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Commit ef4d7217 authored by Vermaat's avatar Vermaat
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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.
parents d0537ebd c97df55d
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basics/basics.tex
View file @ ef4d7217
......@@ -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 0 → 120000
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../presentation/Makefile
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tips/beamerthemelumc.sty 0 → 120000
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../presentation/beamerthemelumc.sty
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tips/gen2phen_logo.eps 0 → 120000
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../presentation/gen2phen_logo.eps
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tips/git-prompt.sh 0 → 100644
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# 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
}
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\documentclass[slidestop]{beamer}