maint: setting up on wsl2 (opensuse tumbleweed)

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

git/gitconfig

@@ -2,8 +2,7 @@
     name = Matthew Dillon
     email = matthewrdillon@gmail.com
 [core]
-    editor = vim
+    editor = nvim
-    excludesfile = /Users/matthew/.gitignore_global
 [color]
     diff = auto
     status = auto

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

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

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', '-', '<cmd>Telescope find_files<CR>', { 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 = {
+          ['<C-d>'] = cmp.mapping.scroll_docs(-4),
+          ['<C-f>'] = cmp.mapping.scroll_docs(4),
+          ['<C-Space>'] = cmp.mapping.complete(),
+          ['<C-e>'] = cmp.mapping.close(),
+          ['<CR>'] = 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)

nvim_init.vim

@@ -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', '-', '<cmd>Telescope find_files<CR>', { 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 = {
-      ['<C-d>'] = cmp.mapping.scroll_docs(-4),
-      ['<C-f>'] = cmp.mapping.scroll_docs(4),
-      ['<C-Space>'] = cmp.mapping.complete(),
-      ['<C-e>'] = cmp.mapping.close(),
-      ['<CR>'] = 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

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"

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

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-option -g default-shell $SHELL
-set -g default-command "reattach-to-user-namespace -l ${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