Advanced Git#

This chapter covers some advanced uses of git that go beyond what is required to work with branches. These features can be used in Sage development, but are not really necessary to contribute to Sage. If you are just getting started with Sage development, you should read Development Walk-through and Git Basics instead.

Detached heads and reviewing PRs#

Each commit is a snapshot of the Sage source tree at a certain point. So far, we always used commits organized in branches. But secretly the branch is just a shortcut for a particular commit, the head commit of the branch. But you can just go to a particular commit without a branch, this is called “detached head”. If you have the commit already in your local history, you can directly check it out without requiring internet access:

[alice@localhost sage]$ git checkout f9a0d54099d758ccec731a38929902b2b9d0b988
Note: switching to 'f9a0d54099d758ccec731a38929902b2b9d0b988'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at f9a0d54099 Fix a slow doctest in

If it is not stored in your local Git repository, you need to download it from the upstream repo first:

[alice@localhost sage]$ git fetch upstream f9a0d54099d758ccec731a38929902b2b9d0b988
 * branch                  f9a0d54099d758ccec731a38929902b2b9d0b988 -> FETCH_HEAD
[alice@localhost sage]$ git checkout FETCH_HEAD
HEAD is now at f9a0d54099 Fix a slow doctest in

Either way, you end up with your current HEAD and working directory that is not associated to any local branch:

[alice@localhost sage]$ git status
HEAD detached at f9a0d54099
nothing to commit, working tree clean

This is perfectly fine. You can switch to an existing branch (with the usual git checkout my_branch) and back to your detached head.

Detached heads can be used to your advantage when reviewing PRs. Just check out the commit (look at the “Commits” tab of the PR) that you are reviewing as a detached head. Then you can look at the changes and run tests in the detached head. When you are finished with the review, you just abandon the detached head. That way you never create a new local branch, so you don’t have to type git branch -D my_branch at the end to delete the local branch that you created only to review the ticket.

Update branch to latest Sage version#

  • You have a compiled and working new SageMath version n, and

  • you want to work on a branch some_code which is based on some old SageMath version o

  • by updating this branch from version o to n

  • with only recompiling changed files (and not all touched files from o to n),

  • then continue reading this section.


When developing, quite frequently one ends up with a branch which is not based on the latest (beta) version of SageMath.


Continue working on a feature based on an old branch is perfectly fine and usually there is no need to merge in this latest SageMath version.

However sometimes there is a need for a merge, for example

  • if there are conflicts with the latest version or

  • one needs a recent feature or

  • simply because the old SageMath version is not available on your machine any longer.

Then merging in the latest SageMath version has to be done.

Merge in the latest Sage version#

(This is the easy way without minimizing the recompilation time.)

Suppose we are on our current working branch some_code (branch is checked out). Then

git merge develop

does the merging, i.e. we merge the latest development version into our working branch.

However, after this merge, we need to (partially) recompile SageMath. Sometimes this can take ages (as many files are touched and their timestamps are renewed) and there is a way to avoid it.

Minimize the recompilation time#

Suppose we are on some new SageMath (e.g. on branch develop) which was already compiled and runs successfully, and we have an “old” branch some_code, that we want to bring onto this SageMath version (without triggering unnecessary recompilations).

We first create a new working tree in a directory new_worktree and switch to this directory:

[alice@localhost sage]$ git worktree add new_worktree
[alice@localhost sage]$ cd new_worktree

Here we have a new copy of our source files. Thus no timestamps etc. of the original repository will be changed. Now we do the merge:

[alice@localhost sage/new_worktree]$ git checkout some_code
[alice@localhost sage/new_worktree]$ git merge develop

And go back to our original repository:

[alice@localhost sage/new_worktree]$ git checkout develop
[alice@localhost sage/new_worktree]$ cd ..

We can now safely checkout some_code:

[alice@localhost sage]$ git checkout some_code

We still need to call

[alice@localhost sage]$ make

but only changed files will be recompiled.

To remove the new working tree simply use

[alice@localhost sage]$ rm -r new_worktree

Why not merging the other way round?#

Being on some new SageMath (e.g. on branch develop) which runs successfully, it would be possible to merge in our branch some_code into develop. This would produce the same source files and avoid unnecessary recompilations. However, it makes reading Git’s history very unpleasant: For example, it is hard to keep track of changes etc., as one cannot simply pursue the first parent of each Git commit (git log --first-parent).

Reset and recovery#

Git makes it very hard to truly mess up. Here is a short way to get back onto your feet, no matter what. First, if you just want to go back to a working Sage installation you can always abandon your working branch by switching to your local copy of the develop branch:

[alice@localhost sage]$ git checkout develop

As long as you did not make any changes to the develop branch directly, this will give you back a working Sage.

If you want to keep your branch but go back to a previous commit you can use the reset command. For this, look up the commit in the log which is some 40-digit hexadecimal number (the SHA1 hash). Then use git reset --hard to revert your files back to the previous state:

[alice@localhost sage]$ git log
commit eafaedad5b0ae2013f8ae1091d2f1df58b72bae3
Author: First Last <[email protected]>
Date:   Sat Jul 20 21:57:33 2013 -0400

    Commit message
[alice@localhost sage]$ git reset --hard eafae


Any uncommitted changes will be lost!

You only need to type the first couple of hex digits, Git will complain if this does not uniquely specify a commit. Also, there is the useful abbreviation HEAD~ for the previous commit and HEAD~n, with some integer n, for the n-th previous commit.

Finally, perhaps the ultimate human error recovery tool is the reflog. This is a chronological history of Git operations that you can undo if needed. For example, let us assume we messed up the git reset command and went back too far (say, 5 commits back). And, on top of that, deleted a file and committed that:

[alice@localhost sage]$ git reset --hard HEAD~5
[alice@localhost sage]$ git rm sage
[alice@localhost sage]$ git commit -m "I shot myself into my foot"

Now we cannot just checkout the repository from before the reset, because it is no longer in the history. However, here is the reflog:

[alice@localhost sage]$ git reflog
2eca2a2 HEAD@{0}: commit: I shot myself into my foot
b4d86b9 HEAD@{1}: reset: moving to HEAD~5
af353bb HEAD@{2}: checkout: moving from some_branch to master
1142feb HEAD@{3}: checkout: moving from other_branch to some_branch

The HEAD@{n} revisions are shortcuts for the history of Git operations. Since we want to rewind to before the erroneous git reset command, we just have to reset back into the future:

[alice@localhost sage]$ git reset --hard HEAD@{2}

Rewriting history#

Git allows you to rewrite history, but be careful: the SHA1 hash of a commit includes the parent’s hash. This means that the hash really depends on the entire content of the working directory; every source file is in exactly the same state as when the hash was computed. This also means that you can’t change history without modifying the hash. If others branched off your code and then you rewrite history, then the others are thoroughly screwed. So, ideally, you would only rewrite history on branches that you have not yet pushed to a public repo.

As an advanced example, consider three commits A, B, C that were made on top of each other. For simplicity, we’ll assume they just added a file named,, and

[alice@localhost sage]$ git log --oneline
9621dae added file C
7873447 added file B
bf817a5 added file A
5b5588e base commit

Now, let’s assume that the commit B was really independent and ought to be on a separate ticket. So we want to move it to a new branch, which we’ll call second_branch. First, branch off at the base commit before we added A:

[alice@localhost sage]$ git checkout 5b5588e
Note: checking out '5b5588e'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b new_branch_name

HEAD is now at 5b5588e... base commit
[alice@localhost sage]$ git checkout -b second_branch
Switched to a new branch 'second_branch'
[alice@localhost sage]$ git branch
* second_branch
[alice@localhost sage]$ git log --oneline
5b5588e base commit

Now, we make a copy of commit B in the current branch:

[alice@localhost sage]$ git cherry-pick 7873447
[second_branch 758522b] added file B
 1 file changed, 1 insertion(+)
 create mode 100644
[alice@localhost sage]$ git log --oneline
758522b added file B
5b5588e base commit

Note that this changes the SHA1 of the commit B, since its parent changed! Also, cherry-picking copies commits, it does not remove them from the source branch. So we now have to modify the first branch to exclude commit B, otherwise there will be two commits adding and our two branches would conflict later when they are being merged into Sage. Hence, we first reset the first branch back to before B was added:

[alice@localhost sage]$ git checkout first_branch
Switched to branch 'first_branch'
[alice@localhost sage]$ git reset --hard bf817a5
HEAD is now at bf817a5 added file A

Now we still want commit C, so we cherry-pick it again. Note that this works even though commit C is, at this point, not included in any branch:

[alice@localhost sage]$ git cherry-pick 9621dae
[first_branch 5844535] added file C
 1 file changed, 1 insertion(+)
 create mode 100644
[alice@localhost sage]$ git log --oneline
5844535 added file C
bf817a5 added file A
5b5588e base commit

And, again, we note that the SHA1 of commit C changed because its parent changed. Voila, now you have two branches where the first contains commits A, C and the second contains commit B.

Interactively rebasing#

An alternative approach to Rewriting history is to use the interactive rebase feature. This will open an editor where you can modify the most recent commits. Again, this will naturally modify the hash of all changed commits and all of their children.

Now we start by making an identical branch to the first branch:

[alice@localhost sage]$ git log --oneline
9621dae added file C
7873447 added file B
bf817a5 added file A
5b5588e base commit
[alice@localhost sage]$ git checkout -b second_branch
Switched to a new branch 'second_branch'
[alice@localhost sage]$ git rebase -i HEAD~3

This will open an editor with the last 3 (corresponding to HEAD~3) commits and instuctions for how to modify them:

pick bf817a5 added file A
pick 7873447 added file B
pick 9621dae added file C

# Rebase 5b5588e..9621dae onto 5b5588e
# Commands:
#  p, pick = use commit
#  r, reword = use commit, but edit the commit message
#  e, edit = use commit, but stop for amending
#  s, squash = use commit, but meld into previous commit
#  f, fixup = like "squash", but discard this commit's log message
#  x, exec = run command (the rest of the line) using shell
# These lines can be re-ordered; they are executed from top to bottom.
# If you remove a line here THAT COMMIT WILL BE LOST.
# However, if you remove everything, the rebase will be aborted.
# Note that empty commits are commented out

To only use commit B, we delete the first and third line. Then save and quit your editor, and your branch now consists only of the B commit.

You still have to delete the B commit from the first branch, so you would go back (git checkout first_branch) and then run the same git rebase -i command and delete the B commit.