diff --git a/README.md b/README.md index c679009..1cf893e 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,31 @@ # dotfiles +## opensuse tumbleweed + +```bash +$ sudo visudo # add /opt/miniconda3/bin to secure_paths +$ sudo zypper install git libopenssl-1_1-devel tree zsh ripgrep +$ sudo zypper install -t pattern devel_C_C++ +$ sudo chsh -s $(which zsh) +$ sudo hostname rattusrattus +$ sudo systemd-tmpfiles --create +$ sudo echo "[interop]\nappendWindowsPath = false" > /etc/wsl.conf +$ git clone --origin pingo ssh://git@pingo.thermokar.st/dotfiles ~/.dotfiles +$ git clone https://github.com/chriskempson/base16-shell.git ~/.config/base16-shell +$ git clone --recursive https://github.com/sorin-ionescu/prezto.git "${ZDOTDIR:-$HOME}/.zprezto" +$ cd ~/.dotfiles +$ ./install +$ source ~/.zshrc +$ base16_ashes +$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh +$ sudo sh Miniconda3-latest-Linux-x86_64.sh -p /opt/miniconda3 -b +$ sudo conda update conda +$ wget https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py38-linux-conda.yml +$ conda env create -n q2dev --file qiime2-latest-py38-linux-conda.yml +``` + +## macos + ```bash $ wget -O gwar https://github.com/thermokarst/gwar/releases/download/0.0.1/gwar-macos $ chmod +x gwar diff --git a/git/gitconfig b/git/gitconfig index 28da453..237d112 100644 --- a/git/gitconfig +++ b/git/gitconfig @@ -2,8 +2,7 @@ name = Matthew Dillon email = matthewrdillon@gmail.com [core] - editor = vim - excludesfile = /Users/matthew/.gitignore_global + editor = nvim [color] diff = auto status = auto diff --git a/install.conf.yaml b/install.conf.yaml index d837ac9..e5a3023 100644 --- a/install.conf.yaml +++ b/install.conf.yaml @@ -10,7 +10,9 @@ - link: ~/.tmux.conf: tmux.conf ~/.gitconfig: git/gitconfig - ~/.gitignore_global: git/gitignore_global + ~/.config/git/ignore: + create: true + path: git/gitignore_global ~/.npmrc: npmrc ~/.psqlrc: psqlrc ~/.vimrc: vimrc @@ -34,4 +36,13 @@ path: kakrc ~/.config/nvim/init.vim: create: true - path: nvim_init.vim + path: nvim/init.vim + ~/.config/nvim/init.vim: + create: true + path: nvim/init.vim + ~/.config/nvim/lua/plugins.lua: + create: true + path: nvim/plugins.lua + ~/bin/safe-reattach-to-user-namespace: + create: true + path: safe-reattach-to-user-namespace.sh diff --git a/nvim/init.vim b/nvim/init.vim new file mode 100644 index 0000000..fe32b9f --- /dev/null +++ b/nvim/init.vim @@ -0,0 +1,25 @@ +" Stick with vimscript file at the moment, but prefer lua for config + +" TODO: fix this vimscript fallback +set backupdir=~/.vim-tmp +set directory=~/.vim-tmp + +lua << EOF +local set = vim.opt + +set.number = true +set.autoindent = true +set.colorcolumn = {80, 100, 120} +set.cursorline = true +set.expandtab = true +set.backup = true + +set.writebackup = true +set.list = true +set.listchars = { trail = '~', tab = '>=' } +set.mouse = 'a' +set.completeopt = { 'menu', 'menuone', 'noselect' } +set.termguicolors = true + +require('plugins') +EOF diff --git a/nvim/plugins.lua b/nvim/plugins.lua new file mode 100644 index 0000000..894e486 --- /dev/null +++ b/nvim/plugins.lua @@ -0,0 +1,141 @@ +local fn = vim.fn + +local install_path = fn.stdpath('data')..'/site/pack/packer/start/packer.nvim' + +if fn.empty(fn.glob(install_path)) > 0 then + packer_bootstrap = fn.system({ + 'git', 'clone', '--depth', '1', 'https://github.com/wbthomason/packer.nvim', install_path + }) +end + +return require('packer').startup(function() + ----------------------------------------------------------------------------- + use 'wbthomason/packer.nvim' + + ----------------------------------------------------------------------------- + use 'wakatime/vim-wakatime' + + ----------------------------------------------------------------------------- + use { + 'neovim/nvim-lspconfig', + config = function() + lspconfig = require('lspconfig') + + lspconfig.pyright.setup({ + settings = { + python = { + venvPath = "~/.conda/envs", + analysis = { + useLibraryCodeForTypes = true, + } + } + } + }) + + lspconfig.rust_analyzer.setup({}) + end, + } + + ----------------------------------------------------------------------------- + use { + 'chriskempson/base16-vim', + config = function() + vim.cmd('source ~/.vimrc_background') + vim.g.base16colorspace = 256 + end, + } + + ----------------------------------------------------------------------------- + use { + 'nvim-telescope/telescope.nvim', + requires = { + { 'nvim-lua/plenary.nvim' }, + { 'kyazdani42/nvim-web-devicons' }, + }, + config = function() + vim.api.nvim_set_keymap('n', '-', 'Telescope find_files', { noremap = true }) + end, + } + + ----------------------------------------------------------------------------- + use { 'nvim-treesitter/nvim-treesitter', run = ':TSUpdate' } + + ----------------------------------------------------------------------------- + use { + 'hrsh7th/nvim-cmp', + requires = { + { 'hrsh7th/cmp-vsnip', after = "nvim-cmp" }, + { 'hrsh7th/cmp-nvim-lsp', after = "nvim-cmp" }, + { 'hrsh7th/cmp-buffer', after = "nvim-cmp" }, + { 'hrsh7th/vim-vsnip', after = "nvim-cmp" }, + }, + config = function() + local cmp = require('cmp') + cmp.setup({ + snippet = { + expand = function(args) + vim.fn["vsnip#anonymous"](args.body) + end, + }, + mapping = { + [''] = cmp.mapping.scroll_docs(-4), + [''] = cmp.mapping.scroll_docs(4), + [''] = cmp.mapping.complete(), + [''] = cmp.mapping.close(), + [''] = cmp.mapping.confirm({ select = true }), + }, + sources = { + { name = 'nvim_lsp' }, + { name = 'vsnip' }, + { name = 'buffer' }, + } + }) + end, + } + + ----------------------------------------------------------------------------- + use { + 'lewis6991/gitsigns.nvim', + requires = { { 'nvim-lua/plenary.nvim' } }, + config = function() + require('gitsigns').setup({}) + end, + } + + ----------------------------------------------------------------------------- + use { + 'simrat39/rust-tools.nvim', + requires = { + { 'nvim-lua/popup.nvim' }, + { 'nvim-lua/plenary.nvim' }, + }, + config = function() + require('rust-tools').setup({}) + end, + } + + ----------------------------------------------------------------------------- + use { + 'GustavoKatel/sidebar.nvim', + requires = { { 'GustavoKatel/todo-comments.nvim' } }, + config = function() + require('sidebar-nvim').setup({ + side = 'right', + sections = { 'datetime', 'git-status', 'lsp-diagnostics', 'todos' } + }) + end, + } + + ----------------------------------------------------------------------------- + use { + 'famiu/feline.nvim', + config = function() + require('feline').setup({ preset = 'noicon' }) + end, + } + + ----------------------------------------------------------------------------- + if packer_bootstrap then + require('packer').sync() + end +end) diff --git a/nvim_init.vim b/nvim_init.vim deleted file mode 100644 index 23e3a34..0000000 --- a/nvim_init.vim +++ /dev/null @@ -1,120 +0,0 @@ -" Stick with vimscript at the moment, but prefer lua for config - -lua << EOF -local set = vim.opt - -set.number = true -set.autoindent = true -set.colorcolumn = {80, 100, 120} -set.cursorline = true -set.expandtab = true -set.backup = true -set.backupdir = { '~/.vim-tmp', '~/.tmp', '~/tmp', '/var/tmp', '/tmp' } -set.backupskip = { '/tmp/*', '/private/tmp/*' } -set.directory = { '~/.vim-tmp', '~/.tmp', '~/tmp', '/var/tmp', '/tmp' } -set.writebackup = true -set.list = true -set.listchars = { trail = '~', tab = '>=' } -set.mouse = 'a' -set.completeopt = { 'menu', 'menuone', 'noselect' } -set.termguicolors = true - -require('packer').startup(function() - ----------------------------------------------------------------------------- - use 'wbthomason/packer.nvim' - - ----------------------------------------------------------------------------- - use 'wakatime/vim-wakatime' - - ----------------------------------------------------------------------------- - use 'neovim/nvim-lspconfig' - require('lspconfig').pyright.setup({ - settings = { - python = { - venvPath = "~/.conda/envs", - analysis = { - useLibraryCodeForTypes = true, - } - } - } - }) - require('lspconfig').rust_analyzer.setup({}) - - ----------------------------------------------------------------------------- - use 'chriskempson/base16-vim' - vim.cmd('source ~/.vimrc_background') - vim.g.base16colorspace = 256 - - ----------------------------------------------------------------------------- - use { - 'nvim-telescope/telescope.nvim', - requires = { - { 'nvim-lua/plenary.nvim' }, - { 'kyazdani42/nvim-web-devicons' } - } - } - vim.api.nvim_set_keymap('n', '-', 'Telescope find_files', { noremap = true }) - - ----------------------------------------------------------------------------- - use { 'nvim-treesitter/nvim-treesitter', run = ':TSUpdate' } - - ----------------------------------------------------------------------------- - use 'hrsh7th/nvim-cmp' - use 'hrsh7th/cmp-nvim-lsp' - use 'hrsh7th/cmp-buffer' - use 'hrsh7th/cmp-vsnip' - use 'hrsh7th/vim-vsnip' - local cmp = require('cmp') - cmp.setup({ - snippet = { - expand = function(args) - vim.fn["vsnip#anonymous"](args.body) - end, - }, - mapping = { - [''] = cmp.mapping.scroll_docs(-4), - [''] = cmp.mapping.scroll_docs(4), - [''] = cmp.mapping.complete(), - [''] = cmp.mapping.close(), - [''] = cmp.mapping.confirm({ select = true }), - }, - sources = { - { name = 'nvim_lsp' }, - { name = 'vsnip' }, - { name = 'buffer' }, - } - }) - - ----------------------------------------------------------------------------- - use { - 'lewis6991/gitsigns.nvim', - requires = { { 'nvim-lua/plenary.nvim' } } - } - require('gitsigns').setup({}) - - ----------------------------------------------------------------------------- - use { - 'simrat39/rust-tools.nvim', - requires = { - { 'nvim-lua/popup.nvim' }, - { 'nvim-lua/plenary.nvim' } - } - } - require('rust-tools').setup({}) - - ----------------------------------------------------------------------------- - use { - 'GustavoKatel/sidebar.nvim', - requires = { { 'GustavoKatel/todo-comments.nvim' } } - } - require('sidebar-nvim').setup({ - side = 'right', - sections = { 'datetime', 'git-status', 'lsp-diagnostics', 'todos' } - }) - - ----------------------------------------------------------------------------- - use 'famiu/feline.nvim' - require('feline').setup({ preset = 'noicon' }) - -end) -EOF diff --git a/repos.toml b/repos.toml index c7f03ed..ef47db9 100644 --- a/repos.toml +++ b/repos.toml @@ -1,6 +1,6 @@ # personal [[workspace]] -path = "$HOME/Desktop/projects/personal" +path = "$HOME/projects/personal" ssh_key_path = "$HOME/.ssh/id_ecdsa" origin.base_addr = "ssh://git@pingo.thermokar.st" origin.name = "pingo" @@ -19,7 +19,7 @@ remotes = [] # personal-dokku [[workspace]] -path = "$HOME/Desktop/projects/personal" +path = "$HOME/projects/personal" ssh_key_path = "$HOME/.ssh/id_ecdsa" origin.base_addr = "ssh://git@pingo.thermokar.st" origin.name = "pingo" @@ -35,7 +35,7 @@ remotes = [ # mds [[workspace]] -path = "$HOME/Desktop/projects/mds" +path = "$HOME/projects/mds" ssh_key_path = "$HOME/.ssh/id_ecdsa" origin.base_addr = "ssh://git@pingo.thermokar.st" origin.name = "pingo" @@ -55,7 +55,7 @@ remotes = [] # github-thermokarst-personal [[workspace]] -path = "$HOME/Desktop/projects/personal" +path = "$HOME/projects/personal" ssh_key_path = "$HOME/.ssh/id_ecdsa" origin.base_addr = "ssh://git@github.com/thermokarst" origin.name = "thermokarst" @@ -66,7 +66,7 @@ remotes = [] # github-thermokarst-qiime2 [[workspace]] -path = "$HOME/Desktop/projects/qiime2" +path = "$HOME/projects/qiime2" ssh_key_path = "$HOME/.ssh/id_ecdsa" origin.base_addr = "ssh://git@github.com/thermokarst" origin.name = "thermokarst" @@ -78,7 +78,7 @@ remotes = [] # github-thermokarst-forks-qiime2 [[workspace]] -path = "$HOME/Desktop/projects/qiime2" +path = "$HOME/projects/qiime2" ssh_key_path = "$HOME/.ssh/id_ecdsa" origin.base_addr = "ssh://git@github.com/qiime2" origin.name = "qiime2" @@ -93,6 +93,7 @@ repos = [ "environment-files", "library", "logos", + "package-integration", "paper1", "paper2", "q2-alignment", @@ -150,7 +151,7 @@ remotes = [ # github-thermokarst-forks-caporaso-lab [[workspace]] -path = "$HOME/Desktop/projects/qiime2" +path = "$HOME/projects/qiime2" ssh_key_path = "$HOME/.ssh/id_ecdsa" origin.base_addr = "ssh://git@github.com/caporaso-lab" origin.name = "caporaso-lab" @@ -169,7 +170,7 @@ remotes = [ # github-thermokarst-forks-biocore [[workspace]] -path = "$HOME/Desktop/projects/qiime2" +path = "$HOME/projects/qiime2" ssh_key_path = "$HOME/.ssh/id_ecdsa" origin.base_addr = "ssh://git@github.com/biocore" origin.name = "biocore" @@ -186,7 +187,7 @@ remotes = [ # github-thermokarst-forks-bokulich-lab [[workspace]] -path = "$HOME/Desktop/projects/qiime2" +path = "$HOME/projects/qiime2" ssh_key_path = "$HOME/.ssh/id_ecdsa" origin.base_addr = "ssh://git@github.com/bokulich-lab" origin.name = "bokulich-lab" @@ -200,7 +201,7 @@ remotes = [ # github-thermokarst-forks-conda-forge [[workspace]] -path = "$HOME/Desktop/projects/qiime2" +path = "$HOME/projects/qiime2" ssh_key_path = "$HOME/.ssh/id_ecdsa" origin.base_addr = "ssh://git@github.com/conda-forge" origin.name = "conda-forge" @@ -215,7 +216,7 @@ remotes = [ # github-gregcaporaso [[workspace]] -path = "$HOME/Desktop/projects/qiime2" +path = "$HOME/projects/qiime2" ssh_key_path = "$HOME/.ssh/id_ecdsa" origin.base_addr = "ssh://git@github.com/gregcaporaso" origin.name = "gregcaporaso" diff --git a/safe-reattach-to-user-namespace.sh b/safe-reattach-to-user-namespace.sh new file mode 100755 index 0000000..c4200fd --- /dev/null +++ b/safe-reattach-to-user-namespace.sh @@ -0,0 +1,8 @@ +#!/usr/bin/env zsh + +# If reattach-to-user-namespace is not available, just run the command. +if [ -n "$(command -v reattach-to-user-namespace)" ]; then + reattach-to-user-namespace $@ +else + exec "$@" +fi diff --git a/tmux.conf b/tmux.conf index acb896e..82d47a0 100644 --- a/tmux.conf +++ b/tmux.conf @@ -1,8 +1,11 @@ +# need to set escape-time first, for wsl deploys +set -sg escape-time 50 setw -g automatic-rename -set-option -g default-shell /bin/zsh -set -g default-command "reattach-to-user-namespace -l ${SHELL}" +set-option -g default-shell $SHELL +# set -g default-command "~/bin/safe-reattach-to-user-namespace -l ${SHELL}" set -g default-terminal "screen-256color" +set -ga terminal-overrides ",xterm-256color*:Tc" set -g prefix C-a unbind C-b @@ -37,7 +40,6 @@ set -g status-right '\ #[fg=white,bg=default]%a %l:%M:%S %p#[default] #[fg=blue]%Y-%m-%d' set-option -g renumber-windows on -set -sg escape-time 0 set-option -g destroy-unattached 'off' # Enable mouse control (clickable windows, panes, resizable panes) @@ -45,5 +47,6 @@ set -g mouse on bind-key -T copy-mode-vi 'v' send -X begin-selection bind-key -T copy-mode-vi 'y' send -X copy-selection-and-cancel +# NOTE: the following line is for macos, but its presence doesnt seem to be a prob. on linux bind-key -T copy-mode-vi 'y' send-keys -X copy-pipe-and-cancel 'reattach-to-user-namespace pbcopy' bind-key p paste-buffer