diff --git a/basics/basics.tex b/basics/basics.tex
index 67eabac00e7ec025915c74bafb31addff73d3f49..1d736f11193164795f722330399cad32e306d0fb 100644
--- a/basics/basics.tex
+++ b/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
diff --git a/tips/Makefile b/tips/Makefile
new file mode 120000
index 0000000000000000000000000000000000000000..199dff7226a84dcdd0c281699009a50ee16432d5
--- /dev/null
+++ b/tips/Makefile
@@ -0,0 +1 @@
+../presentation/Makefile
\ No newline at end of file
diff --git a/tips/beamerthemelumc.sty b/tips/beamerthemelumc.sty
new file mode 120000
index 0000000000000000000000000000000000000000..999deb4e197ab5cd127d06a12d63c324f88ec711
--- /dev/null
+++ b/tips/beamerthemelumc.sty
@@ -0,0 +1 @@
+../presentation/beamerthemelumc.sty
\ No newline at end of file
diff --git a/tips/gen2phen_logo.eps b/tips/gen2phen_logo.eps
new file mode 120000
index 0000000000000000000000000000000000000000..0f2636661f1c186560f22691e6a5172e1bc3f7a8
--- /dev/null
+++ b/tips/gen2phen_logo.eps
@@ -0,0 +1 @@
+../presentation/gen2phen_logo.eps
\ No newline at end of file
diff --git a/tips/git-prompt.sh b/tips/git-prompt.sh
new file mode 100644
index 0000000000000000000000000000000000000000..9d684b10a67ea663410db3ba68482c1a52bbc367
--- /dev/null
+++ b/tips/git-prompt.sh
@@ -0,0 +1,513 @@
+# 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
+}
diff --git a/tips/lgtc_logo.eps b/tips/lgtc_logo.eps
new file mode 120000
index 0000000000000000000000000000000000000000..1732a7e9e5917e6840c9e5977fcff78334758d07
--- /dev/null
+++ b/tips/lgtc_logo.eps
@@ -0,0 +1 @@
+../presentation/lgtc_logo.eps
\ No newline at end of file
diff --git a/tips/lumc_logo.eps b/tips/lumc_logo.eps
new file mode 120000
index 0000000000000000000000000000000000000000..28075f649e2e97c354f0edcb8499aaa716802566
--- /dev/null
+++ b/tips/lumc_logo.eps
@@ -0,0 +1 @@
+../presentation/lumc_logo.eps
\ No newline at end of file
diff --git a/tips/lumc_logo_small.eps b/tips/lumc_logo_small.eps
new file mode 120000
index 0000000000000000000000000000000000000000..a5544fe55e1326788ad0ab37c560dc40c9adf29e
--- /dev/null
+++ b/tips/lumc_logo_small.eps
@@ -0,0 +1 @@
+../presentation/lumc_logo_small.eps
\ No newline at end of file
diff --git a/tips/nbic_logo.eps b/tips/nbic_logo.eps
new file mode 120000
index 0000000000000000000000000000000000000000..8780a0131e16e899fa17c12d886c4135f36e933d
--- /dev/null
+++ b/tips/nbic_logo.eps
@@ -0,0 +1 @@
+../presentation/nbic_logo.eps
\ No newline at end of file
diff --git a/tips/ngi_logo.eps b/tips/ngi_logo.eps
new file mode 120000
index 0000000000000000000000000000000000000000..2a2e1ea9b13da5f50916f33c34e8b5607022962d
--- /dev/null
+++ b/tips/ngi_logo.eps
@@ -0,0 +1 @@
+../presentation/ngi_logo.eps
\ No newline at end of file
diff --git a/tips/nwo_logo_en.eps b/tips/nwo_logo_en.eps
new file mode 120000
index 0000000000000000000000000000000000000000..adcf12fd16e511dbe8213f21ba684611f13291bf
--- /dev/null
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diff --git a/tips/pics b/tips/pics
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diff --git a/tips/tips.tex b/tips/tips.tex
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+\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
+
+% First page of the presentation.
+\section{Introduction}
+\begin{frame}[fragile]
+ \frametitle{}
+
+ We have only been playing with some of what git offers. In reality,
+ you can do much more with it. It also allows for a wide array of
+ customizations.
+ \bigskip
+
+ We will look into some of these customizations now.
+\end{frame}
+
+
+\section{Custom Prompt}
+\begin{frame}[fragile]
+ \frametitle{}
+
+ Checking which branch you are working on and its status is
+ a routine task.
+ \bigskip
+ \pause
+
+ ``\bt{git status}'' is useful, but quickly feels repetitive.
+ \begin{lstlisting}[language=none, caption=Routine git checking]
+ $ git branch
+ * master
+ $ git status
+ nothing to commit, working directory clean
+ \end{lstlisting}
+ \bigskip
+ \pause
+
+ Solution: use a custom shell prompt that displays git status.
+ \begin{lstlisting}[language=none, caption=Git checking with custom prompt]
+ (master) $ git st
+ nothing to commit, working directory clean
+ \end{lstlisting}
+ \bigskip
+
+\end{frame}
+
+
+\section{Custom Prompt}
+\begin{frame}[fragile]
+ \frametitle{}
+
+ The git-approved way to do this is to use the ``\bt{\_\_git\_ps1}''
+ shell function defined in the ``\bt{git-prompt.sh}'' file.
+ \bigskip
+ \pause
+
+ The location of this file depends on your OS and git version. For now,
+ you can download a copy of this file from our GitLab.
+ \bigskip
+ \pause
+
+ Then, in you ``\bt{.bashrc}'' file, add ``\bt{\_\_git\_ps1}'' to the
+ ``\bt{PS1}'' variable, and source your ``\bt{.bashrc}'' again.
+ \bigskip
+\end{frame}
+
+
+\section{Useful git commands}
+\begin{frame}[fragile]
+ \frametitle{git blame}
+
+ Git tracks each line of each file in its repository.
+ \bigskip
+ \pause
+
+ You can view who committed the line change, the commit hash,
+ and the commit time using ``\bt{git blame}''
+ \begin{lstlisting}[language=none, caption=git blame command]
+ $ git blame README
+ a4394d28 (bow 2014-06 ...) Second version.
+ \end{lstlisting}
+ \bigskip
+\end{frame}
+
+
+\section{Useful git commands}
+\begin{frame}[fragile]
+ \frametitle{git tag}
+
+ Sometimes, it is practical to refer to a commit with a name
+ instead of a hash.
+ \bigskip
+ \pause
+
+ Official releases, for example, are better referred as v1.0
+ than a76a0fx.
+ \bigskip
+ \pause
+
+ This can be done using ``\bt{git tag}''.
+\end{frame}
+
+
+\section{Useful git commands}
+\begin{frame}[fragile]
+ \frametitle{git tag}
+
+ \begin{lstlisting}[language=none, caption=Adding a tag]
+ $ git tag "v0.0.1"
+ $ git show v0.0.1
+ commit a4394d28e6ba30be19318ee74f732a103b8ffdf2
+ Author: bow <bow@bow.web.id>
+ Date: Sat Jun 21 13:47:03 2014 +0200
+
+ Second commit
+
+ diff --git a/README b/README
+ index efe6f7c..4fe6328 100644
+ --- a/README
+ +++ b/README
+ @@ -1 +1 @@
+ -First version.
+ +Second version.
+ \end{lstlisting}
+ \bigskip
+\end{frame}
+
+
+\section{Useful git commands}
+\begin{frame}[fragile]
+ \frametitle{git tag}
+
+ What we did previously is to add what is called a lightweight tag.
+ Lightweight tags are essentially commit aliases.
+ \bigskip
+ \pause
+
+ There is another type of tag, called the annotated tag.
+ \bigskip
+ \pause
+
+ Annotated tags contain more information: tagger identity,
+ tagging message, tagging date, and can be verified with GPG.
+ \bigskip
+\end{frame}
+
+
+\section{Useful git commands}
+\begin{frame}[fragile]
+ \frametitle{git tag}
+ \begin{lstlisting}[language=none, caption=Adding an annotated tag]
+ $ git tag -a "v0.0.1" -m "Alpha version"
+ tag v0.1.0
+ Tagger: bow <bow@bow.web.id>
+ Date: Sat Jun 21 15:11:53 2014 +0200
+
+ Alpha version
+
+ commit a4394d28e6ba30be19318ee74f732a103b8ffdf2
+ Author: bow <bow@bow.web.id>
+ Date: Sat Jun 21 13:47:03 2014 +0200
+
+ Second commit
+
+ diff --git a/README b/README
+ index efe6f7c..4fe6328 100644
+ --- a/README
+ +++ b/README
+ @@ -1 +1 @@
+ -First version.
+ +Second version.
+ \end{lstlisting}
+ \bigskip
+\end{frame}
+
+
+\section{Useful git options}
+\begin{frame}[fragile]
+ \frametitle{git diff -w}
+
+ Sometimes, you want to hide whitespace differences when using
+ ``\bt{git diff}''.
+ \bigskip
+ \pause
+
+ This can be done via ``\bt{git diff -w}''
+ \begin{lstlisting}[language=none, caption=git diff without whitespace]
+ $ git diff -w
+ \end{lstlisting}
+ \bigskip
+ \pause
+
+ Note that while this aids visualization of the diff, git will still
+ commit the whitespace change.
+ \bigskip
+\end{frame}
+
+
+\section{Useful git options}
+\begin{frame}[fragile]
+ \frametitle{git commit --amend}
+
+ Git gives you total control over your history, which means you can also
+ change them.
+ \bigskip
+ \pause
+
+ This practice is potentially dangerous and should not be part of your
+ regular workflow. This is especially true for public commits.
+ \bigskip
+ \pause
+
+ Still, there are times when changing that one last commit makes more
+ sense than doing a ``\bt{git revert}''
+ \bigskip
+ \pause
+
+ ``\bt{git commit --amend}'' allows you to do that: changing your last
+ commit.
+ \bigskip
+\end{frame}
+
+
+\section{Useful git options}
+\begin{frame}[fragile]
+ \frametitle{git commit --amend}
+
+ When run on a clean branch (no uncommitted changes),
+ ``\bt{git commit --amend}'' allows you to change your last commit message.
+ \bigskip
+ \pause
+
+ You can also use the command to meld current staged changes to your last
+ committed change.
+ \begin{lstlisting}[language=none, caption=git blame command]
+ $ git status
+ Changes to be committed:
+ modified: README
+ $ git commit --amend -m "Update README"
+ [master b60437d] Second update
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+ \end{lstlisting}
+ \bigskip
+\end{frame}
+
+
+\section{Useful git options}
+\begin{frame}[fragile]
+ \frametitle{git add --patch}
+
+ Often, uncommited change overextends. You start with the intention of
+ fixing bug A, but in the middle found that you can implement feature B
+ and feature C while also squashing bug D.
+ \bigskip
+ \pause
+
+ At the end of the day, only ``\bt{git commit -am "Updates"}'' is done
+ and the whole change is saved in a single comit.
+ \bigskip
+ \pause
+
+ This defeats the purpose of tracking your changes in commits. Commits
+ ideally represents a single, functional update, which you can understand
+ later on.
+ \bigskip
+\end{frame}
+
+
+\section{Useful git options}
+\begin{frame}[fragile]
+ \frametitle{git add --patch}
+
+ You can, infact, commit the line changes selectively. This helps
+ split a mesh of changes into separate commits.
+ \begin{lstlisting}[language=none, caption=git add --patch]
+ $ git add --patch
+ \end{lstlisting}
+ \bigskip
+\end{frame}
+
+
+\section{Main Configuration File}
+\begin{frame}[fragile]
+ \frametitle{Viewing}
+
+ In Linux, git uses the ``\bt{~/.gitconfig}'' file as its main
+ configuration file.
+ \bigskip
+ \pause
+
+ To see the current configuration values, use ``\bt{git config --list}''.
+ \begin{lstlisting}[language=none, caption=Git config values]
+ $ git config --list
+ user.name=bow
+ user.email=bow@bow.web.id
+ color.ui=auto
+ \end{lstlisting}
+ \bigskip
+\end{frame}
+
+
+\section{Main Configuration File}
+\begin{frame}[fragile]
+ \frametitle{Modifying}
+
+ To edit the file directly, open ``\bt{~/.gitconfig}'' in a text editor
+ and save your changes.
+ \begin{lstlisting}[language=none, caption=Modifying the config file]
+ $ vim ~/.gitconfig
+ \end{lstlisting}
+ \bigskip
+ \pause
+
+ You can also use the ``\bt{git config --global}'' to set the values via the shell.
+ \begin{lstlisting}[language=none, caption=Modifying via the shell]
+ $ git config --global user.name "Linus Torvalds"
+ \end{lstlisting}
+ \bigskip
+\end{frame}
+
+
+\section{Main Configuration File}
+\begin{frame}[fragile]
+ \frametitle{Modifying: global ignore}
+
+ We will look at two examples now: setting a global ignore file and
+ setting aliases.
+ \bigskip
+ \pause
+
+ In addition to setting a directory-specific ``\bt{.gitignore}'' file,
+ you can also set a global ignore file.
+ \bigskip
+ \pause
+
+ You can name this file anything. The convention is to use
+ ``\bt{.gitignore\_global}'' and place the file in your home directory.
+ \bigskip
+\end{frame}
+
+
+\section{Main Configuration File}
+\begin{frame}[fragile]
+ \frametitle{}
+
+ The global ignore file has the same format as the per-directory
+ ``\bt{.gitignore}'' file, only visible to all git repositories.
+ \bigskip
+ \pause
+
+ \begin{lstlisting}[language=none, caption=Setting the global ignore file]
+ $ echo "*.out" > ~/.gitignore_global
+ $ echo "testing.txt" > ~/.gitignore_global
+ $ git config --global core.excludesfile \
+ "~/.gitignore_global"
+ \end{lstlisting}
+ \bigskip
+ \pause
+
+ \begin{lstlisting}[language=none, caption=Ignoring via the global file]
+ $ echo "Is this the real life?" > this.out
+ $ touch testing.txt
+ $ git status
+ nothing to commit, working directory clean
+ \end{lstlisting}
+ \bigskip
+\end{frame}
+
+
+\section{Main Configuration File}
+\begin{frame}[fragile]
+ \frametitle{Aliases}
+
+ You can alias simple commands.
+ \begin{lstlisting}[language=none, caption=Simple alias]
+ $ git config --global alias.st status
+ $ git st
+ nothing to commit, working directory clean
+ \end{lstlisting}
+ \bigskip
+ \pause
+
+ Or more complex commands.
+ \begin{lstlisting}[language=none, caption=Complex alias]
+ $ git config --global alias.qlog \
+ "log --pretty=oneline"
+ $ git qlog
+ a4394d28e... Second commit
+ 80eafd7e6... First commit
+ \end{lstlisting}
+ \bigskip
+\end{frame}
+
+
+\section{GitLab and GitHub}
+\begin{frame}[fragile]
+ \frametitle{Demo time!}
+\end{frame}
+
+
+\section{Questions?}
+\lastpagetemplate
+\begin{fframe}
+ \begin{center}
+ Acknowledgements:
+ \bigskip
+ \bigskip
+
+ Martijn Vermaat
+
+ Jeroen F. J. Laros
+
+ \end{center}
+
+ \vfill
+ \permfoot{http://git-scm.com/book}
+\end{fframe}
+
+\end{document}
diff --git a/tips/ul_logo.eps b/tips/ul_logo.eps
new file mode 120000
index 0000000000000000000000000000000000000000..cd04dcb9c72ebdde50fda7ee41e375e053fc31b9
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+++ b/tips/ul_logo.eps
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+../presentation/ul_logo.eps
\ No newline at end of file