minor update

doc/LectureNotes/_build/html/reports/chapter1.err.log

@@ -0,0 +1,90 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
+    return loop.run_until_complete(inner)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, 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:
+------------------
+%matplotlib inline
+
+# Importing various packages
+import numpy as np
+import matplotlib.pyplot as plt
+from sklearn.linear_model import LinearRegression
+
+x = np.random.rand(100,1)
+y = 2*x+np.random.randn(100,1)
+linreg = LinearRegression()
+linreg.fit(x,y)
+# This is our new x-array to which we test our model
+xnew = np.array([[0],[1]])
+ypredict = linreg.predict(xnew)
+
+plt.plot(xnew, ypredict, "r-")
+plt.plot(x, y ,'ro')
+plt.axis([0,1.0,0, 5.0])
+plt.xlabel(r'$x$')
+plt.ylabel(r'$y$')
+plt.title(r'Simple Linear Regression')
+plt.show()
+------------------
+
+
+---------------------------------------------------------------------------
+ModuleNotFoundError                       Traceback (most recent call last)
+Cell In[1], line 1
+----> 1 get_ipython().run_line_magic('matplotlib', 'inline')
+      3 # Importing various packages
+      4 import numpy as np
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth)
+   2430     kwargs['local_ns'] = self.get_local_scope(stack_depth)
+   2431 with self.builtin_trap:
+-> 2432     result = fn(*args, **kwargs)
+   2434 # The code below prevents the output from being displayed
+   2435 # when using magics with decorator @output_can_be_silenced
+   2436 # when the last Python token in the expression is a ';'.
+   2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line)
+     97     print("Available matplotlib backends: %s" % backends_list)
+     98 else:
+---> 99     gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui)
+    100     self._show_matplotlib_backend(args.gui, backend)
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui)
+   3585 def enable_matplotlib(self, gui=None):
+   3586     """Enable interactive matplotlib and inline figure support.
+   3587 
+   3588     This takes the following steps:
+   (...)
+   3604         display figures inline.
+   3605     """
+-> 3606     from matplotlib_inline.backend_inline import configure_inline_support
+   3608     from IPython.core import pylabtools as pt
+   3609     gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select)
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1
+----> 1 from . import backend_inline, config  # noqa
+      2 __version__ = "0.1.6"  # noqa
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6
+      1 """A matplotlib backend for publishing figures via display_data"""
+      3 # Copyright (c) IPython Development Team.
+      4 # Distributed under the terms of the BSD 3-Clause License.
+----> 6 import matplotlib
+      7 from matplotlib import colors
+      8 from matplotlib.backends import backend_agg
+
+ModuleNotFoundError: No module named 'matplotlib'
+

doc/LectureNotes/_build/html/reports/chapter1.log

@@ -0,0 +1,71 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run
+    return loop.run_until_complete(coro)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, 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:
+------------------
+# Read the experimental data with Pandas
+Masses = pd.read_fwf(infile, usecols=(2,3,4,6,11),
+              names=('N', 'Z', 'A', 'Element', 'Ebinding'),
+              widths=(1,3,5,5,5,1,3,4,1,13,11,11,9,1,2,11,9,1,3,1,12,11,1),
+              header=39,
+              index_col=False)
+
+# Extrapolated values are indicated by '#' in place of the decimal place, so
+# the Ebinding column won't be numeric. Coerce to float and drop these entries.
+Masses['Ebinding'] = pd.to_numeric(Masses['Ebinding'], errors='coerce')
+Masses = Masses.dropna()
+# Convert from keV to MeV.
+Masses['Ebinding'] /= 1000
+
+# Group the DataFrame by nucleon number, A.
+Masses = Masses.groupby('A')
+# Find the rows of the grouped DataFrame with the maximum binding energy.
+Masses = Masses.apply(lambda t: t[t.Ebinding==t.Ebinding.max()])
+------------------
+
+---------------------------------------------------------------------------
+ValueError                                Traceback (most recent call last)
+Input In [8], in <cell line: 2>()
+      1 # Read the experimental data with Pandas
+----> 2 Masses = pd.read_fwf(infile, usecols=(2,3,4,6,11),
+      3               names=('N', 'Z', 'A', 'Element', 'Ebinding'),
+      4               widths=(1,3,5,5,5,1,3,4,1,13,11,11,9,1,2,11,9,1,3,1,12,11,1),
+      5               header=39,
+      6               index_col=False)
+      8 # Extrapolated values are indicated by '#' in place of the decimal place, so
+      9 # the Ebinding column won't be numeric. Coerce to float and drop these entries.
+     10 Masses['Ebinding'] = pd.to_numeric(Masses['Ebinding'], errors='coerce')
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/pandas/util/_decorators.py:311, in deprecate_nonkeyword_arguments.<locals>.decorate.<locals>.wrapper(*args, **kwargs)
+    305 if len(args) > num_allow_args:
+    306     warnings.warn(
+    307         msg.format(arguments=arguments),
+    308         FutureWarning,
+    309         stacklevel=stacklevel,
+    310     )
+--> 311 return func(*args, **kwargs)
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/pandas/io/parsers/readers.py:871, in read_fwf(filepath_or_buffer, colspecs, widths, infer_nrows, **kwds)
+    869                     len_index = len(index_col)
+    870         if len(names) + len_index != len(colspecs):
+--> 871             raise ValueError("Length of colspecs must match length of names")
+    873 kwds["colspecs"] = colspecs
+    874 kwds["infer_nrows"] = infer_nrows
+
+ValueError: Length of colspecs must match length of names
+ValueError: Length of colspecs must match length of names
+

doc/LectureNotes/_build/html/reports/chapter10.err.log

@@ -0,0 +1,112 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
+    return loop.run_until_complete(inner)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, 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:
+------------------
+%matplotlib inline
+
+# import necessary packages
+import numpy as np
+import matplotlib.pyplot as plt
+from sklearn import datasets
+
+
+# ensure the same random numbers appear every time
+np.random.seed(0)
+
+# display images in notebook
+%matplotlib inline
+plt.rcParams['figure.figsize'] = (12,12)
+
+
+# download MNIST dataset
+digits = datasets.load_digits()
+
+# define inputs and labels
+inputs = digits.images
+labels = digits.target
+
+print("inputs = (n_inputs, pixel_width, pixel_height) = " + str(inputs.shape))
+print("labels = (n_inputs) = " + str(labels.shape))
+
+
+# flatten the image
+# the value -1 means dimension is inferred from the remaining dimensions: 8x8 = 64
+n_inputs = len(inputs)
+inputs = inputs.reshape(n_inputs, -1)
+print("X = (n_inputs, n_features) = " + str(inputs.shape))
+
+
+# choose some random images to display
+indices = np.arange(n_inputs)
+random_indices = np.random.choice(indices, size=5)
+
+for i, image in enumerate(digits.images[random_indices]):
+    plt.subplot(1, 5, i+1)
+    plt.axis('off')
+    plt.imshow(image, cmap=plt.cm.gray_r, interpolation='nearest')
+    plt.title("Label: %d" % digits.target[random_indices[i]])
+plt.show()
+------------------
+
+
+---------------------------------------------------------------------------
+ModuleNotFoundError                       Traceback (most recent call last)
+Cell In[1], line 1
+----> 1 get_ipython().run_line_magic('matplotlib', 'inline')
+      3 # import necessary packages
+      4 import numpy as np
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth)
+   2430     kwargs['local_ns'] = self.get_local_scope(stack_depth)
+   2431 with self.builtin_trap:
+-> 2432     result = fn(*args, **kwargs)
+   2434 # The code below prevents the output from being displayed
+   2435 # when using magics with decorator @output_can_be_silenced
+   2436 # when the last Python token in the expression is a ';'.
+   2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line)
+     97     print("Available matplotlib backends: %s" % backends_list)
+     98 else:
+---> 99     gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui)
+    100     self._show_matplotlib_backend(args.gui, backend)
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui)
+   3585 def enable_matplotlib(self, gui=None):
+   3586     """Enable interactive matplotlib and inline figure support.
+   3587 
+   3588     This takes the following steps:
+   (...)
+   3604         display figures inline.
+   3605     """
+-> 3606     from matplotlib_inline.backend_inline import configure_inline_support
+   3608     from IPython.core import pylabtools as pt
+   3609     gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select)
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1
+----> 1 from . import backend_inline, config  # noqa
+      2 __version__ = "0.1.6"  # noqa
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6
+      1 """A matplotlib backend for publishing figures via display_data"""
+      3 # Copyright (c) IPython Development Team.
+      4 # Distributed under the terms of the BSD 3-Clause License.
+----> 6 import matplotlib
+      7 from matplotlib import colors
+      8 from matplotlib.backends import backend_agg
+
+ModuleNotFoundError: No module named 'matplotlib'
+

doc/LectureNotes/_build/html/reports/chapter10.log

@@ -0,0 +1,30 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run
+    return loop.run_until_complete(coro)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, 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:
+------------------
+conda create -n tf tensorflow
+conda activate tf
+------------------
+
+  Input In [12]
+    conda create -n tf tensorflow
+          ^
+SyntaxError: invalid syntax
+
+SyntaxError: invalid syntax (2259440937.py, line 1)
+

doc/LectureNotes/_build/html/reports/chapter11.err.log

@@ -0,0 +1,214 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
+    return loop.run_until_complete(inner)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, 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:
+------------------
+%matplotlib inline
+
+import autograd.numpy as np
+from autograd import grad, elementwise_grad
+import autograd.numpy.random as npr
+from matplotlib import pyplot as plt
+
+def sigmoid(z):
+    return 1/(1 + np.exp(-z))
+
+# Assuming one input, hidden, and output layer
+def neural_network(params, x):
+
+    # Find the weights (including and biases) for the hidden and output layer.
+    # Assume that params is a list of parameters for each layer.
+    # The biases are the first element for each array in params,
+    # and the weights are the remaning elements in each array in params.
+
+    w_hidden = params[0]
+    w_output = params[1]
+
+    # Assumes input x being an one-dimensional array
+    num_values = np.size(x)
+    x = x.reshape(-1, num_values)
+
+    # Assume that the input layer does nothing to the input x
+    x_input = x
+
+    ## Hidden layer:
+
+    # Add a row of ones to include bias
+    x_input = np.concatenate((np.ones((1,num_values)), x_input ), axis = 0)
+
+    z_hidden = np.matmul(w_hidden, x_input)
+    x_hidden = sigmoid(z_hidden)
+
+    ## Output layer:
+
+    # Include bias:
+    x_hidden = np.concatenate((np.ones((1,num_values)), x_hidden ), axis = 0)
+
+    z_output = np.matmul(w_output, x_hidden)
+    x_output = z_output
+
+    return x_output
+
+# The trial solution using the deep neural network:
+def g_trial(x,params, g0 = 10):
+    return g0 + x*neural_network(params,x)
+
+# The right side of the ODE:
+def g(x, g_trial, gamma = 2):
+    return -gamma*g_trial
+
+# The cost function:
+def cost_function(P, x):
+
+    # Evaluate the trial function with the current parameters P
+    g_t = g_trial(x,P)
+
+    # Find the derivative w.r.t x of the neural network
+    d_net_out = elementwise_grad(neural_network,1)(P,x)
+
+    # Find the derivative w.r.t x of the trial function
+    d_g_t = elementwise_grad(g_trial,0)(x,P)
+
+    # The right side of the ODE
+    func = g(x, g_t)
+
+    err_sqr = (d_g_t - func)**2
+    cost_sum = np.sum(err_sqr)
+
+    return cost_sum / np.size(err_sqr)
+
+# Solve the exponential decay ODE using neural network with one input, hidden, and output layer
+def solve_ode_neural_network(x, num_neurons_hidden, num_iter, lmb):
+    ## Set up initial weights and biases
+
+    # For the hidden layer
+    p0 = npr.randn(num_neurons_hidden, 2 )
+
+    # For the output layer
+    p1 = npr.randn(1, num_neurons_hidden + 1 ) # +1 since bias is included
+
+    P = [p0, p1]
+
+    print('Initial cost: %g'%cost_function(P, x))
+
+    ## Start finding the optimal weights using gradient descent
+
+    # Find the Python function that represents the gradient of the cost function
+    # w.r.t the 0-th input argument -- that is the weights and biases in the hidden and output layer
+    cost_function_grad = grad(cost_function,0)
+
+    # Let the update be done num_iter times
+    for i in range(num_iter):
+        # Evaluate the gradient at the current weights and biases in P.
+        # The cost_grad consist now of two arrays;
+        # one for the gradient w.r.t P_hidden and
+        # one for the gradient w.r.t P_output
+        cost_grad =  cost_function_grad(P, x)
+
+        P[0] = P[0] - lmb * cost_grad[0]
+        P[1] = P[1] - lmb * cost_grad[1]
+
+    print('Final cost: %g'%cost_function(P, x))
+
+    return P
+
+def g_analytic(x, gamma = 2, g0 = 10):
+    return g0*np.exp(-gamma*x)
+
+# Solve the given problem
+if __name__ == '__main__':
+    # Set seed such that the weight are initialized
+    # with same weights and biases for every run.
+    npr.seed(15)
+
+    ## Decide the vales of arguments to the function to solve
+    N = 10
+    x = np.linspace(0, 1, N)
+
+    ## Set up the initial parameters
+    num_hidden_neurons = 10
+    num_iter = 10000
+    lmb = 0.001
+
+    # Use the network
+    P = solve_ode_neural_network(x, num_hidden_neurons, num_iter, lmb)
+
+    # Print the deviation from the trial solution and true solution
+    res = g_trial(x,P)
+    res_analytical = g_analytic(x)
+
+    print('Max absolute difference: %g'%np.max(np.abs(res - res_analytical)))
+
+    # Plot the results
+    plt.figure(figsize=(10,10))
+
+    plt.title('Performance of neural network solving an ODE compared to the analytical solution')
+    plt.plot(x, res_analytical)
+    plt.plot(x, res[0,:])
+    plt.legend(['analytical','nn'])
+    plt.xlabel('x')
+    plt.ylabel('g(x)')
+    plt.show()
+------------------
+
+
+---------------------------------------------------------------------------
+ModuleNotFoundError                       Traceback (most recent call last)
+Cell In[1], line 1
+----> 1 get_ipython().run_line_magic('matplotlib', 'inline')
+      3 import autograd.numpy as np
+      4 from autograd import grad, elementwise_grad
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth)
+   2430     kwargs['local_ns'] = self.get_local_scope(stack_depth)
+   2431 with self.builtin_trap:
+-> 2432     result = fn(*args, **kwargs)
+   2434 # The code below prevents the output from being displayed
+   2435 # when using magics with decorator @output_can_be_silenced
+   2436 # when the last Python token in the expression is a ';'.
+   2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line)
+     97     print("Available matplotlib backends: %s" % backends_list)
+     98 else:
+---> 99     gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui)
+    100     self._show_matplotlib_backend(args.gui, backend)
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui)
+   3585 def enable_matplotlib(self, gui=None):
+   3586     """Enable interactive matplotlib and inline figure support.
+   3587 
+   3588     This takes the following steps:
+   (...)
+   3604         display figures inline.
+   3605     """
+-> 3606     from matplotlib_inline.backend_inline import configure_inline_support
+   3608     from IPython.core import pylabtools as pt
+   3609     gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select)
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1
+----> 1 from . import backend_inline, config  # noqa
+      2 __version__ = "0.1.6"  # noqa
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6
+      1 """A matplotlib backend for publishing figures via display_data"""
+      3 # Copyright (c) IPython Development Team.
+      4 # Distributed under the terms of the BSD 3-Clause License.
+----> 6 import matplotlib
+      7 from matplotlib import colors
+      8 from matplotlib.backends import backend_agg
+
+ModuleNotFoundError: No module named 'matplotlib'
+

doc/LectureNotes/_build/html/reports/chapter11.log

@@ -0,0 +1,39 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 730, in _async_poll_for_reply
+    msg = await ensure_async(self.kc.shell_channel.get_msg(timeout=new_timeout))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 96, in ensure_async
+    result = await obj
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_client/channels.py", line 230, in get_msg
+    raise Empty
+_queue.Empty
+
+During handling of the above exception, another exception occurred:
+
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run
+    return loop.run_until_complete(coro)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 949, in async_execute_cell
+    exec_reply = await self.task_poll_for_reply
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 754, in _async_poll_for_reply
+    await self._async_handle_timeout(timeout, cell)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 801, in _async_handle_timeout
+    raise CellTimeoutError.error_from_timeout_and_cell(
+nbclient.exceptions.CellTimeoutError: A cell timed out while it was being executed, after 30 seconds.
+The message was: Cell execution timed out.
+Here is a preview of the cell contents:
+-------------------
+['import autograd.numpy as np', 'from autograd import jacobian,hessian,grad', 'import autograd.numpy.random as npr', 'from matplotlib import cm', 'from matplotlib import pyplot as plt']
+...
+['    plt.plot(x, res3)', '    plt.plot(x,res_analytical3)', "    plt.legend(['dnn','analytical'])", '', '    plt.show()']
+-------------------
+

doc/LectureNotes/_build/html/reports/chapter12.err.log

@@ -0,0 +1,87 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
+    return loop.run_until_complete(inner)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, 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:
+------------------
+%matplotlib inline
+
+import numpy as np
+import math
+from scipy import signal
+import matplotlib.pyplot as plt
+
+# number of points                                                                                       
+n = 500
+# start and final times                                                                                  
+t0 = 0.0
+tn = 1.0
+# Period                                                                                                 
+t = np.linspace(t0, tn, n, endpoint=False)
+SqrSignal = np.zeros(n)
+SqrSignal = 1.0+signal.square(2*np.pi*5*t)
+plt.plot(t, SqrSignal)
+plt.ylim(-0.5, 2.5)
+plt.show()
+------------------
+
+
+---------------------------------------------------------------------------
+ModuleNotFoundError                       Traceback (most recent call last)
+Cell In[1], line 1
+----> 1 get_ipython().run_line_magic('matplotlib', 'inline')
+      3 import numpy as np
+      4 import math
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth)
+   2430     kwargs['local_ns'] = self.get_local_scope(stack_depth)
+   2431 with self.builtin_trap:
+-> 2432     result = fn(*args, **kwargs)
+   2434 # The code below prevents the output from being displayed
+   2435 # when using magics with decorator @output_can_be_silenced
+   2436 # when the last Python token in the expression is a ';'.
+   2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line)
+     97     print("Available matplotlib backends: %s" % backends_list)
+     98 else:
+---> 99     gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui)
+    100     self._show_matplotlib_backend(args.gui, backend)
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui)
+   3585 def enable_matplotlib(self, gui=None):
+   3586     """Enable interactive matplotlib and inline figure support.
+   3587 
+   3588     This takes the following steps:
+   (...)
+   3604         display figures inline.
+   3605     """
+-> 3606     from matplotlib_inline.backend_inline import configure_inline_support
+   3608     from IPython.core import pylabtools as pt
+   3609     gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select)
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1
+----> 1 from . import backend_inline, config  # noqa
+      2 __version__ = "0.1.6"  # noqa
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6
+      1 """A matplotlib backend for publishing figures via display_data"""
+      3 # Copyright (c) IPython Development Team.
+      4 # Distributed under the terms of the BSD 3-Clause License.
+----> 6 import matplotlib
+      7 from matplotlib import colors
+      8 from matplotlib.backends import backend_agg
+
+ModuleNotFoundError: No module named 'matplotlib'
+

doc/LectureNotes/_build/html/reports/chapter12.log

@@ -0,0 +1,39 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 730, in _async_poll_for_reply
+    msg = await ensure_async(self.kc.shell_channel.get_msg(timeout=new_timeout))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 96, in ensure_async
+    result = await obj
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_client/channels.py", line 230, in get_msg
+    raise Empty
+_queue.Empty
+
+During handling of the above exception, another exception occurred:
+
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run
+    return loop.run_until_complete(coro)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 949, in async_execute_cell
+    exec_reply = await self.task_poll_for_reply
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 754, in _async_poll_for_reply
+    await self._async_handle_timeout(timeout, cell)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 801, in _async_handle_timeout
+    raise CellTimeoutError.error_from_timeout_and_cell(
+nbclient.exceptions.CellTimeoutError: A cell timed out while it was being executed, after 30 seconds.
+The message was: Cell execution timed out.
+Here is a preview of the cell contents:
+-------------------
+['CNN_keras = np.zeros((len(eta_vals), len(lmbd_vals)), dtype=object)', '        ', 'for i, eta in enumerate(eta_vals):', '    for j, lmbd in enumerate(lmbd_vals):', '        CNN = create_convolutional_neural_network_keras(input_shape, receptive_field,']
+...
+['        ', '        print("Learning rate = ", eta)', '        print("Lambda = ", lmbd)', '        print("Test accuracy: %.3f" % scores[1])', '        print()']
+-------------------
+

doc/LectureNotes/_build/html/reports/chapter13.err.log

@@ -0,0 +1,138 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
+    return loop.run_until_complete(inner)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, 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:
+------------------
+%matplotlib inline
+
+# Start importing packages
+import pandas as pd
+import numpy as np
+import matplotlib.pyplot as plt
+import tensorflow as tf
+from tensorflow.keras import datasets, layers, models
+from tensorflow.keras.layers import Input
+from tensorflow.keras.models import Model, Sequential 
+from tensorflow.keras.layers import Dense, SimpleRNN, LSTM, GRU
+from tensorflow.keras import optimizers     
+from tensorflow.keras import regularizers           
+from tensorflow.keras.utils import to_categorical 
+
+
+
+# convert into dataset matrix
+def convertToMatrix(data, step):
+ X, Y =[], []
+ for i in range(len(data)-step):
+  d=i+step  
+  X.append(data[i:d,])
+  Y.append(data[d,])
+ return np.array(X), np.array(Y)
+
+step = 4
+N = 1000    
+Tp = 800    
+
+t=np.arange(0,N)
+x=np.sin(0.02*t)+2*np.random.rand(N)
+df = pd.DataFrame(x)
+df.head()
+
+plt.plot(df)
+plt.show()
+
+values=df.values
+train,test = values[0:Tp,:], values[Tp:N,:]
+
+# add step elements into train and test
+test = np.append(test,np.repeat(test[-1,],step))
+train = np.append(train,np.repeat(train[-1,],step))
+ 
+trainX,trainY =convertToMatrix(train,step)
+testX,testY =convertToMatrix(test,step)
+trainX = np.reshape(trainX, (trainX.shape[0], 1, trainX.shape[1]))
+testX = np.reshape(testX, (testX.shape[0], 1, testX.shape[1]))
+
+model = Sequential()
+model.add(SimpleRNN(units=32, input_shape=(1,step), activation="relu"))
+model.add(Dense(8, activation="relu")) 
+model.add(Dense(1))
+model.compile(loss='mean_squared_error', optimizer='rmsprop')
+model.summary()
+
+model.fit(trainX,trainY, epochs=100, batch_size=16, verbose=2)
+trainPredict = model.predict(trainX)
+testPredict= model.predict(testX)
+predicted=np.concatenate((trainPredict,testPredict),axis=0)
+
+trainScore = model.evaluate(trainX, trainY, verbose=0)
+print(trainScore)
+
+index = df.index.values
+plt.plot(index,df)
+plt.plot(index,predicted)
+plt.axvline(df.index[Tp], c="r")
+plt.show()
+------------------
+
+
+---------------------------------------------------------------------------
+ModuleNotFoundError                       Traceback (most recent call last)
+Cell In[1], line 1
+----> 1 get_ipython().run_line_magic('matplotlib', 'inline')
+      3 # Start importing packages
+      4 import pandas as pd
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth)
+   2430     kwargs['local_ns'] = self.get_local_scope(stack_depth)
+   2431 with self.builtin_trap:
+-> 2432     result = fn(*args, **kwargs)
+   2434 # The code below prevents the output from being displayed
+   2435 # when using magics with decorator @output_can_be_silenced
+   2436 # when the last Python token in the expression is a ';'.
+   2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line)
+     97     print("Available matplotlib backends: %s" % backends_list)
+     98 else:
+---> 99     gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui)
+    100     self._show_matplotlib_backend(args.gui, backend)
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui)
+   3585 def enable_matplotlib(self, gui=None):
+   3586     """Enable interactive matplotlib and inline figure support.
+   3587 
+   3588     This takes the following steps:
+   (...)
+   3604         display figures inline.
+   3605     """
+-> 3606     from matplotlib_inline.backend_inline import configure_inline_support
+   3608     from IPython.core import pylabtools as pt
+   3609     gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select)
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1
+----> 1 from . import backend_inline, config  # noqa
+      2 __version__ = "0.1.6"  # noqa
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6
+      1 """A matplotlib backend for publishing figures via display_data"""
+      3 # Copyright (c) IPython Development Team.
+      4 # Distributed under the terms of the BSD 3-Clause License.
+----> 6 import matplotlib
+      7 from matplotlib import colors
+      8 from matplotlib.backends import backend_agg
+
+ModuleNotFoundError: No module named 'matplotlib'
+

doc/LectureNotes/_build/html/reports/chapter13.log

@@ -0,0 +1,39 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 730, in _async_poll_for_reply
+    msg = await ensure_async(self.kc.shell_channel.get_msg(timeout=new_timeout))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 96, in ensure_async
+    result = await obj
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_client/channels.py", line 230, in get_msg
+    raise Empty
+_queue.Empty
+
+During handling of the above exception, another exception occurred:
+
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run
+    return loop.run_until_complete(coro)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 949, in async_execute_cell
+    exec_reply = await self.task_poll_for_reply
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 754, in _async_poll_for_reply
+    await self._async_handle_timeout(timeout, cell)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 801, in _async_handle_timeout
+    raise CellTimeoutError.error_from_timeout_and_cell(
+nbclient.exceptions.CellTimeoutError: A cell timed out while it was being executed, after 30 seconds.
+The message was: Cell execution timed out.
+Here is a preview of the cell contents:
+-------------------
+['%matplotlib inline', '', '# Start importing packages', 'import pandas as pd', 'import numpy as np']
+...
+['index = df.index.values', 'plt.plot(index,df)', 'plt.plot(index,predicted)', 'plt.axvline(df.index[Tp], c="r")', 'plt.show()']
+-------------------
+

doc/LectureNotes/_build/html/reports/chapter2.err.log

@@ -0,0 +1,44 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
+    return loop.run_until_complete(inner)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, 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 numpy as np
+import pandas as pd
+n = 10
+x = np.random.normal(size=n)
+x = x - np.mean(x)
+y = 4+3*x+np.random.normal(size=n)
+y = y - np.mean(y)
+# Note that we transpose the matrix in order to stay with our ordering n x p
+X = (np.vstack((x, y))).T
+print(X)
+Xpd = pd.DataFrame(X)
+print(Xpd)
+correlation_matrix = Xpd.corr()
+print(correlation_matrix)
+------------------
+
+
+---------------------------------------------------------------------------
+ModuleNotFoundError                       Traceback (most recent call last)
+Cell In[7], line 2
+      1 import numpy as np
+----> 2 import pandas as pd
+      3 n = 10
+      4 x = np.random.normal(size=n)
+
+ModuleNotFoundError: No module named 'pandas'
+

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@@ -0,0 +1,290 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run
+    return loop.run_until_complete(coro)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, 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:
+------------------
+from cvxopt import matrix, spdiag, mul, div, sqrt, normal, setseed
+from cvxopt import blas, lapack, solvers, sparse, spmatrix
+import math
+
+try:
+    import mosek
+    import sys
+    __MOSEK = True
+except: __MOSEK = False
+
+if __MOSEK:
+
+    def l1regls_mosek(A, b):
+        """
+
+        Returns the solution of l1-norm regularized least-squares problem
+
+            minimize    || A*x - b ||_2^2  + e'*u
+
+            subject to  -u <= x <= u
+
+        """
+
+        m, n = A.size
+
+        env  = mosek.Env()
+        task = env.Task(0,0)
+        task.set_Stream(mosek.streamtype.log, lambda x: sys.stdout.write(x))
+
+        task.appendvars( 2*n)            # number of variables
+        task.appendcons( 2*n)            # number of constraints
+
+        # input quadratic objective
+        Q = matrix(0.0, (n,n)) 
+        blas.syrk(A, Q, alpha = 2.0, trans='T')
+
+        I = []
+        for i in range(n):
+            I.extend(range(i,n))
+
+        J = []
+        for i in range(n):
+            J.extend((n-i)*[i])
+
+        task.putqobj(I, J, list(Q[matrix(I) + matrix(J)*n]))
+        task.putclist(range(2*n), list(-2*A.T*b) + n*[1.0])  # setup linear objective
+
+        # input constraint matrix row by row
+        for i in range(n):
+            task.putarow(   i, [i, n+i], [1.0, -1.0])
+            task.putarow( n+i, [i, n+i], [1.0,  1.0])
+
+        # setup bounds on constraints
+        task.putboundslice(mosek.accmode.con,
+                           0, n, n*[mosek.boundkey.up], n*[0.0], n*[0.0])
+        task.putboundslice(mosek.accmode.con,
+                           n, 2*n, n*[mosek.boundkey.lo], n*[0.0], n*[0.0])
+
+        # setup variable bounds
+        task.putboundslice(mosek.accmode.var,
+                           0, 2*n, 2*n*[mosek.boundkey.fr], 2*n*[0.0], 2*n*[0.0])
+
+        # optimize the task
+        task.putobjsense(mosek.objsense.minimize)
+        task.optimize()
+        task.solutionsummary(mosek.streamtype.log)
+        x = n*[0.0]
+        task.getsolutionslice(mosek.soltype.itr, mosek.solitem.xx, 0, n, x)
+
+        return matrix(x)
+
+    def l1regls_mosek2(A, b):
+        """
+
+        Returns the solution of l1-norm regularized least-squares problem
+
+            minimize     w'*w + e'*u
+
+            subject to  -u <= x <= u
+
+                         A*x - w = b
+
+        """
+
+        m, n = A.size
+
+        env  = mosek.Env()
+        task = env.Task(0,0)
+        task.set_Stream(mosek.streamtype.log, lambda x: sys.stdout.write(x))
+
+        task.appendvars(2*n + m)     # number of variables
+        task.appendcons(2*n + m)     # number of constraints
+
+        # input quadratic objective
+        task.putqobj(range(2*n,2*n+m), range(2*n,2*n+m), m*[2.0])
+
+        task.putclist(range(2*n+m), n*[0.0] + n*[1.0] + m*[0.0])  # setup linear objective
+
+        # input constraint matrix row by row
+        for i in range(n):
+            task.putarow(   i, [i, n+i], [1.0, -1.0])
+            task.putarow( n+i, [i, n+i], [1.0,  1.0])
+
+        for i in range(m):
+            task.putarow( 2*n+i, range(n) + [2*n+i], list(A[i,:]) + [-1.0])
+
+        # setup bounds on constraints
+        task.putboundslice(mosek.accmode.con,
+                           0, n, n*[mosek.boundkey.up], n*[0.0], n*[0.0])
+        task.putboundslice(mosek.accmode.con,
+                           n, 2*n, n*[mosek.boundkey.lo], n*[0.0], n*[0.0])
+        task.putboundslice(mosek.accmode.con,
+                           2*n, 2*n+m, m*[mosek.boundkey.fx], list(b), list(b))
+
+        # setup variable bounds
+        task.putboundslice(mosek.accmode.var, 0, 2*n+m, (2*n+m)*[mosek.boundkey.fr], 
+                           (2*n+m)*[0.0], (2*n+m)*[0.0])
+
+        # optimize the task
+        task.putobjsense(mosek.objsense.minimize)
+        task.optimize()
+        task.solutionsummary(mosek.streamtype.log)
+        x = n*[0.0]
+        task.getsolutionslice(mosek.soltype.itr, mosek.solitem.xx, 0, n, x)
+
+        return matrix(x)
+
+def l1regls(A, b):
+    """
+    
+    Returns the solution of l1-norm regularized least-squares problem
+  
+        minimize || A*x - b ||_2^2  + || x ||_1.
+
+    """
+
+    m, n = A.size
+    q = matrix(1.0, (2*n,1))
+    q[:n] = -2.0 * A.T * b
+
+    def P(u, v, alpha = 1.0, beta = 0.0 ):
+        """
+            v := alpha * 2.0 * [ A'*A, 0; 0, 0 ] * u + beta * v 
+        """
+        v *= beta
+        v[:n] += alpha * 2.0 * A.T * (A * u[:n])
+
+
+    def G(u, v, alpha=1.0, beta=0.0, trans='N'):
+        """
+            v := alpha*[I, -I; -I, -I] * u + beta * v  (trans = 'N' or 'T')
+        """
+
+        v *= beta
+        v[:n] += alpha*(u[:n] - u[n:])
+        v[n:] += alpha*(-u[:n] - u[n:])
+
+    h = matrix(0.0, (2*n,1))
+
+
+    # Customized solver for the KKT system 
+    #
+    #     [  2.0*A'*A  0    I      -I     ] [x[:n] ]     [bx[:n] ]
+    #     [  0         0   -I      -I     ] [x[n:] ]  =  [bx[n:] ].
+    #     [  I        -I   -D1^-1   0     ] [zl[:n]]     [bzl[:n]]
+    #     [ -I        -I    0      -D2^-1 ] [zl[n:]]     [bzl[n:]]
+    #
+    # where D1 = W['di'][:n]**2, D2 = W['di'][:n]**2.
+    #    
+    # We first eliminate zl and x[n:]:
+    #
+    #     ( 2*A'*A + 4*D1*D2*(D1+D2)^-1 ) * x[:n] = 
+    #         bx[:n] - (D2-D1)*(D1+D2)^-1 * bx[n:] + 
+    #         D1 * ( I + (D2-D1)*(D1+D2)^-1 ) * bzl[:n] - 
+    #         D2 * ( I - (D2-D1)*(D1+D2)^-1 ) * bzl[n:]           
+    #
+    #     x[n:] = (D1+D2)^-1 * ( bx[n:] - D1*bzl[:n]  - D2*bzl[n:] ) 
+    #         - (D2-D1)*(D1+D2)^-1 * x[:n]         
+    #
+    #     zl[:n] = D1 * ( x[:n] - x[n:] - bzl[:n] )
+    #     zl[n:] = D2 * (-x[:n] - x[n:] - bzl[n:] ).
+    #
+    # The first equation has the form
+    #
+    #     (A'*A + D)*x[:n]  =  rhs
+    #
+    # and is equivalent to
+    #
+    #     [ D    A' ] [ x:n] ]  = [ rhs ]
+    #     [ A   -I  ] [ v    ]    [ 0   ].
+    #
+    # It can be solved as 
+    #
+    #     ( A*D^-1*A' + I ) * v = A * D^-1 * rhs
+    #     x[:n] = D^-1 * ( rhs - A'*v ).
+
+    S = matrix(0.0, (m,m))
+    Asc = matrix(0.0, (m,n))
+    v = matrix(0.0, (m,1))
+
+    def Fkkt(W):
+
+        # Factor 
+        #
+        #     S = A*D^-1*A' + I 
+        #
+        # where D = 2*D1*D2*(D1+D2)^-1, D1 = d[:n]**-2, D2 = d[n:]**-2.
+
+        d1, d2 = W['di'][:n]**2, W['di'][n:]**2
+
+        # ds is square root of diagonal of D
+        ds = math.sqrt(2.0) * div( mul( W['di'][:n], W['di'][n:]), 
+            sqrt(d1+d2) )
+        d3 =  div(d2 - d1, d1 + d2)
+     
+        # Asc = A*diag(d)^-1/2
+        Asc = A * spdiag(ds**-1)
+
+        # S = I + A * D^-1 * A'
+        blas.syrk(Asc, S)
+        S[::m+1] += 1.0 
+        lapack.potrf(S)
+
+        def g(x, y, z):
+
+            x[:n] = 0.5 * ( x[:n] - mul(d3, x[n:]) + 
+                mul(d1, z[:n] + mul(d3, z[:n])) - mul(d2, z[n:] - 
+                mul(d3, z[n:])) )
+            x[:n] = div( x[:n], ds) 
+
+            # Solve
+            #
+            #     S * v = 0.5 * A * D^-1 * ( bx[:n] - 
+            #         (D2-D1)*(D1+D2)^-1 * bx[n:] + 
+            #         D1 * ( I + (D2-D1)*(D1+D2)^-1 ) * bzl[:n] - 
+            #         D2 * ( I - (D2-D1)*(D1+D2)^-1 ) * bzl[n:] )
+                
+            blas.gemv(Asc, x, v)
+            lapack.potrs(S, v)
+            
+            # x[:n] = D^-1 * ( rhs - A'*v ).
+            blas.gemv(Asc, v, x, alpha=-1.0, beta=1.0, trans='T')
+            x[:n] = div(x[:n], ds)
+
+            # x[n:] = (D1+D2)^-1 * ( bx[n:] - D1*bzl[:n]  - D2*bzl[n:] ) 
+            #         - (D2-D1)*(D1+D2)^-1 * x[:n]         
+            x[n:] = div( x[n:] - mul(d1, z[:n]) - mul(d2, z[n:]), d1+d2 )\
+                - mul( d3, x[:n] )
+                
+            # zl[:n] = D1^1/2 * (  x[:n] - x[n:] - bzl[:n] )
+            # zl[n:] = D2^1/2 * ( -x[:n] - x[n:] - bzl[n:] ).
+            z[:n] = mul( W['di'][:n],  x[:n] - x[n:] - z[:n] ) 
+            z[n:] = mul( W['di'][n:], -x[:n] - x[n:] - z[n:] ) 
+
+        return g
+
+    return solvers.coneqp(P, q, G, h, kktsolver = Fkkt)['x'][:n]
+------------------
+
+---------------------------------------------------------------------------
+ModuleNotFoundError                       Traceback (most recent call last)
+<ipython-input-12-d670a873ab0c> in <module>
+----> 1 from cvxopt import matrix, spdiag, mul, div, sqrt, normal, setseed
+      2 from cvxopt import blas, lapack, solvers, sparse, spmatrix
+      3 import math
+      4 
+      5 try:
+
+ModuleNotFoundError: No module named 'cvxopt'
+ModuleNotFoundError: No module named 'cvxopt'
+

doc/LectureNotes/_build/html/reports/chapter3.err.log

@@ -0,0 +1,96 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
+    return loop.run_until_complete(inner)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, 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:
+------------------
+%matplotlib inline
+
+import numpy as np
+from time import time
+from scipy.stats import norm
+import matplotlib.pyplot as plt
+
+# Returns mean of bootstrap samples 
+# Bootstrap algorithm
+def bootstrap(data, datapoints):
+    t = np.zeros(datapoints)
+    n = len(data)
+    # non-parametric bootstrap         
+    for i in range(datapoints):
+        t[i] = np.mean(data[np.random.randint(0,n,n)])
+    # analysis    
+    print("Bootstrap Statistics :")
+    print("original           bias      std. error")
+    print("%8g %8g %14g %15g" % (np.mean(data), np.std(data),np.mean(t),np.std(t)))
+    return t
+
+# We set the mean value to 100 and the standard deviation to 15
+mu, sigma = 100, 15
+datapoints = 10000
+# We generate random numbers according to the normal distribution
+x = mu + sigma*np.random.randn(datapoints)
+# bootstrap returns the data sample                                    
+t = bootstrap(x, datapoints)
+------------------
+
+
+---------------------------------------------------------------------------
+ModuleNotFoundError                       Traceback (most recent call last)
+Cell In[2], line 1
+----> 1 get_ipython().run_line_magic('matplotlib', 'inline')
+      3 import numpy as np
+      4 from time import time
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth)
+   2430     kwargs['local_ns'] = self.get_local_scope(stack_depth)
+   2431 with self.builtin_trap:
+-> 2432     result = fn(*args, **kwargs)
+   2434 # The code below prevents the output from being displayed
+   2435 # when using magics with decorator @output_can_be_silenced
+   2436 # when the last Python token in the expression is a ';'.
+   2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line)
+     97     print("Available matplotlib backends: %s" % backends_list)
+     98 else:
+---> 99     gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui)
+    100     self._show_matplotlib_backend(args.gui, backend)
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui)
+   3585 def enable_matplotlib(self, gui=None):
+   3586     """Enable interactive matplotlib and inline figure support.
+   3587 
+   3588     This takes the following steps:
+   (...)
+   3604         display figures inline.
+   3605     """
+-> 3606     from matplotlib_inline.backend_inline import configure_inline_support
+   3608     from IPython.core import pylabtools as pt
+   3609     gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select)
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1
+----> 1 from . import backend_inline, config  # noqa
+      2 __version__ = "0.1.6"  # noqa
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6
+      1 """A matplotlib backend for publishing figures via display_data"""
+      3 # Copyright (c) IPython Development Team.
+      4 # Distributed under the terms of the BSD 3-Clause License.
+----> 6 import matplotlib
+      7 from matplotlib import colors
+      8 from matplotlib.backends import backend_agg
+
+ModuleNotFoundError: No module named 'matplotlib'
+

doc/LectureNotes/_build/html/reports/chapter3.log

@@ -0,0 +1,30 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run
+    return loop.run_until_complete(coro)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, 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:
+------------------
+scipy.misc.imread
+------------------
+
+---------------------------------------------------------------------------
+NameError                                 Traceback (most recent call last)
+Input In [31], in <cell line: 1>()
+----> 1 scipy.misc.imread
+
+NameError: name 'scipy' is not defined
+NameError: name 'scipy' is not defined
+

doc/LectureNotes/_build/html/reports/chapter4.err.log

@@ -0,0 +1,124 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
+    return loop.run_until_complete(inner)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, 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:
+------------------
+%matplotlib inline
+
+# Common imports
+import os
+import numpy as np
+import pandas as pd
+import matplotlib.pyplot as plt
+from sklearn.linear_model import LinearRegression, Ridge, Lasso
+from sklearn.model_selection import train_test_split
+from sklearn.utils import resample
+from sklearn.metrics import mean_squared_error
+from IPython.display import display
+from pylab import plt, mpl
+plt.style.use('seaborn')
+mpl.rcParams['font.family'] = 'serif'
+
+# 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("chddata.csv"),'r')
+
+# Read the chd data as  csv file and organize the data into arrays with age group, age, and chd
+chd = pd.read_csv(infile, names=('ID', 'Age', 'Agegroup', 'CHD'))
+chd.columns = ['ID', 'Age', 'Agegroup', 'CHD']
+output = chd['CHD']
+age = chd['Age']
+agegroup = chd['Agegroup']
+numberID  = chd['ID'] 
+display(chd)
+
+plt.scatter(age, output, marker='o')
+plt.axis([18,70.0,-0.1, 1.2])
+plt.xlabel(r'Age')
+plt.ylabel(r'CHD')
+plt.title(r'Age distribution and Coronary heart disease')
+plt.show()
+------------------
+
+
+---------------------------------------------------------------------------
+ModuleNotFoundError                       Traceback (most recent call last)
+Cell In[1], line 1
+----> 1 get_ipython().run_line_magic('matplotlib', 'inline')
+      3 # Common imports
+      4 import os
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth)
+   2430     kwargs['local_ns'] = self.get_local_scope(stack_depth)
+   2431 with self.builtin_trap:
+-> 2432     result = fn(*args, **kwargs)
+   2434 # The code below prevents the output from being displayed
+   2435 # when using magics with decorator @output_can_be_silenced
+   2436 # when the last Python token in the expression is a ';'.
+   2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line)
+     97     print("Available matplotlib backends: %s" % backends_list)
+     98 else:
+---> 99     gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui)
+    100     self._show_matplotlib_backend(args.gui, backend)
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui)
+   3585 def enable_matplotlib(self, gui=None):
+   3586     """Enable interactive matplotlib and inline figure support.
+   3587 
+   3588     This takes the following steps:
+   (...)
+   3604         display figures inline.
+   3605     """
+-> 3606     from matplotlib_inline.backend_inline import configure_inline_support
+   3608     from IPython.core import pylabtools as pt
+   3609     gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select)
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1
+----> 1 from . import backend_inline, config  # noqa
+      2 __version__ = "0.1.6"  # noqa
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6
+      1 """A matplotlib backend for publishing figures via display_data"""
+      3 # Copyright (c) IPython Development Team.
+      4 # Distributed under the terms of the BSD 3-Clause License.
+----> 6 import matplotlib
+      7 from matplotlib import colors
+      8 from matplotlib.backends import backend_agg
+
+ModuleNotFoundError: No module named 'matplotlib'
+

doc/LectureNotes/_build/html/reports/chapter4.log

@@ -0,0 +1,77 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run
+    return loop.run_until_complete(coro)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, 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 matplotlib.pyplot as plt
+import numpy as np
+from sklearn.model_selection import  train_test_split 
+from sklearn.datasets import load_breast_cancer
+from sklearn.linear_model import LogisticRegression
+
+# Load the data
+cancer = load_breast_cancer()
+
+X_train, X_test, y_train, y_test = train_test_split(cancer.data,cancer.target,random_state=0)
+print(X_train.shape)
+print(X_test.shape)
+# Logistic Regression
+logreg = LogisticRegression(solver='lbfgs')
+logreg.fit(X_train, y_train)
+print("Test set accuracy with Logistic Regression: {:.2f}".format(logreg.score(X_test,y_test)))
+#now scale the data
+from sklearn.preprocessing import StandardScaler
+scaler = StandardScaler()
+scaler.fit(X_train)
+X_train_scaled = scaler.transform(X_train)
+X_test_scaled = scaler.transform(X_test)
+# Logistic Regression
+logreg.fit(X_train_scaled, y_train)
+print("Test set accuracy Logistic Regression with scaled data: {:.2f}".format(logreg.score(X_test_scaled,y_test)))
+
+
+from sklearn.preprocessing import LabelEncoder
+from sklearn.model_selection import cross_validate
+#Cross validation
+accuracy = cross_validate(logreg,X_test_scaled,y_test,cv=10)['test_score']
+print(accuracy)
+print("Test set accuracy with Logistic Regression  and scaled data: {:.2f}".format(logreg.score(X_test_scaled,y_test)))
+
+
+import scikitplot as skplt
+y_pred = logreg.predict(X_test_scaled)
+skplt.metrics.plot_confusion_matrix(y_test, y_pred, normalize=True)
+plt.show()
+y_probas = logreg.predict_proba(X_test_scaled)
+skplt.metrics.plot_roc(y_test, y_probas)
+plt.show()
+skplt.metrics.plot_cumulative_gain(y_test, y_probas)
+plt.show()
+------------------
+
+---------------------------------------------------------------------------
+ModuleNotFoundError                       Traceback (most recent call last)
+Input In [8], in <cell line: 36>()
+     32 print(accuracy)
+     33 print("Test set accuracy with Logistic Regression  and scaled data: {:.2f}".format(logreg.score(X_test_scaled,y_test)))
+---> 36 import scikitplot as skplt
+     37 y_pred = logreg.predict(X_test_scaled)
+     38 skplt.metrics.plot_confusion_matrix(y_test, y_pred, normalize=True)
+
+ModuleNotFoundError: No module named 'scikitplot'
+ModuleNotFoundError: No module named 'scikitplot'
+

doc/LectureNotes/_build/html/reports/chapter5.err.log

@@ -0,0 +1,136 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
+    return loop.run_until_complete(inner)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, 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:
+------------------
+%matplotlib inline
+
+from sklearn import datasets
+from sklearn.svm import SVC, LinearSVC
+from sklearn.linear_model import SGDClassifier
+from sklearn.preprocessing import StandardScaler
+import matplotlib
+import matplotlib.pyplot as plt
+plt.rcParams['axes.labelsize'] = 14
+plt.rcParams['xtick.labelsize'] = 12
+plt.rcParams['ytick.labelsize'] = 12
+
+
+iris = datasets.load_iris()
+X = iris["data"][:, (2, 3)]  # petal length, petal width
+y = iris["target"]
+
+setosa_or_versicolor = (y == 0) | (y == 1)
+X = X[setosa_or_versicolor]
+y = y[setosa_or_versicolor]
+
+
+
+C = 5
+alpha = 1 / (C * len(X))
+
+lin_clf = LinearSVC(loss="hinge", C=C, random_state=42)
+svm_clf = SVC(kernel="linear", C=C)
+sgd_clf = SGDClassifier(loss="hinge", learning_rate="constant", eta0=0.001, alpha=alpha,
+                        max_iter=100000, random_state=42)
+
+scaler = StandardScaler()
+X_scaled = scaler.fit_transform(X)
+
+lin_clf.fit(X_scaled, y)
+svm_clf.fit(X_scaled, y)
+sgd_clf.fit(X_scaled, y)
+
+print("LinearSVC:                   ", lin_clf.intercept_, lin_clf.coef_)
+print("SVC:                         ", svm_clf.intercept_, svm_clf.coef_)
+print("SGDClassifier(alpha={:.5f}):".format(sgd_clf.alpha), sgd_clf.intercept_, sgd_clf.coef_)
+
+# Compute the slope and bias of each decision boundary
+w1 = -lin_clf.coef_[0, 0]/lin_clf.coef_[0, 1]
+b1 = -lin_clf.intercept_[0]/lin_clf.coef_[0, 1]
+w2 = -svm_clf.coef_[0, 0]/svm_clf.coef_[0, 1]
+b2 = -svm_clf.intercept_[0]/svm_clf.coef_[0, 1]
+w3 = -sgd_clf.coef_[0, 0]/sgd_clf.coef_[0, 1]
+b3 = -sgd_clf.intercept_[0]/sgd_clf.coef_[0, 1]
+
+# Transform the decision boundary lines back to the original scale
+line1 = scaler.inverse_transform([[-10, -10 * w1 + b1], [10, 10 * w1 + b1]])
+line2 = scaler.inverse_transform([[-10, -10 * w2 + b2], [10, 10 * w2 + b2]])
+line3 = scaler.inverse_transform([[-10, -10 * w3 + b3], [10, 10 * w3 + b3]])
+
+# Plot all three decision boundaries
+plt.figure(figsize=(11, 4))
+plt.plot(line1[:, 0], line1[:, 1], "k:", label="LinearSVC")
+plt.plot(line2[:, 0], line2[:, 1], "b--", linewidth=2, label="SVC")
+plt.plot(line3[:, 0], line3[:, 1], "r-", label="SGDClassifier")
+plt.plot(X[:, 0][y==1], X[:, 1][y==1], "bs") # label="Iris-Versicolor"
+plt.plot(X[:, 0][y==0], X[:, 1][y==0], "yo") # label="Iris-Setosa"
+plt.xlabel("Petal length", fontsize=14)
+plt.ylabel("Petal width", fontsize=14)
+plt.legend(loc="upper center", fontsize=14)
+plt.axis([0, 5.5, 0, 2])
+
+plt.show()
+------------------
+
+
+---------------------------------------------------------------------------
+ModuleNotFoundError                       Traceback (most recent call last)
+Cell In[1], line 1
+----> 1 get_ipython().run_line_magic('matplotlib', 'inline')
+      3 from sklearn import datasets
+      4 from sklearn.svm import SVC, LinearSVC
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth)
+   2430     kwargs['local_ns'] = self.get_local_scope(stack_depth)
+   2431 with self.builtin_trap:
+-> 2432     result = fn(*args, **kwargs)
+   2434 # The code below prevents the output from being displayed
+   2435 # when using magics with decorator @output_can_be_silenced
+   2436 # when the last Python token in the expression is a ';'.
+   2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line)
+     97     print("Available matplotlib backends: %s" % backends_list)
+     98 else:
+---> 99     gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui)
+    100     self._show_matplotlib_backend(args.gui, backend)
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui)
+   3585 def enable_matplotlib(self, gui=None):
+   3586     """Enable interactive matplotlib and inline figure support.
+   3587 
+   3588     This takes the following steps:
+   (...)
+   3604         display figures inline.
+   3605     """
+-> 3606     from matplotlib_inline.backend_inline import configure_inline_support
+   3608     from IPython.core import pylabtools as pt
+   3609     gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select)
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1
+----> 1 from . import backend_inline, config  # noqa
+      2 __version__ = "0.1.6"  # noqa
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6
+      1 """A matplotlib backend for publishing figures via display_data"""
+      3 # Copyright (c) IPython Development Team.
+      4 # Distributed under the terms of the BSD 3-Clause License.
+----> 6 import matplotlib
+      7 from matplotlib import colors
+      8 from matplotlib.backends import backend_agg
+
+ModuleNotFoundError: No module named 'matplotlib'
+

doc/LectureNotes/_build/html/reports/chapter5.log

@@ -0,0 +1,41 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run
+    return loop.run_until_complete(coro)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, 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 the necessary packages
+import numpy
+from cvxopt import matrix
+from cvxopt import solvers
+P = matrix(numpy.diag([1,0]), tc=’d’)
+q = matrix(numpy.array([3,4]), tc=’d’)
+G = matrix(numpy.array([[-1,0],[0,-1],[-1,-3],[2,5],[3,4]]), tc=’d’)
+h = matrix(numpy.array([0,0,-15,100,80]), tc=’d’)
+# Construct the QP, invoke solver
+sol = solvers.qp(P,q,G,h)
+# Extract optimal value and solution
+sol[’x’] 
+sol[’primal objective’]
+------------------
+
+  Input In [5]
+    P = matrix(numpy.diag([1,0]), tc=’d’)
+                                     ^
+SyntaxError: invalid character '’' (U+2019)
+
+SyntaxError: invalid character '’' (U+2019) (3974140161.py, line 5)
+

doc/LectureNotes/_build/html/reports/chapter6.err.log

@@ -0,0 +1,158 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
+    return loop.run_until_complete(inner)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, 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:
+------------------
+%matplotlib inline
+
+import numpy as np
+import matplotlib.pyplot as plt
+from sklearn.preprocessing import PolynomialFeatures
+from sklearn.linear_model import LinearRegression
+
+steps=250
+
+distance=0
+x=0
+distance_list=[]
+steps_list=[]
+while x<steps:
+    distance+=np.random.randint(-1,2)
+    distance_list.append(distance)
+    x+=1
+    steps_list.append(x)
+plt.plot(steps_list,distance_list, color='green', label="Random Walk Data")
+
+steps_list=np.asarray(steps_list)
+distance_list=np.asarray(distance_list)
+
+X=steps_list[:,np.newaxis]
+
+#Polynomial fits
+
+#Degree 2
+poly_features=PolynomialFeatures(degree=2, include_bias=False)
+X_poly=poly_features.fit_transform(X)
+
+lin_reg=LinearRegression()
+poly_fit=lin_reg.fit(X_poly,distance_list)
+b=lin_reg.coef_
+c=lin_reg.intercept_
+print ("2nd degree coefficients:")
+print ("zero power: ",c)
+print ("first power: ", b[0])
+print ("second power: ",b[1])
+
+z = np.arange(0, steps, .01)
+z_mod=b[1]*z**2+b[0]*z+c
+
+fit_mod=b[1]*X**2+b[0]*X+c
+plt.plot(z, z_mod, color='r', label="2nd Degree Fit")
+plt.title("Polynomial Regression")
+
+plt.xlabel("Steps")
+plt.ylabel("Distance")
+
+#Degree 10
+poly_features10=PolynomialFeatures(degree=10, include_bias=False)
+X_poly10=poly_features10.fit_transform(X)
+
+poly_fit10=lin_reg.fit(X_poly10,distance_list)
+
+y_plot=poly_fit10.predict(X_poly10)
+plt.plot(X, y_plot, color='black', label="10th Degree Fit")
+
+plt.legend()
+plt.show()
+
+
+#Decision Tree Regression
+from sklearn.tree import DecisionTreeRegressor
+regr_1=DecisionTreeRegressor(max_depth=2)
+regr_2=DecisionTreeRegressor(max_depth=5)
+regr_3=DecisionTreeRegressor(max_depth=7)
+regr_1.fit(X, distance_list)
+regr_2.fit(X, distance_list)
+regr_3.fit(X, distance_list)
+
+X_test = np.arange(0.0, steps, 0.01)[:, np.newaxis]
+y_1 = regr_1.predict(X_test)
+y_2 = regr_2.predict(X_test)
+y_3=regr_3.predict(X_test)
+
+# Plot the results
+plt.figure()
+plt.scatter(X, distance_list, s=2.5, c="black", label="data")
+plt.plot(X_test, y_1, color="red",
+         label="max_depth=2", linewidth=2)
+plt.plot(X_test, y_2, color="green", label="max_depth=5", linewidth=2)
+plt.plot(X_test, y_3, color="m", label="max_depth=7", linewidth=2)
+
+plt.xlabel("Data")
+plt.ylabel("Darget")
+plt.title("Decision Tree Regression")
+plt.legend()
+plt.show()
+------------------
+
+
+---------------------------------------------------------------------------
+ModuleNotFoundError                       Traceback (most recent call last)
+Cell In[1], line 1
+----> 1 get_ipython().run_line_magic('matplotlib', 'inline')
+      3 import numpy as np
+      4 import matplotlib.pyplot as plt
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth)
+   2430     kwargs['local_ns'] = self.get_local_scope(stack_depth)
+   2431 with self.builtin_trap:
+-> 2432     result = fn(*args, **kwargs)
+   2434 # The code below prevents the output from being displayed
+   2435 # when using magics with decorator @output_can_be_silenced
+   2436 # when the last Python token in the expression is a ';'.
+   2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line)
+     97     print("Available matplotlib backends: %s" % backends_list)
+     98 else:
+---> 99     gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui)
+    100     self._show_matplotlib_backend(args.gui, backend)
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui)
+   3585 def enable_matplotlib(self, gui=None):
+   3586     """Enable interactive matplotlib and inline figure support.
+   3587 
+   3588     This takes the following steps:
+   (...)
+   3604         display figures inline.
+   3605     """
+-> 3606     from matplotlib_inline.backend_inline import configure_inline_support
+   3608     from IPython.core import pylabtools as pt
+   3609     gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select)
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1
+----> 1 from . import backend_inline, config  # noqa
+      2 __version__ = "0.1.6"  # noqa
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6
+      1 """A matplotlib backend for publishing figures via display_data"""
+      3 # Copyright (c) IPython Development Team.
+      4 # Distributed under the terms of the BSD 3-Clause License.
+----> 6 import matplotlib
+      7 from matplotlib import colors
+      8 from matplotlib.backends import backend_agg
+
+ModuleNotFoundError: No module named 'matplotlib'
+

doc/LectureNotes/_build/html/reports/chapter6.log

@@ -0,0 +1,100 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run
+    return loop.run_until_complete(coro)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, 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:
+------------------
+# Common imports
+import numpy as np
+import pandas as pd
+import matplotlib.pyplot as plt
+from sklearn.tree import DecisionTreeClassifier
+from sklearn.model_selection import train_test_split
+from sklearn.tree import export_graphviz
+from sklearn.preprocessing import StandardScaler, OneHotEncoder
+from sklearn.compose import ColumnTransformer
+from IPython.display import Image 
+from pydot import graph_from_dot_data
+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("rideclass.csv"),'r')
+
+# Read the experimental data with Pandas
+from IPython.display import display
+ridedata = pd.read_csv(infile,names = ('Outlook','Temperature','Humidity','Wind','Ride'))
+ridedata = pd.DataFrame(ridedata)
+
+# Features and targets
+X = ridedata.loc[:, ridedata.columns != 'Ride'].values
+y = ridedata.loc[:, ridedata.columns == 'Ride'].values
+
+# Create the encoder.
+encoder = OneHotEncoder(handle_unknown="ignore")
+# Assume for simplicity all features are categorical.
+encoder.fit(X)    
+# Apply the encoder.
+X = encoder.transform(X)
+print(X)
+# Then do a Classification tree
+tree_clf = DecisionTreeClassifier(max_depth=2)
+tree_clf.fit(X, y)
+print("Train set accuracy with Decision Tree: {:.2f}".format(tree_clf.score(X,y)))
+#transfer to a decision tree graph
+export_graphviz(
+    tree_clf,
+    out_file="DataFiles/ride.dot",
+    rounded=True,
+    filled=True
+)
+cmd = 'dot -Tpng DataFiles/cancer.dot -o DataFiles/cancer.png'
+os.system(cmd)
+------------------
+
+---------------------------------------------------------------------------
+FileNotFoundError                         Traceback (most recent call last)
+Input In [6], in <cell line: 37>()
+     34 def save_fig(fig_id):
+     35     plt.savefig(image_path(fig_id) + ".png", format='png')
+---> 37 infile = open(data_path("rideclass.csv"),'r')
+     39 # Read the experimental data with Pandas
+     40 from IPython.display import display
+
+FileNotFoundError: [Errno 2] No such file or directory: 'DataFiles/rideclass.csv'
+FileNotFoundError: [Errno 2] No such file or directory: 'DataFiles/rideclass.csv'
+

doc/LectureNotes/_build/html/reports/chapter7.err.log

@@ -0,0 +1,43 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
+    return loop.run_until_complete(inner)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, 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:
+------------------
+heads_proba = 0.51
+coin_tosses = (np.random.rand(10000, 10) < heads_proba).astype(np.int32)
+cumulative_heads_ratio = np.cumsum(coin_tosses, axis=0) / np.arange(1, 10001).reshape(-1, 1)
+plt.figure(figsize=(8,3.5))
+plt.plot(cumulative_heads_ratio)
+plt.plot([0, 10000], [0.51, 0.51], "k--", linewidth=2, label="51%")
+plt.plot([0, 10000], [0.5, 0.5], "k-", label="50%")
+plt.xlabel("Number of coin tosses")
+plt.ylabel("Heads ratio")
+plt.legend(loc="lower right")
+plt.axis([0, 10000, 0.42, 0.58])
+save_fig("votingsimple")
+plt.show()
+------------------
+
+
+---------------------------------------------------------------------------
+NameError                                 Traceback (most recent call last)
+Cell In[1], line 2
+      1 heads_proba = 0.51
+----> 2 coin_tosses = (np.random.rand(10000, 10) < heads_proba).astype(np.int32)
+      3 cumulative_heads_ratio = np.cumsum(coin_tosses, axis=0) / np.arange(1, 10001).reshape(-1, 1)
+      4 plt.figure(figsize=(8,3.5))
+
+NameError: name 'np' is not defined
+

doc/LectureNotes/_build/html/reports/chapter7.log

@@ -0,0 +1,45 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run
+    return loop.run_until_complete(coro)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, 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:
+------------------
+heads_proba = 0.51
+coin_tosses = (np.random.rand(10000, 10) < heads_proba).astype(np.int32)
+cumulative_heads_ratio = np.cumsum(coin_tosses, axis=0) / np.arange(1, 10001).reshape(-1, 1)
+plt.figure(figsize=(8,3.5))
+plt.plot(cumulative_heads_ratio)
+plt.plot([0, 10000], [0.51, 0.51], "k--", linewidth=2, label="51%")
+plt.plot([0, 10000], [0.5, 0.5], "k-", label="50%")
+plt.xlabel("Number of coin tosses")
+plt.ylabel("Heads ratio")
+plt.legend(loc="lower right")
+plt.axis([0, 10000, 0.42, 0.58])
+save_fig("votingsimple")
+plt.show()
+------------------
+
+---------------------------------------------------------------------------
+NameError                                 Traceback (most recent call last)
+Input In [1], in <cell line: 2>()
+      1 heads_proba = 0.51
+----> 2 coin_tosses = (np.random.rand(10000, 10) < heads_proba).astype(np.int32)
+      3 cumulative_heads_ratio = np.cumsum(coin_tosses, axis=0) / np.arange(1, 10001).reshape(-1, 1)
+      4 plt.figure(figsize=(8,3.5))
+
+NameError: name 'np' is not defined
+NameError: name 'np' is not defined
+

doc/LectureNotes/_build/html/reports/chapter8.err.log

@@ -0,0 +1,43 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
+    return loop.run_until_complete(inner)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, 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 numpy as np
+import pandas as pd
+n = 10
+x = np.random.normal(size=n)
+x = x - np.mean(x)
+y = 4+3*x+np.random.normal(size=n)
+y = y - np.mean(y)
+X = (np.vstack((x, y))).T
+print(X)
+Xpd = pd.DataFrame(X)
+print(Xpd)
+correlation_matrix = Xpd.corr()
+print(correlation_matrix)
+------------------
+
+
+---------------------------------------------------------------------------
+ModuleNotFoundError                       Traceback (most recent call last)
+Cell In[3], line 2
+      1 import numpy as np
+----> 2 import pandas as pd
+      3 n = 10
+      4 x = np.random.normal(size=n)
+
+ModuleNotFoundError: No module named 'pandas'
+

doc/LectureNotes/_build/html/reports/chapter9.err.log

@@ -0,0 +1,144 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
+    return loop.run_until_complete(inner)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, 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:
+------------------
+%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()
+
+"""Sine Function"""
+z = numpy.arange(-2*mt.pi, 2*mt.pi, 0.1)
+t = numpy.sin(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('sine function')
+
+plt.show()
+
+"""Plots a graph of the squashing function used by a rectified linear
+unit"""
+z = numpy.arange(-2, 2, .1)
+zero = numpy.zeros(len(z))
+y = numpy.max([zero, z], axis=0)
+
+fig = plt.figure()
+ax = fig.add_subplot(111)
+ax.plot(z, y)
+ax.set_ylim([-2.0, 2.0])
+ax.set_xlim([-2.0, 2.0])
+ax.grid(True)
+ax.set_xlabel('z')
+ax.set_title('Rectified linear unit')
+
+plt.show()
+------------------
+
+
+---------------------------------------------------------------------------
+ModuleNotFoundError                       Traceback (most recent call last)
+Cell In[1], line 1
+----> 1 get_ipython().run_line_magic('matplotlib', 'inline')
+      3 """The sigmoid function (or the logistic curve) is a 
+      4 function that takes any real number, z, and outputs a number (0,1).
+      5 It is useful in neural networks for assigning weights on a relative scale.
+      6 The value z is the weighted sum of parameters involved in the learning algorithm."""
+      8 import numpy
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth)
+   2430     kwargs['local_ns'] = self.get_local_scope(stack_depth)
+   2431 with self.builtin_trap:
+-> 2432     result = fn(*args, **kwargs)
+   2434 # The code below prevents the output from being displayed
+   2435 # when using magics with decorator @output_can_be_silenced
+   2436 # when the last Python token in the expression is a ';'.
+   2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line)
+     97     print("Available matplotlib backends: %s" % backends_list)
+     98 else:
+---> 99     gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui)
+    100     self._show_matplotlib_backend(args.gui, backend)
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui)
+   3585 def enable_matplotlib(self, gui=None):
+   3586     """Enable interactive matplotlib and inline figure support.
+   3587 
+   3588     This takes the following steps:
+   (...)
+   3604         display figures inline.
+   3605     """
+-> 3606     from matplotlib_inline.backend_inline import configure_inline_support
+   3608     from IPython.core import pylabtools as pt
+   3609     gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select)
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1
+----> 1 from . import backend_inline, config  # noqa
+      2 __version__ = "0.1.6"  # noqa
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6
+      1 """A matplotlib backend for publishing figures via display_data"""
+      3 # Copyright (c) IPython Development Team.
+      4 # Distributed under the terms of the BSD 3-Clause License.
+----> 6 import matplotlib
+      7 from matplotlib import colors
+      8 from matplotlib.backends import backend_agg
+
+ModuleNotFoundError: No module named 'matplotlib'
+

doc/LectureNotes/_build/html/reports/chapteroptimization.err.log

@@ -0,0 +1,90 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
+    return loop.run_until_complete(inner)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, 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:
+------------------
+%matplotlib inline
+
+import numpy as np
+import numpy.linalg as la
+
+import scipy.optimize as sopt
+
+import matplotlib.pyplot as pt
+from mpl_toolkits.mplot3d import axes3d
+
+def f(x):
+    return 0.5*x[0]**2 + 2.5*x[1]**2
+
+def df(x):
+    return np.array([x[0], 5*x[1]])
+
+fig = pt.figure()
+ax = fig.gca(projection="3d")
+
+xmesh, ymesh = np.mgrid[-2:2:50j,-2:2:50j]
+fmesh = f(np.array([xmesh, ymesh]))
+ax.plot_surface(xmesh, ymesh, fmesh)
+------------------
+
+
+---------------------------------------------------------------------------
+ModuleNotFoundError                       Traceback (most recent call last)
+Cell In[1], line 1
+----> 1 get_ipython().run_line_magic('matplotlib', 'inline')
+      3 import numpy as np
+      4 import numpy.linalg as la
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth)
+   2430     kwargs['local_ns'] = self.get_local_scope(stack_depth)
+   2431 with self.builtin_trap:
+-> 2432     result = fn(*args, **kwargs)
+   2434 # The code below prevents the output from being displayed
+   2435 # when using magics with decorator @output_can_be_silenced
+   2436 # when the last Python token in the expression is a ';'.
+   2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line)
+     97     print("Available matplotlib backends: %s" % backends_list)
+     98 else:
+---> 99     gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui)
+    100     self._show_matplotlib_backend(args.gui, backend)
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui)
+   3585 def enable_matplotlib(self, gui=None):
+   3586     """Enable interactive matplotlib and inline figure support.
+   3587 
+   3588     This takes the following steps:
+   (...)
+   3604         display figures inline.
+   3605     """
+-> 3606     from matplotlib_inline.backend_inline import configure_inline_support
+   3608     from IPython.core import pylabtools as pt
+   3609     gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select)
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1
+----> 1 from . import backend_inline, config  # noqa
+      2 __version__ = "0.1.6"  # noqa
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6
+      1 """A matplotlib backend for publishing figures via display_data"""
+      3 # Copyright (c) IPython Development Team.
+      4 # Distributed under the terms of the BSD 3-Clause License.
+----> 6 import matplotlib
+      7 from matplotlib import colors
+      8 from matplotlib.backends import backend_agg
+
+ModuleNotFoundError: No module named 'matplotlib'
+

doc/LectureNotes/_build/html/reports/chapteroptimization.log

@@ -0,0 +1,84 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run
+    return loop.run_until_complete(coro)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, 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 autograd.numpy as np
+from autograd import grad
+def f9(a): # Assume a is an array with 2 elements
+    b = np.array([1.0,2.0])
+    return a.dot(b)
+
+f9_grad = grad(f9)
+
+x = np.array([1.0,0.0])
+
+print("The derivative of f9 is:",f9_grad(x))
+------------------
+
+---------------------------------------------------------------------------
+AttributeError                            Traceback (most recent call last)
+Input In [23], in <cell line: 11>()
+      7 f9_grad = grad(f9)
+      9 x = np.array([1.0,0.0])
+---> 11 print("The derivative of f9 is:",f9_grad(x))
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/autograd/wrap_util.py:20, in unary_to_nary.<locals>.nary_operator.<locals>.nary_f(*args, **kwargs)
+     18 else:
+     19     x = tuple(args[i] for i in argnum)
+---> 20 return unary_operator(unary_f, x, *nary_op_args, **nary_op_kwargs)
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/autograd/differential_operators.py:25, in grad(fun, x)
+     18 @unary_to_nary
+     19 def grad(fun, x):
+     20     """
+     21     Returns a function which computes the gradient of `fun` with respect to
+     22     positional argument number `argnum`. The returned function takes the same
+     23     arguments as `fun`, but returns the gradient instead. The function `fun`
+     24     should be scalar-valued. The gradient has the same type as the argument."""
+---> 25     vjp, ans = _make_vjp(fun, x)
+     26     if not vspace(ans).size == 1:
+     27         raise TypeError("Grad only applies to real scalar-output functions. "
+     28                         "Try jacobian, elementwise_grad or holomorphic_grad.")
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/autograd/core.py:10, in make_vjp(fun, x)
+      8 def make_vjp(fun, x):
+      9     start_node = VJPNode.new_root()
+---> 10     end_value, end_node =  trace(start_node, fun, x)
+     11     if end_node is None:
+     12         def vjp(g): return vspace(x).zeros()
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/autograd/tracer.py:10, in trace(start_node, fun, x)
+      8 with trace_stack.new_trace() as t:
+      9     start_box = new_box(x, t, start_node)
+---> 10     end_box = fun(start_box)
+     11     if isbox(end_box) and end_box._trace == start_box._trace:
+     12         return end_box._value, end_box._node
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/autograd/wrap_util.py:15, in unary_to_nary.<locals>.nary_operator.<locals>.nary_f.<locals>.unary_f(x)
+     13 else:
+     14     subargs = subvals(args, zip(argnum, x))
+---> 15 return fun(*subargs, **kwargs)
+
+Input In [23], in f9(a)
+      3 def f9(a): # Assume a is an array with 2 elements
+      4     b = np.array([1.0,2.0])
+----> 5     return a.dot(b)
+
+AttributeError: 'ArrayBox' object has no attribute 'dot'
+AttributeError: 'ArrayBox' object has no attribute 'dot'
+

doc/LectureNotes/_build/html/reports/clustering.err.log

@@ -0,0 +1,79 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
+    return loop.run_until_complete(inner)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, 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:
+------------------
+%matplotlib inline
+
+import time
+import numpy as np
+import tensorflow as tf
+from matplotlib import image
+import matplotlib.pyplot as plt
+from sklearn.cluster import KMeans
+from IPython.display import display
+
+np.random.seed(2021)
+------------------
+
+
+---------------------------------------------------------------------------
+ModuleNotFoundError                       Traceback (most recent call last)
+Cell In[1], line 1
+----> 1 get_ipython().run_line_magic('matplotlib', 'inline')
+      3 import time
+      4 import numpy as np
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth)
+   2430     kwargs['local_ns'] = self.get_local_scope(stack_depth)
+   2431 with self.builtin_trap:
+-> 2432     result = fn(*args, **kwargs)
+   2434 # The code below prevents the output from being displayed
+   2435 # when using magics with decorator @output_can_be_silenced
+   2436 # when the last Python token in the expression is a ';'.
+   2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line)
+     97     print("Available matplotlib backends: %s" % backends_list)
+     98 else:
+---> 99     gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui)
+    100     self._show_matplotlib_backend(args.gui, backend)
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui)
+   3585 def enable_matplotlib(self, gui=None):
+   3586     """Enable interactive matplotlib and inline figure support.
+   3587 
+   3588     This takes the following steps:
+   (...)
+   3604         display figures inline.
+   3605     """
+-> 3606     from matplotlib_inline.backend_inline import configure_inline_support
+   3608     from IPython.core import pylabtools as pt
+   3609     gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select)
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1
+----> 1 from . import backend_inline, config  # noqa
+      2 __version__ = "0.1.6"  # noqa
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6
+      1 """A matplotlib backend for publishing figures via display_data"""
+      3 # Copyright (c) IPython Development Team.
+      4 # Distributed under the terms of the BSD 3-Clause License.
+----> 6 import matplotlib
+      7 from matplotlib import colors
+      8 from matplotlib.backends import backend_agg
+
+ModuleNotFoundError: No module named 'matplotlib'
+

doc/LectureNotes/_build/html/reports/clustering.log

@@ -0,0 +1,239 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run
+    return loop.run_until_complete(coro)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, 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:
+------------------
+%matplotlib inline
+
+import time
+import numpy as np
+import tensorflow as tf
+from matplotlib import image
+import matplotlib.pyplot as plt
+from sklearn.cluster import KMeans
+from IPython.display import display
+
+np.random.seed(2021)
+------------------
+
+---------------------------------------------------------------------------
+AttributeError                            Traceback (most recent call last)
+Input In [1], in <cell line: 5>()
+      3 import time
+      4 import numpy as np
+----> 5 import tensorflow as tf
+      6 from matplotlib import image
+      7 import matplotlib.pyplot as plt
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/tensorflow/__init__.py:51, in <module>
+     49 from ._api.v2 import autograph
+     50 from ._api.v2 import bitwise
+---> 51 from ._api.v2 import compat
+     52 from ._api.v2 import config
+     53 from ._api.v2 import data
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/tensorflow/_api/v2/compat/__init__.py:37, in <module>
+      3 """Compatibility functions.
+      4 
+      5 The `tf.compat` module contains two sets of compatibility functions.
+   (...)
+     32 
+     33 """
+     35 import sys as _sys
+---> 37 from . import v1
+     38 from . import v2
+     39 from tensorflow.python.compat.compat import forward_compatibility_horizon
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/tensorflow/_api/v2/compat/v1/__init__.py:30, in <module>
+     28 from . import autograph
+     29 from . import bitwise
+---> 30 from . import compat
+     31 from . import config
+     32 from . import data
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/tensorflow/_api/v2/compat/v1/compat/__init__.py:37, in <module>
+      3 """Compatibility functions.
+      4 
+      5 The `tf.compat` module contains two sets of compatibility functions.
+   (...)
+     32 
+     33 """
+     35 import sys as _sys
+---> 37 from . import v1
+     38 from . import v2
+     39 from tensorflow.python.compat.compat import forward_compatibility_horizon
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/tensorflow/_api/v2/compat/v1/compat/v1/__init__.py:47, in <module>
+     45 from tensorflow._api.v2.compat.v1 import layers
+     46 from tensorflow._api.v2.compat.v1 import linalg
+---> 47 from tensorflow._api.v2.compat.v1 import lite
+     48 from tensorflow._api.v2.compat.v1 import logging
+     49 from tensorflow._api.v2.compat.v1 import lookup
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/tensorflow/_api/v2/compat/v1/lite/__init__.py:9, in <module>
+      6 import sys as _sys
+      8 from . import constants
+----> 9 from . import experimental
+     10 from tensorflow.lite.python.lite import Interpreter
+     11 from tensorflow.lite.python.lite import OpHint
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/tensorflow/_api/v2/compat/v1/lite/experimental/__init__.py:8, in <module>
+      3 """Public API for tf.lite.experimental namespace.
+      4 """
+      6 import sys as _sys
+----> 8 from . import authoring
+      9 from tensorflow.lite.python.analyzer import ModelAnalyzer as Analyzer
+     10 from tensorflow.lite.python.lite import OpResolverType
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/tensorflow/_api/v2/compat/v1/lite/experimental/authoring/__init__.py:8, in <module>
+      3 """Public API for tf.lite.experimental.authoring namespace.
+      4 """
+      6 import sys as _sys
+----> 8 from tensorflow.lite.python.authoring.authoring import compatible
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/tensorflow/lite/python/authoring/authoring.py:43, in <module>
+     39 import functools
+     42 # pylint: disable=g-import-not-at-top
+---> 43 from tensorflow.lite.python import convert
+     44 from tensorflow.lite.python import lite
+     45 from tensorflow.lite.python.metrics import converter_error_data_pb2
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/tensorflow/lite/python/convert.py:29, in <module>
+     26 import six
+     28 from tensorflow.lite.python import lite_constants
+---> 29 from tensorflow.lite.python import util
+     30 from tensorflow.lite.python import wrap_toco
+     31 from tensorflow.lite.python.convert_phase import Component
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/tensorflow/lite/python/util.py:51, in <module>
+     47 # Jax functions used by TFLite
+     48 # pylint: disable=g-import-not-at-top
+     49 # pylint: disable=unused-import
+     50 try:
+---> 51   from jax import xla_computation as _xla_computation
+     52 except ImportError:
+     53   _xla_computation = None
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/__init__.py:116, in <module>
+     40 from ._src.config import (
+     41   config as config,
+     42   enable_checks as enable_checks,
+   (...)
+     51   numpy_rank_promotion as numpy_rank_promotion,
+     52 )
+     53 from ._src.api import (
+     54   ad,  # TODO(phawkins): update users to avoid this.
+     55   checkpoint as checkpoint,
+   (...)
+    114   xla_computation as xla_computation,
+    115 )
+--> 116 from .experimental.maps import soft_pmap as soft_pmap
+    117 from .version import __version__ as __version__
+    119 # These submodules are separate because they are in an import cycle with
+    120 # jax and rely on the names imported above.
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/experimental/maps.py:26, in <module>
+     23 from functools import wraps, partial, partialmethod
+     24 from enum import Enum
+---> 26 from .. import numpy as jnp
+     27 from .. import core
+     28 from .. import linear_util as lu
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/numpy/__init__.py:19, in <module>
+      1 # Copyright 2018 Google LLC
+      2 #
+      3 # Licensed under the Apache License, Version 2.0 (the "License");
+   (...)
+     17 
+     18 # flake8: noqa: F401
+---> 19 from . import fft as fft
+     20 from . import linalg as linalg
+     22 from jax.interpreters.xla import DeviceArray as DeviceArray
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/numpy/fft.py:17, in <module>
+      1 # Copyright 2020 Google LLC
+      2 #
+      3 # Licensed under the Apache License, Version 2.0 (the "License");
+   (...)
+     14 
+     15 # flake8: noqa: F401
+---> 17 from jax._src.numpy.fft import (
+     18   ifft as ifft,
+     19   ifft2 as ifft2,
+     20   ifftn as ifftn,
+     21   ifftshift as ifftshift,
+     22   ihfft as ihfft,
+     23   irfft as irfft,
+     24   irfft2 as irfft2,
+     25   irfftn as irfftn,
+     26   fft as fft,
+     27   fft2 as fft2,
+     28   fftfreq as fftfreq,
+     29   fftn as fftn,
+     30   fftshift as fftshift,
+     31   hfft as hfft,
+     32   rfft as rfft,
+     33   rfft2 as rfft2,
+     34   rfftfreq as rfftfreq,
+     35   rfftn as rfftn,
+     36 )
+     38 # Module initialization is encapsulated in a function to avoid accidental
+     39 # namespace pollution.
+     40 _NOT_IMPLEMENTED = []
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/_src/numpy/fft.py:19, in <module>
+     16 import operator
+     17 import numpy as np
+---> 19 from jax import lax
+     20 from jax._src.lib import xla_client
+     21 from jax._src.util import safe_zip
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/lax/__init__.py:332, in <module>
+    299 from jax._src.lax.lax import (_reduce_sum, _reduce_max, _reduce_min, _reduce_or,
+    300                   _reduce_and, _reduce_window_sum, _reduce_window_max,
+    301                   _reduce_window_min, _reduce_window_prod,
+   (...)
+    306                   _upcast_fp16_for_computation, _broadcasting_shape_rule,
+    307                   _eye, _tri, _delta, _ones, _zeros, _dilate_shape)
+    308 from jax._src.lax.control_flow import (
+    309   associative_scan as associative_scan,
+    310   cond as cond,
+   (...)
+    330   while_p as while_p,
+    331 )
+--> 332 from jax._src.lax.fft import (
+    333   fft as fft,
+    334   fft_p as fft_p,
+    335 )
+    336 from jax._src.lax.parallel import (
+    337   all_gather as all_gather,
+    338   all_to_all as all_to_all,
+   (...)
+    355   xeinsum as xeinsum,
+    356 )
+    357 from jax._src.lax.other import (
+    358   conv_general_dilated_patches as conv_general_dilated_patches
+    359 )
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/jax/_src/lax/fft.py:145, in <module>
+    143 batching.primitive_batchers[fft_p] = fft_batching_rule
+    144 if pocketfft:
+--> 145   xla.backend_specific_translations['cpu'][fft_p] = pocketfft.pocketfft
+
+AttributeError: module 'jaxlib.pocketfft' has no attribute 'pocketfft'
+AttributeError: module 'jaxlib.pocketfft' has no attribute 'pocketfft'
+

doc/LectureNotes/_build/html/reports/exercisesweek34.err.log

@@ -0,0 +1,30 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
+    return loop.run_until_complete(inner)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, 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:
+------------------
+x = np.random.rand(100,1)
+y = 2.0+5*x*x+0.1*np.random.randn(100,1)
+------------------
+
+
+---------------------------------------------------------------------------
+NameError                                 Traceback (most recent call last)
+Cell In[1], line 1
+----> 1 x = np.random.rand(100,1)
+      2 y = 2.0+5*x*x+0.1*np.random.randn(100,1)
+
+NameError: name 'np' is not defined
+

doc/LectureNotes/_build/html/reports/exercisesweek34.log

@@ -0,0 +1,32 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run
+    return loop.run_until_complete(coro)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, 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:
+------------------
+x = np.random.rand(100,1)
+y = 2.0+5*x*x+0.1*np.random.randn(100,1)
+------------------
+
+---------------------------------------------------------------------------
+NameError                                 Traceback (most recent call last)
+Input In [1], in <cell line: 1>()
+----> 1 x = np.random.rand(100,1)
+      2 y = 2.0+5*x*x+0.1*np.random.randn(100,1)
+
+NameError: name 'np' is not defined
+NameError: name 'np' is not defined
+

doc/LectureNotes/_build/html/reports/linalg.err.log

@@ -0,0 +1,81 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
+    return loop.run_until_complete(inner)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, 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:
+------------------
+%matplotlib inline
+
+import numpy as np
+import matplotlib.pyplot as plt
+from scipy import sparse
+eye = np.eye(4)
+print(eye)
+sparse_mtx = sparse.csr_matrix(eye)
+print(sparse_mtx)
+x = np.linspace(-10,10,100)
+y = np.sin(x)
+plt.plot(x,y,marker='x')
+plt.show()
+------------------
+
+
+---------------------------------------------------------------------------
+ModuleNotFoundError                       Traceback (most recent call last)
+Cell In[15], line 1
+----> 1 get_ipython().run_line_magic('matplotlib', 'inline')
+      3 import numpy as np
+      4 import matplotlib.pyplot as plt
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth)
+   2430     kwargs['local_ns'] = self.get_local_scope(stack_depth)
+   2431 with self.builtin_trap:
+-> 2432     result = fn(*args, **kwargs)
+   2434 # The code below prevents the output from being displayed
+   2435 # when using magics with decorator @output_can_be_silenced
+   2436 # when the last Python token in the expression is a ';'.
+   2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line)
+     97     print("Available matplotlib backends: %s" % backends_list)
+     98 else:
+---> 99     gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui)
+    100     self._show_matplotlib_backend(args.gui, backend)
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui)
+   3585 def enable_matplotlib(self, gui=None):
+   3586     """Enable interactive matplotlib and inline figure support.
+   3587 
+   3588     This takes the following steps:
+   (...)
+   3604         display figures inline.
+   3605     """
+-> 3606     from matplotlib_inline.backend_inline import configure_inline_support
+   3608     from IPython.core import pylabtools as pt
+   3609     gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select)
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1
+----> 1 from . import backend_inline, config  # noqa
+      2 __version__ = "0.1.6"  # noqa
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6
+      1 """A matplotlib backend for publishing figures via display_data"""
+      3 # Copyright (c) IPython Development Team.
+      4 # Distributed under the terms of the BSD 3-Clause License.
+----> 6 import matplotlib
+      7 from matplotlib import colors
+      8 from matplotlib.backends import backend_agg
+
+ModuleNotFoundError: No module named 'matplotlib'
+

doc/LectureNotes/_build/html/reports/linalg.log

@@ -0,0 +1,31 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run
+    return loop.run_until_complete(coro)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, 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 numpy as np
+x = np.log(np.array([4.0, 7.0, 8.0])
+print(x)
+------------------
+
+  File "<ipython-input-6-f6d7a289d493>", line 3
+    print(x)
+    ^
+SyntaxError: invalid syntax
+
+SyntaxError: invalid syntax (<ipython-input-6-f6d7a289d493>, line 3)
+

doc/LectureNotes/_build/html/reports/project1.err.log

@@ -0,0 +1,109 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
+    return loop.run_until_complete(inner)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, 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:
+------------------
+%matplotlib inline
+
+from mpl_toolkits.mplot3d import Axes3D
+import matplotlib.pyplot as plt
+from matplotlib import cm
+from matplotlib.ticker import LinearLocator, FormatStrFormatter
+import numpy as np
+from random import random, seed
+
+fig = plt.figure()
+ax = fig.gca(projection='3d')
+
+# Make data.
+x = np.arange(0, 1, 0.05)
+y = np.arange(0, 1, 0.05)
+x, y = np.meshgrid(x,y)
+
+
+def FrankeFunction(x,y):
+    term1 = 0.75*np.exp(-(0.25*(9*x-2)**2) - 0.25*((9*y-2)**2))
+    term2 = 0.75*np.exp(-((9*x+1)**2)/49.0 - 0.1*(9*y+1))
+    term3 = 0.5*np.exp(-(9*x-7)**2/4.0 - 0.25*((9*y-3)**2))
+    term4 = -0.2*np.exp(-(9*x-4)**2 - (9*y-7)**2)
+    return term1 + term2 + term3 + term4
+
+
+z = FrankeFunction(x, y)
+
+# Plot the surface.
+surf = ax.plot_surface(x, y, z, cmap=cm.coolwarm,
+                       linewidth=0, antialiased=False)
+
+# Customize the z axis.
+ax.set_zlim(-0.10, 1.40)
+ax.zaxis.set_major_locator(LinearLocator(10))
+ax.zaxis.set_major_formatter(FormatStrFormatter('%.02f'))
+
+# Add a color bar which maps values to colors.
+fig.colorbar(surf, shrink=0.5, aspect=5)
+
+plt.show()
+------------------
+
+
+---------------------------------------------------------------------------
+ModuleNotFoundError                       Traceback (most recent call last)
+Cell In[1], line 1
+----> 1 get_ipython().run_line_magic('matplotlib', 'inline')
+      3 from mpl_toolkits.mplot3d import Axes3D
+      4 import matplotlib.pyplot as plt
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth)
+   2430     kwargs['local_ns'] = self.get_local_scope(stack_depth)
+   2431 with self.builtin_trap:
+-> 2432     result = fn(*args, **kwargs)
+   2434 # The code below prevents the output from being displayed
+   2435 # when using magics with decorator @output_can_be_silenced
+   2436 # when the last Python token in the expression is a ';'.
+   2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line)
+     97     print("Available matplotlib backends: %s" % backends_list)
+     98 else:
+---> 99     gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui)
+    100     self._show_matplotlib_backend(args.gui, backend)
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui)
+   3585 def enable_matplotlib(self, gui=None):
+   3586     """Enable interactive matplotlib and inline figure support.
+   3587 
+   3588     This takes the following steps:
+   (...)
+   3604         display figures inline.
+   3605     """
+-> 3606     from matplotlib_inline.backend_inline import configure_inline_support
+   3608     from IPython.core import pylabtools as pt
+   3609     gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select)
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1
+----> 1 from . import backend_inline, config  # noqa
+      2 __version__ = "0.1.6"  # noqa
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6
+      1 """A matplotlib backend for publishing figures via display_data"""
+      3 # Copyright (c) IPython Development Team.
+      4 # Distributed under the terms of the BSD 3-Clause License.
+----> 6 import matplotlib
+      7 from matplotlib import colors
+      8 from matplotlib.backends import backend_agg
+
+ModuleNotFoundError: No module named 'matplotlib'
+

doc/LectureNotes/_build/html/reports/project1.log

@@ -0,0 +1,30 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run
+    return loop.run_until_complete(coro)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, 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:
+------------------
+scipy.misc.imread
+------------------
+
+---------------------------------------------------------------------------
+NameError                                 Traceback (most recent call last)
+Input In [2], in <cell line: 1>()
+----> 1 scipy.misc.imread
+
+NameError: name 'scipy' is not defined
+NameError: name 'scipy' is not defined
+

doc/LectureNotes/_build/html/reports/statistics.err.log

@@ -0,0 +1,107 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
+    return loop.run_until_complete(inner)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, 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:
+------------------
+%matplotlib inline
+
+import numpy as np
+from math import acos, exp, sqrt
+from  matplotlib import pyplot as plt
+from matplotlib import rc, rcParams
+import matplotlib.units as units
+import matplotlib.ticker as ticker
+rc('text',usetex=True)
+rc('font',**{'family':'serif','serif':['Gaussian distribution']})
+font = {'family' : 'serif',
+        'color'  : 'darkred',
+        'weight' : 'normal',
+        'size'   : 16,
+        }
+pi = acos(-1.0)
+mu0 = 0.0
+sigma0 = 1.0
+mu1= 1.0
+sigma1 = 2.0
+mu2 = 2.0
+sigma2 = 4.0
+
+x = np.linspace(-20.0, 20.0)
+v0 = np.exp(-(x*x-2*x*mu0+mu0*mu0)/(2*sigma0*sigma0))/sqrt(2*pi*sigma0*sigma0)
+v1 = np.exp(-(x*x-2*x*mu1+mu1*mu1)/(2*sigma1*sigma1))/sqrt(2*pi*sigma1*sigma1)
+v2 = np.exp(-(x*x-2*x*mu2+mu2*mu2)/(2*sigma2*sigma2))/sqrt(2*pi*sigma2*sigma2)
+plt.plot(x, v0, 'b-', x, v1, 'r-', x, v2, 'g-')
+plt.title(r'{\bf Gaussian distributions}', fontsize=20)
+plt.text(-19, 0.3, r'Parameters: $\mu = 0$, $\sigma = 1$', fontdict=font)
+plt.text(-19, 0.18, r'Parameters: $\mu = 1$, $\sigma = 2$', fontdict=font)
+plt.text(-19, 0.08, r'Parameters: $\mu = 2$, $\sigma = 4$', fontdict=font)
+plt.xlabel(r'$x$',fontsize=20)
+plt.ylabel(r'$p(x)$ [MeV]',fontsize=20)
+
+# Tweak spacing to prevent clipping of ylabel                                                                       
+plt.subplots_adjust(left=0.15)
+plt.savefig('gaussian.pdf', format='pdf')
+plt.show()
+------------------
+
+
+---------------------------------------------------------------------------
+ModuleNotFoundError                       Traceback (most recent call last)
+Cell In[1], line 1
+----> 1 get_ipython().run_line_magic('matplotlib', 'inline')
+      3 import numpy as np
+      4 from math import acos, exp, sqrt
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth)
+   2430     kwargs['local_ns'] = self.get_local_scope(stack_depth)
+   2431 with self.builtin_trap:
+-> 2432     result = fn(*args, **kwargs)
+   2434 # The code below prevents the output from being displayed
+   2435 # when using magics with decorator @output_can_be_silenced
+   2436 # when the last Python token in the expression is a ';'.
+   2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line)
+     97     print("Available matplotlib backends: %s" % backends_list)
+     98 else:
+---> 99     gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui)
+    100     self._show_matplotlib_backend(args.gui, backend)
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui)
+   3585 def enable_matplotlib(self, gui=None):
+   3586     """Enable interactive matplotlib and inline figure support.
+   3587 
+   3588     This takes the following steps:
+   (...)
+   3604         display figures inline.
+   3605     """
+-> 3606     from matplotlib_inline.backend_inline import configure_inline_support
+   3608     from IPython.core import pylabtools as pt
+   3609     gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select)
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1
+----> 1 from . import backend_inline, config  # noqa
+      2 __version__ = "0.1.6"  # noqa
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6
+      1 """A matplotlib backend for publishing figures via display_data"""
+      3 # Copyright (c) IPython Development Team.
+      4 # Distributed under the terms of the BSD 3-Clause License.
+----> 6 import matplotlib
+      7 from matplotlib import colors
+      8 from matplotlib.backends import backend_agg
+
+ModuleNotFoundError: No module named 'matplotlib'
+

doc/LectureNotes/_build/html/reports/statistics.log

@@ -0,0 +1,58 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run
+    return loop.run_until_complete(coro)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, 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)
+------------------
+
+  File "<ipython-input-6-2ff97f4bf03b>", line 2
+    @timeFunction
+    ^
+IndentationError: unexpected indent
+
+IndentationError: unexpected indent (<ipython-input-6-2ff97f4bf03b>, line 2)
+

doc/LectureNotes/_build/html/reports/week34.err.log

@@ -0,0 +1,81 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
+    return loop.run_until_complete(inner)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, 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:
+------------------
+%matplotlib inline
+
+import numpy as np
+import matplotlib.pyplot as plt
+from scipy import sparse
+eye = np.eye(4)
+print(eye)
+sparse_mtx = sparse.csr_matrix(eye)
+print(sparse_mtx)
+x = np.linspace(-10,10,100)
+y = np.sin(x)
+plt.plot(x,y,marker='x')
+plt.show()
+------------------
+
+
+---------------------------------------------------------------------------
+ModuleNotFoundError                       Traceback (most recent call last)
+Cell In[16], line 1
+----> 1 get_ipython().run_line_magic('matplotlib', 'inline')
+      3 import numpy as np
+      4 import matplotlib.pyplot as plt
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth)
+   2430     kwargs['local_ns'] = self.get_local_scope(stack_depth)
+   2431 with self.builtin_trap:
+-> 2432     result = fn(*args, **kwargs)
+   2434 # The code below prevents the output from being displayed
+   2435 # when using magics with decorator @output_can_be_silenced
+   2436 # when the last Python token in the expression is a ';'.
+   2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line)
+     97     print("Available matplotlib backends: %s" % backends_list)
+     98 else:
+---> 99     gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui)
+    100     self._show_matplotlib_backend(args.gui, backend)
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui)
+   3585 def enable_matplotlib(self, gui=None):
+   3586     """Enable interactive matplotlib and inline figure support.
+   3587 
+   3588     This takes the following steps:
+   (...)
+   3604         display figures inline.
+   3605     """
+-> 3606     from matplotlib_inline.backend_inline import configure_inline_support
+   3608     from IPython.core import pylabtools as pt
+   3609     gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select)
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1
+----> 1 from . import backend_inline, config  # noqa
+      2 __version__ = "0.1.6"  # noqa
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6
+      1 """A matplotlib backend for publishing figures via display_data"""
+      3 # Copyright (c) IPython Development Team.
+      4 # Distributed under the terms of the BSD 3-Clause License.
+----> 6 import matplotlib
+      7 from matplotlib import colors
+      8 from matplotlib.backends import backend_agg
+
+ModuleNotFoundError: No module named 'matplotlib'
+

doc/LectureNotes/_build/html/reports/week34.log

@@ -0,0 +1,71 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run
+    return loop.run_until_complete(coro)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, 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:
+------------------
+# Read the experimental data with Pandas
+Masses = pd.read_fwf(infile, usecols=(2,3,4,6,11),
+              names=('N', 'Z', 'A', 'Element', 'Ebinding'),
+              widths=(1,3,5,5,5,1,3,4,1,13,11,11,9,1,2,11,9,1,3,1,12,11,1),
+              header=39,
+              index_col=False)
+
+# Extrapolated values are indicated by '#' in place of the decimal place, so
+# the Ebinding column won't be numeric. Coerce to float and drop these entries.
+Masses['Ebinding'] = pd.to_numeric(Masses['Ebinding'], errors='coerce')
+Masses = Masses.dropna()
+# Convert from keV to MeV.
+Masses['Ebinding'] /= 1000
+
+# Group the DataFrame by nucleon number, A.
+Masses = Masses.groupby('A')
+# Find the rows of the grouped DataFrame with the maximum binding energy.
+Masses = Masses.apply(lambda t: t[t.Ebinding==t.Ebinding.max()])
+------------------
+
+---------------------------------------------------------------------------
+ValueError                                Traceback (most recent call last)
+Input In [30], in <cell line: 2>()
+      1 # Read the experimental data with Pandas
+----> 2 Masses = pd.read_fwf(infile, usecols=(2,3,4,6,11),
+      3               names=('N', 'Z', 'A', 'Element', 'Ebinding'),
+      4               widths=(1,3,5,5,5,1,3,4,1,13,11,11,9,1,2,11,9,1,3,1,12,11,1),
+      5               header=39,
+      6               index_col=False)
+      8 # Extrapolated values are indicated by '#' in place of the decimal place, so
+      9 # the Ebinding column won't be numeric. Coerce to float and drop these entries.
+     10 Masses['Ebinding'] = pd.to_numeric(Masses['Ebinding'], errors='coerce')
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/pandas/util/_decorators.py:311, in deprecate_nonkeyword_arguments.<locals>.decorate.<locals>.wrapper(*args, **kwargs)
+    305 if len(args) > num_allow_args:
+    306     warnings.warn(
+    307         msg.format(arguments=arguments),
+    308         FutureWarning,
+    309         stacklevel=stacklevel,
+    310     )
+--> 311 return func(*args, **kwargs)
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/pandas/io/parsers/readers.py:871, in read_fwf(filepath_or_buffer, colspecs, widths, infer_nrows, **kwds)
+    869                     len_index = len(index_col)
+    870         if len(names) + len_index != len(colspecs):
+--> 871             raise ValueError("Length of colspecs must match length of names")
+    873 kwds["colspecs"] = colspecs
+    874 kwds["infer_nrows"] = infer_nrows
+
+ValueError: Length of colspecs must match length of names
+ValueError: Length of colspecs must match length of names
+

doc/LectureNotes/_build/html/reports/week35.err.log

@@ -0,0 +1,110 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
+    return loop.run_until_complete(inner)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, 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:
+------------------
+%matplotlib inline
+
+import os
+import numpy as np
+import pandas as pd
+import matplotlib.pyplot as plt
+from sklearn.model_selection import train_test_split
+
+
+def R2(y_data, y_model):
+    return 1 - np.sum((y_data - y_model) ** 2) / np.sum((y_data - np.mean(y_data)) ** 2)
+def MSE(y_data,y_model):
+    n = np.size(y_model)
+    return np.sum((y_data-y_model)**2)/n
+
+x = np.random.rand(100)
+y = 2.0+5*x*x+0.1*np.random.randn(100)
+
+
+#  The design matrix now as function of a fourth-order polynomial
+X = np.zeros((len(x),5))
+X[:,0] = 1.0
+X[:,1] = x
+X[:,2] = x**2
+X[:,3] = x**3
+X[:,4] = x**4
+# We split the data in test and training data
+X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2)
+# matrix inversion to find beta
+beta = np.linalg.inv(X_train.T @ X_train) @ X_train.T @ y_train
+print(beta)
+# and then make the prediction
+ytilde = X_train @ beta
+print("Training R2")
+print(R2(y_train,ytilde))
+print("Training MSE")
+print(MSE(y_train,ytilde))
+ypredict = X_test @ beta
+print("Test R2")
+print(R2(y_test,ypredict))
+print("Test MSE")
+print(MSE(y_test,ypredict))
+------------------
+
+
+---------------------------------------------------------------------------
+ModuleNotFoundError                       Traceback (most recent call last)
+Cell In[7], line 1
+----> 1 get_ipython().run_line_magic('matplotlib', 'inline')
+      3 import os
+      4 import numpy as np
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth)
+   2430     kwargs['local_ns'] = self.get_local_scope(stack_depth)
+   2431 with self.builtin_trap:
+-> 2432     result = fn(*args, **kwargs)
+   2434 # The code below prevents the output from being displayed
+   2435 # when using magics with decorator @output_can_be_silenced
+   2436 # when the last Python token in the expression is a ';'.
+   2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line)
+     97     print("Available matplotlib backends: %s" % backends_list)
+     98 else:
+---> 99     gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui)
+    100     self._show_matplotlib_backend(args.gui, backend)
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui)
+   3585 def enable_matplotlib(self, gui=None):
+   3586     """Enable interactive matplotlib and inline figure support.
+   3587 
+   3588     This takes the following steps:
+   (...)
+   3604         display figures inline.
+   3605     """
+-> 3606     from matplotlib_inline.backend_inline import configure_inline_support
+   3608     from IPython.core import pylabtools as pt
+   3609     gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select)
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1
+----> 1 from . import backend_inline, config  # noqa
+      2 __version__ = "0.1.6"  # noqa
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6
+      1 """A matplotlib backend for publishing figures via display_data"""
+      3 # Copyright (c) IPython Development Team.
+      4 # Distributed under the terms of the BSD 3-Clause License.
+----> 6 import matplotlib
+      7 from matplotlib import colors
+      8 from matplotlib.backends import backend_agg
+
+ModuleNotFoundError: No module named 'matplotlib'
+

doc/LectureNotes/_build/html/reports/week35.log

@@ -0,0 +1,32 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run
+    return loop.run_until_complete(coro)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, 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:
+------------------
+fit = np.linalg.lstsq(X, Energies, rcond =None)[0]
+ytildenp = np.dot(fit,X.T)
+------------------
+
+---------------------------------------------------------------------------
+NameError                                 Traceback (most recent call last)
+Input In [2], in <cell line: 1>()
+----> 1 fit = np.linalg.lstsq(X, Energies, rcond =None)[0]
+      2 ytildenp = np.dot(fit,X.T)
+
+NameError: name 'Energies' is not defined
+NameError: name 'Energies' is not defined
+

doc/LectureNotes/_build/html/reports/week36.err.log

@@ -0,0 +1,38 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
+    return loop.run_until_complete(inner)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, 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 numpy as np
+X = np.array( [ [1,2,3],[2,4,5],[3,5,6]])
+Xinv = np.linlag.pinv(X)
+------------------
+
+
+---------------------------------------------------------------------------
+AttributeError                            Traceback (most recent call last)
+Cell In[1], line 3
+      1 import numpy as np
+      2 X = np.array( [ [1,2,3],[2,4,5],[3,5,6]])
+----> 3 Xinv = np.linlag.pinv(X)
+
+File ~/miniforge3/lib/python3.9/site-packages/numpy/__init__.py:313, in __getattr__(attr)
+    310     from .testing import Tester
+    311     return Tester
+--> 313 raise AttributeError("module {!r} has no attribute "
+    314                      "{!r}".format(__name__, attr))
+
+AttributeError: module 'numpy' has no attribute 'linlag'
+

doc/LectureNotes/_build/html/reports/week36.log

@@ -0,0 +1,40 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run
+    return loop.run_until_complete(coro)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, 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 numpy as np
+X = np.array( [ [1,2,3],[2,4,5],[3,5,6]])
+Xinv = np.linlag.pinv(X)
+------------------
+
+---------------------------------------------------------------------------
+AttributeError                            Traceback (most recent call last)
+Input In [1], in <cell line: 3>()
+      1 import numpy as np
+      2 X = np.array( [ [1,2,3],[2,4,5],[3,5,6]])
+----> 3 Xinv = np.linlag.pinv(X)
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/numpy/__init__.py:315, in __getattr__(attr)
+    312     from .testing import Tester
+    313     return Tester
+--> 315 raise AttributeError("module {!r} has no attribute "
+    316                      "{!r}".format(__name__, attr))
+
+AttributeError: module 'numpy' has no attribute 'linlag'
+AttributeError: module 'numpy' has no attribute 'linlag'
+

doc/LectureNotes/_build/html/reports/week37.err.log

@@ -0,0 +1,96 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
+    return loop.run_until_complete(inner)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, 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:
+------------------
+%matplotlib inline
+
+import numpy as np
+from time import time
+from scipy.stats import norm
+import matplotlib.pyplot as plt
+
+# Returns mean of bootstrap samples 
+# Bootstrap algorithm
+def bootstrap(data, datapoints):
+    t = np.zeros(datapoints)
+    n = len(data)
+    # non-parametric bootstrap         
+    for i in range(datapoints):
+        t[i] = np.mean(data[np.random.randint(0,n,n)])
+    # analysis    
+    print("Bootstrap Statistics :")
+    print("original           bias      std. error")
+    print("%8g %8g %14g %15g" % (np.mean(data), np.std(data),np.mean(t),np.std(t)))
+    return t
+
+# We set the mean value to 100 and the standard deviation to 15
+mu, sigma = 100, 15
+datapoints = 10000
+# We generate random numbers according to the normal distribution
+x = mu + sigma*np.random.randn(datapoints)
+# bootstrap returns the data sample                                    
+t = bootstrap(x, datapoints)
+------------------
+
+
+---------------------------------------------------------------------------
+ModuleNotFoundError                       Traceback (most recent call last)
+Cell In[1], line 1
+----> 1 get_ipython().run_line_magic('matplotlib', 'inline')
+      3 import numpy as np
+      4 from time import time
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth)
+   2430     kwargs['local_ns'] = self.get_local_scope(stack_depth)
+   2431 with self.builtin_trap:
+-> 2432     result = fn(*args, **kwargs)
+   2434 # The code below prevents the output from being displayed
+   2435 # when using magics with decorator @output_can_be_silenced
+   2436 # when the last Python token in the expression is a ';'.
+   2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line)
+     97     print("Available matplotlib backends: %s" % backends_list)
+     98 else:
+---> 99     gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui)
+    100     self._show_matplotlib_backend(args.gui, backend)
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui)
+   3585 def enable_matplotlib(self, gui=None):
+   3586     """Enable interactive matplotlib and inline figure support.
+   3587 
+   3588     This takes the following steps:
+   (...)
+   3604         display figures inline.
+   3605     """
+-> 3606     from matplotlib_inline.backend_inline import configure_inline_support
+   3608     from IPython.core import pylabtools as pt
+   3609     gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select)
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1
+----> 1 from . import backend_inline, config  # noqa
+      2 __version__ = "0.1.6"  # noqa
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6
+      1 """A matplotlib backend for publishing figures via display_data"""
+      3 # Copyright (c) IPython Development Team.
+      4 # Distributed under the terms of the BSD 3-Clause License.
+----> 6 import matplotlib
+      7 from matplotlib import colors
+      8 from matplotlib.backends import backend_agg
+
+ModuleNotFoundError: No module named 'matplotlib'
+

doc/LectureNotes/_build/html/reports/week37.log

@@ -0,0 +1,92 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run
+    return loop.run_until_complete(coro)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, 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:
+------------------
+from sklearn import linear_model
+np.random.seed(2018)
+n = 10
+d = 2
+Lambda = 0.01
+
+# Make data set.
+x = np.linspace(-3, 3, n)
+y = 2.0 + 0.5*x + 5.0*(x**2)+ np.random.randn(n)
+
+# Design matrix X does not include the intercept. 
+X = np.zeros((n, d))
+for p in range(d):     
+    X[:, p] = x ** (p+1)
+
+#Split data in train and test
+X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2)
+# Scale data by subtracting mean value of the input using scikit-learn
+scaler = StandardScaler(with_std=False)
+scaler.fit(X_train)
+X_train_mean = np.mean(X_train,axis=0)
+X_train_scaled = scaler.transform(X_train)
+X_test_scaled = scaler.transform(X_test)
+# We scale also the output, here by our own code
+y_scaler = np.mean(y_train)
+y_train_scaled = y_train - y_scaler
+y_test_scaled = y_test- y_scaler
+
+#Calculate beta
+OLS = LinearRegression()
+betaOLS=OLS.fit(X_train_scaled,y_train_scaled)
+ypredictOLS = OLS.predict(X_test_scaled)
+linear_model.Ridge(Lambda)
+RegRidge.fit(X_train_scaled,y_train_scaled)
+ypredictRidge = RegRidge.predict(X_test_scaled)
+betaOLS = OLS.coef_
+betaRidge = RegRidge.coef_
+print(betaOLS)
+print(betaRidge)
+interceptOLS = np.mean(y_train) - X_train_mean @ betaOLS
+interceptRidge = y_scaler - X_train_mean @ betaRidge
+print(interceptOLS)
+print(interceptRidge)
+#predict value 
+ytilde_test_Ridge = X_test_scaled @ betaRidge+y_scaler
+ytilde_test_OLS = X_test_scaled @ betaOLS+y_scaler
+
+#Calculate MSE
+print("  ")
+print("test MSE of OLS")
+print(MSE(y_test,ytilde_test_OLS))
+print("  ")
+print("test MSE of Ridge")
+print(MSE(y_test,ytilde_test_Ridge))
+plt.scatter(x,y,label='Data')
+plt.plot(x, X @ RegRidge.coef_ + RegRidge.intercept_ , label="Ridge_Fit")
+plt.grid()
+plt.legend()
+plt.show()
+------------------
+
+---------------------------------------------------------------------------
+NameError                                 Traceback (most recent call last)
+Input In [11], in <cell line: 34>()
+     32 ypredictOLS = OLS.predict(X_test_scaled)
+     33 linear_model.Ridge(Lambda)
+---> 34 RegRidge.fit(X_train_scaled,y_train_scaled)
+     35 ypredictRidge = RegRidge.predict(X_test_scaled)
+     36 betaOLS = OLS.coef_
+
+NameError: name 'RegRidge' is not defined
+NameError: name 'RegRidge' is not defined
+

doc/LectureNotes/_build/html/reports/week38.err.log

@@ -0,0 +1,159 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
+    return loop.run_until_complete(inner)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, 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:
+------------------
+%matplotlib inline
+
+import numpy as np
+import matplotlib.pyplot as plt
+from sklearn.model_selection import KFold
+from sklearn.linear_model import Ridge
+from sklearn.model_selection import cross_val_score
+from sklearn.preprocessing import PolynomialFeatures
+
+# A seed just to ensure that the random numbers are the same for every run.
+# Useful for eventual debugging.
+np.random.seed(3155)
+
+# Generate the data.
+nsamples = 100
+x = np.random.randn(nsamples)
+y = 3*x**2 + np.random.randn(nsamples)
+
+## Cross-validation on Ridge regression using KFold only
+
+# Decide degree on polynomial to fit
+poly = PolynomialFeatures(degree = 6)
+
+# Decide which values of lambda to use
+nlambdas = 500
+lambdas = np.logspace(-3, 5, nlambdas)
+
+# Initialize a KFold instance
+k = 5
+kfold = KFold(n_splits = k)
+
+# Perform the cross-validation to estimate MSE
+scores_KFold = np.zeros((nlambdas, k))
+
+i = 0
+for lmb in lambdas:
+    ridge = Ridge(alpha = lmb)
+    j = 0
+    for train_inds, test_inds in kfold.split(x):
+        xtrain = x[train_inds]
+        ytrain = y[train_inds]
+
+        xtest = x[test_inds]
+        ytest = y[test_inds]
+
+        Xtrain = poly.fit_transform(xtrain[:, np.newaxis])
+        ridge.fit(Xtrain, ytrain[:, np.newaxis])
+
+        Xtest = poly.fit_transform(xtest[:, np.newaxis])
+        ypred = ridge.predict(Xtest)
+
+        scores_KFold[i,j] = np.sum((ypred - ytest[:, np.newaxis])**2)/np.size(ypred)
+
+        j += 1
+    i += 1
+
+
+estimated_mse_KFold = np.mean(scores_KFold, axis = 1)
+
+## Cross-validation using cross_val_score from sklearn along with KFold
+
+# kfold is an instance initialized above as:
+# kfold = KFold(n_splits = k)
+
+estimated_mse_sklearn = np.zeros(nlambdas)
+i = 0
+for lmb in lambdas:
+    ridge = Ridge(alpha = lmb)
+
+    X = poly.fit_transform(x[:, np.newaxis])
+    estimated_mse_folds = cross_val_score(ridge, X, y[:, np.newaxis], scoring='neg_mean_squared_error', cv=kfold)
+
+    # cross_val_score return an array containing the estimated negative mse for every fold.
+    # we have to the the mean of every array in order to get an estimate of the mse of the model
+    estimated_mse_sklearn[i] = np.mean(-estimated_mse_folds)
+
+    i += 1
+
+## Plot and compare the slightly different ways to perform cross-validation
+
+plt.figure()
+
+plt.plot(np.log10(lambdas), estimated_mse_sklearn, label = 'cross_val_score')
+plt.plot(np.log10(lambdas), estimated_mse_KFold, 'r--', label = 'KFold')
+
+plt.xlabel('log10(lambda)')
+plt.ylabel('mse')
+
+plt.legend()
+
+plt.show()
+------------------
+
+
+---------------------------------------------------------------------------
+ModuleNotFoundError                       Traceback (most recent call last)
+Cell In[1], line 1
+----> 1 get_ipython().run_line_magic('matplotlib', 'inline')
+      3 import numpy as np
+      4 import matplotlib.pyplot as plt
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth)
+   2430     kwargs['local_ns'] = self.get_local_scope(stack_depth)
+   2431 with self.builtin_trap:
+-> 2432     result = fn(*args, **kwargs)
+   2434 # The code below prevents the output from being displayed
+   2435 # when using magics with decorator @output_can_be_silenced
+   2436 # when the last Python token in the expression is a ';'.
+   2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line)
+     97     print("Available matplotlib backends: %s" % backends_list)
+     98 else:
+---> 99     gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui)
+    100     self._show_matplotlib_backend(args.gui, backend)
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui)
+   3585 def enable_matplotlib(self, gui=None):
+   3586     """Enable interactive matplotlib and inline figure support.
+   3587 
+   3588     This takes the following steps:
+   (...)
+   3604         display figures inline.
+   3605     """
+-> 3606     from matplotlib_inline.backend_inline import configure_inline_support
+   3608     from IPython.core import pylabtools as pt
+   3609     gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select)
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1
+----> 1 from . import backend_inline, config  # noqa
+      2 __version__ = "0.1.6"  # noqa
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6
+      1 """A matplotlib backend for publishing figures via display_data"""
+      3 # Copyright (c) IPython Development Team.
+      4 # Distributed under the terms of the BSD 3-Clause License.
+----> 6 import matplotlib
+      7 from matplotlib import colors
+      8 from matplotlib.backends import backend_agg
+
+ModuleNotFoundError: No module named 'matplotlib'
+

doc/LectureNotes/_build/html/reports/week38.log

@@ -0,0 +1,32 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run
+    return loop.run_until_complete(coro)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, 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:
+------------------
+x = 2*np.random.rand(m,1)
+y = 4+3*x+np.random.randn(m,1)
+------------------
+
+---------------------------------------------------------------------------
+NameError                                 Traceback (most recent call last)
+Input In [13], in <cell line: 1>()
+----> 1 x = 2*np.random.rand(m,1)
+      2 y = 4+3*x+np.random.randn(m,1)
+
+NameError: name 'm' is not defined
+NameError: name 'm' is not defined
+

doc/LectureNotes/_build/html/reports/week39.err.log

@@ -0,0 +1,90 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1305, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
+    return loop.run_until_complete(inner)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 705, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 1058, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/lib/python3.9/site-packages/nbclient/client.py", line 914, 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:
+------------------
+%matplotlib inline
+
+import numpy as np
+import numpy.linalg as la
+
+import scipy.optimize as sopt
+
+import matplotlib.pyplot as pt
+from mpl_toolkits.mplot3d import axes3d
+
+def f(x):
+    return x[0]**2 + 3.0*x[1]**2
+
+def df(x):
+    return np.array([2*x[0], 6*x[1]])
+
+fig = pt.figure()
+ax = fig.gca(projection="3d")
+
+xmesh, ymesh = np.mgrid[-3:3:50j,-3:3:50j]
+fmesh = f(np.array([xmesh, ymesh]))
+ax.plot_surface(xmesh, ymesh, fmesh)
+------------------
+
+
+---------------------------------------------------------------------------
+ModuleNotFoundError                       Traceback (most recent call last)
+Cell In[1], line 1
+----> 1 get_ipython().run_line_magic('matplotlib', 'inline')
+      3 import numpy as np
+      4 import numpy.linalg as la
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:2432, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth)
+   2430     kwargs['local_ns'] = self.get_local_scope(stack_depth)
+   2431 with self.builtin_trap:
+-> 2432     result = fn(*args, **kwargs)
+   2434 # The code below prevents the output from being displayed
+   2435 # when using magics with decorator @output_can_be_silenced
+   2436 # when the last Python token in the expression is a ';'.
+   2437 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/magics/pylab.py:99, in PylabMagics.matplotlib(self, line)
+     97     print("Available matplotlib backends: %s" % backends_list)
+     98 else:
+---> 99     gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui)
+    100     self._show_matplotlib_backend(args.gui, backend)
+
+File ~/miniforge3/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3606, in InteractiveShell.enable_matplotlib(self, gui)
+   3585 def enable_matplotlib(self, gui=None):
+   3586     """Enable interactive matplotlib and inline figure support.
+   3587 
+   3588     This takes the following steps:
+   (...)
+   3604         display figures inline.
+   3605     """
+-> 3606     from matplotlib_inline.backend_inline import configure_inline_support
+   3608     from IPython.core import pylabtools as pt
+   3609     gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select)
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/__init__.py:1
+----> 1 from . import backend_inline, config  # noqa
+      2 __version__ = "0.1.6"  # noqa
+
+File ~/miniforge3/lib/python3.9/site-packages/matplotlib_inline/backend_inline.py:6
+      1 """A matplotlib backend for publishing figures via display_data"""
+      3 # Copyright (c) IPython Development Team.
+      4 # Distributed under the terms of the BSD 3-Clause License.
+----> 6 import matplotlib
+      7 from matplotlib import colors
+      8 from matplotlib.backends import backend_agg
+
+ModuleNotFoundError: No module named 'matplotlib'
+

doc/LectureNotes/_build/html/reports/week39.log

@@ -0,0 +1,32 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run
+    return loop.run_until_complete(coro)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, 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:
+------------------
+x = 2*np.random.rand(m,1)
+y = 4+3*x+np.random.randn(m,1)
+------------------
+
+---------------------------------------------------------------------------
+NameError                                 Traceback (most recent call last)
+Input In [6], in <cell line: 1>()
+----> 1 x = 2*np.random.rand(m,1)
+      2 y = 4+3*x+np.random.randn(m,1)
+
+NameError: name 'm' is not defined
+NameError: name 'm' is not defined
+

doc/LectureNotes/_build/html/reports/week40.log

@@ -0,0 +1,84 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run
+    return loop.run_until_complete(coro)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, 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 autograd.numpy as np
+from autograd import grad
+def f8(x): # Assume x is an array
+    x[2] = 3
+    return x*2
+
+f8_grad = grad(f8)
+
+x = 8.4
+
+print("The derivative of f8 is:",f8_grad(x))
+------------------
+
+---------------------------------------------------------------------------
+TypeError                                 Traceback (most recent call last)
+Input In [13], in <cell line: 11>()
+      7 f8_grad = grad(f8)
+      9 x = 8.4
+---> 11 print("The derivative of f8 is:",f8_grad(x))
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/autograd/wrap_util.py:20, in unary_to_nary.<locals>.nary_operator.<locals>.nary_f(*args, **kwargs)
+     18 else:
+     19     x = tuple(args[i] for i in argnum)
+---> 20 return unary_operator(unary_f, x, *nary_op_args, **nary_op_kwargs)
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/autograd/differential_operators.py:25, in grad(fun, x)
+     18 @unary_to_nary
+     19 def grad(fun, x):
+     20     """
+     21     Returns a function which computes the gradient of `fun` with respect to
+     22     positional argument number `argnum`. The returned function takes the same
+     23     arguments as `fun`, but returns the gradient instead. The function `fun`
+     24     should be scalar-valued. The gradient has the same type as the argument."""
+---> 25     vjp, ans = _make_vjp(fun, x)
+     26     if not vspace(ans).size == 1:
+     27         raise TypeError("Grad only applies to real scalar-output functions. "
+     28                         "Try jacobian, elementwise_grad or holomorphic_grad.")
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/autograd/core.py:10, in make_vjp(fun, x)
+      8 def make_vjp(fun, x):
+      9     start_node = VJPNode.new_root()
+---> 10     end_value, end_node =  trace(start_node, fun, x)
+     11     if end_node is None:
+     12         def vjp(g): return vspace(x).zeros()
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/autograd/tracer.py:10, in trace(start_node, fun, x)
+      8 with trace_stack.new_trace() as t:
+      9     start_box = new_box(x, t, start_node)
+---> 10     end_box = fun(start_box)
+     11     if isbox(end_box) and end_box._trace == start_box._trace:
+     12         return end_box._value, end_box._node
+
+File ~/miniforge3/envs/myenv/lib/python3.9/site-packages/autograd/wrap_util.py:15, in unary_to_nary.<locals>.nary_operator.<locals>.nary_f.<locals>.unary_f(x)
+     13 else:
+     14     subargs = subvals(args, zip(argnum, x))
+---> 15 return fun(*subargs, **kwargs)
+
+Input In [13], in f8(x)
+      3 def f8(x): # Assume x is an array
+----> 4     x[2] = 3
+      5     return x*2
+
+TypeError: 'ArrayBox' object does not support item assignment
+TypeError: 'ArrayBox' object does not support item assignment
+

doc/LectureNotes/_build/html/reports/week42.log

@@ -0,0 +1,29 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run
+    return loop.run_until_complete(coro)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, 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:
+------------------
+pip3 install tensorflow
+------------------
+
+  Input In [14]
+    pip3 install tensorflow
+         ^
+SyntaxError: invalid syntax
+
+SyntaxError: invalid syntax (2357089093.py, line 1)
+

doc/LectureNotes/_build/html/reports/week43.log

@@ -0,0 +1,119 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run
+    return loop.run_until_complete(coro)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 965, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 862, 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:
+------------------
+# to categorical turns our integer vector into a onehot representation
+from sklearn.metrics import accuracy_score
+
+# one-hot in numpy
+def to_categorical_numpy(integer_vector):
+    n_inputs = len(integer_vector)
+    n_categories = np.max(integer_vector) + 1
+    onehot_vector = np.zeros((n_inputs, n_categories))
+    onehot_vector[range(n_inputs), integer_vector] = 1
+    
+    return onehot_vector
+
+#Y_train_onehot, Y_test_onehot = to_categorical(Y_train), to_categorical(Y_test)
+Y_train_onehot, Y_test_onehot = to_categorical_numpy(Y_train), to_categorical_numpy(Y_test)
+
+def feed_forward_train(X):
+    # weighted sum of inputs to the hidden layer
+    z_h = np.matmul(X, hidden_weights) + hidden_bias
+    # activation in the hidden layer
+    a_h = sigmoid(z_h)
+    
+    # weighted sum of inputs to the output layer
+    z_o = np.matmul(a_h, output_weights) + output_bias
+    # softmax output
+    # axis 0 holds each input and axis 1 the probabilities of each category
+    exp_term = np.exp(z_o)
+    probabilities = exp_term / np.sum(exp_term, axis=1, keepdims=True)
+    
+    # for backpropagation need activations in hidden and output layers
+    return a_h, probabilities
+
+def backpropagation(X, Y):
+    a_h, probabilities = feed_forward_train(X)
+    
+    # error in the output layer
+    error_output = probabilities - Y
+    # error in the hidden layer
+    error_hidden = np.matmul(error_output, output_weights.T) * a_h * (1 - a_h)
+    
+    # gradients for the output layer
+    output_weights_gradient = np.matmul(a_h.T, error_output)
+    output_bias_gradient = np.sum(error_output, axis=0)
+    
+    # gradient for the hidden layer
+    hidden_weights_gradient = np.matmul(X.T, error_hidden)
+    hidden_bias_gradient = np.sum(error_hidden, axis=0)
+
+    return output_weights_gradient, output_bias_gradient, hidden_weights_gradient, hidden_bias_gradient
+
+print("Old accuracy on training data: " + str(accuracy_score(predict(X_train), Y_train)))
+
+eta = 0.01
+lmbd = 0.01
+for i in range(1000):
+    # calculate gradients
+    dWo, dBo, dWh, dBh = backpropagation(X_train, Y_train_onehot)
+    
+    # regularization term gradients
+    dWo += lmbd * output_weights
+    dWh += lmbd * hidden_weights
+    
+    # update weights and biases
+    output_weights -= eta * dWo
+    output_bias -= eta * dBo
+    hidden_weights -= eta * dWh
+    hidden_bias -= eta * dBh
+
+print("New accuracy on training data: " + str(accuracy_score(predict(X_train), Y_train)))
+------------------
+
+---------------------------------------------------------------------------
+RuntimeWarning                            Traceback (most recent call last)
+Input In [26], in <cell line: 54>()
+     53 lmbd = 0.01
+     54 for i in range(1000):
+     55     # calculate gradients
+---> 56     dWo, dBo, dWh, dBh = backpropagation(X_train, Y_train_onehot)
+     58     # regularization term gradients
+     59     dWo += lmbd * output_weights
+
+Input In [26], in backpropagation(X, Y)
+     32 def backpropagation(X, Y):
+---> 33     a_h, probabilities = feed_forward_train(X)
+     35     # error in the output layer
+     36     error_output = probabilities - Y
+
+Input In [26], in feed_forward_train(X)
+     18 z_h = np.matmul(X, hidden_weights) + hidden_bias
+     19 # activation in the hidden layer
+---> 20 a_h = sigmoid(z_h)
+     22 # weighted sum of inputs to the output layer
+     23 z_o = np.matmul(a_h, output_weights) + output_bias
+
+Input In [25], in sigmoid(x)
+      3 def sigmoid(x):
+----> 4     return 1/(1 + np.exp(-x))
+
+RuntimeWarning: overflow encountered in exp
+RuntimeWarning: overflow encountered in exp
+

doc/LectureNotes/_build/html/reports/week44.log

@@ -0,0 +1,39 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 730, in _async_poll_for_reply
+    msg = await ensure_async(self.kc.shell_channel.get_msg(timeout=new_timeout))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 96, in ensure_async
+    result = await obj
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_client/channels.py", line 230, in get_msg
+    raise Empty
+_queue.Empty
+
+During handling of the above exception, another exception occurred:
+
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run
+    return loop.run_until_complete(coro)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 949, in async_execute_cell
+    exec_reply = await self.task_poll_for_reply
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 754, in _async_poll_for_reply
+    await self._async_handle_timeout(timeout, cell)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 801, in _async_handle_timeout
+    raise CellTimeoutError.error_from_timeout_and_cell(
+nbclient.exceptions.CellTimeoutError: A cell timed out while it was being executed, after 30 seconds.
+The message was: Cell execution timed out.
+Here is a preview of the cell contents:
+-------------------
+['CNN_keras = np.zeros((len(eta_vals), len(lmbd_vals)), dtype=object)', '        ', 'for i, eta in enumerate(eta_vals):', '    for j, lmbd in enumerate(lmbd_vals):', '        CNN = create_convolutional_neural_network_keras(input_shape, receptive_field,']
+...
+['        ', '        print("Learning rate = ", eta)', '        print("Lambda = ", lmbd)', '        print("Test accuracy: %.3f" % scores[1])', '        print()']
+-------------------
+

doc/LectureNotes/_build/html/reports/week45.log

@@ -0,0 +1,39 @@
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 730, in _async_poll_for_reply
+    msg = await ensure_async(self.kc.shell_channel.get_msg(timeout=new_timeout))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 96, in ensure_async
+    result = await obj
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_client/channels.py", line 230, in get_msg
+    raise Empty
+_queue.Empty
+
+During handling of the above exception, another exception occurred:
+
+Traceback (most recent call last):
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
+    executenb(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 1204, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 84, in wrapped
+    return just_run(coro(*args, **kwargs))
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/util.py", line 62, in just_run
+    return loop.run_until_complete(coro)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
+    return future.result()
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 663, in async_execute
+    await self.async_execute_cell(
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 949, in async_execute_cell
+    exec_reply = await self.task_poll_for_reply
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 754, in _async_poll_for_reply
+    await self._async_handle_timeout(timeout, cell)
+  File "/Users/mhjensen/miniforge3/envs/myenv/lib/python3.9/site-packages/nbclient/client.py", line 801, in _async_handle_timeout
+    raise CellTimeoutError.error_from_timeout_and_cell(
+nbclient.exceptions.CellTimeoutError: A cell timed out while it was being executed, after 30 seconds.
+The message was: Cell execution timed out.
+Here is a preview of the cell contents:
+-------------------
+['# Start importing packages', 'import pandas as pd', 'import numpy as np', 'import matplotlib.pyplot as plt', 'import tensorflow as tf']
+...
+['trainScore = model.evaluate(trainX, trainY, verbose=0)', 'print(trainScore)', 'plt.plot(df)', 'plt.plot(predicted)', 'plt.show()']
+-------------------
+

doc/LectureNotes/week45.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "7e9869f2",
+   "id": "967cdaca",
    "metadata": {
     "editable": true
    },
@@ -14,7 +14,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "fca263d7",
+   "id": "7f44e4d0",
    "metadata": {
     "editable": true
    },
@@ -27,7 +27,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "8c3d9fea",
+   "id": "3094316d",
    "metadata": {
     "editable": true
    },
@@ -58,6 +58,10 @@
     "\n",
     "    * These lecture notes\n",
     "\n",
+    "    * [Video of lecture](https://youtu.be/z0x-vgyAZUk)\n",
+    "\n",
+    "    * [Whiteboard notes](https://github.com/CompPhysics/MachineLearning/blob/master/doc/HandWrittenNotes/2023/NotesNov9.pdf)\n",
+    "\n",
     "    * For a more in depth discussion on  neural networks we recommend Goodfellow et al chapter 10. See also chapter 11 and 12 on practicalities and applications    \n",
     "\n",
     "     * Reading suggestions for implementation of RNNs: [Aurelien Geron's chapter 14](https://github.com/CompPhysics/MachineLearning/blob/master/doc/Textbooks/TensorflowML.pdf).\n",
@@ -69,7 +73,7 @@
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   {
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-   "id": "d0107e8f",
+   "id": "46b1e9db",
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@@ -79,7 +83,7 @@
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   {
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+   "id": "19315bd5",
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@@ -98,7 +102,7 @@
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    "execution_count": 1,
-   "id": "7d202a1c",
+   "id": "d03a6f44",
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@@ -155,7 +159,7 @@
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   {
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+   "id": "e6cbd4ca",
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@@ -167,7 +171,7 @@
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   {
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-   "id": "693475c8",
+   "id": "1ea723fc",
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@@ -182,7 +186,7 @@
   {
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    "execution_count": 2,
-   "id": "cdd8cf73",
+   "id": "0ebb62df",
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     "editable": true
@@ -235,7 +239,7 @@
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   {
    "cell_type": "markdown",
-   "id": "51ef3976",
+   "id": "0fb161e1",
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@@ -250,7 +254,7 @@
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   {
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-   "id": "033bda9d",
+   "id": "8bdb137e",
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@@ -270,7 +274,7 @@
   {
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    "execution_count": 3,
-   "id": "0a320c52",
+   "id": "af61779f",
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@@ -324,7 +328,7 @@
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   {
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-   "id": "bcd8ea70",
+   "id": "89f07674",
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@@ -339,7 +343,7 @@
   {
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-   "id": "6fe70002",
+   "id": "37c8ca05",
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@@ -366,7 +370,7 @@
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   {
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+   "id": "509bf7a9",
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@@ -380,7 +384,7 @@
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-   "id": "96a74e80",
+   "id": "e9d06a0c",
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@@ -425,7 +429,7 @@
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+   "id": "ab1f9810",
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@@ -450,7 +454,7 @@
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-   "id": "d00d3339",
+   "id": "d8a5dabe",
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@@ -462,7 +466,7 @@
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+   "id": "69fd6511",
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@@ -473,7 +477,7 @@
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-   "id": "382459a0",
+   "id": "b74de9e5",
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@@ -485,7 +489,7 @@
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+   "id": "24e267e4",
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@@ -498,7 +502,7 @@
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@@ -531,7 +535,7 @@
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@@ -545,7 +549,7 @@
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@@ -557,7 +561,7 @@
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@@ -569,7 +573,7 @@
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@@ -581,7 +585,7 @@
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@@ -591,7 +595,7 @@
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+   "id": "0f77aa9a",
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@@ -603,7 +607,7 @@
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@@ -613,7 +617,7 @@
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@@ -625,7 +629,7 @@
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+   "id": "24aec375",
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@@ -636,7 +640,7 @@
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+   "id": "8d288b9d",
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@@ -655,7 +659,7 @@
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   {
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-   "id": "6dcb34a4",
+   "id": "e1663205",
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@@ -667,7 +671,7 @@
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   {
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-   "id": "a975cae8",
+   "id": "b34d890c",
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@@ -677,7 +681,7 @@
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   {
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-   "id": "d4971baf",
+   "id": "14e7f314",
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@@ -689,7 +693,7 @@
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-   "id": "a4bd001d",
+   "id": "879bac6b",
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@@ -701,7 +705,7 @@
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   {
    "cell_type": "markdown",
-   "id": "a8b1f114",
+   "id": "31d2b3b7",
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@@ -713,7 +717,7 @@
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   {
    "cell_type": "markdown",
-   "id": "959cdbff",
+   "id": "34fd7537",
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@@ -723,7 +727,7 @@
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   {
    "cell_type": "markdown",
-   "id": "59ee7f47",
+   "id": "4bebbe84",
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@@ -735,7 +739,7 @@
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   {
    "cell_type": "markdown",
-   "id": "5cdba722",
+   "id": "690c8d76",
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@@ -763,7 +767,7 @@
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   {
    "cell_type": "markdown",
-   "id": "35390ed4",
+   "id": "12d8a75e",
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@@ -775,7 +779,7 @@
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   {
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-   "id": "b1651ea3",
+   "id": "1df29154",
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@@ -800,7 +804,7 @@
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-   "id": "1bfac852",
+   "id": "9083178e",
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@@ -818,7 +822,7 @@
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+   "id": "e7719466",
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@@ -829,7 +833,7 @@
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    "execution_count": 8,
-   "id": "31f4ee21",
+   "id": "bcddf060",
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@@ -872,7 +876,7 @@
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-   "id": "098bfaec",
+   "id": "6ec55e94",
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@@ -882,7 +886,7 @@
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   {
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-   "id": "55cc0e20",
+   "id": "690b1a08",
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@@ -909,7 +913,7 @@
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   {
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-   "id": "8860da9c",
+   "id": "825bc136",
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@@ -920,7 +924,7 @@
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    "execution_count": 9,
-   "id": "7252c0b8",
+   "id": "ce956b33",
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@@ -993,7 +997,7 @@
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   {
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+   "id": "002c4d99",
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@@ -1013,7 +1017,7 @@
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-   "id": "1c5b70a2",
+   "id": "6572c07f",
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@@ -1029,7 +1033,7 @@
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-   "id": "29c129fe",
+   "id": "fbd8e269",
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@@ -1051,7 +1055,7 @@
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   {
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-   "id": "c2bc1aa3",
+   "id": "919bb09e",
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@@ -1069,7 +1073,7 @@
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   {
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-   "id": "01ef7e17",
+   "id": "6e3360db",
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@@ -1115,7 +1119,7 @@
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-   "id": "8dd26bf6",
+   "id": "0f284cbd",
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@@ -1136,7 +1140,7 @@
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+   "id": "b5e9785e",
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@@ -1197,7 +1201,7 @@
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+   "id": "50a43c30",
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@@ -1222,7 +1226,7 @@
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+   "id": "f3e0d31b",
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@@ -1241,7 +1245,7 @@
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+   "id": "b1571231",
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@@ -1265,7 +1269,7 @@
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+   "id": "e7886dd3",
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@@ -1347,7 +1351,7 @@
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+   "id": "f878b195",
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@@ -1363,7 +1367,7 @@
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-   "id": "9365f92f",
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@@ -1402,7 +1406,7 @@
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@@ -1446,7 +1450,7 @@
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@@ -1529,7 +1533,7 @@
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@@ -1540,7 +1544,7 @@
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@@ -1642,7 +1646,7 @@
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@@ -1664,7 +1668,7 @@
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-   "id": "22123a0f",
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@@ -1761,7 +1765,7 @@
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@@ -1787,7 +1791,7 @@
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