Text editor: Difference between revisions

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== radian: alternative R console ==
== radian: alternative R console ==
https://github.com/randy3k/radian. Written in Python.
https://github.com/randy3k/radian. Written in Python.
* q() will not ask to save the workspace
* If we try to change the default prompt, it will lose all the features. See [https://github.com/randy3k/radian/issues/270 Update radian prompt e.g. via options() #270].


== Rmd file and R-IDE ==
== Rmd file and R-IDE ==

Revision as of 21:02, 27 June 2022

Comparison

Stack Overflow Developer Survey 2021

Platforms Pros Cons
Atom Cross built-in markdown file preview
Bluefish Cross remote file, project support crash when I try Print->Preview
Brackets Cross good for web designer
Emacs Cross split the buffers
Gedit Cross print preview (incorrect when landscape but pdf is right) no code folding
Geany Cross print preview; Terminal; split window
IntelliJ IDEA Cross
Notepad++ Win print line numbers, Right-click menu R syntax highlight not work with most themes
Qt Creator Cross split a window (even same file)
RStudio Cross folding, best IDE for R coding not support drag and drop a file but SendTo works
Sublime Cross menu -> Goto -> Bookmarks -> Toggle bookmarks (Ctrl + F2)
Typora Cross Markdown editor (Preview, TOC, LaTex)
vim Cross
Visual Studio Code Cross Integrated Terminal,

Markdown preview. Github markdown extension.

CMD+K and V to open the preview panel side by side.

"minimap" can be removed from menu -> View.


HTML editors: see here.

Atom

  • Markdown preview feature is OK but it cannot export to pdf or HTML.
  • pandoc conversion to html/PDF is not good; scripts part has no rectangle, tables have no separate lines.

Packages

To install a new package, go to Preferences -> Install -> type the package name and hit ENTER.

To remove a package, just delete the related folder. 

rm -rf ~/.atom/packages/markdown-toc
  • Markdown Preview Enhanced. It allows to view in browser (html) or export to PDF. Use r instead of R for R language syntax highlight. Another nice feature is the scrollings of the markdown file and preview are together.
  • Markdown TOC. It messes up the # sign in script blocks :( So I switch to RStudio which has a good support to create the TOC (YAML header).

Emacs

$ cat ~/.emacs
;disable backup
(setq backup-inhibited t)
;disable auto save
(setq auto-save-default nil)
(load-theme 'manoj-dark)

Gedit

  • Homebrew or Macport on Mac. Windows binary is available too.
  • To create a new tab, Ctrl + t.
  • Preferences
    • View: display line numbers, highlight current line
    • Font and colors: change to font size 14, color scheme = Cobalt
    • Plugins: External Tools
  • To split a screen, Do "Documents -> New Tab Group. No extra plugin is needed to download. I am using version 3.10.4 from Ubuntu 14.04.
  • Restore tabs plugin. It works on my gedit 3.4 (ubuntu 12.04). Follow the instruction there exactly.
  • Source code browser plugin. This makes gedit a good IDE for developing C++/Java code since the left panel can show symbols. Click F9 to show the side panel.
  • Darkmate theme.
cd /usr/share/gtksourceview-3.0/styles
sudo gedit darkermate.xml

gedit > Edit > preferences > font and colors > color scheme.

Launch from a command line

gksu gedit XXXX

Plugins

markdown preview plugin

How To Add Markdown Support To Gedit Using `Markdown Preview` Plugin

Geany

Geany can be used to run a bash script file line by line. See Debugging_Scripts.

Display special characters

Geany has a way to show special characters (Tabs/LF/CR). Edit > Preferences > Display > Tick, Show whitespace (tabs) & Show Line endings(CR/LF).

For DOS text file, the line ending is CR+LF.

For Unix text file, the line ending is LF.

Font size

Users can use either one of the following methods

  1. Edit -> Preferences -> Interface -> Fonts to adjust the font size.
  2. Keyboard bindings: Ctrl + Shift + '+' to increase the font size or Ctrl + '-' to decrease the font size. This does not affect the font size in Preferences.

Printing

The font size in Preferences affects the printing. The font size changed by using the keyboard bindings does not affect printing.

Remove vertical line

Edit -> Preferences -> Editor -> Display -> Uncheck Long line marker.

Sublime

My settings file which takes care of the scheme, font size and word wrap. 

{
	"color_scheme": "Packages/Color Scheme - Default/Monokai.sublime-color-scheme",
	"font_size": 16,
	"open_files_in_new_window": false,
	"word_wrap": true,
	"theme": "Default.sublime-theme"
}

Tips from youtube

  • View - Groups/Focus Group (^1, ^2)
    • This shortcuts are consistent with RStudio. ^1 moves to source code & ^2 moves to R console.
  • Alt key to show the menu
  • base16 color scheme (Enter)
  • select color scheme (Arrow keys to cycle through)
    • goog (Pick base16-google-dark for example)
  • install package - Cyanide theme (Enter)
  • select theme (Arrow keys to cycle through)
  • Alt (to see the menu bar) - Preference - Settings
    • Left = default settings, right = custom settings
    • change the settings (eg font size) on RHS panel.
    • "font_size": 16,
    • "highlight_line": true,
    • Ctr + s to save.
  • Ctrl+b to run the code
  • ESC to close the output pane (did not stop the run)
  • Preference - Color scheme - Monokai
  • Preference - Theme - Adaptive.sublime-theme
  • Tools - Build System - Python (or Automatic)
  • Preference - Key binding
  • C+S+p - Package Control
  • F11/fn + F11 full screen mode

License key

Preferences/settings

On my mac & Sublime Text 4 (don't add "~/" to the path), 

$ cd
$ ls "Library/Application Support/Sublime Text/Packages"                                                     
Citer           User            markupsafe      ptyprocess      pyte            pyyaml
R-IDE           backrefs        mdpopups        pygments        python-jinja2   wcmatch
SendCode        bracex          pathlib         pymdownx        python-markdown wcwidth
$ ls "Library/Application Support/Sublime Text/Packages/User"                                              
Package Control.sublime-settings Preferences.sublime-settings     SendCode.sublime-settings
Package Control.user-ca-bundle   R-IDE                            Terminus

Projects

Package Control

File explorer

standard file browser in sidebar. Go to menu View > Side Bar > Show Side Bar. Then, open windows explorer and drag the root folder into the Side Bar, The folders should now be available on the Side Bar. (it works on Sublime Text 4 macOS)

Terminus package

SendCode

  • https://github.com/randy3k/SendCode. It is not specific to R code.
  • See a screenshot Meta-Analysis in R with {metafor}
  • A guide to using R in Sublime Text. It does not mention about R-box or R-IDE.
  • SendCode will work automatically next time when I use it to send statements from an R or Rmd file. I just need to manually open Terminus window.
  • (Outdated) R-Box. R-Box is succeeded by R-IDE
    • Cannot Uninstall R-box. You could remove it manually - Run Browse Packages and then go to User/R-Box and remove the menu file. (it works)
  • In summary for a new sublime session
    • Open Terminus (Shift + CMD + p) by typing "Terminus: Open Default Shell in Tab (View)"
    • cd $ProjectFolder (can I edit Project Setting to automate this process?)
    • Type "R"
    • Open an R/Rmd file. Make sure Terminus is where "SendCode" will send code (Shift + CMD + p, SendCode: Choose Program - Terminus). Now I can use CMD + Enter to send a line or a function to Terminus.

radian: alternative R console

https://github.com/randy3k/radian. Written in Python.

Rmd file and R-IDE

  • (2021) *Scientific writing made easy - Sublime and R-IDE. This will add R-IDE to the menu bar.
    • I found when I edit an rmd file, sublime recognized it as a text file. So I need to click on the bottom right corner and select R Markdown as a language syntax. After the change, SendCode works again. Once I've done this one time, a new rmd file will be recognized as R Markdown automatically.
  • R-IDE: Make Sublime Text a perfect IDE for R
  • It seems R-IDE provides a menu to give shortcuts to render R Markdown to HTML/PDF. Many (9) menu items related to package development are grayed out for some reasons.
  • (2015, outdated) R Markdown: Syntax Highlighting for Sublime Text. Install package -> type "r-box". (Re)load Rmd files. This will add R-Box to the menu bar.
  • Compare to RStudio, R-IDE still cannot
    • Quickly jump to one chunk
    • Preview figure files in Rmd files without knitting them

Memory requirement

On my mac, it uses only 55MB when running Sublime without turning on R. So I can leave Sublime on and use it as an R console at any time.

If we use RStudio IDE with Docker, the total memory allocation used by Docker can be controlled in Docker Desktop Settings/Resource (the default is 2 GB). If we check the process com.docker.hyperkit in system monitor we can see its memory usage is close to (a litter larger than) the specified value.

Graphics Device (Quartz)

Don't 'x' the graphics window/tabs. If you x the graphics window, it will trigger *** caught segfault *** and forcibly to take one of possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace

The graphics device will be closed automatically when you exit R in Terminus.

nano editor

Build/upgrade it

wget https://www.nano-editor.org/dist/v4/nano-4.2.tar.gz
sudo nano /etc/apt/sources.list # Uncomment 'deb-src http://us.archive.ubuntu.com/ubuntu/ xenial main restricted'
                                # The source package is at 'main'. See https://packages.ubuntu.com/xenial/nano
sudo apt-get build-dep nano
sudo apt-get install libmagic-dev
tar -xzvf nano-4.2.tar.gz
cd nano-4.2
./configure --enable-utf8
make
sudo apt-get remove nano
sudo make install
# In case we want to remove the manually installed nano
# sudo apt-get autoremove nano
# sudo rm /etc/nanorc
  • Tested using nano 3.2 on CentOS 7.6.
./configure --prefix=/home/USERNAME/bin/nano
make
make install
nano  ~/.bashrc
# alias nano="~/bin/nano/bin/nano -c --softwrap"

Change as default editor

Keyboard shortcuts

Actually there is no need to memorize them because the common shortcuts are always displayed at the bottom of the screen (ctrl+g to get more).

  • Ctrl+c: cur pos
  • Ctrl+y: prev screen
  • Ctrl+v: next screen
  • Ctrl+k: cut
  • Ctrl+u: paste
  • Ctrl+w: search. Alt+w: find next occurrence
  • Ctrl+q: search backward. Alt+q: find next occurrence backward
  • Ctrl+r: insert another file at cur
  • Alt+r: search and replace
  • Alt+u (Option+u): Undo [There is a hint at bottom right, M-u where M stands for meta]. Require nano 2.3.5 (2014)
  • Alt+e (Option+e): Redo

Permission denied and sudoedit command

When I run 'nano tmp', I got a message: Error reading /home/odroid/.nano/search_history: Permission denied. Press Enter to continue. 

odroid@odroid:~$ ls -ld /home/odroid/.nano
drwxr-xr-x 2 root root 4096 Feb 12 08:01 /home/odroid/.nano
odroid@odroid:~$ ls -l /home/odroid/.nano
total 4
-rw------- 1 root root 15 Feb 12 08:01 search_history

A simple solution is 

sudo chown -R odroid:odroid /home/odroid/.nano  # note '-R' has to be capital

This seems to be a bug in nano after we use 'sudo nano [file]' (eg 'sudo nano /etc/chromium-browser/default') when the 'nano' program has not been run before.

The bottom line is use something like below for editing system files 

EDITOR=nano sudoedit /etc/chromium-browser/default

Enable soft line wrapping

nano -$ FILENAME
nano --softwrap FILENAME

Not that

  1. "-$" is the same as "--softwrap". The option "-s" has a different meaning; see below.
  2. "-s program" means to use this alternative spell checker command.
  3. these options are not available on the NIH/Biowulf. I need to use emacs/vi/joe. The keyboard shortcuts for joe can be found here.

show line number/cursor position

Use the -c option for cursor position. 

nano -c FILENAME

This does not add line numbers on the left hand side.

Show line number on the left hand side like vi & .nanorc

  • Alt/option + n (according to the help Ctrl+g where 'Alt' is the meta key (option), on mac) OR Shift + Alt + 3
  • Add set linenumbers to .nanorc to make it permanent. So my ~/.nanorc looks like 
    set linenumbers
set softwrap
include /usr/share/nano/sh.nanorc
include /usr/share/nano/c.nanorc
include ~/bin/r.nanorc

See

syntax highlight & .nanorc

Add a syntax highlight support for some languages 

$ ls /usr/share/nano/
asm.nanorc    html.nanorc  mutt.nanorc    perl.nanorc    ruby.nanorc
c.nanorc      java.nanorc  nanorc.nanorc  pov.nanorc     sh.nanorc
groff.nanorc  man.nanorc   patch.nanorc   python.nanorc  tex.nanorc
$ cat ~/.nanorc
include /usr/share/nano/sh.nanorc
include /usr/share/nano/c.nanorc
include ~/r.nanorc

Note that on mac, replace /usr/share/nano/ with /usr/local/share/nano/.

R syntax highlight file r.nanorc. Note that I have to comment out line 29 starting with 'header'. A personal copy is saved in github. Grab it using wget https://gist.githubusercontent.com/arraytools/8b52cc749c2fa6d45c16/raw/22af7ac21581604a2418875b4308a6cc65065ddd/r.nanorc -O ~/Downloads/nano-4.2/syntax/R.nanorc

Since I am using my compiled nano, my ~/.nanorc file becomes 

set linenumbers
set softwrap
include ~/Downloads/nano-4.2/syntax/sh.nanorc
include ~/Downloads/nano-4.2/syntax/c.nanorc
include ~/Downloads/nano-4.2/syntax/R.nanorc

To disable syntax highlight (useful if we use a terminal app on an Android ebook reader such as Boox), add -Ynone parameter.

Delete multiple lines

Nano does not delete lines. It only cuts lines.

ctrl + shift + 6 to mark the beginning of the block and use mouse to mark the end of the block. Hit ctrl+k to cut lines.

vim editor

One advantage over nano

When I copy text (say from a shell script), long line won't break when I paste it to a terminal. Even I copy the text from the output of "cat" command, it has the same problem.

Keys

  • quit without saving: ":q!"
  • save and quit: ":x" or ":wq" (note that ":qw" won't work; you want to write and then quit!)
  • Page down: ctrl +f. Page up: Ctrl +b
  • ^: beginning of a line. $: end of a line.
  • Moving around
    • line beginning: "0"
    • line end: "$"
    • last row: "G"
  • delete a character under the cursor: "x". Delete the remainder of line: "D". Delete entire line: "dd"
  • undo: "u"
  • search forward: "/pattern" (case sensitive). Hit "n" to repeat search.
  • Highlight search ":set hlsearch". To disable highlight ":set nohlsearch"
  • search backward: "?pattern" (case sensitive). Hit "n" to repeat search.
  • save: ":w"
  • quit: ":q"
  • Run external command ":! command"
  • Display line numbers ":set nu" or ":set number". To hide the line numbers ":set nonu" or ":set nonumber". Add "set number" to your .vimrc file in your home directory.
  • Ignore cases when searching ":set ic"

Some helps

color schemes

On my Mint 18.2, the color syntax is off. It does not work if I try to enable it.

The solution is install vim (sudo apt-get install vim). After that, the syntax highlight works automatically; no need to turn it on manually.

To change the color scheme on-the-fly, type :colorscheme then Space followed by TAB. The 'darkblue' looks cool.

The list can be found at /usr/share/vim/vimNN/colors.

On Raspbian OS , we should use the method described here. That is, sudo nano /etc/vim/vimrc and uncomment out the line containing syntax on.

plugin

On Mac, I need to run mkdir ~/.vim/plugin'. Then I can put the downloaded .vim file (e.g. R syntax highlight) there.

Also I may need to modify ~/.vimrc file by adding some options, 

syntax on
filetype plugin on

How to Install a Plugin In Vim

view: read-only mode

  • ctrl+f - forward next page
  • ctrl+b - backward
  • :q - quit

Nvim-R

neovim

micro

Theme

Write or Code Faster in Your Linux Text Editor With Custom Themes

Visual Studio Code/VS code

Change to use as the default text editor

Visual Studio Code on Linux 

xdg-mime default code.desktop text/plain

Untitled tab

New Project

File → New Window. Open folder...

Workspace

Activity Bar (User Interface): left most

This is the bar on the left hand side. See User Interface. We can toggle it use View > Appearance.

The Activity Bar on the left lets you quickly switch between Views. You can also reorder Views by dragging and dropping them on the Activity Bar or remove a View entirely (right click Hide from Activity Bar). By default, it contains Explorer, Search, Git, Debug and Extensions.

If you right click on the Activity Bar, we can see a right-click menu for several options.

The 'gear' icon at the bottom shows a bunch of shortcuts: Command Palette, Settings, Extensions, Keyboard Shortcuts, User Snippets, Color Theme, File Icon Theme and Check for Updates.

Explorer: left pane (OUTLINE view, switch open files)

https://code.visualstudio.com/docs/getstarted/userinterface#_explorer

I can use it to switch opened files through OPEN EDITORS.

It has an OUTLINE view On the left bottom corner. Useful for me to switch to any section of my document. I need to click "..." to change to sort by position.

R markdown files

How to review the outline of `.rmd` file in vs code?

Markdown preview

use the Command Palette (Ctrl+Shift+P) to run the Markdown: Open Preview to the Side command.

Tab to space conversion

How can I customize the tab-to-space conversion factor?. Take a look at the bottom right-hand side of the screen. You should see something that says Spaces or Tab-Size. For the HTML file I am editing, I need to change the spaces from the default 4 to 8. Note that the spacing of HTML file edited by using nano or vi looks the same (a tab represents 8 spaces).

Markdown TOC (table of contents) extension

https://marketplace.visualstudio.com/items?itemName=AlanWalk.markdown-toc and Github page

  1. Follow the instruction here to fix a problem of extra 'autoauto' words in TOC
    • File > Preferences > Settings
    • Filter setting by typing 'eol'
    • Make appropriate changes ('auto' to '\n')
  2. Modify the setting to start the level from 2 instead of 1. Change the anchor mode from Github to Bitbucket.

Python Extension

Docker Extension

Live Server extension

Live Server extension and github

Hide the left most pane/side bar

Use mouse to drag the boundary between two panes. Once one pane is too narrow, it will disappear.

Command palette

Ctrl + Shift + p. Or View -> Command Palette.

From there we can quickly try different color theme (use arrow key to select but do not use mouse to click). See the video VS Code - Customization.

Open a file from the command line

macOS instruction. Press "F1" or Shift + CMD + p and type "shell Command" to find the Shell Command: Install 'code' command in PATH command.

This will create a soft link file </usr/local/bin/code> which links to </Applications/Visual Studio Code.app/Contents/Resources/app/bin/code>.

Restart the terminal for the new $PATH value to take effect.

You'll be able to type code FileName in any folder to start editing files in Visual Studio Code.

Integrated Terminal

R and code remotely

  • R Extension for Visual Studio Code by Yuki Ueda
    • install.packages("languageserver") # need to install on the remote server
    • Click the brick icon on LHS & type ext:R, install R extension for VS. Or we can follow the instruction on the extension web page (1 time only on my local machine)
    • Ctrl + Shift + P (or View → Command Palette) and choose R: create R terminal
    • Select lines and Ctrl + Enter to send the code to R terminal (cursor will auto move to the next line)
    • For some reason, it just add another empty line in the source panel without sending the line.
  • https://github.com/REditorSupport/vscode-R/wiki
  • How to enable using R Programming with Visual Studio VS Code
    • Source (Ctrl + Shift + S)
    • Run selected lines (Ctrl + Enter). It works!
    • On Mac, Ctrl = CMD
  • Note it is possible to show HTML help (top right pane) by clicking R icon on the sidebar and clicking HELP PAGES -> HOME). It is also possible to use rmarkdown::run("XXX.Rmd") to show a shiny app (it's shown next to my Rmd file) in VS code.

VscodeR.png

Toggle between editor and terminal

Toggle Sidebar

Ctrl + b. Or View -> Appearance -> Toggle Side Bar.

Cloud/server IDE

Coding remotely

Notepad ++

Add line breaks in large XML file in one line

Notepad Next

Notepad Next is a Reimplementation of Notepad++ for Linux Users

Text editor with navigation

7 Best Note-Taking Tools for Programmers

http://www.makeuseof.com/tag/best-note-taking-tools-programmers/

RStudio

Code -> Insert Section

We can create different levels of sections.

Netbeans and navigator

On ODroid (ARM works too!) Ubuntu 16.04 

# Note: OpenJDK 8 will not work
# We have to install Oracle Java
sudo add-apt-repository ppa:webupd8team/java
sudo apt-get update
sudo apt-get install oracle-java8-installer

sudo apt-get install netbeans # version 8.1 in my case

See screenshots

Note:

  • Netbeans has a built-in support for HTML/XML files. XML has an advantage over HTML since HTML cannot have any tags you want.
  • We need to download a plugin for markdown file support. Go to Tools -> Plugins. In the 'Settings' tab make sure the 3 items are checked. Go to 'Available plugins' tab

search 'markdown'. Install 'Markdown support'. It works on Netbeans 8.0 on x64 Ubuntu 14.04 and Netbeans 8.1 on my ARM Ubuntu 16.04.

  • For Markdown or XML, the comment syntax can be found here.
  • For some reason, the order of headlines on the navigator pane is not the same as they appeared on the file. So it is better to use XML file format.
  • My hack on Netbeans options (change to use a dark color on background).
    • Profile: NetBeans
    • Syntax. Default: Foreground=White, Background=Dark Gray. Comment: Foreground=cyan. Keyword: Foreground=Orange.
    • Highlighting. Highlight Caret Row: Foreground=Dark Gray. Background=Pink.
  • For choosing colors, go to Google: rgb to hex
  • For some reason, it makes my graphical Mint desktop unstable. I have to use Ctrl + Alt + F1 and Ctrl + Alt + F8 to fix it temporarily. Deal breaker!

Netbeans.png NetbeansMarkdown.png

IntelliJ IDEA

It requires JDK. The community version is free. Download the tarball. Extract it and run bin/idea.sh. It even identifies a mismatch in my XML documentation that netbeans does not find.

  • Viewing Structure of a Source File or Alt + 7
  • Open a terminal at the bottom; Alt + F12
  • SOLARIZED color. Copy icls file to ~/.IdeaIC2016.2/config/colors directory. Restart Intellij IDEA. Go to File -> Settings -> Editor -> Colors & Fonts -> Font.
  • To deactivate spelling checking: Ctrl + Alt + s -> Editor -> Inspections -> Spelling -> Typo. Uncheck it.
  • We need to create a project for IntelliJ IDEA to automatically open the file we are working on. IDEA will create a hidden folder call .idea. For git repository, we shall create the .gitignore file contains
.idea/workspace.xml
.idea/misc.xml

Zim

  • Available in Linux, Windows & Mac.
  • The side panel contains a hierarchical view of the pages.
  • Right click on the page tab, we can create a new page or sub page.
  • On Ubuntu, the title bar is on the top of the desktop.
  • Auto save. Auto re-open the last session.
  • Handles several types of markup, like headings, bullet lists and of course bold, italic and highlighted. This markup is saved as wiki text so you can easily edit it with other editors.
  • Toggle notebook editable.
  • Insert image (cannot resize)
  • Plugins, e.g. Equation editor, R plot,
  • The default folder for storing the notes is ~/Notebook. Each page has its own file in storage.
~/Notebooks/Notes/
~/Notebooks/Notes/notebook.zim
~/Notebooks/Notes/Home.txt

If we create a 2nd page called 'Home2' with sub pages 'Subpage1' and 'subpage2' we will have 

~/Notebooks/Notes/Home2.txt
~/Notebooks/Notes/Home2
~/Notebooks/Notes/Home2/subpage1.txt
~/Notebooks/Notes/Home2/subpage2.txt

Cherrytree - a hierarchical note taking application

featuring rich text and syntax highlighting, storing data in a single xml or sqlite file.

Vim

with the Tagbar plugin.

The instruction works for cpp file.

Unfortunately xml files are not supported from my testing. See its wiki for supported filetypes.

Lime

Maybe

Note taking

Best Note Taking Apps for Linux (some of them are cross-platform)

Online IDEs

The 13 Best Browser IDEs Every Programmer Should Know About

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