The Sage Trac Server

All changes to Sage source code have to go through the Sage trac development server. The purpose of the Sage trac server is to

  1. Provide a place for discussion on issues and store a permanent record.
  2. Provide a repository of source code and all proposed changes.
  3. Link these two together.

There is also a wiki for more general organizational web pages, like Sage development workshops.

Thus if you find a bug in Sage, if you have new code to submit, want to review new code already written but not yet included in Sage, or if you have corrections for the documentation, you should post on the trac server. Items on the server are called tickets, and anyone may search or browse the tickets. For a list of recent changes, just visit the Sage trac timeline.

Authentication

There are two avenues to prove to the trac server that you are who you claim to be. First, to change the ticket web pages you need to log in to trac using a username/password. Second, there is public key cryptography used by git when copying new source files to the repository. This section will show you how to setup both.

Obtaining an Account

You first need to open an account if you want to change anything on the Sage trac server, even if you just want to comment on a ticket. Part of the process is to prove that you are a human to keep spam at a minimum. To get an account read the developer manual (this document) and then send an email to sage-trac-account@googlegroups.com that contains all of the following:

  • your full name,
  • preferred username,
  • contact email,
  • and reason for needing a trac account.

Your trac account also grants you access to the sage wiki. Make sure you understand the review process, and the procedures for opening and closing tickets before making changes. The remainder of this chapter contains various guidelines on using the trac server.

Generating and Uploading your SSH Keys

The git installation on the development server uses SSH keys to decide if and where you are allowed to upload code. No SSH key is required to report a bug or comment on a ticket, but as soon as you want to contribute code yourself you need to provide trac with the public half of your own personal key. In recent versions of Sage, you can use Sage to generate an upload an SSH key

sage: dev.upload_ssh_key()
The trac git server requires your SSH public key to be able to identify you.
Upload "/home/vbraun/.ssh/id_dsa.pub" to trac? [Yes/no] y
Trac username: user
Trac password:
Your key has been uploaded.

You can also manually generate an SSH key and upload it to trac. This is described in the following two sections.

Manually Generating your SSH Keys

If you don’t have a private key yet, you can create it with the ssh-keygen tool:

[user@localhost ~]$ ssh-keygen
Generating public/private rsa key pair.
Enter file in which to save the key (/home/user/.ssh/id_rsa):
Enter passphrase (empty for no passphrase):
Enter same passphrase again:
Your identification has been saved in /home/user/.ssh/id_rsa.
Your public key has been saved in /home/user/.ssh/id_rsa.pub.
The key fingerprint is:
ce:32:b3:de:38:56:80:c9:11:f0:b3:88:f2:1c:89:0a user@localhost
The key's randomart image is:
+--[ RSA 2048]----+
|  ....           |
|   ..            |
|   .o+           |
| o o+o.          |
|E + .  .S        |
|+o .   o.        |
|. o   +.o        |
|      oB         |
|     o+..        |
+-----------------+

This will generate a new random private RSA key in the .ssh folder in your home directory. By default, they are

~/.ssh/id_rsa
Your private key. Keep safe. Never hand it out to anybody.
~/.ssh/id_rsa.pub
The corresponding public key. This and only this file can be safely disclosed to third parties.

The ssh-keygen tool will let you generate a key with a different file name, or protect it with a passphrase. Depending on how much you trust your own computer or system administrator, you can leave the passphrase empty to be able to login without any human intervention.

If you have accounts on multiple computers you can use the SSH keys to log in. Just copy the public key file (ending in .pub) to ~/.ssh/authorized_keys on the remote computer and make sure that the file is only read/writeable by yourself. Voila, the next time you ssh into that machine you don’t have to provide your password.

Manually Linking your Public Key to your Trac Account

The Sage trac server needs to know one of your public keys. You can upload it in the preferences, that is

  1. Go to http://trac.sagemath.org
  2. Log in with your trac username/password
  3. Click on “Preferences”
  4. Go to the “SSH Keys” tab
  5. Paste the content of your public key file (e.g. ~/.ssh/id_rsa.pub)
  6. Click on “Save changes”

Note that this does not allow you to ssh into any account on trac, it is only used to authenticate you to the gitolite installation on trac. You can test that you are being authenticated correctly by issuing some basic gitolite commands, for example:

[user@localhost ~]$ ssh git@trac.sagemath.org info
hello user, this is git@trac running gitolite3 (unknown) on git 1.7.9.5

 R W      sage
[user@localhost ~]$ ssh git@trac.sagemath.org help
hello user, this is gitolite3 (unknown) on git 1.7.9.5

list of remote commands available:

    desc
    help
    info
    perms
    writable

Reporting Bugs

If you think you have found a bug in Sage, you should first search through the following Google groups for postings related to your possible bug:

Maybe the problem you have encountered has already been discussed. You should also search the trac server to see if anyone else has opened a ticket about your bug.

If you do not find anything, and you are not sure that you have found a bug, ask about it on sage-devel. You might be asked to open a new ticket on the trac server. As mentioned above, you need an account to do this. To report a bug, login and click on the “New ticket” button. Type a meaningful one-liner in the “Short summary” box, with more information in the larger box below. You should include at least one explicit, reproducible example illustrating your bug (and/or the steps required to reproduce the buggy behavior). You should also include the version of Sage (and any relevant packages) you are using, and operating system information, being precise as possible (32-bit, 64-bit, ...).

Between the “Summary” and “Full description” boxes, there is a place to choose the “Type” of the ticket: “Defect”, “Enhancement”, or “Task”. Use your best judgment here; a bug should probably be reported as a “Defect”.

Also pick a component for your bug; this is sometimes straightforward. If your bug deals with Sage’s calculus implementation, choose “calculus”. If it is not obvious, do your best. Choose a milestone; if you are not sure what to choose, just choose the numbered version of Sage from the menu (“sage-5.10”, for example). Type in some helpful keywords. In the box labeled “Assign to”, type “somebody” if you are not sure what else to do.

Hit the “Preview” button to make sure everything looks okay, and then hit “Submit ticket”.

If you do not have an account on the trac system to report directly, you are still encouraged to report any possible bug to the sage-devel mailing list at sage-devel@googlegroups.com. The list is moderated for new users and requires subscription. In your bug report to sage-devel, make sure to include the following information:

  • operating system: as precise as possible and architecture (32-bit, 64-bit, ...)
  • affected version: the exact version number and the downloaded package (source, precompiled, virtual machine image, or an upgrade from a previous version (which one?))
  • provide a reproducible example and/or define the steps to reproduce the erroneous behaviour.

Thank you in advance for reporting bugs to improve Sage in the future!

Guidelines for Opening Tickets

In addition to bug reports, you should also open a ticket if you have some new code which extends Sage’s capabilities. If you have a feature request, start a discussion on sage-devel first, and then if there seems to be general agreement that you have a good idea, open a ticket describing the idea.

When you consider opening a new ticket, please bear the following points in mind.

  • Before opening a ticket, make sure that nobody else has opened a ticket about the same or closely related issue.
  • It is much better to open several specific tickets than one that is very broad. Indeed, a single ticket which deals with lots of different issues can be quite problematic, and should be avoided.
  • Be precise: If foo does not work on OS X but is fine on Linux, mention that in the title. Use the keyword option so that searches will pick up the issue.
  • The problem described in the ticket must be solvable. For example, it would be silly to open a ticket whose purpose was “Make Sage the best mathematical software in the world”. There is no metric to measure this properly and it is highly subjective.
  • If appropriate, provide URLs to background information or email threads relevant to the problem you are reporting.

The Ticket Fields

When you open a new ticket or change an existing ticket, you will find a variety of fields that can be changed. Here is a comprehensive overview:

  • Reported by: The trac account name of whoever created the ticket. Cannot be changed.
  • Owned by: Trac account name of owner, by default the person in charge of the Component:. Generally not used in the Sage trac.
  • Priority: The priority of the ticket. Keep in mind that the “blocker” label should be used very sparingly.
  • Milestone: Milestones are usually goals to be met while working toward a release. In Sage’s trac, we use milestones instead of releases. Each ticket must have a milestone assigned. If you are unsure, assign it to the current milestone.
  • Component: A list of components of Sage, pick one that most closely matches the ticket.
  • Keywords: List of keywords. Fill in any keywords that you think will make your ticket easier to find. Tickets that have been worked on at Sage days NN (some number) ofter have sdNN as keyword.
  • Cc: List of trac user names to Cc (send emails for changes on the ticket). Note that users that enter a comment are automatically substcribed to email updates and don’t need to be listed under Cc.
  • Merged in: The Sage release where the ticket was merged in. Only changed by the release manager.
  • Authors: Real name of the ticket author (or list of authors).
  • Reviewers: Real name of the ticket reviewer (or list of reviewers).
  • Report Upstream: If the ticket is a bug in an upstream component of Sage, this field is used to summarize the communication with the upstream developers.
  • Work issues: Issues that need to be resolved before the ticket can leave the “needs work” status.
  • Branch: See Branching Out
  • Dependencies: Does the ticket depend on another ticket? Sometimes, a ticket requires that another ticket be applied first. If this is the case, put the dependencies as a comma-separated list (#1234, #5678) into the “Dependencies:” field.
  • Stopgaps: See Stopgaps.

Stopgaps

If a component of Sage produces a mathematical error, you should open two tickets: a main ticket with all available details, and also a “stopgap” ticket. This second ticket should have a patch which will be merged into Sage if no one fixes the main issue; this patch should print a warning when anyone uses the relevant code. To produce the warning message, use code like the following:

from sage.misc.stopgap import stopgap
stopgap("This code contains bugs and may be mathematically unreliable.",
    TICKET_NUM)

Replace TICKET_NUM by the ticket number for the main ticket. See trac ticket #12699, for example. On the main trac ticket, you should also enter the ticket number for the stopgap ticket in the “Stopgaps” field. Stopgap tickets should be marked as blockers.

Note

If mathematically valid code causes Sage to raise an error or crash, for example, there is no need for a stopgap. Rather, stopgaps are to warn users that they may be using buggy code; if Sage crashes, this is not an issue.

Working on Tickets

If you manage to fix a bug or enhance Sage you are our hero. See Sage Development Process for making changes to the Sage source code, uploading them to the Sage trac server, and finally putting your new branch on the trac ticket. The following are some other relevant issues:

  • The Patch buildbot wil automatically test your ticket. See the patchbot wiki for more information about its features and limitations. Make sure that you look at the log, especially if the patch buildbot did not give you the green blob.
  • Every bug fixed should result in a doctest.
  • This is not an issue with defects, but there are many enhancements possible for Sage and too few developers to implement all the good ideas. The trac server is useful for keeping ideas in a central place because in the Google groups they tend to get lost once they drop off the first page.
  • If you are a developer, be nice and try to solve a stale/old ticket every once in a while.
  • Some people regularly do triage. In this context, this means that we look at new bugs and classify them according to our perceived priority. It is very likely that different people will see priorities of bugs very differently from us, so please let us know if you see a problem with specific tickets.

Reviewing Patches

All code that goes into Sage is peer-reviewed, to ensure that the conventions discussed in this manual are followed, to make sure that there are sufficient examples and doctests in the documentation, and to try to make sure that the code does, mathematically, what it is supposed to.

If someone (other than you) has posted a git branch for a ticket on the trac server, you can review it! Look at the branch diff (by clicking on the ) to see if it makes sense. Download it (see Reviewing) and build Sage with the new code. Now ask yourself questions such as the following:

  • Does the new source code make sense?
  • When you run it in Sage, does it fix the problem reported on the ticket?
  • Does it introduce any new problems?
  • Is it documented sufficiently, including both explanation and doctests? All code in Sage must have doctests, so if the ticket author changes code which did not have a doctest before, the new version must include one. In particular, all new code must be 100% doctested. Use the command sage -coverage <files> to see the coverage percentage of <files>.
  • In particular, is there a doctest illustrating that the bug has been fixed? If a function used to give the wrong answer and this ticket fixes that, then it should include a doctest illustrating its new success. The surrounding docstring shoud contain the ticket number, for example See :trac:`12345`.
  • If the ticket claims to speed up some computation, does the ticket contain code examples to illustrate the claim? The ticket should explain the speed efficiency before applying the patch. It should also explain the speed efficiency gained after applying the patch.
  • Does the reference manual build without errors? You can test the reference manual using the command sage -docbuild reference html to build the HTML version. The PDF version of the reference manual must also build without errors. Use the command sage -docbuild reference pdf to test it out. The latter command requires that you have LaTeX installed on your system.
  • Do all doctests pass without errors? It is difficult to predict which components of Sage will be affected by a given patch and you should run tests on the whole library—including those flagged as #long—before giving a positive review. You can test the Sage library with make ptestlong. See Doctesting the Sage Library for more information.
  • Do the code and documentation follow conventions documented in the following sections?

If the answers to these and other such reasonable questions are yes, then you might want to give the patch a positive review. On the main ticket page, write a comment in the box explaining your review. If you don’t feel experienced enough for this, make a comment explaining what you checked, and end by asking if someone more experienced will take a look. If you think there are issues with the patch, explain them in the comment box and change the status to “needs work”. Browse the tickets on the trac server to see how things are done.

Note

“The perfect is the enemy of the good”

The point of the review is to ensure that the Sage code guidelines are followed and that the the implementation is mathematically correct. Please refrain from aditional feature requests or open-ended discussion about alternative implementations. If you want the patch written differently, your suggestion should be a clear and actionable request.

Closing Tickets

Only the Sage release manager will close tickets. Most likely, this is not you nor will your trac account have the necessary permissions. If you feel strongly that a ticket should be closed or deleted, then change the status of the ticket to needs review and change the milestone to sage-duplictate/invalid/wontfix. You should also comment on the ticket, explaining why it should be closed. If another developer agrees, he sets the ticket to positive review.

A related issue is re-opening tickets. You should refrain from re-opening a ticket that is already closed. Instead, open a new ticket and provide a link in the description to the old ticket.

Reasons to Invalidate Tickets

One Issue Per Ticket: A ticket must cover only one issue and should not be a laundry list of unrelated issues. If a ticket covers more than one issue, we cannot close it and while some of the patches have been applied to a given release, the ticket would remain in limbo.

No Patch Bombs: Code that goes into Sage is peer-reviewed. If you show up with an 80,000 lines of code bundle that completely rips out a subsystem and replaces it with something else, you can imagine that the review process will be a little tedious. These huge patch bombs are problematic for several reasons and we prefer small, gradual changes that are easy to review and apply. This is not always possible (e.g. coercion rewrite), but it is still highly recommended that you avoid this style of development unless there is no way around it.

Sage Specific: Sage’s philosophy is that we ship everything (or close to it) in one source tarball to make debugging possible. You can imagine the combinatorial explosion we would have to deal with if you replaced only ten components of Sage with external packages. Once you start replacing some of the more essential components of Sage that are commonly packaged (e.g. Pari, GAP, lisp, gmp), it is no longer a problem that belongs in our tracker. If your distribution’s Pari package is buggy for example, file a bug report with them. We are usually willing and able to solve the problem, but there are no guarantees that we will help you out. Looking at the open number of tickets that are Sage specific, you hopefully will understand why.

No Support Discussions: The trac installation is not meant to be a system to track down problems when using Sage. Tickets should be clearly a bug and not “I tried to do X and I couldn’t get it to work. How do I do this?” That is usually not a bug in Sage and it is likely that sage-support can answer that question for you. If it turns out that you did hit a bug, somebody will open a concise and to-the-point ticket.

Solution Must Be Achievable: Tickets must be achievable. Many times, tickets that fall into this category usually ran afoul to some of the other rules listed above. An example would be to “Make Sage the best CAS in the world”. There is no metric to measure this properly and it is highly subjective.