vim, git, etc.

Common workflows with git

• Use git to manage and backup your work
• Accept someone else's edits to your code
• Pull Requests
  • You cannot push your code to others
  • Ask to have your code edits accepted using a pull request (PR)

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Use git to manage and backup your work

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Accept someone else's (dvklopfenstein's) edits to your (raefcon's) code

git pull is 'git fetchthengit merge'

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Ask somebody (dvklopfenstein) to accept your (scbarrera) edits to their code

You cannot push your code to others (as a contributor)

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Ask (dvklopfenstein) to have your (scbarrera) code edits accepted using a pull request

vim

• :ls see the list of current buffers
• :reg see the current contents of your registers
• `:global/pat/normal O/insert

•  `:g/pat/norm Oinserttxt
  

• gUiw # global UPPERCASE inner(for entire word no matter cursor) word

Placing current line at top/center/bottom of screen in vim

:help scroll-cursor
:set scrolloff?
:set so?

keystroke	description
z[enter]	puts current line to top of screen
zt	puts current line to top of screen, but leave cursor in same col
z.	puts current line to center of screen
zz	puts current line to center of screen, but leave cursor in same col
z-	puts current line to bottom of screen
zb	puts current line to bottom of screen, but leave cursor in same col
z<t	z

Character based motions on the current line

• 3fa move forward to the third occurrence of character a
• ta move forward to the character just before a
• 3tx move forward to the character just before the third occurrence of character x
• Fa move backward to the character a
• Ta move backward to the character just after a
• ; repeat previous f or F or t or T motion in the same direction
• , repeat previous f or F or t or T motion in the opposite direction

Insert a line above a line that matches a pattern

:g/^def /norm O# some_comment<CR>
or in sed
$ sed -i '/^def /i # some_comment' filename.py

gpg

Checking GCC download

0. https://ftp.gnu.org/gnu/gcc/gcc-13.2.0/ # Download latest compiler
1. gpg gcc-13.2.0.tar.gz.sig # Get public key name (01234578)
2. gpg --keyserver hkps://keyserver.ubuntu.com --recv-keys 01234567 # Download public key
3. gpg gcc-13.2.0.tar.gz.sig # Look for "Good signature" this validates the download

Games

• https://vim-adventures

Links

• Learn vim script the hard way

git

• `git commit --amend -m 'Replaces last commit msg'
• git merge fast-forward vs git rebase
• Resolving a merge conflict using the command line

Undo a commit & redo

$ git commit -m "Something terribly misguided" # (0: Your Accident)
$ git reset HEAD~                              # undo commit. LEAVE FILES ALONE AS IS. Will need to redo 'git add'
[ edit files as necessary ]                    # 
$ git add .                                    # Need to redo 'git add'
$ git commit -c ORIG_HEAD                      # Commit changes, reusing old commit msg OR
$ git --amend -m 'New commit msg'              # Commit changes, using new commit msg

Pull Requests (PR)

https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/reviewing-changes-in-pull-requests/checking-out-pull-requests-locally

git fetch origin pull/$PRID/head:$BRANCHNAME  # BRANCHNAME is new branch that you want to create
git fetch origin pull/$PRID/head:$BRANCHNAME --update-head-ok  # if fatal: refusing to fetch into branch 'refs/heads/main' checked out at ...
git fetch origin pull/13/head:PR13

# Get the filenames of new files from PR (leave out the deleted files)
git --no-pager diff --diff-filter=D --name-only FETCH_HEAD $$(git merge-base FETCH_HEAD main)

Find deleted files

$ git log --diff-filter=D --summary --reverse | grep delete
$ git log --summary --reverse -- src/bin/bash_text_colors.py
$ git show [hash] -- src/bin/bash_text_colors.py | tee bash_text_colors.py
$ git checkout [hash]~1 -- src/bin/bash_text_colors.py

git show

$ git show HEX:filename

• https://stackoverflow.com/questions/424071/how-do-i-list-all-the-files-in-a-commit

$ git diff-tree --no-commit-id --name-only HEX -r # List all the files in a commit (plumbing)
$ git show --pretty="" --name-only HEX            # List all the files in a commit (porcelain)

git log

####See things missing in main that are on dvk_git Try to delete branch, dvk_git, while on branch main. But dvk_git has commits main does not. See a graph using git log of what you are missing...

$ git branch
  dvk_git
* main

$ git log --graph --left-right --cherry-pick --oneline main...dvk_git
< 3b19970 (HEAD -> main) Add copyright & clean up makefile
> 36e20e4 (origin/dvk_git, dvk_git) Added forks
>   d7ece74 (upstream/main) Merge branch 'dvk_git' of dvklopfenstein/OMICS_dev into main
|\
| > 6ce87e7 Add make target for adding upstream remote (source repo)
| > ae2b839 Add links to Instructor git flow
> fcc49d5 Merge branch 'main' of dvklopfenstein/OMICS_dev into main

Make a branch tree visual

$ git log --all --graph --decorate --oneline --simplify-by-decoration

Remotes

• https://stackoverflow.com/questions/14290113/git-pushing-code-to-two-remotes ''' $ git remote -v $ git remote add dampierlab [ssh] $ git push dampierlab main $ git push dampierlab $ git remote add both [ssh] $ git remote set-url --push both [http] '''

$ git config --list
$ git config user.name
$ git config user.email
$ git config --global user.name <user_name>
$ git config --local user.name <user_name>

git pull

https://git-scm.com/book/en/v2/Git-Branching-Rebasing

$ git pull
  git config pull.rebase false  # merge             $ git pull --no-rebase
  git config pull.rebase true   # rebase            $ git pull --rebase
  git config pull.ff only       # fast-forward only $ git pull --ff-only

Sync a forked origin to upstream

$ git remote -v
$ git remote add upstream https://github.com/whoever/repo.git
$ git fetch upstream main
$ git checkout main
$ git merge upstream/main

### Create a new repository on the command line

touch README.md git init git add README.md git commit -m "first commit" git remote add origin https://github.com/OMICS_dev.git git push -u origin main

### Backup onto a local repo

Create a bare repo, which is optimized for sharing and has no working dir

$ git init --bare ~/backup/myproject.git $ cd /path/to/existing/repo $ git remote add origin ~/backup/myproject.git $ git push origin main $ git clone ~/backup/myproject.git

### Push an existing repository from the command line

git remote add origin http://github.com/OMICS_dev.git git push -u origin main

### Branches

$ git branch -d <branch_name> # Delete local branch if it has been fully merged $ git branch -D <branch_name> # Delete local branch irrespective of its merged status $ git push <remote_name> --delete <branch_name> # or $ git push -d <remote_name> <branch_name>

## bash
### args

!^ first argument !$ last argument !* all arguments !:2 second argument

!:2-3 second to third arguments !:2-$ second to last arguments !:2* second to last arguments !:2- second to next to last arguments

!:0 the command !! repeat the previous line

## git
### How can I print a plain list of all files that were part of a given commit?
* git diff-tree --no-commit-id --name-only -r bd61ad98 # Preferred (plumbing command) programmatic
* git diff-tree --no-commit-id --name-only -r bd61ad98 # Porcelain; user facing

### List files tracked by git
* git checkout $(git ls-files -m)
* git ls-files # List files tracked by git
* git ls-files --other # List files NOT tracked by git
* git diff --name-only --diff-filter=U  # Show Unmerged files (--relative to show paths from cwd)
* git diff --check     # show the list of files containing conflict markers including line numbers.
* git diff --name-only --diff-filter=u  # Show modified, unstaged files, and only the filenames
* git diff --name-only --diff-filter=u --cached # Show modified, staged/cached files, and only the filenames
* git diff --name-only --diff-filter=AM HEAD  # list 'git status -s' filenames only

### color diff
* git diff --color-words README.md
* git diff --color-words old.txt new.txt

### If default branch on GitHub is renamed (master->main), do this on your local clone to update:
git branch -m master main
git fetch origin
git branch -u origin/main main
git remote set-head origin -a

## git plumbing
description  # Only used by GitWeb program
HEAD         # ref: refs/heads/main        Points to current branch
config
objects/     # All repo content
objects/info # All repo content
objects/pack # All repo content
refs/        # Stores pointers to commint objects (branches, tags, remotes, ...)
info/
hooks/

$ git ls-files    # Show .git/index: a sorted list of path names w/permissions and SHA1 of blob
$ git cat-file -p 4b825dc642cb6eb9a060e54bf8d69288fbee4904
$ git cat-file -s 4b825dc642cb6eb9a060e54bf8d69288fbee4904
$ git cat-file -t 4b825dc642cb6eb9a060e54bf8d69288fbee4904
$ git count-objects -v
$ git log --pretty=oneline
$ git reflog
$ git log -g
$ git gc --auto
$ git fsck --full


## git and Jupter notebooks
* http://timstaley.co.uk/posts/making-git-and-jupyter-notebooks-play-nice/ nbconvert_jq
* https://www.reviewnb.com/git-jupyter-notebook-ultimate-guide

## grep
* grep -B 10 -A 5 build README.md  # report 10 lines before and 5 lines after lines containing build
* grep -C 5 build README.md        # report  5 lines before and after lines containing build

## Bash cursor
* ctrl-a Go to beginning of line
* ctrl-e Go to end of line

## awk
gene_result.txt is from NCBI Gene search: (HIV) AND 9606[Taxonomy ID]    
("Human immunodeficiency virus 1"[Organism] OR "Human immunodeficiency virus 2"[Organism] OR "Simian-Human immunodeficiency virus"[Organism] OR HIV[All Fields]) AND 9606[Taxonomy ID] AND ("genetype protein coding"[Properties] AND alive[prop])    
* awk -F '\t' '{printf "%15-s %s\n", $6, $8}' gene_result.txt   # Print Gene Symbol and Description
* awk -F"\t" '{print $1, $2, $3, $4, $5}' notebooks/goea_0.05_*_proteincoding_partof_sig_goids.txt
* cut -f1-5 notebooks/goea_0.05_*_proteincoding_partof_sig_goids.txt

* awk '{print NR-1 "," $0}' README.md                    # print lines w/lnum prefixed (NR starts at 1)
* awk '3288<=NR && NR<=3291 {print NR-1 ": " $0}' *.sam  # print specific line numbers
* awk '3288<=NR && NR<=3291' *.sam                       # print specific line numbers
* sed -n '3288,3291p' *.sam

## find
* find ~+ -type d   # Use bash's Tilde Expansion to get the absolute path of the surrent working directory
* find . -name notebooks -exec find {} -name \*.py \;