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init.vim
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let $NVIM_TUI_ENABLE_TRUE_COLOR=1
"vim-plug instructions----------------
"Install plugins：:PlugInstall
"Update plugins：:PlugUpdate
"Remove plugins：:PlugClean (" first)
"Check the plugin status：:PlugStatus
"Upgrade vim-plug itself：:PlugUpgrade
""Plug Ins start----------------------
call plug#begin('~/.vim/plugged')
Plug 'bling/vim-airline'
Plug 'tpope/vim-fugitive'
Plug 'edkolev/promptline.vim'
Plug 'airblade/vim-gitgutter'
Plug 'ryanoasis/vim-devicons'
Plug 'preservim/nerdtree'
Plug 'tiagofumo/vim-nerdtree-syntax-highlight'
Plug 'neoclide/coc.nvim', {'branch': 'release'}
Plug 'kassio/neoterm'
Plug 'vim-pandoc/vim-pandoc'
Plug 'vim-pandoc/vim-pandoc-syntax'
Plug 'vim-pandoc/vim-rmarkdown'
Plug 'snakemake/snakemake', {'rtp': 'misc/vim'}
Plug 'junegunn/fzf'
Plug 'junegunn/fzf.vim'
Plug 'snakemake/snakefmt'
"Plug 'plasticboy/vim-markdown'
" Plug 'jalvesaq/Nvim-R'
call plug#end()
"Plug Ins end------------------------
" Enable transparent background, needed on mac/iterm2?
hi Normal ctermbg=none
" Select colorscheme
colorscheme cobalt
" colorscheme base16-eighties
"autocmd vimenter * ++nested colorscheme gruvbox
let g:airline_powerline_fonts = 1
set clipboard+=unnamedplus " use clipboard rather then +/* registers
set number " turn on line numbering
"set timeoutlen=50 " make mode swithcing faster
set wildmenu " visual autocomplete for command menu
" set cursorline " highlight current line
set showmatch " highlight matching [{()}]
set hlsearch " highlight matches
set splitright " vsplit on the right
set inccommand=nosplit " turn on live substitution
" move vertically by visual line
nnoremap j gj
nnoremap k gk
" incremental search
set incsearch
" backspace clears search
nmap <silent> <BS> :nohlsearch<CR>
" get rid of carets in airline
set fillchars+=stl:\ ,stlnc:\
" if neovim then map quick terminal/window navigation, and terminal mode exit
" if neovim also fix terminal mode Alt+b and Alt+f line navigation and Alt+.
" for last argument
" if vim then map window navigation only
if exists(':tnoremap')
tnoremap <Esc> <C-\><C-n>
tnoremap <A-h> <C-\><C-n><C-w>h
tnoremap <A-j> <C-\><C-n><C-w>j
tnoremap <A-k> <C-\><C-n><C-w>k
tnoremap <A-l> <C-\><C-n><C-w>l
tnoremap <A-b> <Esc>b
tnoremap <A-f> <Esc>f
tnoremap <A-.> <Esc>.
nnoremap <A-h> <C-w>h
nnoremap <A-j> <C-w>j
nnoremap <A-k> <C-w>k
nnoremap <A-l> <C-w>l
else
nnoremap <Esc>h <C-w>h
nnoremap <Esc>j <C-w>j
nnoremap <Esc>k <C-w>k
nnoremap <Esc>l <C-w>l
endif
" get rid of line numbers after opening terminal in a split
autocmd TermOpen * set nonumber
" Use tab and shift-tab to cycle through windows.
nnoremap <Tab> <C-W>w
nnoremap <S-Tab> <C-W>W
" testing neovim mappings
"nnoremap <c-c><c-c> :TREPLSendLine
"nnoremap <c-c><c-c> :TREPLSendLine<CR>
nnoremap <SPACE> <Nop>
let mapleader=" "
" update: this is a problem
" it remaps delete line and insert
" nnoremap <C-s> :TREPLSendLine<CR>
" vnoremap <C-s> :TREPLSendSelection<CR>
let g:neoterm_default_mod = 'vertical'
nnoremap , :TREPLSendLine<CR>
vnoremap , :TREPLSendSelection<CR>
" set the neoterm python repl
" --no-autoindent was necessary before implementation of bracketed paste
"let g:neoterm_repl_python = 'ipython --no-autoindent'
let g:neoterm_repl_python = 'ipython'
"let g:neoterm_bracketed_paste = 1
" had to turn off bracketed paste as it breaks :TREPLSendLine in R
" use paste magic instead of the exec command (can't remember why though)
" presumably to handle the pasting of indented code
let g:neoterm_repl_ipython_magic = 1
" promptline config---------------------------
" in combination with ~/.zshrc prompts:
" PS1='%n@%m:$ '
" RPROMPT='%~'
" for changes to take effect run:
" :PromptlineSnapshot ~/.promptline.sh
" append theme is desired:
" :PromptlineSnapshot ~/.promptline.sh airline
" the file is then sourced, e.g. in ~/.zshrc
" source ~/.promptline.sh
let g:promptline_preset = {
\'b' : [ promptline#slices#user() ],
\'z' : [ promptline#slices#cwd({ 'dir_limit': 4 }) ],
\'warn' : [ promptline#slices#last_exit_code() ],
\'a' : [ '%m' ],
\'c' : [ promptline#slices#git_status(), promptline#slices#conda_env() ],
\'y' : [ promptline#slices#vcs_branch() ]}
let g:promptline_theme = {
\'a' : [188, 234],
\'b' : [231, 240],
\'c' : [188, 234],
\'x' : [188, 234],
\'y' : [231, 240],
\'z' : [188, 234],
\'warn' : [232, 166]}
"end promptline config------------------------
"coc config-----------------------------------
"inoremap <expr> <Tab> pumvisible() ? "\<C-n>" : "\<Tab>"
"inoremap <expr> <S-Tab> pumvisible() ? "\<C-p>" : "\<S-Tab>"
"coc config end-------------------------------
" use <tab> for trigger completion and navigate to the next complete item
"function! s:check_back_space() abort
" let col = col('.') - 1
" return !col || getline('.')[col - 1] =~ '\s'
"endfunction
"
"inoremap <silent><expr> <Tab>
" \ pumvisible() ? "\<C-n>" :
" \ <SID>check_back_space() ? "\<Tab>" :
" \ coc#refresh()
"
"played around with the config a lot
"for now, try autoomplete remapped to tab
"this keeps enter for new lines and prevents
"accidentally completion when begininning a newline
"cycle through completions with C-n and C-p
"inoremap <silent><expr> <tab> pumvisible() ? coc#_select_confirm() : "\<C-g>u\<TAB>"
"inoremap <silent><expr> <cr> "\<c-g>u\<CR>"
"end coc config--------------------------------
" Use tab for trigger completion with characters ahead and navigate.
" NOTE: Use command ':verbose imap <tab>' to make sure tab is not mapped by
" other plugin before putting this into your config.
inoremap <silent><expr> <TAB>
\ pumvisible() ? "\<C-n>" :
\ <SID>check_back_space() ? "\<TAB>" :
\ coc#refresh()
inoremap <expr><S-TAB> pumvisible() ? "\<C-p>" : "\<C-h>"
function! s:check_back_space() abort
let col = col('.') - 1
return !col || getline('.')[col - 1] =~# '\s'
endfunction
" Use <c-space> to trigger completion.
inoremap <silent><expr> <c-space> coc#refresh()
" Use <cr> to confirm completion, `<C-g>u` means break undo chain at current
" position. Coc only does snippet and additional edit on confirm.
" <cr> could be remapped by other vim plugin, try `:verbose imap <CR>`.
if exists('*complete_info')
inoremap <expr> <cr> complete_info()["selected"] != "-1" ? "\<C-y>" : "\<C-g>u\<CR>"
else
inoremap <expr> <cr> pumvisible() ? "\<C-y>" : "\<C-g>u\<CR>"
endif
highlight clear SignColumn " git gutter same color as background
" Send RMarkdown code chunk.
" taken from https://github.com/daler/dotfiles
" When inside a code chunk, <Leader>cd selects the chunk and sends to neoterm.
" Breaking this down...
"
" /```{<CR> -> search for chunk delimiter (recall <CR> is Enter)
" N -> find the *previous* match to ```{
" j -> move down one line from the previous match
" V -> enter visual line-select mode
" /^```\n<CR> -> select until the next chunk delimiter by itself on the line (which should be the end)
" k -> go up one line from that match so we don't include that line
" <Plug>(neoterm-repl-send)<CR> -> send the selection to the neoterm terminal
" /```{r<CR> -> go to the start of the next chunk
nmap <Leader>cd /```{<CR>NjV/```\n<CR>k<Plug>(neoterm-repl-send)<CR>/```{r<CR>
" default timeout length seems to be too short for me to use the above mapping
" had to comment this out again because it slowed down neoterm send too much
"set timeout timeoutlen=3000 ttimeoutlen=100
let g:pandoc#spell#enabled = 0
" if neovim then map quick terminal/window navigation, and terminal mode exit
" if neovim also fix terminal mode Alt+b and Alt+f line navigation and Alt+.
" for last argument
" if vim then map window navigation only
if exists(':tnoremap')
tnoremap <Esc> <C-\><C-n>
tnoremap <A-h> <C-\><C-n><C-w>h
tnoremap <A-j> <C-\><C-n><C-w>j
tnoremap <A-k> <C-\><C-n><C-w>k
tnoremap <A-l> <C-\><C-n><C-w>l
tnoremap <A-b> <Esc>b
tnoremap <A-f> <Esc>f
tnoremap <A-.> <Esc>.
nnoremap <A-h> <C-w>h
nnoremap <A-j> <C-w>j
nnoremap <A-k> <C-w>k
nnoremap <A-l> <C-w>l
else
nnoremap <Esc>h <C-w>h
nnoremap <Esc>j <C-w>j
nnoremap <Esc>k <C-w>k
nnoremap <Esc>l <C-w>l
endif
" fzf.vim shortcut for :Files
" it is a hangover from ctrlp.vim
" look at https://vim.fandom.com/wiki/Unused_keys
" consider shortcuts for :Buffers etc
nnoremap <C-p> :Files<Cr>
" Jump to open buffer
let g:fzf_buffers_jump = 1
" disable arrows for time being
" note this also disables scrolling
noremap <Up> <nop>
noremap <Down> <nop>
noremap <Left> <nop>
noremap <Right> <nop>
let g:pandoc#syntax#conceal#use = 1
let g:pandoc#syntax#codeblocks#embeds#langs = ["R=r", "bash=sh", "vim", "python"]