Git Resources#

Git is central to astropy development. While Git is undeniably complex and at times inscrutable, in practice there is only a very small subset of commands that you will need to know to make contributions to Astropy. This page provides Astropy-specific guidance to using Git along with a list of resources for learning more about Git.

If you have never used git or have limited experience with it, take a few minutes to look at Git Basics, part of a much longer git book.

Essential git commands#

Here are a few git commands you are likely to encounter in contributing to Astropy. In general if you google “git <command>” you will get the appropriate documentation page from git-scm.com.

git fetch gets the latest development version of Astropy, which you will use as the basis for making your changes.
git pull will fetch from and integrate with another repository or a local branch.
git switch changes to a different development branch, optionally creating it.
git add stages files you have changed or created for addition to git.
git commit adds your staged changes to the repository.
git push copies the changes you committed to GitHub
git status to see a list of files that have been modified or created.

Note

A good graphical interface to git makes some of these steps much easier. You might find this list of GUI Clients to be helpful. You may also consider using an Interactive Development Environment (IDE) like PyCharm or Visual Studio Code. Both of these IDEs have built-in Git support.

If something goes wrong#

git provides a number of ways to recover from errors. If you end up making a git mistake, do not hesitate to ask for help. An additional resource that walks you through recovering from git mistakes is the git choose-your-own-adventure.

Tutorials and summaries#

GitHub Help has an excellent series of how-to guides.
learn.github has an excellent series of tutorials
The pro git book is a good in-depth book on git.
A git cheat sheet is a page giving summaries of common commands.
The git user manual
The git tutorial
The git community book
git casts — video snippets giving git how-tos.
The git parable is an easy read explaining the concepts behind git.
git foundation expands on the git parable.
Fernando Perez’s ipython notebook on using git in science
A good but technical page on git concepts

Additional Tips and Tricks#

About Names in git #

Important

tl;dr: Never work in your main branch, always work in a feature branch.

git is a distributed version control system. Each clone of a repository is, itself, a repository. That can lead to some confusion, especially for the branch called main. If you list all of the branches your clone of git knows about with git branch -a you will see there are three different branches called main:

* main                              # this is main in your local repo
remotes/upstream/main               # the official main branch of Astropy
remotes/origin/main                 # main on your fork of Astropy on GitHub

The naming scheme used by git will also be used here. A plain branch name, like main means a branch in your local copy of Astropy. A branch on a remote, like upstream , is labeled by that remote, upstream/main.

This duplication of names can get very confusing when working with pull requests, especially when the official main branch, upstream/main, changes due to other contributions before your contributions are merged in.

Delete a branch on GitHub#

git strongly encourages making a new branch each time you make a change in the code. At some point you will need to clean up the branches you no longer need– that point is after your changes have been accepted if you made a pull request for those changes.

There are two places to delete the branch: in your local repo and on GitHub.

You can do these independent of each other.

To delete both your local copy AND the GitHub copy from the command line follow these instructions:

# change to the main branch (if you still have one, otherwise change to
# another branch)
git switch main

# delete branch locally
# Note: -d tells git to check whether your branch has been merged somewhere
# if it hasn't, and you delete it, it is gone forever.
#
# Use -D instead to force deletion regardless of merge status
git branch -d my-unwanted-branch

# delete branch on GitHub
git push origin :my-unwanted-branch

(Note the colon : before test-branch.) See Github’s instructions for deleting a branch if you want to delete the GitHub copy through GitHub.

Explore your repository#

To see a graphical representation of the repository branches and commits:

gitk --all

To see a linear list of commits for this branch:

git log

You can also look at the network graph visualizer for your GitHub repo.

Rebasing on main#

Let’s say you thought of some work you’d like to do. You git fetch upstream --tags and Make a new feature branch called cool-feature. At this stage main is at some commit, let’s call it E. Now you make some new commits on your cool-feature branch, let’s call them A, B, C. Maybe your changes take a while, or you come back to them after a while. In the meantime, main has progressed from commit E to commit (say) G:

      A---B---C cool-feature
     /
D---E---F---G main

At this stage you consider merging main into your feature branch, and you remember that this here page sternly advises you not to do that, because the history will get messy. Most of the time you can just ask for a review, and not worry that main has got a little ahead. But sometimes, the changes in main might affect your changes, and you need to harmonize them. In this situation you may prefer to do a rebase.

Rebase takes your changes (A, B, C) and replays them as if they had been made to the current state of main. In other words, in this case, it takes the changes represented by A, B, C and replays them on top of G. After the rebase, your history will look like this:

              A'--B'--C' cool-feature
             /
D---E---F---G main

See rebase without tears for more detail.

To do a rebase on main:

# Update the mirror of main
git fetch upstream

# Go to the feature branch
git switch cool-feature

# Make a backup in case you mess up
git branch tmp cool-feature

# Rebase cool-feature onto main
git rebase --onto upstream/main upstream/main cool-feature

In this situation, where you are already on branch cool-feature, the last command can be written more succinctly as:

git rebase upstream/main

When all looks good you can delete your backup branch:

git branch -D tmp

If it doesn’t look good you may need to have a look at Recovering from mess-ups.

If you have made changes to files that have also changed in main, this may generate merge conflicts that you need to resolve - see the git rebase man page for some instructions at the end of the “Description” section. There is some related help on merging in the git user manual - see resolving a merge.

If your feature branch is already on GitHub and you rebase, you will have to force push the branch; a normal push would give an error. If the branch you rebased is called cool-feature and your GitHub fork is available as the remote called origin, you use this command to force-push:

git push --force origin cool-feature

Note that this will overwrite the branch on GitHub, i.e. this is one of the few ways you can actually lose commits with git. Also note that it is never allowed to force push to the main astropy repo (typically called upstream), because this would re-write commit history and thus cause problems for all others.

Recovering from mess-ups#

Sometimes, you mess up merges or rebases. Luckily, in git it is relatively straightforward to recover from such mistakes.

If you mess up during a rebase:

git rebase --abort

If you notice you messed up after the rebase:

# Reset branch back to the saved point
git reset --hard tmp

If you forgot to make a backup branch:

# Look at the reflog of the branch
git reflog show cool-feature

8630830 cool-feature@{0}: commit: BUG: io: close file handles immediately
278dd2a cool-feature@{1}: rebase finished: refs/heads/my-feature-branch onto 11ee694744f2552d
26aa21a cool-feature@{2}: commit: BUG: lib: make seek_gzip_factory not leak gzip obj
...

# Reset the branch to where it was before the botched rebase
git reset --hard cool-feature@{2}

Rewriting commit history#

Note

Do this only for your own feature branches.

There’s an embarrassing typo in a commit you made? Or perhaps the you made several false starts you would like the posterity not to see.

This can be done via interactive rebasing.

Suppose that the commit history looks like this:

git log --oneline
eadc391 Fix some remaining bugs
a815645 Modify it so that it works
2dec1ac Fix a few bugs + disable
13d7934 First implementation
6ad92e5 * masked is now an instance of a new object, MaskedConstant
29001ed Add pre-nep for a couple of structured_array_extensions.
...

and 6ad92e5 is the last commit in the cool-feature branch. Suppose we want to make the following changes:

Rewrite the commit message for 13d7934 to something more sensible.
Combine the commits 2dec1ac, a815645, eadc391 into a single one.

We do as follows:

# make a backup of the current state
git branch tmp HEAD
# interactive rebase
git rebase -i 6ad92e5

This will open an editor with the following text in it:

pick 13d7934 First implementation
pick 2dec1ac Fix a few bugs + disable
pick a815645 Modify it so that it works
pick eadc391 Fix some remaining bugs

# Rebase 6ad92e5..eadc391 onto 6ad92e5
#
# 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
#
# If you remove a line here THAT COMMIT WILL BE LOST.
# However, if you remove everything, the rebase will be aborted.
#

To achieve what we want, we will make the following changes to it:

r 13d7934 First implementation
pick 2dec1ac Fix a few bugs + disable
f a815645 Modify it so that it works
f eadc391 Fix some remaining bugs

This means that (i) we want to edit the commit message for 13d7934, and (ii) collapse the last three commits into one. Now we save and quit the editor.

Git will then immediately bring up an editor for editing the commit message. After revising it, we get the output:

[detached HEAD 721fc64] FOO: First implementation
 2 files changed, 199 insertions(+), 66 deletions(-)
[detached HEAD 0f22701] Fix a few bugs + disable
 1 files changed, 79 insertions(+), 61 deletions(-)
Successfully rebased and updated refs/heads/my-feature-branch.

and the history looks now like this:

0f22701 Fix a few bugs + disable
721fc64 ENH: Sophisticated feature
6ad92e5 * masked is now an instance of a new object, MaskedConstant

If it went wrong, recovery is again possible as explained above.

Merge commits and cherry picks#

Let’s say that you have a fork (origin) on GitHub of the main Astropy repository (upstream). Your fork is up to date with upstream’s main branch and you’ve made some commits branching off from it on your own branch:

upstream:

   main
      |
A--B--C

origin:

 upstream/main
      |
A--B--C
       \
        D--E
           |
       issue-branch

Then say you make a pull request of issue-branch against Astroy’s main, and the pull request is accepted and merged. When GitHub merges the pull request it’s basically doing the following in the upstream repository:

$ git switch main
$ git remote add yourfork file:///path/to/your/fork/astropy
$ git fetch yourfork
$ git merge --no-ff yourfork/issue-branch

Because it always uses --no-ff we always get a merge commit (it is possible to manually do a fast-forward merge of a pull request, but we rarely ever do that). Now the main Astropy repository looks like this:

upstream:

          main
             |
A--B--C------F
       \    /
        D--E
           |
    yourfork/issue-branch

where “F” is the merge commit GitHub just made in upstream.

When you do cherry-pick of a non-merge commit, say you want to just cherry-pick “D” from the branch, what happens is it does a diff of “D” with its parent (in this case “C”) and applies that diff as a patch to whatever your HEAD is.

The problem with a merge commit, such as “F”, is that “F” has two parents: “C” and “E”. It doesn’t know whether to apply the diff of “F” with “C” or the diff of “F” with “E”. Clearly in this case of backporting a pull request to a bug fix branch we want to apply everything that changed on main from the merge, so we want the diff of “F” with “C”.

Since GitHub was on main when it did git merge yourfork/issue-branch, the last commit in main is the first parent. Basically whatever HEAD you’re on when you do the merge is the first parent, and the tip you’re merging from is the second parent (octopus merge gets more complicated but only a little, and that doesn’t apply to pull requests). Since parents are numbered starting from “1” then we will always cherry-pick merge commits with -m 1 in this case.

That’s not to say that the cherry-pick will always apply cleanly. Say in upstream we also have a backport branch that we want to cherry pick “F” onto:

upstream:

  backport
     |
     G       main
    /          |
A--B----C------F
         \    /
          D--E

We would do:

$ git switch backport
$ git cherry-pick -m 1 F

But this applies the diff of “F” with “C”, not of “F” with “G”. So clearly there’s potential for conflicts and incongruity here. But this will work like any merge that has conflicts–you can resolve any conflicts manually and then commit. As long as the fix being merged is reasonably self-contained this usually requires little effort.

Git mailmap#

If you need to edit .mailmap and know how to do it then you can open a pull request for that. Please run git shortlog -es locally first with your changes to make sure your edit is correct, and you only appear in the list once.