Code, notes, and writeup

• publications are projects stored in a self contained git repo that contain code as well as write-up

following - http://www.itk.org/Wiki/ITK/Git/Develop

• BUG: Fix for runtime crash or incorrect result
• COMP: Compiler error or warning fix
• DOC: Documentation change
• ENH: New functionality
• PERF: Performance improvement
• STYLE: No logic impact (indentation, comments)
• WIP: Work In Progress not ready for merge

following - http://www.itk.org/Wiki/ITK/Coding_Style_Guide#Naming_Conventions

• Names are constructed by using case change to indicate separate words, as in TimeStamp (versus Time Stamp).
• Underscores are not used.
• Variable names are chosen carefully with the intention to convey the meaning behind the code.
• Names are generally spelled out
• Use of abbreviations is discouraged. (Abbreviation are allowable when in common use, and should be in uppercase as in RGB.) While this does result in long names, it self-documents the code.
• If you learn how to use name completion in your editor (e.g.,Vim, Emacs), this inconvenience can be minimized.

http://git-scm.com/book/en/v2/Git-Tools-Submodules#Starting-with-Submodules

• proposals and pdf presentations stored as single git repo organized by funding source

  • submodules are used to point to publications within funding source

  git submodule add git@github.com:ImageGuidedTherapyLab/IrreversibleElectroporationSpine.git publications/IrreversibleElectroporationSpine git commit -am 'DOC: ire paper'

http://git-scm.com/book/en/v2/Git-Tools-Submodules#Cloning-a-Project-with-Submodules

http://stackoverflow.com/questions/3796927/how-to-git-clone-including-submodules

$ git submodule update --init --recursive

git remote update --prune

git checkout -b fuentesdt

git checkout -b fuentesdt origin/fuentesdt

git branch --set-upstream origin/fuentesdt fuentesdt

git push origin fuentesdt

git checkout master git merge --no-ff fuentesdt git push origin master

https://help.github.com/articles/remove-sensitive-data/

• run from top of repo and push changes

  git filter-branch --force --index-filter 'git rm --cached --ignore-unmatch path/to/largefiles/*' --prune-empty --tag-name-filter cat -- --all git push origin --force --all

• other forks/branchnes need to rebase to the master... dangerous ? (http://git-scm.com/book/en/v2/Git-Branching-Rebasing)

  git pull --rebase origin master

https://help.github.com/articles/splitting-a-subfolder-out-into-a-new-repository/

• git filter-branch --prune-empty --subdirectory-filter YOUR_FOLDER_NAME master
• git push my-new-repo -f .

http://stackoverflow.com/questions/13040958/merge-two-git-repositories-without-breaking-file-history

Here's a way that doesn't rewrite any history, so all commit IDs will remain valid. The end-result is that the second repo's files will end up in a subdirectory.

1. Add the second repo as a remote:

   cd firstgitrepo/ git remote add -f secondrepo username@servername:andsoon

2. Create a local branch from the second repo's branch:

   git branch branchfromsecondrepo secondrepo/master; git checkout branchfromsecondrepo

3. Move all its files into a subdirectory:

   mkdir subdir/ git ls-tree -z --name-only HEAD | xargs -0 -I {} git mv {} subdir/

4. Merge the second branch into the first repo's master branch:

git commit -m "STYLE: organizing files"; git checkout master; git merge branchfromsecondrepo

5. clean up

   git branch -D branchfromsecondrepo; git remote rm secondrepo

6. git log --follow file

   Continue listing the history of a file beyond renames (works only for a single file).