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\documentclass[a4paper,12pt]{article}
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\usepackage[utf8]{inputenc}
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%\usepackage[T1]{fontenc}
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\usepackage[english]{babel}
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\usepackage[dvips,pdftex]{graphicx}
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\usepackage{dirtree}
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\usepackage[top=2cm, bottom=2cm, left=1cm, right=1cm]{geometry}
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\usepackage{url}
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\usepackage[dvips,
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pdftex,
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colorlinks=true,
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urlcolor=blue,
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bookmarks=true]{hyperref}
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\hypersetup{
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pdfauthor=Debian-Med Group,
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pdftitle=Debian-Med Policy
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}
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\graphicspath{{../img/}}
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\newcommand{\HRule}{\rule{\linewidth}{0.5mm}}
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% Title Page
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\title{Debian-Med Policy}
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\author{Debian-Med Group}
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\begin{document}
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\begin{center}
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\includegraphics[scale=0.5]{debian-med}
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\HRule \\[0.4cm]
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{\huge \bfseries Group Policy}
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\HRule \\[1.5cm]
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\begin{minipage}[t]{0.4\textwidth}
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\begin{flushleft}
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\large \emph{Author:}\\
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David \textsc{Paleino}
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\end{flushleft}
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\end{minipage}
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\begin{minipage}[t]{0.4\textwidth}
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\begin{flushright}
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\large \emph{Supervisors:}\\
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Nelson A. \textsc{de Oliveira} \\
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Charles \textsc{Plessy} \\
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Andreas \textsc{Tille} \\
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Foo \textsc{Bar} \\
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\end{flushright}
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\end{minipage}
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\rule[-5mm]{\linewidth}{0.5mm}
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\end{center}
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\section{Introduction}
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Debian-Med is a ``\href{http://people.debian.org/~tille/cdd}{Custom Debian Distribution}'' with the aim to develop Debian into an operating system that is particularly well fit for the requirements for medical practice and research. \\ \\
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The Debian-Med project presents packages that are associated with medicine, pre-clinical research, and life science. Its developments are mostly focused on three areas for the moment: medical practice, imaging and bioinformatics. \\ \\
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Over the previous years, several initiatives have spawned that address the scientific disciplines like chemistry or bioinformatics. Debian-Med is not a competition to these efforts but a platform to present the packages to the community as a Custom Debian Distribution.
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\section{How to Contribute}
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From the developer to the user, there is a long chain of tasks in which we always welcome participation. First we must keep ourselves informed about the software landscape in biology and medicine. Software to be packaged is chosen according to criteria such as users' need and the consistency of the distribution. Once in Debian, the software is monitored for its quality and bugs are fixed, if possible in collaboration with the upstream maintainer(s). All this work would not be very useful if it remains confidential. We also dedicate some time to advertise it to the world via \url{http://www.debian.org} and to ease the integration of new members through this wiki. \\ \\
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Please contact us on \href{mailto:debian-med@lists.debian.org}{debian-med@lists.debian.org} if you want to help to make medical and biological software available to Debian users. Read the \textbf{Membership} section if you're interested in joining us. \\ \\
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If you speak a language other than English, you can contribute rightaway with translations of package descriptions at \url{http://ddtp.debian.org}. When working on these, you will find immediate targets for improvements of the original English versions, too. For these, though, you need access to Debian-Med's source code repository. Very welcome are tutorials that guide Debian users towards the use of packages to their immediate benefit. You may also consider to write respective articles for Magazines, be they online or in print.
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\subsection{Membership}
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To request membership to this group, please go on our \href{http://alioth.debian.org/projects/debian-med}{\emph{Alioth page}}, or directly follow this \href{http://alioth.debian.org/project/request.php?group_id=30063}{link}. Remember that you \textbf{must} have an Alioth account before requesting membership.
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\section{Subversion}
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Our Subversion (SVN) repository is currently hosted on \href{http://alioth.debian.org}{\emph{Alioth}}, the hosting facility provided by Debian to free software developers. You can have a look at the repository through Alioth's \href{http://svn.debian.org/wsvn/debian-med}{web interface}.
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\subsection{Give me the source!}
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To check sources out from SVN, please do:
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\begin{itemize}
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\item if you are a member of Debian-Med:
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\begin{verbatim}
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svn co svn+ssh://user@alioth.debian.org/svn/debian-med/trunk/...
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\end{verbatim}
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\item are \textbf{NOT} a member of Debian-Med:
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\begin{verbatim}
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svn co svn://svn.debian.org/svn/debian-med/trunk/...
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\end{verbatim}
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\end{itemize}
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\subsection{Repository structure}
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The SVN repository is structured as follows: \\
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\dirtree{%
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.1 debian-med/.
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.2 trunk/.
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.3 community/.
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.4 debtags/.
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.4 infrastructure/.
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.4 website/.
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.3 packages/.
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.4 <package>/.
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.5 branches/.
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.5 tags/.
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.5 trunk/.
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.6 debian/.
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}
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\section{Packaging}
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\subsection{Announcing intent to package}
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If you intent to work on a Debian package you should follow the
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\href{http://www.debian.org/devel/wnpp/#l1}{normal Debian rules} and
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file a \texttt{WNPP} bug report. It is a good idea to keep the
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Debian-Med mailing list
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\href{mailto:debian-med@lists.debian.org}{debian-med@lists.debian.org}
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in CC or forward the response of the BTS that includes the bug number
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to the mailing list to keep your co-workers informed.
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In addition to this you should add a user tag to this WNPP bug to
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make sure that your intent is in focus of the Debian-Med team. This
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can be done by sending a mail to
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\href{mailto:request@bugs.debian.org}{request@bugs.debian.org} with
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the following content:
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\begin{verbatim}
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user debian-med@lists.debian.org
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usertag <bug-number> + wnpp med-<task>
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thanks
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\end{verbatim}
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For instance if you want to tag an ITP with bug number \#123456 for
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Debian-Med section biology you would do the following:
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\begin{verbatim}
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mailx -s "Tagging bug #123456" request@bugs.debian.org <<...
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user debian-med@lists.debian.org
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usertag 123456 + wnpp med-bio
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thanks
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...
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\end{verbatim}
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\subsection{Conventions}
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Please, in \texttt{debian/control}, use these values:
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\begin{verbatim}
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...
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Section: ...
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Priority: ...
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Maintainer: Debian-Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
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XS-DM-Upload-Allowed: yes
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Uploaders: <yourname> <youremail>
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Standards-Version: 3.7.3
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Homepage: http://...
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Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/<package>/trunk/
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Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/<package>/trunk/?rev=0&sc=0
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...
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\end{verbatim}
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Make sure you use the right Section and Priority fields for the package. Also, be sure to use the latest Standards-Version. Please also add the Homepage field, we aim at having our packages the most complete as they can be.
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\subsection{Uploading a new package}
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To upload a new package to the SVN repository, you must have write access to it; i.e. you must be a member of this group. \\
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You can upload a new package only \emph{after} successfully building it with \textbf{dpkg-buildpackage} (or any wrapper around it). Then you can:
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\begin{verbatim}
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$ svn-inject package.dsc svn+ssh://user@alioth.debian.org/svn/debian-med/trunk/packages/
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\end{verbatim}
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The \texttt{svn-inject} command is found in the
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\texttt{svn-buildpackage} package (just \texttt{apt-get} it). \\
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Once you uploaded a new package please make sure that it is mentioned
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in the apropriate tasks file in the package source of the debian-med
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package
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\href{http://svn.debian.org/wsvn/cdd/projects/med/trunk/debian-med/tasks/?rev=0&sc=0}{in
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SVN}. Normally maintainer watch the changes in the Debian-Med
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packaging pool but it helps if the maintainer of a certain package
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verifies that everything is in the right place.
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\subsection{Building the packages}
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To build the package, just use the tools that \texttt{svn-buildpackage} carries. First of all, we suggest you to define some aliases for the most common commands:
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\begin{verbatim}
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alias svn-b='svn-buildpackage -us -uc -rfakeroot --svn-ignore'
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alias svn-br='svn-b --svn-dont-purge --svn-reuse'
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alias svn-bt='svn-buildpackage --svn-tag -rfakeroot'
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\end{verbatim}
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You're ready now to checkout the sources (see the proper section). \\ \\
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Once done, you're ready to do the work. First, cd to the \texttt{trunk} directory, and download the upstream sources (if there is a debian/watch file):
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\begin{verbatim}
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echo "origDir=.." >> .svn/deb-layout && uscan --force-download
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\end{verbatim}
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Alternatively, you can try this, it depends on how the package was built (again, from the \texttt{trunk} directory:
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\begin{verbatim}
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debian/rules get-orig-source
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\end{verbatim}
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Once done, edit the files you need, and then build the package with \texttt{svn-b} or \texttt{svn-br}. \\ \\
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If you're a Debian-Med member, you can commit your changes:
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\begin{verbatim}
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svn commit
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\end{verbatim}
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(also \texttt{svn ci}). \\
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Otherwise, you can ask to be added to the group (see the Membership section), or send the result of \texttt{svn diff} to the \href{mailto:debian-med@lists.debian.org}{mailing list} (gzip it, if it's too large).
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\subsection{Tagging packages}
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It may happen that a package version has been uploaded to Debian repositories, and you forgot to tag the last build with
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\begin{verbatim}
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svn-buildpackage --svn-tag
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\end{verbatim}
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You can tag this package also retroactively. A first step, creating the \texttt{tags/} directory, can be achieved in two ways:
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\begin{itemize}
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\item create it locally (it is a sibling of \texttt{trunk/}), and commit:
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\begin{verbatim}
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svn mkdir tags
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svn commit
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\end{verbatim}
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\item create it remotely:
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\begin{verbatim}
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svn mkdir svn+ssh://user@svn.debian.org/svn/debian-med/trunk/packages/<package>/tags
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\end{verbatim}
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\end{itemize}
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After the \texttt{tags/} directory has been created, you're ready to tag the package:
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\begin{verbatim}
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svn-buildpackage --svn-tag-only --svn-no-autodch
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\end{verbatim}
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(\texttt{--svn-autodch} avoids \texttt{debian/changelog} to be marked as \texttt{UNRELEASED}).
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\subsection{Handling patches}
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Often happens that the upstream code doesn't fit well into the Debian distribution: be this wrong paths, missing features, anything that implies editing the source files. When you directly edit upstream's source files, your changes will be put into a \texttt{.diff.gz} file, which should instead contain only \texttt{debian/}. Because of this, it's best using a \emph{patch handling system}. The most known are \texttt{dpatch} and \texttt{quilt}.
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\subsubsection{Using \texttt{dpatch}}
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\paragraph{Creating a patch}
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\texttt{dpatch-edit-patch}\\
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\paragraph{Applying and unapplying patches}
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\texttt{apply(-all)}, \texttt{unapply(-all)}, \texttt{status}\\
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\paragraph{Editing a patch}
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\texttt{dpatch-edit-patch}\\
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\subsubsection{Using \texttt{quilt}}
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Using \texttt{quilt} is rather easy (easier than \texttt{dpatch}, I'd say). \\
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First, make sure you have correctly setup quilt: open \texttt{.quiltrc} in your home directory (create it if you don't have one), and make sure it looks like this:
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\begin{verbatim}
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QUILT_DIFF_ARGS="--no-timestamps --no-index"
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QUILT_REFRESH_ARGS="--no-timestamps --no-index"
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QUILT_PATCH_OPTS="--unified-reject-files"
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QUILT_PATCHES="debian/patches"
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\end{verbatim}
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After this, you're ready to start working with quilt.
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\paragraph{Creating a patch}
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\texttt{new}, \texttt{edit}, \texttt{refresh}\\
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To create a patch, use the \texttt{new} command. Run:
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\begin{verbatim}
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quilt new <patch_name>.patch
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\end{verbatim}
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This will create (if it doesn't exist yet) a \texttt{debian/patches/series} file, which contains all the patches to be applied by quilt. Moreover, the new patch is also the \emph{topmost} (the currently applied). \\ \\
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Now start editing files, with:
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\begin{verbatim}
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quilt edit <file>
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\end{verbatim}
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and repeat the process for each file the patch is involved with. At the end, run
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\begin{verbatim}
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quilt refresh
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\end{verbatim}
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This will compare the noted state of the edited files with the current state, and will produce a patch in \texttt{debian/patches}. Remember: the patch is currently \textbf{applied} (you can check this with \texttt{quilt applied}).
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\paragraph{Applying and unapplying patches}
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\texttt{push}, \texttt{pop}, \texttt{applied}, \texttt{unapplied}\\
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Just two easy commands to do the job: \\ \\
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\texttt{quilt pop} will unapply the topmost patch. \\
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\texttt{quilt push} will apply the next patch in \texttt{debian/patches/series}. \\
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You can just add a ``-a'' flag to the commands above, to respectively apply/unapply \textbf{all} patches in the series. \\ \\
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You can check which patches are applied / unapplied with, respectively, \texttt{quilt applied} and \texttt{quilt unapplied}.
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\paragraph{Editing patches}
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\texttt{push}, \texttt{pop}, \texttt{edit}, \texttt{refresh}\\
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To edit a patch, first make it the topmost:
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\begin{verbatim}
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quilt push <patch_name>
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\end{verbatim}
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If the patch is already applied, but is not the topmost, run \texttt{quilt pop} until it becomes the currently applied one. \\ \\
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You can now run \texttt{quilt edit} on the files you want to change, and, when you're done, \texttt{quilt refresh}.
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\paragraph{Renaming patches}
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\texttt{rename}\\
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Sometimes it's useful to rename a patch. Without any hassle, do:
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\begin{verbatim}
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quilt rename -P <old_name>.patch <new_name>.patch
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\end{verbatim}
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\paragraph{Other commands}
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.\\
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Please see \texttt{man 1 quilt} to have a comprehensive list of commands.
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\subsubsection{Integration in the build process}
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TODO:
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\begin{verbatim}
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include /usr/share/{quilt,dpatch}/{quilt,dpatch}.make
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\end{verbatim}
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\texttt{\$(QUILT\_STAMPFN)}
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...
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\end{document}
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