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Jan 18, 2015
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Unescape the less than and greater than inequalities #1

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2afa6da
Unescape the less than and greater than inequalities
peterjc Dec 19, 2014
7020c6a
Unescape single quotes
peterjc Jan 15, 2015
fa6864e
Fixing another escaped greater-than
peterjc Jan 15, 2015
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6 changes: 3 additions & 3 deletions 01-numpy.html
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Expand Up @@ -28,7 +28,7 @@
<h1 class="title">Programming with Python</h1>
<h2 class="subtitle">Analyzing Patient Data</h2>
<div id="learning-objectives" class="objectives objectives">
<h2>Learning Objectives</h2>
<h2 id="learning-objectives" class="objectives objectives">Learning Objectives</h2>
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@aaren aaren Jan 15, 2015

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Does this need to change with this PR? I know it is happening automatically, but could you move it to a different commit?

<ul>
<li>Explain what a library is, and what libraries are used for.</li>
<li>Load a Python library and use the things it contains.</li>
Expand All @@ -43,7 +43,7 @@ <h2>Learning Objectives</h2>
<p>In order to load our inflammation data, we need to <strong>import</strong> a library called NumPy. In general you should use this library if you want to do fancy things with numbers, especially if you have matrices. We can load NumPy using:</p>
<pre class="sourceCode python"><code class="sourceCode python"><span class="ch">import</span> numpy</code></pre>
<p>Importing a library is like getting a piece of lab equipment out of a storage locker and setting it up on the bench. Once it's done, we can ask the library to read our data file for us:</p>
<pre class="sourceCode python"><code class="sourceCode python">numpy.loadtxt(fname=&amp;<span class="co">#39;inflammation-01.csv&amp;#39;, delimiter=&amp;#39;,&amp;#39;)</span></code></pre>
<pre class="sourceCode python"><code class="sourceCode python">numpy.loadtxt(fname=<span class="st">&#39;inflammation-01.csv&#39;</span>, delimiter=<span class="st">&#39;,&#39;</span>)</code></pre>
<pre class="output"><code>array([[ 0., 0., 1., ..., 3., 0., 0.],
[ 0., 1., 2., ..., 1., 0., 1.],
[ 0., 1., 1., ..., 2., 1., 1.],
Expand Down Expand Up @@ -93,7 +93,7 @@ <h2>Learning Objectives</h2>
[ 0. 0. 1. ..., 1. 1. 0.]]</code></pre>
<p>Now that our data is in memory, we can start doing things with it. First, let's ask what <strong>type</strong> of thing <code>data</code> refers to:</p>
<pre class="sourceCode python"><code class="sourceCode python"><span class="dt">print</span> <span class="dt">type</span>(data)</code></pre>
<pre class="output"><code>&amp;lt;type &#39;numpy.ndarray&#39;&amp;gt;</code></pre>
<pre class="output"><code>&lt;type &#39;numpy.ndarray&#39;&gt;</code></pre>
<p>The output tells us that <code>data</code> currently refers to an N-dimensional array created by the NumPy library. We can see what its <strong>shape</strong> is like this:</p>
<pre class="sourceCode python"><code class="sourceCode python"><span class="dt">print</span> data.shape</code></pre>
<pre class="output"><code>(60, 40)</code></pre>
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4 changes: 2 additions & 2 deletions 01-numpy.md
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Expand Up @@ -36,7 +36,7 @@ Once it's done,
we can ask the library to read our data file for us:

~~~ {.python}
numpy.loadtxt(fname=&#39;inflammation-01.csv&#39;, delimiter=&#39;,&#39;)
numpy.loadtxt(fname='inflammation-01.csv', delimiter=',')
~~~
~~~ {.output}
array([[ 0., 0., 1., ..., 3., 0., 0.],
Expand Down Expand Up @@ -189,7 +189,7 @@ let's ask what **type** of thing `data` refers to:
print type(data)
~~~
~~~ {.output}
&lt;type 'numpy.ndarray'&gt;
<type 'numpy.ndarray'>
~~~

The output tells us that `data` currently refers to an N-dimensional array created by the NumPy library.
Expand Down
38 changes: 19 additions & 19 deletions 02-func.html
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Expand Up @@ -124,8 +124,8 @@ <h2 id="the-call-stack">The Call Stack</h2>
<pre class="sourceCode python"><code class="sourceCode python"><span class="dt">print</span> <span class="st">&#39;final value of temp after all function calls:&#39;</span>, temp</code></pre>
<pre class="error"><code>---------------------------------------------------------------------------
NameError Traceback (most recent call last)
&amp;lt;ipython-input-12-ffd9b4dbd5f1&amp;gt; in &amp;lt;module&amp;gt;()
----&amp;gt; 1 print &#39;final value of temp after all function calls:&#39;, temp
&lt;ipython-input-12-ffd9b4dbd5f1&gt; in &lt;module&gt;()
----&gt; 1 print &#39;final value of temp after all function calls:&#39;, temp

NameError: name &#39;temp&#39; is not defined</code></pre>
<pre class="output"><code>final value of temp after all function calls:</code></pre>
Expand Down Expand Up @@ -195,15 +195,15 @@ <h2 id="testing-and-documenting">Testing and Documenting</h2>
<p>A string like this is called a <strong>docstring</strong>. We don't need to use triple quotes when we write one, but if we do, we can break the string across multiple lines:</p>
<pre class="sourceCode python"><code class="sourceCode python"><span class="kw">def</span> center(data, desired):
<span class="co">&#39;&#39;&#39;Return a new array containing the original data centered around the desired value.</span>
<span class="co"> Example: center([1, 2, 3], 0) =&amp;gt; [-1, 0, 1]&#39;&#39;&#39;</span>
<span class="co"> Example: center([1, 2, 3], 0) =&gt; [-1, 0, 1]&#39;&#39;&#39;</span>
<span class="kw">return</span> (data - data.mean()) + desired

<span class="dt">help</span>(center)</code></pre>
<pre class="output"><code>Help on function center in module __main__:

center(data, desired)
Return a new array containing the original data centered around the desired value.
Example: center([1, 2, 3], 0) =&amp;gt; [-1, 0, 1]
Example: center([1, 2, 3], 0) =&gt; [-1, 0, 1]
</code></pre>
<h2 id="defining-defaults">Defining Defaults</h2>
<p>We have passed parameters to functions in two ways: directly, as in <code>span(data)</code>, and by name, as in <code>numpy.loadtxt(fname='something.csv', delimiter=',')</code>. In fact, we can pass the filename to <code>loadtxt</code> without the <code>fname=</code>:</p>
Expand All @@ -213,21 +213,21 @@ <h2 id="defining-defaults">Defining Defaults</h2>
<pre class="sourceCode python"><code class="sourceCode python">numpy.loadtxt(<span class="st">&#39;inflammation-01.csv&#39;</span>, <span class="st">&#39;,&#39;</span>)</code></pre>
<pre class="error"><code>---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
&amp;lt;ipython-input-26-e3bc6cf4fd6a&amp;gt; in &amp;lt;module&amp;gt;()
----&amp;gt; 1 numpy.loadtxt(&#39;inflammation-01.csv&#39;, &#39;,&#39;)
&lt;ipython-input-26-e3bc6cf4fd6a&gt; in &lt;module&gt;()
----&gt; 1 numpy.loadtxt(&#39;inflammation-01.csv&#39;, &#39;,&#39;)

/Users/gwilson/anaconda/lib/python2.7/site-packages/numpy/lib/npyio.pyc in loadtxt(fname, dtype, comments, delimiter, converters, skiprows, usecols, unpack, ndmin)
775 try:
776 # Make sure we&#39;re dealing with a proper dtype
--&amp;gt; 777 dtype = np.dtype(dtype)
--&gt; 777 dtype = np.dtype(dtype)
778 defconv = _getconv(dtype)
779

TypeError: data type &quot;,&quot; not understood</code></pre>
<p>To understand what's going on, and make our own functions easier to use, let's re-define our <code>center</code> function like this:</p>
<pre class="sourceCode python"><code class="sourceCode python"><span class="kw">def</span> center(data, desired=<span class="fl">0.0</span>):
<span class="co">&#39;&#39;&#39;Return a new array containing the original data centered around the desired value (0 by default).</span>
<span class="co"> Example: center([1, 2, 3], 0) =&amp;gt; [-1, 0, 1]&#39;&#39;&#39;</span>
<span class="co"> Example: center([1, 2, 3], 0) =&gt; [-1, 0, 1]&#39;&#39;&#39;</span>
<span class="kw">return</span> (data - data.mean()) + desired</code></pre>
<p>The key change is that the second parameter is now written <code>desired=0.0</code> instead of just <code>desired</code>. If we call the function with two arguments, it works as it did before:</p>
<pre class="sourceCode python"><code class="sourceCode python">test_data = numpy.zeros((<span class="dv">2</span>, <span class="dv">2</span>))
Expand Down Expand Up @@ -267,7 +267,7 @@ <h2 id="defining-defaults">Defining Defaults</h2>
<pre class="sourceCode python"><code class="sourceCode python"><span class="dt">help</span>(numpy.loadtxt)</code></pre>
<pre class="output"><code>Help on function loadtxt in module numpy.lib.npyio:

loadtxt(fname, dtype=&amp;lt;type &#39;float&#39;&amp;gt;, comments=&#39;#&#39;, delimiter=None, converters=None, skiprows=0, usecols=None, unpack=False, ndmin=0)
loadtxt(fname, dtype=&lt;type &#39;float&#39;&gt;, comments=&#39;#&#39;, delimiter=None, converters=None, skiprows=0, usecols=None, unpack=False, ndmin=0)
Load data from a text file.

Each row in the text file must have the same number of values.
Expand Down Expand Up @@ -331,23 +331,23 @@ <h2 id="defining-defaults">Defining Defaults</h2>

Examples
--------
&amp;gt;&amp;gt;&amp;gt; from StringIO import StringIO # StringIO behaves like a file object
&amp;gt;&amp;gt;&amp;gt; c = StringIO(&quot;0 1\n2 3&quot;)
&amp;gt;&amp;gt;&amp;gt; np.loadtxt(c)
&gt;&gt;&gt; from StringIO import StringIO # StringIO behaves like a file object
&gt;&gt;&gt; c = StringIO(&quot;0 1\n2 3&quot;)
&gt;&gt;&gt; np.loadtxt(c)
array([[ 0., 1.],
[ 2., 3.]])

&amp;gt;&amp;gt;&amp;gt; d = StringIO(&quot;M 21 72\nF 35 58&quot;)
&amp;gt;&amp;gt;&amp;gt; np.loadtxt(d, dtype={&#39;names&#39;: (&#39;gender&#39;, &#39;age&#39;, &#39;weight&#39;),
&gt;&gt;&gt; d = StringIO(&quot;M 21 72\nF 35 58&quot;)
&gt;&gt;&gt; np.loadtxt(d, dtype={&#39;names&#39;: (&#39;gender&#39;, &#39;age&#39;, &#39;weight&#39;),
... &#39;formats&#39;: (&#39;S1&#39;, &#39;i4&#39;, &#39;f4&#39;)})
array([(&#39;M&#39;, 21, 72.0), (&#39;F&#39;, 35, 58.0)],
dtype=[(&#39;gender&#39;, &#39;|S1&#39;), (&#39;age&#39;, &#39;&amp;lt;i4&#39;), (&#39;weight&#39;, &#39;&amp;lt;f4&#39;)])
dtype=[(&#39;gender&#39;, &#39;|S1&#39;), (&#39;age&#39;, &#39;&lt;i4&#39;), (&#39;weight&#39;, &#39;&lt;f4&#39;)])

&amp;gt;&amp;gt;&amp;gt; c = StringIO(&quot;1,0,2\n3,0,4&quot;)
&amp;gt;&amp;gt;&amp;gt; x, y = np.loadtxt(c, delimiter=&#39;,&#39;, usecols=(0, 2), unpack=True)
&amp;gt;&amp;gt;&amp;gt; x
&gt;&gt;&gt; c = StringIO(&quot;1,0,2\n3,0,4&quot;)
&gt;&gt;&gt; x, y = np.loadtxt(c, delimiter=&#39;,&#39;, usecols=(0, 2), unpack=True)
&gt;&gt;&gt; x
array([ 1., 3.])
&amp;gt;&amp;gt;&amp;gt; y
&gt;&gt;&gt; y
array([ 2., 4.])
</code></pre>
<p>There's a lot of information here, but the most important part is the first couple of lines:</p>
Expand Down
38 changes: 19 additions & 19 deletions 02-func.md
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Expand Up @@ -291,8 +291,8 @@ print 'final value of temp after all function calls:', temp
~~~ {.error}
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
&lt;ipython-input-12-ffd9b4dbd5f1&gt; in &lt;module&gt;()
----&gt; 1 print 'final value of temp after all function calls:', temp
<ipython-input-12-ffd9b4dbd5f1> in <module>()
----> 1 print 'final value of temp after all function calls:', temp

NameError: name 'temp' is not defined
~~~
Expand Down Expand Up @@ -478,7 +478,7 @@ we can break the string across multiple lines:
~~~ {.python}
def center(data, desired):
'''Return a new array containing the original data centered around the desired value.
Example: center([1, 2, 3], 0) =&gt; [-1, 0, 1]'''
Example: center([1, 2, 3], 0) => [-1, 0, 1]'''
return (data - data.mean()) + desired

help(center)
Expand All @@ -488,7 +488,7 @@ Help on function center in module __main__:

center(data, desired)
Return a new array containing the original data centered around the desired value.
Example: center([1, 2, 3], 0) =&gt; [-1, 0, 1]
Example: center([1, 2, 3], 0) => [-1, 0, 1]

~~~

Expand Down Expand Up @@ -520,13 +520,13 @@ numpy.loadtxt('inflammation-01.csv', ',')
~~~ {.error}
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
&lt;ipython-input-26-e3bc6cf4fd6a&gt; in &lt;module&gt;()
----&gt; 1 numpy.loadtxt('inflammation-01.csv', ',')
<ipython-input-26-e3bc6cf4fd6a> in <module>()
----> 1 numpy.loadtxt('inflammation-01.csv', ',')

/Users/gwilson/anaconda/lib/python2.7/site-packages/numpy/lib/npyio.pyc in loadtxt(fname, dtype, comments, delimiter, converters, skiprows, usecols, unpack, ndmin)
775 try:
776 # Make sure we're dealing with a proper dtype
--&gt; 777 dtype = np.dtype(dtype)
--> 777 dtype = np.dtype(dtype)
778 defconv = _getconv(dtype)
779

Expand All @@ -540,7 +540,7 @@ let's re-define our `center` function like this:
~~~ {.python}
def center(data, desired=0.0):
'''Return a new array containing the original data centered around the desired value (0 by default).
Example: center([1, 2, 3], 0) =&gt; [-1, 0, 1]'''
Example: center([1, 2, 3], 0) => [-1, 0, 1]'''
return (data - data.mean()) + desired
~~~

Expand Down Expand Up @@ -622,7 +622,7 @@ help(numpy.loadtxt)
~~~ {.output}
Help on function loadtxt in module numpy.lib.npyio:

loadtxt(fname, dtype=&lt;type 'float'&gt;, comments='#', delimiter=None, converters=None, skiprows=0, usecols=None, unpack=False, ndmin=0)
loadtxt(fname, dtype=<type 'float'>, comments='#', delimiter=None, converters=None, skiprows=0, usecols=None, unpack=False, ndmin=0)
Load data from a text file.

Each row in the text file must have the same number of values.
Expand Down Expand Up @@ -686,23 +686,23 @@ loadtxt(fname, dtype=&lt;type 'float'&gt;, comments='#', delimiter=None, convert

Examples
--------
&gt;&gt;&gt; from StringIO import StringIO # StringIO behaves like a file object
&gt;&gt;&gt; c = StringIO("0 1\n2 3")
&gt;&gt;&gt; np.loadtxt(c)
>>> from StringIO import StringIO # StringIO behaves like a file object
>>> c = StringIO("0 1\n2 3")
>>> np.loadtxt(c)
array([[ 0., 1.],
[ 2., 3.]])

&gt;&gt;&gt; d = StringIO("M 21 72\nF 35 58")
&gt;&gt;&gt; np.loadtxt(d, dtype={'names': ('gender', 'age', 'weight'),
>>> d = StringIO("M 21 72\nF 35 58")
>>> np.loadtxt(d, dtype={'names': ('gender', 'age', 'weight'),
... 'formats': ('S1', 'i4', 'f4')})
array([('M', 21, 72.0), ('F', 35, 58.0)],
dtype=[('gender', '|S1'), ('age', '&lt;i4'), ('weight', '&lt;f4')])
dtype=[('gender', '|S1'), ('age', '<i4'), ('weight', '<f4')])

&gt;&gt;&gt; c = StringIO("1,0,2\n3,0,4")
&gt;&gt;&gt; x, y = np.loadtxt(c, delimiter=',', usecols=(0, 2), unpack=True)
&gt;&gt;&gt; x
>>> c = StringIO("1,0,2\n3,0,4")
>>> x, y = np.loadtxt(c, delimiter=',', usecols=(0, 2), unpack=True)
>>> x
array([ 1., 3.])
&gt;&gt;&gt; y
>>> y
array([ 2., 4.])

~~~
Expand Down
4 changes: 2 additions & 2 deletions 03-loop.html
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Expand Up @@ -90,8 +90,8 @@ <h2 id="for-loops">For Loops</h2>
</ol>
<pre class="sourceCode python"><code class="sourceCode python">print_characters(<span class="st">&#39;tin&#39;</span>)</code></pre>
<h2 id="section" class="error"><sub>~</sub></h2>
<p>IndexError Traceback (most recent call last) &lt;ipython-input-13-5bc7311e0bf3&gt; in &lt;module&gt;() ----&gt; 1 print_characters('tin')</p>
<p>&lt;ipython-input-12-11460561ea56&gt; in print_characters(element) 3 print element[1] 4 print element[2] ----&gt; 5 print element[3] 6 7 print_characters('lead')</p>
<p>IndexError Traceback (most recent call last) <ipython-input-13-5bc7311e0bf3> in <module>() ----&gt; 1 print_characters('tin')</p>
<p><ipython-input-12-11460561ea56> in print_characters(element) 3 print element[1] 4 print element[2] ----&gt; 5 print element[3] 6 7 print_characters('lead')</p>
<p>IndexError: string index out of range <sub>~</sub> {.output} t i n <sub>~</sub></p>
<p>Here's a better approach:</p>
<pre class="sourceCode python"><code class="sourceCode python"><span class="kw">def</span> print_characters(element):
Expand Down
8 changes: 4 additions & 4 deletions 03-loop.md
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Expand Up @@ -100,13 +100,13 @@ print_characters('tin')
~~~ {.error}
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
&lt;ipython-input-13-5bc7311e0bf3&gt; in &lt;module&gt;()
----&gt; 1 print_characters('tin')
<ipython-input-13-5bc7311e0bf3> in <module>()
----> 1 print_characters('tin')

&lt;ipython-input-12-11460561ea56&gt; in print_characters(element)
<ipython-input-12-11460561ea56> in print_characters(element)
3 print element[1]
4 print element[2]
----&gt; 5 print element[3]
----> 5 print element[3]
6
7 print_characters('lead')

Expand Down
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