_reply['content'])
-nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
------------------
-# Common imports
-import numpy as np
-import pandas as pd
-import matplotlib.pyplot as plt
-import sklearn.linear_model as skl
-from sklearn.model_selection import train_test_split
-from sklearn.metrics import mean_squared_error, r2_score, mean_absolute_error
-import os
-
-# Where to save the figures and data files
-PROJECT_ROOT_DIR = "Results"
-FIGURE_ID = "Results/FigureFiles"
-DATA_ID = "DataFiles/"
-
-if not os.path.exists(PROJECT_ROOT_DIR):
-    os.mkdir(PROJECT_ROOT_DIR)
-
-if not os.path.exists(FIGURE_ID):
-    os.makedirs(FIGURE_ID)
-
-if not os.path.exists(DATA_ID):
-    os.makedirs(DATA_ID)
-
-def image_path(fig_id):
-    return os.path.join(FIGURE_ID, fig_id)
-
-def data_path(dat_id):
-    return os.path.join(DATA_ID, dat_id)
-
-def save_fig(fig_id):
-    plt.savefig(image_path(fig_id) + ".png", format='png')
-
-infile = open(data_path("MassEval2016.dat"),'r')
------------------
-
-[0;31m---------------------------------------------------------------------------[0m
-[0;31mFileNotFoundError[0m                         Traceback (most recent call last)
-[0;32m<ipython-input-28-3cd19a0768e1>[0m in [0;36m<module>[0;34m[0m
-[1;32m     31[0m     [0mplt[0m[0;34m.[0m[0msavefig[0m[0;34m([0m[0mimage_path[0m[0;34m([0m[0mfig_id[0m[0;34m)[0m [0;34m+[0m [0;34m".png"[0m[0;34m,[0m [0mformat[0m[0;34m=[0m[0;34m'png'[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m
-[1;32m     32[0m [0;34m[0m[0m
-[0;32m---> 33[0;31m [0minfile[0m [0;34m=[0m [0mopen[0m[0;34m([0m[0mdata_path[0m[0;34m([0m[0;34m"MassEval2016.dat"[0m[0;34m)[0m[0;34m,[0m[0;34m'r'[0m[0;34m)[0m[0;34m[0m[0;34m[0m[0m
-[0m
-[0;31mFileNotFoundError[0m: [Errno 2] No such file or directory: 'DataFiles/MassEval2016.dat'
-FileNotFoundError: [Errno 2] No such file or directory: 'DataFiles/MassEval2016.dat'
-
@@ -0,0 +1,230 @@
+;;; -*- mode: lisp; coding: utf-8; -*-
+
+;; Unfortunately xindy is out-of-the-box hyperref-incompatible.  This
+;; configuration is a workaround, which requires to pass option
+;; hyperindex=false to hyperref.
+;; textit and emph not currently used, spxpagem replaces former textbf
+(define-attributes (("textbf" "textit" "emph" "spxpagem" "default")))
+(markup-locref :open "\textbf{\hyperpage{" :close "}}" :attr "textbf")
+(markup-locref :open "\textit{\hyperpage{" :close "}}" :attr "textit")
+(markup-locref :open "\emph{\hyperpage{" :close "}}" :attr "emph")
+(markup-locref :open "\spxpagem{\hyperpage{" :close "}}" :attr "spxpagem")
+(markup-locref :open "\hyperpage{" :close "}" :attr "default")
+
+(require "numeric-sort.xdy")
+
+;; xindy base module latex.xdy loads tex.xdy and the latter instructs
+;; xindy to ignore **all** TeX macros in .idx entries, except those
+;; explicitely described in merge rule.  But when after applying all
+;; merge rules an empty string results, xindy raises an error:
+
+;;   ERROR: CHAR: index 0 should be less than the length of the string
+
+;; For example when using pdflatex with utf-8 characters the index
+;; file will contain \IeC macros and they will get ignored except if
+;; suitable merge rules are loaded early.  The texindy script coming
+;; with xindy provides this, but only for Latin scripts.  The texindy
+;; man page says to use rather xelatex or lualatex in case of Cyrillic
+;; scripts.
+
+;; Sphinx contributes LICRcyr2utf8.xdy to provide support for Cyrillic
+;; scripts for the pdflatex engine.
+
+;; Another issue caused by xindy ignoring all TeX macros except those
+;; explicitely declared reveals itself when attempting to index ">>>",
+;; as the ">" is converted to "\textgreater{}" by Sphinx's LaTeX
+;; escaping.
+
+;; To fix this, Sphinx does **not** use texindy, and does not even
+;; load the xindy latex.xdy base module.
+
+;(require "latex.xdy")
+
+;; Rather it incorporates some suitable extracts from latex.xdy and
+;; tex.xdy with additional Sphinx contributed rules.
+
+;; But, this means for pdflatex and Latin scripts that the xindy file
+;; tex/inputenc/uf8.xdy is not usable because it refers to the macro
+;; \IeC only sporadically, and as tex.xdy is not loaded, a rule such as
+;;     (merge-rule "\'e" "é" :string)
+;; does not work, it must be
+;;     (merge-rule "\IeC {\'e}" "é" :string)
+;; So Sphinx contributes LICRlatin2utf8.xdy to mitigate that problem.
+
+;;;;;;;; extracts from tex.xdy (discarding most original comments):
+
+;;;
+;;; TeX conventions
+;;;
+
+;; Discard leading and trailing white space. Collapse multiple white
+;; space characters to blank.
+
+(merge-rule "^ +" "" :eregexp)
+(merge-rule " +$" "" :eregexp)
+(merge-rule "  +" " " :eregexp)
+
+;; Handle TeX markup
+
+(merge-rule "\\([{}$%&#])" "\1" :eregexp)
+
+;;;;;;;; end of extracts from xindy's tex.xdy
+
+;;;;;;;; extracts from latex.xdy:
+
+;; Standard location classes: arabic and roman numbers, and alphabets.
+
+(define-location-class "arabic-page-numbers" ("arabic-numbers"))
+(define-location-class "roman-page-numbers"  ("roman-numbers-lowercase"))
+(define-location-class "Roman-page-numbers"  ("roman-numbers-uppercase"))
+(define-location-class "alpha-page-numbers"  ("alpha"))
+(define-location-class "Alpha-page-numbers"  ("ALPHA"))
+
+;; Output Markup
+
+(markup-letter-group-list :sep "~n~n  \indexspace~n")
+
+(markup-indexentry :open "~n  \item "           :depth 0)
+(markup-indexentry :open "~n    \subitem "      :depth 1)
+(markup-indexentry :open "~n      \subsubitem " :depth 2)
+
+(markup-locclass-list :open ", " :sep ", ")
+(markup-locref-list   :sep ", ")
+
+;;;;;;;; end of extracts from latex.xdy
+
+;; The LaTeX \index command turns \ into normal character so the TeX macros
+;; written to .idx files are not followed by a blank. This is different
+;; from non-ascii letters which end up (with pdflatex) as \IeC macros in .idx
+;; file, with a blank space after \IeC
+
+;; Details of the syntax are explained at
+;;     http://xindy.sourceforge.net/doc/manual-3.html
+;; In absence of :string, "xindy uses an auto-detection mechanism to decide,
+;; if the pattern is a regular expression or not". But it is not obvious to
+;; guess, for example "\\_" is not detected as RE but "\\P\{\}" is, so for
+;; being sure we apply the :string switch everywhere and do not use \\ etc...
+
+;; Go back from sphinx.util.texescape TeX macros to UTF-8
+
+(merge-rule "\sphinxleftcurlybrace{}" "{" :string)
+(merge-rule "\sphinxrightcurlybrace{}" "}" :string)
+(merge-rule "\_" "_" :string)
+(merge-rule "{[}" "[" :string)
+(merge-rule "{]}" "]" :string)
+(merge-rule "\textbackslash{}" "\" :string)  ; " for Emacs syntax highlighting
+(merge-rule "\textasciitilde{}" "~~" :string); the ~~ escape is needed here
+(merge-rule "\textasciicircum{}" "^" :string)
+(merge-rule "\sphinxhyphen{}" "-" :string)
+(merge-rule "\textquotesingle{}" "'" :string)
+(merge-rule "\textasciigrave{}" "`" :string)
+(merge-rule "\textless{}" "<" :string)
+(merge-rule "\textgreater{}" ">" :string)
+(merge-rule "\P{}" "¶" :string)
+(merge-rule "\S{}" "§" :string)
+(merge-rule "\texteuro{}" "€" :string)
+(merge-rule "\(\infty\)" "∞" :string)
+(merge-rule "\(\pm\)" "±" :string)
+(merge-rule "\(\rightarrow\)" "→" :string)
+(merge-rule "\(\checkmark\)" "✓" :string)
+(merge-rule "\textendash{}" "–" :string)
+(merge-rule "\textbar{}" "|" :string)
+(merge-rule "\(\sp{\text{0}}\)" "⁰" :string)
+(merge-rule "\(\sp{\text{1}}\)" "¹" :string)
+(merge-rule "\(\sp{\text{2}}\)" "²" :string)
+(merge-rule "\(\sp{\text{3}}\)" "³" :string)
+(merge-rule "\(\sp{\text{4}}\)" "⁴" :string)
+(merge-rule "\(\sp{\text{5}}\)" "⁵" :string)
+(merge-rule "\(\sp{\text{6}}\)" "⁶" :string)
+(merge-rule "\(\sp{\text{7}}\)" "⁷" :string)
+(merge-rule "\(\sp{\text{8}}\)" "⁸" :string)
+(merge-rule "\(\sp{\text{9}}\)" "⁹" :string)
+(merge-rule "\(\sb{\text{0}}\)" "₀" :string)
+(merge-rule "\(\sb{\text{1}}\)" "₁" :string)
+(merge-rule "\(\sb{\text{2}}\)" "₂" :string)
+(merge-rule "\(\sb{\text{3}}\)" "₃" :string)
+(merge-rule "\(\sb{\text{4}}\)" "₄" :string)
+(merge-rule "\(\sb{\text{5}}\)" "₅" :string)
+(merge-rule "\(\sb{\text{6}}\)" "₆" :string)
+(merge-rule "\(\sb{\text{7}}\)" "₇" :string)
+(merge-rule "\(\sb{\text{8}}\)" "₈" :string)
+(merge-rule "\(\sb{\text{9}}\)" "₉" :string)
+(merge-rule "\IeC {\textalpha }" "α" :string)
+(merge-rule "\IeC {\textbeta }" "β" :string)
+(merge-rule "\IeC {\textgamma }" "γ" :string)
+(merge-rule "\IeC {\textdelta }" "δ" :string)
+(merge-rule "\IeC {\textepsilon }" "ε" :string)
+(merge-rule "\IeC {\textzeta }" "ζ" :string)
+(merge-rule "\IeC {\texteta }" "η" :string)
+(merge-rule "\IeC {\texttheta }" "θ" :string)
+(merge-rule "\IeC {\textiota }" "ι" :string)
+(merge-rule "\IeC {\textkappa }" "κ" :string)
+(merge-rule "\IeC {\textlambda }" "λ" :string)
+(merge-rule "\IeC {\textmu }" "μ" :string)
+(merge-rule "\IeC {\textnu }" "ν" :string)
+(merge-rule "\IeC {\textxi }" "ξ" :string)
+(merge-rule "\IeC {\textomicron }" "ο" :string)
+(merge-rule "\IeC {\textpi }" "π" :string)
+(merge-rule "\IeC {\textrho }" "ρ" :string)
+(merge-rule "\IeC {\textsigma }" "σ" :string)
+(merge-rule "\IeC {\texttau }" "τ" :string)
+(merge-rule "\IeC {\textupsilon }" "υ" :string)
+(merge-rule "\IeC {\textphi }" "φ" :string)
+(merge-rule "\IeC {\textchi }" "χ" :string)
+(merge-rule "\IeC {\textpsi }" "ψ" :string)
+(merge-rule "\IeC {\textomega }" "ω" :string)
+(merge-rule "\IeC {\textAlpha }" "Α" :string)
+(merge-rule "\IeC {\textBeta }" "Β" :string)
+(merge-rule "\IeC {\textGamma }" "Γ" :string)
+(merge-rule "\IeC {\textDelta }" "Δ" :string)
+(merge-rule "\IeC {\textEpsilon }" "Ε" :string)
+(merge-rule "\IeC {\textZeta }" "Ζ" :string)
+(merge-rule "\IeC {\textEta }" "Η" :string)
+(merge-rule "\IeC {\textTheta }" "Θ" :string)
+(merge-rule "\IeC {\textIota }" "Ι" :string)
+(merge-rule "\IeC {\textKappa }" "Κ" :string)
+(merge-rule "\IeC {\textLambda }" "Λ" :string)
+(merge-rule "\IeC {\textMu }" "Μ" :string)
+(merge-rule "\IeC {\textNu }" "Ν" :string)
+(merge-rule "\IeC {\textTheta }" "Θ" :string)
+(merge-rule "\IeC {\textIota }" "Ι" :string)
+(merge-rule "\IeC {\textKappa }" "Κ" :string)
+(merge-rule "\IeC {\textLambda }" "Λ" :string)
+(merge-rule "\IeC {\textMu }" "Μ" :string)
+(merge-rule "\IeC {\textNu }" "Ν" :string)
+(merge-rule "\IeC {\textXi }" "Ξ" :string)
+(merge-rule "\IeC {\textOmicron }" "Ο" :string)
+(merge-rule "\IeC {\textPi }" "Π" :string)
+(merge-rule "\IeC {\textRho }" "Ρ" :string)
+(merge-rule "\IeC {\textSigma }" "Σ" :string)
+(merge-rule "\IeC {\textTau }" "Τ" :string)
+(merge-rule "\IeC {\textUpsilon }" "Υ" :string)
+(merge-rule "\IeC {\textPhi }" "Φ" :string)
+(merge-rule "\IeC {\textChi }" "Χ" :string)
+(merge-rule "\IeC {\textPsi }" "Ψ" :string)
+(merge-rule "\IeC {\textOmega }" "Ω" :string)
+(merge-rule "\IeC {\textohm }" "Ω" :string)
+
+;; This xindy module provides some basic support for "see"
+(require "makeindex.xdy")
+
+;; This creates one-letter headings and works fine with utf-8 letters.
+;; For Cyrillic with pdflatex works thanks to LICRcyr2utf8.xdy
+(require "latin-lettergroups.xdy")
+
+;; currently we don't (know how to easily) separate "Numbers" from
+;; "Symbols" with xindy as is the case with makeindex.
+(markup-index :open  "\begin{sphinxtheindex}
+\let\lettergroup\sphinxstyleindexlettergroup
+\let\lettergroupDefault\sphinxstyleindexlettergroupDefault
+\let\spxpagem\sphinxstyleindexpagemain
+\let\spxentry\sphinxstyleindexentry
+\let\spxextra\sphinxstyleindexextra
+
+"
+	      :close "
+
+\end{sphinxtheindex}
+"
+	      :tree)
+
@@ -0,0 +1,55 @@
+%% CYRILLIC IN NON-CYRILLIC DOCUMENTS (pdflatex only)
+%
+% refs: https://tex.stackexchange.com/q/460271/
+\ProvidesPackage{sphinxcyrillic}%
+  [2018/11/21 v2.0 support for Cyrillic in non-Cyrillic documents]
+\RequirePackage{kvoptions}
+\SetupKeyvalOptions{prefix=spx@cyropt@} % use \spx@cyropt@ prefix
+\DeclareBoolOption[false]{Xtwo}
+\DeclareBoolOption[false]{TtwoA}
+\DeclareDefaultOption{\@unknownoptionerror}
+\ProcessLocalKeyvalOptions* % ignore class options
+
+\ifspx@cyropt@Xtwo
+% original code by tex.sx user egreg (updated 2019/10/28):
+%   https://tex.stackexchange.com/a/460325/
+% 159 Cyrillic glyphs as available in X2 TeX 8bit font encoding
+% This assumes inputenc loaded with utf8 option, or LaTeX release
+% as recent as 2018/04/01 which does it automatically. 
+  \@tfor\next:=%
+    {Ё}{Ђ}{Є}{Ѕ}{І}{Ј}{Љ}{Њ}{Ћ}{Ў}{Џ}{А}{Б}{В}{Г}{Д}{Е}{Ж}{З}{И}{Й}%
+    {К}{Л}{М}{Н}{О}{П}{Р}{С}{Т}{У}{Ф}{Х}{Ц}{Ч}{Ш}{Щ}{Ъ}{Ы}{Ь}{Э}{Ю}%
+    {Я}{а}{б}{в}{г}{д}{е}{ж}{з}{и}{й}{к}{л}{м}{н}{о}{п}{р}{с}{т}{у}%
+    {ф}{х}{ц}{ч}{ш}{щ}{ъ}{ы}{ь}{э}{ю}{я}{ё}{ђ}{є}{ѕ}{і}{ј}{љ}{њ}{ћ}%
+    {ў}{џ}{Ѣ}{ѣ}{Ѫ}{ѫ}{Ѵ}{ѵ}{Ґ}{ґ}{Ғ}{ғ}{Ҕ}{ҕ}{Җ}{җ}{Ҙ}{ҙ}{Қ}{қ}{Ҝ}{ҝ}%
+    {Ҟ}{ҟ}{Ҡ}{ҡ}{Ң}{ң}{Ҥ}{ҥ}{Ҧ}{ҧ}{Ҩ}{ҩ}{Ҫ}{ҫ}{Ҭ}{ҭ}{Ү}{ү}{Ұ}{ұ}{Ҳ}{ҳ}%
+    {Ҵ}{ҵ}{Ҷ}{ҷ}{Ҹ}{ҹ}{Һ}{һ}{Ҽ}{ҽ}{Ҿ}{ҿ}{Ӏ}{Ӄ}{ӄ}{Ӆ}{ӆ}{Ӈ}{ӈ}{Ӌ}{ӌ}%
+    {Ӎ}{ӎ}{Ӕ}{ӕ}{Ә}{ә}{Ӡ}{ӡ}{Ө}{ө}\do
+  {%
+    \begingroup\def\IeC{\protect\DeclareTextSymbolDefault}%
+    \protected@edef\@temp{\endgroup
+    \@ifl@t@r{\fmtversion}{2019/10/01}{\csname u8:\next\endcsname}{\next}}%
+    \@temp{X2}%
+  }%
+\else
+\ifspx@cyropt@TtwoA
+% original code by tex.sx user jfbu:
+%   https://tex.stackexchange.com/a/460305/
+% 63*2+1=127 Cyrillic glyphs as found in T2A 8bit TeX font-encoding
+  \@tfor\@tempa:=%
+    {ae}{a}{b}{chrdsc}{chvcrs}{ch}{c}{dje}{dze}{dzhe}{d}{erev}{ery}{e}%
+    {f}{ghcrs}{gup}{g}{hdsc}{hrdsn}{h}{ie}{ii}{ishrt}{i}{je}%
+    {kbeak}{kdsc}{kvcrs}{k}{lje}{l}{m}{ndsc}{ng}{nje}{n}{otld}{o}{p}{r}%
+    {schwa}{sdsc}{sftsn}{shch}{shha}{sh}{s}{tshe}{t}{ushrt}{u}{v}%
+    {ya}{yhcrs}{yi}{yo}{yu}{y}{zdsc}{zhdsc}{zh}{z}\do
+  {%
+    \expandafter\DeclareTextSymbolDefault\expandafter
+               {\csname cyr\@tempa\endcsname}{T2A}%
+    \expandafter\uppercase\expandafter{\expandafter
+                 \def\expandafter\@tempa\expandafter{\@tempa}}%
+    \expandafter\DeclareTextSymbolDefault\expandafter
+      {\csname CYR\@tempa\endcsname}{T2A}%
+  }%
+  \DeclareTextSymbolDefault{\CYRpalochka}{T2A}%
+\fi\fi
+\endinput
@@ -0,0 +1,105 @@
+\NeedsTeXFormat{LaTeX2e}[1995/12/01]
+\ProvidesPackage{sphinxhighlight}[2016/05/29 stylesheet for highlighting with pygments]
+
+
+\makeatletter
+\def\PYG@reset{\let\PYG@it=\relax \let\PYG@bf=\relax%
+    \let\PYG@ul=\relax \let\PYG@tc=\relax%
+    \let\PYG@bc=\relax \let\PYG@ff=\relax}
+\def\PYG@tok#1{\csname PYG@tok@#1\endcsname}
+\def\PYG@toks#1+{\ifx\relax#1\empty\else%
+    \PYG@tok{#1}\expandafter\PYG@toks\fi}
+\def\PYG@do#1{\PYG@bc{\PYG@tc{\PYG@ul{%
+    \PYG@it{\PYG@bf{\PYG@ff{#1}}}}}}}
+\def\PYG#1#2{\PYG@reset\PYG@toks#1+\relax+\PYG@do{#2}}
+
+\expandafter\def\csname PYG@tok@w\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.73,0.73}{##1}}}
+\expandafter\def\csname PYG@tok@c\endcsname{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.25,0.50,0.56}{##1}}}
+\expandafter\def\csname PYG@tok@cp\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}}
+\expandafter\def\csname PYG@tok@cs\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.25,0.50,0.56}{##1}}\def\PYG@bc##1{\setlength{\fboxsep}{0pt}\colorbox[rgb]{1.00,0.94,0.94}{\strut ##1}}}
+\expandafter\def\csname PYG@tok@k\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}}
+\expandafter\def\csname PYG@tok@kp\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}}
+\expandafter\def\csname PYG@tok@kt\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.56,0.13,0.00}{##1}}}
+\expandafter\def\csname PYG@tok@o\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
+\expandafter\def\csname PYG@tok@ow\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}}
+\expandafter\def\csname PYG@tok@nb\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}}
+\expandafter\def\csname PYG@tok@nf\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.02,0.16,0.49}{##1}}}
+\expandafter\def\csname PYG@tok@nc\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.05,0.52,0.71}{##1}}}
+\expandafter\def\csname PYG@tok@nn\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.05,0.52,0.71}{##1}}}
+\expandafter\def\csname PYG@tok@ne\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}}
+\expandafter\def\csname PYG@tok@nv\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.38,0.84}{##1}}}
+\expandafter\def\csname PYG@tok@no\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.38,0.68,0.84}{##1}}}
+\expandafter\def\csname PYG@tok@nl\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.13,0.44}{##1}}}
+\expandafter\def\csname PYG@tok@ni\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.84,0.33,0.22}{##1}}}
+\expandafter\def\csname PYG@tok@na\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}}
+\expandafter\def\csname PYG@tok@nt\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.02,0.16,0.45}{##1}}}
+\expandafter\def\csname PYG@tok@nd\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.33,0.33,0.33}{##1}}}
+\expandafter\def\csname PYG@tok@s\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}}
+\expandafter\def\csname PYG@tok@sd\endcsname{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}}
+\expandafter\def\csname PYG@tok@si\endcsname{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.44,0.63,0.82}{##1}}}
+\expandafter\def\csname PYG@tok@se\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}}
+\expandafter\def\csname PYG@tok@sr\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.14,0.33,0.53}{##1}}}
+\expandafter\def\csname PYG@tok@ss\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.32,0.47,0.09}{##1}}}
+\expandafter\def\csname PYG@tok@sx\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.78,0.36,0.04}{##1}}}
+\expandafter\def\csname PYG@tok@m\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.13,0.50,0.31}{##1}}}
+\expandafter\def\csname PYG@tok@gh\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.00,0.50}{##1}}}
+\expandafter\def\csname PYG@tok@gu\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.50,0.00,0.50}{##1}}}
+\expandafter\def\csname PYG@tok@gd\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.63,0.00,0.00}{##1}}}
+\expandafter\def\csname PYG@tok@gi\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.63,0.00}{##1}}}
+\expandafter\def\csname PYG@tok@gr\endcsname{\def\PYG@tc##1{\textcolor[rgb]{1.00,0.00,0.00}{##1}}}
+\expandafter\def\csname PYG@tok@ge\endcsname{\let\PYG@it=\textit}
+\expandafter\def\csname PYG@tok@gs\endcsname{\let\PYG@bf=\textbf}
+\expandafter\def\csname PYG@tok@gp\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.78,0.36,0.04}{##1}}}
+\expandafter\def\csname PYG@tok@go\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.20,0.20,0.20}{##1}}}
+\expandafter\def\csname PYG@tok@gt\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.27,0.87}{##1}}}
+\expandafter\def\csname PYG@tok@err\endcsname{\def\PYG@bc##1{\setlength{\fboxsep}{0pt}\fcolorbox[rgb]{1.00,0.00,0.00}{1,1,1}{\strut ##1}}}
+\expandafter\def\csname PYG@tok@kc\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}}
+\expandafter\def\csname PYG@tok@kd\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}}
+\expandafter\def\csname PYG@tok@kn\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}}
+\expandafter\def\csname PYG@tok@kr\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}}
+\expandafter\def\csname PYG@tok@bp\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}}
+\expandafter\def\csname PYG@tok@fm\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.02,0.16,0.49}{##1}}}
+\expandafter\def\csname PYG@tok@vc\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.38,0.84}{##1}}}
+\expandafter\def\csname PYG@tok@vg\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.38,0.84}{##1}}}
+\expandafter\def\csname PYG@tok@vi\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.38,0.84}{##1}}}
+\expandafter\def\csname PYG@tok@vm\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.38,0.84}{##1}}}
+\expandafter\def\csname PYG@tok@sa\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}}
+\expandafter\def\csname PYG@tok@sb\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}}
+\expandafter\def\csname PYG@tok@sc\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}}
+\expandafter\def\csname PYG@tok@dl\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}}
+\expandafter\def\csname PYG@tok@s2\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}}
+\expandafter\def\csname PYG@tok@sh\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}}
+\expandafter\def\csname PYG@tok@s1\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}}
+\expandafter\def\csname PYG@tok@mb\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.13,0.50,0.31}{##1}}}
+\expandafter\def\csname PYG@tok@mf\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.13,0.50,0.31}{##1}}}
+\expandafter\def\csname PYG@tok@mh\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.13,0.50,0.31}{##1}}}
+\expandafter\def\csname PYG@tok@mi\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.13,0.50,0.31}{##1}}}
+\expandafter\def\csname PYG@tok@il\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.13,0.50,0.31}{##1}}}
+\expandafter\def\csname PYG@tok@mo\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.13,0.50,0.31}{##1}}}
+\expandafter\def\csname PYG@tok@ch\endcsname{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.25,0.50,0.56}{##1}}}
+\expandafter\def\csname PYG@tok@cm\endcsname{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.25,0.50,0.56}{##1}}}
+\expandafter\def\csname PYG@tok@cpf\endcsname{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.25,0.50,0.56}{##1}}}
+\expandafter\def\csname PYG@tok@c1\endcsname{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.25,0.50,0.56}{##1}}}
+
+\def\PYGZbs{\char`\\}
+\def\PYGZus{\char`\_}
+\def\PYGZob{\char`\{}
+\def\PYGZcb{\char`\}}
+\def\PYGZca{\char`\^}
+\def\PYGZam{\char`\&}
+\def\PYGZlt{\char`\<}
+\def\PYGZgt{\char`\>}
+\def\PYGZsh{\char`\#}
+\def\PYGZpc{\char`\%}
+\def\PYGZdl{\char`\$}
+\def\PYGZhy{\char`\-}
+\def\PYGZsq{\char`\'}
+\def\PYGZdq{\char`\"}
+\def\PYGZti{\char`\~}
+% for compatibility with earlier versions
+\def\PYGZat{@}
+\def\PYGZlb{[}
+\def\PYGZrb{]}
+\makeatother
+
+\renewcommand\PYGZsq{\textquotesingle}
@@ -0,0 +1,102 @@
+%
+% sphinxhowto.cls for Sphinx (http://sphinx-doc.org/)
+%
+
+\NeedsTeXFormat{LaTeX2e}[1995/12/01]
+\ProvidesClass{sphinxhowto}[2019/12/01 v2.3.0 Document class (Sphinx howto)]
+
+% 'oneside' option overriding the 'twoside' default
+\newif\if@oneside
+\DeclareOption{oneside}{\@onesidetrue}
+% Pass remaining document options to the parent class.
+\DeclareOption*{\PassOptionsToClass{\CurrentOption}{\sphinxdocclass}}
+\ProcessOptions\relax
+
+% Default to two-side document
+\if@oneside
+% nothing to do (oneside is the default)
+\else
+\PassOptionsToClass{twoside}{\sphinxdocclass}
+\fi
+
+\LoadClass{\sphinxdocclass}
+
+% Set some sane defaults for section numbering depth and TOC depth.  You can
+% reset these counters in your preamble.
+%
+\setcounter{secnumdepth}{2}
+\setcounter{tocdepth}{2}% i.e. section and subsection
+
+% Adapt \and command to the flushright context of \sphinxmaketitle, to
+% avoid ragged line endings if author names do not fit all on one single line
+\DeclareRobustCommand{\and}{%
+    \end{tabular}\kern-\tabcolsep
+    \allowbreak
+    \hskip\dimexpr1em+\tabcolsep\@plus.17fil\begin{tabular}[t]{c}%
+}%
+% If it is desired that each author name be on its own line, use in preamble:
+%\DeclareRobustCommand{\and}{%
+%   \end{tabular}\kern-\tabcolsep\\\begin{tabular}[t]{c}%
+%}%
+% Change the title page to look a bit better, and fit in with the fncychap
+% ``Bjarne'' style a bit better.
+%
+\newcommand{\sphinxmaketitle}{%
+  \noindent\rule{\textwidth}{1pt}\par
+    \begingroup % for PDF information dictionary
+       \def\endgraf{ }\def\and{\& }%
+       \pdfstringdefDisableCommands{\def\\{, }}% overwrite hyperref setup
+       \hypersetup{pdfauthor={\@author}, pdftitle={\@title}}%
+    \endgroup
+  \begin{flushright}
+    \sphinxlogo
+    \py@HeaderFamily
+    {\Huge \@title }\par
+    {\itshape\large \py@release \releaseinfo}\par
+    \vspace{25pt}
+    {\Large
+      \begin{tabular}[t]{c}
+        \@author
+      \end{tabular}\kern-\tabcolsep}\par
+    \vspace{25pt}
+    \@date \par
+    \py@authoraddress \par
+  \end{flushright}
+  \@thanks
+  \setcounter{footnote}{0}
+  \let\thanks\relax\let\maketitle\relax
+  %\gdef\@thanks{}\gdef\@author{}\gdef\@title{}
+}
+
+\newcommand{\sphinxtableofcontents}{%
+  \begingroup
+    \parskip \z@skip
+    \sphinxtableofcontentshook
+    \tableofcontents
+  \endgroup
+  \noindent\rule{\textwidth}{1pt}\par
+  \vspace{12pt}%
+}  
+\newcommand\sphinxtableofcontentshook{}
+\pagenumbering{arabic}
+
+% Fix the bibliography environment to add an entry to the Table of
+% Contents.
+% For an article document class this environment is a section,
+% so no page break before it.
+%
+\newenvironment{sphinxthebibliography}[1]{%
+  % \phantomsection % not needed here since TeXLive 2010's hyperref
+  \begin{thebibliography}{#1}%
+  \addcontentsline{toc}{section}{\ifdefined\refname\refname\else\ifdefined\bibname\bibname\fi\fi}}{\end{thebibliography}}
+
+
+% Same for the indices.
+% The memoir class already does this, so we don't duplicate it in that case.
+%
+\@ifclassloaded{memoir}
+ {\newenvironment{sphinxtheindex}{\begin{theindex}}{\end{theindex}}}
+ {\newenvironment{sphinxtheindex}{%
+    \phantomsection % needed because no chapter, section, ... is created by theindex
+    \begin{theindex}%
+    \addcontentsline{toc}{section}{\indexname}}{\end{theindex}}}
--- a/Show More
+++ b/Show More
				`@@ -0,0 +1,2 @@`

				`<meta http-equiv="Refresh" content="0; url=chapter1.html" />`