Autobuild

Author: ThomasCarroll

docs/exercises/answers/Exercise2_answers.html

@@ -645,7 +645,7 @@ <h4 class="date"><a href="https://rockefelleruniversity.github.io/Intro_To_Pytho
 between the two?</li>
 </ul>
 <div class="sourceCode" id="cb48"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb48-1"><a href="#cb48-1" tabindex="-1"></a>my_set1.intersection(my_set2) </span></code></pre></div>
-<pre><code>## {&#39;PKM&#39;, &#39;MCM10&#39;, &#39;GSS&#39;}</code></pre>
+<pre><code>## {&#39;GSS&#39;, &#39;MCM10&#39;, &#39;PKM&#39;}</code></pre>
 
 
 

docs/exercises/exercises/Exercise2_exercise.html

@@ -480,7 +480,7 @@ <h4 class="date"><a href="https://rockefelleruniversity.github.io/Intro_To_Pytho
 <li>These are genes of interest from two experiments. What genes overlap
 between the two?</li>
 </ul>
-<pre><code>## {&#39;PKM&#39;, &#39;MCM10&#39;, &#39;GSS&#39;}</code></pre>
+<pre><code>## {&#39;GSS&#39;, &#39;MCM10&#39;, &#39;PKM&#39;}</code></pre>
 
 
 

docs/index.html

@@ -485,7 +485,7 @@ <h2>Course Overview</h2>
 <p><br></p>
 <div id="course-integrity" class="section level3">
 <h3>Course Integrity</h3>
-<p><strong>This course is compiled automatically on <em>2026-01-22</em>
+<p><strong>This course is compiled automatically on <em>2026-01-26</em>
 </strong> <br> <a
 href="https://github.com/RockefellerUniversity/Intro_To_Python/actions/workflows/selfTest.yml"><img
 src="https://github.com/RockefellerUniversity/Intro_To_Python/actions/workflows/selfTest.yml/badge.svg"

docs/presentations/r_code/Session1.R

@@ -245,15 +245,15 @@ if(params$isSlides == "yes"){
 ## list2
 ## list3
 
-## biglist = my_strs + my_ints
+## biglist = my_ints + my_strs
 ## biglist
 
-## biglist = my_strs
-## biglist += my_ints
-## biglist
+## biglist2 = [1,2,3,4,5]
+## biglist2 += my_strs
+## biglist2
 
-## biglist = my_strs * 5
-## biglist
+## biglist3 = my_strs * 5
+## biglist3
 
 ## my_strs.append('f')
 ## my_strs
@@ -267,12 +267,12 @@ if(params$isSlides == "yes"){
 ## my_strs.remove('c')
 ## my_strs
 
+## my_strs.index('c')
+
 ## del my_strs[3]
 ## my_strs
 
-## my_strs.index('c')
-
-## my_strs.append("f")
+## "a" in my_strs
 
 ## my_list = [1,4,9,4,11,12,6]
 ## my_list.sort()

docs/presentations/singlepage/Session1.html

@@ -1634,111 +1634,111 @@ <h2>Reading/writing files</h2>
 Gene_a
 </td>
 <td style="text-align:right;">
-4.172365
+3.166541
 </td>
 <td style="text-align:right;">
-4.036224
+4.886880
 </td>
 <td style="text-align:right;">
-3.459136
+4.606144
 </td>
 </tr>
 <tr>
 <td style="text-align:left;">
 Gene_b
 </td>
 <td style="text-align:right;">
-4.666711
+2.342709
 </td>
 <td style="text-align:right;">
-2.498400
+6.603740
 </td>
 <td style="text-align:right;">
-5.089345
+4.268355
 </td>
 </tr>
 <tr>
 <td style="text-align:left;">
 Gene_c
 </td>
 <td style="text-align:right;">
-3.108345
+4.147176
 </td>
 <td style="text-align:right;">
-4.798711
+3.900358
 </td>
 <td style="text-align:right;">
-4.562888
+4.833181
 </td>
 </tr>
 <tr>
 <td style="text-align:left;">
 Gene_d
 </td>
 <td style="text-align:right;">
-3.188671
+4.368126
 </td>
 <td style="text-align:right;">
-4.394748
+3.428708
 </td>
 <td style="text-align:right;">
-2.946436
+5.866756
 </td>
 </tr>
 <tr>
 <td style="text-align:left;">
 Gene_e
 </td>
 <td style="text-align:right;">
-9.470627
+12.240208
 </td>
 <td style="text-align:right;">
-10.896368
+11.012076
 </td>
 <td style="text-align:right;">
-10.461258
+10.342122
 </td>
 </tr>
 <tr>
 <td style="text-align:left;">
 Gene_f
 </td>
 <td style="text-align:right;">
-10.469845
+10.308645
 </td>
 <td style="text-align:right;">
-11.160107
+9.751059
 </td>
 <td style="text-align:right;">
-11.321652
+11.166391
 </td>
 </tr>
 <tr>
 <td style="text-align:left;">
 Gene_g
 </td>
 <td style="text-align:right;">
-9.564607
+8.889014
 </td>
 <td style="text-align:right;">
-10.943613
+9.860780
 </td>
 <td style="text-align:right;">
-8.815916
+9.617840
 </td>
 </tr>
 <tr>
 <td style="text-align:left;">
 Gene_h
 </td>
 <td style="text-align:right;">
-9.633494
+9.838351
 </td>
 <td style="text-align:right;">
-9.724424
+8.941217
 </td>
 <td style="text-align:right;">
-11.069627
+9.474184
 </td>
 </tr>
 </tbody>

docs/presentations/singlepage/Session2.html

@@ -841,33 +841,33 @@
 
 
 ``` python
-biglist = my_strs + my_ints
+biglist = my_ints + my_strs
 biglist
 ```
 
 ```
-## ['a', 'b', 'c', 'd', 'e', 1, 2, 3, 4, 5]
+## [1, 2, 3, 4, 5, 'a', 'b', 'c', 'd', 'e']
 ```
 
 
 ``` python
-biglist = my_strs 
-biglist += my_ints
-biglist
+biglist2 = [1,2,3,4,5] 
+biglist2 += my_strs
+biglist2
 ```
 
 ```
-## ['a', 'b', 'c', 'd', 'e', 1, 2, 3, 4, 5]
+## [1, 2, 3, 4, 5, 'a', 'b', 'c', 'd', 'e']
 ```
 
 
 ``` python
-biglist = my_strs * 5
-biglist
+biglist3 = my_strs * 5
+biglist3
 ```
 
 ```
-## ['a', 'b', 'c', 'd', 'e', 1, 2, 3, 4, 5, 'a', 'b', 'c', 'd', 'e', 1, 2, 3, 4, 5, 'a', 'b', 'c', 'd', 'e', 1, 2, 3, 4, 5, 'a', 'b', 'c', 'd', 'e', 1, 2, 3, 4, 5, 'a', 'b', 'c', 'd', 'e', 1, 2, 3, 4, 5]
+## ['a', 'b', 'c', 'd', 'e', 'a', 'b', 'c', 'd', 'e', 'a', 'b', 'c', 'd', 'e', 'a', 'b', 'c', 'd', 'e', 'a', 'b', 'c', 'd', 'e']
 ```
 
 ---
@@ -882,7 +882,7 @@
 ```
 
 ```
-## ['a', 'b', 'c', 'd', 'e', 1, 2, 3, 4, 5, 'f']
+## ['a', 'b', 'c', 'd', 'e', 'f']
 ```
 
 
@@ -892,7 +892,7 @@
 ```
 
 ```
-## ['a', 'b', 'c', 'd', 'e', 1, 2, 3, 4, 5, 'f', 1]
+## ['a', 'b', 'c', 'd', 'e', 'f', 1]
 ```
 
 ---
@@ -909,7 +909,7 @@
 ```
 
 ```
-## ['a', 'b', 'c', 'c', 'd', 'e', 1, 2, 3, 4, 5, 'f', 1]
+## ['a', 'b', 'c', 'c', 'd', 'e', 'f', 1]
 ```
 
 * `.remove()` removes something from the list, but will only remove the first instance 
@@ -921,20 +921,10 @@
 ```
 
 ```
-## ['a', 'b', 'c', 'd', 'e', 1, 2, 3, 4, 5, 'f', 1]
+## ['a', 'b', 'c', 'd', 'e', 'f', 1]
 ```
 
-* the generic `del` statement removes an argument from a specific position in the list
-
-
-``` python
-del my_strs[3]
-my_strs
-```
 
-```
-## ['a', 'b', 'c', 'e', 1, 2, 3, 4, 5, 'f', 1]
-```
 
 ---
 ## Functions and lists
@@ -952,11 +942,27 @@
 ## 2
 ```
 
-* `.append()` will append the supplied argument to the list
+* the generic `del` statement removes an argument from a specific position in the list
+
+
+``` python
+del my_strs[3]
+my_strs
+```
+
+```
+## ['a', 'b', 'c', 'e', 'f', 1]
+```
+
+* we can also test membership of an element with the `in` operator
 
 
 ``` python
-my_strs.append("f")
+"a" in my_strs
+```
+
+```
+## True
 ```
 
 ---
@@ -1360,7 +1366,7 @@
 ```
 
 ```
-## {'a', 'd', 'c', 'b'}
+## {'d', 'a', 'c', 'b'}
 ```
 
 
@@ -1393,7 +1399,7 @@
 ---
 ## Sets are unique
 
-Even if you provide duplicate entries to a set, the set wil only contain unique values. 
+Even if you provide duplicate entries to a set, the set will only contain unique values. 
 
 
 ``` python
@@ -1570,6 +1576,10 @@
 arr
 ```
 
+```
+## array(['a', '2', '3'], dtype='<U21')
+```
+
 ---
 ## Adding Dimensions
 
@@ -1614,7 +1624,7 @@
 ## (3, 3)
 ```
 
-The shape of an array can easily be changed with the `reshape` method. Note that you will get an error if the number of values in the array doesn't fit int othe dimensions specified.
+The shape of an array can easily be changed with the `reshape` method. Note that you will get an error if the number of values in the array doesn't fit into the dimensions specified.
 
 
 ``` python
@@ -1837,7 +1847,7 @@
 * Tuples - If you want to create an immutable version of a list as some kind of reference.  
 * Sets - Similar to Tuples, but if you do not want any repeating values.   
 * Dictionaries - If you have complex data i.e. different shape and size, and you will have some kind of key/lookup values. 
-* Arrays - When you have rectangular data i.e. a table. 
+* Arrays - When you have rectangular data i.e. a table, need to perform math on elements or interface with more advanced computational libraries (stats, ML, etc) 
 
 ---
 class: inverse, center, middle
@@ -1867,6 +1877,8 @@
 * `code` - the start of the code is indicated by a colon, new line and indentation. 
 * `return` - this is the result that you wish to be delivered from the function. 
 
+NOTE: In python functions, indentation after defining the function is required. Otherwise you will get an error. 
+
 
 ``` python
 def myFirstFunction(num1, num2):
@@ -2058,7 +2070,8 @@
 
 Once I have made a function and I want to keep reusing it I can easily save it i.e. I have a function that I want to use regularly to process some data in the same way. To do this you save it as a script. 
 
-First open a new script: File > New File > Python Script. We can then add our orginal function and save the python script as *myFirstFunction.py*.
+First open a new script: File > New File > Python Script. We can then add our original function and save the python script as *myFirstFunction.py*. 
+
 
 
 ``` python
@@ -2075,6 +2088,7 @@
 First open a new script: File > New File > Python Script. We can then add our orginal function and save the python script as *myFirstFunction_script.py*.
 
 
+
 ``` python
 import myFirstFunction_script