R IDE for R statistics, data analysis and a bit of Nim

init.vim

This is the second version of my R as an IDE for stats using R. It is built on three tools: treesitter, lsp, and Nvim-R.
One has to manually run :TSInstall markdown, :TSInstall R, and :LspInstall R. Will update this with more time in the future
but the code is mostly self explaining:

```vimscript
" Installation  {{{
call plug#begin(stdpath('data') . 'vimplug')
  Plug 'EdenEast/nightfox.nvim'
  Plug 'kristijanhusak/orgmode.nvim'
  Plug 'scrooloose/nerdtree'
  Plug 'github/copilot.vim'
  Plug 'skywind3000/asynctasks.vim'
  Plug 'skywind3000/asyncrun.vim'
  Plug 'jistr/vim-nerdtree-tabs'
  Plug 'nvim-lua/plenary.nvim'
  Plug 'nvim-lua/popup.nvim'
  Plug 'nvim-telescope/telescope.nvim'
  Plug 'neovim/nvim-lspconfig'
  Plug 'kabouzeid/nvim-lspinstall'
  Plug 'glepnir/lspsaga.nvim'
  Plug 'nvim-treesitter/nvim-treesitter', {'do': ':TSUpdate'}
  Plug 'nvim-treesitter/nvim-treesitter-textobjects'
  Plug 'lifepillar/vim-mucomplete'
  Plug 'glepnir/galaxyline.nvim', { 'branch': 'main' }
  Plug 'kyazdani42/nvim-web-devicons'  " needed for galaxyline icons
  Plug 'tpope/vim-ragtag'
  Plug 'tpope/vim-surround'
  Plug 'tpope/vim-unimpaired'
  Plug 'imkmf/ctrlp-branches'
  Plug 'hara/ctrlp-colorscheme'
  Plug 'simplenote-vim/simplenote.vim'
  Plug 'tpope/vim-eunuch'
  Plug 'tpope/vim-fugitive'
  Plug 'rhysd/vim-grammarous'
  Plug 'yegappan/greplace'
  Plug 'tomtom/tcomment_vim'
  Plug 'ompugao/ctrlp-locate'
  Plug 'endel/ctrlp-filetype.vim'
  Plug 'suy/vim-ctrlp-commandline'
  Plug 'mbbill/desertex'
  Plug 'mhinz/vim-startify'
  Plug 'jalvesaq/Nvim-R'
  Plug 'metakirby5/codi.vim'
  Plug 'ctrlpvim/ctrlp.vim'
  Plug 'ryanoasis/vim-devicons'
  Plug 'tacahiroy/ctrlp-funky'
  Plug 'dbeecham/ctrlp-commandpalette.vim'
  Plug 'dense-analysis/ale'
  Plug 'https://github.com/prashanthellina/follow-markdown-links'
  Plug 'phongnh/ctrlp-fzy-matcher'
  Plug 'halkn/ripgrep.vim'
call plug#end()
 " }}}

" General settings {{{
if exists('+termguicolors')
  let &t_8f = "\<Esc>[38;2;%lu;%lu;%lum"
  let &t_8b = "\<Esc>[48;2;%lu;%lu;%lum"
  set termguicolors
endif



colorscheme duskfox

set guifont=Iosevka:h12
let g:molokai_original=1
let g:blamer_enabled = 1
let g:webdevicons_enable_ctrlp = 1
let g:disco_nobright = 1
let g:disco_red_error_only = 1
set bg=dark
let g:yui_comments = "fade"
let g:mapleader = "\<Space>"
let maplocalleader = "\<Space>"

set autochdir
set sessionoptions-=blank " This fixes a problem with nerdtree and sessions
set modelines=1
set spell
set spelllang=en
set mouse=a                   " Enable mouse support in insert mode.
set clipboard+=unnamedplus    " Use clipboard
set guioptions+=a
set backspace=indent,eol,start  " To make backscape work in all conditions.
set ma                          " To set mark a at current cursor location.
" set number                      " To switch the line numbers on.
set expandtab                   " To enter spaces when tab is pressed.
set smarttab                    " To use smart tabs.
set tabstop=2                   " Two chars for a tab
set shiftwidth=2
set autoindent                  " To copy indentation from current line
set si                          " To switch on smart indentation.
set ignorecase                  " To ignore case when searching.
set smartcase                   " When searching try to be smart about cases.
set hlsearch                    " To highlight search results.
set incsearch                   " To make search act like search in modern browsers.
set magic                       " For regular expressions turn magic on.
set showmatch                   " To show matching brackets when text indicator
set mat=2                       " How many tenths of a second to blink
syntax enable                   " Enable syntax highlighting.
set encoding=utf-8 fileencodings=ucs-bom,utf-8,gbk,gb18030,latin1 termencoding=utf-8
"set nobackup                     " Turn off backup.
"set nowb                         " Don't backup before overwriting a file.
"set noswapfile                   " Don't create a swap file.
"set ffs=unix,dos,mac             " Use Unix as the standard file type.
"au! BufWritePost $MYVIMRC source %      " auto source when writing to init.vm alternatively you can run :source $MYVIMRC
autocmd CursorHold,CursorHoldI * update " Saves when changing from insert mode

set undofile " Maintain undo history between sessions
set undodir=~/.vim/undodir


" Return to last edit position when opening files
au BufReadPost * if line("'\"") > 1 && line("'\"") <= line("$") | exe "normal! g'\"" | endif

" Reload vimrc on save
au BufWritePost ~/.config/nvim/*.{vim,lua} so $MYVIMRC
"map q :quit<CR>                 " Quit with q

" FIXME: (broken) ctrl s to save
noremap  <C-S> :update<CR>
vnoremap <C-S> <C-C>:update<CR>
inoremap <C-S> <Esc>:update<CR>

" exit insert mode
" inoremap <C-c> <Esc>

" Find
map <C-f> /

" indent / deindent after selecting the text with (⇧ v), (.) to repeat.
vnoremap <Tab> >
vnoremap <S-Tab> <

" Cut, Paste, Copy
vmap <C-x> d
vmap <C-v> p
vmap <C-c> y

" Undo, Redo (broken)
nnoremap <C-z>  :undo<CR>
inoremap <C-z>  <Esc>:undo<CR>
nnoremap <C-y>  :redo<CR>
inoremap <C-y>  <Esc>:redo<CR>


  " This mapping makes Ctrl-Tab switch between tabs.
  " Ctrl-Shift-Tab goes the other way.
  noremap <C-Tab> :tabnext<CR>
  noremap <C-S-Tab> :tabprev<CR>

  map <C-t> :tabnew<cr>

  " switch between tabs with cmd+1, cmd+2,..."
  map <C-1> 1gt
  map <C-2> 2gt
  map <C-3> 3gt
  map <C-4> 4gt
  map <C-5> 5gt
  map <C-6> 6gt
  map <C-7> 7gt
  map <C-8> 8gt
  map <C-9> 9gt

  " until we have default MacVim shortcuts this is the only way to use it in
  " insert mode
  imap <C-1> <esc>1gt
  imap <C-2> <esc>2gt
  imap <C-3> <esc>3gt
  imap <C-4> <esc>4gt
  imap <C-5> <esc>5gt
  imap <C-6> <esc>6gt
  imap <C-7> <esc>7gt
  imap <C-8> <esc>8gt
  imap <C-9> <esc>9gt


set completeopt=noselect,noinsert,menuone,preview

" >> Lsp key bindings
nnoremap <silent> gd    <cmd>lua vim.lsp.buf.definition()<CR>
nnoremap <silent> <C-]> <cmd>lua vim.lsp.buf.definition()<CR>
nnoremap <silent> gD    <cmd>lua vim.lsp.buf.declaration()<CR>
nnoremap <silent> gr    <cmd>lua vim.lsp.buf.references()<CR>
nnoremap <silent> gi    <cmd>lua vim.lsp.buf.implementation()<CR>
nnoremap <silent> K     <cmd>Lspsaga hover_doc<CR>
nnoremap <silent> <C-l> <cmd>lua vim.lsp.buf.signature_help()<CR>
nnoremap <silent> <C-k> <cmd>Lspsaga diagnostic_jump_prev<CR>
nnoremap <silent> <C-j> <cmd>Lspsaga diagnostic_jump_next<CR>
nnoremap <silent> gf    <cmd>lua vim.lsp.buf.formatting()<CR>
nnoremap <silent> gn    <cmd>lua vim.lsp.buf.rename()<CR>
nnoremap <silent> ga    <cmd>Lspsaga code_action<CR>
xnoremap <silent> ga    <cmd>Lspsaga range_code_action<CR>
nnoremap <silent> gs    <cmd>Lspsaga signature_help<CR>

lua <<EOF
require("lsp")
require("treesitter")
require("statusbar")
EOF


" require("completion")
" }}}

" R configuration - Nvim-R {{{
let g:rout_follow_colorscheme = 1 " R output is highlighted with current colorscheme
let g:Rout_more_colors = 1 " R commands in R output are highlighted
let g:R_pdfviewer="evince"
" let R_show_args = 1 " show the arguments for functions with autocompletion
let g:R_objbr_opendf = 0
let g:R_objbr_openlist = 0

" let R_set_omnifunc = ["rnoweb", "rhelp", "rrst"]

autocmd VimLeave * if exists("g:SendCmdToR") && string(g:SendCmdToR) != "function('SendCmdToR_fake')" | call RQuit("nosave") | endif " exit R when you exit the vim
autocmd FileType rmd set foldmarker=```{,```
autocmd FileType rmd setlocal foldmethod=marker


vmap <Space><Space> <Plug>RDSendSelection
nmap <Space><Space> <Plug>RDSendLine


" Workaround to get auto omni completion FIXME very buggy
" from so/q/35837990/
" function! OpenCompletion()
"     if ((v:char >= 'a' && v:char <= 'z') || (v:char >= 'A' && v:char <= 'Z'))
"         call feedkeys("\<C-x>\<C-o>", 'n')
"     endif
" endfunction
"
" autocmd FileType rmd autocmd InsertCharPre * call OpenCompletion()
" autocmd FileType r autocmd InsertCharPre * call OpenCompletion()
" autocmd FileType Rmd autocmd InsertCharPre * call OpenCompletion()
" autocmd FileType R autocmd InsertCharPre * call OpenCompletion()
" }}}

" CtrlP interface {{{
if executable('rg')
  let g:ctrlp_user_command = 'rg --files %s'
  let g:ctrlp_use_caching = 0
  let g:ctrlp_working_path_mode = 'rw'
endif

let g:ctrlp_match_func = { 'match': 'fzy_matcher#match' }


let g:ctrlp_map = '<C-p>'
let g:ctrlp_cmd = 'CtrlPCommandPalette'
let g:ctrlp_extensions = ['mixed',  'line', 'filetype', 'commandline', 'colorscheme', 'funky', 'branches']
let g:ripgrep_options='--hidden
                      \ -g "!/cache/*"
                      \ -g "!/data/*"
                      \ -g "!/reports/*"
                      \ -g "!/.git/*"
                      \ -- '

let g:commandPalette = {
    \ 'Ignorecase: Toggle': 'set ignorecase!',
    \ 'File: save and close': 'wq',
    \ 'Start R':  'call StartR("R")',
    \ 'Start Object Browser': 'call RObjBrowser()',
    \ 'Start Inim':  'T inim',
    \ 'Search files': 'CtrlPMixed',
    \ 'MRU': 'CtrlPMRU',
    \ 'Search within project': 'call feedkeys(":CtrlPRg ")',
    \ 'Search in this file': 'CtrlPLine',
    \ 'Commend lines': 'TComment',
    \ 'Check grammar': 'GrammarousCheck',
    \ 'Set filetype': 'CtrlPFiletype',
    \ 'Bye!': 'qa!',
    \ 'Command history': 'call ctrlp#init(ctrlp#commandline#id())',
    \ 'Find file anywhere in system': 'CtrlPLocate',
    \ 'Colorschemes': 'CtrlPColorscheme',
    \ 'Unfold all lines': 'call feedkeys("\<Space>zR\<CR>")',
    \ 'Fold all lines': 'call feedkeys("\<Space>zM\<CR>")',
    \ 'Unfold here': 'call feedkeys("\<Space>zo\<CR>")',
    \ 'Navigate sections of this file': 'CtrlPFunkyMulti',
    \ 'Run!': 'call feedkeys("\<Space>B\<CR>")',
    \ 'More!': 'Telescope builtin',
    \ 'Branches': 'CtrlPBranches'}
let g:ctrlp_match_window = 'results:100'



set wildignore+=*/.git/*,*/.hg/*,*/.svn/*
" }}}

" Startify {{{
function! s:gitModified()
    let files = systemlist('git ls-files -m 2>/dev/null')
    return map(files, "{'line': v:val, 'path': v:val}")
endfunction

" same as above, but show untracked files, honouring .gitignore
function! s:gitUntracked()
    let files = systemlist('git ls-files -o --exclude-standard 2>/dev/null')
    return map(files, "{'line': v:val, 'path': v:val}")
endfunction

let g:startify_lists = [
        \ { 'type': 'files',     'header': ['   MRU']            },
        \ { 'type': 'sessions',  'header': ['   Sessions']       },
        \ ]
" }}}

" Nerdtree {{{
nnoremap <C-n> :NERDTreeTabsToggle<CR>
" Start NERDTree when Vim starts with a directory argument.
autocmd StdinReadPre * let s:std_in=1
autocmd VimEnter * if argc() == 1 && isdirectory(argv()[0]) && !exists('s:std_in') |
    \ execute 'NERDTree' argv()[0] | wincmd p | enew | execute 'cd '.argv()[0] | endif

"autocmd bufenter * if (winnr("$") == 1 && exists("b:NERDTree") && b:NERDTree.isTabTree()) | q | endif
" Exit Vim if NERDTree is the only window left.
autocmd BufEnter * if tabpagenr('$') == 1 && winnr('$') == 1 && exists('b:NERDTree') && b:NERDTree.isTabTree() |
    \ quit | endif
let g:NERDTreeChDirMode       = 2
" If another buffer tries to replace NERDTree, put it in the other window, and bring back NERDTree.
autocmd BufEnter * if bufname('#') =~ 'NERD_tree_\d\+' && bufname('%') !~ 'NERD_tree_\d\+' && winnr('$') > 1 |
    \ let buf=bufnr() | buffer# | execute "normal! \<C-W>w" | execute 'buffer'.buf | endif
autocmd BufWinEnter * silent NERDTreeMirror " Open the existing NERDTree on each new tab.

" }}}

" ALE {{{
let g:ale_linters = {
\   'nim': ['nimlsp', 'nimcheck'],
\   'sh': ['shellcheck']
\}

let g:ale_fixers = {
\   '*': ['remove_trailing_lines', 'trim_whitespace'],
\   'rmd': ['styler'],
\   'nim': ['nimpretty'],
\}

let g:ale_fix_on_save = 1
let g:ale_linters_explicit = 1
let g:ale_set_loclist = 0
let g:ale_set_quickfix = 1
let g:ale_lint_on_text_changed = 'never'
let g:ale_lint_on_insert_leave = 0
let g:ale_fix_on_save = 1
let g:ale_sign_error = '✖✖'
let g:ale_sign_warning = '⚠⚠'
highlight ALEErrorSign guifg=Red
highlight ALEWarningSign guifg=Yellow



" }}}

" Nim configuration - asyncomplete {{{
au User asyncomplete_setup call asyncomplete#register_source({
    \ 'name': 'nim',
    \ 'whitelist': ['nim'],
    \ 'completor': {opt, ctx -> nim#suggest#sug#GetAllCandidates({start, candidates -> asyncomplete#complete(opt['name'], ctx, start, candidates)})}
    \ })
" }}}

" Nim configuration - CodeRunner and TREPL {{{

let g:CodeRunnerCommandMap = {
      \ 'nim' : 'nim c -r $fileName'
      \}


let g:code_runner_save_before_execute = 1

let g:neoterm_callbacks = {}
function! g:neoterm_callbacks.before_new()
  if winwidth('.') > 100
    let g:neoterm_default_mod = 'botright vertical'
  else
    let g:neoterm_default_mod = 'botright'
  end
endfunction



nmap <silent><leader>B <plug>CodeRunner
autocmd FileType nim nmap <leader>d :TREPLSendLine<CR>

" }}}

" Grammarous {{{
"let $PATH.=':/usr/lib64/openjdk-11/bin/'
"let $MYVIMRC='/home/luis/.config/nvim/init.vim'


"let g:SimplenoteUsername = ""
let g:SimplenotePassword = ""
" }}}

" MUCOMPLETE {{{
let g:mucomplete#enable_auto_at_startup = 1
let g:mucomplete#chains = {
            \ 'default' : ['omni', 'path', 'c-n'],
            \ }

let g:mucomplete#chains['rmd'] = {
            \ 'default' : ['user', 'path', 'uspl'],
            \ 'rmdrChunk' : ['omni', 'path'],
            \ }

" }}}

" Async Run {{{
augroup renderRmd | au!
    autocmd BufWritePost *.Rmd call Render()
  augroup end

function! Render() abort
  :AsyncTask render
endfunction

" function! Render() abort
"   :tabnew | te Rscript -e "rmarkdown::render(<afile>:p:S)"
"   :tabprev
" endfunction

let g:asyncrun_open = 6
" }}}


" Treesitter {{{
lua << EOF
local parser_config = require "nvim-treesitter.parsers".get_parser_configs()
parser_config.org = {
  install_info = {
    url = 'https://github.com/milisims/tree-sitter-org',
    revision = 'main',
    files = {'src/parser.c', 'src/scanner.cc'},
  },
  filetype = 'org',
}

require'nvim-treesitter.configs'.setup {
  -- If TS highlights are not enabled at all, or disabled via `disable` prop, highlighting will fallback to default Vim syntax highlighting
  highlight = {
    enable = true,
    disable = {'org'}, -- Remove this to use TS highlighter for some of the highlights (Experimental)
    additional_vim_regex_highlighting = {'org'}, -- Required since TS highlighter doesn't support all syntax features (conceal)
  },
  ensure_installed = {'org'}, -- Or run :TSUpdate org
}

require('orgmode').setup({
  org_agenda_files = {'~/Documents/org/*'},
  org_default_notes_file = '~/Documents/org/refile.org',
})
EOF

" }}}



" vim:foldmethod=marker:foldlevel=0
```