Software Carpentry:             American University
Dates:                                     Monday through Thursday, Nov 9-12
Time:                                      10 am - 3 pm ET
Workshop website:                https://annajiat.github.io/2020-11-09-american-online/
Lesson website:                      https://software-carpentry.org/lessons/
Etherpad (this document):    https://pad.carpentries.org/2020-11-09-american-online
Feedback form:                      Please fill up the following form at the end of each day to help us improve  https://docs.google.com/forms/d/e/1FAIpQLScS2cxi4ArrrDNfbktURliIvMwFseyjxtqFCUv0d2IjKBaDHQ/viewform

Welcome to Software Carpentry
	* We will use this Etherpad for sharing links, code snippets, notes, ask/answer questions, etc. 
	* From the upper right corner of this screen, please change "anonymous" to yourname and if you wish, please choose a color for your writing.
	* There is a chat window at the bottom right corner. In case of zoom difficulties, please notify us using that.
	* In this part at the left, we will keep adding our notes as we go through the workshop. You can also add your notes/questions here as well. This pad is synchronized as you type, so that everyone viewing this page sees the same text. This allows us to collaborate seamlessly on this document. 
	* From the upper right corner, you can choose to save your own copy of this document by clicking the double arrow and choosing HTML or other formats.
	* In case this page keeps showing error, please keep it closed for few minutes and open again.
	* Both this page and the lesson pages will remain available online after the workshop. In case you need to review anything, please feel free to visit the links again!

Host
	* Melissa L. Becher, American University

Instructors
	* Annajiat Alim Rasel, Brac University, @annajiat
	* Elnaz AMANZADEH: elibio449@gmail.com
	* Jesse Johnston (he/him), Univ. of Michigan (supporting instructor) @jesseajohnston, https://orcid.org/0000-0003-2617-0166

Helpers
	* Amanda Steadman, American University
	* Stefan Kramer, American University

Code of conduct
	* Use welcoming and inclusive language
	* Be respectful of different viewpoints and experiences
	* Gracefully accept constructive criticism
	* Focus on what is best for the community
	* Show courtesy and respect towards other community members
	* More details at https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html

Guidelines
	* Zoom chat can be used to ask questions or provide comments or express difficulties during the lesson. Type “hand” in the chat, or type the question into the chat, or use a “raise hand”. To request assistance, message helper or indicate the red x "no" in the participants chat.
		* Helpers may continue to reply there or via zoom private chat as needed.
		* If necessary, helpers may temporarily move to a zoom breakout room with you to discuss in details using audio/screen sharing. You can return to the main session by leaving the breakout room.
	* You can participate in the polls during the lesson by clicking Zoom Participants Panel and clicking on yes/no.
	* If we are going too fast/slow, please indicate by clicking >>>go faster or <<<go slower.
	* Use a second screen (phone, laptop, tab) to open the lessons or other windows.
	* For a single screen, it can be split to have the zoom window and the window where we'll be working, both open side by side.
	* Please rename yourself to add the Operating System (OS) after your name in zoom. e.g. Annajiat (Linux)
	* Having a Great Online Learning Experience: A Guide for Students, https://carpentries.org/blog/2020/04/great-online-learning-student/


 ---------------------------------------------------------------------------------------------------
								  Day 1: November 9, Monday
 ---------------------------------------------------------------------------------------------------
 Icebreaker activity: 
 please list your name, pronouns, email/twitter, affiliation, and ... your favorite icebreaker activity! Please tell us a bit more about yourself as well!
 
	*  Annajiat Alim Rasel, he/him/his, annajiat@gmail.com, Brac University. My favorite icebreaker activity is discussing about favorite books! The least favorite gift that I have received at events is stickers! I love to volunteer in learning activities, if you are organizing one, please count me in! I am super excited to go through the workshop lessons and to learn along with you! 
	* Jesse, he/him, @jesseajohnston (twitter), University of Michigan - I love/hate the icebreaker where each person gives their name, then the next person has to repeat each name - it's great to be one of the first people, but i dread being the last person. these text-based intros are much easier for me! :)
	* Amanda, she/hers, ajstead@american.edu, American University. My favorite icebreaker is naming a favorite movie (mine is Back to the Future!). 
	* Stefan Kramer, he/him/his, skramer@american.edu, Assoc. Dir. for Research Data Services@ American U. Library. Favorite icebreaker: tell about a crazy - good or bad- trip, e.g., 4 flight/train layovers to get from city A to B. 
	* Marissa, she/her, personal email mlbeller@icloud.com, Cleveland State, 2 truths and a lie!
	* Jennifer Lopez, She/her, email - jl0049a@student.american.edu, American University, top wrestling walk-out song
	* Donna, 
	* Fred Bruhweiler, 
	* Silvina Guidoni (she,her), American University, I am bad at ice-breakers ... :) 

Lesson:
http://swcarpentry.github.io/shell-novice/01-intro/index.html

Notes:
	* You can usually customize the colors and font sizes in your shell
	* control+L (or cmd+L) clears the shell/terminal screen and so does the "clear" command
	* Basic shell syntax: [command] [options, also called "flag", indicate with a hyphen] [argument - additional information to the command, like where you want to go]
		* example: ls [command] -F [flags] [this one does not require additional information or "argument"]
		* syntax = the way to put word commands together in a way that the shell system will understand them
	* Commands we covered:
		* pwd - print the current location, like "you are here" (= print working directory)
		* ls [+ path] - use to "list" the files in your current directory (or provide an argument with another location you want to list)
		* cd [path as argument] - use with an argument to "change directory" (that is, move around the file system)
			* "." and ".." refer respectively to "here" (single dot) and "up one directory" (double dot)
			* if used without any argument (that is, "cd"), this moves to the user's home directory
		* mkdir
		* touch
		* mv
		* cp
		* cat
		* head
		* tail
		* wc
		* sort
	* use the "-h" or "--help" flags to learn more about a command; on MacOS, you can use "man" to show the "manual"
	* ~ is the root for the user which is usually called home directory/folder, instead of being called a root
	* / is for the root for the whole computer system, it is the top most folder/directory in a computer, it is usually refered to as the root directory
	* man is short for manual. This command may not work on Git Bash shell on Windows. Uers may wish to try the online man pages from by searching online, for example: https://man7.org/linux/man-pages/man1/ls.1.html
	* use the `Tab` key for autocomplete... very helpful for completing paths in the shell interface!
	* absolute/relative paths: absolute is a definite location in relation to the root ("full path" beginning from the root location); relative commands (like "." or ".." or incomplete paths), will change meaning depending on your current location (identify this with `pwd`)

Current point in lesson:
http://swcarpentry.github.io/shell-novice/02-filedir/index.html

Excercise 1: what is the usage of "ls -l"? 
	* Donna:  list of files with modification dates/times
	* Fred:   I'm an astrophysicist, who is supposed to be retired, buyt have several active grants.  I've been using IDL extensiviely with associAted libraries.  I see a lot of people moving to Python for data ewduction and analysis.  This is pretty much where i'm at.
	* 
	* Jennifer - ls gives you a list of files, and adding -l shows you the owner and other details like when it was last modified
	* Marissa:  List file in a long list format
	* Silvina: Gives the size of files, gives you more info for each file

Excercise 2:
second question: 
Donna:
Fred:
Jennifer:The first command was within that directory while the second was in the root directory
Marissa:
Silvina: command could not understand the path?

How we kno flags of "mkdir" command?
Donna:
Fred:
Jennifer:
Marissa:
Silvina: man mkdir


Excercise 3:
The homework of first day: 
please run "ls -S -r" what is the output?
Relative Path Resolution
*ls Reading Comprehension


Lunch break is going on, we'll try to resume at 12:55 pm ET (5:55 pm UTC)
If you are back early from lunch, please try out the last few tasks from http://swcarpentry.github.io/shell-novice/03-create/index.html

RE: http://swcarpentry.github.io/shell-novice/04-pipefilter/index.html:
note that this sorting includes the "total" from the earlier wc -l output … that's not the size of one file. With many more files to work with in a directory, that could trip up a reader, thinking there's a file called "total" that's the largest of them all. ;-)
Outside of this lesson, in a real project, you would probably also want to put the "metadata"-files you generate (like lengths.txt) into a separate directory from the original files whose attributes were used to put into those "metadata"-files.

For cat lovers, you could run the command
	alias meow=cat
and then
	meow lengths.txt
would also work. That's not officially a part of this lesson. :-)
lol! :) love this :meow:

	* A classis use case for using the shell interface: you could create a script running the cp command on a number of files to copy them to a different directory, to run a recurring backup.


Topics to cover in first section on Day 2 
	* If possible, please join may be 10 minutes earlier on Day 2, so that we can review, answer QA 
	* may be discuss a bit about last two episodes.of the shell lesson
	* please try to come up with an example of a task you would benefit from automation through shell scripting

---------------------------------------------------------------------------------------------------
								  Day 2: November 10, Tuesday
 ---------------------------------------------------------------------------------------------------

Intros (please add name again, so we know who's here)
Stefan Kramer, skramer@american.edu, http://orcid.org/0000-0001-5795-7629, helper
Jesse Johnston, @jesseajohnston, supporting instructor
Annajiat Alim Rasel, @annajiat, looking forward to learn more python, the language headed to be the top one.

Melissa Becher, she/her, helper/host
Marissa Beller, she/her, learner, have experience with R through Data Carpentries and would like to learn other languages used by data professionals
Fred Bruhweiler, learner-interested in learning Python
Donna Femenella, she/her, learner
Jennifer Lopez, she/her, learner. 

Shell scripts: http://swcarpentry.github.io/shell-novice/06-script/index.html
Shell find & search: http://swcarpentry.github.io/shell-novice/07-find/index.html 
Python lesson: http://swcarpentry.github.io/python-novice-gapminder/ 
Python data: http://swcarpentry.github.io/python-novice-gapminder/files/python-novice-gapminder-data.zip (see the setup page for info on installation: http://swcarpentry.github.io/python-novice-gapminder/setup.html)

Notes

Day 2:
Data File: http://swcarpentry.github.io/python-novice-gapminder/files/python-novice-gapminder-data.zip
ANACONDA Download link: http://swcarpentry.github.io/python-novice-gapminder/setup.html
Lesson1: http://swcarpentry.github.io/python-novice-gapminder/01-run-quit/index.html

I'm wondering why the Python code:
	print(name, 'is', age, '.')
generates 
	Jesse is 40 .
with a space between 40 and the period ...?  How could that be avoided if necessary?

Observation: in the Unix shell, we had to precede a defined variable with a $ sign to extract its value, but not so in Python.
Good question: in this case, you can use the comma or plus to do similar things - the comma is basic output with space between each thing, but the + directly concatenates the values of strings together

Question: what happens with age = '30' if we try to use the addition operation?

Marissa 
Donna 
Jennifer - Error because '30' is a string variable not an integer. 
Fred - "2 is an integer" -> error


Why don’t max and min return None when they are given no arguments?
Marissa it would not be enough information to troubleshoot, in case someone accidentally forgot to add an argument
Donna 
Jennifer  - 
Fred -

Questions from the morning?

JJ to all: Did we answer the question about different types of division?

You want to select a random character from a string. 
	1. Which standard library module could help you? see https://docs.python.org/3/library/

Silvina: random libraries, searched for word "rand
om" in the list of libraries

Code: 
*import math as m
angle = ____.degrees(____.pi / 2)
print(____)

	1. What method call will display the first three rows of this data?
	2. What method call will display the last three columns of this data? (Hint: you may need to change your view of the data.)

Write an expression to find the Per Capita GDP of Serbia in 2007.

Useful for working through on your own: "Practice with Selection" exercise

Data from Gapminder: https://www.gapminder.org/data/


---------------------------------------------------------------------------------------------------
								  Day 3: November 11, Wednesday
 ---------------------------------------------------------------------------------------------------
 
 Roll call:
	* Jesse (supporting instructor)
	* Amanda (helper)
	* Jennifer Lopez (learner)
	* Fred (learner) 
	* Melissa Becher (helper/host)
	* Elnaz (instructor)
	* Annajiat (instructor)

Any questions from Day 2? 

	* Matplotlib documentation: https://matplotlib.org/3.3.2/index.html  
	* information on how to modify the ticks on the axes: https://matplotlib.org/3.3.2/api/_as_gen/matplotlib.axes.Axes.autoscale_view.html#matplotlib.axes.Axes.autoscale_view
	* https://matplotlib.org/3.3.2/api/_as_gen/matplotlib.pyplot.locator_params.html#matplotlib.pyplot.locator_params
	* Here is the parameter for matplotlib that allows you to modify the tick values: https://matplotlib.org/3.3.2/api/ticker_api.html#matplotlib.ticker.MultipleLocator 

Notes for Day 3
	* Lessons: Starting at python "lists" http://swcarpentry.github.io/python-novice-gapminder/11-lists/index.html 
	* Annajiat shared information about python conventions: http://swcarpentry.github.io/python-novice-gapminder/11-lists/index.html 
	* Loops: http://swcarpentry.github.io/python-novice-gapminder/12-for-loops/index.html
	* Resource for tracking variables during execution of loops & programs: http://pythontutor.com/visualize.html#mode=edit 
	* Conditionals: http://swcarpentry.github.io/python-novice-gapminder/13-conditionals/index.html
	* Functions (http://swcarpentry.github.io/python-novice-gapminder/16-writing-functions/index.html)
		* Common syntax of functions:
			* starts with def
			* requires a name() (you define the name)
			* inside parens, specify if the function takes any arguments (can be used within the function)
			* the "activity" of the function is indented under the line beginning with "def"
			* One way to describe the function is as a recipe (instructions on what to do), and the arguments are like the ingredients (the things that go into the function)
		* Every function call produces some result.
		* If the function doesn’t have a useful result to return, it usually returns the special value None.



Exercise:
#Fill in the blanks so that the program below produces the output shown.
values = ____
values.____(1)
values.____(3)
values.____(5)
print('first time:', values)
values = values[____]
print('second time:', values)
#first time: [1, 3, 5]
#second time: [3, 5]

Useful resources:
	* https://annajiat.blogspot.com/2020/08/python-code-convention-or-style-guide.html
	* http://pythontutor.com/visualize.html#mode=edit

*
Day3: Afternoon Session lessons: 1. http://swcarpentry.github.io/python-novice-gapminder/16-writing-functions/index.html
2. http://swcarpentry.github.io/python-novice-gapminder/17-scope/index.html
3. http://swcarpentry.github.io/python-novice-gapminder/18-style/index.html

extra useful links: 1. http://swcarpentry.github.io/python-novice-gapminder/04-built-in/
2. https://www.python.org/dev/peps/pep-0008/
3. https://docs.python.org/3/



Question: Please write down three points about the code which you see in my Jupyter Notebook.

	* Marissa : 
	* Donna :
	* Jennifer : (1) The code is separating out eggs based on mass. (2) Starts out with an if function, continues on with else if based on size. (3) Finishes with the eggs that did not fit into any category with the else function and labels them "small."
	* Fred : This is an egg sorter, which does it by mass. The smallones are considered to be spoiled or unfit.
 

     Q2: Why we get "None" when we run code: result = print_date(1871, 3, 19)
print('result of call is:', result)

	* Marissa :
	* Jennifer :
	* Fred :



	* Marissa :
	* Jennifer :
	* Fred :

---------------------------------------------------------------------------------------------------
								  Day 4: November 12, Thursday
 ---------------------------------------------------------------------------------------------------
 
 Version control with Git: https://swcarpentry.github.io/git-novice/ 
 
 GitHub repository links:
 
https://github.com/annajiat/planets
https://github.com/morskyjezek/planets 
https://github.com/jennlopez49/planets - @jesse added venus.txt
https://github.com/mlbecher/planets
https://github.com/ajsteadm/planets