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1.BasicPython.slides.html
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<h1 id="Introductory-Python">Introductory Python<a class="anchor-link" href="#Introductory-Python">¶</a></h1>
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<h4 id="Quentin-CAUDRON-----Ecology-and-Evolutionary-Biology----qcaudron@princeton.edu----@QuentinCAUDRON">Quentin CAUDRON <br /> <br /> Ecology and Evolutionary Biology <br /> <br /> [email protected] <br /> <br /> @QuentinCAUDRON<a class="anchor-link" href="#Quentin-CAUDRON-----Ecology-and-Evolutionary-Biology----qcaudron@princeton.edu----@QuentinCAUDRON">¶</a></h4>
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<p>This section moves quickly. I'm assuming that everyone speaks at least one programming language well, and / or has introductory Python experience, and so this chapter gives a lightning intro to syntax in Python. The sections are subheaded, but they really overlap quite a lot, so they're there more as a page reference...</p>
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<h2 id="Variables-and-Arithmetic">Variables and Arithmetic<a class="anchor-link" href="#Variables-and-Arithmetic">¶</a></h2>
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<div class=" highlight hl-ipython3"><pre><span class="nb">print</span><span class="p">(</span><span class="s">"He said, 'what ?'"</span><span class="p">)</span>
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<pre>He said, 'what ?'
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<p>Strings are delimited by <code>"</code>, but can also use <code>'</code>. This is useful because you can now use one set of quotes inside another, and it'll still be one big string.</p>
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<div class=" highlight hl-ipython3"><pre><span class="n">s</span> <span class="o">=</span> <span class="s">"This is a string."</span>
<span class="nb">print</span><span class="p">(</span><span class="n">s</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="nb">type</span><span class="p">(</span><span class="n">s</span><span class="p">))</span>
<span class="nb">print</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">s</span><span class="p">))</span>
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<pre>This is a string.
<class 'str'>
17
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<div class=" highlight hl-ipython3"><pre><span class="n">s</span> <span class="o">=</span> <span class="mi">42</span>
<span class="nb">print</span><span class="p">(</span><span class="n">s</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="nb">type</span><span class="p">(</span><span class="n">s</span><span class="p">))</span>
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<pre>42
<class 'int'>
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<p>Variables don't need to be given a type, as Python is <em>dynamically-typed</em>. That means if I wanted to reuse <code>s</code> as an integer, Python would have no issue with that.</p>
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<div class=" highlight hl-ipython3"><pre><span class="nb">print</span><span class="p">(</span><span class="n">s</span> <span class="o">*</span> <span class="mi">2</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">s</span> <span class="o">+</span> <span class="mi">7</span><span class="p">)</span>
<span class="c"># Neither statement modify the variable.</span>
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<pre>84
49
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<p>Single-line comments use <code>#</code>.</p>
<p>Arithmetic uses the standard operators : <code>+</code>, <code>-</code>, <code>*</code>, <code>/</code>.</p>
<p>You can take powers using <code>**</code>.</p>
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<p>Python also allows <code>+=</code> syntax :</p>
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<div class=" highlight hl-ipython3"><pre><span class="n">s</span> <span class="o">+=</span> <span class="mi">2</span><span class="o">**</span><span class="mi">3</span> <span class="c"># s is being incremented by 2^3</span>
<span class="nb">print</span><span class="p">(</span><span class="s">"Same as s = s + 2**3"</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">s</span><span class="p">)</span>
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<pre>Same as s = s + 2**3
50
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<p>This statement is equivalent to saying <code>s = s + 2**3</code>, it's just shorthand. Also works with <code>-=</code>, <code>*=</code>, <code>/=</code>, <code>**=</code></p>
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<div class=" highlight hl-ipython3"><pre><span class="nb">print</span><span class="p">(</span><span class="n">s</span> <span class="o">==</span> <span class="mi">42</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">s</span> <span class="o">==</span> <span class="mi">50</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">s</span> <span class="o">></span> <span class="mi">10</span><span class="p">)</span>
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<pre>False
True
True
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<p>The <code>==</code> operator is the <em>comparison</em> operator. Here, we also see Python's syntax for logical statements : <code>True</code> and <code>False</code>. As with any programming syntax, capitalisation is important. In Python, <code>1</code> is also <code>True</code>, and <code>0</code> is also <code>False</code>.</p>
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<div class=" highlight hl-ipython3"><pre><span class="n">x</span> <span class="o">=</span> <span class="s">"Blah"</span>
<span class="nb">print</span><span class="p">(</span><span class="n">x</span> <span class="o">+</span> <span class="n">x</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">x</span><span class="p">))</span>
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<pre>BlahBlah
4
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<p>Strings can be concatenated using the <code>+</code> operator. The <code>len()</code> function returns the length of a string.</p>
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<h2 id="Lists">Lists<a class="anchor-link" href="#Lists">¶</a></h2>
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<div class=" highlight hl-ipython3"><pre><span class="n">mylist</span> <span class="o">=</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mf">2.41341</span><span class="p">]</span>
<span class="n">mylist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">"We can mix types !"</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">mylist</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="nb">type</span><span class="p">(</span><span class="n">mylist</span><span class="p">))</span>
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<pre>[1, 2.41341, 'We can mix types !']
<class 'list'>
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<p>Python accesses elements in lists from 0, not from 1 as in Matlab or R. This will be familiar to C and Java users.</p>
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<div class=" highlight hl-ipython3"><pre><span class="nb">print</span><span class="p">(</span><span class="n">mylist</span><span class="p">,</span> <span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">mylist</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
<span class="nb">print</span><span class="p">(</span><span class="n">mylist</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
<span class="nb">print</span><span class="p">(</span><span class="n">mylist</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
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<pre>[1, 2.41341, 'We can mix types !']
1
2.41341
We can mix types !
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<p>Lists have several methods ( <code>count</code>, <code>sort</code>, <code>reverse</code>, <code>pop</code>, <code>insert</code>, <code>remove</code>, ... ). Here are a few.</p>
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<div class=" highlight hl-ipython3"><pre><span class="nb">print</span><span class="p">(</span><span class="s">"Length is {} long.</span><span class="se">\n</span><span class="s">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">mylist</span><span class="p">)))</span>
<span class="nb">print</span><span class="p">(</span><span class="s">"There are {} ones in this list.</span><span class="se">\n</span><span class="s">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">mylist</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="mi">1</span><span class="p">)))</span>
<span class="n">mylist</span><span class="o">.</span><span class="n">reverse</span><span class="p">()</span>
<span class="nb">print</span><span class="p">(</span><span class="s">"Reversed ! {}"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">mylist</span><span class="p">))</span>
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<pre>Length is 3 long.
There are 1 ones in this list.
Reversed ! ['We can mix types !', 2.41341, 1]
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<h2 id="Control-Structures">Control Structures<a class="anchor-link" href="#Control-Structures">¶</a></h2>
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<p>Python objects like lists are <em>iterables</em>. That is, we can directly iterate over them :</p>
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<div class=" highlight hl-ipython3"><pre><span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">mylist</span> <span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s">"Hello</span><span class="se">\n</span><span class="s">"</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s">"Finished"</span><span class="p">)</span>
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<pre>We can mix types !
Hello
2.41341
Hello
1
Hello
Finished
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<p><em>Note the indentation</em>. Loops in Python don't get delimited by brackets like in C or R. Each block gets its own indentation.</p>
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<p>Typically, people use tabs, but you can use any amount of whitespace you want <em>as long as you are consistent</em>. To end the loop, simply unindent. We'll see that in a few lines.</p>
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<p>Users of languages like C or Java, where code blocks are delimited by curly braces, sometimes ask that they be made available in Python.</p>
<pre><code>for i in range {
do something to i
}
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<p>Python's <code>__future__</code> module has already taken care of this.</p>
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<div class=" highlight hl-ipython3"><pre><span class="kn">from</span> <span class="nn">__future__</span> <span class="k">import</span> <span class="n">braces</span>
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<pre>
<span class="ansicyan"> File </span><span class="ansigreen">"<ipython-input-12-2aebb3fc8ecf>"</span><span class="ansicyan">, line </span><span class="ansigreen">1</span>
<span class="ansired"> from __future__ import braces</span>
<span class="ansired">SyntaxError</span><span class="ansired">:</span> not a chance
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<p>The keyword <code>in</code> can also be used to check whether something is in a container :</p>
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<div class=" highlight hl-ipython3"><pre><span class="nb">print</span><span class="p">(</span><span class="mi">1</span> <span class="ow">in</span> <span class="n">mylist</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="mi">2</span> <span class="ow">in</span> <span class="n">mylist</span><span class="p">)</span>
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<pre>True
False
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<p>If you wanted to loop by indexing the list, we can use <code>range()</code>, which, in its simplest ( single-argument ) form, returns a list from 0 to that element minus 1.</p>
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<div class=" highlight hl-ipython3"><pre><span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">mylist</span><span class="p">))</span> <span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">mylist</span><span class="p">[</span><span class="n">i</span><span class="p">])</span>
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<pre>0 We can mix types !
1 2.41341
2 1
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<p>Another way to do this is the <code>enumerate</code> function :</p>
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<div class=" highlight hl-ipython3"><pre><span class="k">for</span> <span class="n">index</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">mylist</span><span class="p">)</span> <span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="s">"Element number {} in the list has the value {}"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">index</span><span class="p">,</span> <span class="n">value</span><span class="p">))</span>
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<pre>Element number 0 in the list has the value We can mix types !
Element number 1 in the list has the value 2.41341
Element number 2 in the list has the value 1
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<p>What about if statements ?</p>
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<div class=" highlight hl-ipython3"><pre><span class="n">x</span> <span class="o">=</span> <span class="mi">5</span>
<span class="k">if</span> <span class="n">x</span> <span class="o">></span> <span class="mi">3</span> <span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="s">"x is greater than 3."</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">x</span> <span class="o">==</span> <span class="mi">5</span> <span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="s">"We aren't going to see this. Why ?"</span><span class="p">)</span>
<span class="k">else</span> <span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="s">"x is not greater than 3."</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s">"We can see this, it's not in the if statement."</span><span class="p">)</span>
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<pre>x is greater than 3.
We can see this, it's not in the if statement.
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