cheatsheets.knit

class: title-slide
count: false

.title[
  # Cheat Sheets
]
.subtitle[
  ## Open Science Tools
]

.author[
  ### Claudio Zandonella & Davide Massidda
]

.institute[

]

---
## RStudio Keyboard Shortcuts

.pull-left-50[
<table class="table" style="font-size: 15px; width: auto !important; margin-left: auto; margin-right: auto;">
 <thead>
  <tr>
   <th style="text-align:left;"> Command </th>
   <th style="text-align:left;"> Windows &amp; Linux </th>
   <th style="text-align:left;"> MacOS </th>
  </tr>
 </thead>
<tbody>
  <tr grouplength="4"><td colspan="3" style="border-bottom: 1px solid;"><strong>Basic</strong></td></tr>
<tr>
   <td style="text-align:left;padding-left: 2em;" indentlevel="1"> Run current line </td>
   <td style="text-align:left;"> Ctrl+Enter </td>
   <td style="text-align:left;"> Cmd+Return </td>
  </tr>
  <tr>
   <td style="text-align:left;padding-left: 2em;" indentlevel="1"> Jump to Word </td>
   <td style="text-align:left;"> Ctrl+Left/Right </td>
   <td style="text-align:left;"> Option+Left/Right </td>
  </tr>
  <tr>
   <td style="text-align:left;padding-left: 2em;" indentlevel="1"> Jump to Start/End </td>
   <td style="text-align:left;"> Ctrl+Home/End </td>
   <td style="text-align:left;"> Cmd+Home/End </td>
  </tr>
  <tr>
   <td style="text-align:left;padding-left: 2em;" indentlevel="1"> Delete Line </td>
   <td style="text-align:left;"> Ctrl+D </td>
   <td style="text-align:left;"> Cmd+D </td>
  </tr>
  <tr grouplength="8"><td colspan="3" style="border-bottom: 1px solid;"><strong>Life Hack</strong></td></tr>
<tr>
   <td style="text-align:left;padding-left: 2em;" indentlevel="1"> Insert assignment operator </td>
   <td style="text-align:left;"> Alt+- </td>
   <td style="text-align:left;"> Option+- </td>
  </tr>
  <tr>
   <td style="text-align:left;padding-left: 2em;" indentlevel="1"> Insert pipe operator </td>
   <td style="text-align:left;"> Ctrl+Shift+M </td>
   <td style="text-align:left;"> Cmd+Shift+M </td>
  </tr>
  <tr>
   <td style="text-align:left;padding-left: 2em;" indentlevel="1"> Comment/uncomment </td>
   <td style="text-align:left;"> Ctrl+Shift+C </td>
   <td style="text-align:left;"> Cmd+Shift+C </td>
  </tr>
  <tr>
   <td style="text-align:left;padding-left: 2em;" indentlevel="1"> Reflow Comment </td>
   <td style="text-align:left;"> Ctrl+Shift+/ </td>
   <td style="text-align:left;"> Cmd+Shift+/ </td>
  </tr>
  <tr>
   <td style="text-align:left;padding-left: 2em;" indentlevel="1"> Reformat Selection </td>
   <td style="text-align:left;"> Ctrl+Shift+A </td>
   <td style="text-align:left;"> Cmd+Shift+A </td>
  </tr>
  <tr>
   <td style="text-align:left;padding-left: 2em;" indentlevel="1"> Find in Files </td>
   <td style="text-align:left;"> Ctrl+Shift+F </td>
   <td style="text-align:left;"> Cmd+Shift+F </td>
  </tr>
  <tr>
   <td style="text-align:left;padding-left: 2em;" indentlevel="1"> Show help for function at cursor </td>
   <td style="text-align:left;"> F1 </td>
   <td style="text-align:left;"> F1 </td>
  </tr>
  <tr>
   <td style="text-align:left;padding-left: 2em;" indentlevel="1"> Check Spelling </td>
   <td style="text-align:left;"> F7 </td>
   <td style="text-align:left;"> F7 </td>
  </tr>
</tbody>
</table>

]
.pull-right-50[
<table class="table" style="font-size: 15px; width: auto !important; margin-left: auto; margin-right: auto;">
 <thead>
  <tr>
   <th style="text-align:left;"> Command </th>
   <th style="text-align:left;"> Windows &amp; Linux </th>
   <th style="text-align:left;"> MacOS </th>
  </tr>
 </thead>
<tbody>
  <tr grouplength="4"><td colspan="3" style="border-bottom: 1px solid;"><strong>Pro Tricks</strong></td></tr>
<tr>
   <td style="text-align:left;padding-left: 2em;" indentlevel="1"> Move Lines Up/Down </td>
   <td style="text-align:left;"> Alt+Up/Down </td>
   <td style="text-align:left;"> Option+Up/Down </td>
  </tr>
  <tr>
   <td style="text-align:left;padding-left: 2em;" indentlevel="1"> Copy Lines Up/Down </td>
   <td style="text-align:left;"> Shift+Alt+Up/Down </td>
   <td style="text-align:left;"> Cmd+Option+Up/Down </td>
  </tr>
  <tr>
   <td style="text-align:left;padding-left: 2em;" indentlevel="1"> Add Cursor Above/below </td>
   <td style="text-align:left;"> Ctrl+Alt+Up/Down </td>
   <td style="text-align:left;"> Ctrl+Option+Up/Down </td>
  </tr>
  <tr>
   <td style="text-align:left;padding-left: 2em;" indentlevel="1"> Add Cursor Selection </td>
   <td style="text-align:left;"> Alt+mouse selction </td>
   <td style="text-align:left;"> Option+mouse selction </td>
  </tr>
  <tr grouplength="2"><td colspan="3" style="border-bottom: 1px solid;"><strong>RMarkdown</strong></td></tr>
<tr>
   <td style="text-align:left;padding-left: 2em;" indentlevel="1"> Knit Document </td>
   <td style="text-align:left;"> Ctrl+Shift+K </td>
   <td style="text-align:left;"> Cmd+Shift+K </td>
  </tr>
  <tr>
   <td style="text-align:left;padding-left: 2em;" indentlevel="1"> Insert R chunk </td>
   <td style="text-align:left;"> Ctrl+Alt+I </td>
   <td style="text-align:left;"> Command+Option+I </td>
  </tr>
  <tr grouplength="4"><td colspan="3" style="border-bottom: 1px solid;"><strong>Devtools</strong></td></tr>
<tr>
   <td style="text-align:left;padding-left: 2em;" indentlevel="1"> Load All </td>
   <td style="text-align:left;"> Ctrl+Shift+L </td>
   <td style="text-align:left;"> Cmd+Shift+L </td>
  </tr>
  <tr>
   <td style="text-align:left;padding-left: 2em;" indentlevel="1"> Test Package </td>
   <td style="text-align:left;"> Ctrl+Shift+T </td>
   <td style="text-align:left;"> Cmd+Shift+T </td>
  </tr>
  <tr>
   <td style="text-align:left;padding-left: 2em;" indentlevel="1"> Document Package </td>
   <td style="text-align:left;"> Ctrl+Shift+D </td>
   <td style="text-align:left;"> Cmd+Shift+D </td>
  </tr>
  <tr>
   <td style="text-align:left;padding-left: 2em;" indentlevel="1"> Insert Roxygen Skeleton </td>
   <td style="text-align:left;"> Ctrl+Alt+Shift+R </td>
   <td style="text-align:left;"> Cmd+Option+Shift+R </td>
  </tr>
</tbody>
</table>

]

---
## Bash Cheatsheet

.pull-left-70[
.code-size-12[
```bash
#----    Navigating    ----#

pwd                       # Print working directory
cd      <directory>       # Change directory
ls      <directory>       # List files
    -l   # Long list with details
    -a   # List also hidden files and directories
    -h   # Return file size in readable units

#----    Modifying    ----#

mkdir   <directory>       # Create directory
touch   <file>            # Create file
mv      <source><dest>    # Move (or rename) file or directory
cp      <source><dest>    # Copy file 
    -r   # For directories
rm      <file>            # Remove file
rmdir   <directory>       # Remove directory

#-----   Other    -----#

echo    <message>         # Print message in console
cat     <file>            # Print file in console
less    <file>            # Open file in a screen
```
]
]

---
## Git Cheatsheet

.move-up-30[
.pull-left-50[
.code-small[
```bash
#----    Configure Settings    ----#

git config --list         # Check configuration settings

git config --global user.name "<My Name>"          # Configure username
git config --global user.email "<user@email.com>"  # Configure email
git config --global merge.conflictstyle diff3      # Configure conflict style

#----    Initialize Git Repo    ----#

git init <path>             # Initialize local repository
git clone <repository-URL>  # Clone remote repository

#----    Tracking Files    ----#

git status               # Check repository status

# Staging
git add <files>          # Add selected files to staging area
git add --all            # Add all files to staging area

git rm --cached <file>   # Remove selected files from staging area
git reset                # Remove all files from staging area

# Commit
git commit               # Create commit
    # Options
    -a               # Commit all changes of tracked files
    -m "<message>"   # Inline commit message

git log                  # Get commit history
git log --oneline        # Get commit history (compact)
```
]
]
.pull-right-50[
.code-small[
```bash
git diff                              # Changes since the last commit
git diff <commit-ID>                  # Changes since a specified commit
git diff <commit-ID-A> <commit-ID-B>  # Changes from commit-A to commit-B.

git checkout <commit-ID>  # Point HEAD to specific commit/branch
git revert <commit-ID>    # Undo commit (forward-way)
git reset <commit-ID>     # Undo commit (disruptive-way)

#----    Collaboration    ----#

git remote -v                # List remote (verbose)
git remote add <name> <url>  # Add remote

git pull <remote-name> <branch-name>  # Pull commits from remote
git push <remote-name> <branch-name>  # Push commit to remote
         -u       # Set upstream remote branch

git branch --set-upstream-to="<remote/branch>"  # Set  upstream remote branch

#----    Branching    ----#

git branch          # List branches
git branch -vv      # List branches (verbose)
git branch -vvr       # List remote branches (verbose)
    
git branch <branch-name>           # Create new branch
git checkout -b <new-branch-name>  # Create and move to new branch
    
git merge <branch-name>            # Merge target branch
git merge --abort                  # Abort merge

git branch -d <branch-name>                    # Delete local Branch
git push <remote-name> --delete <branch-name>  # Delete remote Branch

```
]
]
]

---
.pull-left-50[
## `targets` Cheatsheet

.code-size-12[

```r

# Define targets
tar_target(<target_name>, <expression>)
tar_target(<target_name>, <path-to-file>, format = "file")
tarchetypes::tar_render(
  <target_name>, <path-to-document>
  )

# Check pipeline
tar_manifest()
tar_visnetwork()

# Run analysis
tar_make()

# Load Results
tar_read()
tar_load()
```
]
]
.pull-right-50[
## `renv` Cheatsheet

.code-size-12[

```r
# Initialize project
init()

# Install package
install.packages()

# Capture dependencies
snapshot()

# Restore dependencies
restore()
```
]
]
---
## Docker Cheatsheet

.pull-left-50[
.code-small[
```bash
#----    Images    ----#

docker build -t <name-image>:<tag> .   # Build an image from Dockerfile

docker images                          # List all images
docker image ls                        # List all images
docker image rm <id-image>             # Remove Image

#----    Container    ----#

docker run --name <container-name> <image>:<tag> # Run a container from an Image
           # Other flags and options
           --rm     # Remove at exit      
           -it      # Interactive terminal
           -d       # Detached mode
           -v <host-path>:<container-path>  # Attach a volume or bind mount
           -e <name>=<value>                # Define environment variable
           -p <host-port>:<container-port>  # Map port

docker ps -a              # List all containers
docker container ls  -a     # List all containers

docker stop <container-name>    # Stop container
docker start <container-name>   # Start container
docker rm <container-name>        # Remove container

docker cp <container-name>:<path> <host-path> # Copy from container to host
docker cp <host-path> <container-name>:<path> # Copy from host to container
docker exec -it <name-container> bin/bash     # Connect to container bin/bash

```

]
]
.pull-right-50[
.code-small[
```bash
#----    Volumes    ----#

docker volume create <name-volume>  # Create named volume
docker volume ls                    # List all volumes
docker volume rm <volume id>        # Remove volume

#----   Docker Compose    ----#
docker-compose up    # Start service
docker-compose down  # Stop service

#----    Docker Hub    ----#

docker pull  <username>/<name-repo>:<tag>   # Pull image
docker push  <username>/<name-repo>         # Push image

docker login --username=<username> --email=<email@com>  # Login  
docker tag <image-id> <username>/<name-repo>:<tag> # Tag image for repository
```
]
]
---
class: inverse, center
# God Progammer Mode Achieved!