Dear Bioconductors, We're pleased to announce the availability of Bioconductor Git Mirrors. These are read-only GitHub repositories (available under https://github.com/Bioconductor-mirror) for every Bioconductor software package. These repositories are synchronized with our Subversion repository. Package maintainers (or anyone else) can fork these repositories and do their development on the fork. Complete documentation of the mirrors is at http://bioconductor.org/developers/how-to/git-mirror/ These mirrors supersede the Git-SVN bridge, which is now deprecated. Creation of new bridges is disabled and maintainers who are using the bridge should migrate to the Git mirrors as soon as it's convenient, as the bridge will eventually go away. Instructions for migrating can be found at the above link. Some features of the new Git Mirrors, and why we feel they are a better solution than the Git-SVN bridge: - The mirrors contain complete commit history. - The mirrors contain release branches for Bioconductor 3.0 and 3.1, and new releases will be added as they happen. You will no longer need separate repositories for release and devel. - Setup is easy and you no longer have to grant any permissions on your repository to other users. You can commit directly to Subversion using git-svn (https://git-scm.com/docs/git-svn). - Each git commit appears in the SVN log as a distinct SVN commit; commits are no longer grouped together as they were with the bridge. Each git commit can be mapped to a specific svn commit, and vice versa. - The Git mirrors are much more reliable. - Use is flexible. You can use git locally (without GitHub) or you can use GitHub as well, to take advantage of all its social coding features. - Using GitHub's code search, you can search the entire Bioconductor codebase. Here's a sample search: https://goo.gl/jI92Ys - Subversion is fully supported and remains the cannonical repository; use of Git and GitHub is optional. We are excited about these new mirrors (brought to you by the hard work of Jim Hester) and we hope you are too. Questions and comments are welcome on the bioc-devel mailing list. Dan
[Bioc-devel] Bioconductor Git/GitHub Mirrors
17 messages · Ryan, Leonardo Collado Torres, Dan Tenenbaum +3 more
Correct link is http://bioconductor.org/developers/how-to/git-mirrors/ On Tue, Jun 16, 2015 at 3:00 PM Dan Tenenbaum <dtenenba at fredhutch.org> wrote:
Dear Bioconductors, We're pleased to announce the availability of Bioconductor Git Mirrors. These are read-only GitHub repositories (available under https://github.com/Bioconductor-mirror) for every Bioconductor software package. These repositories are synchronized with our Subversion repository. Package maintainers (or anyone else) can fork these repositories and do their development on the fork. Complete documentation of the mirrors is at http://bioconductor.org/developers/how-to/git-mirror/ These mirrors supersede the Git-SVN bridge, which is now deprecated. Creation of new bridges is disabled and maintainers who are using the bridge should migrate to the Git mirrors as soon as it's convenient, as the bridge will eventually go away. Instructions for migrating can be found at the above link. Some features of the new Git Mirrors, and why we feel they are a better solution than the Git-SVN bridge: - The mirrors contain complete commit history. - The mirrors contain release branches for Bioconductor 3.0 and 3.1, and new releases will be added as they happen. You will no longer need separate repositories for release and devel. - Setup is easy and you no longer have to grant any permissions on your repository to other users. You can commit directly to Subversion using git-svn (https://git-scm.com/docs/git-svn). - Each git commit appears in the SVN log as a distinct SVN commit; commits are no longer grouped together as they were with the bridge. Each git commit can be mapped to a specific svn commit, and vice versa. - The Git mirrors are much more reliable. - Use is flexible. You can use git locally (without GitHub) or you can use GitHub as well, to take advantage of all its social coding features. - Using GitHub's code search, you can search the entire Bioconductor codebase. Here's a sample search: https://goo.gl/jI92Ys - Subversion is fully supported and remains the cannonical repository; use of Git and GitHub is optional. We are excited about these new mirrors (brought to you by the hard work of Jim Hester) and we hope you are too. Questions and comments are welcome on the bioc-devel mailing list. Dan
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
This is great to hear. I sometimes want to delve into the source code of a package's internals, but doing so through the SVN web interface is clunky. Being able to use Github's repo browsing functionality for Bioc packages is great.
On 06/16/2015 12:00 PM, Dan Tenenbaum wrote:
Dear Bioconductors, We're pleased to announce the availability of Bioconductor Git Mirrors. These are read-only GitHub repositories (available under https://github.com/Bioconductor-mirror) for every Bioconductor software package. These repositories are synchronized with our Subversion repository. Package maintainers (or anyone else) can fork these repositories and do their development on the fork. Complete documentation of the mirrors is at http://bioconductor.org/developers/how-to/git-mirror/ These mirrors supersede the Git-SVN bridge, which is now deprecated. Creation of new bridges is disabled and maintainers who are using the bridge should migrate to the Git mirrors as soon as it's convenient, as the bridge will eventually go away. Instructions for migrating can be found at the above link. Some features of the new Git Mirrors, and why we feel they are a better solution than the Git-SVN bridge: - The mirrors contain complete commit history. - The mirrors contain release branches for Bioconductor 3.0 and 3.1, and new releases will be added as they happen. You will no longer need separate repositories for release and devel. - Setup is easy and you no longer have to grant any permissions on your repository to other users. You can commit directly to Subversion using git-svn (https://git-scm.com/docs/git-svn). - Each git commit appears in the SVN log as a distinct SVN commit; commits are no longer grouped together as they were with the bridge. Each git commit can be mapped to a specific svn commit, and vice versa. - The Git mirrors are much more reliable. - Use is flexible. You can use git locally (without GitHub) or you can use GitHub as well, to take advantage of all its social coding features. - Using GitHub's code search, you can search the entire Bioconductor codebase. Here's a sample search: https://goo.gl/jI92Ys - Subversion is fully supported and remains the cannonical repository; use of Git and GitHub is optional. We are excited about these new mirrors (brought to you by the hard work of Jim Hester) and we hope you are too. Questions and comments are welcome on the bioc-devel mailing list. Dan
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Hi, This sounds great! Not having to setup all those bridges everytime a new BioC version is released should be a great feature, plus keeping the commit history tidy. And we can still use Travis or other things like Slack notifications on our own bridges. I guess that it'd be good to remind users to pull new content from the bioc remote before trying to commit to svn. Anyhow, great work! I'm having a few problems with this new setup which hopefully are easy to iron out. Basically, I am stuck at the "git svn rebase && git svn dcommit --add-author-from" step. See 2b) below. 1) My git was pointing to an older version even after updated with brew. This was because I still had MacPorts around. How to diagnose: $ which git Wrong version was pointing to /opt/local/bin/git instead of /usr/local/bin/git Can also see by running $ git --version ## if it doesn't match the version number you installed from brew Solution: * Uninstall all of MacPorts following instructions from https://guide.macports.org/chunked/installing.macports.uninstalling.html * Follow part of http://stackoverflow.com/questions/20648235/error-linking-git-to-homebrew $ sudo brew prune $ brew update $ brew install git $ brew unlink git && brew link git You might want to update subversion. http://blog.victorquinn.com/fix-git-svn-in-mountain-lion might be relevant for you. 2) Test case: derfinderHelper. Smallest and simplest package I have, which won't matter much if things break because it's stable. a) You might want to delete update_remotes.sh after using it. * I deleted the git-svn bridges to both https://github.com/leekgroup/derfinderHelper and https://github.com/leekgroup/derfinderHelper-release * On https://github.com/leekgroup/derfinderHelper I removed bioc as a collaborator and deleted the push-hook since it seems like we don't need this anymore * Download and ran update_remotes.sh as instructed. It doesn't seem like we need it anymore after that point. If you leave it there, it seems to give problems. Easy to solve, but might want to clarify in the instructions. b) Following the section "Use Git Locally And Publicly" I get stuck on the "git svn rebase && git svn dcommit --add-author-from" step as shown at https://gist.github.com/lcolladotor/ac8838b25955caeebcf1. The "CONFLICT (add/add): Merge conflict" message lead me to http://stackoverflow.com/questions/19475387/how-to-handle-fix-git-add-add-conflicts from where I could resolve the initial problem that I saw using "git diff". But was basically the changes between the very first version of README.md and the very latest version of it. There must be a way to not have to go through every single commit and/or file one by one. Using "git rebase --continue" doesn't help. c) Given the issue with b, the devel branch already has a merge commit. Using http://stackoverflow.com/questions/927358/how-to-undo-the-last-commit I cleaned things up. I don't think it's needed, but I don't want to run into more issues. $ git rebase --abort $ git reset HEAD~1 As you can tell, I'm no "git rebase" expert. From http://git-scm.com/docs/git-rebase it seems like the "ours" option might be useful. But right now I prefer to get some pointers on how to proceed before playing around further :P Thanks, Leo PS At the "Unable to determine upstream SVN information" section, I believe that there is a typo. "git svn dcomit" should be "git svn dcommit"
On Tue, Jun 16, 2015 at 3:20 PM, Ryan C. Thompson <rct at thompsonclan.org> wrote:
This is great to hear. I sometimes want to delve into the source code of a package's internals, but doing so through the SVN web interface is clunky. Being able to use Github's repo browsing functionality for Bioc packages is great. On 06/16/2015 12:00 PM, Dan Tenenbaum wrote:
Dear Bioconductors, We're pleased to announce the availability of Bioconductor Git Mirrors. These are read-only GitHub repositories (available under https://github.com/Bioconductor-mirror) for every Bioconductor software package. These repositories are synchronized with our Subversion repository. Package maintainers (or anyone else) can fork these repositories and do their development on the fork. Complete documentation of the mirrors is at http://bioconductor.org/developers/how-to/git-mirror/ These mirrors supersede the Git-SVN bridge, which is now deprecated. Creation of new bridges is disabled and maintainers who are using the bridge should migrate to the Git mirrors as soon as it's convenient, as the bridge will eventually go away. Instructions for migrating can be found at the above link. Some features of the new Git Mirrors, and why we feel they are a better solution than the Git-SVN bridge: - The mirrors contain complete commit history. - The mirrors contain release branches for Bioconductor 3.0 and 3.1, and new releases will be added as they happen. You will no longer need separate repositories for release and devel. - Setup is easy and you no longer have to grant any permissions on your repository to other users. You can commit directly to Subversion using git-svn (https://git-scm.com/docs/git-svn). - Each git commit appears in the SVN log as a distinct SVN commit; commits are no longer grouped together as they were with the bridge. Each git commit can be mapped to a specific svn commit, and vice versa. - The Git mirrors are much more reliable. - Use is flexible. You can use git locally (without GitHub) or you can use GitHub as well, to take advantage of all its social coding features. - Using GitHub's code search, you can search the entire Bioconductor codebase. Here's a sample search: https://goo.gl/jI92Ys - Subversion is fully supported and remains the cannonical repository; use of Git and GitHub is optional. We are excited about these new mirrors (brought to you by the hard work of Jim Hester) and we hope you are too. Questions and comments are welcome on the bioc-devel mailing list. Dan
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
On Tue, Jun 16, 2015 at 8:55 PM, Leonardo Collado Torres
<lcollado at jhu.edu> wrote:
Hi, This sounds great! Not having to setup all those bridges everytime a new BioC version is released should be a great feature, plus keeping the commit history tidy. And we can still use Travis or other things like Slack notifications on our own bridges.
I meant repos here I guess that it'd be good
to remind users to pull new content from the bioc remote before trying to commit to svn. Anyhow, great work! I'm having a few problems with this new setup which hopefully are easy to iron out. Basically, I am stuck at the "git svn rebase && git svn dcommit --add-author-from" step. See 2b) below. 1) My git was pointing to an older version even after updated with brew. This was because I still had MacPorts around. How to diagnose: $ which git Wrong version was pointing to /opt/local/bin/git instead of /usr/local/bin/git Can also see by running $ git --version ## if it doesn't match the version number you installed from brew Solution: * Uninstall all of MacPorts following instructions from https://guide.macports.org/chunked/installing.macports.uninstalling.html * Follow part of http://stackoverflow.com/questions/20648235/error-linking-git-to-homebrew $ sudo brew prune $ brew update $ brew install git $ brew unlink git && brew link git You might want to update subversion. http://blog.victorquinn.com/fix-git-svn-in-mountain-lion might be relevant for you. 2) Test case: derfinderHelper. Smallest and simplest package I have, which won't matter much if things break because it's stable. a) You might want to delete update_remotes.sh after using it. * I deleted the git-svn bridges to both https://github.com/leekgroup/derfinderHelper and https://github.com/leekgroup/derfinderHelper-release * On https://github.com/leekgroup/derfinderHelper I removed bioc as a collaborator and deleted the push-hook since it seems like we don't need this anymore * Download and ran update_remotes.sh as instructed. It doesn't seem like we need it anymore after that point. If you leave it there, it seems to give problems. Easy to solve, but might want to clarify in the instructions. b) Following the section "Use Git Locally And Publicly" I get stuck on the "git svn rebase && git svn dcommit --add-author-from" step as shown at https://gist.github.com/lcolladotor/ac8838b25955caeebcf1. The "CONFLICT (add/add): Merge conflict" message lead me to http://stackoverflow.com/questions/19475387/how-to-handle-fix-git-add-add-conflicts from where I could resolve the initial problem that I saw using "git diff". But was basically the changes between the very first version of README.md and the very latest version of it. There must be a way to not have to go through every single commit and/or file one by one. Using "git rebase --continue" doesn't help. c) Given the issue with b, the devel branch already has a merge commit. Using http://stackoverflow.com/questions/927358/how-to-undo-the-last-commit I cleaned things up. I don't think it's needed, but I don't want to run into more issues. $ git rebase --abort $ git reset HEAD~1 As you can tell, I'm no "git rebase" expert. From http://git-scm.com/docs/git-rebase it seems like the "ours" option might be useful. But right now I prefer to get some pointers on how to proceed before playing around further :P Thanks, Leo PS At the "Unable to determine upstream SVN information" section, I believe that there is a typo. "git svn dcomit" should be "git svn dcommit" On Tue, Jun 16, 2015 at 3:20 PM, Ryan C. Thompson <rct at thompsonclan.org> wrote:
This is great to hear. I sometimes want to delve into the source code of a package's internals, but doing so through the SVN web interface is clunky. Being able to use Github's repo browsing functionality for Bioc packages is great. On 06/16/2015 12:00 PM, Dan Tenenbaum wrote:
Dear Bioconductors, We're pleased to announce the availability of Bioconductor Git Mirrors. These are read-only GitHub repositories (available under https://github.com/Bioconductor-mirror) for every Bioconductor software package. These repositories are synchronized with our Subversion repository. Package maintainers (or anyone else) can fork these repositories and do their development on the fork. Complete documentation of the mirrors is at http://bioconductor.org/developers/how-to/git-mirror/ These mirrors supersede the Git-SVN bridge, which is now deprecated. Creation of new bridges is disabled and maintainers who are using the bridge should migrate to the Git mirrors as soon as it's convenient, as the bridge will eventually go away. Instructions for migrating can be found at the above link. Some features of the new Git Mirrors, and why we feel they are a better solution than the Git-SVN bridge: - The mirrors contain complete commit history. - The mirrors contain release branches for Bioconductor 3.0 and 3.1, and new releases will be added as they happen. You will no longer need separate repositories for release and devel. - Setup is easy and you no longer have to grant any permissions on your repository to other users. You can commit directly to Subversion using git-svn (https://git-scm.com/docs/git-svn). - Each git commit appears in the SVN log as a distinct SVN commit; commits are no longer grouped together as they were with the bridge. Each git commit can be mapped to a specific svn commit, and vice versa. - The Git mirrors are much more reliable. - Use is flexible. You can use git locally (without GitHub) or you can use GitHub as well, to take advantage of all its social coding features. - Using GitHub's code search, you can search the entire Bioconductor codebase. Here's a sample search: https://goo.gl/jI92Ys - Subversion is fully supported and remains the cannonical repository; use of Git and GitHub is optional. We are excited about these new mirrors (brought to you by the hard work of Jim Hester) and we hope you are too. Questions and comments are welcome on the bioc-devel mailing list. Dan
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
----- Original Message -----
From: "Leonardo Collado Torres" <lcollado at jhu.edu> To: "Ryan C. Thompson" <rct at thompsonclan.org> Cc: "Dan Tenenbaum" <dtenenba at fredhutch.org>, "bioc-devel" <bioc-devel at r-project.org> Sent: Tuesday, June 16, 2015 5:55:05 PM Subject: Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors Hi, This sounds great! Not having to setup all those bridges everytime a new BioC version is released should be a great feature, plus keeping the commit history tidy. And we can still use Travis or other things like Slack notifications on our own bridges. I guess that it'd be good to remind users to pull new content from the bioc remote before trying to commit to svn. Anyhow, great work! I'm having a few problems with this new setup which hopefully are easy to iron out. Basically, I am stuck at the "git svn rebase && git svn dcommit --add-author-from" step. See 2b) below. 1) My git was pointing to an older version even after updated with brew. This was because I still had MacPorts around. How to diagnose: $ which git Wrong version was pointing to /opt/local/bin/git instead of /usr/local/bin/git Can also see by running $ git --version ## if it doesn't match the version number you installed from brew Solution: * Uninstall all of MacPorts following instructions from https://guide.macports.org/chunked/installing.macports.uninstalling.html * Follow part of http://stackoverflow.com/questions/20648235/error-linking-git-to-homebrew $ sudo brew prune $ brew update $ brew install git $ brew unlink git && brew link git
Good to know. Things seem to work on the Macs I have tested with the vanilla git-svn that ships with the OS.
You might want to update subversion. http://blog.victorquinn.com/fix-git-svn-in-mountain-lion might be relevant for you.
I haven't needed to update svn.
2) Test case: derfinderHelper. Smallest and simplest package I have, which won't matter much if things break because it's stable. a) You might want to delete update_remotes.sh after using it. * I deleted the git-svn bridges to both https://github.com/leekgroup/derfinderHelper and https://github.com/leekgroup/derfinderHelper-release * On https://github.com/leekgroup/derfinderHelper I removed bioc as a collaborator and deleted the push-hook since it seems like we don't need this anymore
Yes, you can delete the push hook. Leaving it does no harm as long as the bridge has been deleted (nobody will listen to the hook on the other end once the bridge is deleted).
* Download and ran update_remotes.sh as instructed. It doesn't seem like we need it anymore after that point. If you leave it there, it seems to give problems.
Can you explain what problems?
Easy to solve, but might want to clarify in the instructions.
I do this in a separate directory: git clone https://github.com/Bioconductor/mirror.git and then I have a repos containing the script where I can run 'git pull' if it ever changes. You could also symlink to it in /usr/local/bin. We'll see about changing the docs for this.
b) Following the section "Use Git Locally And Publicly" I get stuck on the "git svn rebase && git svn dcommit --add-author-from" step as shown at https://gist.github.com/lcolladotor/ac8838b25955caeebcf1. The "CONFLICT (add/add): Merge conflict" message lead me to http://stackoverflow.com/questions/19475387/how-to-handle-fix-git-add-add-conflicts from where I could resolve the initial problem that I saw using "git diff". But was basically the changes between the very first version of README.md and the very latest version of it. There must be a way to not have to go through every single commit and/or file one by one. Using "git rebase --continue" doesn't help.
I didn't have this problem. Here is what I did, which should be the same as what you did: forked derfinderHelper to my personal (dtenenba) account cloned the fork ran the update_remotes.sh script in the fork git checkout devel git svn rebase git merge master --no-edit git svn rebase git svn dcommit --add-author-from None of these lines gave any errors and the last line said: Committing to https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/derfinderHelper ... Doesn't seem like it actually needed to commit anything.
c) Given the issue with b, the devel branch already has a merge commit. Using http://stackoverflow.com/questions/927358/how-to-undo-the-last-commit I cleaned things up. I don't think it's needed, but I don't want to run into more issues. $ git rebase --abort $ git reset HEAD~1 As you can tell, I'm no "git rebase" expert. From http://git-scm.com/docs/git-rebase it seems like the "ours" option might be useful. But right now I prefer to get some pointers on how to proceed before playing around further :P
Well, since I can't reproduce this situation I'm not exactly sure what to tell you. If you know you want all the changes from git and none from svn (or vice versa) then the --ours and --theirs options are appropriate. But you might just want to start over and see if the problem goes away. Here are my relevant versions: $ git --version git version 1.9.5 (Apple Git-50.3) $ git svn --version git-svn version 1.9.5 (Apple Git-50.3) (svn 1.7.19) $ svn --version svn, version 1.8.11 (r1643975) $ uname -a Darwin viper 13.4.0 Darwin Kernel Version 13.4.0: Wed Mar 18 16:20:14 PDT 2015; root:xnu-2422.115.14~1/RELEASE_X86_64 x86_64 It does look like on this particular machine I have a non-standard svn: $ which svn /opt/subversion/bin/svn Looks like it came from: https://www.wandisco.com/subversion/os/downloads
Thanks, Leo PS At the "Unable to determine upstream SVN information" section, I believe that there is a typo. "git svn dcomit" should be "git svn dcommit"
Will fix. Thanks for the comments and for trying it out. Dan
On Tue, Jun 16, 2015 at 3:20 PM, Ryan C. Thompson <rct at thompsonclan.org> wrote:
This is great to hear. I sometimes want to delve into the source code of a package's internals, but doing so through the SVN web interface is clunky. Being able to use Github's repo browsing functionality for Bioc packages is great. On 06/16/2015 12:00 PM, Dan Tenenbaum wrote:
Dear Bioconductors, We're pleased to announce the availability of Bioconductor Git Mirrors. These are read-only GitHub repositories (available under https://github.com/Bioconductor-mirror) for every Bioconductor software package. These repositories are synchronized with our Subversion repository. Package maintainers (or anyone else) can fork these repositories and do their development on the fork. Complete documentation of the mirrors is at http://bioconductor.org/developers/how-to/git-mirror/ These mirrors supersede the Git-SVN bridge, which is now deprecated. Creation of new bridges is disabled and maintainers who are using the bridge should migrate to the Git mirrors as soon as it's convenient, as the bridge will eventually go away. Instructions for migrating can be found at the above link. Some features of the new Git Mirrors, and why we feel they are a better solution than the Git-SVN bridge: - The mirrors contain complete commit history. - The mirrors contain release branches for Bioconductor 3.0 and 3.1, and new releases will be added as they happen. You will no longer need separate repositories for release and devel. - Setup is easy and you no longer have to grant any permissions on your repository to other users. You can commit directly to Subversion using git-svn (https://git-scm.com/docs/git-svn). - Each git commit appears in the SVN log as a distinct SVN commit; commits are no longer grouped together as they were with the bridge. Each git commit can be mapped to a specific svn commit, and vice versa. - The Git mirrors are much more reliable. - Use is flexible. You can use git locally (without GitHub) or you can use GitHub as well, to take advantage of all its social coding features. - Using GitHub's code search, you can search the entire Bioconductor codebase. Here's a sample search: https://goo.gl/jI92Ys - Subversion is fully supported and remains the cannonical repository; use of Git and GitHub is optional. We are excited about these new mirrors (brought to you by the hard work of Jim Hester) and we hope you are too. Questions and comments are welcome on the bioc-devel mailing list. Dan
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
----- Original Message -----
From: "Leonardo Collado Torres" <lcollado at jhu.edu> To: "Ryan C. Thompson" <rct at thompsonclan.org> Cc: "Dan Tenenbaum" <dtenenba at fredhutch.org>, "bioc-devel" <bioc-devel at r-project.org> Sent: Tuesday, June 16, 2015 5:55:05 PM Subject: Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors Hi, This sounds great! Not having to setup all those bridges everytime a new BioC version is released should be a great feature, plus keeping the commit history tidy. And we can still use Travis or other things like Slack notifications on our own bridges. I guess that it'd be good to remind users to pull new content from the bioc remote before trying to commit to svn.
PS., the docs do say this: 2. git svn rebase to get the latest SVN changes. However, you are reminding me that we should make sure we document that you should merge any changes from back into master after you dcommit. Dan
----- Original Message -----
From: "Dan Tenenbaum" <dtenenba at fredhutch.org> To: "Leonardo Collado Torres" <lcollado at jhu.edu> Cc: "bioc-devel" <bioc-devel at r-project.org>, "Ryan C. Thompson" <rct at thompsonclan.org> Sent: Tuesday, June 16, 2015 7:02:36 PM Subject: Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors ----- Original Message -----
From: "Leonardo Collado Torres" <lcollado at jhu.edu> To: "Ryan C. Thompson" <rct at thompsonclan.org> Cc: "Dan Tenenbaum" <dtenenba at fredhutch.org>, "bioc-devel" <bioc-devel at r-project.org> Sent: Tuesday, June 16, 2015 5:55:05 PM Subject: Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors Hi, This sounds great! Not having to setup all those bridges everytime a new BioC version is released should be a great feature, plus keeping the commit history tidy. And we can still use Travis or other things like Slack notifications on our own bridges. I guess that it'd be good to remind users to pull new content from the bioc remote before trying to commit to svn. Anyhow, great work! I'm having a few problems with this new setup which hopefully are easy to iron out. Basically, I am stuck at the "git svn rebase && git svn dcommit --add-author-from" step. See 2b) below. 1) My git was pointing to an older version even after updated with brew. This was because I still had MacPorts around. How to diagnose: $ which git Wrong version was pointing to /opt/local/bin/git instead of /usr/local/bin/git Can also see by running $ git --version ## if it doesn't match the version number you installed from brew Solution: * Uninstall all of MacPorts following instructions from https://guide.macports.org/chunked/installing.macports.uninstalling.html * Follow part of http://stackoverflow.com/questions/20648235/error-linking-git-to-homebrew $ sudo brew prune $ brew update $ brew install git $ brew unlink git && brew link git
Good to know. Things seem to work on the Macs I have tested with the vanilla git-svn that ships with the OS.
You might want to update subversion. http://blog.victorquinn.com/fix-git-svn-in-mountain-lion might be relevant for you.
I haven't needed to update svn.
2) Test case: derfinderHelper. Smallest and simplest package I have, which won't matter much if things break because it's stable. a) You might want to delete update_remotes.sh after using it. * I deleted the git-svn bridges to both https://github.com/leekgroup/derfinderHelper and https://github.com/leekgroup/derfinderHelper-release * On https://github.com/leekgroup/derfinderHelper I removed bioc as a collaborator and deleted the push-hook since it seems like we don't need this anymore
Yes, you can delete the push hook. Leaving it does no harm as long as the bridge has been deleted (nobody will listen to the hook on the other end once the bridge is deleted).
* Download and ran update_remotes.sh as instructed. It doesn't seem like we need it anymore after that point. If you leave it there, it seems to give problems.
Can you explain what problems?
Easy to solve, but might want to clarify in the instructions.
I do this in a separate directory: git clone https://github.com/Bioconductor/mirror.git and then I have a repos containing the script where I can run 'git pull' if it ever changes. You could also symlink to it in /usr/local/bin. We'll see about changing the docs for this.
b) Following the section "Use Git Locally And Publicly" I get stuck on the "git svn rebase && git svn dcommit --add-author-from" step as shown at https://gist.github.com/lcolladotor/ac8838b25955caeebcf1. The "CONFLICT (add/add): Merge conflict" message lead me to http://stackoverflow.com/questions/19475387/how-to-handle-fix-git-add-add-conflicts from where I could resolve the initial problem that I saw using "git diff". But was basically the changes between the very first version of README.md and the very latest version of it. There must be a way to not have to go through every single commit and/or file one by one. Using "git rebase --continue" doesn't help.
I didn't have this problem.
Sorry, I wasn't following along correctly, I didn't start with your github repos (formerly bridged). What's the link to it? Dan
----- Original Message -----
From: "Dan Tenenbaum" <dtenenba at fredhutch.org> To: "Leonardo Collado Torres" <lcollado at jhu.edu> Cc: "bioc-devel" <bioc-devel at r-project.org> Sent: Tuesday, June 16, 2015 8:05:37 PM Subject: Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors ----- Original Message -----
From: "Dan Tenenbaum" <dtenenba at fredhutch.org> To: "Leonardo Collado Torres" <lcollado at jhu.edu> Cc: "bioc-devel" <bioc-devel at r-project.org>, "Ryan C. Thompson" <rct at thompsonclan.org> Sent: Tuesday, June 16, 2015 7:02:36 PM Subject: Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors ----- Original Message -----
From: "Leonardo Collado Torres" <lcollado at jhu.edu> To: "Ryan C. Thompson" <rct at thompsonclan.org> Cc: "Dan Tenenbaum" <dtenenba at fredhutch.org>, "bioc-devel" <bioc-devel at r-project.org> Sent: Tuesday, June 16, 2015 5:55:05 PM Subject: Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors Hi, This sounds great! Not having to setup all those bridges everytime a new BioC version is released should be a great feature, plus keeping the commit history tidy. And we can still use Travis or other things like Slack notifications on our own bridges. I guess that it'd be good to remind users to pull new content from the bioc remote before trying to commit to svn. Anyhow, great work! I'm having a few problems with this new setup which hopefully are easy to iron out. Basically, I am stuck at the "git svn rebase && git svn dcommit --add-author-from" step. See 2b) below. 1) My git was pointing to an older version even after updated with brew. This was because I still had MacPorts around. How to diagnose: $ which git Wrong version was pointing to /opt/local/bin/git instead of /usr/local/bin/git Can also see by running $ git --version ## if it doesn't match the version number you installed from brew Solution: * Uninstall all of MacPorts following instructions from https://guide.macports.org/chunked/installing.macports.uninstalling.html * Follow part of http://stackoverflow.com/questions/20648235/error-linking-git-to-homebrew $ sudo brew prune $ brew update $ brew install git $ brew unlink git && brew link git
Good to know. Things seem to work on the Macs I have tested with the vanilla git-svn that ships with the OS.
You might want to update subversion. http://blog.victorquinn.com/fix-git-svn-in-mountain-lion might be relevant for you.
I haven't needed to update svn.
2) Test case: derfinderHelper. Smallest and simplest package I have, which won't matter much if things break because it's stable. a) You might want to delete update_remotes.sh after using it. * I deleted the git-svn bridges to both https://github.com/leekgroup/derfinderHelper and https://github.com/leekgroup/derfinderHelper-release * On https://github.com/leekgroup/derfinderHelper I removed bioc as a collaborator and deleted the push-hook since it seems like we don't need this anymore
Yes, you can delete the push hook. Leaving it does no harm as long as the bridge has been deleted (nobody will listen to the hook on the other end once the bridge is deleted).
* Download and ran update_remotes.sh as instructed. It doesn't seem like we need it anymore after that point. If you leave it there, it seems to give problems.
Can you explain what problems?
Easy to solve, but might want to clarify in the instructions.
I do this in a separate directory: git clone https://github.com/Bioconductor/mirror.git and then I have a repos containing the script where I can run 'git pull' if it ever changes. You could also symlink to it in /usr/local/bin. We'll see about changing the docs for this.
b) Following the section "Use Git Locally And Publicly" I get stuck on the "git svn rebase && git svn dcommit --add-author-from" step as shown at https://gist.github.com/lcolladotor/ac8838b25955caeebcf1. The "CONFLICT (add/add): Merge conflict" message lead me to http://stackoverflow.com/questions/19475387/how-to-handle-fix-git-add-add-conflicts from where I could resolve the initial problem that I saw using "git diff". But was basically the changes between the very first version of README.md and the very latest version of it. There must be a way to not have to go through every single commit and/or file one by one. Using "git rebase --continue" doesn't help.
I didn't have this problem.
Sorry, I wasn't following along correctly, I didn't start with your github repos (formerly bridged). What's the link to it?
Answering my own question: https://github.com/leekgroup/derfinderHelper I can reproduce the issue, this is the first time it has come up in all the formerly-bridged repos I have tested. Will get back to you. Dan
Dan
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
On Tue, Jun 16, 2015 at 10:02 PM, Dan Tenenbaum <dtenenba at fredhutch.org> wrote:
----- Original Message -----
From: "Leonardo Collado Torres" <lcollado at jhu.edu> To: "Ryan C. Thompson" <rct at thompsonclan.org> Cc: "Dan Tenenbaum" <dtenenba at fredhutch.org>, "bioc-devel" <bioc-devel at r-project.org> Sent: Tuesday, June 16, 2015 5:55:05 PM Subject: Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors Hi, This sounds great! Not having to setup all those bridges everytime a new BioC version is released should be a great feature, plus keeping the commit history tidy. And we can still use Travis or other things like Slack notifications on our own bridges. I guess that it'd be good to remind users to pull new content from the bioc remote before trying to commit to svn. Anyhow, great work! I'm having a few problems with this new setup which hopefully are easy to iron out. Basically, I am stuck at the "git svn rebase && git svn dcommit --add-author-from" step. See 2b) below. 1) My git was pointing to an older version even after updated with brew. This was because I still had MacPorts around. How to diagnose: $ which git Wrong version was pointing to /opt/local/bin/git instead of /usr/local/bin/git Can also see by running $ git --version ## if it doesn't match the version number you installed from brew Solution: * Uninstall all of MacPorts following instructions from https://guide.macports.org/chunked/installing.macports.uninstalling.html * Follow part of http://stackoverflow.com/questions/20648235/error-linking-git-to-homebrew $ sudo brew prune $ brew update $ brew install git $ brew unlink git && brew link git
Good to know. Things seem to work on the Macs I have tested with the vanilla git-svn that ships with the OS.
Yeah, I've had mine for a while and forgot I still had MacPorts around.
You might want to update subversion. http://blog.victorquinn.com/fix-git-svn-in-mountain-lion might be relevant for you.
I haven't needed to update svn.
Ok, I just did it to be safe. Link is about those updating to Mountain Lion or Mavericks and having to re-download Xcode then setting up the command line tools and them some potential perl issues which I didn't have.
2) Test case: derfinderHelper. Smallest and simplest package I have, which won't matter much if things break because it's stable. a) You might want to delete update_remotes.sh after using it. * I deleted the git-svn bridges to both https://github.com/leekgroup/derfinderHelper and https://github.com/leekgroup/derfinderHelper-release * On https://github.com/leekgroup/derfinderHelper I removed bioc as a collaborator and deleted the push-hook since it seems like we don't need this anymore
Yes, you can delete the push hook. Leaving it does no harm as long as the bridge has been deleted (nobody will listen to the hook on the other end once the bridge is deleted).
Ok!
* Download and ran update_remotes.sh as instructed. It doesn't seem like we need it anymore after that point. If you leave it there, it seems to give problems.
Can you explain what problems?
Git complains that you have an untracked file in the repo when running git svn rebase. There's no need to actually track it, or even exclude it with a .gitignore file, so I simply deleted it. I did check that the remotes had been added using "git remote -v".
Easy to solve, but might want to clarify in the instructions.
I do this in a separate directory: git clone https://github.com/Bioconductor/mirror.git and then I have a repos containing the script where I can run 'git pull' if it ever changes. You could also symlink to it in /usr/local/bin. We'll see about changing the docs for this.
b) Following the section "Use Git Locally And Publicly" I get stuck on the "git svn rebase && git svn dcommit --add-author-from" step as shown at https://gist.github.com/lcolladotor/ac8838b25955caeebcf1. The "CONFLICT (add/add): Merge conflict" message lead me to http://stackoverflow.com/questions/19475387/how-to-handle-fix-git-add-add-conflicts from where I could resolve the initial problem that I saw using "git diff". But was basically the changes between the very first version of README.md and the very latest version of it. There must be a way to not have to go through every single commit and/or file one by one. Using "git rebase --continue" doesn't help.
I didn't have this problem. Here is what I did, which should be the same as what you did: forked derfinderHelper to my personal (dtenenba) account
Ok, maybe this is why you don't have the problem. I didn't fork https://github.com/Bioconductor-mirror/derfinderHelper into my personal (or organization, doesn't matter here) account. I did all of this with my local clone of https://github.com/leekgroup/derfinderHelper which already existed. https://github.com/leekgroup/derfinderHelper has the full commit history since I've been using git from the beginning, instead of the aggregated svn commit history. If I fork https://github.com/Bioconductor-mirror/derfinderHelper then I'll lose the detailed commit history, right? In terms of the deprecated git-svn bridge, I want git to win unconditionally on the merge. I'm not sure how I would do that. Another reason why I would like to avoid doing a fork is that several users already "watch", starred the original github repo, or created issues (some might be open still, others closed with info others might want to read). Well, not really with the tiny derfinderHelper. But I guess that this is just really a weak argument since I could just let svn win while preserving the original github repo.
cloned the fork ran the update_remotes.sh script in the fork git checkout devel git svn rebase git merge master --no-edit git svn rebase git svn dcommit --add-author-from None of these lines gave any errors and the last line said: Committing to https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/derfinderHelper ... Doesn't seem like it actually needed to commit anything.
c) Given the issue with b, the devel branch already has a merge commit. Using http://stackoverflow.com/questions/927358/how-to-undo-the-last-commit I cleaned things up. I don't think it's needed, but I don't want to run into more issues. $ git rebase --abort $ git reset HEAD~1 As you can tell, I'm no "git rebase" expert. From http://git-scm.com/docs/git-rebase it seems like the "ours" option might be useful. But right now I prefer to get some pointers on how to proceed before playing around further :P
Well, since I can't reproduce this situation I'm not exactly sure what to tell you. If you know you want all the changes from git and none from svn (or vice versa) then the --ours and --theirs options are appropriate. But you might just want to start over and see if the problem goes away.
Ahh, ok. Sounds like what I want! http://stackoverflow.com/questions/2959443/why-is-the-meaning-of-ours-and-theirs-reversed-with-git-svn seems like a good starting point
Here are my relevant versions: $ git --version git version 1.9.5 (Apple Git-50.3) $ git svn --version git-svn version 1.9.5 (Apple Git-50.3) (svn 1.7.19) $ svn --version svn, version 1.8.11 (r1643975) $ uname -a Darwin viper 13.4.0 Darwin Kernel Version 13.4.0: Wed Mar 18 16:20:14 PDT 2015; root:xnu-2422.115.14~1/RELEASE_X86_64 x86_64 It does look like on this particular machine I have a non-standard svn: $ which svn /opt/subversion/bin/svn Looks like it came from: https://www.wandisco.com/subversion/os/downloads
Thanks, Leo PS At the "Unable to determine upstream SVN information" section, I believe that there is a typo. "git svn dcomit" should be "git svn dcommit"
Will fix. Thanks for the comments and for trying it out. Dan
On Tue, Jun 16, 2015 at 3:20 PM, Ryan C. Thompson <rct at thompsonclan.org> wrote:
This is great to hear. I sometimes want to delve into the source code of a package's internals, but doing so through the SVN web interface is clunky. Being able to use Github's repo browsing functionality for Bioc packages is great. On 06/16/2015 12:00 PM, Dan Tenenbaum wrote:
Dear Bioconductors, We're pleased to announce the availability of Bioconductor Git Mirrors. These are read-only GitHub repositories (available under https://github.com/Bioconductor-mirror) for every Bioconductor software package. These repositories are synchronized with our Subversion repository. Package maintainers (or anyone else) can fork these repositories and do their development on the fork. Complete documentation of the mirrors is at http://bioconductor.org/developers/how-to/git-mirror/ These mirrors supersede the Git-SVN bridge, which is now deprecated. Creation of new bridges is disabled and maintainers who are using the bridge should migrate to the Git mirrors as soon as it's convenient, as the bridge will eventually go away. Instructions for migrating can be found at the above link. Some features of the new Git Mirrors, and why we feel they are a better solution than the Git-SVN bridge: - The mirrors contain complete commit history. - The mirrors contain release branches for Bioconductor 3.0 and 3.1, and new releases will be added as they happen. You will no longer need separate repositories for release and devel. - Setup is easy and you no longer have to grant any permissions on your repository to other users. You can commit directly to Subversion using git-svn (https://git-scm.com/docs/git-svn). - Each git commit appears in the SVN log as a distinct SVN commit; commits are no longer grouped together as they were with the bridge. Each git commit can be mapped to a specific svn commit, and vice versa. - The Git mirrors are much more reliable. - Use is flexible. You can use git locally (without GitHub) or you can use GitHub as well, to take advantage of all its social coding features. - Using GitHub's code search, you can search the entire Bioconductor codebase. Here's a sample search: https://goo.gl/jI92Ys - Subversion is fully supported and remains the cannonical repository; use of Git and GitHub is optional. We are excited about these new mirrors (brought to you by the hard work of Jim Hester) and we hope you are too. Questions and comments are welcome on the bioc-devel mailing list. Dan
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
----- Original Message -----
From: "Dan Tenenbaum" <dtenenba at fredhutch.org> To: "Leonardo Collado Torres" <lcollado at jhu.edu> Cc: "bioc-devel" <bioc-devel at r-project.org> Sent: Tuesday, June 16, 2015 8:10:56 PM Subject: Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors ----- Original Message -----
From: "Dan Tenenbaum" <dtenenba at fredhutch.org> To: "Leonardo Collado Torres" <lcollado at jhu.edu> Cc: "bioc-devel" <bioc-devel at r-project.org> Sent: Tuesday, June 16, 2015 8:05:37 PM Subject: Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors ----- Original Message -----
From: "Dan Tenenbaum" <dtenenba at fredhutch.org> To: "Leonardo Collado Torres" <lcollado at jhu.edu> Cc: "bioc-devel" <bioc-devel at r-project.org>, "Ryan C. Thompson" <rct at thompsonclan.org> Sent: Tuesday, June 16, 2015 7:02:36 PM Subject: Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors ----- Original Message -----
From: "Leonardo Collado Torres" <lcollado at jhu.edu> To: "Ryan C. Thompson" <rct at thompsonclan.org> Cc: "Dan Tenenbaum" <dtenenba at fredhutch.org>, "bioc-devel" <bioc-devel at r-project.org> Sent: Tuesday, June 16, 2015 5:55:05 PM Subject: Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors Hi, This sounds great! Not having to setup all those bridges everytime a new BioC version is released should be a great feature, plus keeping the commit history tidy. And we can still use Travis or other things like Slack notifications on our own bridges. I guess that it'd be good to remind users to pull new content from the bioc remote before trying to commit to svn. Anyhow, great work! I'm having a few problems with this new setup which hopefully are easy to iron out. Basically, I am stuck at the "git svn rebase && git svn dcommit --add-author-from" step. See 2b) below. 1) My git was pointing to an older version even after updated with brew. This was because I still had MacPorts around. How to diagnose: $ which git Wrong version was pointing to /opt/local/bin/git instead of /usr/local/bin/git Can also see by running $ git --version ## if it doesn't match the version number you installed from brew Solution: * Uninstall all of MacPorts following instructions from https://guide.macports.org/chunked/installing.macports.uninstalling.html * Follow part of http://stackoverflow.com/questions/20648235/error-linking-git-to-homebrew $ sudo brew prune $ brew update $ brew install git $ brew unlink git && brew link git
Good to know. Things seem to work on the Macs I have tested with the vanilla git-svn that ships with the OS.
You might want to update subversion. http://blog.victorquinn.com/fix-git-svn-in-mountain-lion might be relevant for you.
I haven't needed to update svn.
2) Test case: derfinderHelper. Smallest and simplest package I have, which won't matter much if things break because it's stable. a) You might want to delete update_remotes.sh after using it. * I deleted the git-svn bridges to both https://github.com/leekgroup/derfinderHelper and https://github.com/leekgroup/derfinderHelper-release * On https://github.com/leekgroup/derfinderHelper I removed bioc as a collaborator and deleted the push-hook since it seems like we don't need this anymore
Yes, you can delete the push hook. Leaving it does no harm as long as the bridge has been deleted (nobody will listen to the hook on the other end once the bridge is deleted).
* Download and ran update_remotes.sh as instructed. It doesn't seem like we need it anymore after that point. If you leave it there, it seems to give problems.
Can you explain what problems?
Easy to solve, but might want to clarify in the instructions.
I do this in a separate directory: git clone https://github.com/Bioconductor/mirror.git and then I have a repos containing the script where I can run 'git pull' if it ever changes. You could also symlink to it in /usr/local/bin. We'll see about changing the docs for this.
b) Following the section "Use Git Locally And Publicly" I get stuck on the "git svn rebase && git svn dcommit --add-author-from" step as shown at https://gist.github.com/lcolladotor/ac8838b25955caeebcf1. The "CONFLICT (add/add): Merge conflict" message lead me to http://stackoverflow.com/questions/19475387/how-to-handle-fix-git-add-add-conflicts from where I could resolve the initial problem that I saw using "git diff". But was basically the changes between the very first version of README.md and the very latest version of it. There must be a way to not have to go through every single commit and/or file one by one. Using "git rebase --continue" doesn't help.
I didn't have this problem.
Sorry, I wasn't following along correctly, I didn't start with your github repos (formerly bridged). What's the link to it?
Answering my own question: https://github.com/leekgroup/derfinderHelper I can reproduce the issue, this is the first time it has come up in all the formerly-bridged repos I have tested. Will get back to you.
Laurent Gatto, helping me with a separate but (probably) related issue, may have helped with this one too. Try starting over again. Remove your local repository and do a fresh clone: git clone https://github.com/leekgroup/derfinderHelper.git cd derfinderHelper bash /path/to/update_remotes.sh git checkout devel git svn rebase git merge master --no-edit git svn dcommit --add-author-from That all worked for me and did not end up committing anything. The difference between this and our documentation is that here there is no rebase in between the merge and dcommit. You can then review the commits in devel (with git log) and see if you want to merge them into master. If so, do git checkout master git merge devel git status will now show that master is 30 commits ahead of origin/master. Push if you want. Not sure if you want to as you said you wanted git to "win". But note that we are no longer in the land of one SCM unconditionally "winning" over another. That was a concept from the git-svn bridge (a somewhat dangerous one) which in any case only applied to the initial setup of a bridge. With git-svn you have complete control over what goes where. So anyway, try the above and if it works we will discuss whether and how the documentation needs to be updated. Thanks, Dan
Dan
Dan
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
It would be cool if we could somehow get the equivalent of the bioconductor package page to show up as the "readme" on the github page. Or at least, if there could be a very obvious link from the mirror repository to the maintainer repository, without having to click through to the Bioconductor package page, which might confuse new users a bit.
On Tue, Jun 16, 2015 at 12:00 PM, Dan Tenenbaum <dtenenba at fredhutch.org> wrote:
Dear Bioconductors, We're pleased to announce the availability of Bioconductor Git Mirrors. These are read-only GitHub repositories (available under https://github.com/Bioconductor-mirror) for every Bioconductor software package. These repositories are synchronized with our Subversion repository. Package maintainers (or anyone else) can fork these repositories and do their development on the fork. Complete documentation of the mirrors is at http://bioconductor.org/developers/how-to/git-mirror/ These mirrors supersede the Git-SVN bridge, which is now deprecated. Creation of new bridges is disabled and maintainers who are using the bridge should migrate to the Git mirrors as soon as it's convenient, as the bridge will eventually go away. Instructions for migrating can be found at the above link. Some features of the new Git Mirrors, and why we feel they are a better solution than the Git-SVN bridge: - The mirrors contain complete commit history. - The mirrors contain release branches for Bioconductor 3.0 and 3.1, and new releases will be added as they happen. You will no longer need separate repositories for release and devel. - Setup is easy and you no longer have to grant any permissions on your repository to other users. You can commit directly to Subversion using git-svn (https://git-scm.com/docs/git-svn). - Each git commit appears in the SVN log as a distinct SVN commit; commits are no longer grouped together as they were with the bridge. Each git commit can be mapped to a specific svn commit, and vice versa. - The Git mirrors are much more reliable. - Use is flexible. You can use git locally (without GitHub) or you can use GitHub as well, to take advantage of all its social coding features. - Using GitHub's code search, you can search the entire Bioconductor codebase. Here's a sample search: https://goo.gl/jI92Ys - Subversion is fully supported and remains the cannonical repository; use of Git and GitHub is optional. We are excited about these new mirrors (brought to you by the hard work of Jim Hester) and we hope you are too. Questions and comments are welcome on the bioc-devel mailing list. Dan
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Why not write your own *readme.md* file for the package and put the link there? There is nothing stopping the maintainer from having a README file in the package. Although it does not show up on the Bioconductor page, it shows up nicely on Github: My package: https://github.com/Bioconductor-mirror/categoryCompare https://github.com/rmflight/categoryCompare -Robert On Wed, Jun 17, 2015 at 8:43 AM Michael Lawrence <lawrence.michael at gene.com> wrote:
It would be cool if we could somehow get the equivalent of the bioconductor package page to show up as the "readme" on the github page. Or at least, if there could be a very obvious link from the mirror repository to the maintainer repository, without having to click through to the Bioconductor package page, which might confuse new users a bit. On Tue, Jun 16, 2015 at 12:00 PM, Dan Tenenbaum <dtenenba at fredhutch.org> wrote:
Dear Bioconductors, We're pleased to announce the availability of Bioconductor Git Mirrors. These are read-only GitHub repositories (available under
for every Bioconductor software package. These repositories are
synchronized with our
Subversion repository. Package maintainers (or anyone else) can fork
these repositories
and do their development on the fork. Complete documentation of the
mirrors is at
http://bioconductor.org/developers/how-to/git-mirror/ These mirrors supersede the Git-SVN bridge, which is now deprecated. Creation of new bridges is disabled and maintainers who are using the
bridge
should migrate to the Git mirrors as soon as it's convenient, as the
bridge
will eventually go away. Instructions for migrating can be found at the
above link.
Some features of the new Git Mirrors, and why we feel they are a better
solution than the Git-SVN bridge:
- The mirrors contain complete commit history. - The mirrors contain release branches for Bioconductor 3.0 and 3.1, and new releases will be added as they happen. You will no longer need separate repositories for release and devel. - Setup is easy and you no longer have to grant any permissions on your repository to other users. You can commit directly to Subversion using git-svn (https://git-scm.com/docs/git-svn). - Each git commit appears in the SVN log as a distinct SVN commit;
commits
are no longer grouped together as they were with the bridge. Each git commit can be mapped to a specific svn commit, and vice versa. - The Git mirrors are much more reliable. - Use is flexible. You can use git locally (without GitHub) or you can use GitHub as well, to take advantage of all its social coding
features.
- Using GitHub's code search, you can search the entire Bioconductor
codebase.
Here's a sample search: https://goo.gl/jI92Ys - Subversion is fully supported and remains the cannonical repository;
use
of Git and GitHub is optional. We are excited about these new mirrors (brought to you by the hard work of Jim Hester) and we hope you are too. Questions and comments are welcome on the bioc-devel mailing list. Dan
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
I have (in the past couple of minutes) added a more detailed description to all of the GitHub pages. If you have URL or BugReports fields in your package DESCRIPTION those are used to provide links to the project page and bug tracker if they are available, see Roberts https://github.com/Bioconductor-mirror/categoryCompare for an example. I would also recommend doing as Robert suggests and adding a link in a README.md file if you would like to direct users elsewhere. These files are automatically rendered by GitHub and users are used to looking at them for project documentation. Thank you all for being patient as we roll out this functionality. Jim On Wed, Jun 17, 2015 at 9:06 AM, Robert M. Flight <rflight79 at gmail.com> wrote:
Why not write your own *readme.md* file for the package and put the link there? There is nothing stopping the maintainer from having a README file in the package. Although it does not show up on the Bioconductor page, it shows up nicely on Github: My package: https://github.com/Bioconductor-mirror/categoryCompare https://github.com/rmflight/categoryCompare -Robert On Wed, Jun 17, 2015 at 8:43 AM Michael Lawrence < lawrence.michael at gene.com> wrote:
It would be cool if we could somehow get the equivalent of the bioconductor package page to show up as the "readme" on the github page. Or at least, if there could be a very obvious link from the mirror repository to the maintainer repository, without having to click through to the Bioconductor package page, which might confuse new users a bit. On Tue, Jun 16, 2015 at 12:00 PM, Dan Tenenbaum <dtenenba at fredhutch.org> wrote:
Dear Bioconductors, We're pleased to announce the availability of Bioconductor Git Mirrors. These are read-only GitHub repositories (available under
for every Bioconductor software package. These repositories are
synchronized with our
Subversion repository. Package maintainers (or anyone else) can fork
these repositories
and do their development on the fork. Complete documentation of the
mirrors is at
http://bioconductor.org/developers/how-to/git-mirror/ These mirrors supersede the Git-SVN bridge, which is now deprecated. Creation of new bridges is disabled and maintainers who are using the
bridge
should migrate to the Git mirrors as soon as it's convenient, as the
bridge
will eventually go away. Instructions for migrating can be found at the
above link.
Some features of the new Git Mirrors, and why we feel they are a better
solution than the Git-SVN bridge:
- The mirrors contain complete commit history. - The mirrors contain release branches for Bioconductor 3.0 and 3.1,
and
new releases will be added as they happen. You will no longer need separate repositories for release and devel. - Setup is easy and you no longer have to grant any permissions on
your
repository to other users. You can commit directly to Subversion using git-svn (https://git-scm.com/docs/git-svn). - Each git commit appears in the SVN log as a distinct SVN commit;
commits
are no longer grouped together as they were with the bridge. Each
git
commit can be mapped to a specific svn commit, and vice versa. - The Git mirrors are much more reliable. - Use is flexible. You can use git locally (without GitHub) or you can use GitHub as well, to take advantage of all its social coding
features.
- Using GitHub's code search, you can search the entire Bioconductor
codebase.
Here's a sample search: https://goo.gl/jI92Ys - Subversion is fully supported and remains the cannonical repository;
use
of Git and GitHub is optional. We are excited about these new mirrors (brought to you by the hard work of Jim Hester) and we hope you are too. Questions and comments are welcome on the bioc-devel mailing list. Dan
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
2 days later
So this seems to work quite nicely. But in my own testing of committing with my categoryCompare package, there is one interesting issue of Github complaining about how many commits ahead / behind the fork is. So I moved my old github repo, and then made a fresh fork from the Bioconductor mirror, and made a new clone of that fork on my local machine, and ran update_remotes.sh. Made some changes to the readme (pointing to personal repo for issues) and committed in *master git push origin master (push back up to my personal copy) git checkout devel git svn rebase git merge master --no-edit git svn rebase && git svn dcommit --add-author-from When I looked at my personal fork, it shows 1 commit ahead & behind the original. So I pulled from *bioc* remote into master (and merge it), and then pushed back up to master. I still have this message: This branch is 2 commits ahead of Bioconductor-mirror:master, but there are no file differences. Does anyone know how to make this message go away? Should I just use my own repo instead of a *fork* of the Bioconductor-mirror? -Robert On Wed, Jun 17, 2015 at 10:10 AM Jim Hester <james.f.hester at gmail.com> wrote:
I have (in the past couple of minutes) added a more detailed description to all of the GitHub pages. If you have URL or BugReports fields in your package DESCRIPTION those are used to provide links to the project page and bug tracker if they are available, see Roberts https://github.com/Bioconductor-mirror/categoryCompare for an example. I would also recommend doing as Robert suggests and adding a link in a README.md file if you would like to direct users elsewhere. These files are automatically rendered by GitHub and users are used to looking at them for project documentation. Thank you all for being patient as we roll out this functionality. Jim On Wed, Jun 17, 2015 at 9:06 AM, Robert M. Flight <rflight79 at gmail.com> wrote:
Why not write your own *readme.md* file for the package and put the link there? There is nothing stopping the maintainer from having a README file in the package. Although it does not show up on the Bioconductor page, it shows up nicely on Github: My package: https://github.com/Bioconductor-mirror/categoryCompare https://github.com/rmflight/categoryCompare -Robert On Wed, Jun 17, 2015 at 8:43 AM Michael Lawrence < lawrence.michael at gene.com> wrote:
It would be cool if we could somehow get the equivalent of the bioconductor package page to show up as the "readme" on the github page. Or at least, if there could be a very obvious link from the mirror repository to the maintainer repository, without having to click through to the Bioconductor package page, which might confuse new users a bit. On Tue, Jun 16, 2015 at 12:00 PM, Dan Tenenbaum <dtenenba at fredhutch.org wrote:
Dear Bioconductors, We're pleased to announce the availability of Bioconductor Git
Mirrors.
These are read-only GitHub repositories (available under
for every Bioconductor software package. These repositories are
synchronized with our
Subversion repository. Package maintainers (or anyone else) can fork
these repositories
and do their development on the fork. Complete documentation of the
mirrors is at
http://bioconductor.org/developers/how-to/git-mirror/ These mirrors supersede the Git-SVN bridge, which is now deprecated. Creation of new bridges is disabled and maintainers who are using the
bridge
should migrate to the Git mirrors as soon as it's convenient, as the
bridge
will eventually go away. Instructions for migrating can be found at
the
above link.
Some features of the new Git Mirrors, and why we feel they are a
better
solution than the Git-SVN bridge:
- The mirrors contain complete commit history. - The mirrors contain release branches for Bioconductor 3.0 and 3.1,
and
new releases will be added as they happen. You will no longer need separate repositories for release and devel. - Setup is easy and you no longer have to grant any permissions on
your
repository to other users. You can commit directly to Subversion using git-svn (https://git-scm.com/docs/git-svn). - Each git commit appears in the SVN log as a distinct SVN commit;
commits
are no longer grouped together as they were with the bridge. Each
git
commit can be mapped to a specific svn commit, and vice versa. - The Git mirrors are much more reliable. - Use is flexible. You can use git locally (without GitHub) or you can use GitHub as well, to take advantage of all its social coding
features.
- Using GitHub's code search, you can search the entire Bioconductor
codebase.
Here's a sample search: https://goo.gl/jI92Ys - Subversion is fully supported and remains the cannonical
repository;
use
of Git and GitHub is optional. We are excited about these new mirrors (brought to you by the hard work of Jim Hester) and we hope you are too. Questions and comments
are
welcome on the bioc-devel mailing list. Dan
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
I think these are unavoidable artifacts with the current setup. The commits from the Bioconductor-mirror are coming from SVN after being translated so they have extra metadata attached to the commit message, while your original commits do not have this. Therefore GitHub cannot properly disambiguate the two commits, and you get this message. You will also notice you get the same commit twice in your log ( https://github.com/rmflight/categoryCompare/commits/master) due to the same reason. Using your own repo instead of forking Bioconductor-mirror will make the message go away and you should also not have the issue with double commits I believe. On Fri, Jun 19, 2015 at 10:23 AM, Robert M. Flight <rflight79 at gmail.com> wrote:
So this seems to work quite nicely. But in my own testing of committing with my categoryCompare package, there is one interesting issue of Github complaining about how many commits ahead / behind the fork is. So I moved my old github repo, and then made a fresh fork from the Bioconductor mirror, and made a new clone of that fork on my local machine, and ran update_remotes.sh. Made some changes to the readme (pointing to personal repo for issues) and committed in *master git push origin master (push back up to my personal copy) git checkout devel git svn rebase git merge master --no-edit git svn rebase && git svn dcommit --add-author-from When I looked at my personal fork, it shows 1 commit ahead & behind the original. So I pulled from *bioc* remote into master (and merge it), and then pushed back up to master. I still have this message: This branch is 2 commits ahead of Bioconductor-mirror:master, but there are no file differences. Does anyone know how to make this message go away? Should I just use my own repo instead of a *fork* of the Bioconductor-mirror? -Robert On Wed, Jun 17, 2015 at 10:10 AM Jim Hester <james.f.hester at gmail.com> wrote:
I have (in the past couple of minutes) added a more detailed description to all of the GitHub pages. If you have URL or BugReports fields in your package DESCRIPTION those are used to provide links to the project page and bug tracker if they are available, see Roberts https://github.com/Bioconductor-mirror/categoryCompare for an example. I would also recommend doing as Robert suggests and adding a link in a README.md file if you would like to direct users elsewhere. These files are automatically rendered by GitHub and users are used to looking at them for project documentation. Thank you all for being patient as we roll out this functionality. Jim On Wed, Jun 17, 2015 at 9:06 AM, Robert M. Flight <rflight79 at gmail.com> wrote:
Why not write your own *readme.md* file for the package and put the link there? There is nothing stopping the maintainer from having a README file in the package. Although it does not show up on the Bioconductor page, it shows up nicely on Github: My package: https://github.com/Bioconductor-mirror/categoryCompare https://github.com/rmflight/categoryCompare -Robert On Wed, Jun 17, 2015 at 8:43 AM Michael Lawrence < lawrence.michael at gene.com> wrote:
It would be cool if we could somehow get the equivalent of the bioconductor package page to show up as the "readme" on the github page. Or at least, if there could be a very obvious link from the mirror repository to the maintainer repository, without having to click through to the Bioconductor package page, which might confuse new users a bit. On Tue, Jun 16, 2015 at 12:00 PM, Dan Tenenbaum <
dtenenba at fredhutch.org>
wrote:
Dear Bioconductors, We're pleased to announce the availability of Bioconductor Git
Mirrors.
These are read-only GitHub repositories (available under
for every Bioconductor software package. These repositories are
synchronized with our
Subversion repository. Package maintainers (or anyone else) can fork
these repositories
and do their development on the fork. Complete documentation of the
mirrors is at
http://bioconductor.org/developers/how-to/git-mirror/ These mirrors supersede the Git-SVN bridge, which is now deprecated. Creation of new bridges is disabled and maintainers who are using the
bridge
should migrate to the Git mirrors as soon as it's convenient, as the
bridge
will eventually go away. Instructions for migrating can be found at
the
above link.
Some features of the new Git Mirrors, and why we feel they are a
better
solution than the Git-SVN bridge:
- The mirrors contain complete commit history. - The mirrors contain release branches for Bioconductor 3.0 and
3.1, and
new releases will be added as they happen. You will no longer need separate repositories for release and devel. - Setup is easy and you no longer have to grant any permissions on
your
repository to other users. You can commit directly to Subversion using git-svn (https://git-scm.com/docs/git-svn). - Each git commit appears in the SVN log as a distinct SVN commit;
commits
are no longer grouped together as they were with the bridge. Each
git
commit can be mapped to a specific svn commit, and vice versa. - The Git mirrors are much more reliable. - Use is flexible. You can use git locally (without GitHub) or you can use GitHub as well, to take advantage of all its social coding
features.
- Using GitHub's code search, you can search the entire Bioconductor
codebase.
Here's a sample search: https://goo.gl/jI92Ys - Subversion is fully supported and remains the cannonical
repository;
use
of Git and GitHub is optional. We are excited about these new mirrors (brought to you by the hard work of Jim Hester) and we hope you are too. Questions and comments
are
welcome on the bioc-devel mailing list. Dan
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Hmmm, ok. I kind of liked having the message about being a fork of the Bioc-mirror, but the difference message makes it a little messy. Oh well. Was an interesting experiment. On Fri, Jun 19, 2015 at 11:19 AM Jim Hester <james.f.hester at gmail.com> wrote:
I think these are unavoidable artifacts with the current setup. The commits from the Bioconductor-mirror are coming from SVN after being translated so they have extra metadata attached to the commit message, while your original commits do not have this. Therefore GitHub cannot properly disambiguate the two commits, and you get this message. You will also notice you get the same commit twice in your log ( https://github.com/rmflight/categoryCompare/commits/master) due to the same reason. Using your own repo instead of forking Bioconductor-mirror will make the message go away and you should also not have the issue with double commits I believe. On Fri, Jun 19, 2015 at 10:23 AM, Robert M. Flight <rflight79 at gmail.com> wrote:
So this seems to work quite nicely. But in my own testing of committing with my categoryCompare package, there is one interesting issue of Github complaining about how many commits ahead / behind the fork is. So I moved my old github repo, and then made a fresh fork from the Bioconductor mirror, and made a new clone of that fork on my local machine, and ran update_remotes.sh. Made some changes to the readme (pointing to personal repo for issues) and committed in *master git push origin master (push back up to my personal copy) git checkout devel git svn rebase git merge master --no-edit git svn rebase && git svn dcommit --add-author-from When I looked at my personal fork, it shows 1 commit ahead & behind the original. So I pulled from *bioc* remote into master (and merge it), and then pushed back up to master. I still have this message: This branch is 2 commits ahead of Bioconductor-mirror:master, but there are no file differences. Does anyone know how to make this message go away? Should I just use my own repo instead of a *fork* of the Bioconductor-mirror? -Robert On Wed, Jun 17, 2015 at 10:10 AM Jim Hester <james.f.hester at gmail.com> wrote:
I have (in the past couple of minutes) added a more detailed description to all of the GitHub pages. If you have URL or BugReports fields in your package DESCRIPTION those are used to provide links to the project page and bug tracker if they are available, see Roberts https://github.com/Bioconductor-mirror/categoryCompare for an example. I would also recommend doing as Robert suggests and adding a link in a README.md file if you would like to direct users elsewhere. These files are automatically rendered by GitHub and users are used to looking at them for project documentation. Thank you all for being patient as we roll out this functionality. Jim On Wed, Jun 17, 2015 at 9:06 AM, Robert M. Flight <rflight79 at gmail.com> wrote:
Why not write your own *readme.md* file for the package and put the link there? There is nothing stopping the maintainer from having a README file in the package. Although it does not show up on the Bioconductor page, it shows up nicely on Github: My package: https://github.com/Bioconductor-mirror/categoryCompare https://github.com/rmflight/categoryCompare -Robert On Wed, Jun 17, 2015 at 8:43 AM Michael Lawrence < lawrence.michael at gene.com> wrote:
It would be cool if we could somehow get the equivalent of the bioconductor package page to show up as the "readme" on the github page. Or at least, if there could be a very obvious link from the mirror repository to the maintainer repository, without having to click through to the Bioconductor package page, which might confuse new users a bit. On Tue, Jun 16, 2015 at 12:00 PM, Dan Tenenbaum <
dtenenba at fredhutch.org>
wrote:
Dear Bioconductors, We're pleased to announce the availability of Bioconductor Git
Mirrors.
These are read-only GitHub repositories (available under
for every Bioconductor software package. These repositories are
synchronized with our
Subversion repository. Package maintainers (or anyone else) can fork
these repositories
and do their development on the fork. Complete documentation of the
mirrors is at
http://bioconductor.org/developers/how-to/git-mirror/ These mirrors supersede the Git-SVN bridge, which is now deprecated. Creation of new bridges is disabled and maintainers who are using
the
bridge
should migrate to the Git mirrors as soon as it's convenient, as the
bridge
will eventually go away. Instructions for migrating can be found at
the
above link.
Some features of the new Git Mirrors, and why we feel they are a
better
solution than the Git-SVN bridge:
- The mirrors contain complete commit history. - The mirrors contain release branches for Bioconductor 3.0 and
3.1, and
new releases will be added as they happen. You will no longer
need
separate repositories for release and devel. - Setup is easy and you no longer have to grant any permissions on
your
repository to other users. You can commit directly to Subversion using git-svn (https://git-scm.com/docs/git-svn). - Each git commit appears in the SVN log as a distinct SVN commit;
commits
are no longer grouped together as they were with the bridge.
Each git
commit can be mapped to a specific svn commit, and vice versa. - The Git mirrors are much more reliable. - Use is flexible. You can use git locally (without GitHub) or you can use GitHub as well, to take advantage of all its social
coding
features.
- Using GitHub's code search, you can search the entire
Bioconductor
codebase.
Here's a sample search: https://goo.gl/jI92Ys - Subversion is fully supported and remains the cannonical
repository;
use
of Git and GitHub is optional. We are excited about these new mirrors (brought to you by the hard work of Jim Hester) and we hope you are too. Questions and comments
are
welcome on the bioc-devel mailing list. Dan
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel