Cheatsheet

The commands you meet when you work on marisco with the agent

Stage 2 explains what each tool does. In the commands below, replace <...> with your own value.

Terminal

Command	What it does
pwd	Print the current folder
ls, ls -la	List the current folder. -la adds hidden files, sizes and dates
cd <folder>, cd .., cd ~	Go into a folder, up one level, or to your home folder
mkdir <folder>	Create a folder
cat <file>, less <file>	Print a file, or page through it (q quits)
cp <from> <to>, mv <from> <to>	Copy, or move or rename
rm <file>	Delete a file. There is no trash bin and no undo
which <command>	Print where the shell finds a program
Ctrl+C	Stop the running command
Up arrow, Tab	Recall the previous command, or complete a name

Git

Command	What it does
git status	Show the current branch, and the changed and staged files
git diff, git diff --staged	Show changes not yet staged, or staged changes
git log --oneline -10	Show the last 10 commits
git switch main	Go to the main branch
git switch -c <branch>	Create a branch and go to it
git add <file>	Stage a change for the next commit
git commit -m "<message>"	Record the staged changes as a commit
git push -u origin <branch>	Send a new branch to GitHub
git push	Send new commits on the current branch to GitHub
git pull	Bring in new commits from GitHub
git branch -d <branch>	Delete a branch that is already merged
git stash, git stash pop	Put uncommitted changes aside, and bring them back

These commands discard work. Approve them only when you know what they discard:

Command	What it discards
git restore <file>	Uncommitted changes to the file
git reset --hard	All uncommitted changes, in every file
git clean -fd	Files that Git does not track
git branch -D <branch>	A branch, even if it is not merged
git push --force	Commits on GitHub that your folder does not have

GitHub CLI

Command	What it does
gh issue list	List open issues
gh issue view <number>	Show an issue and its comments
gh issue create	Open a new issue
gh pr create	Open a PR for the current branch
gh pr list	List open PRs
gh pr view --web	Open the current branch’s PR in the browser
gh pr checks	Show the CI results of the current branch’s PR
gh pr checkout <number>	Get the branch of a PR, to try it out

Workspace

Command	What it does
source ~/aai-ws/.venv/bin/activate	Activate the workspace environment in this terminal
ws-sync	Pull every repository in the workspace and update the Python packages
ws-status	Show uncommitted changes in every repository of the workspace
which python	Show which Python environment is active

nbdev

Command	What it does
nbdev-export	Regenerate the package in marisco/ from the notebooks
nbdev-clean	Remove Jupyter metadata from the notebooks
nbdev-test	Run the tests of every notebook
nbdev-test <notebook>	Run the tests of one notebook
nbdev-readme	Regenerate README.md from nbs/index.ipynb

marisco

Command	What it does
marisco-ingest <handler> <output>	Encode a provider dataset as a MARIS NetCDF file
marisco-ingest <handler> <output> --src <file>	The same, for handlers that read a local file
marisco-ingest not-a-handler	List the handlers
marisco-export <file.nc>	Write one CSV file for each sample type in a NetCDF file

Claude Code

Command	What it does
claude	Start the agent in the current folder
Esc	Stop what the agent is doing
Shift+Tab	Switch permission mode: manual, accept edits, plan, auto. The status bar shows the current mode
/clear	Start a new conversation
/help	List the commands
/exit	Quit