Diff for "TentativeConventions"

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:

• Everyone can see/read everyone else's branches on Trac.

• Everyone can create/move/write any branch named public/<whatever>, where <whatever> is (almost) any string. We may refer to these branches as being in the Trac "public" space.

• The user mguaypaq can create/move/write any branch named u/mguaypaq/<whatever>. No one else can do this. We may refer to these branches as being in a Trac "user" space.

• However, any user can take any branch named u/mguaypaq/<whatever> and create a copy of it in the "public" space or in their own "user" space.

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

• In your user space, feel free to call your branches u/<username>/<whatever>, where <username> is your user name, and <whatever> is practically any string, including characters like /-_.

• If your branch is related to combinat, feel free to call it u/<username>/combinat/<topic>. If you have an associated Trac ticket number, you can append it to the name: u/<username>/combinat/<topic>-<number>, but please keep the <topic> part of the name next to the /combinat/ part of the name.

• If you are working on a combinat branch with some collaborators, a good central place to push and pull from (in addition to your personal u/<username>/combinat/<topic>) would be the public branch name public/combinat/<topic>.

• If your branch corresponds to a non-combinat ticket, a good default name may be public/ticket/<ticket>-<whatever>, like public/ticket/10305-farahat-higman.

These conventions make it easy to:

• Browse through the list of all branches on Trac (or all combinat branches) and get an idea of what is there.

• Search through the list of all branches on Trac (or all combinat branches) using grep or other automated tools.

• Find the corresponding Trac tickets easily.

In summary:

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

• If aardvarks is a local branch on Alice's computer, then it belongs only to Alice, and she is free to rebase it. Bob could never even see it to use as a base for his work.

• If aardvarks lives on Trac in Alice's user space (branches starting with u/alice/) and it is marked as a "work-in-progress" (abbreviated "wip", for example, u/alice/wip/aardvarks or u/alice/aardvarks-wip), then it belongs only to Alice, and she is free to rebase it. In this case, Bob could technically see the branch and use it as a base for his work, but then Bob has full responsibility for the consequences. Two reasons for this:

  • The user space branches on Trac may be a convenient way for Alice to synchronize her personal messy development work between her own laptop and her own desktop computer.
  • The user space branches on Trac may be a convenient way for Alice to share her personal messy development work with her colleague Carl.

• If aardvarks is listed as the official branch on a Trac ticket (in the "branch" field), then it belongs to the community, and Alice should not rebase it. This is true even if the branch is in Alice's user space (for example, u/alice/aardvarks). Two reasons for this:

  • At this point, Bob may well find the branch by browsing Trac and see that it fixes a bug that is crucial to his feature. If he could not reuse Alice's code as a base, he would have to duplicate Alice's work and likely create merge conflicts for Alice.
  • Bob may also decide to review the patch, and give it a positive review after adding a reviewer patch.

• If aardvarks lives on Trac in the public space (branches starting with public/, like public/combinat/aardvarks), then it belongs to the community, and Alice should not rebase it. This is true even if there is no associated Trac ticket.

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:

• If aardvarks lives on Trac in Alice's user space, is not marked "wip", and has never been in the "branch" field of a Trac ticket (so: u/alice/aardvarks), does it belong to Alice only, or to the community?

There is also the following corollary:

• If aardvarks is marked as work-in-progress (say u/alice/wip/aardvarks), then it should not also be in the "branch" field of a Trac ticket. Before setting it in the "branch" field of a ticket, the branch should be renamed.

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:

• http://trac.sagemath.org/wiki/QuickStartSageGit

• http://sagemath.github.io/git-developer-guide/

• http://sagemath.org/doc/installation/source.html

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.

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 the /usr directory, and we choose to put the sage tree in the /usr/sage-git directory.

/usr$ git clone git@trac.sagemath.org: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.
/usr$ cd sage-git
/usr/sage-git$ ls
build  COPYING.txt  Makefile  README.txt  sage  src  VERSION.txt

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:

• Your global configuration options, in $HOME/.gitconfig, which apply to all your git projects (not just sage). Mine looks like this. The [user] section is the most important, and contains my real name and my real email address. The other sections are really optional, but you can simply copy and paste them:

  • The [core] section has an option that sets my favorite text editor.

  • The [alias] section defines some shortcut commands (like git lg for a very pretty history graph).

  • The [merge] section has an option that makes for more informative merge commit messages.

  • The [push] section contains an option that makes git only update the current branch when pushing to the Trac git server.

/usr/sage-git$ cat $HOME/.gitconfig
[user]
  name = Mathieu Guay-Paquet
  email = mathieu.guaypaquet@gmail.com
[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

• Your sage-specific configurations options, in $SAGE_ROOT/.git/config. Mine looks like this. The parts that should be copied very exactly are:

  • the url option of the [remote "origin"] section, which tells git how it should synchronize the information on your local machine with the information on the Trac git server,

  • the [branch "master"] section, which tells git how your local master branch corresponds to the master branch on the Trac git server.

/usr/sage-git$ cat .git/config
[core]
  repositoryformatversion = 0
  filemode = true
  bare = false
  logallrefupdates = true
[remote "origin"]
  fetch = +refs/heads/*:refs/remotes/origin/*
  url = git@trac.sagemath.org: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

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

The result should look something like:

/usr/sage-git/src/bin/sage-spkg: line 310: cd: /usr/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
/usr/sage-git/local/var/tmp/sage/build/ccache-3.1.9
touch: cannot touch `/usr/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:

• If you already have Atlas libraries built somewhere, you can tell sage to re-use them instead of re-building them. This is controlled by the SAGE_ATLAS_LIB environment variable.

• If you have a computer with many cores and you want to use them to build sage in parallel, you can tell it to do so.

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:

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

/usr/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

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

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

Basic git commands

Getting the latest version of Sage

First get the latest information about all the branches published on trac

$ git remote update origin

Then get the latest version of Sage itself

$ git checkout master
$ git pull --ff-only
$ make start

The option --ff-only for the 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.

Pushing and pulling branches to and from trac

If you have a local branch on your personal computer that you would like to push to trac, there are four options:

$ git push --set-upstream origin <mybranch>:u/<mytracname>/<mybranch>
$ git push --set-upstream origin <mybranch>:public/combinat/<mybranch>
$ git push --set-upstream origin <mybranch>:public/combinat/<ticketnumber>-<mybranch>
$ git push --set-upstream origin <mybranch>:public/ticket/<ticketnumber>-<mybranch>

Use the first option for code you personally work on. The second option is for collaborative code with other combinat people. Use the third option if you already have a ticket number for combinat-related code. The fourth option is for tickets unrelated to combinat.

The first time you pull a branch from trac onto your local computer:

$ git remote update origin
$ git checkout -b 10305-partition origin/public/ticket/10305-partition

The -b option builds the remote branch locally.

After the initial pull or push, this is the workflow to push your local changes to trac:

$ git checkout <mybranch>
$ git pull --ff-only
$ git status
$ git add '<your file>'
$ git commit -m '<your commit message>'
$ git push

The 'git status' command will tell you which files have changed. Then use the 'git add' command to add the files whose changes you want to push to trac.

If the pull command produces an error, you can use these commands:

$ git checkout <mybranch>
$ git pull --ff-only
*git complains*
$ git fetch
$ git merge FETCH_HEAD
...
*resolve any merge conflicts*
*or give up and say: "git merge --abort"*
...
$ git status
...
*some output???*
...
$ git commit -a -m '<some message>'
$ git push

The git fetch command downloads a list of latest commits for the branch you are on, it does not change the state of your local branch. The command git merge FETCH_HEAD updates your branch to the latest version of the branch on Trac.

Deleting branches

If you want to delete a local branch:

$ git checkout <somethingelse>
$ git branch -d <mybranch>

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:

$ git branch -D <mybranch>

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

To delete a remote branch:

$ git push origin :u/aschilling/<something>

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

$ 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>.

Resetting unwanted changes

If you accidentally edited master and want to undo your change

$ git branch -m master <mybranch>
$ git branch master origin/master

If you do not care about the changes you can do a hard reset

$ git reset --hard origin/master

Checking your last few commits

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

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

Branch naming conventions

On Trac

See the section about naming conventions on trac.

Local machine

On your local machine you can call your branches however you like. However, it might be useful to use the same names that you use on trac.

Naming and searching

The branch name should be descriptive. If you have a ticket number (say 10305) that should be the first part of the name. The rest should describe what is in the branch, so people can easily search it

public/combinat/10305-partition-tableaux

Consistently using these naming conventions among all (sage-combinat) developers will make it easier to search for stuff. For example, trying to find all branches related to combinatorics can be found as follows

$ git ls-remote origin '*combinat*'
5feebdbfa73f64dafe28a5e4fe0144ab36083ab0        refs/heads/public/combinat/15361-branching-rules
7f974aeb3446206c029ac047c31938d55d86e651        refs/heads/u/aschilling/combinat/kschur

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

$ git remote update origin
$ git log --all --author="Bump" --since=1.day
commit 5feebdbfa73f64dafe28a5e4fe0144ab36083ab0
Author: Daniel Bump <bump@match.stanford.edu>
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

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

$ git log --remotes='origin/u/mguaypaq/ticket/*' ^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

$ 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

$ git branch --merged=master 
  master

Tornado branches

Sometimes you might want to share certain features that are not yet in main-sage with a collaborator who is not a developer. Suppose these features are in two different branches on trac. Then you can create a tornado branch by merging the two. Note, that you want to make sure that other developers will not base other code on those, so please label them as tornado branches!

Go to one of the two branches you would like to merge

$ git checkout kschur
$ git branch
  combinat/kschur
  master
* public/combinat/15361-branching-rules
  ticket/15300

From there create your new tornado branch

$ git checkout -b tornado-kschur-branching
$ git branch
  combinat/kschur
  master
  public/combinat/15361-branching-rules
  ticket/15300
* tornado-kschur-branching

Now merge in the other branch

$ git merge combinat/kschur
$ git log
commit 510520a52e44bace997784370cacbfdd75ae4473
Merge: 5feebdb 7f974ae
Author: Anne Schilling <anne@lolita-4.local>
Date:   Wed Nov 6 21:59:20 2013 -0800

    Merge branch 'combinat/kschur' into tornado-kschur-branching

Finally push to trac

$ git push --set-upstream origin tornado-kschur-branching:u/aschilling/tornado-kschur-branching
Counting objects: 44, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (5/5), done.
Writing objects: 100% (5/5), 523 bytes | 0 bytes/s, done.
Total 5 (delta 4), reused 0 (delta 0)
To git@trac.sagemath.org:sage.git
 * [new branch]      tornado-kschur-branching -> u/aschilling/tornado-kschur-branching
Branch tornado-kschur-branching set up to track remote branch u/aschilling/tornado-kschur-branching from origin.

Example workflow

Basic collaboration example

Suppose developers A and B collaborate on branch branch_AB. Developer A wants to work on the project and does

$ git checkout branch_AB
$ git pull

then edits files in the sage file system. Once finished A makes a commit

$ git commit -a -m"changed everything"

and pushes to Trac

$ git push

B has been working at the same time and wants to base her work on A's, but is not sure whether there will be conflicts. She only wants to commit changes in file.py for now. So she does

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

Then she pulls using

$ git pull --ff-only

If there was no problem she can push her changes

$ git push

Moving a ticket from patches to git

Make sure that your file has the header data by 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

$ git checkout -b <mybranch> master

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

$ git checkout <mybranch>

Next import your hg patch.

Import patch from a local file

If your patch is on your local computer at /pathname/patchname.patch then

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

Import patch from url

If your patch is on trac or on the internet at a url

$ 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 first.

Moving 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 loose author information if the patch does not have the appropriate meta information.

Here is a sample workflow on how to transform your patch to git:

Export hg patch

First make sure that your patch has the correct meta data by exporting it.

Create new local branch

Make a new branch on your local machine:

$ git checkout -b combinat/kschur master
$ git branch
* combinat/kschur
  master
  ticket/15300

Import patch from queue

Next import the patch from the queue

$ sage --dev import-patch --local-file /Applications/sage-5.13.beta2/devel/sage-combinat/.hg/patches/kschur-as.patch

Create branch on trac

Now we create a branch on trac

$ 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 git@trac.sagemath.org: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.

Mark patch in series file

Mark the patch in the sage-combinat series file as moved to git by changing

kschur-as.patch

to

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