Differences between revisions 1 and 32 (spanning 31 versions)

The Sage-Combinat patch server: step by step instructions

This page is meant as a step-by-step tutorial on using the Sage-Combinat patch server, from basic installation to contributing new patches:

Contents

Installation and basic usage
Looking and selecting the patches
Creating and contributing patches

For technical background on the patch server, see http:/combinat/Mercurial.

1. Installation and basic usage

1.1. Prerequisites

We assume that:

Sage 3.2 or higher is already installed (say in /opt/sage), and can be started by typing sage at the command line
- (it is recommended to use the most recent stable version)
The user has write access on the Sage installation tree
The user has access to: http://sage.math.washington.edu:2144/

Open (or create, if it does not exist yet) your Mercurial configuration file (~/.hgrc in your home directory), insert the following, and edit the username:

[ui]
username = Simon Cussonnet <Simon.Cussonnet at lycee-technique.torrez.eure.fr>
[extensions]
hgext.mq =
extdiff =
alias =
[alias]
qstatus = status --rev -2:.
[hooks]
pre-qrefresh = (echo "Are you sure you want to refresh the following changes:"; sage -hg status; echo -n "into the patch: "; hg qtop; read -p "(y/n)" answer; test "$answer" = "y"  )
[extdiff]
cmd.interdiff = hg-interdiff

1.2. Getting usage information

sage -combinat --help

1.3. Downloading and installing the Sage-combinat patches

sage -combinat install

1.4. Updating the Sage-Combinat patches

To update the Sage-Combinat patches to the latest version, you can run:

sage -combinat update

It is possible to simultaneously upgrade Sage to the latest version:

sage -combinat upgrade

1.5. Uninstalling the Sage-combinat patches

sage -b main

Now, you may destroy .../sage/devel/sage-combinat/ (after checking that you do not have local changes!)

2. Looking and selecting the patches

2.1. The Sage-combinat stack of patches

Sage-combinat is a collection of experimental patches (i.e. extensions) on top of Sage. Each patch describes a relatively atomic modification which may span several files; it may fix a bug, implement a new feature, improve some documentation, ...

TODO: insert a short example here:

The patches are organized as a (totally ordered) stack, each being applied on top of the previous one. The most stable are at the bottom, while the most experimental ones are on top. In practice, they are managed as a Mercurial queue. Let's look at a typical stack of patches:

hg qseries

It will display something like:

sage-3.1.3.patch
sage-3.2.patch
...
lazy_attributes-4371-nt.patch
copy_on_write_fh.patch
discrete_function-nt.patch
crystals_alcove_path_model_bj.patch
words_new_fcts_sl.patch

sage-3.1.3 is at the bottom of the stack, and is applied first, while words_new_fcts_sl.patch is applied last. The patch sage-3.2.patch contains all the sage-combinat patches that have readilly been integrated in sage 3.2 (see "using sage-combinat with older versions of sage"). The patch lazy_attributes-4371-nt.patch is about lazy attributes, related to ticket number 4371 on Sage trac, and is owned by Nicolas Thiéry (nt).

2.2. Top, applied and unapplied patches

It is possible to move up and down the stack, applying only the patches up to a given one.

hg qpush             # Apply the first patch in the series which is not currently applied
hg qpop              # Unapply the most recently applied patch
hg qpush -a          # Apply all the patches
hg qpop -a           # Unapply all the patches

If you get confused, the following can tell you which patches are applied or not:

hg qtop               # Top applied patch
hg qapplied         # Currently applied patches
hg qunapplied     # Currently unapplied patches

Note that after moving around the stack of patches, it is necessary to rebuild sage before using it :

sage -b
sage

2.3. Looking inside patches

The content of the current top patch can be retrieved with

hg qdiff

while a brief summary of the modifed files is given by

hg qstatus

2.4. Using the sage-combinat patches with an older version of sage

For the convenience of the user, it is possible to use the sage-combinat patches with an older version of sage. The intent is only to temporarily support one or two older versions of sage (that is about one month old); there is no guarantee whatsoever.

This is the purpose of the patches like sage-3.0.2.patch. This particular patch contains all the sage-combinat patches that have been integrated into Sage 3.0.2, and is only applied if Sage's version is strictly less than 3.0.2. This is achieved through guards (see the next section), and is taken care of automatically by sage -combinat, and in particular by:

sage -combinat qselect

2.5. Selecting guarded patches

Some patches may be guarded since they are experimental, not yet finished, or should be only applied for certain versions of sage. Guarded patches are not applied unless explicitly chosen. For example if one would like to apply patches labeled [+experimental] one can use the following steps:

hg qselect experimental
sage -combinat qselect

Then reapply the appropriate patches, typically with:

hg qpop -a
hg qpush -a

To disregard all guarded patches one uses instead:

hg qselect -n
sage -combinat qselect

3. Creating and contributing patches

3.1. Patch naming convention

Each patch should be of the form:

    <theme>_<feature/fix>_<trac ref if any>_<rev if any>_<owner or final or closed>.patch

Examples:

root-systems-lattices_nt.patch 
partitions_fix_3244_mh.patch 
crystals-affine_as.patch 
free-modules_1_mh.patch 
free-modules_2_mh.patch 
free-modules_final.patch 
dyck-words_closed.patch

A series of patches like the free_modules one above is intended to be progressively folded together into a single patch free_modules.patch before submission to sage (see patch folding below). The name free_modules_final indicates that the owner of this patch will no longer edit it, and it is ready to be posted to trac. The name *_closed.patch indicates that this patch has been posted to trac and the corresponding ticket has been closed.

3.2. Creating a new patch (qnew)

The first step is to create a new patch. It is easier to create it before doing any modifications to the sage sources. Never modify a patch that you do not own

hg qnew my_improvement_ab.patch

where ab are your initials. The new patch is created on top of the most recently applied patch. You may use qpush and qpop first to choose where your patch is created.

3.3. Editing the Sage sources

It is recommended to double check that the current top patch is yours and is the one you want to add your modifications to (see qtop and qpop/qpush). """using qpop and qpush become tricky to use once you started modifications'".

Now you can edit the Sage sources files to your taste in $SAGE_ROOT/devel/sage-combinat/sage/. At any time, you can review your modifications since the creation of the patch (or since the last qrefresh, see below) by doing:

hg diff           #complete modifications since last qrefresh
hg status         #list the modified files since last qrefresh

If you added a new source file, you must declare it using the command:

hg add <filename>

3.4. Refreshing your patch (qrefresh)

Currently, the modifications are still not part of the patch as may be seen with the commands

hg qdiff
hg qstatus

Use

hg qrefresh

to put the actual modifications in the current top patch. You can check that they have been included in the patch with:

hg qdiff
hg qstatus

Also, they should appear anymore in:

hg diff
hg status

After qrefresh, you can use qpop and qpush again and modify the same patch or some other patch you already created.

3.5. Removing a patch

In case you want to discard your patch, you may use:

$ hg qremove my_improvement_AB.patch

You may use

$ hg qseries

to confirm that the patch is removed.

3.6. Pushing patches to the sage-combinat server

Go to the sage-combinat directory, and make sure that there is no local changes (hg status):

cd $SAGE_ROOT/devel/sage-combinat
hg status

Otherwise dicard them (hg revert) or save them in your favorite patch (hg qrefresh).

Pull the latest version of the patches from the server, and make sure that everything is working fine after applying all patches:

sage -combinat update -f
hg qpush -a
sage -br  # Make sure this works
sage -t filenames # If you believe your tests should pass, check them.

The -f is to tell sage -combinat to run even if your patch directory is modified, which it probably is.

When pulling from the server, your changes will be merged with those from the server. You may get conflicts in the series file, or patches that do not apply anymore. Fix the patches that you own, and get in touch with the owners of the other broken patches.

When everything is ready, double check that you are up to date:

sage -combinat update -f

and then:

cd .hg/patches
hg commit
hg push

In case you have been unlucky, and there has been a change on the patch server between your last pull and your commit, push will fail with an error like "abort: push creates new remote heads! did you forget to merge?". You then have to merge your local modifications with the remote ones:

cd .ht/patches
hg pull -u
hg merge

If the merge goes through automatically, just commit with "Merge" as message, and push. Otherwise, well, feel free to ask for help!

3.7. Exporting Patches for use with trac

When a patch is ready to be applied to Sage, you should first verify that it will apply cleanly. If you want to be able to undo anything you do in this step, you should run hg qcommit before beginning.

The first step is, from the PATCHES directory, manually edit the series file so that your patch (or patches) are applied only to patches labelled *_closed. Then (from the source directories) use qpush and qpop to bring the first of your patches to the top of the stack (ie, only one of your patches should be applied). Suppose your patches were called 1.patch and 2.patch, and you currently have 1.patch at the top of the stack, and 2.patch as the next patch to be applied. The command $ hg qfold 2.patch will incorporate the changes from 2.patch into 1.patch, and then delete 2.patch. You should repeat this process until all patches working on one particular issue have been incorporated.

Then you should make sure that sage builds, runs, and passes tests, with just this patch applied only to patches that have already been closed. Don't forget to also commit and push your changes to the server.

The next step is to export your patch for submission. Running "hg export" includes extra information in the patch such as the author of the patch.

cd $SAGE_ROOT/devel/sage-combinat
hg export new_feature.patch > /path/to/new_feature_for_trac.patch

You would then upload the file new_feature_for_trac.patch to the appropriate ticket on the Sage Trac server, creating the ticket if necessary. Procedures for using the trac system are described here: http://wiki.sagemath.org/TracGuidelines

-  ⇤ ← Revision 1 as of 2008-10-13 10:41:49 → 
  Size: 1609
  Editor: NicolasThiery
  Comment: New page with basic instructions on the patch server
+   ← Revision 32 as of 2009-01-28 18:31:30 → ⇥
  Size: 11854
  Editor: NicolasThiery
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-= The Sage-combinat patch server: basic instructions =

This page describes how to install and update the Sage-combinat experimental patches.

For advanced usage of the patch server, see [combinat/Mercurial].

== Install the Sage-combinat patches

We assume sage is already installed (say in /opt/sage), and that the user has write access on the installation tree.

Edit your Mercurial configuration file (~/.hgrc in your home directory), and insert the following (if not yet there):
+#pragma section-numbers 2

= The Sage-Combinat patch server: step by step instructions =

This page is meant as a step-by-step tutorial on using the Sage-Combinat patch server, from basic installation to contributing new patches:
<<TableOfContents(3)>>

For technical background on the patch server, see http:/combinat/Mercurial.

== Installation and basic usage ==

=== Prerequisites ===

We assume that:
 * Sage 3.2 or higher is already installed  (say in {{{/opt/sage}}}), and can be started by typing {{{sage}}} at the command line
   (it is recommended to use the most recent stable version)
 * The user has write access on the {{{Sage}}} installation tree
 * The user has access to: http://sage.math.washington.edu:2144/

/* * Mercurial is already installed ({{{sudo apt-get install mercurial}}} on Debian) */

Open (or create, if it does not exist yet) your Mercurial configuration file ({{{~/.hgrc}}} in your home directory), insert the following, and edit the username:
-Line 14:
+Line 25:
-username = YourFirstName YourLastName <YourEmail>
+username = Simon Cussonnet <Simon.Cussonnet at lycee-technique.torrez.eure.fr>
-Line 20:
+Line 30:
-Line 23:
+Line 32:
-Line 26:
+Line 34:
 [extdiff]
-Line 31:
+Line 38:
-Download the attachment:sage-combinat script, and run from anywhere:
{{{
python sage-combinat install
}}}

In case Sage or python is not in the user's path, you may have to specify where they are, as in:
{{{
/opt/sage/sage-python sage-combinat install --sage=/opt/sage/sage
}}}

Note: starting from sage 3.1.3, the sage-combinat script is readily included in the sage distribution,
and you can run it with:
+=== Getting usage information ===
{{{
sage -combinat --help
}}}

=== Downloading and installing the Sage-combinat patches ===
-Line 47:
+Line 48:
-Some help is available with:
{{{
/opt/sage/sage-python sage-combinat --help
}}}


== Update the Sage-combinat patches

{{{
python sage-combinat update
}}}

== Upgrade Sage and update the Sage-combinat patches

{{{
python sage-combinat upgrade
}}}
+=== Updating the Sage-Combinat patches ===

To update the Sage-Combinat patches to the latest version, you can run:
{{{
sage -combinat update
}}}

It is possible to simultaneously upgrade Sage to the latest version:
{{{
sage -combinat upgrade
}}}

=== Uninstalling the Sage-combinat patches ===
{{{
sage -b main
}}}
Now, you may destroy {{{.../sage/devel/sage-combinat/}}} (after checking that you do not have local changes!)

== Looking and selecting the patches ==

=== The Sage-combinat stack of patches ===

Sage-combinat is a collection of experimental patches (i.e. extensions) on top of Sage. Each patch describes a relatively atomic modification which may span several files; it may fix a bug, implement a new feature, improve some documentation, ...

TODO: insert a short example here:

The patches are organized as a (totally ordered) stack, each being applied on top of the previous one. The most stable are at the bottom, while the most experimental ones are on top. In practice, they are managed as a Mercurial queue. Let's look at a typical stack of patches:
{{{
hg qseries
}}}
It will display something like:
{{{
sage-3.1.3.patch
sage-3.2.patch
...
lazy_attributes-4371-nt.patch
copy_on_write_fh.patch
discrete_function-nt.patch
crystals_alcove_path_model_bj.patch
words_new_fcts_sl.patch
}}}

sage-3.1.3 is at the bottom of the stack, and is applied first, while words_new_fcts_sl.patch is applied last.
The patch sage-3.2.patch contains all the sage-combinat patches that have readilly been integrated in sage 3.2 (see "using sage-combinat with older versions of sage").
The patch lazy_attributes-4371-nt.patch is about lazy attributes, related to [[http://sagetrac.org/sage_trac/ticket/4371|  ticket number 4371 on Sage trac]], and is owned by Nicolas Thiéry (nt).

=== Top, applied and unapplied patches ===

It is possible to move up and down the stack, applying only the patches up to a given one.
{{{
hg qpush             # Apply the first patch in the series which is not currently applied
hg qpop              # Unapply the most recently applied patch
hg qpush -a          # Apply all the patches
hg qpop -a           # Unapply all the patches
}}}

If you get confused, the following can tell you which patches are applied or not:
{{{
hg qtop               # Top applied patch
hg qapplied         # Currently applied patches
hg qunapplied     # Currently unapplied patches
}}}

Note that after moving around the stack of patches, it is necessary to rebuild sage before using it :
{{{
sage -b
sage
}}}

=== Looking inside patches ===

The content of the current top patch can be retrieved with
{{{
hg qdiff
}}}
while a brief summary of the modifed files is given by
{{{
hg qstatus
}}}

=== Using the sage-combinat patches with an older version of sage ===

For the convenience of the user, it is possible to use the sage-combinat patches with an older version of sage.
The intent is only to temporarily support one or two older versions of sage (that is about one month old); there is no guarantee whatsoever.

This is the purpose of the patches like {{{sage-3.0.2.patch}}}. This particular patch contains all the sage-combinat patches that have been integrated into Sage 3.0.2, and is only applied if Sage's version is strictly less than 3.0.2. This is achieved through guards (see the next section), and is taken care of automatically by {{{sage -combinat}}}, and in particular by:
{{{
sage -combinat qselect
}}}

=== Selecting guarded patches ===

Some patches may be guarded since they are experimental, not yet finished, or should be only applied for certain versions of sage.
Guarded patches are not applied unless explicitly chosen. For example if one would like to apply patches labeled
[+experimental] one can use the following steps:

{{{
hg qselect experimental
sage -combinat qselect
}}}
Then reapply the appropriate patches, typically with:
{{{
hg qpop -a
hg qpush -a
}}}

To disregard all guarded patches one uses instead:
{{{
hg qselect -n
sage -combinat qselect
}}}


== Creating and contributing patches ==

=== Patch naming convention ===

Each patch should be of the form:
{{{
    <theme>_<feature/fix>_<trac ref if any>_<rev if any>_<owner or final or closed>.patch 
}}}

Examples: 
{{{
root-systems-lattices_nt.patch 
partitions_fix_3244_mh.patch 
crystals-affine_as.patch 
free-modules_1_mh.patch 
free-modules_2_mh.patch 
free-modules_final.patch 
dyck-words_closed.patch 
}}}

A series of patches like the free_modules one above is intended to be progressively folded together into a single patch free_modules.patch before submission to sage (see patch folding below). The name free_modules_final indicates that the owner of this patch will no longer edit it, and it is ready to be posted to trac. The name *_closed.patch indicates that this patch has been posted to trac and the corresponding ticket has been closed.

=== Creating a new patch (qnew) ===

The first step is to create a new patch. It is easier to create it before doing any modifications to the sage sources.
'''Never modify a patch that you do not own'''
{{{
hg qnew my_improvement_ab.patch
}}}
where ab are your initials. The new patch is created on top of the most recently applied patch. You may use {{{qpush}}} and {{{qpop}}} first to choose where your patch is created.

=== Editing the Sage sources ===

It is recommended to double check that the current top patch is yours and is the one you want to add your modifications to
(see {{{qtop}}} and {{{qpop/qpush}}}). """using {{{qpop}}} and {{{qpush}}} become tricky to use once you started modifications'".

Now you can edit the Sage sources files to your taste in {{{$SAGE_ROOT/devel/sage-combinat/sage/}}}. At any time, you can review your modifications since the creation of the patch (or since the last {{{qrefresh}}}, see below) by doing:
{{{
hg diff           #complete modifications since last qrefresh
hg status         #list the modified files since last qrefresh
}}}
If you added a new source file, you must declare it using the command:
{{{
hg add <filename>
}}}

=== Refreshing your patch (qrefresh) ===

Currently, the modifications are still not part of the patch as may be seen with the commands
{{{
hg qdiff
hg qstatus
}}}
Use 
{{{
hg qrefresh
}}}
to put the actual modifications in the current top patch. You can check that they have been included in the patch with:
{{{
hg qdiff
hg qstatus
}}}
Also, they should appear anymore in:
{{{
hg diff
hg status
}}}

After {{{qrefresh}}}, you can use {{{qpop}}} and {{{qpush}}} again and modify the same patch or some other patch you already created.

=== Removing a patch ===

In case you want to discard your patch, you may use:
{{{
$ hg qremove my_improvement_AB.patch
}}}
You may use
{{{
$ hg qseries
}}}
to confirm that the patch is removed.

=== Pushing patches to the sage-combinat server ===

Go to the sage-combinat directory, and make sure that there is no local changes (hg status):
{{{
cd $SAGE_ROOT/devel/sage-combinat
hg status
}}}
Otherwise dicard them (hg revert) or save them in your favorite patch (hg qrefresh).

Pull the latest version of the patches from the server, and make sure that everything is working fine after applying all patches:
{{{
sage -combinat update -f
hg qpush -a
sage -br  # Make sure this works
sage -t filenames # If you believe your tests should pass, check them.
}}}
The -f is to tell sage -combinat to run even if your patch directory is modified, which it probably is.

When pulling from the server, your changes will be merged with those from the server. You may
get conflicts in the series file, or patches that do not apply anymore. Fix the patches that you own,
and get in touch with the owners of the other broken patches.

When everything is ready, double check that you are up to date:
{{{
sage -combinat update -f
}}}
and then:
{{{
cd .hg/patches
hg commit
hg push
}}}

In case you have been unlucky, and there has been a change on the patch server between your
last pull and your commit, push will fail with an error like "abort: push creates new remote heads!
did you forget to merge?". You then have to merge your local modifications with the remote ones:
{{{
cd .ht/patches
hg pull -u
hg merge
}}}
If the merge goes through automatically, just commit with "Merge" as message, and push.
Otherwise, well, feel free to ask for help!

=== Exporting Patches for use with trac ===

When a patch is ready to be applied to {{{Sage}}}, you should first verify that it will apply cleanly.   If you want to be able to undo anything you do in this step, you should run {{{hg qcommit }}} before beginning.

The first step is, from the {{{PATCHES}}} directory, manually edit the {{{series }}} file so that your patch (or patches) are applied only to patches labelled *_closed.  Then (from the source directories) use {{{qpush}}} and {{{qpop}}} to bring the first of your patches to the top of the stack (ie, only one of your patches should be applied).  Suppose your patches were called 1.patch and 2.patch, and you currently have 1.patch at the top of the stack, and 2.patch as the next patch to be applied.  The command {{{$ hg qfold 2.patch}}} will incorporate the changes from 2.patch into 1.patch, and then delete 2.patch.  You should repeat this process until all patches working on one particular issue have been incorporated.

Then you should make sure that sage builds, runs, and passes tests, with just this patch applied only to patches that have already been closed.
Don't forget to also commit and push your changes to the server.

The next step is to export your patch for submission.  Running "hg export" includes extra information in the patch such as the author of the patch.
{{{
cd $SAGE_ROOT/devel/sage-combinat
hg export new_feature.patch > /path/to/new_feature_for_trac.patch
}}}
You would then upload the file new_feature_for_trac.patch to the appropriate ticket on the Sage Trac server, creating the ticket if necessary.  Procedures for using the trac system are described here: http://wiki.sagemath.org/TracGuidelines

Diff for "combinat/MercurialBasic"