This is the most important thing to understand Git!
You must:
- be able to visualize the commit tree
- understand how each git command modifies the commit DAG
Some people like merges, but they are ugly and stupid. Rebase instead and keep linear history.
Linear history:
5 master
|
4
|
3
|
2
|
1 first commitBranched history:
7 master
|\
| \
6 \
|\ \
| | |
3 4 5
| | |
| / /
|/ /
2 /
| /
1/ first commitWhich type of tree do you think will be easier to understand and maintain?
????
????????????
You may disconnect now if you still like branched history.
Generate a minimal test repo. You should get in the habit of doing this to test stuff out.
#!/usr/bin/env bash
mkdir git-tips
cd git-tips
git init
for i in 1 2 3 4 5; do
echo $i > f
git add f
git commit -m $i
done
git checkout HEAD~2
git checkout -b my-feature
for i in 6 7; do
echo $i > f
git add f
git commit -m $i
done
GPU accelerated, simulates the Craig's minimized M. genitalium, JCVI-syn3A at a particle basis of some kind.
Lab head is the cutest-looking lady ever: chemistry.illinois.edu/zan, Zaida (Zan) Luthey-Schulten.
- 2022 paper: www.cell.com/cell/fulltext/S0092-8674(21)01488-4 Fundamental behaviors emerge from simulations of a living minimal cell by Thornburg et al. (2022) published on Cell
- faculty.scs.illinois.edu/schulten/lm/ actual source code. No Version control and non-code drop release, openess and best practices haven't reached such far obscure reaches of academia yet. One day.
- blogs.nvidia.com/blog/2022/01/20/living-cell-simulation/ Nvidia announcement. That's how they do business, it is quite interesting how they highlight this kind of research.
www.wholecellviz.org/viz.php awesome visualization of simtk, paper: www.ncbi.nlm.nih.gov/pmc/articles/PMC3413483/ A Whole-Cell Computational Model Predicts Phenotype from Genotype - 2013 - Jonathan R. Karr.
Followed up by the E. Coli Whole Cell Model by Covert Lab.
For the strong.
git log --abbrev-commit --decorate --graph --pretty=oneline master HEADOutput:
* b4ec057 (master) 5
* 0b37c1b 4
| * fbfbfe8 (HEAD -> my-feature) 7
| * 7b0f59d 6
|/
* 661cfab 3
* 6d748a9 2
* c5f8a2c 1If we also add the As we can see, this removes any commit that is neither:
--simplify-by-decoration, which you very often want want on a real repository with many commits:* b4ec057 (master) 5
| * fbfbfe8 (HEAD -> my-feature) 7
|/
* c5f8a2c 1- under a branch or tag
- at the intersection of too branches or tags
Before:
5 master
|
4 7 my-feature HEAD
| |
3 6
|/
2
|
1Action:
git rebaseAfter:Ready to push with linear history!
7 my-feature HEAD
|
6
|
5 master
|
4
|
3
|
2
|
1Before:
7 my-feature HEAD
|
6
|
5 master
|
4
|
3
|
2
|
1Oh, commit 6 was crap:
git rebase -i HEAD~2Mark
6 to be modified.After:Better now, ready to push.
7 my-feature HEAD
|
6v2
|
5 master
|
4
|
3
|
2
|
1In order to solve conflicts, you just have to understand what commit you are trying to move where.
E.g. if from:we do:what happens step by step is first 6 is moved on top of 5:and then 7 is moved on top of the new 6:
5 master
|
4 7 my-feature HEAD
| |
3 6
|/
2
|
1git rebase master6on5 HEAD
|
5 master
|
4 7 my-feature
| |
3 6
| |
2-----------------+
|
17on5 HEAD
|
6on5
|
5 master
|
4 7 my-feature
| |
3 6
| |
2-----------------+
|
17on5 my-feature HEAD
|
6on5
|
5 master
|
4
|
3
|
2
|
1Quick facts:
- Nationalities: Italian and Brazilian
- Grew up in: Brazil
- Relationship status 2017-: married
- Given name pronunciation: take your pick from Ciro Santilli's given name
- Chinese name: 三西猴, means "three western monkeys". Phonetic approximation to SANtilli CIRO. More info at: Ciro Santilli's Chinese name. Semi-unintentionally reminds Chinese people of Sun Wukong (孙悟空). This association is further slightly strengthened by the phonetic choice of 三 San, which Ciro later noticed matches the middle character of Tang Sanzang (唐三藏), the monk in Journey to the West. The given name 西猴 was given by Ciro Santilli's wife, then recent girlfriend, as a semi-joke, and he took it up because the best way to take a joke is to play along with the joker. 三 was chosen by Ciro himself.
- laptop: high end Lenovo ThinkPad
- distro: latest Ubuntu release
- Vim or Emacs: vi/vim. But for The Love, will someone please make an open source C++ integrated development environment that actually just works?
- tabs or spaces: spaces
- Mailing list or Git(Hub|Lab): Git(Hub|Lab), with passion, see Section "Mailing list"
- system or unit tests: system
- programming languages: Python and C++. He'll learn Rust and Haskell once he's rich. As of the 2020s, Rust was picking up some serious steam, so Ciro might end up eating his own words there.
- musical instruments to listen: Chinese Guqin and electric Jazz-fusion guitar
- metric or imperial: metric, for The Love. Science? Standardization? 21st century anyone?
- QWERTY or Dvorak: QWERTY, alas
- birth name: Ciro Duran Santilli
Other people with the same name are listed at Section "Ciro Santilli's homonyms".
19th century illustration of the Journey to the West protagonist Sun Wukong
. Source. Sun Wukong (孙悟空) is a playful and obscenely powerful monkey Journey to the West. He protects Buddhist monk Tang Sanzang, and likes eating fruit, just like Ciro. Oh, and Goku from Dragon Ball is based on him. His japanese name is "Sun Wukong" (same Chinese characters with different Japanese pronunciation) for the love. His given name "Wukong" means literally "the one who mastered the void", which is clearly a Dharma name and fucking awesome in multiple ways. This is another sad instance of a Chinese thing better known in the West as Japanese.
It is worth noting however that although Wukong is extremely charming, Ciro's favorite novel of the Four Great Classic Novels is Water Margin. Journey to the West is just a monster of the week for kids, but Water Margin is a fight for justice saga. Sorry Wukong!
Ciro Santilli playing with a pipette at the University of Cambridge circa 2017
. The photo was taken in an open event organized by the awesome Cambridge Synthetic Biology outreach group, more or less the same people who organize: www.meetup.com/Cambridge-Synthetic-Biology-Meetup/ and who helped organize Section "How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it".
Taking part in such activities is what Ciro tries to do to overcome his lifelong regret of not having done more experimental stuff at university. Would he have had the patience to handle all the bullshit of the physical word without going back to the informational sciences? Maybe, maybe not. But now he will probably never know?!
Notice the orange high visibility cycling jersey under the lab coat, from someone who had just ridden in from work as fast as possible as part of his "lunch break". It is more fun when it is hard.
Scribe Jean Miélot, 15th century
. Ciro Santilli fantasizes that he would have make a good scribe in the middle ages, partly due to his self diagnosed graphomania, but also appreciation for foreign languages, and his mild obsession with the natural sciences.
OurBigBook.com is Ciro's view of a modern day scriptorium, except that now the illuminations are YouTube videos.
Chill and eat your bread in peace comes to mind. A scribe, in a library, reading and writing the entire day in peace and quiet. The life!
The job of a Internet-age scribe is basically that of making knowledge more open, legally extracting it from closed copyrighted sources, and explaining your understanding of it to the wider world under Creative Commons licenses on the web. And in the process of greater openness, given a well organized system, we are able combine the knowledge of many different people, and thus make things more understandable than any single/few creator closed source source could ever achieve.
Ciro Santilli waving hello in infrared.
More info at: Figure "Ciro Santilli waving hello in infrared".Based on JCVI-syn3.0, they've added a few genes back to give better phenotypes, including slightly faster duplication time. Because the development cycle time is your God is also true in biology.
As of essential metabolism for a minimal cell (2019) it had only 91 genes of unknown function! So funny.
Bibliograpy:
JCVI-syn3A during cell division by David Goodsell (2022)
Source. A description is present at: cdn.rcsb.org/pdb101/goodsell/2022_JCVI-syn3A.pdf Integrative Illustration of a JCVI-syn3A Minimal Cell by David Goodsell (2022) which describes everything in the picture.phenomena.nationalgeographic.com/2016/04/21/we-built-the-worlds-simplest-cell-but-dunno-how-it-works/ likely talks about it.
Stuff built on top:
Pinned article: Introduction to the OurBigBook Project
Welcome to the OurBigBook Project! Our goal is to create the perfect publishing platform for STEM subjects, and get university-level students to write the best free STEM tutorials ever.
Everyone is welcome to create an account and play with the site: ourbigbook.com/go/register. We belive that students themselves can write amazing tutorials, but teachers are welcome too. You can write about anything you want, it doesn't have to be STEM or even educational. Silly test content is very welcome and you won't be penalized in any way. Just keep it legal!
Intro to OurBigBook
. Source. We have two killer features:
- topics: topics group articles by different users with the same title, e.g. here is the topic for the "Fundamental Theorem of Calculus" ourbigbook.com/go/topic/fundamental-theorem-of-calculusArticles of different users are sorted by upvote within each article page. This feature is a bit like:
- a Wikipedia where each user can have their own version of each article
- a Q&A website like Stack Overflow, where multiple people can give their views on a given topic, and the best ones are sorted by upvote. Except you don't need to wait for someone to ask first, and any topic goes, no matter how narrow or broad
This feature makes it possible for readers to find better explanations of any topic created by other writers. And it allows writers to create an explanation in a place that readers might actually find it.
Figure 1. Screenshot of the "Derivative" topic page. View it live at: ourbigbook.com/go/topic/derivativeVideo 2. OurBigBook Web topics demo. Source. - local editing: you can store all your personal knowledge base content locally in a plaintext markup format that can be edited locally and published either:This way you can be sure that even if OurBigBook.com were to go down one day (which we have no plans to do as it is quite cheap to host!), your content will still be perfectly readable as a static site.
- to OurBigBook.com to get awesome multi-user features like topics and likes
- as HTML files to a static website, which you can host yourself for free on many external providers like GitHub Pages, and remain in full control
Figure 3. Visual Studio Code extension installation.
Figure 4. Visual Studio Code extension tree navigation.
Figure 5. Web editor. You can also edit articles on the Web editor without installing anything locally.Video 3. Edit locally and publish demo. Source. This shows editing OurBigBook Markup and publishing it using the Visual Studio Code extension.Video 4. OurBigBook Visual Studio Code extension editing and navigation demo. Source. 
- Infinitely deep tables of contents:
All our software is open source and hosted at: github.com/ourbigbook/ourbigbook
Further documentation can be found at: docs.ourbigbook.com
Feel free to reach our to us for any help or suggestions: docs.ourbigbook.com/#contact