T if you have trouble viewing this presentation.Sage Days 28
Orsay, France, January 17-19th 2011
Sage is distributed under the terms of the GNU General Public License version 2 (GPLv2) which provides four kinds of freedom:
- Freedom to :red:`run the program`
- Freedom to :red:`access the code`
- Freedom to :red:`redistribute the program to anyone`
- Freedom to :red:`improve the software`
While all users of Sage make use of the first freedom, in this talk, we will see :red:`how to appropriate the other three`.
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That's the easiest part. Choose one amongst this
selection of unreported documentation bugs
made for Sage Days 28 or browse the
Open Beginner Tickets.
During this talk, instead of fixing a bug I am going to introduce one in the inverse method of a permutation.
In Sage, modifications are tracked on a web site called Sage trac. Every bug gets assigned a number. For instance, the number #10484 refers to the bug called :fuchsia:`Chinese remainder code raises an error when called with Python ints`. On the ticket, one can see that:
- The bug was reported and solved by David Loeffler (UK) in December 2010.
- The ticket was positively reviewed by Robert Bradshaw (USA) and Mike Hansen.
- The solution was merged in
sage-4.6.2by Jeroen Demeyer (Belgium) on January 11th 2011.
One can also look at the :red:`solution`, :red:`download it`, :red:`test it`, etc.
In order to create a ticket:
- Create an account on http://trac.sagemath.org/sage_trac/register
- Login to your account
- Make sure the ticket :red:`does not already exists`.
- Create ticket
- In the description field, explain how should someone else understand and/or reproduce the bug.
I create the imaginary ticket #12345 for introducing a useless print
statement in the method that computes the inverse of a permutation.
- Clone Sage and create your branch (:red:`Do it right now because it might take some time`)
sage -clone slabbe
This creates a :red:`new directory` called sage-slabbe in the devel repository:
slabbe@pol ~/Applications/sage-4.6.1/devel $ ls -l drwxr-xr-x 2 slabbe staff 68 14 jan 03:59 old/ lrwxr-xr-x 1 slabbe staff 9 18 jan 15:01 sage -> sage-main/ drwxr-xr-x 23 slabbe staff 782 18 jan 01:42 sage-main/ drwxr-xr-x 24 slabbe staff 816 17 jan 01:50 sage-slabbe/ lrwxr-xr-x 1 slabbe staff 11 14 jan 03:42 sagenb -> sagenb-main/ drwxr-xr-x 21 slabbe staff 714 14 jan 03:41 sagenb-main/
| Build the main branch | Build my branch slabbe | Print the current branch |
sage -b main |
sage -b slabbe |
sage -branch |
Sage uses the program :red:`Mercurial` ( hg or sage -hg ) to manage all of its source code. Mercurial stores the evolution of every single file of Sage since the beginning.
Since I am too lazy to write sage -hg every time I use Mercurial, I added
the following line to my ~/.bashrc file:
alias hg='sage -hg'
I verify that it works:
slabbe@pol ~ $ hg --version Mercurial Distributed SCM (version 1.6.4) Copyright (C) 2005-2010 Matt Mackall <[email protected]> and others This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
- hg log
- Print the revision history of the specified files or the entire project.
slabbe@pol ~/Applications/sage-4.6.1/devel/sage-main $ hg log changeset: 15205:f24ce048fa66 tag: tip user: Jeroen Demeyer date: Tue Jan 11 08:10:26 2011 +0100 summary: 4.6.1 ... changeset: 0:039f6310c6fe user: tornaria date: Sat Feb 11 01:13:08 2006 +0000 summary: [project @ original sage-0.10.12]
- hg update
- Update the repository's working directory to the specified changeset.
Mercurial queues is an extension to Mercurial that allows one to easily
work with collections of patches. To allow Mercurial queues, edit (or create)
the file ~/.hgrc and make sure it contains the line :red:`hgext.mq =` in
the extensions section:
[ui] username = Sebastien Labbe <hidden email> [extensions] hgext.mq = color = [alias] qstatus = status --rev -2:.
Warning
The line hgext.mq= is an indispensable for the next steps.
cd to your branch:
cd Applications/sage-4.6.1/devel/sage-slabbe
Create a new empty patch:
hg qnew trac_12345-add_useless_print-sl.patch
Find the file containing the bug
Personnally I found the file permutation.py here:
sage-4.6.1/devel/sage-slabbe/sage/combinat/permutation.py
Find the solution to the bug
Edit the source code accordingly, save and quit
Now, you may use the following Mercurial commands to look at your local changes.
hg status shows changed files since last hg qnew (or hg qrefresh):
slabbe@pol ~/Applications/sage-4.6.1/devel/sage-combinat/sage/combinat $ hg status M sage/combinat/permutation.py
hg diff shows differences since last hg qnew (or hg qrefresh)
slabbe@pol ~/Applications/sage-4.6.1/devel/sage-combinat/sage/combinat $ hg diff
diff --git a/sage/combinat/permutation.py b/sage/combinat/permutation.py
--- a/sage/combinat/permutation.py
+++ b/sage/combinat/permutation.py
@@ -1208,6 +1208,7 @@ class Permutation_class(CombinatorialObj
sage: Permutation([2, 4, 1, 5, 3]).inverse()
[3, 1, 5, 2, 4]
"""
+ print("YO !!!! Let's inverse some permutations !!!")
w = range(len(self))
for i,j in enumerate(self):
w[j-1] = i+1
- Build sage
sage -b- Verify the effects of the modification
- Run
sage
sage: p = Permutation([4,3,2,5,1]) sage: p.inverse() YO !!!! Let's inverse some permutations !!! [5, 3, 2, 1, 4]
That's great: we are now able to :red:`modify` Sage.
- Make sure that all examples in the source code still work
sage -t <files>
slabbe@pol ~/Applications/sage-4.6.1/devel/sage-slabbe/sage/combinat $ sage -t permutation.py
sage -t "devel/sage-slabbe/sage/combinat/permutation.py"
**********************************************************************
File "/Users/slabbe/Applications/sage-4.6.1/devel/sage-slabbe/sage/combinat/permutation.py", line 1206:
sage: Permutation([3,8,5,10,9,4,6,1,7,2]).inverse()
Expected:
[8, 10, 1, 6, 3, 7, 9, 2, 5, 4]
Got:
YO !!!! Let's inverse some permutations !!!
[8, 10, 1, 6, 3, 7, 9, 2, 5, 4]
----------------------------------------------------------------------
The following tests failed:
sage -t "devel/sage-slabbe/sage/combinat/permutation.py"
Total time for all tests: 10.4 seconds
If :red:`tests failed`, one should edit files again...
Build the documentation and make sure there are no errors or warnings:
sage -b && sage -docbuild reference html
Open the html version of documentation in your browser and make sure the documentation looks OK:
open ~/Applications/sage-4.6.1/devel/sage/doc/output/html/en/reference/sage/combinat/permutation.html
When the bug is fixed, once we made sure every tests pass and that the documentation builds fine, then we can :red:`update the current patch` with hg qrefresh to reflect the changes:
hg qrefresh
No changes are shown anymore by hg status or hg diff:
hg status hg diff
Modifications are now in the patch. See hg qstatus or hg qdiff:
hg qstatus hg qdiff
:red:`Add a commit message` to the patch:
hg qrefresh -m "#12345: add a useless print in the inverse method of a permutation"
Export the patch with hg export:
hg export trac_12345-add_useless_print-sl.patch >
~/Documents/tmp/trac_12345-add_useless_print-sl.patch
The command hg export also adds information in the patch (author name, date, ...).
Note
Personally, I added the following alias to my ~/.bashrc:
alias qtoptotmp='hg export `hg qtop` > ~/Documents/tmp/`hg qtop`'
Here is an example of a patch exported by Mercurial for the imaginary ticket #12345. It contains information about the :red:`author`, the :red:`date`, the :red:`commit message` we just wrote and finally the complete :red:`diff`.
trac_12345-add_useless_print-sl.patch:
# HG changeset patch
# User Sebastien Labbe <hidden email>
# Date 1295311529 -3600
# Node ID 4a6379cf0c965e1ce309846cbcb9f864932a3b6c
# Parent 83e5e45a8935ac627c45ed14042bbebafeb1a800
#12345: add a useless print in the inverse method of a permutation
diff --git a/sage/combinat/permutation.py b/sage/combinat/permutation.py
--- a/sage/combinat/permutation.py
+++ b/sage/combinat/permutation.py
@@ -1208,6 +1208,7 @@ class Permutation_class(CombinatorialObj
sage: Permutation([2, 4, 1, 5, 3]).inverse()
[3, 1, 5, 2, 4]
"""
+ print("YO !!!! Let's inverse some permutations !!!")
w = range(len(self))
for i,j in enumerate(self):
w[j-1] = i+1
Upload the patch on Sage trac
You can mention things like "tested on sage-4.6.1" in the text box when uploading the ticket.
Make sure the patch was correctly uploaded by :red:`looking at it` directly on the web page.
Set the ticket to needs review
You may ask somebody to review your ticket.
Other useful Mercurial commands when patches multiplies:
- hg qnew
- Create a new patch
- hg qnew
- ...
- hg qpop
- Move a patch from the applied stack to the unapplied one
- hg qpush
- Move a patch from the unapplied stack to the applied one
- hg qtop
- Show the current patch
- hg qseries
- Print all of the patches in order
A feature available on a Sage Trac ticket interests you? You want to review a ticket?
Insert a patch into the series after the last applied patch with hg qimport:
hg qimport ~/Downloads/trac_65321-nice-feature-AA.patch
Warning
Do :red:`NOT` use the command hg import as it will import the changes in the current patch.
You can change the order in which the patches are applied. To do so, simply edit the series file:
slabbe@pol ~/Applications/sage-4.6.1/devel/sage-slabbe $ cd .hg/patches/ slabbe@pol ~/Applications/sage-4.6.1/devel/sage-slabbe/.hg/patches $ vim series
Make sure the patch you are reviewing is :red:`the first patch` to be applied:
slabbe@pol ~/Applications/sage-4.6.1/devel/sage-slabbe/.hg/patches $ cat series trac_65321-nice-feature-AA.patch A.patch B.patch C.patch
Warning
Visit the Reviewing a patch Section of the Sage Developer's Guide. Also, make sure you read William Stein's blog post about reviewing a Sage trac ticket.
- Make sure the patch applies on Sage without conflicts:
hg qpushandhg qpop
Experiment the functionality proposed in the patch.
- Make sure the bug described in the ticket is fixed.
- Make sure the patch does not introduce any new bug.
- Run tests on the affected files.
sage -t <affected_files>
- Test the entire Sage library.
sage --testall --long- Ensure that the documentation builds fine:
sage -docbuild reference html- Check for full 100% doctest coverage:
sage -coverage <file>
Once you’ve tested the patch, report any failures on the Trac page for the ticket. Make suggestions about simplifying the code or fixing typos you noticed.
Three cases may happen:
- Needs work
- Mark it as needs work if there is anything to do.
- Positive review
- Otherwise, mark it as positive review, and mention in a comment all the things you checked.
- Delegate
- If you don’t feel experienced enough for that, add a comment on the Trac page explaining what you have checked, what the results were, and that you think someone more experienced should take a look.
Note
Delete an (unapplied) patch from the queue:
hg qdelete trac_65321-nice-feature-AA.patch
Erase your branch. Of course, do this only if you don't care about your local changes:
rm -rf sage-slabbe
Reviewing a Sage trac ticket, William Stein's blog post, October 31, 2010.
This talk was generated
- by Docutils
- from ReStructuredText source
- to a Simple Standards-based Slide Show System (S5) format.
Sébastien Labbé, Sage Days 28, Orsay, France, January 17-19th 2011.