The general problem

m1-m2-m3 # the master branch
       \
        x11-x12-x13 # example branch_1
                  \
                   y21-y22-y23 # example branch_2 that depends on branch_1

After a squash and merge the Git DAG looks like this

m1-m2-m3-s1 # master branch + squash-merge
       \
        x11-x12-x13 # commits from branch_1 still exist
                  \
                   y21-y22-y23 # commits from branch_2 still exist

You can’t simply just squash merge branch_2, becuase the commits from branch_1 are technically still part of the history of branch_2, so a rebase of branch_2 against the new master will cause conflicts, and I’ll have duplicate messages if I do another squash+merge of branch_2.

If you did a rebase you’ll end up with this:

git checkout branch_2 # make sure you're on branch_2
git rebase master
# fix conflicts
# so many conflicts

m1-m2-m3-s1 # master branch + squash-merge
          \
           x11-x12-x13-y21-y22-y23 # commits from branch_1 and branch_2

Instead, you need to git cherry-pick the commits against the updated master with just the commits from branch_2.

git checkout master # go to master branch so you can cherry-pick commits on top
git cherry-pick y21^..y23 # this is how to cherry-pick multiple commits
# (note the ^ to also include commit y21, otherwise it is left exclusive)

m1-m2-m3-s1 # master branch + squash-merge
       \  \
        \  y21-y22-y23 # cherry-pick commits from branch_2 # this is good
         \
          x11-x12-x13 # commits from branch_1 still exist # already in s1

We don’t need the commits from branch one anymore (x11 to x13 in the example), so we can deleate that branch using git branch -D branch_1, note you have to use a force delete with the -D flag, because git does not think that branch_1 was merged because we did a squash+merge. Otherwise you would’ve been able to use the lowercase -d flag to delete the branch.

m1-m2-m3-s1 # master branch + squash-merge
          \
           y21-y22-y23 # cherry-pick commits from branch_2 # yay!

Now we finally get everthing up to date, and can re-update the pull request for branch 2 by doing a force push: git push -f origin master.

In the real world

The PR process is the same as usual:

1. Create a branch
2. Push the branch to the remote (i.e., Github, in this case)
3. Pull request!

However, Github now gives you an option of which green button you want! Specifically, the option to “Squash and merge”

This is fine when you have a totally independent PR and there’s no other work that is based of the current work on that branch. However here’s an example where I created separate branches for each “feature”, but they all rely on the previous feature.

Output of my git log --oneline --graph --decorate --all, which I have aliased as git l

Here’s the current state we’re in after we perform a squash+merge on GitHub

              vignettes
             /
older_commits
             \
              master

Here’s what the actual state of the repository looks like.

dchen@longclaw [~/git/hub/gradethis]  (vignettes) 
[10:51:06] $ git l
* 16f4b6b (HEAD -> vignettes) intro to gradethis for learnr docs
* b4e2873 (origin/vignettes) emphasize not to use ==
* f66aa39 i don't want to stash
| * feb82b3 (origin/gh-pages) Deploy rstudio-education/gradethis to github.com/rstudio-education/gradethis.git:gh-pages
| * a195fa3 (origin/master, origin/HEAD) fix gradethis demo (#70)
| | * 4aaee31 (origin/compare_default_formals, compare_default_formals) call_standarise_formals
| | * 19354dd refactor is_code_same to is_code_identical
| | * 5591ae8 rename fxn code_is_same -> is_code_same
| |/  
| | * 91cf16e (update_grading_demo) fix gradethis demo
| |/  
| * 9083fc8 (me/master, master) rename functions per #65 update docs and tests (#72)
| * 5ec1144 Docs to markdown per #68 by @andrie + Barret changes (#69)
| * 9cc3d6d Test result api fixes#60 (#63)
|/  
* d5cf9de Doc fixes (#62) and function pruning

What we want is something like this:

older_commits
             \
              master
                    \
                     vignettes

First we pull and update master

dchen@longclaw [~/git/hub/gradethis]  (master) 
[10:51:18] $ git pull origin master
From github.com:rstudio-education/gradethis
 * branch            master     -> FETCH_HEAD
Updating 9083fc8..a195fa3
Fast-forward
 inst/tutorials/grading-demo/grading-demo.Rmd | 249 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-----------------------------------------------------------------------------------------------------
 1 file changed, 112 insertions(+), 137 deletions(-)

Now that master is up to date,

              vignettes
             /
older_commits
             \
              master-master # master has moved up a commit from pull

we can cherry-pick the commits of interest

dchen@longclaw [~/git/hub/gradethis]  (master) 
[10:51:30] $ git cherry-pick f66aa39^..16f4b6b
[master 28c7ebe] i don't want to stash
 Date: Wed Aug 14 10:03:25 2019 -0400
 3 files changed, 72 insertions(+)
 create mode 100644 vignettes/000-introduction_to_gradethis.Rmd
 create mode 100644 vignettes/010-using_equal.Rmd
 create mode 100644 vignettes/990-developers_guide.Rmd
[master 9b84be6] emphasize not to use ==
 Date: Wed Aug 14 11:44:36 2019 -0400
 1 file changed, 4 insertions(+), 4 deletions(-)
[master 846bb18] intro to gradethis for learnr docs
 Date: Tue Aug 27 10:51:06 2019 -0400
 1 file changed, 151 insertions(+), 9 deletions(-)

Note that I used the <commit>^..<commit> notation while cherry-picking. The ^ means to also include that commit, otherwise it will start from that commit, but not include it (i.e., left exclusive).

If you wanted to not use the ^ you need to pick the previous commit hash. In my case it would’ve been d5cf9de.

Now, we need to clean up the references to our branch. Since we cherry-picked commits on master we’re actually still on master. So we need to do update where our branches are pointing to by using `git reset –hard

First we checkout the vignettes branch,

dchen@longclaw [~/git/hub/gradethis]  (master) 
[10:51:46] $ git checkout vignettes 
Switched to branch 'vignettes'

dchen@longclaw [~/git/hub/gradethis]  (vignettes) 
[10:51:52] $ git l
* 846bb18 (master) intro to gradethis for learnr docs
* 9b84be6 emphasize not to use ==
* 28c7ebe i don't want to stash
* a195fa3 (origin/master, origin/HEAD) fix gradethis demo (#70)
| * 16f4b6b (HEAD -> vignettes) intro to gradethis for learnr docs
| * b4e2873 (origin/vignettes) emphasize not to use ==
| * f66aa39 i don't want to stash
| | * feb82b3 (origin/gh-pages) Deploy rstudio-education/gradethis to github.com/rstudio-education/gradethis.git:gh-pages
| | * 4aaee31 (origin/compare_default_formals, compare_default_formals) call_standarise_formals
| | * 19354dd refactor is_code_same to is_code_identical
| | * 5591ae8 rename fxn code_is_same -> is_code_same
| |/  
|/|   
| | * 91cf16e (update_grading_demo) fix gradethis demo
| |/  
|/|   
* | 9083fc8 (me/master) rename functions per #65 update docs and tests (#72)
* | 5ec1144 Docs to markdown per #68 by @andrie + Barret changes (#69)
* | 9cc3d6d Test result api fixes#60 (#63)
|/  
* d5cf9de Doc fixes (#62) and function pruning

and then set it to the correct commit location.

dchen@longclaw [~/git/hub/gradethis]  (vignettes) 
[10:52:04] $ git reset --hard 846bb18
HEAD is now at 846bb18 intro to gradethis for learnr docs

We then repeat the process for the master branch.

First checkout master

dchen@longclaw [~/git/hub/gradethis]  (vignettes) 
[10:52:07] $ git checkout master
Switched to branch 'master'
Your branch is ahead of 'origin/master' by 3 commits.
  (use "git push" to publish your local commits)

Then reset --hard to the correct location:

dchen@longclaw [~/git/hub/gradethis]  (master) 
[10:52:11] $ git reset --hard a195fa3
HEAD is now at a195fa3 fix gradethis demo (#70)

Now everything is in the right place

older_commits
             \
              master
                    \
                     vignettes

dchen@longclaw [~/git/hub/gradethis]  (master) 
[10:52:21] $ git l
* 846bb18 (vignettes) intro to gradethis for learnr docs
* 9b84be6 emphasize not to use ==
* 28c7ebe i don't want to stash
* a195fa3 (HEAD -> master, origin/master, origin/HEAD) fix gradethis demo (#70)
| * feb82b3 (origin/gh-pages) Deploy rstudio-education/gradethis to github.com/rstudio-education/gradethis.git:gh-pages
| * 4aaee31 (origin/compare_default_formals, compare_default_formals) call_standarise_formals
| * 19354dd refactor is_code_same to is_code_identical
| * 5591ae8 rename fxn code_is_same -> is_code_same
|/  
| * 91cf16e (update_grading_demo) fix gradethis demo
|/  
* 9083fc8 (me/master) rename functions per #65 update docs and tests (#72)
* 5ec1144 Docs to markdown per #68 by @andrie + Barret changes (#69)
* 9cc3d6d Test result api fixes#60 (#63)
| * b4e2873 (origin/vignettes) emphasize not to use ==
| * f66aa39 i don't want to stash
|/  
* d5cf9de Doc fixes (#62) and function pruning

Finally, we can update the GitHub remote by force bushing the branch (remember to be on the branch before pushing).

dchen@longclaw [~/git/hub/gradethis]  (master) 
[10:53:25] $ git checkout vignettes 
Switched to branch 'vignettes'

dchen@longclaw [~/git/hub/gradethis]  (vignettes) 
[10:53:30] $ git push -f origin vignettes 
Enumerating objects: 15, done.
Counting objects: 100% (15/15), done.
Delta compression using up to 4 threads
Compressing objects: 100% (14/14), done.
Writing objects: 100% (14/14), 3.27 KiB | 3.27 MiB/s, done.
Total 14 (delta 7), reused 0 (delta 0)
remote: Resolving deltas: 100% (7/7), completed with 1 local object.
To github.com:rstudio-education/gradethis.git
 + b4e2873...846bb18 vignettes -> vignettes (forced update)

The final Graph now looks like this

dchen@longclaw [~/git/hub/gradethis]  (vignettes) 
[10:54:13] $ git l
* 846bb18 (HEAD -> vignettes, origin/vignettes) intro to gradethis for learnr docs
* 9b84be6 emphasize not to use ==
* 28c7ebe i don't want to stash
* a195fa3 (origin/master, origin/HEAD, master) fix gradethis demo (#70)
| * feb82b3 (origin/gh-pages) Deploy rstudio-education/gradethis to github.com/rstudio-education/gradethis.git:gh-pages
| * 4aaee31 (origin/compare_default_formals, compare_default_formals) call_standarise_formals
| * 19354dd refactor is_code_same to is_code_identical
| * 5591ae8 rename fxn code_is_same -> is_code_same
|/  
| * 91cf16e (update_grading_demo) fix gradethis demo
|/  
* 9083fc8 (me/master) rename functions per #65 update docs and tests (#72)
* 5ec1144 Docs to markdown per #68 by @andrie + Barret changes (#69)

Conclusion

It’s taken me many years to be comfortable with Git. My previous go-to method was to rebase one branch on top of the other, but with the squash-and-merge method, a lot of commits get repeated, and it just makes rebaseing a pain with all the commits and merge conflicts.

In this particular workflow I found cherry-pick to be way more convenient, and led to fewer merge conflicts.

Again, the notation for cherry-pick is weird, in that it is left exclusive unless you put in the ^, i.e.,

git cherry-pick <commit-start>^..<commit-end>

not

git cherry-pick <commit-start>..<commit-end>