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The goal of the Subversion (SVN) project is to build a version control system that is a compelling replacement for CVS in the open source community. The software is released under an Apache/BSD-style open source license. Subversion is meant to be a better CVS, so it has most of CVS's features. Generally, Subversion's interface to a particular feature is similar to CVS's, except where there's a compelling reason to do otherwise. [http://subversion.tigris.org/]  * Subversion is a free/open source version control system. That is, Subversion manages files and directories, and the changes made to them, over time. [[http://subversion.apache.org/]]
 * General SVN documentation is available here: [[http://subversion.apache.org/docs/]] and a nice online book can be found here: [[http://svnbook.red-bean.com/]].
 * In order to access an SVN repository, you must install a special piece of software called an SVN client; SVN clients are available for most any operating system.
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In order to access an SVN repository, you must install a special piece of software called an SVN client; SVN clients are available for most any operating system. General SVN documentation is available on this [http://subversion.tigris.org/servlets/ProjectDocumentList?folderID=254&expandFolder=254&folderID=257] and a nice online book can be found here: [http://svnbook.red-bean.com/]. === Browsing SVN ===
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You can browse the source repository with a web browser: [[http://chianti.ucsd.edu/svn/cytoscape]]
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== SVN Access == === SVN Access ===
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If you're remote you can check code out using ssh:
{{{
svn co svn+ssh://gamay.ucsd.edu/cellar/common/svn/cytoscape/trunk cytoscape
}}}

You can check out code anonymously: 		If you do not have a username on grenache you can check out code anonymously. '''Note''' that you are not able to check code '''IN''' through chianti. This is meant to be a public resource for people other than cytoscape developers.
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You can also browse the source repository with a normal web browser: If you're a cytoscape developer, you should use grenache to check code in and out.
{{{
svn co svn+ssh://grenache.ucsd.edu/cellar/common/svn/cytoscape/trunk cytoscape
}}}
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[http://chianti.ucsd.edu/svn/cytoscape] If this doesn't work, you may need to specify your user account, as defined on grenache. For example:
{{{
svn co svn+ssh://username@grenache.ucsd.edu/cellar/common/svn/cytoscape/trunk cytoscape
}}}

Or, to check out a specific branch:
{{{
svn co svn+ssh://grenache.ucsd.edu/cellar/common/svn/cytoscape/branches/Cyto-2.7.x_release_branch/ cytoscape_2_7
}}}
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1. Setup Subversion plugin 1. Setup subclipse plugin: [[http://subclipse.tigris.org/]]
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[http://subclipse.tigris.org/install.html]  * Update site for Eclipse 3.2/Callisto, 3.3/Europa, 3.4/Ganymede, 3.5/Galileo +: [[http://subclipse.tigris.org/update_1.6.x]]
 * Installation instructions can be found here: [[http://subclipse.tigris.org/servlets/ProjectProcess?pageID=p4wYuA]]
 * In Eclipse, Window>Preferences>Team>SVN. Set SVN Interface to "JavaSVN (Pure Java)"
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Remote site
 * For 3.1: [http://subclipse.tigris.org/update_1.0.x]
 * For 3.2: [http://subclipse.tigris.org/update_1.2.x] (Still beta?)


2. Check out project from UCSD Repository:
 - File --> New --> Project
 - Select "SVN"
 - Create new repository. URL is:
 		2. Check out project from UCSD Repository (chianti or grenache):
 * File --> New --> Project
 * Select "SVN"
 * Create new repository. If you have developer account, URL is:
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 svn+ssh://gamay.ucsd.edu/cellar/common/svn  svn+ssh://grenache.ucsd.edu/cellar/common/svn
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 - You can use default values for port number etc.
 - ID and password: same as CVS id & pw for gammay 		Otherwise, you can check out project anonymously from:
{{{
http://chianti.ucsd.edu/svn
}}}
 * You can use default values for port number etc.
 * ID and password are required on grenache, and not required for anonymous checkout on chiante. These are same as CVS id & password.
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== Tips and Troubleshooting == === Tips and Troubleshooting ===
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General advice for those who have difficulties getting SVN access in the Eclipse environment. These are not meant to be sequential steps. These are just 4 independent tips that address a range of issues, in no particular order. If just doing #1 works, then you're done. But if not, then #2-4 provide other things to try, leads derived from solutions found in various forums and FAQs. General advice for those who have difficulties getting SVN access via the Subclipse in the Eclipse environment. These are not meant to be sequential steps. These are just 4 independent tips that address a range of issues, in no particular order. If just doing #1 works, then you're done. But if not, then #2-4 provide other things to try, leads derived from solutions found in various forums and FAQs.
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3. Request a new password from Mike Smoot. Some old passwords may not work (mine didn't!) 3. Request a new password from MikeSmoot. Some old passwords may not work (mine didn't!)
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4. Try alternative plugin: TortoiseSVN: [http://www.tabaquismo.freehosting.net/ignacio/eclipse/tortoise-svn/subversion.html]   4. Try alternative plugins:
  * TortoiseSVN: [[http://www.tabaquismo.freehosting.net/ignacio/eclipse/tortoise-svn/subversion.html]]
  * Subversive: [[http://www.eclipse.org/subversive/]] use this url for the Remote Site in the update manager: http://www.polarion.org/download/p_subversive/update-site/
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== What to Check In ==

In general you should only check in source files and the files needed to compile the source (e.g. library jar files). You should '''NOT''' check in generated files such as jar files that you compiled in your project or .class files. Since these files are created directly from the source, there is no need to check them in and is a waste of disk space.

It can also be problematic to check in IDE configuration files. It is OK to check in the configuration file for that particular project, but anything that is specific to your machine (e.g. lists a specific class path) should be avoided since this will not work in other people's configurations.

== Creating New Projects ==

Given the current configuration of our system, it is rare that you should be creating a new top-level project. In general, you will want to add files to an existing project rather than creating a new project. This holds for new plugins or libraries for cytoscape. To add new files, simple check out the existing project, move your new files into the directory that you'd like to add to the project, and then run {{{svn add directory-to-add}}} to add the files to the project.

If you find that you do need to run the {{{svn import}}} command, then please contact MikeSmoot before doing so.
 

About SVN

  • Subversion is a free/open source version control system. That is, Subversion manages files and directories, and the changes made to them, over time. http://subversion.apache.org/

  • General SVN documentation is available here: http://subversion.apache.org/docs/ and a nice online book can be found here: http://svnbook.red-bean.com/.

  • In order to access an SVN repository, you must install a special piece of software called an SVN client; SVN clients are available for most any operating system.

Browsing SVN

You can browse the source repository with a web browser: http://chianti.ucsd.edu/svn/cytoscape

SVN Access

If you do not have a username on grenache you can check out code anonymously. Note that you are not able to check code IN through chianti. This is meant to be a public resource for people other than cytoscape developers. 

svn co http://chianti.ucsd.edu/svn/cytoscape/trunk cytoscape

If you're a cytoscape developer, you should use grenache to check code in and out. 

svn co svn+ssh://grenache.ucsd.edu/cellar/common/svn/cytoscape/trunk cytoscape

If this doesn't work, you may need to specify your user account, as defined on grenache. For example: 

svn co svn+ssh://username@grenache.ucsd.edu/cellar/common/svn/cytoscape/trunk cytoscape

Or, to check out a specific branch: 

svn co svn+ssh://grenache.ucsd.edu/cellar/common/svn/cytoscape/branches/Cyto-2.7.x_release_branch/ cytoscape_2_7

SVN Access in Eclipse

1. Setup subclipse plugin: http://subclipse.tigris.org/

2. Check out project from UCSD Repository (chianti or grenache):

  • File --> New --> Project

  • Select "SVN"
  • Create new repository. If you have developer account, URL is: 

 svn+ssh://grenache.ucsd.edu/cellar/common/svn

Otherwise, you can check out project anonymously from: 

http://chianti.ucsd.edu/svn
  • You can use default values for port number etc.

  • ID and password are required on grenache, and not required for anonymous checkout on chiante. These are same as CVS id & password.

3. Check in code

  • - Almost same as GUI for CVS. Select "Team" menu item for more detail.

Tips and Troubleshooting

General advice for those who have difficulties getting SVN access via the Subclipse in the Eclipse environment. These are not meant to be sequential steps. These are just 4 independent tips that address a range of issues, in no particular order. If just doing #1 works, then you're done. But if not, then #2-4 provide other things to try, leads derived from solutions found in various forums and FAQs.

1. SVN Interface:

  • In Eclipse, Window>Preferences>Team>SVN. Set SVN Interface to "JavaSVN (Pure Java)"

2. Define SSH Client for Subversion:

  1. Edit C:\Documents and Settings\*user*\Application Data\Subversion\config and add "ssh = C:\Program Files\TortoiseSVN\bin\TortoisePlink.exe" after "[tunnels]" heading.

  2. Set environment variable "SVN_SSH" to "C:\Program Files\TortoiseSVN\bin\TortoisePlink.exe"

3. Request a new password from MikeSmoot. Some old passwords may not work (mine didn't!)

4. Try alternative plugins:

Common Error Messages:

  • Subclipse:
    1. "tunneling" problem. Solution = see #1 above.
    2. "malformed network data" = may be password problem
    3. "std output (err)" issue = may be password problem

What to Check In

In general you should only check in source files and the files needed to compile the source (e.g. library jar files). You should NOT check in generated files such as jar files that you compiled in your project or .class files. Since these files are created directly from the source, there is no need to check them in and is a waste of disk space.

It can also be problematic to check in IDE configuration files. It is OK to check in the configuration file for that particular project, but anything that is specific to your machine (e.g. lists a specific class path) should be avoided since this will not work in other people's configurations.

Creating New Projects

Given the current configuration of our system, it is rare that you should be creating a new top-level project. In general, you will want to add files to an existing project rather than creating a new project. This holds for new plugins or libraries for cytoscape. To add new files, simple check out the existing project, move your new files into the directory that you'd like to add to the project, and then run svn add directory-to-add to add the files to the project.

If you find that you do need to run the svn import command, then please contact MikeSmoot before doing so.

SVN_Access (last edited 2010-08-03 10:37:00 by 46-116-188-160)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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