Merge branch 'updates_bow' into 'master'

Updates bow

Slight delay because yesterday some things took more time than I predicted..

But I think the tips presentation is ready now :). I added the git-prompt.sh file (which comes with a git install) to the repository just to be sure we have a backup in case the file is not available in the laptops.

Other than that, I skipped the autocrlf / safecrlf config since it seems more complicated for first-time git users. Instead, I added some slides about `git add --patch` for selective commits of line changes, which I think is more useful (and easier to grasp).

Anyway, comments are welcomed.

basics/basics.tex

@@ -2,7 +2,7 @@
 
 \title{Git Basics}
 \providecommand{\myConference}{Git course}
-\providecommand{\myDate}{Monday, October 14, 2013}
+\providecommand{\myDate}{Monday, June 23, 2014}
 \author{Jeroen F. J. Laros}
 \providecommand{\myGroup}{Leiden Genome Technology Center}
 \providecommand{\myDepartment}{Department of Human Genetics}
@@ -39,6 +39,7 @@
   \bigskip
  
   \begin{lstlisting}[language=none, caption=Make a new repository.]
+    $ cd ~/projects
     $ git init
     Initialized empty Git repository in <path>/.git/
   \end{lstlisting}
@@ -186,6 +187,43 @@
   \end{lstlisting}
 \end{frame}
 
+\begin{frame}[fragile]
+  \frametitle{Undoing changes.}
+
+  Keep in mind that ``\bt{git reset}'' by default sets a staged file back to unstaged.
+  \begin{lstlisting}[language=none, caption=Unstage a file.]
+    $ git reset README
+    $ git status
+    # Changes not staged for commit:
+    #       modified:   README
+  \end{lstlisting}
+  \bigskip
+  \pause
+
+  To discard all changes in an unstaged file, you can use ``\bt{git checkout}''
+  \begin{lstlisting}[language=none, caption=Discarding changes.]
+    $ git checkout -- .
+    $ git status
+    nothing to commit, working directory clean
+  \end{lstlisting}
+  
+\end{frame}
+
+\begin{frame}[fragile]
+  \frametitle{Undoing changes.}
+
+  For now, let's commit our change and move on.
+  \bigskip
+
+  \begin{lstlisting}[language=none, caption=Adding a new version of a file.]
+    $ echo Second version. > README
+    $ git commit
+    $ git status
+    nothing to commit, working directory clean
+  \end{lstlisting}
+  \bigskip
+\end{frame}
+
 \begin{frame}[fragile]
   \frametitle{Viewing the history.}
 
@@ -193,8 +231,6 @@
   \bigskip
 
   \begin{lstlisting}[language=none, caption=The log of our project.]
-    $ git add README
-    $ git commit
     $ git log
     commit cc61ee7cd72590f3bebcc9e1ff3e9435c7f7dd28
     Author: J.F.J. Laros <j.f.j.laros@lumc.nl>
@@ -228,7 +264,7 @@
   \bigskip
   \pause
 
-  You can also use an unique prefix of this hash, usually six characters is
+  You can also use a unique prefix of this hash, usually six characters is
   enough.
 \end{frame}
 
@@ -341,6 +377,8 @@
 
     Zuotian Tatum
 
+    Wibowo Arindrarto
+
   \end{center}
 
   \vfill

tips/Makefile

+../presentation/Makefile
\ No newline at end of file

tips/beamerthemelumc.sty

+../presentation/beamerthemelumc.sty
\ No newline at end of file

tips/gen2phen_logo.eps

+../presentation/gen2phen_logo.eps
\ No newline at end of file

tips/git-prompt.sh

+# bash/zsh git prompt support
+#
+# Copyright (C) 2006,2007 Shawn O. Pearce <spearce@spearce.org>
+# Distributed under the GNU General Public License, version 2.0.
+#
+# This script allows you to see repository status in your prompt.
+#
+# To enable:
+#
+#    1) Copy this file to somewhere (e.g. ~/.git-prompt.sh).
+#    2) Add the following line to your .bashrc/.zshrc:
+#        source ~/.git-prompt.sh
+#    3a) Change your PS1 to call __git_ps1 as
+#        command-substitution:
+#        Bash: PS1='[\u@\h \W$(__git_ps1 " (%s)")]\$ '
+#        ZSH:  setopt PROMPT_SUBST ; PS1='[%n@%m %c$(__git_ps1 " (%s)")]\$ '
+#        the optional argument will be used as format string.
+#    3b) Alternatively, for a slightly faster prompt, __git_ps1 can
+#        be used for PROMPT_COMMAND in Bash or for precmd() in Zsh
+#        with two parameters, <pre> and <post>, which are strings
+#        you would put in $PS1 before and after the status string
+#        generated by the git-prompt machinery.  e.g.
+#        Bash: PROMPT_COMMAND='__git_ps1 "\u@\h:\w" "\\\$ "'
+#          will show username, at-sign, host, colon, cwd, then
+#          various status string, followed by dollar and SP, as
+#          your prompt.
+#        ZSH:  precmd () { __git_ps1 "%n" ":%~$ " "|%s" }
+#          will show username, pipe, then various status string,
+#          followed by colon, cwd, dollar and SP, as your prompt.
+#        Optionally, you can supply a third argument with a printf
+#        format string to finetune the output of the branch status
+#
+# The repository status will be displayed only if you are currently in a
+# git repository. The %s token is the placeholder for the shown status.
+#
+# The prompt status always includes the current branch name.
+#
+# In addition, if you set GIT_PS1_SHOWDIRTYSTATE to a nonempty value,
+# unstaged (*) and staged (+) changes will be shown next to the branch
+# name.  You can configure this per-repository with the
+# bash.showDirtyState variable, which defaults to true once
+# GIT_PS1_SHOWDIRTYSTATE is enabled.
+#
+# You can also see if currently something is stashed, by setting
+# GIT_PS1_SHOWSTASHSTATE to a nonempty value. If something is stashed,
+# then a '$' will be shown next to the branch name.
+#
+# If you would like to see if there're untracked files, then you can set
+# GIT_PS1_SHOWUNTRACKEDFILES to a nonempty value. If there're untracked
+# files, then a '%' will be shown next to the branch name.  You can
+# configure this per-repository with the bash.showUntrackedFiles
+# variable, which defaults to true once GIT_PS1_SHOWUNTRACKEDFILES is
+# enabled.
+#
+# If you would like to see the difference between HEAD and its upstream,
+# set GIT_PS1_SHOWUPSTREAM="auto".  A "<" indicates you are behind, ">"
+# indicates you are ahead, "<>" indicates you have diverged and "="
+# indicates that there is no difference. You can further control
+# behaviour by setting GIT_PS1_SHOWUPSTREAM to a space-separated list
+# of values:
+#
+#     verbose       show number of commits ahead/behind (+/-) upstream
+#     name          if verbose, then also show the upstream abbrev name
+#     legacy        don't use the '--count' option available in recent
+#                   versions of git-rev-list
+#     git           always compare HEAD to @{upstream}
+#     svn           always compare HEAD to your SVN upstream
+#
+# By default, __git_ps1 will compare HEAD to your SVN upstream if it can
+# find one, or @{upstream} otherwise.  Once you have set
+# GIT_PS1_SHOWUPSTREAM, you can override it on a per-repository basis by
+# setting the bash.showUpstream config variable.
+#
+# If you would like to see more information about the identity of
+# commits checked out as a detached HEAD, set GIT_PS1_DESCRIBE_STYLE
+# to one of these values:
+#
+#     contains      relative to newer annotated tag (v1.6.3.2~35)
+#     branch        relative to newer tag or branch (master~4)
+#     describe      relative to older annotated tag (v1.6.3.1-13-gdd42c2f)
+#     default       exactly matching tag
+#
+# If you would like a colored hint about the current dirty state, set
+# GIT_PS1_SHOWCOLORHINTS to a nonempty value. The colors are based on
+# the colored output of "git status -sb" and are available only when
+# using __git_ps1 for PROMPT_COMMAND or precmd.
+
+# check whether printf supports -v
+__git_printf_supports_v=
+printf -v __git_printf_supports_v -- '%s' yes >/dev/null 2>&1
+
+# stores the divergence from upstream in $p
+# used by GIT_PS1_SHOWUPSTREAM
+__git_ps1_show_upstream ()
+{
+	local key value
+	local svn_remote svn_url_pattern count n
+	local upstream=git legacy="" verbose="" name=""
+
+	svn_remote=()
+	# get some config options from git-config
+	local output="$(git config -z --get-regexp '^(svn-remote\..*\.url|bash\.showupstream)$' 2>/dev/null | tr '\0\n' '\n ')"
+	while read -r key value; do
+		case "$key" in
+		bash.showupstream)
+			GIT_PS1_SHOWUPSTREAM="$value"
+			if [[ -z "${GIT_PS1_SHOWUPSTREAM}" ]]; then
+				p=""
+				return
+			fi
+			;;
+		svn-remote.*.url)
+			svn_remote[$((${#svn_remote[@]} + 1))]="$value"
+			svn_url_pattern="$svn_url_pattern\\|$value"
+			upstream=svn+git # default upstream is SVN if available, else git
+			;;
+		esac
+	done <<< "$output"
+
+	# parse configuration values
+	for option in ${GIT_PS1_SHOWUPSTREAM}; do
+		case "$option" in
+		git|svn) upstream="$option" ;;
+		verbose) verbose=1 ;;
+		legacy)  legacy=1  ;;
+		name)    name=1 ;;
+		esac
+	done
+
+	# Find our upstream
+	case "$upstream" in
+	git)    upstream="@{upstream}" ;;
+	svn*)
+		# get the upstream from the "git-svn-id: ..." in a commit message
+		# (git-svn uses essentially the same procedure internally)
+		local -a svn_upstream
+		svn_upstream=($(git log --first-parent -1 \
+					--grep="^git-svn-id: \(${svn_url_pattern#??}\)" 2>/dev/null))
+		if [[ 0 -ne ${#svn_upstream[@]} ]]; then
+			svn_upstream=${svn_upstream[${#svn_upstream[@]} - 2]}
+			svn_upstream=${svn_upstream%@*}
+			local n_stop="${#svn_remote[@]}"
+			for ((n=1; n <= n_stop; n++)); do
+				svn_upstream=${svn_upstream#${svn_remote[$n]}}
+			done
+
+			if [[ -z "$svn_upstream" ]]; then
+				# default branch name for checkouts with no layout:
+				upstream=${GIT_SVN_ID:-git-svn}
+			else
+				upstream=${svn_upstream#/}
+			fi
+		elif [[ "svn+git" = "$upstream" ]]; then
+			upstream="@{upstream}"
+		fi
+		;;
+	esac
+
+	# Find how many commits we are ahead/behind our upstream
+	if [[ -z "$legacy" ]]; then
+		count="$(git rev-list --count --left-right \
+				"$upstream"...HEAD 2>/dev/null)"
+	else
+		# produce equivalent output to --count for older versions of git
+		local commits
+		if commits="$(git rev-list --left-right "$upstream"...HEAD 2>/dev/null)"
+		then
+			local commit behind=0 ahead=0
+			for commit in $commits
+			do
+				case "$commit" in
+				"<"*) ((behind++)) ;;
+				*)    ((ahead++))  ;;
+				esac
+			done
+			count="$behind	$ahead"
+		else
+			count=""
+		fi
+	fi
+
+	# calculate the result
+	if [[ -z "$verbose" ]]; then
+		case "$count" in
+		"") # no upstream
+			p="" ;;
+		"0	0") # equal to upstream
+			p="=" ;;
+		"0	"*) # ahead of upstream
+			p=">" ;;
+		*"	0") # behind upstream
+			p="<" ;;
+		*)	    # diverged from upstream
+			p="<>" ;;
+		esac
+	else
+		case "$count" in
+		"") # no upstream
+			p="" ;;
+		"0	0") # equal to upstream
+			p=" u=" ;;
+		"0	"*) # ahead of upstream
+			p=" u+${count#0	}" ;;
+		*"	0") # behind upstream
+			p=" u-${count%	0}" ;;
+		*)	    # diverged from upstream
+			p=" u+${count#*	}-${count%	*}" ;;
+		esac
+		if [[ -n "$count" && -n "$name" ]]; then
+			__git_ps1_upstream_name=$(git rev-parse \
+				--abbrev-ref "$upstream" 2>/dev/null)
+			if [ $pcmode = yes ] && [ $ps1_expanded = yes ]; then
+				p="$p \${__git_ps1_upstream_name}"
+			else
+				p="$p ${__git_ps1_upstream_name}"
+				# not needed anymore; keep user's
+				# environment clean
+				unset __git_ps1_upstream_name
+			fi
+		fi
+	fi
+
+}
+
+# Helper function that is meant to be called from __git_ps1.  It
+# injects color codes into the appropriate gitstring variables used
+# to build a gitstring.
+__git_ps1_colorize_gitstring ()
+{
+	if [[ -n ${ZSH_VERSION-} ]]; then
+		local c_red='%F{red}'
+		local c_green='%F{green}'
+		local c_lblue='%F{blue}'
+		local c_clear='%f'
+	else
+		# Using \[ and \] around colors is necessary to prevent
+		# issues with command line editing/browsing/completion!
+		local c_red='\[\e[31m\]'
+		local c_green='\[\e[32m\]'
+		local c_lblue='\[\e[1;34m\]'
+		local c_clear='\[\e[0m\]'
+	fi
+	local bad_color=$c_red
+	local ok_color=$c_green
+	local flags_color="$c_lblue"
+
+	local branch_color=""
+	if [ $detached = no ]; then
+		branch_color="$ok_color"
+	else
+		branch_color="$bad_color"
+	fi
+	c="$branch_color$c"
+
+	z="$c_clear$z"
+	if [ "$w" = "*" ]; then
+		w="$bad_color$w"
+	fi
+	if [ -n "$i" ]; then
+		i="$ok_color$i"
+	fi
+	if [ -n "$s" ]; then
+		s="$flags_color$s"
+	fi
+	if [ -n "$u" ]; then
+		u="$bad_color$u"
+	fi
+	r="$c_clear$r"
+}
+
+__git_eread ()
+{
+	f="$1"
+	shift
+	test -r "$f" && read "$@" <"$f"
+}
+
+# __git_ps1 accepts 0 or 1 arguments (i.e., format string)
+# when called from PS1 using command substitution
+# in this mode it prints text to add to bash PS1 prompt (includes branch name)
+#
+# __git_ps1 requires 2 or 3 arguments when called from PROMPT_COMMAND (pc)
+# in that case it _sets_ PS1. The arguments are parts of a PS1 string.
+# when two arguments are given, the first is prepended and the second appended
+# to the state string when assigned to PS1.
+# The optional third parameter will be used as printf format string to further
+# customize the output of the git-status string.
+# In this mode you can request colored hints using GIT_PS1_SHOWCOLORHINTS=true
+__git_ps1 ()
+{
+	local pcmode=no
+	local detached=no
+	local ps1pc_start='\u@\h:\w '
+	local ps1pc_end='\$ '
+	local printf_format=' (%s)'
+
+	case "$#" in
+		2|3)	pcmode=yes
+			ps1pc_start="$1"
+			ps1pc_end="$2"
+			printf_format="${3:-$printf_format}"
+		;;
+		0|1)	printf_format="${1:-$printf_format}"
+		;;
+		*)	return
+		;;
+	esac
+
+	# ps1_expanded:  This variable is set to 'yes' if the shell
+	# subjects the value of PS1 to parameter expansion:
+	#
+	#   * bash does unless the promptvars option is disabled
+	#   * zsh does not unless the PROMPT_SUBST option is set
+	#   * POSIX shells always do
+	#
+	# If the shell would expand the contents of PS1 when drawing
+	# the prompt, a raw ref name must not be included in PS1.
+	# This protects the user from arbitrary code execution via
+	# specially crafted ref names.  For example, a ref named
+	# 'refs/heads/$(IFS=_;cmd=sudo_rm_-rf_/;$cmd)' might cause the
+	# shell to execute 'sudo rm -rf /' when the prompt is drawn.
+	#
+	# Instead, the ref name should be placed in a separate global
+	# variable (in the __git_ps1_* namespace to avoid colliding
+	# with the user's environment) and that variable should be
+	# referenced from PS1.  For example:
+	#
+	#     __git_ps1_foo=$(do_something_to_get_ref_name)
+	#     PS1="...stuff...\${__git_ps1_foo}...stuff..."
+	#
+	# If the shell does not expand the contents of PS1, the raw
+	# ref name must be included in PS1.
+	#
+	# The value of this variable is only relevant when in pcmode.
+	#
+	# Assume that the shell follows the POSIX specification and
+	# expands PS1 unless determined otherwise.  (This is more
+	# likely to be correct if the user has a non-bash, non-zsh
+	# shell and safer than the alternative if the assumption is
+	# incorrect.)
+	#
+	local ps1_expanded=yes
+	[ -z "$ZSH_VERSION" ] || [[ -o PROMPT_SUBST ]] || ps1_expanded=no
+	[ -z "$BASH_VERSION" ] || shopt -q promptvars || ps1_expanded=no
+
+	local repo_info rev_parse_exit_code
+	repo_info="$(git rev-parse --git-dir --is-inside-git-dir \
+		--is-bare-repository --is-inside-work-tree \
+		--short HEAD 2>/dev/null)"
+	rev_parse_exit_code="$?"
+
+	if [ -z "$repo_info" ]; then
+		if [ $pcmode = yes ]; then
+			#In PC mode PS1 always needs to be set
+			PS1="$ps1pc_start$ps1pc_end"
+		fi
+		return
+	fi
+
+	local short_sha
+	if [ "$rev_parse_exit_code" = "0" ]; then
+		short_sha="${repo_info##*$'\n'}"
+		repo_info="${repo_info%$'\n'*}"
+	fi
+	local inside_worktree="${repo_info##*$'\n'}"
+	repo_info="${repo_info%$'\n'*}"
+	local bare_repo="${repo_info##*$'\n'}"
+	repo_info="${repo_info%$'\n'*}"
+	local inside_gitdir="${repo_info##*$'\n'}"
+	local g="${repo_info%$'\n'*}"
+
+	local r=""
+	local b=""
+	local step=""
+	local total=""
+	if [ -d "$g/rebase-merge" ]; then
+		__git_eread "$g/rebase-merge/head-name" b
+		__git_eread "$g/rebase-merge/msgnum" step
+		__git_eread "$g/rebase-merge/end" total
+		if [ -f "$g/rebase-merge/interactive" ]; then
+			r="|REBASE-i"
+		else
+			r="|REBASE-m"
+		fi
+	else
+		if [ -d "$g/rebase-apply" ]; then
+			__git_eread "$g/rebase-apply/next" step
+			__git_eread "$g/rebase-apply/last" total
+			if [ -f "$g/rebase-apply/rebasing" ]; then
+				__git_eread "$g/rebase-apply/head-name" b
+				r="|REBASE"
+			elif [ -f "$g/rebase-apply/applying" ]; then
+				r="|AM"
+			else
+				r="|AM/REBASE"
+			fi
+		elif [ -f "$g/MERGE_HEAD" ]; then
+			r="|MERGING"
+		elif [ -f "$g/CHERRY_PICK_HEAD" ]; then
+			r="|CHERRY-PICKING"
+		elif [ -f "$g/REVERT_HEAD" ]; then
+			r="|REVERTING"
+		elif [ -f "$g/BISECT_LOG" ]; then
+			r="|BISECTING"
+		fi
+
+		if [ -n "$b" ]; then
+			:
+		elif [ -h "$g/HEAD" ]; then
+			# symlink symbolic ref
+			b="$(git symbolic-ref HEAD 2>/dev/null)"
+		else
+			local head=""
+			if ! __git_eread "$g/HEAD" head; then
+				if [ $pcmode = yes ]; then
+					PS1="$ps1pc_start$ps1pc_end"
+				fi
+				return
+			fi
+			# is it a symbolic ref?
+			b="${head#ref: }"
+			if [ "$head" = "$b" ]; then
+				detached=yes
+				b="$(
+				case "${GIT_PS1_DESCRIBE_STYLE-}" in
+				(contains)
+					git describe --contains HEAD ;;
+				(branch)
+					git describe --contains --all HEAD ;;
+				(describe)
+					git describe HEAD ;;
+				(* | default)
+					git describe --tags --exact-match HEAD ;;
+				esac 2>/dev/null)" ||
+
+				b="$short_sha..."
+				b="($b)"
+			fi
+		fi
+	fi
+
+	if [ -n "$step" ] && [ -n "$total" ]; then
+		r="$r $step/$total"
+	fi
+
+	local w=""
+	local i=""
+	local s=""
+	local u=""
+	local c=""
+	local p=""
+
+	if [ "true" = "$inside_gitdir" ]; then
+		if [ "true" = "$bare_repo" ]; then
+			c="BARE:"
+		else
+			b="GIT_DIR!"
+		fi
+	elif [ "true" = "$inside_worktree" ]; then
+		if [ -n "${GIT_PS1_SHOWDIRTYSTATE-}" ] &&
+		   [ "$(git config --bool bash.showDirtyState)" != "false" ]
+		then
+			git diff --no-ext-diff --quiet --exit-code || w="*"
+			if [ -n "$short_sha" ]; then
+				git diff-index --cached --quiet HEAD -- || i="+"
+			else
+				i="#"
+			fi
+		fi
+		if [ -n "${GIT_PS1_SHOWSTASHSTATE-}" ] &&
+		   [ -r "$g/refs/stash" ]; then
+			s="$"
+		fi
+
+		if [ -n "${GIT_PS1_SHOWUNTRACKEDFILES-}" ] &&
+		   [ "$(git config --bool bash.showUntrackedFiles)" != "false" ] &&
+		   git ls-files --others --exclude-standard --error-unmatch -- '*' >/dev/null 2>/dev/null
+		then
+			u="%${ZSH_VERSION+%}"
+		fi
+
+		if [ -n "${GIT_PS1_SHOWUPSTREAM-}" ]; then
+			__git_ps1_show_upstream
+		fi
+	fi
+
+	local z="${GIT_PS1_STATESEPARATOR-" "}"
+
+	# NO color option unless in PROMPT_COMMAND mode
+	if [ $pcmode = yes ] && [ -n "${GIT_PS1_SHOWCOLORHINTS-}" ]; then
+		__git_ps1_colorize_gitstring
+	fi
+
+	b=${b##refs/heads/}
+	if [ $pcmode = yes ] && [ $ps1_expanded = yes ]; then
+		__git_ps1_branch_name=$b
+		b="\${__git_ps1_branch_name}"
+	fi
+
+	local f="$w$i$s$u"
+	local gitstring="$c$b${f:+$z$f}$r$p"
+
+	if [ $pcmode = yes ]; then
+		if [ "${__git_printf_supports_v-}" != yes ]; then
+			gitstring=$(printf -- "$printf_format" "$gitstring")
+		else
+			printf -v gitstring -- "$printf_format" "$gitstring"
+		fi
+		PS1="$ps1pc_start$gitstring$ps1pc_end"
+	else
+		printf -- "$printf_format" "$gitstring"
+	fi
+}

tips/lgtc_logo.eps

+../presentation/lgtc_logo.eps
\ No newline at end of file

tips/lumc_logo.eps

+../presentation/lumc_logo.eps
\ No newline at end of file

tips/lumc_logo_small.eps

+../presentation/lumc_logo_small.eps
\ No newline at end of file

tips/nbic_logo.eps

+../presentation/nbic_logo.eps
\ No newline at end of file

tips/ngi_logo.eps

+../presentation/ngi_logo.eps
\ No newline at end of file

tips/nwo_logo_en.eps

+../presentation/nwo_logo_en.eps
\ No newline at end of file

tips/pics

+../pics/
\ No newline at end of file

tips/tips.tex

+\documentclass[slidestop]{beamer}
+
+\title{Git Tips and Tricks}
+\providecommand{\myConference}{Git course}
+\providecommand{\myDate}{Monday, June 23, 2014}
+\author{Wibowo Arindrarto}
+\providecommand{\myGroup}{Sequencing Analysis Support Core}
+\providecommand{\myDepartment}{}
+\providecommand{\myCenter}{}
+\providecommand{\lastCenterLogo}{
+  \raisebox{-0.1cm}{
+    \includegraphics[height=1cm]{lgtc_logo}
+    %\includegraphics[height=0.7cm]{ngi_logo}
+  }
+}
+\providecommand{\lastRightLogo}{
+  %\includegraphics[height=0.7cm]{nbic_logo}
+  %\includegraphics[height=0.8cm]{nwo_logo_en}
+  %\hspace{1.5cm}\includegraphics[height=0.7cm]{gen2phen_logo}
+}
+
+\usetheme{lumc}
+
+\begin{document}
+
+% This disables the \pause command, handy in the editing phase.
+%\renewcommand{\pause}{}
+
+% Make the title page.
+\bodytemplate
+