1 Analogy For Microsoft Word Users 2 Brief Background on Version
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1. I want to start a folder for documentation projects Im working on The first document I put into the new folder will be this file you are reading right now cd SVN repo mkdir HOWIQ docs cd HOWIO docs cp SVN intro lyx cd PA AA HW 12 The cd command takes me back to the main repository directory where I see HOWTO docs as a sub directory I want to add that and all of its files to the repository In the previous section I noticed that when I added a directory svn did not automatically add the files inside the directory into the repository So I individually added the files Since then I ve re read the manual and I ve learned that the add command can work recursively if I add the depth option svn add depth infinity HOWIG docs A HOWIO docs A HOWIO docs SVN intro lyx That adds the directory and files to the repository framework but it does not upload them We have to force a commit or check in like so ci commit svn ci m initial pauljohn hpc quant ku edu s password Adding HOWIQ docs Adding HOWIQ docs SVN intro lyx Transmitting file data Committed revision 1 Various programs I use like Emacs and LyX are SVN aware which means they have menus to check out files and check them back in to the repository I often prefer to avoid those conveniences to feel sure things are working I d rather just type svn commands in the terminal But your mileage may vary Now2. find it confusing at this point The result is Sending rawdata txt Transmitting file data Committed revision 2 Back out of there cd 5 4 Lets Beat The Example Into the Ground Completely Create yet one more working directory We will test the newly uploaded file mkdir TmpWorkDir3 cd TmpWorkDir3 This downloads a current snapshot of the repository svn co svn ssh hpc quant ku edu home pauljohn tmp PJtestsvn A PJtestsvn rawdata txt A PJtestsvn coolcode R A PJtestsvn something txt Checked out revision 2 Use cat to display the contents of the file rawdata txt See it is still the same bunch of crap I started with cat PJtestsvn rawdata txt iasdf ajsdkfl ajdsf asfdl jaskf aj asdfk asjdf Good The file is there Then I edit rawdata txt with nano cd PJtestsvn nano rawdata txt and put in some different crapola Then I send it to the repository svn commit m some random crapola Sending rawdata txt Transmitting file data Committed revision 3 Now If I go to the other working directory and run svn update It should find the new information in the repository and integrate it with your current working version 5 5 Add Files and Directories to the Repository The only way to add material in a repository is to check out a working copy and then make the desired changes and then add the new files to the repository Lets try to add a directory I am currently sti
3. if you want to grab your own working copy of my SVN repository go to some computer and tell it you want it If you are a member of crmda on hpc you can have it Run this on a Linux workstation svn co svn ssh hpc quant ku edu crmda users pauljohn SVN repo If you are in Windows or a Mac your interface will be different but I m pretty sure the part the program will need is svnt tssh hpc quant ku edu crmda users pauljohn SVN repo Now I could with a completely clear conscience throw this laptop computer off a bridge and forget about it Because I am secure in the knowledge that the file SVN intro lyx is saved in my repository on HPC All I need to do is get another laptop check out a new working directory and I m back in business 9 There s a Lot More to Do amp Learn Subversion is an industrial sized team ready production tool It can do all kinds of stuff most ordinary humans like you and me never really need When a program is finished and ready for packaging it can be tagged with a version number and then exported Revisions can be created on branches and changes can be merged back onto the main trunk of the project 13 We do that kind of stuff in software development but you probably won t need to if you are just using Subversion to keep track of your personal software and document development If you decide to convert your R code into an R package well the additional power of SVN wi
4. there on HPC Let s experiment in a safe way where it is easy to erase mistakes and erase them and start over We will create a repository within your personal user account SVN is already installed and configured on hpc quant ku edu If you happen to google and find a bunch of instructions about setting up Apache or Unix user groups or svn just ignore that part We did it already You just need to use it From what I can tell it will be necessary for you to actually log into hpc and manually create the repository in your personal account That is a very easy process as I will demonstrate in the next section After that you can use any SVN client program to get the files when you want them and send them back when you are finished More on that later First I will walk through the process of logging on to hpc quant ku edu and creating the archive Later I will learn how to use the free Windows program TortoiseSVN and see what it can do 5 1 Start a test repository on HPC This is a nice way to get your feet wet in Linux It is not a completely stupid task it is useful and it is not too difficult either On a workstation use some terminal program Putty in Windows is OK xterm or gnome terminal in Linux is OK On a Linux workstation d just open the terminal and type this to go over to HPC gt ssh username hpc quant ku edu For username I put pauljohn It is not necess
5. user manual I suspect 1 was in large part driven by 2 In the early 2000s the software experts started to want more features and a proliferation of version control systems emerged Linus Torvalds the author of the original Linux kernel proposed a program git There are many others bazaar mercurial and so forth I have not used them At the current time the version control system that is most like CVS is called SVN short for Subversion The commands that are used to interact with Subversion are almost the same as CVS so as a simple user with simple needs I don t notice much difference But I have to admit it is a hassle to get started with version control but after you do it for a while you will never want to go back The alternative is to make a full copy of your project and set it aside frequently If you have ever done that then you know it has strengths and weaknesses You do need a Subversion Server running somewhere I have Subversion installed in my personal computer so I can just create a repository on my hard disk If your system does not have Subversion then you need to use a remote server That sounds frightening but it is not too hard At the University of Kansas we have Subversion installed on the cluster system known as hpc quant ku edu Users can create their own personal SVN archives or they can participate in the communal programming effort via SVN 3 Conceptual Time Flow of V
6. using in the late 1980s and 1990s If you don t do this SVN will get mad and it won t work right If you don t already have a temporary directory tmp make one mkdir tmp Then change to the tmp folder as the working directory cd tmp Create an SVN repository for testing Mine is named PJtestsvn svnadmin create PJtestsvn PJtestsvn appears as a directory inside my tmp folder which is in my HOME so the full path to it is home pauljohn tmp PJtestsvn The command cd by itself bumps you back to your home folder See what I mean Run the command pwd to see where you are cd pwd 5 2 Import some content into the SVN repository Now create some empty files somewhere so we have something to test with mkdir TmpWorkDir cd TmpWorkDir touch rawdata txt touch coolcode R PAA HK touch something txt The touch command has the effect of creating an empty file if none exists or if one does exist it gives it a current time stamp We tell the svn repository that we want to add these files in the repository s top folder svn import m initial svn ssh hpc quant ku edu home pauljohn tmp PJtestsvn When that works you see this output Adding rawdata txt Adding coolcode R Adding something txt About my svn command The backslash is only needed because my command ran onto a second line It is not needed if yours fits on one line The option m initial is option
7. Version Control Systems and Subversion SVN Paul Johnson Nov 24 2010 1 Analogy For Microsoft Word Users I often forget that the people I m trying to help have a completely different experience than I do I often plunge into a massive explanation that is completely useless This section is my effort to avoid that Have you ever used change tracking in an MS Word document That s handy because you can see what changes have been made you can reject a suggested change and go back Version control is a bit like saving your place in a video game actually If your character gets killed you can start again from a previous saved position Version control is somewhat like that except it is more thorough A version control system keeps track of all of your changes and allows you to grab any past version of a file A version control system allows teamwork several people can edit the same set of files at once and the system tries to reconcile the changes The system tracks who makes changes It asks them to explain the changes they make And it allows rollbacks Version control is harder to set up the first time It is not automatic 2 Brief Background on Version Control There are many different programs for version control The time honored standard was CVS Concurrent Version System Of all of the free software programs I have used that one had 1 the longest run as the dominant widely used program and 2 the best
8. al If I don t do that then the svn system wants to make me open an editor and type out an explanation of what these files are The m initial option just lets me give the message initial so I will be able to tell in the future this is the initial check in 5 3 Check out a Sandbox Working Copy Now test that the repository works Back out of TmpWorkDir We might as well stay in character and create TmpWorkDir2 to use for another sandbox cd mkdir TmpWorkDir2 cd TmpWorkDir2 svn checkout svn ssh hpc quant ku edu home pauljohn tmp PJtestsvn A PJtestsvn rawdata txt A PJtestsvn coolcode R A PJtestsvn something txt Checked out revision 1 ls you should see that a new directory called PJtestsvn was created That s your working copy of the repository Change into that directory cd PJtestsvn The program nano is a text editor It is patterned after the editor that was used in an email program called pine that we used to use in the 1980s nano rawdata txt Put some stuff in there anything you want save it Control O close nano Control X I just put in gibberish like iasdf ajsdkfl to see that the svn system works Then commit it to the repository svn commit m Some random characters I chose The m option gives a check in message If I don t do that svn will aske me to interactively type in change log I don t mind that but you might
9. ary to include username but I try to remember to do that in case I m logged in with a different user name If you only have one login name on all systems it will be OK to just let the system assume you always have the same name Run gt ssh hpc quant ku edu If you are in Windows there is a free program called Putty and if you double click the icon for that and make sure the ssh button is selected then it will give you the right menu you need to log in After giving a password you see this Last login Thu Sep 30 15 50 44 2010 from 129 237 46 125 Access to electronic resources at the University of Kansas is restricted to employees students or individuals authorized by the University or its affiliates Use of this system is subject to all policies and procedures set forth by the University located at www policy ku edu Unauthorized use is prohibited and may result in administrative or legal action The University may monitor the use of this system for purposes related to security management system operations and intellectual property compliance username hpc The dollar sign is the prompt Type there One silly preliminary Run this export SVN_EDITOR nano The SVN system will want to know what editor you will use when you need to interact with it I suggest the simple editor nano for now nano is based on the editor that was used in the email system pine which virtually everybody at KU was
10. copies before committing changes rarely run afoul of others work That rarity is nonetheless accounted for by Subversion with conflict resolution features built in It also supports easy branching of modified versions of the main development trunk merging of divergent development branches varying levels of checkout and update permissions for various classes of user and a number of other useful features that project managers often find invaluable Personal document management Another benefit of version control systems is that they allow you to work on a single project from a number of different locations using a number of different computers without having to keep any USB storage devices or CD RW media on you at all times As long as you have a version control client installed on the computer where you re going to work and have access to the server where the version control magic happens you can check out the current version of the project and get to work Because of the fact that multiple copies of the same data are automatically synchronized to the same state when the checked out copy is updated on multiple client machines a version control system like Subversion can also serve as an excellent backup sys tem for a collection of files This covers your everyday personal documents as well as source code that is if you interpret project to mean any relatively small collection of data small enough so that you don t require a bandw
11. ersion Control This document is not a substitute for a comprehensive SVN manual but it should help us to get off the ground First Create the repository That s the vault where all the code and changes are recorded Second Go somewhere else and download or check out a working copy of the repository Let s call that the initial working directory That s like a sandbox You can change whatever you want Add files add directories Third Add those new files to the repository That is called committing or checking in your files Fourth Make sure the whole thing worked Go to another computer check out a new snapshot of your repository Fiddle around with those files in the sandbox When you are ready you commit those changes into the repository The repository keeps a current version and it also keeps the previous versions which you can recover if you want to Fifth Go back to the initial working directory and bring it up to date You should see that the changes you made from your other computer will appear in this updated working directory You can fiddle around with those files commit the changes and walk away The SVN repository of course should not be deleted But you can feel free to delete any working directories This means that if you take some project and make a bunch of mistakes you don t have to worry You can always check out the repository again If you want to yo
12. hing inside that and so forth cd svn add depth infinity SomethingElse svn commit m here is everything that has been updated or added 6 Accessing Your Personal Repository from MS Windows with TortoiseSVN A free program called TortoiseSVN is available It is easy to install and it runs as a Windows File Explorer addon After installing TortoiseSVN I wondered if I could recover the files from my repository I made a Windows folder navigated into it and then right clicked on the background There should be two TortoiseSVN related options Click the one with the little arrow by it and choose Repo Browser We can use that to go see what we left on HPC syn ssh pauljohn hpc quant ku edu home pauljohn tmp PJtestsvn The only really annoying part of this is that it asks me for my password three times in a row You can navigate the repository in the usual way and when you get to the directory that you want to work with right click and choose check out TortoiseSVN will then ask you where you want to keep your working copy I chose C Users pauljohn Desktop whatever The current versions of the SVN files are downloaded and I could edit them When I created a folder or files in a folder I noticed I could right click choose the TortoiseSVN commit and then a menu appeared asking me if I wanted to add some files or directories to the SVN repository I did so it uploaded them Then I
13. hn chmod g s pauljohn I ran ls la to make sure I had this tightened down In the end what I want to see is the following cd pauljohn ls la drwxr s 10 pauljohn crmda 10 Nov 24 11 58 drwxr xr x 113 root admin 113 Nov 22 13 03 drwxr xr x 3 pauljohn crmda 13 Apr 13 2010 acadiau drwxr xr x 6 pauljohn crmda 7 Nov 1 19 19 RandBlas drwxr xr x 6 pauljohn crmda 8 Nov 24 11 26 SVN repo The current working directory is now crmda users pauljohn That is where I will create the svn repository called SVN repo export SVN_EDITOR nano svnadmin create SVN repo That creates a repository in a folder SVN repo that is sitting in my share on hpc I can access that from anywhere to check out a working copy and then check back in my changes Now I go through the check out step on my laptop That just first place where I want to use those files I ll also make checkouts on my home PC my PC in Blake Hall and probably on some workstations in the CRMDA On the laptop I changed to my directory where I keep course material and I run the command to check out the whole hierarchy under SVN repo cd ps svn co svn ssh hpc quant ku edu crmda users pauljohn SVN repo pauljohn hpc quant ku edu s password pauljohn hpc quant ku edu s password Checked out revision Q0 T ll test out the process of adding new content before I quit In that working copy on my laptop
14. idth optimized weekly backup to minimize the time spent copying your data A personal documents directory usually fits this description perfectly especially when you don t keep many files that tend toward multiple megabyte file sizes such as music video and high resolution image files If you are the type of computer user who understands that regular backups are extremely important as a precaution against hardware or file system failures but just find yourself putting off regular backups because of the effort involved in configuring a traditional backup system or copying data to huge stacks of CD R media Subversion could be just what the doctor ordered The simplicity of a tool like Subversion for personal document backups can save you from yourself or at least from your own tendency to procrastinate and all you need is a second computer running the Subversion server software Because Subversion is not tied to a single purpose specific graphical user interface the way many proprietary systems like Visual SourceSafe and ClearCase are it is easily adapted to nonstandard uses such as standard document control as well You can still have your GUI environment however because there are a number of stand alone GUI clients for Subversion and Subversion has been integrated with a number of other GUI tools such as Eclipse and even Microsoft s Windows Explorer file browser via the TortoiseSVN client 5 Create Your Repository over
15. ll help you out Finally yes I realize there are abbreviations and shortcuts that will work to make some of the commands here shorter Inside one system it is not generally necessary to access files through svn ssh because a more simple access protocol is available for example But if svn ssh does work why bother learning another style For abbreviations it is true that one replace commit with ci and checkout with co Run svn help to see a list of abbreviations 14
16. ll in the last sandbox home pauljohn tmp Tm pWorkDir3 Run pwd to make sure Check what I ve got so far ls PJtestsvn Good that s the copy of the repository Change in there cd PJtestsvn It appears I have the right stuff ls coolcode R rawdata txt something txt Create a new folder mkdir SomethingElse Add that to the repository svn add SomethingElse A SomethingElse Go into SomethingElse and create a file cd SomethingElse touch anotherFile txt cd svn commit m here s something SomethingElse Adding SomethingElse Committed revision 4 cd SomethingElse svn status anotherFile txt That means the svn system does not recognise anotherFile txt I can manually add that particular file though svn add anotherFile txt A anotherFile txt And then commit this version svn commit m here is some file anotherFile txt Adding anotherFile txt Transmitting file data Committed revision 5 I think it is useful to see that we can add an individual file and check it in with commit but usually I don t deal with files individually Usually I create a folder of material and I want to add everything in the repository That s useful when there are a lot of files involved This should do it The option depth infinity on the add command means that svn will absorb SomethingElse and everything that is inside it and everything that is inside everyt
17. ly different format but the key idea is the same The address you need to check out is probably going to be svnt tssh pauljohn hpc quant ku edu projects svn repos md 8 I m Shooting with Real Bullets Now Recently I realized that my course writeups my handouts my slide shows have degenerated into a completly unmanageable mess There are different versions floating about I can t remember which version of my regression handout is current etc I decided to start an SVN repository on hpc where I would re organize my writeups I decided to put this archive in the crmda share where members of the crmda group can check out working copies if they want to Here s the embarrassing part Even though I wrote this guide only two weeks ago I had to read it step by step to remember how to do this So first I logged into hpc quant ku edu went into my folder re set permissions so group members will have read access cd crmda users chown pauljohn crmda pauljohn Unfortunately that seems to give everybody in the crmda group write permission on my folder so I need to tighten things up First I need to revoke write permission from the group I m doing this recursively hence the capital R option chmod R g w pauljohn 11 I also want every file I create within there to have the group assigned as crmda and the way to do that is to assign the sticky bit for the group marker on the folder pauljo
18. u can check out the repository as it was on some date in the past 4 SVN Why bother From Chad Perrin Use open source Subversion for personal document management March 14 2007 http articles techrepublic com com 5100 10878_11 6167205 html A mechanism for automatic revision history management is probably most likely to be familiar to non programmers because the most famous examples of wiki software employ such a technique for tracking changes to content and allowing undesirable changes to be reversed As part of the revision history mechanism a version control system such as Subversion not only maintains a central data repository copy of the current version of files that have been entrusted to version control but also maintains a log of changes that have been made from the present all the way back to the moment the files entered version control Anyone who has been doing software development work for very long should be able to tell you how important the ability to roll back a file to a known good state can be This is in fact the central feature of any version control software the primary reason it exists Subversion does this and much more For instance it also provides the ability to resolve version conflicts when two people have been editing the same file at the same time In the real world users who employ good practices such as making regular commits when working on files in version control and updating local
19. went to another system grabbed the same repository and the new stuff was in it Problem solved Because TortoiseSVN is point and click inside the Explorer it is not so easy to tell you exactly what to do But I suppose the point of that is that you should be able to figure it out on your own if you can point and click at it 7 Sharing a Repository with Other Users This is the way big time software development works People expect cooperative work effort on a common set of files In the next section I describe the steps I ve taken to create a new repository in my user share on hpc to allow other people to download my course notes I probably will never give other people permission to write in that folder but I don t mind sharing If I want a folder that other people can both read and write then I need to be a bit more careful On HPC we have set aside a folder in the common storage system for this purpose The system wide SVN repository is stored in projects svn As of November 2010 the following SVN registered projects exist hpcexample md HPC example is a collection of programs that use cluster computing md is the missing data simulation project Ordinary users in the HPC system are not allowed to create new project folders but they can make requests for new projects to clusterhelp ittc ku edu The permissions on those folders are set as follows drwxr xr x 6 pauljohn pauljohn 8 Jun 2 11 53 hpce
20. xample drwxrwxr x 6 pauljohn mdgroup 8 May 7 2010 md 10 The hpcexample folder is owned by pauljohn and the group is pauljohn that means as it currently stands only pauljohn can write in there but other system users are able to read that material That means any user in HPC can check out hpcexample but cannot commit changes to it Rather than repeat myself about access to hpcexample I would refer the reader to the web page where the details have already been committed http pj freefaculty org cgi bin mw index php title Cluster Main A_Collection_of_ Simple_Working Examples_Using Qsub_and_Multi core 2Fthreading Perhaps at some point in the future there will be other qualified users and a group can be created to make changes in hpcexample The md folder is owned by pauljohn but its group is mdgroup Note the group permissions are rwx so that anybody in the mdgroup can check in changes The permissions for others are rx which means that other people are allowed to check out a copy of the archive but they cannot write changes back onto it People who want to make contributions will have to request membership in the Unix user group called md To grab a snapshot of the md directory from a Linux workstation this command should do it svn co svn ssh pauljohn hpc quant ku edu projects svn repos md If you are in Windows or a Mac system your client program will want the options in a slight
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