2023 June UCSD Carpentries Bootcamp - Python, Unix Shell, & Git

--- tags: ucsd-carpentries --- # 2023 June UCSD Carpentries Bootcamp - Python, Unix Shell, & Git **Workshop Details** Dates: June 26th - 29th, 2023 Days: Mon-Thurs Time: 1-4pm Location: Virtual via Zoom **Workshop Agenda:** https://ucsdlib.github.io/2023-06-26-UCSD/ **Workshop Lessons Reviewed** Plotting and Programming in Python - http://swcarpentry.github.io/python-novice-gapminder/ Library Carpentries: The Unix Shell - https://librarycarpentry.org/lc-shell/index.html Library Carpentries: Introduction to Git - https://librarycarpentry.org/lc-git/ Version Control with Git: Conflicts - https://swcarpentry.github.io/git-novice/09-conflict/index.html **Software Installation:** [software downloads ](https://hackmd.io/@U2NG/SJkaMk2t7) **Lesson Data (download)** [Gapminder data](http://swcarpentry.github.io/python-novice-gapminder/files/python-novice-gapminder-data.zip) [Shell lesson data](https://librarycarpentry.org/lc-shell/data/shell-lesson.zip) ## NOTES: A copy of the instructor live session notes will be made available to participants upon request at the end of the workshop. Jupyterlab will be used for the lessons [m] Markdown cell = notes [#]also works in code cell for notes [b] = add cell below [a] is above [r]Raw cells cannot have text edits (for Python lessons) https://www.markdownguide.org/getting-started/ https://www.markdownguide.org/basic-syntax/ ## Workshop Day 1 ### First name and Last Name/Organization/Dept./Email | Name (first & last) | Organization | Dept. | Email | | ------------------------- | ------------ | ----- | --------------- | | (example) Kimberly Thomas | UCSD | IT | kkt008@ucsd.edu | | Hoang Nguyen |UCSD |Chemistry and Biochemistry|hon005@ucsd.edu | | Cindy Zhong | UCSD | Biology | l3zhong@ucsd.edu | | Yipeng Li | UCSD |Bioeng |y9li@ucsd.edu | |Jessica Fong | UCSD | Bioengineering | j6fong@ucsd.edu | | Alexis Morales Flores | UCSD | CSE |amoralesflores@ucsd.edu| | Yevgeniy Yakusevich | UCSD | MAE | yyakusevich@ucsd.edu | | Daiwei Wang | UCSD | Biology |daw008@ucsd.edu | |Hamed Mojtahed| UCSD|ECE|hmojtahed(at)ucsd.edu| | Saurabh Parab | UCSD | MATS |saparab@ucsd.edu | |Samantha Kruse | UCSD | Chem | smkruse@ucsd.edu | Celeste Kanne|UCSD|BMS|ckanne@ucsd.edu |Tony Guan | UCSD | ECE | jug054@ucsd.edu | Maya Morris | UCSD | chem |mnmorris@ucsd.edu |Kanuri Roundtree | UCSD | Chemistry | kroundtree@ucsd.edu | | | | Gerald Henderson| UCSD | RMAS | | gehenderson@health.ucsd.edu | |Eranda Somathilake |UCSD | MAE |esomathilake@ucsd.edu| |Emily Zhu |UCSD |Math |e9zhu@ucsd.edu | |Melina Basilio Flores |UCSD |Chemistry |mbasilio@ucsd.ed| | Lisa Rhodes|UCSD|HTTC|lmrhodes@ucsd.edu | | | | | | | | | | Jose Sandoval Ortega | UCSD | Math CS | jsandovalortega@ucsd.edu | |Syeda Ullah | UCSD |Rady School of Management |sullah@ucsd.edu | |Daniel Mansour |UCSD |MAE |dmansour@ucsd.edu | |Paulina De la Garza| UCSD| Biological Sciences| pdelagarza@ucsd.edu |Isaac Kreitzer | UCSD | Structural Engineering | ikreitzer@ucsd.edu | | Heidy Vega | UCSD | Biochemistry and Chemistry | hvega@ucsd.edu | |Chang Han | UCSD | Bioengineering | c4han@ucsd.edu | |Andrew Keller |UCSD |MAE |akeller@ucsd.edu | |Yifan Xiao |UCSD |Math |yix001@ucsd.edu | |Chuqing Shi |UCSD |Math |chs139@ucsd.edu | |James Findley de Regt|UCSD|Nanoengineering| jfindleyderegt@ucsd.edu| |Nurikemu Gulinihali |UCSD |Electrical Engineering |ngulinihali@ucsd.edu | |Nuri Chung |UCSD |BE |nuchung@ucsd.edu | Shreesamarth Srivatsa| UCSD | Bioengineering | ssrivatsa@ucsd.edu | |Anugrah Jo Joshy | UCSD | MAE | ajoshy@eng.ucsd.edu | |Sai Jannamaraju | UC San Diego Health | HTTC | scjannamaraju@health.ucsd.edu |Mingyue Zhang | UCSD | Structural Engineering| miz005@eng.ucsd.edu |Anthony Cai | UCSD | Chemistry and Biochemistry| aycai@ucsd.edu | Christopher Frobenius | UCSD | Chemistry & Biochemistry | cfrobeni@ucsd.edu |Justin Hamlin|UCSD | Chemistry and Biochemistry | jdhamlin@ucsd.edu| Tiffany Chu | UCSD | Biomedical Sciences | t2chu@ucsd.edu | Leesa Anzaldo | UCSD | Math |lbanzaldo@ucsd.edu | Quincy Lyons| UCSD| BENG| qulyons@ucsd.edu| |Rana Hegazy|UCSD|ECE|rhegazy@ucsd.edu| | Ari Lin | UCSD | ECE | chl177@ucsd.edu | | Asuka Zumi Alvarado | SBP | Snyder Lab | aalvarado@sbpdiscovery.org | | Tung Vu | UCSD | ECE | tmv001@ucsd.edu | |Luciann Valencia|UCSD|math-cs|l2valencia@ucsd.edu | Maya Vasishth | UCSD SBP | Biomedical Sciences Snyder Lab | mvasishth@heakth.UCSD.edu | |Kassra Eshragh|| UCSD MATS | keshragh@eng.ucsd.edu Leila El Masri | UCSD | chem | lelmasri@ucsd.edu |Jeremy Shek | UCSD | Biomedical Sciences | jshek@ucsd.edu Paul Bastaki|UCSD | ECE | pbastaki@ucsd.edu| Diana Tran | UCSD |Chemistry | dit002@ucsd.edu Heng Zhu | UCSD | ECE | hez007@ucsd.edu Runqiu Xu | UCSD | Math | r4xu@ucsd.edu |Yuanshan Wu | UCSD | Bioengineering | yuw100@ucsd.edu Michelle Truong|UCSD|Medicine|mitruong@health.ucsd.edu| Jenny Nicolas | UCSD | MATS | jnicolas@ucsd.edu| chengchangfeng lu | UCSD | ECE | c9lu@ucsd.edu | ## Day 1 Lessons Reviewed *Running and Quitting *Variables and assignments *Data Types and Type Conversion *Built-in Functions and Help ## Day 1 Questions: Please enter any questions not answered during live session here: ### End Day 1 ## Workshop Day 2 ### First name and Last Name/Organization/Dept./Email | Name (first & last) | Organization | Dept. | Email | | ------------------------- | ------------ | ----- | --------------- | | Celeste Allaband | UCSD | Pediatrics | callaban@health.ucsd.edu | | Eranda Somathilake | UCSD | MAE | esomathilake@ucsd.edu | Gerald Henderson|UCSD | RMAS | gehenderson@health.ucsd.edu | | | Maya Morris | UCSD | Chem | mnmorris@ucsd.edu | | | | | | --------------------- | ---- | -------------------------- | ------------------------ | ---------- | ---- | ---- | --------------- | | Anugrah Jo Joshy | UCSD | MAE | ajoshy@eng.ucsd.edu | | | | | | Yipeng Li | UCSD | Bioeng | y9li@ucsd.edu | | | | | | Heidy Vega | UCSD | Biochemistry and Chemistry | hvega@ucsd.edu | | | | | | Jessica Fong | UCSD | Bioengineeering | j6fong@ucsd.edu | | | | | |Nuri Chung| UCSD |BE |nuchung@ucsd.edu | | Nurikemu Gulinihali | UCSD | Electrical Engineering | ngulinihali@ucsd.edu | | | | | | Michelle Truong | UCSD | Medicine | mitruong@health.ucsd.edu | | | | | | Daniel Mansour | UCSD | MAE | dmansour@ucsd.edu | | | | | | Tony Guan | UCSD | ECE | jug054@ucsd.edu | | | | | | Daiwei Wang | UCSD | Biology | daw008@ucsd.edu | | | | | | Leila EL Masri | UCSD | CHem | lelmasri@ucsd.edu | | | | | | Leesa Anzaldo | UCSD | Math | lbanzaldo@ucsd.edu | | | | | | Justin Hamlin | UCSD | Chemistry | jdhamlin@ucsd.edu | | | | | | Hamed Mojtahed | UCSD | ECE | hmojtahed(at)ucsd.edu | | | | | | Jenny Nicolas | UCSD | MATS | jnicolas@ucsd.edu | | | | | | Jeremy Shek | UCSD | Biomedical Sciences | jshek@ucsd.edu | | | | | | Hoang Nguyen | UCSD | Chemistry and Biochemistry | hon005@ucsd.edu | | | | | | Andrew Keller | UCSD | MAE | akeller@ucsd.edu | | | | | | Kanuri Roundtree | UCSD | Chemistry | Kroundtree@ucsd.edu | | | | | | Runqiu Xu | UCSD | MATH | r4xu@ucsd.edu | | | | | | Yevgeniy Yakusevich | UCSD | MAE | yyakusevich@ucsd.edu | | | | | | Chang Han | UCSD | Bioengineering | c4han@ucsd.edu | | | | | | Anthony Cai | UCSD | Chemistry and Biochemistry | aycai@ucsd.edu | | | | | | Jose Sandoval Ortega | UCSD | Math CS | jsandovalortega@ucsd.edu | | | | | | James Findley de Regt | UCSD | Nanoengineering | jfindleyderegt@ucsd.edu | | | | | | Luciann Valencia | UCSD | math-cs | l2valencia@ucsd.edu | | | | | | Yifan Xiao | UCSD | Math | yix001@ucsd.edu | | | | | | Paul Bastaki | UCSD | ECE | pbastaki@ucsd.edu | Yifan Xiao | UCSD | Math | yix001@ucsd.edu | | Quincy Lyons | UCSD | BENG | qulyons@ucsd.edu | | | | | | Diana Tran | UCSD | Chemistry | dit002@ucsd.edu | | | | | | Mingyue Zhang | UCSD | Structural Engineering | miz005@eng.ucsd.edu | | | | | | Ari Lin | UCSD | ECE | chl177@ucsd.edu | | | | | | Tiffany Chu | UCSD | Biomedical Sciences | t2chu@ucsd.edu | | Yuanshan Wu| UCSD | Bioengineering |yuw100@ucsd.edu Syeda Ullah | UCSD| Rady School of Management| sullah@ucsd.edu| chengchangfeng lu| UCSD | ECE | c9lu@ucsd.edu| Saurabh Parab | UCSD|MATS|saparab@ucsd.edu Melina Basilio Flores|UCSD|Chemistry|mbasilio@ucsd.edu ## Day 2 Lessons Reviewed [Gapminder Dataset Needed](http://swcarpentry.github.io/python-novice-gapminder/files/python-novice-gapminder-data.zip) *1. [Libraries](http://swcarpentry.github.io/python-novice-gapminder/06-libraries.html) *2. [Reading Dataframes](http://swcarpentry.github.io/python-novice-gapminder/07-reading-tabular.html) *3. [Working with Pandas Dataframes](http://swcarpentry.github.io/python-novice-gapminder/08-data-frames.html) *4. [Plotting!](http://swcarpentry.github.io/python-novice-gapminder/09-plotting.html) **************** ## Day 2 Lessons Reviewed "*Libraries *Reading Tabular Data into DataFrames *Pandas DataFrames *Plotting" ## Day 2 Questions: Please enter any questions not answered during live session here: 1. ### End Day 2 ## Workshop Day 3 ### First name and Last Name/Organization/Dept./Email | Name (first & last) | Organization | Dept. | Email | | | --------------------- | ------------ | -------------------------- | --------------------------- | --- | | Celeste Allaband | UCSD | Pediatrics | callaban@health.ucsd.edu | | | Gerald Henderson | UCSD | RMAS | gehenderson@health.ucsd.edu | | | Hamed Mojtahed | UCSD | ECE | hmojtahed(at)ucsd.edu | | | Jessica Fong | UCSD | Bioengineering | j6fong@ucsd.edu | | | Daniel Mansour | UCSD | MAE | dmansour@ucsd.edu | | | Tony Guan | UCSD | ECE | jug054@ucsd.edu | | | Andrew Keller | UCSD | MAE | akeller@ucsd.edu | | | Nurikemu Gulinihali | UCSD | Electrical Engineering | ngulinihali@ucsd.edu | | | James Findley de Regt | UCSD | NanoEngineering | jfindleyderegt@ucsd.edu | | | Kanuri Roundtree | UCSD | Chemistry | Kroundtree@ucsd.edu | | | Jose Sandoval | UCSD | Math CS | jsandovalortega@ucsd.edu | | | Chang Han | UCSD | Bioengineering | c4han@ucsd.edu | | | Hoang Nguyen | UCSD | Chemistry and Biochemistry | hon005@ucsd.edu | | | Eranda Somathilake | UCSD | MAE | esomathilake@ucsd.edu | | | Syeda Ullah | UCSD | Rady School of Management | sullah@ucsd.edu | | | Heidy Vega | UCSD | Biochemistry and Chemistry | hvega@ucsd.edu | | | Maya Morris | UCSD | CHEM | mnmorris@ucsd.edu | | | Mingyue Zhang | UCSD | SE | miz005@eng.ucsd.edu | Yuanshan Wu|UCSD |Bioengineering|yuw100@ucsd.edu | Yifan Xiao | UCSD | Math | yix001@ucsd.edu | | | Anthony Cai | UCSD | Chemistry and Biochemistry | aycai@ucsd.edu | | | Jenny Nicolas | UCSD | MATS | jnicolas@ucsd.edu | | | Justin Hamlin | UCSD | Chemistry | jdhamlin@ucsd.edu | | | Ari Lin | UCSD | ECE | chl177@ucsd.edu | | | Anugrah Jo Joshy | UCSD | MAE | ajoshy@eng.ucsd.edu | | | Tiffany Chu | UCSD | Biomedical Sciences | t2chu@ucsd.edu | | | Diana Tran | UCSD | Chemistry | dit002@ucsd.edu | | | Paul Bastaki | UCSD | ECE | pbastaki@ucsd.edu | | | Daiwei Wang | UCSD | Biology | daw008@ucsd.edu | | | Saurabh Parab | UCSD | MATS | saparab@ucsd.edu | | | Leesa Anzaldo | UCSD | Math | lbanzaldo@ucsd.edu | | | Runqiu Xu | UCSD | MATH | R4XU@UCSD.EDU | | | Jeremy Shek | UCSD | Biomedical Sciences | jshek@ucsd.edu | | Yipeng Li | UCSD | Bioeng | y9li@ucsd.edu Melina Basilio Flores|UCSD|Chemistry|mbasilio@ucsd.edu | Yevgeniy Yakusevich | UCSD | MAE | yyakusevich@ucsd.edu| ## Day 3 Lessons Reviewed *1. [Functions](http://swcarpentry.github.io/python-novice-gapminder/16-writing-functions.html) *2. [Lists](http://swcarpentry.github.io/python-novice-gapminder/11-lists.html) *3. [For Loops](http://swcarpentry.github.io/python-novice-gapminder/12-for-loops.html) **************** ## Day 3 Questions: Please enter any questions not answered during live session here: ### End Day 3 ## Workshop Day 4 ### First name and Last Name/Organization/Dept./Email | Name (first & last) | Organization | Dept. | | | | ------------------- | ------------ | ------------------------- | --- | --- | | Kanuri Roundtree | UCSD | Chemistry | | | | Jessica Fong | UCSD | Bioengineering | | | | Yuanshan Wu | UCSD | Bioengineering | yuw100@ucsd.edu | | | Hamed Mojtahed | UCSD | ECE | | | | Chang Han | UCSD | Bioengineering | | | | Maya Morris | UCSD | Chem | | | | Justin Hamlin | UCSD | Chemistry | | | | Nurikemu Gulinihali | UCSD | Electrical Engineering | ngulinihali@ucsd.edu | | | | | | | | Michelle Truong | UCSD | Medicine | | | | Eranda Somathilake | UCSD | MAE | | | | Jenny Nicolas | UCSD | MATS | | | | Syeda Ullah | UCSD | Rady School of Management | | | | Jeremy Shek | UCSD | Biomedical Sciences | jshek@ucsd.edu | | | Paul Bastaki | UCSD | ECE | pbastaki@ucsd.edu | | | Yevgeniy Yakusevich | UCSD | MAE | yyakusevich@ucsd.edu| |Yifan Xiao |UCSD |Math |yix001@ucsd.edu | | |Tiffany Chu | UCSD | Biomedical Sciences |t2chu@ucsd.edu | | | Tony Guan | UCSD | ECE | jug054@ucsd.edu | | | Daiwei Wang |UCSD |Biology |daw008@ucsd.edu | | | Anthony Cai | UCSD | Chemistry and Biochemsitry | aycai@ucsd.edu | | | Andrew Keller | UCSD | MAE |akeller@ucsd.edu | | Ari Lin | UCSD | ECE | chl177@ucsd.edu | | Mingyue Zhang | UCSD | SE | miz005@eng.ucsd.edu | | | James FIndley de Regt | UCSD | Nanoengineering | jfindleyderegt@ucsd.edu | | | Nuri Chung |UCSD |BE |nuchung@ucsd.edu | |Diana Tran |UCSD |Chemistry | dit002@ucsd.edu | | | Saurabh Parab | UCSD | MATS | saparab@ucsd.edu | | | Daibo Zhang | UCSD | MAE | daz045@eng.ucsd.edu | | | Yipeng Li | UCSD | Bioeng | y9li@ucsd.edu | | | | | | | | ## Day 4 Lessons Reviewed *1. [What is the Shell?](https://librarycarpentry.org/lc-shell/01-intro-shell.html) *2. [Navigating the file system](https://librarycarpentry.org/lc-shell/02-navigating-the-filesystem.html) *3. [Working with files and directories](https://librarycarpentry.org/lc-shell/03-working-with-files-and-folders.html) **************** *1. [What is Git/Github?](https://librarycarpentry.org/lc-git/01-what-is-git.html) *2. [Getting started with G****it](https://librarycarpentry.org/lc-git/02-getting-started.html) *3. [Sharing your work](https://librarycarpentry.org/lc-git/03-sharing.html) *5. [GitHub Pages](https://librarycarpentry.org/lc-git/05-github-pages.html) ## Day 4 Questions: Please enter any questions not answered during live session here: 1. ### End Day 4

Syntax	Example	Reference
# Header	Header	基本排版
- Unordered List	Unordered List
1. Ordered List	Ordered List
- [ ] Todo List	Todo List
> Blockquote	Blockquote
Bold font	Bold font
Italics font	Italics font
~~Strikethrough~~	~~Strikethrough~~
19^th^	19^th
H~2~O	H₂O
++Inserted text++	Inserted text
==Marked text==	Marked text
[link text](https:// "title")	Link
![image alt](https:// "title")	Image
`Code`	`Code`	在筆記中貼入程式碼
```javascript var i = 0; ```	`var i = 0;`
:smile:		Emoji list
{%youtube youtube_id %}	Externals
$L^aT_eX$	L^aT_eX
:::info This is a alert area. :::	This is a alert area.