.vimrc

call plug#begin()
 " Plug 'dracula/vim'
 " Visual
 Plug 'morhetz/gruvbox'
 Plug 'vim-airline/vim-airline'
 Plug 'vim-airline/vim-airline-themes'
 " Stuff I like
 Plug 'ryanoasis/vim-devicons'
 Plug 'mhinz/vim-startify'
 Plug 'preservim/nerdtree'
 Plug 'neoclide/coc.nvim', {'branch': 'release'}
 Plug 'pappasam/coc-jedi', { 'do': 'yarn install --frozen-lockfile && yarn build', 'branch': 'main' }
 Plug 'LukeGoodsell/nextflow-vim'
call plug#end()

map <SPACE> <leader>
set expandtab
set ts=4 sw=4
set guifont=fonts-hack-ttf
set modelines=5
let g:airline_theme='simple'
let g:deoplete#enable_at_startup = 1
:inoremap jk <Esc>
:inoremap kj <Esc>
:vnoremap jk <Esc>
:vnoremap kj <Esc>
nnoremap <C-Left> :tabprevious<CR>
nnoremap <C-Right> :tabnext<CR>
nnoremap <leader>a :! git add %
nnoremap <leader>f :vim <C-R>" * <CR>
:map <C-t> :NERDTree <CR>
:map <leader>t :tabnew <CR>
:map <leader>gd :w !diff % - <CR>
nnoremap <leader>p "+p
vnoremap <leader>p "+p
nnoremap <leader>P "+P
vnoremap <leader>P "+P
nnoremap <leader>y "+y
vnoremap <leader>y "+y
nnoremap <leader>Y "+y$

"Run command based on filetype!
"
autocmd FileType groovy nnoremap <F10> :w<CR>:!groovy %<CR>
autocmd FileType python nnoremap <F10> :w<CR>:!python %<CR>
autocmd FileType bash nnoremap <F10> :w<CR>:!bash %<CR>
autocmd FileType sh nnoremap <F10> :w<CR>:!bash %<CR>
autocmd FileType md nnoremap <F10> :w<CR>:!bat %<CR>

autocmd FileType python nnoremap <F8> :w<CR>:!pylint -j2 %<CR>
" Run pylint on save for Python files
autocmd BufWritePost *.py !pylint %
autocmd BufWritePost *.groovy !npm-groovy-lint -l error error --failon error % | sed 's/\x1B\[[0-9;]*[mGKH]//g' -
"
"Copilot mappings for vim

inoremap <silent><script><expr> <PageUp> copilot#Previous()
inoremap <silent><script><expr> <PageDown> copilot#Next()
inoremap <silent><script><expr> <Home> copilot#Accept()
inoremap <silent><script><expr> <End> copilot#Dismiss()
"
inoremap <silent><script><expr> <'-Space> copilot#Trigger()
"
" use <tab> to trigger completion and navigate to the next complete item
function! CheckBackspace() abort
  let col = col('.') - 1
  return !col || getline('.')[col - 1]  =~# '\s'
endfunction

inoremap <silent><expr> <Tab>
      \ coc#pum#visible() ? coc#pum#next(1) :
      \ CheckBackspace() ? "\<Tab>" :
      \ coc#refresh()

function Escape()
  if pumvisible()
    return "\<c-e>"
  else
    call feedkeys("\<esc>","nit")
    return ""
  endif
endfunction

" For local replace
"nnoremap gr gd[{V%::s/\<C-R>///gc<left><left><left>

" For global replace
"nnoremap gR gD:%s/\<C-R>///gc<left><left><left>
"
" Navigate the complete menu items like CTRL+n / CTRL+p would.
"inoremap <expr> <Tab> pumvisible() ? "<C-n>" :"<Tab>"
"inoremap <expr> <S-Tab> pumvisible() ? "<C-p>" :"<S-Tab>"

" Select the complete menu item like CTRL+y would.
"inoremap <expr> <CR> pumvisible() ? "<C-y>" :"<CR>"

" Cancel the complete menu item like CTRL+e would.
"inoremap <expr> <esc> pumvisible() ? "<C-e>" : Escape()
"
"
" color schemes
 if (has("termguicolors"))
 set termguicolors
 endif
 syntax enable
" colorscheme evening
"colorscheme dracula
"colorscheme gruvbox
autocmd vimenter * ++nested colorscheme gruvbox
"open new split panes to right and below

set splitright
set splitbelow

set nocompatible            " disable compatibility to old-time vi
set showmatch               " show matching 
set ignorecase              " case insensitive 
set mouse=v                 " middle-click paste with 
set hlsearch                " highlight search 
set incsearch               " incremental search
set tabstop=4               " number of columns occupied by a tab 
set softtabstop=4           " see multiple spaces as tabstops so <BS> does the right thing
set expandtab               " converts tabs to white space
set shiftwidth=4            " width for autoindents
set autoindent              " indent a new line the same amount as the line just typed
set number                  " add line numbers
set wildmode=longest,list   " get bash-like tab completions
set cc=80                  " set an 80 column border for good coding style
filetype plugin indent on   "allow auto-indenting depending on file type
syntax on                   " syntax highlighting
set mouse=a                 " enable mouse click
set clipboard=unnamedplus   " using system clipboard
filetype plugin on
set cursorline              " highlight current cursorline
set ttyfast                 " Speed up scrolling in Vim
" set spell                 " enable spell check (may need to download language package)
" set noswapfile            " disable creating swap file
" set backupdir=~/.cache/vim " Directory to store backup files.

" Set internal encoding of vim, not needed on neovim, since coc.nvim using some
" unicode characters in the file autoload/float.vim
set encoding=utf-8 " TextEdit might fail if hidden is not set.  set hidden Some servers have issues with backup files, see #649.  set nobackup set nowritebackup Give more space for displaying messages.  set cmdheight=2 Having longer updatetime (default is 4000 ms = 4 s) leads to noticeable delays and poor user experience.  set updatetime=300

" Don't pass messages to |ins-completion-menu|.
set shortmess+=c

" Always show the signcolumn, otherwise it would shift the text each time
" diagnostics appear/become resolved.
if has("nvim-0.5.0") || has("patch-8.1.1564")
  " Recently vim can merge signcolumn and number column into one
  set signcolumn=number
else
  set signcolumn=yes
endif

function! AddGngsTags()
    let gngs_tags = "/home/alex/vcgs/groovy-ngs-utils/src/tags"
    if filereadable(gngs_tags)
      execute "set tags+=" . gngs_tags
    endif
endfunction

function! AddCamelTags()
    let camel_tags = "/home/alex/vcgs/giphub/camelpack/src/tags"
    if filereadable(camel_tags)
      execute "set tags+=" . camel_tags
    endif
endfunction

function! LsCopiedPath()
    " Get the path from the default register
    let path = getreg('"')

    " Call the 'ls' command with the path as an argument
    execute 'ls ' . shellescape(path)
endfunction

" May need for Vim (not Neovim) since coc.nvim calculates byte offset by count
" utf-8 byte sequence
set encoding=utf-8
" Some servers have issues with backup files, see #649
"set nobackup
"set nowritebackup

" Having longer updatetime (default is 4000 ms = 4s) leads to noticeable
" delays and poor user experience
set updatetime=300

" Always show the signcolumn, otherwise it would shift the text each time
" diagnostics appear/become resolved
set signcolumn=yes

" Use tab for trigger completion with characters ahead and navigate
" NOTE: There's always complete item selected by default, you may want to enable
" no select by `"suggest.noselect": true` in your configuration file
" 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>
      \ coc#pum#visible() ? coc#pum#next(1) :
      \ CheckBackspace() ? "\<Tab>" :
      \ coc#refresh()
inoremap <expr><S-TAB> coc#pum#visible() ? coc#pum#prev(1) : "\<C-h>"

" Make <CR> to accept selected completion item or notify coc.nvim to format
" <C-g>u breaks current undo, please make your own choice
inoremap <silent><expr> <CR> coc#pum#visible() ? coc#pum#confirm()
                              \: "\<C-g>u\<CR>\<c-r>=coc#on_enter()\<CR>"

function! CheckBackspace() abort
  let col = col('.') - 1
  return !col || getline('.')[col - 1]  =~# '\s'
endfunction

" Use <c-space> to trigger completion
if has('nvim')
  inoremap <silent><expr> <c-space> coc#refresh()
else
  inoremap <silent><expr> <c-@> coc#refresh()
endif

" Use `[g` and `]g` to navigate diagnostics
" Use `:CocDiagnostics` to get all diagnostics of current buffer in location list
nmap <silent> [g <Plug>(coc-diagnostic-prev)
nmap <silent> ]g <Plug>(coc-diagnostic-next)

" GoTo code navigation
nmap <silent> gd <Plug>(coc-definition)
nmap <silent> gy <Plug>(coc-type-definition)
nmap <silent> gi <Plug>(coc-implementation)
nmap <silent> gr <Plug>(coc-references)

" Use K to show documentation in preview window
nnoremap <silent> K :call ShowDocumentation()<CR>

function! ShowDocumentation()
  if CocAction('hasProvider', 'hover')
    call CocActionAsync('doHover')
  else
    call feedkeys('K', 'in')
  endif
endfunction

" Highlight the symbol and its references when holding the cursor
" autocmd CursorHold * silent call CocActionAsync('highlight')

" Symbol renaming
nmap <space>rn <Plug>(coc-rename)

" Formatting selected code
xmap <space>f  <Plug>(coc-format-selected)
nmap <space>f  <Plug>(coc-format-selected)

augroup mygroup
  autocmd!
  " Setup formatexpr specified filetype(s)
  autocmd FileType typescript,json setl formatexpr=CocAction('formatSelected')
  " Update signature help on jump placeholder
  autocmd User CocJumpPlaceholder call CocActionAsync('showSignatureHelp')
augroup end

" Applying code actions to the selected code block
" Example: `<leader>aap` for current paragraph
xmap <leader>a  <Plug>(coc-codeaction-selected)
nmap <leader>a  <Plug>(coc-codeaction-selected)

" Remap keys for applying code actions at the cursor position
nmap <leader>ac  <Plug>(coc-codeaction-cursor)
" Remap keys for apply code actions affect whole buffer
nmap <leader>as  <Plug>(coc-codeaction-source)
" Apply the most preferred quickfix action to fix diagnostic on the current line
nmap <leader>qf  <Plug>(coc-fix-current)

" Remap keys for applying refactor code actions
nmap <silent> <leader>re <Plug>(coc-codeaction-refactor)
xmap <silent> <leader>r  <Plug>(coc-codeaction-refactor-selected)
nmap <silent> <leader>r  <Plug>(coc-codeaction-refactor-selected)

" Run the Code Lens action on the current line
nmap <leader>cl  <Plug>(coc-codelens-action)

" Map function and class text objects
" NOTE: Requires 'textDocument.documentSymbol' support from the language server
xmap if <Plug>(coc-funcobj-i)
omap if <Plug>(coc-funcobj-i)
xmap af <Plug>(coc-funcobj-a)
omap af <Plug>(coc-funcobj-a)
xmap ic <Plug>(coc-classobj-i)
omap ic <Plug>(coc-classobj-i)
xmap ac <Plug>(coc-classobj-a)
omap ac <Plug>(coc-classobj-a)

" Remap <C-f> and <C-b> to scroll float windows/popups
if has('nvim-0.4.0') || has('patch-8.2.0750')
  nnoremap <silent><nowait><expr> <C-f> coc#float#has_scroll() ? coc#float#scroll(1) : "\<C-f>"
  nnoremap <silent><nowait><expr> <C-b> coc#float#has_scroll() ? coc#float#scroll(0) : "\<C-b>"
  inoremap <silent><nowait><expr> <C-f> coc#float#has_scroll() ? "\<c-r>=coc#float#scroll(1)\<cr>" : "\<Right>"
  inoremap <silent><nowait><expr> <C-b> coc#float#has_scroll() ? "\<c-r>=coc#float#scroll(0)\<cr>" : "\<Left>"
  vnoremap <silent><nowait><expr> <C-f> coc#float#has_scroll() ? coc#float#scroll(1) : "\<C-f>"
  vnoremap <silent><nowait><expr> <C-b> coc#float#has_scroll() ? coc#float#scroll(0) : "\<C-b>"
endif

" Use CTRL-S for selections ranges
" Requires 'textDocument/selectionRange' support of language server
nmap <silent> <C-s> <Plug>(coc-range-select)
xmap <silent> <C-s> <Plug>(coc-range-select)

" Add `:Format` command to format current buffer
command! -nargs=0 Format :call CocActionAsync('format')

" Add `:Fold` command to fold current buffer
command! -nargs=? Fold :call     CocAction('fold', <f-args>)

" Add `:OR` command for organize imports of the current buffer
command! -nargs=0 OR   :call     CocActionAsync('runCommand', 'editor.action.organizeImport')

" Add (Neo)Vim's native statusline support
" NOTE: Please see `:h coc-status` for integrations with external plugins that
" provide custom statusline: lightline.vim, vim-airline
set statusline^=%{coc#status()}%{get(b:,'coc_current_function','')}

" Mappings for CoCList
" Show all diagnostics
nnoremap <silent><nowait> <space>a  :<C-u>CocList diagnostics<cr>
" Manage extensions
nnoremap <silent><nowait> <space>e  :<C-u>CocList extensions<cr>
" Show commands
nnoremap <silent><nowait> <space>c  :<C-u>CocList commands<cr>
" Find symbol of current document
nnoremap <silent><nowait> <space>o  :<C-u>CocList outline<cr>
" Search workspace symbols
nnoremap <silent><nowait> <space>s  :<C-u>CocList -I symbols<cr>
" Do default action for next item
nnoremap <silent><nowait> <space>j  :<C-u>CocNext<CR>
" Do default action for previous item
nnoremap <silent><nowait> <space>k  :<C-u>CocPrev<CR>
" Resume latest coc list
nnoremap <silent><nowait> <space>p  :<C-u>CocListResume<CR>

au BufNewFile,BufRead *.nf set filetype=groovy
au BufNewFile,BufRead *.nf.test set filetype=groovy
au BufNewFile,BufRead nextflow.config set filetype=groovy
au BufNewFile,BufRead bpipe.config set filetype=groovy