Merge branch 'master' of https://github.com/RockefellerUniversity/Intro_To_Python

Author: dougbarrows

IntroToPython/inst/extdata/Descriptions/Session2Overview.Rmd

@@ -7,7 +7,6 @@ The session includes longer exercises and shorter slide decks and so more time s
 
 Session sections:
 
-* Looping Conditional Branching
 * Loading libraries
 * Writing Scripts
 * Getting help

…thon/inst/extdata/data/susbet_dataset.py …thon/inst/extdata/data/subset_dataset.pyIntroToPython/inst/extdata/data/susbet_dataset.py renamed to IntroToPython/inst/extdata/data/subset_dataset.py IntroToPython/inst/extdata/data/susbet_dataset.py renamed to IntroToPython/inst/extdata/data/subset_dataset.py

@@ -91,11 +91,13 @@ Guido van Rossum began working on Python in the late 1980s as a successor to the
 
 One of the most noticeable differences comes from the emphasis on code readability:
 
-  it uses significant indentation 
+<div style="text-indent: 2em;">
+it uses significant indentation.
+</div>
 
 Python 3.0, released in 2008, was a major revision not completely backward-compatible with earlier versions. Python 2.7 and older is officially unsupported but some tools require it. 
 
-<img src="imgs/Python.png" alt="python" height="300" width="300">
+<img src="imgs/Python.png" alt="python" height="250" width="250">
 
 ---
 ## What is Python to you?
@@ -241,15 +243,7 @@ conda install jupyter
 ```
 
 
----
-## Interactive or scripts?
-
-As with many languages you can work with python in two main ways:
-interactive or scripts. 
-
-When people think about coding they are often thinking about the interactive **console**. This is what we saw earlier when we first opened python. When you work in this way lines of code are submitted as you enter them. You often do this when you are developing an analysis and trying out parameters. This is mostly how we will work in the training. 
 
-When you want to automate something, i.e. an analysis workflow, you will write a script. You can then run this script with python and it will run every line of code for you sequentially.
 
 ---
 ## Python and IDEs
@@ -318,6 +312,31 @@ Once the Terminal is open, you can then just open Python, by typing `python` int
 
 There is is an easier shortcut to do this. Once you start developing code the easiest way to open it is to use the `Shift + Enter` shortcut. 
 
+---
+## Why VS code and IDEs
+
+As VS code is an IDE it allows us to access and run python. But also do several other things from the same portal i.e.
+
+- Explore files
+- Open/Write scripts
+- Shortcuts for common python utilities
+- Have a live plotting window
+- GitHub integration
+- Advanced coding features for debugging and LLM support
+
+We won't full dive into everything but getting familiar early is best. 
+
+---
+## Interactive or scripts?
+
+As with many languages you can work with python in two main ways:
+interactive or scripts. 
+
+When people think about coding they are often thinking about the interactive **console**. This is what we saw earlier when we first opened python. When you work in this way lines of code are submitted as you enter them. You often do this when you are developing an analysis and trying out parameters. This is mostly how we will work in the training. 
+
+When you want to automate something, i.e. an analysis workflow, you will write a script. You can then run this script with python and it will run every line of code for you sequentially.
+
+
 ---
 ## Quick Recap
 
@@ -523,6 +542,22 @@ except Exception as e:
   
 ```
 
+---
+## A quick aside
+
+You will run into errors coding. 
+
+DON'T PANIC. 
+
+Most of the time the error messages are very clear. And if they are not a quick google will often clear it up. 
+
+In this case we can break it down:
+
+* ValueError - The content is invalid for the operation. The first statement is the overarching name for the error.
+* invalid literal for int() - Specifically the int() function is expecting something different
+* with base 10 - It is expecting base 10 numbers/integers
+* 'Hello!' - This is what you gave it. We can see it doesn't match the criteria above.
+
 ---
 ## Concatenation
 
@@ -837,14 +872,7 @@ except Exception as e:
   
 ```
 
----
-## A quick aside
-
-You will run into errors coding. 
 
-DON'T PANIC. 
-
-Most of the time the error messages are very clear. And if they are not a quick google will often clear it up. 
 
 ---
 ## Tuple/List coercion
@@ -1228,7 +1256,7 @@ arr
 ---
 ## Adding Dimensions
 
-It is possible to create many kinds of arrays, with differing dimensionality. They can be 1D,2D,3D etc. Typically we think about 2D arrays as this is often the rectangular data we deal with. 
+Typically we think about 2D arrays as this is often the rectangular data we deal with. It is possible to create many kinds of arrays, with differing dimensionality. They can be 1D,2D,3D etc.  
 
 Here we again create a list to coerce into a array. This time we have a list of lists. Each list will become equivalent to a row in our array.
 
@@ -1265,7 +1293,7 @@ arr_2d.reshape(9,1)
 ---
 ## Indexing Arrays
 
-We can use same square brackets we used for other data objects to index our arrays. The big difference is we now have 2 dimensions. We therefore need to provide 2 indexes, separated by a comma. 
+We can use the same square brackets we used for other data objects to index our arrays. The big difference is we now have 2 dimensions. We therefore need to provide 2 indexes, separated by a comma. 
 
 The first number will correspond to row. The second number will correspond to column.
 
@@ -1289,9 +1317,6 @@ arr_2d[0,1:3]
 
 ```
 
-
-
-
 ---
 ## Logical Indexing
 
@@ -1711,7 +1736,7 @@ There are several ways to control how your code is evaluated. There are two main
 
 Conditional branching is the evaluation of a logical to determine whether a chunk of code is executed.
 
-In Python, we use the if statement with the logical to be evaluated immediately after. The dependent code is indicated by a colon, new line and indentation.
+In Python, we use the if statement with the logical to be evaluated immediately after. The dependent code is indicated by a **colon**, **new line** and **indentation**.
 
 ```{python}
 
@@ -1742,6 +1767,7 @@ if x > y:
   print("The value of x is",x,"which is greater than", y)
 
 ```
+
 The message is printed above because x is greater than y.
 
 
@@ -1874,7 +1900,7 @@ To help us write complex code we often use pseudocode as a starting point.
 ---
 ## Pseudocode
 
-When we write pseudocode we are trying to write out each computational step in a human readaBle way. 
+When we write pseudocode we are trying to write out each computational step in a human readable way. 
 
 It is important to be specific, simple, concise and include the control structures that would be in your final code. 
 

…inst/extdata/data/susbet_dataset_args.py …inst/extdata/data/subset_dataset_args.pyIntroToPython/inst/extdata/data/susbet_dataset_args.py renamed to IntroToPython/inst/extdata/data/subset_dataset_args.py IntroToPython/inst/extdata/data/susbet_dataset_args.py renamed to IntroToPython/inst/extdata/data/subset_dataset_args.py

@@ -203,14 +203,18 @@ os.chdir("/Users/mattpaul/Downloads/Intro_To_Python-master/r_course/")
 
 ```
 
-Given that we started at: */Users/mattpaul*, we could have also used. This uses the knowledge that we are in that start position to find where we are going. 
+This absolute pathway is very precise but it contains specific information about my computer. This means this will only work on this computer. 
+
+Given that we started at: */Users/mattpaul*, we could have also used a relative path. This uses the knowledge that we are in that start position to find where we are going. 
 
 ```{python, eval=F}
 
 os.chdir("Downloads/Intro_To_Python-master/r_course/")
 
 ```
 
+If we ensure the code is run from an equivalent position, than we can use relative paths across computers. 
+
 ---
 ## Back to Reading
 
@@ -290,11 +294,13 @@ sex
 
 
 ---
-## Quick Recap
+## Quick Recap - Array Filtering
 
-Once you have performed some analysis you will want to export it into a new file. 
+Once you have performed some analysis you will want to export it into a new file.
 
-Let's do some quick processing based on what we learned yesterday. First we will make a 2D array. 
+Let's do some quick filtering of the data based on what we learned yesterday. We can then export the results later. 
+
+First we will make a 2D array. 
 
 ```{python}
 
@@ -337,7 +343,7 @@ np.savetxt("height-weight_female.csv", subset_array, delimiter=',', fmt='%s')
 
 Though a lot of the time we may use these NumPy approaches, there are specific functions dedicated to a variety of data types. 
 
-The most common is [pandas](https://pandas.pydata.org/docs/getting_started/index.html#getting-started). This is a specialized library for managing data frames. It also has the ability to read/write from excel spreadsheets.  
+The most common is [pandas](https://pandas.pydata.org/docs/getting_started/index.html#getting-started). This is a specialized library for managing data frames. These are similar to arrays but a little more flexible for multiple data types. It also has the ability to read/write from excel spreadsheets.  
 
 [BioPython](https://biopython.org/) and [BioNumPy](https://bionumpy.github.io/bionumpy/menu.html) have a range of utilities for managing biological data types i.e. fasta, fastq, etc.
 
@@ -367,7 +373,7 @@ if(params$isSlides == "yes"){
 
 ## Scripts
 
-So far we have been working interactively with the console: asking it questions and getting answers back immediately. 
+So far we have predominately been working interactively with the console: asking it questions and getting answers back immediately. 
 
 When you want to run all your code, or if you want to start working on automation you can run a whole script instead. In this case we have all our code written out in a *.py document. This is good practice for matured analysis that you have finalized to ensure that you have everything properly documented. 
 
@@ -426,7 +432,7 @@ More traditionally we would invoke python directly and provide the script. You w
 ```
 /Users/mattpaul/Deskt
 op/miniconda3/envs/intro_to_python/bin/python /Users/mattpaul/Documents/RU/Train
-ing/Intro_To_Python/r_course/data/susbet_dataset.py
+ing/Intro_To_Python/r_course/data/subset_dataset.py
 ```
 
 
@@ -463,9 +469,7 @@ np.savetxt("data/height-weight_"+arg1+".csv", subset_array, delimiter=',', fmt='
 To pass the argument to our script when we run it, we simply add it after our python script. 
 
 ```
-/Users/mattpaul/Deskt
-op/miniconda3/envs/intro_to_python/bin/python /Users/mattpaul/Documents/RU/Train
-ing/Intro_To_Python/r_course/data/susbet_dataset_args.py Male
+/Users/mattpaul/Desktop/miniconda3/envs/intro_to_python/bin/python /Users/mattpaul/Documents/RU/Training/Intro_To_Python/r_course/data/subset_dataset_args.py Male
 ```
 
 ---