Abstract

Here are some tentative workflow and naming conventions developed at Sage Days 54, together with some FAQs about using git.

Rationale

Why does this page give instructions using git directly instead of the dev scripts?

Currently, the dev scripts are in a state of flux, and it's easy for a user to get their sage tree into a state where the dev scripts are not working properly, or not working at all. The situation will eventually stabilize, and at that point the scripts will be reliable in addition to being useful. Until then, it's important to know how to work with git directly.

What is a git branch?

In the git model (see Git for computer scientists for a nice description), there is a history graph (that is, a directed acyclic graph), which contains every change to the sage code together with descriptions of these changes. A node in this graph is called a "commit", and in general the history graph only ever grows (gets more nodes/commits). A "branch" is just a movable label to a particular point in the history graph. We think of a branch as pointing to a particular commit, together with all of its ancestors in the history graph.

What is Trac?

Trac is the server that acts as the git repository (it is also refers to the ticket manager). In this document the identifier origin always refers to Trac.

Since this is confusing, let's say it again: Trac refers to the url trac.sagemath.org, which runs two services, namely a git repository (this is our main concern in this document), and a ticket tracker (which is only a secondary concern in this document).

What should I name my branch on Trac?

First, it should be noted that the name of a branch on your computer does not have to match the name of the (corresponding) branch on Trac. Git has the ability to keep track of a mapping between local branch names and remote branch names for convenience. However, some people prefer to keep the same name for local and remote branches, to avoid confusion. Now, the question is: what should you name your remote branches on Trac?

This is mainly important because different people have different permission for reading and writing branches on Trac:

Given this, the discussions at Sage Days 54 settled on some suggestions:

These conventions make it easy to:

In summary:

u/<username>/wip/<mystuff>          # for a single-author, unstable personal branch
u/<username>/combinat/<topic>       # for personal progress on a combinat branch
public/combinat/<topic>             # for public progress on a combinat branch
public/combinat/<topic>-<number>    # for a combinat-related branch with an associated Trac ticket
public/ticket/<number>-<topic>      # for a generic public branch with an associated Trac Ticket

If a branch is on Trac, who does it belong to?

Suppose Alice creates a branch aardvarks starting from origin/master. Then Bob sees this and creates a further branch bowling starting from the branch aardvarks. Later, Alice decides (whether rightly or wrongly) to rebase the branch aardvarks on a more recent version of origin/master, without consulting Bob. This creates a conflict between the new history of aardvarks and the current history of bowling. Who is now responsible for fixing the conflict? (See RebaseVsMerge for more details about this situation.)

Based on discussions at Sage Days 54, the following statements should not be controversial:

This leaves the following question unanswered, because there is currently no consensus. It may be best to avoid such ambiguities for now when naming branches on Trac:

There is also the following corollary:

First-time setup

There is some scattered documentation on how to install and configure the git version of Sage. For convenience, we compile all of the correct (as of November 7, 2013) steps here.

Sources:

Step 1: make sure git is installed on your computer

This step is different for different people, but is described in the git setup section of the new developer guide. Note that to use git with sage, you must always be somewhere in the sage tree (in $SAGE_ROOT, which may be something like /opt/sage-git on your computer) when running any git ... commands.

Note

If you want to set up tab completion for git (which is very useful), check out the nice instructions at the tips and tricks section of the Pro Git book.

Step 2: tell Trac about your ssh key

Follow the excellent directions at the authentication section of the new developer guide (everything starting at the heading "Authentication" and ending before the heading "Reporting bug"). This is necessary if you want to actually push your code changes to the Trac server using git.

Note
When you copy your public key information to Trac (in your user preferences page), make sure you don't copy and paste extra line breaks in your key! Trac allows you to have more than one public key, as long as you put each key on a separate line. Conversely, this means that you cannot spread a single key across multiple lines. To check that you don't have extra line breaks, you can try resizing the textbox on your user preferences page.

Step 3: clone the git repository from Trac

Get a copy of the whole sage tree from the Trac server using git. In the following example, we are working in my home directory (denoted by ~), and we choose to put the sage tree in the ~/sage-git sub-directory.

~$ git clone [email protected]:sage.git sage-git
Cloning into 'sage-git'...
remote: Counting objects: 205444, done.
remote: Compressing objects: 100% (36317/36317), done.
remote: Total 205444 (delta 137341), reused 205055 (delta 137070)
Receiving objects: 100% (205444/205444), 57.55 MiB | 11.18 MiB/s, done.
Resolving deltas: 100% (137341/137341), done.
~$ cd sage-git
~/sage-git$ ls
build  COPYING.txt  Makefile  README.txt  sage  src  VERSION.txt
Important note

If you have any aliases or symbolic links set up for running the sage command on your machine, now would be a very good time to update them. Otherwise, be careful to always run ./sage instead of just plain sage!

Step 4: make sure your git configuration is correct

Git stores some information about default command options and remote repositories in a few places on your computer. For sage, there are two relevant places:

~/sage-git$ cat $HOME/.gitconfig
[user]
  name = Mathieu Guay-Paquet
  email = [email protected]
[core]
  editor = gedit -w -s
[alias]
  ci = commit -a
  co = checkout
  st = status
  br = branch
  wdiff = diff --color-words
  lg = log --graph --pretty=format:'%Cred%h%Creset -%C(yellow)%d%Creset %s %Cgreen(%cr) %C(bold blue)[%an]%Creset' --abbrev-commit --date=relative
[merge]
  log = true
[push]
  default = upstream

~/sage-git$ cat .git/config
[core]
  repositoryformatversion = 0
  filemode = true
  bare = false
  logallrefupdates = true
[remote "origin"]
  fetch = +refs/heads/*:refs/remotes/origin/*
  url = [email protected]:sage.git
[branch "master"]
  remote = origin
  merge = refs/heads/master

Step 5: install ccache to speed up future compilations

The optional sage package ccache makes recompilations of C files much faster, so it is recommended to install it. Thankfully, this is very easy: simply go to the directory containing sage on your computer and say

~/sage-git$ ./sage -i ccache

The result should look something like:

~/sage-git/src/bin/sage-spkg: line 310: cd: ~/sage-git/upstream: No such file or directory
Attempting to download package ccache
>>> Checking online list of optional packages.
2013-11-07 17:11:12 URL:http://www.sagemath.org/spkg/optional/list [1139/1139] -> "-" [1]
>>> Found ccache-3.1.9
>>> Trying to download http://www.sagemath.org/spkg/optional/ccache-3.1.9.spkg

*** lots of output ***

real 0m8.544s
user 0m5.328s
sys 0m1.392s
Successfully installed ccache-3.1.9
Deleting temporary build directory
~/sage-git/local/var/tmp/sage/build/ccache-3.1.9
touch: cannot touch `~/sage-git/local/lib/sage-force-relocate.txt': No such file or directory
Finished installing ccache-3.1.9.spkg

Step 6: build sage and/or the sage documentation

Now we must compile sage for the first time. This will likely take a long time, but subsequent times (such as when reviewing tickets or developing the sage library or upgrading to the latest version of sage) should be much faster.

Note

Whenever you run the git or make commands, make sure you are in the sage directory.

Still, there are two things you can do to significantly speed up building sage:

Both of these options (and many more) are documented in the "environment variables" section of the sage installation guide, but below are some of the salient points.

You can also tell sage to skip building the documentation by giving an option to the make command, as follows:

~/sage-git$ make start    # build sage without documentation and make sure it runs
~/sage-git$ make build    # build sage without documentation
~/sage-git$ make doc      # build the sage documentation
~/sage-git$ make          # build sage and the documentation

I have a pre-compiled version of Atlas in my /opt/atlas-sage directory, containing the following files:

~/sage-git$ ls /opt/atlas-sage
libatlas.a   libcblas.so   libf77blas.so  libptcblas.a
libatlas.so  libclapack.a  liblapack.a    libptf77blas.a
libcblas.a   libf77blas.a  liblapack.so   libtstatlas.a

Note that by default, sage will only download the packages it needs when it tries to install each one. If you want to download everything at once (maybe because you intend to compile sage without an internet connection), you can simply say:

~/sage-git$ make download    # download all the latest standard spkg files

Combining all of this, probably the fastest way to build sage is something like:

~/sage-git$ export SAGE_ATLAS_LIB=/opt/atlas-sage    # this is where my pre-compiled Atlas libraries live
~/sage-git$ export MAKE='make -j6'                   # use many cores (6 in this case)
~/sage-git$ make start                               # build only sage

Quick reference guide: I want to...

Here are some common things you might want to do, together with the relevant git commands.

Note
If you want to know the details of a given git command, use:

$ git help <command>

where <command> is something like push, pull, commit, etc.

Get the latest official stable version and development version of Sage

First, check if you have any unsaved changes by running the command:

~/sage-git$ git status

If you do have unsaved changes, they will be lost! Save them first. To get the latest stable version of Sage run the following commands:

~/sage-git$ git fetch origin           # get the latest repository information from Trac
~/sage-git$ git reset --hard master    # make all your files correspond to the local master branch
~/sage-git$ git clean -d -f            # get rid of any untracked files or directories
~/sage-git$ git checkout master        # switch to the master branch (in case you are not yet on it)
~/sage-git$ git pull --ff-only         # move the local master branch forward to match the information from Trac
~/sage-git$ make start                 # rebuild the parts of Sage that changed

The latest development version of Sage is in the branch develop. It is a good idea to base all new Sage development off the development branch. Before starting to work on a new project, get the latest development version via

~/sage-git$ git fetch origin           # get the latest repository information from Trac
~/sage-git$ git reset --hard develop   # make all your files correspond to the local develop branch
~/sage-git$ git clean -d -f            # get rid of any untracked files or directories
~/sage-git$ git checkout develop       # change to the development branch
~/sage-git$ git pull --ff-only         # move the local master branch forward to match the information from Trac
~/sage-git$ make start                 # rebuild the parts of Sage that changed

The option --ff-only for the git pull command makes sure that if there are big merge conflicts with the new changes on trac, you can handle them manually without messing up your entire branch and your local changes. The make start command is analogous to the usual sage -b command, but is more comprehensive.

Start working on a new feature

To start work on a new feature, you should first get latest official development version of Sage, and use that as the base of your work. Then create a new local branch (named <localname> here, but please pick a better name) to hold your code changes:

~/sage-git$ git checkout develop -b <localname>    # create a new branch <localname> based at the current develop branch

Then, you can go ahead and start making your code changes. Be sure to save your work when you are done!

Also, before running Sage with your modifications, be sure to rebuild the parts that changed with the command:

~/sage-git$ make start

Save my work

See this tutorial on making commits or this tutorial on stashing changes for lots of details on how to save your code changes, but here are the basic commands you need. If your code is in a coherent state, use some combination of the commands:

~/sage-git$ git branch                                      # see if you are on the right branch
~/sage-git$ git status                                      # see what files you have changed
~/sage-git$ git add <filename>                              # if you have created a new file
~/sage-git$ git commit -a -m 'this is my commit message'    # save changes to any modified files

If your code is in a very dirty state, you can instead use a combination of the commands:

~/sage-git$ git stash save 'this is a note to self'    # create a temporary stash of code changes
~/sage-git$ git stash list                             # show a list of existing stashes
~/sage-git$ git stash pop                              # apply the most recent stash to the sage tree
~/sage-git$ git stash drop                             # discard the most recent stash

See also the section on making your code changes available on the Trac git server.

Continue working on a feature

First, check if you have any unsaved changes by running the command:

~/sage-git$ git status

If you don't have any unsaved changes and you would like to work on the branch <localname>, which already exists on your own computer, then do:

~/sage-git$ git checkout <localname>    # move to the correct branch
~/sage-git$ git pull --ff-only          # get any recent changes from the Trac git server

Only do the second command if you have set up a corresponding branch on the Trac git server. If the pull command produces an error, you can use these commands to resolve the conflict between your version of the code, and the version available on Trac:

~/sage-git$ git checkout <mybranch>    # you already ran
~/sage-git$ git pull --ff-only         # these two commands

*** git complains ***

~/sage-git$ git fetch               # save the changes from Trac to FETCH_HEAD
~/sage-git$ git merge FETCH_HEAD    # combine the changes from Trac with your code

*** resolve any merge conflicts ***
*** or give up and say: "git merge --abort" ***

~/sage-git$ git status

*** some output ***

~/sage-git$ git commit -a -m '<some message>'    # save the result of merging
~/sage-git$ git push                             # tell Trac about the result

In any case, before running Sage with your modifications, rebuild the parts that changed with the command:

~/sage-git$ make start

I made a mistake! I want to undo something I just did

If you accidentally edited master and want to undo your change, you can:

~/sage-git$ git branch -m master <mybranch>    # save your current state to a new branch <mybranch>
~/sage-git$ git branch master origin/master    # make a new master branch from the original one

If you deleted a local branch and you want to get it back, your deletion command should have told you the commit hash (something like fb33147) of the deleted branch. To get it back, say:

~/sage-git$ git branch <oldname> <hash>

If you want to see what your last few commits were, type:

~/sage-git$ git reflog
5c7e56d [email protected]{0}: commit: fixed some documentation in kr_tableaux.py
d4cc8e0 [email protected]{1}: pull: Merge made by the 'recursive' strategy.
3813946 [email protected]{2}: commit: removed some whitespace in kr_tableaux.py
307fef1 [email protected]{3}: commit: Removed some whitespaces, beautified code
6aae6bf [email protected]{4}: merge origin/public/combinat/rigged_configurations/13872-bijections: Fast-forward
f2491f1 [email protected]{5}: checkout: moving from master to public/combinat/rigged_configurations/13872-bijections
f2491f1 [email protected]{6}: checkout: moving from tornado-kschur-branching to master
510520a [email protected]{7}: checkout: moving from extended_affine_weyl_groups_sd40 to tornado-kschur-branching
f2491f1 [email protected]{8}: checkout: moving from master to extended_affine_weyl_groups_sd40
f2491f1 [email protected]{9}: checkout: moving from tornado-kschur-branching to master

Make my code available on the Trac git server

If you have a local branch <localname> on your own computer that you would like to push to Trac under the name <remotename>, use the command:

~/sage-git$ git push --set-upstream origin <localname>:<remotename>

For some advice on what <remotename> should be, see the section on branch naming conventions.

Note that with the --set-upstream option, the previous command sets up a mapping on your computer between the names <localname> and origin/<remotename>. This only needs to be done once, and then the following shortcuts should work:

~/sage-git$ git checkout <localname>    # make sure you are on the <localname> branch
~/sage-git$ git pull --ff-only          # get any changes from the Trac git server
~/sage-git$ git push                    # push your changes from the Trac git server

(But see the section on git configuration if git push doesn't work.)

Get someone else's code from the Trac git server

If there is a branch <remotename> on Trac and you would like to have a corresponding branch called <localname> on your own computer, use the commands:

~/sage-git$ git fetch origin                                   # get the latest repository information from Trac
~/sage-git$ git checkout origin/<remotename> -b <localname>    # create the <localname> branch

For some clues on what <remotename> may mean, see the section on branch naming conventions.

The previous command sets up a mapping on your computer between the names <localname> and origin/<remotename>. This only needs to be done once, and then the following shortcuts should work:

~/sage-git$ git checkout <localname>    # make sure you are on the <localname> branch
~/sage-git$ git pull --ff-only          # get any changes from the Trac git server
~/sage-git$ git push                    # push your changes from the Trac git server

(But see the section on git configuration if git push doesn't work.)

In any case, before running Sage, rebuild the parts that changed with the command:

~/sage-git$ make start

It can happen that you might have already compiled the latest development version on your develop branch, but that the branch you want to get from trac is based on a later version of Sage. In this case, just checking out the branch on trac as above will result in a lot of recompilation. In this example public/ticket/18653 is a branch on the git server that is based on an older version than the develop branch. This can be avoided with the following workflow:

~/sage-git$ git checkout develop -b <localname>   # locally create a new branch based on the develop branch
~/sage-git$ git fetch origin                      # get the latest changes from the trac server 
~/sage-git$ git pull origin public/ticket/18653   # pull in the new branch from trac into the current branch <localname>
~/sage-git$ make start

Move/delete/rename a local branch

If you want to delete a local branch <localname>:

~/sage-git$ git checkout master          # move to a different branch
~/sage-git$ git branch -d <localname>    # delete the branch

This might complain if you are trying to delete a branch that has not been merged yet. If nonetheless you would like to delete it, try a hard delete:

~/sage-git$ git branch -D <localname>

Even in a hard delete this can be undone in the next 30 days (before the commits get garbage collected).

If you want to rename a local branch <oldname> to <newname>:

~/sage-git$ git branch -m <oldname> <newname>

Move/delete/rename a branch on the Trac git server

To delete a remote branch <something>:

~/sage-git$ git push origin :<something>

The syntax here may look confusing, so here is a little explanation: it is actually a special case of the syntax

~/sage-git$ git push origin <localbranch>:<remotebranch>

which updates <remotebranch> on the remote server to be the same as <localbranch>. To delete a branch, we make <localbranch> be completely blank and push it onto <remotebranch>.

To rename a remote branch, you have to delete the old name, and create the new name. Use these commands:

~/sage-git$ git fetch origin                             # get the latest info from Trac
~/sage-git$ git checkout origin/<oldname>                # move to the branch to be renamed
~/sage-git$ git push origin HEAD:<newname> :<oldname>    # create <newname> and delete <oldname> on Trac

Note that this will change which branch you are currently on.

Change the mapping between my local branches and branches on the Trac git server

If you have a local branch named <localname> on your own computer which is currently set up to map to the branch <oldremotename> on the Trac git server, and you would rather that it map to the branch <newremotename>, use the following command:

~/sage-git$ git branch <localname> --set-upstream-to origin/<newremotename>
Note
You may have an older version of git, in which case you will get an error message like

error: unknown option `set-upstream-to'
usage: git branch [options] [-r | -a] [--merged | --no-merged]
   or: git branch [options] [-l] [-f] <branchname> [<start-point>]

*** more output ***

In that case, use the following command instead:

~/sage-git$ git branch <localname> --set-upstream origin/<newremotename>
Note

You can also see (and edit) the information about the mapping between local branch names and remote branch names in the file $SAGE_ROOT/.git/config.

Collaborate with others on a combinat feature

Simply use the workflow described in the rest of this document, and pay attention to your naming conventions. For a quick example, see the basic collaboration example below.

See what other people are doing

If people use consistent naming conventions for their branch names on the Trac git server, then it will be easy to search through them. For example, the following commands search through the branch names on Trac for certain patterns:

~/sage-git$ git fetch origin                           # get the latest info from Trac
~/sage-git$ git branch -r | grep '/combinat/'          # search for combinat branches
~/sage-git$ git branch -r | grep '/combinat/kschur'    # search for branches on kschur functions
~/sage-git$ git branch -r | grep '/aschilling/'        # search for Anne Schilling's branches

If you want to see what a specific author did on trac within the last day, you can say:

~/sage-git$ git fetch origin
~/sage-git$ git log --all --author="Bump" --since=1.day
commit 5feebdbfa73f64dafe28a5e4fe0144ab36083ab0
Author: Daniel Bump <[email protected]>
Date:   Wed Nov 6 09:51:08 2013 -0800

    get_branching_rule for F4=>B3 and G2=>A1 should return vectors of the correct length

To see how the ticket branches of author mguaypaq differ from main sage (or origin/master) try:

~/sage-git$ git log --remotes='origin/u/mguaypaq/*' ^origin/master --oneline
1c7458a #15300: Implement Weyl and Clifford algebras.
fb33147 Merge branch 'master' into ticket/10305
405178b Remove extra chunk from farahat_higman.py and fix related formatting issues.
25ff1fd Split off SymmetricGroupAlgebraCenter to its own file.
9b72574 Add rings for the center of the symmetric group algebras.

To see all unmerged branches, say:

~/sage-git$ git branch --no-merged=master
  public/combinat/15361-branching-rules
* public/combinat/rigged_configurations/13872-bijections
  ticket/15300
  u/aschilling/combinat/kschur

To see all merged branches, say:

~/sage-git$ git branch --merged=master
  master

Review a ticket

First, consult the "branch" field on the Trac ticket tracker to see the name of the git branch which contains the code changes to be reviewed. Then, get the code from Trac, and review it as usual. You should be able to easily switch between the `master` branch and the ticket branch. If you have any changes to suggest in a review patch, you can make the changes and push them to the Trac git server then into a new branch, e.g., by using

~/sage-git$ sage -dev push --ticket 12345

This should set the branch field on trac properly to your new branch, though you may anyway check on the Trac ticket that the "branch" field is still up to date. The "commit" field will be updated automatically. Make any comments or status changes as needed on the Trac ticket, and you're done!

Test out many features together (tornado branch)

If you want to test out many features together (perhaps to see what merge conflicts will have to be dealt with, or to share the resulting version of Sage with a colleague), you can create a "tornado" branch which includes all of them. Note that you want to make sure that other developers will not base other code intended for the Sage library on those, so please label them clearly as tornado branches!

First make sure you have no unsaved modifications, then create a new branch (called <tornado> here) based at one of the branches or master:

~/sage-git$ git checkout master -b <tornado>

Next, for each branch <branch1>, <branch2>, etc. that you want to combine, merge them into your tornado branch:

~/sage-git$ git merge <branch1>

*** solve any merge conflicts ***

~/sage-git$ git merge <branch2>

*** solve any merge conflicts ***

*** etc. ***

Finally, you can push your tornado branch to Trac, but make sure it is clearly labelled!

Convert a mercurial patch to a git branch

Make sure that your file has the header data by doing an hg export. Then decide where you want to put your patch: if it is an independent patch, you want to create a new branch:

~/sage-git$ git checkout master -b <mybranch>

If you want to import the hg patch on top of another branch, go into this branch first:

~/sage-git$ git checkout <mybranch>

If your patch is on your local computer at /pathname/patchname.patch then use the Sage development script:

~/sage-git$ ./sage --dev import-patch --local-file /pathname/patchname.patch

If your patch is on the Trac ticket tracker or on the internet at a url, then use a command like:

~/sage-git$ ./sage --dev import-patch --url http://trac.sagemath.org/raw-attachment/ticket/12345/trac_12345-patchname.patch

If you find that the author field is set to unknown user then it could be that the patch needs to be exported and modified first.

To see the commit which corresponds to the patch you just imported, do:

~/sage-git$ git log -1         # view the commit message and information of the most recent commit
~/sage-git$ git diff HEAD^1    # view the actual code modifications

If you are satisfied with the imported patch, you can push your changes to the Trac git server.

Move a patch from the combinat queue to git

All patches in the queue will soon be merged from the sage-combinat queue to git branches on trac. Authors who want to do this themselves are encouraged to do so. The script will by default put the branches to public/combinat/<branchname> and might lose author information if the patch does not have the appropriate meta information. To avoid this, use the following workflow.

First make sure that your patch has the correct meta data by exporting it. This step uses the familiar Mercurial workflow, so we will not describe it here.

Then, follow the instructions above for importing a mercurial patch into a git branch.

When the imported patch looks good, push it to the Trac git server, and make sure you label it as a /combinat/ branch. For example:

$ git push --set-upstream origin combinat/kschur:u/aschilling/combinat/kschur
Counting objects: 47, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (7/7), done.
Writing objects: 100% (7/7), 1.27 KiB | 0 bytes/s, done.
Total 7 (delta 6), reused 0 (delta 0)
To [email protected]:sage.git
 * [new branch]      combinat/kschur -> u/aschilling/combinat/kschur
Branch combinat/kschur set up to track remote branch u/aschilling/combinat/kschur from origin.

Finally, mark your patch in the series file as moved to git by changing, for example,

kschur-as.patch

to

kschur-as.patch # git:u/aschilling/combinat/kschur

Basic collaboration example

Suppose developers Alice and Bob collaborate on branch branch_AB. We assume here that both Alice and Bob have set up a correspondence between their local branches and the branch on Trac. Alice wants to work on the project and does:

~/sage-git$ git checkout branch_AB    # go to the common branch
~/sage-git$ git pull --ff-only        # get any changes from Trac

*** make changes to Sage ***

~/sage-git$ git commit -a -m "changed everything"    # save any local changes
~/sage-git$ git push                                 # tell Trac about the changes

Bob has been working at the same time and wants to base his work on Alice's, but he is not sure whether there will be conflicts. He only wants to commit changes in file.py for now. So he does

~/sage-git$ git add file.py
~/sage-git$ git commit -m "changed everything as well"

When he goes to push his changes to Trac, he will get a notification:

~/sage-git$ git push

*** git complains ***

~/sage-git$ git pull --ff-only    # this will complain again, but save the changes from Trac to FETCH_HEAD anyway

*** git complains again ***

~/sage-git$ git merge FETCH_HEAD

*** resolve any merge conflicts

~/sage-git$ git push

TentativeConventions (last edited 2015-06-11 16:27:31 by aschilling)