antidote + cleanup

install.sh

@@ -1,53 +1,36 @@
 #!/bin/bash
 
-# Make ZSH the default shell environment
-if [ `cat /etc/passwd | grep $USER | awk -F ':' '{print $7}'` != "/usr/bin/zsh" ]; then
-	echo "Changing shell to zsh"
-	chsh -s $(which zsh)
-fi
-
-# zgen Installation
-if [ ! -d "$HOME/.zgen" ]; then
-	echo "Installing zgen"
-	git clone --depth=1 https://github.com/tarjoilija/zgen.git "${HOME}/.zgen"
+if ! type zsh > /dev/null; then
+    echo "Cannnot change default shell to zsh: not installed"
 else
-	echo "zgen already exists."
+    # Make ZSH the default shell environment
+    if [ $(cat /etc/passwd | grep $USER | awk -F ':' '{print substr($7, length($7)-3)}') != "/zsh" ]; then
+        echo "Changing shell to zsh"
+        chsh -s $(which zsh)
+    fi
+
+    # Antidote Installation
+    if [ ! -d "$HOME/.antidote" ]; then
+        echo "Installing antidote"
+
+        # make sure git is installed
+        if ! type git > /dev/null; then
+            echo "Git not installed. Cannot install antidote"
+	else
+             git clone --depth=1 https://github.com/mattmc3/antidote.git $HOME/.antidote
+        fi
+
+    else
+	echo "antidote already exists."
+    fi
 fi
 
-# Conda and pip
-if [ ! -d "$HOME/conda" ]; then
-	echo "Installing Conda"
-	wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /tmp/miniconda.sh
-	bash /tmp/miniconda.sh -b -p ~/conda 
-	rm /tmp/miniconda.sh
-	echo "yes" | conda install pip
-else
-	echo "Conda already installed"
-fi
-
-# Marker
-if [ ! -d "$HOME/.marker" ]; then
-	echo "Installing Marker"
-	git clone --depth=1 https://github.com/pindexis/marker $HOME/.marker
-	$HOME/.marker/install.py
-fi
-
-# fasd 
-if [ ! -d "$HOME/bin" ]; then
-	mkdir -p $HOME/bin
-fi
-if [ ! -f "$HOME/bin/fasd" ]; then
-	echo "Installing fasd"
-	wget https://raw.githubusercontent.com/clvv/fasd/master/fasd
-	mv fasd $HOME/bin/fasd
-	chmod +x $HOME/bin/fasd
-fi
 
 # vundle
 if [ ! -d "$HOME/.vim/bundle" ]; then
+    echo "setup vundle"
     git clone https://github.com/VundleVim/Vundle.vim.git ~/.vim/bundle/Vundle.vim
 fi
 
 # linking dotfiles
 $HOME/.dotfiles/dotfiles.sh link base  
-

profiles/base/.aliases

@@ -1,38 +1,3 @@
 # aliases
-if [ -f .cargo/bin/bat ]; then
-    alias cat='bat'
-fi	
 alias clip='xsel --clipboard'
-alias groclean='rm \#*'
-alias latexclean='for i in `*aux *bbl *blg *fdb_latexmk *fls *lof *log *lot *out *synctex.gz *toc`; do rm $i; done'
 alias ls='ls --color=auto -lh'
-alias workon='source activate' # enable anaconda environ
-alias cwl="cwl-runner"
-
-function gitignore() {
-    for i in "$@"; do
-        echo $i >> .gitignore
-    done
-}
-
-# lhr
-alias squeue="ssh lcluster17 squeue"
-alias csum="ssh lcluster17 csum"
-alias csreport="ssh lcluster17 csreport"
-alias scancel="ssh lcluster17 scancel"
-
-# snakemake use all cores by default
-sm() {
-    if [[ "$*" == *"-j"* || "$*" == *"--jobs"* || "$*" == *"--cores"* ]]; then
-        snakemake $@
-    else
-        snakemake -j all $@
-    fi 
-}
-
-# extract whatever archive
-alias extract="dtrx"
-
-# faster sshfs
-#alias sshfs="sshfs -o Ciphers=arcfour,Compression=no,auto_cache"
-#alias sshfs="sshfs -o Compression=no,auto_cache"

profiles/base/.antigenrc

@@ -1,27 +0,0 @@
-antigen use oh-my-zsh
-
-# bundles
-#antigen bundle git
-#antigen bundle zsh-users/zsh-completions
-#antigen bundle pip
-#antigen bundle zsh-users/zsh-syntax-highlighting
-#antigen bundle zsh-users/zsh-history-substring-search
-
-antigen bundle command-not-found
-
-# theme
-export TERM="xterm-256color"
-DEFAULT_USER=bauer
-POWERLEVEL9K_LEFT_PROMPT_ELEMENTS=(ssh context  dir vcs anaconda)
-POWERLEVEL9K_RIGHT_PROMPT_ELEMENTS=(background_jobs status time)
-
-# Anaconda
-POWERLEVEL9K_ANACONDA_RIGHT_DELIMITER='>'
-POWERLEVEL9K_ANACONDA_LEFT_DELIMITER='<'
-POWERLEVEL9K_ANACONDA_BACKGROUND='24'
-POWERLEVEL9K_ANACONDA_FOREGROUND='111'
-
-POWERLEVEL9K_PROMPT_ON_NEWLINE=true
-antigen theme bhilburn/powerlevel9k powerlevel9k
-
-#antigen apply

profiles/base/.condarc

@@ -1,5 +0,0 @@
-channels:
-  - conda-forge
-  - salilab
-  - defaults
-channel_priority: strict

profiles/base/.environment

@@ -1,19 +1,21 @@
 #!/bin/bash
 
 # system preferences
+export TERM="xterm-256color"
 export LANG=en_US.UTF-8
 export SSH_KEY_PATH="~/.ssh/rsa_id"
 
 # Prefered programs
 export EDITOR='vim'
-export TERMINAL="terminator"
-export BROWSER="firefox"
-export PAGER='most'
-export BAT_PAGER='less'
+if type most > /dev/null; then
+    export PAGER='most'
+else
+    export PAGER='less'
+fi
 
-# Path
-export PATH="${PATH}:$HOME/.cargo/bin"
-export PATH="${PATH}:$HOME/bin" # binaries
-export PATH="${PATH}:$HOME/scripts" # scripts
-export PATH="${PATH}:$HOME/.local/bin" # python executeables
-export PATH="${PATH}:$HOME/bin/pushbullet-bash"
+
+# Change Path
+export PATH="${PATH}:$HOME/.local/bin"
+if [ -d $HOME/.cargo ]; then 
+    export PATH="${PATH}:$HOME/.cargo/bin"
+fi

profiles/base/.gitconfig

@@ -9,6 +9,7 @@
 	tool = kdiff3
 [core]
 	pager = diff-so-fancy | less --tabs=4 -RFX
+	autocrlf = input
 [alias]
 	up = !git pull --rebase --prune $@ && git submodule update --init --recursive
 	cm = !git add -A && git commit -m 

profiles/base/.local/share/marker/user_commands.txt

@@ -1,5 +0,0 @@
-cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/opt/gromacs-2019.1/ -DCMAKE_C_COMPILER=/usr/bin/gcc-4.9 -DCMAKE_CXX_COMPILER=/usr/bin/g++-4.9##gmx_compile
-git clone git@git.compbiol.bio.tu-darmstadt.de:Daniel/md-template.git sim##md-template
-git clone git@git.compbiol.bio.tu-darmstadt.de:Daniel/build_system.git {{folder}} && cd {{folder}}##build_system
-cookiecutter git@git.compbiol.bio.tu-darmstadt.de:Daniel/cookiecutter-md-template.git##cookiecutter-md-template
-cookiecutter git@git.compbiol.bio.tu-darmstadt.de:Daniel/cookiecutter-mpt.git##cookiecutter MPT

profiles/base/.zgenrc

@@ -1,46 +0,0 @@
-#!/usr/bin/zsh
-
-export TERM="xterm-256color"
-
-zmodules=(ssh directory environment git history input utility custom \
-          syntax-highlighting history-substring-search prompt completion fasd autosuggestions)
-
-ZSH_AUTOSUGGEST_STRATEGY=(history completion)
-
-DEFAULT_USER=bauer
-POWERLEVEL9K_LEFT_PROMPT_ELEMENTS=(ssh context  dir vcs anaconda)
-POWERLEVEL9K_RIGHT_PROMPT_ELEMENTS=(background_jobs status time)
-
-# Anaconda
-POWERLEVEL9K_ANACONDA_RIGHT_DELIMITER='>'
-POWERLEVEL9K_ANACONDA_LEFT_DELIMITER='<'
-POWERLEVEL9K_ANACONDA_BACKGROUND='24'
-POWERLEVEL9K_ANACONDA_FOREGROUND='111'
-
-POWERLEVEL9K_PROMPT_ON_NEWLINE=true
-
-source "${HOME}/.zgen/zgen.zsh"
-if ! zgen saved; then
-    echo "generating zgen save"
-    zgen oh-my-zsh
-
-    zgen oh-my-zsh plugins/git
-    zgen oh-my-zsh plugins/sudo
-    zgen oh-my-zsh plugins/command-not-found
-    zgen oh-my-zsh plugins/git
-    zgen oh-my-zsh plugins/debian
-
-    zgen oh-my-zsh plugins/tmux
-    zgen oh-my-zsh plugins/vundle
-    zgen oh-my-zsh plugins/ssh-agent
-    zgen oh-my-zsh plugins/copydir
-
-    zgen load zsh-users/zsh-syntax-highlighting.git
-    zgen load zsh-users/zsh-history-substring-search.git
-    zgen load tarruda/zsh-autosuggestions.git
-
-    zgen load bhilburn/powerlevel9k powerlevel9k
-    zgen save
-fi
-
-

profiles/base/.zsh_plugins.txt

@@ -0,0 +1,14 @@
+rupa/z  # jump into most used directories
+
+belak/zsh-utils path:history  # enable history
+belak/zsh-utils path:editor  # allow vim bindings
+
+# completions and suggestions
+zsh-users/zsh-history-substring-search
+zsh-users/zsh-completions  # additionally completions
+zsh-users/zsh-autosuggestions
+#ZSH_AUTOSUGGEST_STRATEGY=(history completion)
+
+# theme
+romkatv/powerlevel10k
+

profiles/base/.zshrc

@@ -1,45 +1,35 @@
-source "${HOME}/.zgenrc"
-
-# source other dotfiles
-source $HOME/.environment
-if [ -f "$HOME/.environment.local" ]; then
-    source $HOME/.environment.local
+# Enable Powerlevel10k instant prompt. Should stay close to the top of ~/.zshrc.
+# Initialization code that may require console input (password prompts, [y/n]
+# confirmations, etc.) must go above this block; everything else may go below.
+if [[ -r "${XDG_CACHE_HOME:-$HOME/.cache}/p10k-instant-prompt-${(%):-%n}.zsh" ]]; then
+  source "${XDG_CACHE_HOME:-$HOME/.cache}/p10k-instant-prompt-${(%):-%n}.zsh"
 fi
 
-# >>> conda initialize >>>
-# !! Contents within this block are managed by 'conda init' !!
-__conda_setup="$('/home/bauer/conda/bin/conda' 'shell.zsh' 'hook' 2> /dev/null)"
-if [ $? -eq 0 ]; then
-    eval "$__conda_setup"
-else
-    if [ -f "/home/bauer/conda/etc/profile.d/conda.sh" ]; then
-        . "/home/bauer/conda/etc/profile.d/conda.sh"
-    else
-        export PATH="/home/bauer/conda/bin:$PATH"
-    fi
-fi
-unset __conda_setup
-# <<< conda initialize <<<
-
-source $HOME/.aliases
-# config specific to this machine
 if [ -f $HOME/.zshrc_local ]; then
     source $HOME/.zshrc_local
 fi
 
-if [ -n "$GMXRC" ]; then
-    source $GMXRC
+ENV_FILE="$HOME/.environment"
+LOCAL_ENV_FILE="$HOME/.environment.local"
+
+ALIAS_FILE="$HOME/.aliases"
+LOCAL_ALIAS_FILE="$HOME/.aliases.local"
+
+source $ENV_FILE
+if [ -f $LOCAL_ENV_FILE ]; then
+    source $LOCAL_ENV_FILE
+fi
+source $ALIAS_FILE
+if [ -f $LOCAL_ALIAS_FILE ]; then
+    source $LOCAL_ALIAS_FILE
 fi
 
-# fasd autocompletion
-eval "$(fasd --init auto)"
 
-# marker
-[[ -s "$HOME/.local/share/marker/marker.sh" ]] && source "$HOME/.local/share/marker/marker.sh"
+source $HOME/.antidote/antidote.zsh
+antidote load
 
-# snakemake autocomplete
-#if hash snakemake 2>/dev/null; then
-#    compdef _gnu_generic snakemake
-#fi
+# To customize prompt, run `p10k configure` or edit ~/.p10k.zsh.
+[[ ! -f ~/.p10k.zsh ]] || source ~/.p10k.zsh
 
-export PATH="$HOME/.poetry/bin:$PATH"
+# vim mode
+bindkey -v

profiles/base/bin/github_http_to_ssh.sh

@@ -1,33 +0,0 @@
-#/bin/bash
-#-- Script to automate https://help.github.com/articles/why-is-git-always-asking-for-my-password
-# Modified from https://gist.github.com/m14t/3056747 to work on http/https and .git/nothing repos
-
-
-REPO_URL=`git remote -v | grep -m1 '^origin' | sed -Ene's#.*(https*://[^[:space:]]*).*#\1#p'`
-if [ -z "$REPO_URL" ]; then
-  echo "-- ERROR:  Could not identify Repo url."
-  echo "   It is possible this repo is already using SSH instead of HTTPS."
-  exit
-fi
-
-USER=`echo $REPO_URL | sed -Ene's#https*://github.com/([^/]*)/(.*)(\.git)?#\1#p'`
-if [ -z "$USER" ]; then
-  echo "-- ERROR:  Could not identify User."
-  exit
-fi
-
-REPO=`echo $REPO_URL | sed -Ene's#https*://github.com/([^/]*)/(.*)(\.git)?#\2#p'`
-if [ -z "$REPO" ]; then
-  echo "-- ERROR:  Could not identify Repo."
-  exit
-fi
-
-NEW_URL="git@github.com:$USER/$REPO.git"
-echo "Changing repo url from "
-echo "  '$REPO_URL'"
-echo "      to "
-echo "  '$NEW_URL'"
-echo ""
-CHANGE_CMD="git remote set-url origin $NEW_URL"
-`$CHANGE_CMD`
-echo "Success"