I just had a quick look at it, and the following looks downright scary:

+            For backward compatibility, if a permutation group element
+            acts on the integers `\{1,\ldots,n\}` or a subset thereof,
+            the columns are considered as being numbered from `1`::
+
+                sage: G = PermutationGroup(['(1,2,3)(4,5)', '(1,2,3,4,5)'])
+                sage: sigma, tau = G.gens()
+                sage: sigma
+                (1,2,3)(4,5)
+                sage: M = copy(N)
+                sage: M.permute_columns(sigma)
+                sage: M
+                [1 0 1 0 0]
+                [2 2 0 0 0]
+                [0 3 0 0 3]
+                [0 0 0 4 4]
+                [0 0 0 5 0]

note that there is an unpleasant ambiguity here:
namely, if, say in this example you take
G = PermutationGroup(['(1,2,3)'])
how one could tell whether it is meant to permute stuff in [0..2], or in 
[1..3] ?
Do you mean that one must write G = PermutationGroup(['(0),(1,2,3)']) for 
the latter?

Dima




On Wednesday, September 3, 2014 2:46:25 PM UTC+1, Nicolas M. Thiéry wrote:
>
>         Dear Sage devs, 
>
> From the description of ticket #16577: 
>
> Permutation groups used to only handle permutations of 1,..n, and the 
> methods permute_rows and friends of matrices coped with this with an 
> ugly and potentially confusing shift by 1. After this ticket, 
> permutation of 0,...,n-1 are accepted and handled as can be 
> expected. For permutations of 1..n and subsets thereof, the behavior 
> is unchanged for backward compatibility. 
>
> This ticket also includes the following changes: 
>
>     A rewrite of the documentation 
>     New documentation on a related method 
>     Code refactorization to avoid some duplication 
>     The implementation of M.permute_rows_and_columns(sigma) 
>
> The ticket has been reviewed by Karl and is ready to go. This is just 
> a final call in case someone would have some more opinion about it. 
>
> Speak now or forever hold your peace :-) 
>
> Cheers, 
>                                 Nicolas 
> -- 
> Nicolas M. Thiéry "Isil" <nth...@users.sf.net <javascript:>> 
> http://Nicolas.Thiery.name/ 
>

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