[sage-devel] Help fixing doctest warnings

[David Coudert]

Dear all,

I observe some doctest warnings that I don't know how to fix.  This is 
certainly a side effect of the modularization.

File "src/sage/plot/plot.py", line 569, in sage.plot.plot
Warning: Variable 'sig_on_count' referenced here was set only in doctest 
marked '# needs sage.symbolic'
sig_on_count() # check sig_on/off pairings (virtual doctest)
**
File "src/sage/plot/plot.py", line 3623, in sage.plot.plot.graphics_array
Warning: Variable 'x' referenced here was set only in doctest marked '# 
long time, needs sage.symbolic'
L = [plot(sin(k*x), (x,-pi,pi)) for k in [1..3]]
**
File "src/sage/plot/plot.py", line 3669, in sage.plot.plot.graphics_array
Warning: Variable 'x' referenced here was set only in doctest marked '# 
long time, needs sage.symbolic'
p1 = plot(sin(x^2), (x, 0, 6),
  axes_labels=[r'$\theta$', r'$\sin(\theta^2)$'], fontsize=16)
**
File "src/sage/plot/plot.py", line 3671, in sage.plot.plot.graphics_array
Warning: Variable 'x' referenced here was set only in doctest marked '# 
long time, needs sage.symbolic'
p2 = plot(x^3, (x, 1, 100), axes_labels=[r'$x$', r'$y$'],
  scale='semilogy', frame=True, gridlines='minor')


File "src/sage/repl/user_globals.py", line 52, in sage.repl.user_globals
Warning: Variable 'sig_on_count' referenced here was set only in doctest 
marked '# needs sage.modules'
sig_on_count() # check sig_on/off pairings (virtual doctest)
**
File "src/sage/repl/user_globals.py", line 99, in 
sage.repl.user_globals.get_globals
Warning: Variable 'sig_on_count' referenced here was set only in doctest 
marked '# needs sage.modules'
sig_on_count() # check sig_on/off pairings (virtual doctest)


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Re: [sage-devel] Graph([('A','B'),(1,2)]).edges() raises weird traceback

[David Coudert]

@Vincent: yes, the construction of EdgesView is in O(1) and it's nice. 
Unfortunately, I don't know how to check that sorting may lead to an error 
at construction without doing it. At least the current behavior is 
documented.

@Nils: I fully agree with you and soon the default value of parameter sort 
will be False. The deprecation warning will be one year old in a month.

We have already drastically reduce the dependency to orderings, vertex 
label /edge types in the graph module Some remaining issues have been 
identified, so we have some more work to do (and some open PR to review, 
help is more than welcome).

Best,
David.

On Thursday, July 6, 2023 at 6:01:23 PM UTC+2 Nils Bruin wrote:

> On Wednesday, 5 July 2023 at 21:54:03 UTC-7 David Coudert wrote:
>
> The current design choice in `EdgesView` is to sort only when asking for 
> the list of edges, that is when calling `__repr__` if `sort=True`. 
> The alternative is to sort at the initialization of the object and to 
> cache the sorted list of edges in the object.
> Should we go for this alternative implementation ?
>
>
> Perhaps useful in considerations: One contributing factor for the 
> extensive usage of sort in string representations was the desire to have 
> doctests be robust against changes in code, particularly hashes: print 
> order of sets in Py2 was very unpredictable and driven by hash values 
> (especially if those hash values end up being "id", i.e., basically a 
> memory address).
>
> There is the other one that Py2 started out with a tacit assumption that 
> "<" was a total order on all objects, which it of course never was. It did 
> mean that "sort" could often be applied to very diverse lists without error 
> and with results that were relatively consistent between different runs 
> (but not necessarily between different versions).
>
> In Py3, iteration and print order of sets is determined by insertion 
> order. Therefore, the string representation of objects tends to not be 
> dependent on hash values anymore. Furthermore "<" between different types 
> of objects will generally raise an error. Hence, "sort" has become much 
> more problematic to be used by default and one of the motivations to use it 
> by default in sage has become less relevant.
>
> Hence, in my opinion, routines in sage that give access to a set of 
> objects (like edges or vertices) should just return it in the order in 
> which they are encountered, leading to an O(n) algorithm. If the 
> application calls for a sorted version, the O(n*log n) penalty can be 
> incurred by sorting the result. For doctests that need to return the actual 
> result *AS WELL AS* be consistent for checking, wrapping in a sorted(..., 
> key=str) would work just fine. In general it would be better to test some 
> guaranteed invariants of the return value rather than its string 
> representation, though.
>  
>

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Re: [sage-devel] Graph([('A','B'),(1,2)]).edges() raises weird traceback

[David Coudert]

The current design choice in `EdgesView` is to sort only when asking for 
the list of edges, that is when calling `__repr__` if `sort=True`. 
The alternative is to sort at the initialization of the object and to cache 
the sorted list of edges in the object.
Should we go for this alternative implementation ?

On Wednesday, July 5, 2023 at 8:48:05 AM UTC+2 Vincent Delecroix wrote:

> To my mind, this is not the problem. The first command does generate a
> warning (fine)
>
> sage: E = Graph([('A','B'),(1,2)]).edges()
> :1: DeprecationWarning: parameter 'sort'
> will be set to False by default in the future
> See https://github.com/sagemath/sage/issues/27408 for details.
>
> But the EdgesView.__repr__ is buggy (bad)
>
> sage: E
> ) failed:
> TypeError: unsupported operand parent(s) for <: 'Integer Ring' and
> ''>
>
> I think that either E is broken from start and an error should have
> been raised in the first stage or everything is fine and we should
> have a proper string representation.
>
> On Wed, 5 Jul 2023 at 08:33, David Coudert  wrote:
> >
> > There is an active deprecation warning in method edges(). Parameter sort 
> will be set to False in the future. I'm surprised you don't see it.
> >
> > sage: Graph([('A','B'),(1,2)]).edges()
> > :1: DeprecationWarning: parameter 'sort' 
> will be set to False by default in the future See 
> https://github.com/sagemath/sage/issues/27408 for details.
> > Graph([('A','B'),(Integer(1),Integer(2))]).edges() 
> ) failed: TypeError: 
> unsupported operand parent(s) for <: 'Integer Ring' and ''>
> >
> >
> > On Tuesday, July 4, 2023 at 4:29:21 PM UTC+2 Vincent Delecroix wrote:
> >>
> >> https://github.com/sagemath/sage/issues/35897
> >>
> >> On Tue, 4 Jul 2023 at 16:25, Vincent Delecroix
> >> <20100.d...@gmail.com> wrote:
> >> >
> >> > This is a bug in the __repr__ method of EdgesView. Thanks for your 
> report.
> >> >
> >> > On Tue, 4 Jul 2023 at 10:52, Georgi Guninski  
> wrote:
> >> > >
> >> > > Graph([('A','B'),(1,2)]).edges()
> >> > > ) failed:
> >> > > TypeError: unsupported operand parent(s) for <: 'Integer Ring' and
> >> > > ''>
> >> > >
> >> > > I think this is related to sorting the edges.
> >> > >
> >> > > The following works:
> >> > > sage: Graph([("A",1),("B",2)]).edges()
> >> > > [(1, 'A', None), (2, 'B', None)]
> >> > >
> >> > > --
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> Groups "sage-devel" group.
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> send an email to sage-devel+...@googlegroups.com.
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> .
> >
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[sage-devel] Re: Exception in `G=Graph([("A",1)]);G.faces()`

[David Coudert]

I have opened https://github.com/sagemath/sage/issues/35902 to collect such 
kind of issues.
Please use it to share new cases.

On Wednesday, July 5, 2023 at 9:38:28 AM UTC+2 Georgi Guninski wrote:

> Hi sage devs, your daily dose of incomparable objects,
> fix 'em while they are free ;)
>
> G=Graph([("A",1)]);G.faces()
>
> TypeError Traceback (most recent call last)
> Cell In [1], line 1
> > 1 G=Graph([("A",Integer(1))]);G.faces()
>
> File /home/sc_serv/sage/src/sage/graphs/generic_graph.py:6385, in
> GenericGraph.faces(self, embedding)
> 6383 # Storage for face paths
> 6384 faces = []
> -> 6385 minedge = min(edgeset)
> 6386 path = [minedge]
> 6387 edgeset.discard(minedge)
>
> TypeError: '<' not supported between instances of 'int' and 'str'
>

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[sage-devel] Re: grep-ing for sort() in graphs

[David Coudert]

Most of these calls are done on purpose and safe, but some may raise an 
error.

> ./base/static_sparse_backend.pyx:512: vertices.sort() 
It's inside a try ... except...  statement. We may certainly remove it in 
the future.

> ./base/static_sparse_graph.pxd:10: void qsort(void *base, int  nmemb, int 
size, 
This is the declaration of a sort method

> ./base/static_sparse_graph.pyx:293: qsort(g.neighbors[i],  
g.neighbors[i+1] - g.neighbors[i], sizeof(int), compare_uint32_p) 
Sort integers, so it's OK.

> ./graph_decompositions/vertex_separation.pyx:1841: delta.sort() 
The list delta contains only tuples (int, int), so it's fine.

> ./connectivity.pyx:287: c.sort() 
This one is considered in https://github.com/sagemath/sage/pull/35891

> ./generic_graph.py:3413: multi_edges.sort() 
> ./generic_graph.py:12124: output.sort() 

These two calls mays lead to an error when parameter `sort` is set to 
`True` by users. We should at least add parameter `key` to the method -> 
TODO

> ./generic_graph.py:21508: sage: lap.sort(reverse=True) 
Inside a doctest. Done carefully.

> ./generic_graph.py:21521: evals.sort(reverse=True) 
Sorts a list of eigenvalues, so it's fine.

> ./graph.py:2715: e.sort() 
Always sorts integer values. See method  `is_edge_transitive`

> ./graph_database.py:75: degree_sequence.sort() 
Sorts a list of integers (degree sequence), so it's fine.

> ./schnyder.py:278: l.sort() 
> ./schnyder.py:427: ones.sort() 
> ./schnyder.py:428: twos.sort() 
> ./schnyder.py:429: threes.sort() 
I don't know if these calls are safe or not. This code is used only in 
`src/sage/combinat/interval_posets.py`.
Someone with expertise in this code should certainly improve it to make it 
safer and more efficient. 


On Tuesday, July 4, 2023 at 8:36:42 AM UTC+2 Georgi Guninski wrote:

> In a QA attempt I tried to find calling sort() in graphs without
> |key|, which may raise exception.
>
> On sage 9.6:
>
> $cd /usr/lib64/python3.11/site-packages/sage/graphs/
> $grep -rnI 'sort(' . | grep -v 'key=' | grep -v 'topological'
>
> #15 results
>
>
> ./base/static_sparse_backend.pyx:512: vertices.sort()
> ./base/static_sparse_graph.pxd:10: void qsort(void *base, int
> nmemb, int size,
> ./base/static_sparse_graph.pyx:293: qsort(g.neighbors[i],
> g.neighbors[i+1] - g.neighbors[i], sizeof(int), compare_uint32_p)
> ./graph_decompositions/vertex_separation.pyx:1841: delta.sort()
> ./connectivity.pyx:287: c.sort()
> ./generic_graph.py:3413: multi_edges.sort()
> ./generic_graph.py:12124: output.sort()
> ./generic_graph.py:21508: sage: lap.sort(reverse=True)
> ./generic_graph.py:21521: evals.sort(reverse=True)
> ./graph.py:2715: e.sort()
> ./graph_database.py:75: degree_sequence.sort()
> ./schnyder.py:278: l.sort()
> ./schnyder.py:427: ones.sort()
> ./schnyder.py:428: twos.sort()
> ./schnyder.py:429: threes.sort()
>

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Re: [sage-devel] Graph([('A','B'),(1,2)]).edges() raises weird traceback

[David Coudert]

There is an active deprecation warning in method edges(). Parameter sort 
will be set to False in the future. I'm surprised you don't see it.

sage: Graph([('A','B'),(1,2)]).edges()
:1: DeprecationWarning: parameter 'sort' will 
be set to False by default in the future See https://github.com/sagemath/
sage/issues/27408 for details.
Graph([('A','B'),(Integer(1),Integer(2))]).edges() ) failed: TypeError: unsupported operand parent(s) 
for <: 'Integer Ring' and ''>


On Tuesday, July 4, 2023 at 4:29:21 PM UTC+2 Vincent Delecroix wrote:

> https://github.com/sagemath/sage/issues/35897
>
> On Tue, 4 Jul 2023 at 16:25, Vincent Delecroix
> <20100.d...@gmail.com> wrote:
> >
> > This is a bug in the __repr__ method of EdgesView. Thanks for your 
> report.
> >
> > On Tue, 4 Jul 2023 at 10:52, Georgi Guninski  wrote:
> > >
> > > Graph([('A','B'),(1,2)]).edges()
> > > ) failed:
> > > TypeError: unsupported operand parent(s) for <: 'Integer Ring' and
> > > ''>
> > >
> > > I think this is related to sorting the edges.
> > >
> > > The following works:
> > > sage: Graph([("A",1),("B",2)]).edges()
> > > [(1, 'A', None), (2, 'B', None)]
> > >
> > > --
> > > You received this message because you are subscribed to the Google 
> Groups "sage-devel" group.
> > > To unsubscribe from this group and stop receiving emails from it, send 
> an email to sage-devel+...@googlegroups.com.
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> .
>

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Re: [sage-devel] Should I report codepaths leading to comparing incomparable objects?

[David Coudert]

Thanks for reporting this issue. I have opened an issue 
(https://github.com/sagemath/sage/issues/35889) and will propose a fix asap.

On Sunday, July 2, 2023 at 6:37:45 PM UTC+2 Georgi Guninski wrote:

> You definitely can construct graph with incomparable vertices
> and they worked as expected in python2. python3 regressed them
> and devs are doing workarounds.
>
> The new testace is:
> G=Graph([("A",1)])
> G.feedback_vertex_set()
> ===
> File /home/sc_serv/sage/src/sage/graphs/connectivity.pyx:287, in
> sage.graphs.connectivity.connected_component_containing_vertex()
> 285
> 286 if sort:
> --> 287 c.sort()
> 288 return c
>

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Re: [sage-devel] Re: Voting: Block-scoped optional tag and the keyword

[David Coudert]

I vote for (A)

On Friday, June 30, 2023 at 2:59:53 PM UTC+2 David Ayotte wrote:

> I vote for (A)
>
> Le jeudi 29 juin 2023 à 18:47:42 UTC-4, Edgar Costa a écrit :
>
>> I vote for (A)
>>
>> On Thu, Jun 29, 2023 at 6:27 PM Marc Culler  wrote:
>>
>>> I vote for (C).
>>>
>>> On Wednesday, June 28, 2023 at 9:40:07 PM UTC-5 Kwankyu Lee wrote:
>>>
 Hi,

 We spent six days for the preliminary discussion in the sage-devel 
 thread

 https://groups.google.com/g/sage-devel/c/OUnoroIf0qc

 about choosing the keyword triggering block-scoped optional tag needed 
 in 

 https://github.com/sagemath/sage/issues/35750

 We now start the voting with the four candidates (A), (B), (C), (D). 
 The voting will end 7th July 23:59 KST (Korea Standard Time). During the 
 voting, discussions can continue in the linked places but please only your 
 vote (and, if you will, short comment) to this thread.

 (A) "needs"

 sage: # needs sage.rings.number_field
 sage: QQbar(I)^2
 -1
 sage: QQbar(I)^10 # long time
 1

 sage: # needs sage.rings.finite_rings
 sage: F = GF(7)
 sage: F(1) + QQbar(1)  # needs sage.rings.number_field
 ...

 (B) "requires"

 sage: # requires sage.rings.number_field
 sage: QQbar(I)^2
 -1
 sage: QQbar(I)^10  # long time
 1

 sage: # requires sage.rings.finite_rings
 sage: F = GF(7)
 sage: F(1) + QQbar(1)  # requires sage.rings.number_field
 ...

 (C) "uses"

 sage: # uses sage.rings.number_field
 sage: QQbar(I)^2
 -1
 sage: QQbar(I)^10  # long time
 1

 sage: # uses sage.rings.finite_rings
 sage: F = GF(7)
 sage: F(1) + QQbar(1)  # uses sage.rings.number_field
 ...

 (D) "standard"

 sage: # use standard feature - sage.rings.number_field
 sage: QQbar(I)^2
 -1
 sage: QQbar(I)^10  # long time
 1

 sage: # use standard feature - sage.rings.finite_rings
 sage: F = GF(7)
 sage: F(1) + QQbar(1)  # standard - sage.rings.number_field
 ...

 Please just focus on the keyword. Don't worry about minor details or 
 punctuations: the keyword would be recognized, the rest would be ignored 
 noise, in the implementation.

 Thanks for your attention. Happy voting :-)



  

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>>> 
>>> .
>>>
>>

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[sage-devel] Re: New algorithm for graph edge coloring

[David Coudert]

FYI, the current Vizing algorithm is not well tested and the returned edge 
coloring may have an empty set of colors

sage: from sage.graphs.graph_coloring import edge_coloring
sage: G = graphs.PetersenGraph()
sage: edge_coloring(G, vizing=True)
[[(0, 1), (2, 3), (4, 9), (5, 7), (6, 8)],
 [(0, 4), (1, 2), (3, 8), (6, 9)],
 [(0, 5), (2, 7)],
 [(1, 6), (3, 4), (5, 8), (7, 9)]]
sage: G = graphs.StarGraph(4)
sage: edge_coloring(G, vizing=True)
[[(0, 1)], [(0, 2)], [(0, 3)], [(0, 4)], []]



On Tuesday, November 29, 2022 at 7:13:43 AM UTC+1 Matheus Maldonado wrote:

> On Monday, 28 November 2022 at 03:48:18 UTC-3 dmo...@deductivepress.ca 
> wrote:
>
>> I agree that this seems to be a good improvement.  I think it should 
>> replace the current "vizing" algorithm, instead of adding a new function to 
>> the namespace.
>>
>> A minor issue is that (if I understand correctly) the current vizing 
>> algorithm always gives a colouring with Delta + 1 colours.  If that is 
>> correct, then the code may need to be modified to have an option that 
>> matches this behaviour, until the traditional 1-year deprecation period has 
>> passed.
>>
>
> I see. If the algorithm finds a Delta coloring, I just need to change the 
> color of a random edge to a new one. Sounds a little counter-intuitive, but 
> I understand the reason behind it. 
>  
>
>>
>> Also, I think the "hex_colors" option should be deleted. Instead, it 
>> would be nice to put this code into the documentation as an example that 
>> demonstrates how to print the colouring.
>>
>
>  Any specific reason for this? 
>  
>
>> On Sunday, November 27, 2022 at 11:20:35 PM UTC-7 David Coudert wrote:
>>
>>> Feel free to open a ticket for this code. It's seems a good improvement.
>>>
>>> On Sunday, November 27, 2022 at 5:39:34 PM UTC+1 Matheus Maldonado wrote:
>>>
>>>> Hello everyone,
>>>>
>>>> I just developed a new function for coloring graph edges based on 
>>>> this article: 
>>>> https://www.sciencedirect.com/science/article/abs/pii/002001909290041S 
>>>> , and I'd like to know if you think it's a valuable contribution to sage 
>>>> and deserves a trac ticket. I compared the existing edge coloring function 
>>>> and the one I created, and it's a pretty good improvement in processing 
>>>> time for graphs with a lot of edges:
>>>>
>>>> sage: g_list = [graphs RandomGNP(x, 0.7) for x in range(25)]
>>>> sage: %time c = [vizing_edge_coloring(x) for x in g_list]
>>>> CPU times: user 131 ms, sys: 9.94 ms, total: 141 ms
>>>> Wall time: 140 ms
>>>> sage: %time c = [edge_coloring(x, vizing=True) for x in g_list]
>>>> CPU times: user 18.6 s, sys: 134 μs, total: 18.6 s
>>>> Wall time: 18.6 s
>>>>
>>>> I still haven't decided if this function should be standalone or if it 
>>>> should be called when the flag vizing is set on the existing edge_coloring 
>>>> function. If you have an opinion on that, please share :)
>>>>
>>>> I'm pasting the code below for reference, since I haven't created a 
>>>> ticket and pushed my branch yet. Feedback is much appreciated!
>>>>
>>>> def vizing_edge_coloring(g, hex_colors=False):
>>>> r"""
>>>> Compute an edge coloring with at most `\Delta + 1` colors.
>>>>
>>>> INPUT:
>>>>
>>>> - ``g`` -- a graph.
>>>>
>>>> - ``hex_colors`` -- boolean (default: ``False``); when set to 
>>>> ``True``, the
>>>>   partition returned is a dictionary whose keys are colors and 
>>>> whose values
>>>>   are the color classes (ideal for plotting)
>>>>
>>>> OUTPUT:
>>>>
>>>> - Returns a partition of the edge set into at most `\Delta + 1` 
>>>> matchings.
>>>>
>>>> .. SEEALSO::
>>>>
>>>> - :wikipedia:`Edge_coloring` for further details on edge 
>>>> coloring
>>>> - :wikipedia:`Vizing's_theorem` for further details on Vizing's 
>>>> theorem
>>>>
>>>> ALGORITHM:
>>>>
>>>> This function's implementation is based on the algorithm described 
>>>> at [MG1992]_
>>>> 
>>>> EXAMPLES:
>>>>
>>>> Coloring the edges of the Petersen Graph::
>>>>
>>>>sage: from sage.grap

[sage-devel] Re: New algorithm for graph edge coloring

[David Coudert]

Feel free to open a ticket for this code. It's seems a good improvement.

On Sunday, November 27, 2022 at 5:39:34 PM UTC+1 Matheus Maldonado wrote:

> Hello everyone,
>
> I just developed a new function for coloring graph edges based on 
> this article: 
> https://www.sciencedirect.com/science/article/abs/pii/002001909290041S , 
> and I'd like to know if you think it's a valuable contribution to sage and 
> deserves a trac ticket. I compared the existing edge coloring function and 
> the one I created, and it's a pretty good improvement in processing time 
> for graphs with a lot of edges:
>
> sage: g_list = [graphs RandomGNP(x, 0.7) for x in range(25)]
> sage: %time c = [vizing_edge_coloring(x) for x in g_list]
> CPU times: user 131 ms, sys: 9.94 ms, total: 141 ms
> Wall time: 140 ms
> sage: %time c = [edge_coloring(x, vizing=True) for x in g_list]
> CPU times: user 18.6 s, sys: 134 μs, total: 18.6 s
> Wall time: 18.6 s
>
> I still haven't decided if this function should be standalone or if it 
> should be called when the flag vizing is set on the existing edge_coloring 
> function. If you have an opinion on that, please share :)
>
> I'm pasting the code below for reference, since I haven't created a ticket 
> and pushed my branch yet. Feedback is much appreciated!
>
> def vizing_edge_coloring(g, hex_colors=False):
> r"""
> Compute an edge coloring with at most `\Delta + 1` colors.
>
> INPUT:
>
> - ``g`` -- a graph.
>
> - ``hex_colors`` -- boolean (default: ``False``); when set to 
> ``True``, the
>   partition returned is a dictionary whose keys are colors and whose 
> values
>   are the color classes (ideal for plotting)
>
> OUTPUT:
>
> - Returns a partition of the edge set into at most `\Delta + 1` 
> matchings.
>
> .. SEEALSO::
>
> - :wikipedia:`Edge_coloring` for further details on edge coloring
> - :wikipedia:`Vizing's_theorem` for further details on Vizing's 
> theorem
>
> ALGORITHM:
>
> This function's implementation is based on the algorithm described at 
> [MG1992]_
> 
> EXAMPLES:
>
> Coloring the edges of the Petersen Graph::
>
>sage: from sage.graphs.graph_coloring import vizing_edge_coloring
>sage: g = graphs.PetersenGraph()
>sage: vizing_edge_coloring(g)
>[[(0, 1), (2, 7), (3, 4), (6, 9)],
>  [(0, 4), (2, 3), (5, 7), (6, 8)],
>  [(0, 5), (1, 6), (3, 8), (7, 9)],
>  [(1, 2), (4, 9), (5, 8)]]
>sage: vizing_edge_coloring(g, hex_colors=True)
> {'#00': [(0, 5), (1, 6), (3, 8), (7, 9)],
> '#7f00ff': [(1, 2), (4, 9), (5, 8)],
> '#7fff00': [(0, 4), (2, 3), (5, 7), (6, 8)],
> '#ff': [(0, 1), (2, 7), (3, 4), (6, 9)]}
>
> TESTS:
>
> Graph without edge::
>
>sage: g = Graph(2)
>sage: vizing_edge_coloring(g)
>[]
>sage: vizing_edge_coloring(g, hex_colors=True)
>{}
> """
> # finds every color adjacent to vertex v
> def colors_of(v):
> return [x[2] for x in g.edges_incident(v) if x[2] is not None]
>
> # constructs a maximal fan  of X where X is edge[0] and f is 
> edge[1]
> def maximal_fan(edge):
> fan_center, rear = edge
> rear_colors = colors_of(rear)
> cdef list neighbors = [n for n in g.neighbors(fan_center) if 
> g.edge_label(fan_center, n) is not None]
> cdef list fan = [rear]
> can_extend_fan = True
> while can_extend_fan:
> can_extend_fan = False
> for n in neighbors:
> if g.edge_label(fan_center, n) not in rear_colors:
> fan.append(n)
> rear = n
> rear_colors = colors_of(rear)
> can_extend_fan = True
> neighbors.remove(n)
> return fan
>
> # gives each edge Xu in the fan  the color of Xu+ and uncolors Xw
> def rotate_fan(fan_center, fan):
> for i in range(1, len(fan)):
> g.set_edge_label(fan_center, fan[i - 1], 
> g.edge_label(fan_center, fan[i]))
> g.set_edge_label(fan_center, fan[-1], None)
>
> # computes the maximal ab-path starting at v
> def find_path(v, a, b, path=[]):
> path_edge = [x for x in g.edges_incident(v) if x[2] == a]
> if path_edge and path_edge[0] not in path:
> path.append(path_edge[0][0] if path_edge[0][1] == v else 
> path_edge[0][1])
> find_path(path[-1], b, a, path)
> return path
>
> # exchanges the color of every edge on the ab-path starting at v
> def invert_path(v, a, b):
> path = [v] + find_path(v, a, b, [])
> for i in range(1, len(path)):
> g.set_edge_label(path[i-1], path[i], a if 
> g.edge_label(path[i-1], path[i]) == b else b)
>
> # returns the ´smallest´ color free at v
> def find_free_color(v):
> colors = [x[2] for x in g.edges_incident(v) if x[2] is not None]
> for c in 

[sage-devel] Re: View issues

[David Coudert]

The command t.pdf() is not working for me for the following reason:

Warning: `tkz-graph.sty` is not part of this computer's TeX installation.
This package is required to render graphs in LaTeX.
Visit 'https://www.ctan.org/pkg/tkz-graph'.

Warning: `tkz-berge.sty` is not part of this computer's TeX installation.
This package is required to render graphs in LaTeX.
Visit 'https://www.ctan.org/pkg/tkz-berge'.


On Wednesday, September 28, 2022 at 10:56:29 AM UTC+2 Sébastien Labbé wrote:

> With the new latex_standalone.py module in sage misc, you have access to 
> more control on the options to construct a tikzpicture within a latex file 
> with standalone document class. See the documentation here:
>
> https://doc.sagemath.org/html/en/reference/misc/sage/misc/latex_standalone.html
>
> I am curious that you test whether the following example taken from the 
> above documentation works for you:
>
> g = graphs.PetersenGraph()
> s = latex(g)
> from sage.misc.latex_standalone import TikzPicture
> t = TikzPicture(s, standalone_config=["border=4mm"], usepackage=[
> 'tkz-graph'])
> t
> t.pdf()
>
>
> On Tuesday, September 27, 2022 at 9:16:03 PM UTC+2 Ben Salisbury wrote:
>
>> Hi all,
>>
>> I'm having trouble with the view method.  For example, 
>>
>> sage: G = graphs.PetersenGraph()
>> sage: view(G)
>>
>> produced the following error. 
>>
>> An error occurred.
>> This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) 
>> (preloaded format=pdflatex 2022.9.9)  17 SEP 2022 18:58
>> entering extended mode
>> restricted \write18 enabled.
>> %&-line parsing enabled.
>> **\nonstopmode \input{sage.tex}
>> (./sage.tex (/usr/local/texlive/2022/texmf-dist/tex/latex/base/article.cls
>> Document Class: article 2021/10/04 v1.4n Standard LaTeX document class
>> (/usr/local/texlive/2022/texmf-dist/tex/latex/base/size10.clo
>> File: size10.clo 2021/10/04 v1.4n Standard LaTeX file (size option)
>> )
>> \c@part=\count185
>> \c@section=\count186
>> \c@subsection=\count187
>> \c@subsubsection=\count188
>> \c@paragraph=\count189
>> \c@subparagraph=\count190
>> \c@figure=\count191
>> \c@table=\count192
>> \abovecaptionskip=\skip47
>> \belowcaptionskip=\skip48
>> \bibindent=\dimen138
>> )
>> (/usr/local/texlive/2022/texmf-dist/tex/latex/amsmath/amsmath.sty
>> Package: amsmath 2021/10/15 v2.17l AMS math features
>> \@mathmargin=\skip49
>>
>> 
>>
>> ! Undefined control sequence.
>> \@outputpage ...istfalse \@parboxrestore \shipout 
>>  \vbox 
>> {\set@typeset@protec...
>> l.118 \end{document}
>>
>> (That makes 100 errors; please try again.) 
>> Here is how much of TeX's memory you used:
>> 17546 strings out of 478268
>> 364860 string characters out of 5846348
>> 670991 words of memory out of 500
>> 35436 multiletter control sequences out of 15000+60
>> 472216 words of font info for 40 fonts, out of 800 for 9000
>> 1141 hyphenation exceptions out of 8191
>> 94i,9n,104p,428b,907s stack positions out of 
>> 1i,1000n,2p,20b,20s
>>
>> !  ==> Fatal error occurred, no output PDF file produced!
>>
>> Latex error
>>
>> Is there a known error or is my installation messed up (or something 
>> else)?
>>
>> Best,
>> Ben
>>
>

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[sage-devel] Re: Polling for pygments style for our future doc

[David Coudert]

+1 for sphinx

I don't like the italic in tango.

David.

On Thursday, August 4, 2022 at 6:33:27 PM UTC+2 Eric Gourgoulhon wrote:

> Thanks for preparing this poll. I vote for 
>
> (1) tango
>
> Eric.
>

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[sage-devel] Re: Kruskal's Algorithm using Priority Queues

[David Coudert]

You are right, this can be removed too.
And I'm not sure a parallel version of Boruvka's algorithm is needed. We 
already have a large number of spanning tree algorithms.


On Tuesday, April 12, 2022 at 7:56:20 PM UTC+2 patrat...@gmail.com wrote:

> Just wondering if the third TODO (Randomized spanning tree construction) 
> should be removed as well, since I see a function called 
> "random_spanning_tree" 
> exists already.
> On Monday, April 11, 2022 at 8:23:30 AM UTC+1 adarsh.k...@gmail.com wrote:
>
>> Okay, then I think that line should be removed right? It can be 
>> misleading to potential contributors
>>
>> On Monday, April 11, 2022 at 12:31:02 PM UTC+5:30 David Coudert wrote:
>>
>>> This query has been added in https://trac.sagemath.org/ticket/10433.
>>> I don't think that priority queue can be of any help to speed up the 
>>> current code.
>>>
>>> On Sunday, April 10, 2022 at 11:03:41 AM UTC+2 adarsh.k...@gmail.com 
>>> wrote:
>>>
>>>> Hi everyone,
>>>>
>>>> I was going through Sage's codebase, and I came across the file
>>>> ```
>>>> SAGE_ROOT/src/sage/graphs/spanning_tree.pyx
>>>> ```
>>>> [image: Screenshot from 2022-04-10 14-27-45.png]
>>>>
>>>> In the TODO section, it is mentioned that 
>>>> ```
>>>> - Rewrite: func:`kruskal` to use priority queues.
>>>> ```
>>>>
>>>> I looked it up on Google and StackOverFlow, but I didn't come across 
>>>> any such implementation. The standard implementations all prefer to use 
>>>> the 
>>>> DisjointSet data structure. I would like to contribute to Sage and if 
>>>> someone can point me to a good resource which discusses this concept, 
>>>> preferably with a better time complexity than by using Disjoint Sets, that 
>>>> would be really great
>>>>
>>>

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[sage-devel] Re: Kruskal's Algorithm using Priority Queues

[David Coudert]

Sure, feel free to open a ticket to correct this.

On Monday, April 11, 2022 at 4:18:38 PM UTC+2 adarsh.k...@gmail.com wrote:

> I can open a ticket to correct this if you want
>
> On Monday, April 11, 2022 at 12:53:30 PM UTC+5:30 Adarsh Kishore wrote:
>
>> Okay, then I think that line should be removed right? It can be 
>> misleading to potential contributors
>>
>> On Monday, April 11, 2022 at 12:31:02 PM UTC+5:30 David Coudert wrote:
>>
>>> This query has been added in https://trac.sagemath.org/ticket/10433.
>>> I don't think that priority queue can be of any help to speed up the 
>>> current code.
>>>
>>> On Sunday, April 10, 2022 at 11:03:41 AM UTC+2 adarsh.k...@gmail.com 
>>> wrote:
>>>
>>>> Hi everyone,
>>>>
>>>> I was going through Sage's codebase, and I came across the file
>>>> ```
>>>> SAGE_ROOT/src/sage/graphs/spanning_tree.pyx
>>>> ```
>>>> [image: Screenshot from 2022-04-10 14-27-45.png]
>>>>
>>>> In the TODO section, it is mentioned that 
>>>> ```
>>>> - Rewrite: func:`kruskal` to use priority queues.
>>>> ```
>>>>
>>>> I looked it up on Google and StackOverFlow, but I didn't come across 
>>>> any such implementation. The standard implementations all prefer to use 
>>>> the 
>>>> DisjointSet data structure. I would like to contribute to Sage and if 
>>>> someone can point me to a good resource which discusses this concept, 
>>>> preferably with a better time complexity than by using Disjoint Sets, that 
>>>> would be really great
>>>>
>>>

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[sage-devel] Re: Kruskal's Algorithm using Priority Queues

[David Coudert]

This query has been added in https://trac.sagemath.org/ticket/10433.
I don't think that priority queue can be of any help to speed up the 
current code.

On Sunday, April 10, 2022 at 11:03:41 AM UTC+2 adarsh.k...@gmail.com wrote:

> Hi everyone,
>
> I was going through Sage's codebase, and I came across the file
> ```
> SAGE_ROOT/src/sage/graphs/spanning_tree.pyx
> ```
> [image: Screenshot from 2022-04-10 14-27-45.png]
>
> In the TODO section, it is mentioned that 
> ```
> - Rewrite: func:`kruskal` to use priority queues.
> ```
>
> I looked it up on Google and StackOverFlow, but I didn't come across any 
> such implementation. The standard implementations all prefer to use the 
> DisjointSet data structure. I would like to contribute to Sage and if 
> someone can point me to a good resource which discusses this concept, 
> preferably with a better time complexity than by using Disjoint Sets, that 
> would be really great
>

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Re: [sage-devel] trac is not accessible now

[David Coudert]

> In the spam they are! First time I see this in more than 10 years! Thank 
> you.
>

I frequently have emails about sagemath in my spam folder and I have not 
find yet how to change the rules of gmail to avoid that.

Best,
David.
 

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Re: [sage-devel] Failed to build cysignals-1.10.3 and pyzmq-22.2.1 on a Fedora 35 (x86_64)

[David Coudert]

I have the same issues after upgrade a desktop to fedora 35.
I succeed to compile using  https://trac.sagemath.org/ticket/32828
Thanks.
On Monday, November 22, 2021 at 8:22:48 AM UTC+1 enriqu...@gmail.com wrote:

> For cysignals it works using the package from this fork: 
> https://github.com/kliem/cysignals/tree/fix_non_constant_MINSIGSTKSZ 
> (attached) with the changed files for build/pkgs/cysignals
> For pyzmq it has been solved in https://trac.sagemath.org/ticket/32828.
> I got some failed tests but at least a usable build. 
> Following https://trac.sagemath.org/ticket/30767 it is also possible to 
> use Python 3.10 (in this ticket they do not use the system package).
>
> El lunes, 22 de noviembre de 2021 a las 7:26:47 UTC+1, 
> jonatha...@googlemail.com escribió:
>
>> Thanks for the report. For cysignals we have the ticket 
>> https://trac.sagemath.org/ticket/32576 and github issue 
>> https://github.com/sagemath/cysignals/issues/150.
>>
>> furutaka@gmail.com schrieb am Montag, 22. November 2021 um 04:17:55 
>> UTC+1:
>>
>>> Forgot to attach this...
>>>
>>> 2021年11月22日(月) 11:31 Kazuyoshi Furutaka :
>>>
 Hi,

 My build of sage-9.5.beta7 on a Fedora 35 system (x86_64) failed:
 * package: cysignals-1.10.3
   last build time: Nov 22 11:13

 * package: pyzmq-22.2.1
   last build time: Nov 22 11:13

 Logs attached to this message.

 By the way, they've been installed as Fedora packages:
 [root@peart-furu-or-jp furutaka]# dnf list installed \*zmq\* 
 \*cysignals\*
 Installed Packages
 czmq.x86_64  
 4.2.1-6.fc34@fedora
 czmq-devel.x86_64
 4.2.1-6.fc34@fedora
 python3-cysignals.x86_64 
 1.10.3-2.fc35   @fedora
 python3-cysignals-devel.x86_64   
 1.10.3-2.fc35   @fedora
 python3-zmq.x86_64   
 22.2.1-1.fc35   @fedora
 python3-zmq-tests.x86_64 
 22.2.1-1.fc35   @fedora

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 .

>>>
>>>
>>> -- 
>>> Kazuyoshi Furutaka
>>>
>>

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Re: [sage-devel] Teaching with Sagemath

[David Coudert]

Thank you !

On Wednesday, October 6, 2021 at 7:41:02 PM UTC+2 dim...@gmail.com wrote:

> There is 
>
>- *Title* Algorithmic Graph Theory
>- *Authors* David Joyner, Minh Van Nguyen, Nathann Cohen
>- *Publisher:* Google (Last draft on May 10, 2013) 
>- *License(s):* GNU GPL v2 
><http://www.gnu.org/licenses/old-licenses/gpl-2.0.html>
>
> see
> http://static.latexstudio.net/wp-content/uploads/2013/03/book.pdf (from 
> 2013).
>
> It's not clear to me why this is not linked in the wiki.
>
>
> On Wed, Oct 6, 2021 at 4:50 PM David Joyner  wrote:
>
>> On Wed, Oct 6, 2021 at 11:17 AM David Coudert  
>> wrote:
>> >
>> > Dear all,
>> >
>> > a colleague asks me if we have examples of notebooks for teaching 
>> introduction to graph theory with sagemath.
>> > I found this page that is clearly outdated 
>> https://wiki.sagemath.org/Teaching_with_SAGE
>> >
>> > If you are aware of some accessible material, please let me know.
>> >
>>
>> There is some sage code included in these lecture notes:
>> https://yetanothermathblog.com/2018/04/01/calculus-on-graphs/
>>
>> > Best,
>> > David.
>> >
>> > --
>> > You received this message because you are subscribed to the Google 
>> Groups "sage-devel" group.
>> > To unsubscribe from this group and stop receiving emails from it, send 
>> an email to sage-devel+...@googlegroups.com.
>> > To view this discussion on the web visit 
>> https://groups.google.com/d/msgid/sage-devel/5fffb047-6d16-4195-853c-60de102b2932n%40googlegroups.com
>> .
>>
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>> https://groups.google.com/d/msgid/sage-devel/CAEQuuAVX--iJ0aiR2jkcfD-vbqHcj52siQfoF2R4NUT7HeHmnA%40mail.gmail.com
>> .
>>
>

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[sage-devel] Teaching with Sagemath

[David Coudert]

Dear all,

a colleague asks me if we have examples of notebooks for teaching 
introduction to graph theory with sagemath.
I found this page that is clearly 
outdated https://wiki.sagemath.org/Teaching_with_SAGE

If you are aware of some accessible material, please let me know.

Best,
David.

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[sage-devel] Cplex 20.1

[David Coudert]

I tried the last version of cplex (20.1) with sagemath and so far it's 
working well.
The previous version was 12.10.

I had a look at the release note and I don't see any deprecation that may 
be problematic for us 
https://www.ibm.com/docs/en/icos/20.1.0?topic=2010-release-notes-cplex

Best,
David.

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Re: [sage-devel] trac notification emails

[David Coudert]

I discovered today that mails can also be put into quarantine.
Problem solved (I hope).
Best,

Le mercredi 10 mars 2021 à 09:31:59 UTC+1, David Coudert a écrit :

> I will ask the IT service of Inria.
> Thank you Dima. 
>
> Le mercredi 10 mars 2021 à 01:15:15 UTC+1, dim...@gmail.com a écrit :
>
>>
>>
>> On Tue, 9 Mar 2021, 22:41 David Coudert,  wrote:
>>
>>> I don't know why, but apparently I don't receive notification emails 
>>> from the trac server since a couple of days. Did I miss some configuration 
>>> change ?
>>> Are others having the same issue ?
>>>
>>
>> I checked logs, everything is in order on the sender side, your emails 
>> are being delivered.
>> e.g.
>>
>> Mar  9 18:34:12 sagemath smtpd[93054]: 407e223ef83c2266 mta delivery 
>> evpid=519550eedbe2e43f from= to= 
>> rcpt=<-> source="46.23.93.76" relay="192.134.164.98 (
>> mail3-smtp-sop.national.inria.fr)" delay=2s result="Ok" stat="250 ok: 
>>  Message 375249000 accepted"
>>
>> I guess it's your side that has issues. A new spam filter in INRIA?
>>
>> Dima
>>
>> -- 
>>> You received this message because you are subscribed to the Google 
>>> Groups "sage-devel" group.
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>>> an email to sage-devel+...@googlegroups.com.
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>>> https://groups.google.com/d/msgid/sage-devel/83672d87-f599-491e-a8c3-1718f707ec62n%40googlegroups.com
>>>  
>>> <https://groups.google.com/d/msgid/sage-devel/83672d87-f599-491e-a8c3-1718f707ec62n%40googlegroups.com?utm_medium=email_source=footer>
>>> .
>>>
>>

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Re: [sage-devel] trac notification emails

[David Coudert]

I will ask the IT service of Inria.
Thank you Dima. 

Le mercredi 10 mars 2021 à 01:15:15 UTC+1, dim...@gmail.com a écrit :

>
>
> On Tue, 9 Mar 2021, 22:41 David Coudert,  wrote:
>
>> I don't know why, but apparently I don't receive notification emails from 
>> the trac server since a couple of days. Did I miss some configuration 
>> change ?
>> Are others having the same issue ?
>>
>
> I checked logs, everything is in order on the sender side, your emails are 
> being delivered.
> e.g.
>
> Mar  9 18:34:12 sagemath smtpd[93054]: 407e223ef83c2266 mta delivery 
> evpid=519550eedbe2e43f from= to= 
> rcpt=<-> source="46.23.93.76" relay="192.134.164.98 (
> mail3-smtp-sop.national.inria.fr)" delay=2s result="Ok" stat="250 ok: 
>  Message 375249000 accepted"
>
> I guess it's your side that has issues. A new spam filter in INRIA?
>
> Dima
>
> -- 
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>>  
>> <https://groups.google.com/d/msgid/sage-devel/83672d87-f599-491e-a8c3-1718f707ec62n%40googlegroups.com?utm_medium=email_source=footer>
>> .
>>
>

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[sage-devel] trac notification emails

[David Coudert]

I don't know why, but apparently I don't receive notification emails from 
the trac server since a couple of days. Did I miss some configuration 
change ?
Are others having the same issue ?

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Re: [sage-devel] Re: Sage GSoC 2021 Projects

[David Coudert]

I added a project for improving the graph drawing methods we have.


Le mercredi 24 février 2021 à 02:09:46 UTC+1, Travis Scrimshaw a écrit :

> Thank you everyone who has added some projects.
>
> Even if someone has a project later on they want to add, please do so. We 
> can continue to add projects until we select the students in a few months.
>
> Best,
> Travis
>
>
> On Wednesday, February 24, 2021 at 1:03:44 AM UTC+10 mckenz...@gmail.com 
> wrote:
>
>> I've added myself as a mentor for the Small Groups project.  I am willing 
>> to help but haven't been involved enough lately to have my own idea.  
>>
>> Mckenzie
>>
>> On Tuesday, February 23, 2021 at 5:26:08 AM UTC-6 de...@benjamin-hackl.at 
>> wrote:
>>
>>> I have added a project for expanding Sage's asymptotics module to the 
>>> list which Clemens and I are willing to mentor.
>>>
>>> Best wishes,
>>> Benjamin
>>>
>>> Travis Scrimshaw schrieb am Dienstag, 23. Februar 2021 um 00:18:20 UTC+1:
>>>
 Hi Clemens,
Google could look at the projects page at anytime now. So it would 
 be good to add them by the end of the week.

 Best,
 Travis

 On Monday, February 22, 2021 at 8:35:54 PM UTC+10 Clemens Heuberger 
 wrote:

> Hi, 
>
> Am 22.02.21 um 06:08 schrieb 'Travis Scrimshaw' via sage-devel: 
> > Hi everyone, 
> >   With currently only 2 projects (proposed only by me), we do not 
> have a strong 
> > case to be accepted for GSoC this year. It would be great if you 
> could add a 
> > project if you are considering one. 
>
> what are the deadlines? 
>
> Best, 
>
> Clemens 
>
> > 
> > I have been a (co)mentor the past few years and also found the 
> program very 
> > rewarding. This is a great way to get some help with doing 
> improvements to Sage 
> > or with your research, where you can give back to the community. You 
> also do not 
> > need to be a regular Sage developer either. I (or perhaps other 
> developers) can 
> > help you when issues arise. 
> > 
> > Best, 
> > Travis 
> > 
> > 
> > On Monday, February 15, 2021 at 1:54:37 PM UTC+10 Travis Scrimshaw 
> wrote: 
> > 
> > Hi everyone, 
> >I will be the admin for this year's Sage's GSoC program (for more 
> on 
> > GSoC, see https://summerofcode.withgoogle.com/), taking over after 
> the 
> > amazing job Harald has been doing these past years. This year, 
> students will 
> > be working on a 175-hour project over 10 weeks; specifically June 
> 8th to 
> > August 17th. As part of our application, I need your help in 
> constructing a 
> > a list of potential projects and mentors. 
> > 
> > If you are interested in mentoring a student on a project, please 
> add it to 
> > this page (still a bit of a work in progress): 
> > https://wiki.sagemath.org/GSoC/2021 
> > 
> > Note that by adding a project, you are /not/ committing to being a 
> mentor. 
> > Being a mentor typically means weekly meetings, some emails checking 
> > progress, and writing a few progress reports. Even if you are unsure 
> of your 
> > availability, it would be great to add some projects. 
> > 
> > Let me know if you have any questions. 
> > 
> > Best, 
> > Travis 
> > 
>
>

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Re: [sage-devel] issues building pdf documentation: missing encoding file 2004-H

[David Coudert]

After installation of texlive-scheme-full, it's finally working.
Thank you Dima. 

Le samedi 13 février 2021 à 16:10:36 UTC+1, dim...@gmail.com a écrit :

>
>
> On Sat, 13 Feb 2021, 15:02 David Coudert,  wrote:
>
>> Hello,
>>
>> I'm trying to build the pdf documentation (make doc-pdf) on a desktop 
>> with fedora-33.
>> I'm currently having hard time with the Japanese version of 
>> a_tour_of_sage. I'm discovering one after the other the missing packages 
>> for latex.
>>
>> Currently, I'm blocked with the following error:
>> dvipdfmx:fatal: Could not find encoding file "2004-H".
>>
>> does anyone know how to fix this ?
>> I know it's not directly sagemath related, but I assume that anyone 
>> trying to run `make doc-pdf` for the first time will have the same kind of 
>> issues. 
>>
>
> I would have tried installing complete TeXLive (hopefully you are not 
> short on disk space)-  texlive-full package
>
>
>
>> Thanks,
>> David.
>>
>> -- 
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>> email to sage-devel+...@googlegroups.com.
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>> <https://groups.google.com/d/msgid/sage-devel/575e35b2-9c10-431c-b071-fd88a8e27408n%40googlegroups.com?utm_medium=email_source=footer>
>> .
>>
>

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[sage-devel] issues building pdf documentation: missing encoding file 2004-H

[David Coudert]

Hello,

I'm trying to build the pdf documentation (make doc-pdf) on a desktop with 
fedora-33.
I'm currently having hard time with the Japanese version of a_tour_of_sage. 
I'm discovering one after the other the missing packages for latex.

Currently, I'm blocked with the following error:
dvipdfmx:fatal: Could not find encoding file "2004-H".

does anyone know how to fix this ?
I know it's not directly sagemath related, but I assume that anyone trying 
to run `make doc-pdf` for the first time will have the same kind of issues. 

Thanks,
David.

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[sage-devel] Re: [GSoC Mentors Announce] Now Accepting GSoC 2021 Mentoring Organization Applications until Feb 19

[David Coudert]

This year is difficult for all of us and we lack motivation for this 
edition of GSoC.
On the other end, it is more important than ever to push/motivate/help 
students.

Other Sagemath contributors than the usual could be involved in mentoring 
activity.
I think many contributors are not really aware of this program and what it 
means.
Furthermore, this year the GSoC period has been shortened (by half) and so 
it is no longer necessary to be around till end of August.
This could be an extra motivation to attract new mentors.

Concerning the admin part, I don't know how heavy it is, what it means 
exactly, etc.

Of course, if we are too few ready to help/mentor for GSoC this year we can 
pass.

Le lundi 8 février 2021 à 15:17:43 UTC+1, mmarco a écrit :

> I have participated as mentor other years... but this year I just don't 
> think I have the needed energy.
>
> I think Harald's proposal to pass this year and reconsider the next one 
> makes sense (sadly).
> El domingo, 7 de febrero de 2021 a las 17:54:07 UTC+1, 
> harald@gmail.com escribió:
>
>> Hi, a word from my side: I would really like to stop being admin as well 
>> and hope someone else can take over. I'm the one writing the application 
>> each year and I could this time around, but in general I want to focus on 
>> other things after all those years.
>>
>> Despite that, looks like there are only two mentors. Feels like this is 
>> below the threshold where it makes sense to pursue this? Maybe we should 
>> pass this year and re-evaluate for the next one?
>>
>> -- Harald
>>
>>
>>
>>

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Re: [sage-devel] Re: [GSoC Mentors Announce] Now Accepting GSoC 2021 Mentoring Organization Applications until Feb 19

[David Coudert]

I'll be happy to mentor a good student, but would prefer not to be admin.
I already have a huge load of administrative work daily and would 
appreciate not to have extra.

Le jeudi 4 février 2021 à 15:21:06 UTC+1, dim...@gmail.com a écrit :

> On Thu, Feb 4, 2021 at 3:32 AM 'Travis Scrimshaw' via sage-devel
>  wrote:
> >
> > I am happy to mentor, but I am not sure I could take on being an admin 
> this year (next year I could though).
>
> admin is much less work than mentoring, I think.
>
> >
> > Best,
> > Travis
> >
> >
> > On Tuesday, February 2, 2021 at 7:54:01 PM UTC+10 dim...@gmail.com 
> wrote:
> >>
> >> Dear all,
> >>
> >> we are looking for projects and mentors for GSoC 2021.
> >>
> >> Myself, I'll pass this year, though.
> >> This means we need at least one more admin.
> >>
> >> Dima
> >>
> >> -- Forwarded message -
> >> From: 'Stephanie Taylor' via Google Summer of Code Mentors Announce
> >> List 
> >> Date: Tue, Feb 2, 2021 at 7:28 AM
> >> Subject: [GSoC Mentors Announce] Now Accepting GSoC 2021 Mentoring
> >> Organization Applications until Feb 19
> >> To: Google Summer of Code Mentors Announce List
> >> 
> >>
> >>
> >> Hi all,
> >>
> >> Org admins can submit their org's application to be a mentoring
> >> organization for GSoC 2021 at g.co/gsoc from today until Feb 19 at
> >> 1900UTC.
> >>
> >> Please remember for the 2021 GSoC program all projects students will
> >> be working on for the summer should be ~175 hr projects. Please adjust
> >> your Project Ideas as needed. Having a thorough and well thought out
> >> list of Project Ideas is the most important part of your application.
> >> Making sure you having enough mentors excited to mentor student
> >> projects and that are ready to commit to mentoring over the summer is
> >> very important.
> >>
> >> Please encourage other open source orgs to apply -- if you know of
> >> other open source projects that may be interested in applying to GSoC
> >> as a first time org please remind them to check out the available
> >> resources below and have them put your org (or you) down as a
> >> reference.
> >>
> >> Resources:
> >>
> >> Mentor Guide
> >>
> >> Timeline
> >>
> >> FAQs
> >>
> >> Roles and Responsibilities
> >>
> >> Marketing Materials (slide deck, flyers)
> >>
> >> Videos
> >>
> >> If you have any questions please email me at gsoc-s...@google.com
> >>
> >> Best,
> >>
> >> Stephanie Taylor
> >>
> >> GSoC Program Lead
> >>
> >> --
> >> You received this message because you are subscribed to the Google
> >> Groups "Google Summer of Code Mentors Announce List" group.
> >> To unsubscribe from this group and stop receiving emails from it, send
> >> an email to gsoc-mentors-ann...@googlegroups.com.
> >> To view this discussion on the web visit
> >> 
> https://groups.google.com/d/msgid/gsoc-mentors-announce/87b37bc9-4ec0-4e30-a31e-1f47030902d0n%40googlegroups.com
> .
> >
> > --
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[sage-devel] Re: How to compile sparse graph backend with c++

[David Coudert]

I have not tried yet, but isn't it due to the fact that some parts are 
compiled with C and others with C++ ?

Le lundi 11 janvier 2021 à 11:28:47 UTC+1, jonatha...@googlemail.com a 
écrit :

> Super weird. I think it is a cython bug, but I'm not sure.
>
> The problem seems to be that the parent class has the same method. I need 
> to enforce the correct method
> by
>
> self.foo(u) -> SparseGraph.foo(self, u)
>
> This seems to work (compiles and the doctests pass).
>
> jonatha...@googlemail.com schrieb am Freitag, 8. Januar 2021 um 16:31:48 
> UTC+1:
>
>> Prepending 
>> # distutils: language = c++
>> to src/sage/graphs/base/sparse_graph.pyx makes my compilation crash.
>>
>> Does anyone know, how to fix it. I'm on develop and I'm getting the 
>> following compilation error. Does anyone know how to resolve this? Thank 
>> you.
>>
>> Jonathan
>>
>> (I want to see whether cpp set would be a reasonable alternative to our 
>> private tree implementation.)
>>
>> [sagelib-9.3.beta5] [3/3] gcc -Wno-unused-result -Wsign-compare -DNDEBUG 
>> -g -fwrapv -O3 -Wall -Wno-unused -march=native -O2 -g -march=native -O3 -g 
>> -fPIC -I./sage/data_structures 
>> -I/srv/public/kliem/sage/local/lib/python3.8/site-packages/cysignals 
>> -I./sage/cpython -Isage/data_structures 
>> -I/srv/public/kliem/sage/build/pkgs/sagelib/src 
>> -I/srv/public/kliem/sage/local/include/python3.8 
>> -I/srv/public/kliem/sage/local/lib/python3.8/site-packages/numpy/core/include
>>  
>> -Ibuild/cythonized -I/srv/public/kliem/sage/local/include/python3.8 -c 
>> build/cythonized/sage/graphs/base/sparse_graph.cpp -o 
>> build/temp.linux-x86_64-3.8/build/cythonized/sage/graphs/base/sparse_graph.o 
>> -fno-strict-aliasing -DCYTHON_CLINE_IN_TRACEBACK=1 -std=c++11
>> [sagelib-9.3.beta5] build/cythonized/sage/graphs/base/sparse_graph.cpp: 
>> In function ‘PyObject* 
>> __pyx_f_4sage_6graphs_4base_12sparse_graph_11SparseGraph_add_arc_label(__pyx_obj_4sage_6graphs_4base_12sparse_graph_SparseGraph*,
>>  
>> int, int, int, 
>> __pyx_opt_args_4sage_6graphs_4base_12sparse_graph_11SparseGraph_add_arc_label*)’:
>> [sagelib-9.3.beta5] 
>> build/cythonized/sage/graphs/base/sparse_graph.cpp:6543:94: error: cannot 
>> convert ‘__pyx_obj_4sage_6graphs_4base_7c_graph_CGraph*’ to 
>> ‘__pyx_obj_4sage_6graphs_4base_12sparse_graph_SparseGraph*’
>> [sagelib-9.3.beta5]__pyx_t_6 = 
>> __pyx_f_4sage_6graphs_4base_12sparse_graph_11SparseGraph_add_arc_label_unsafe(((struct
>>  
>> __pyx_obj_4sage_6graphs_4base_7c_graph_CGraph *)__pyx_v_self), __pyx_v_u, 
>> __pyx_v_v, __pyx_v_l); if (unlikely(__pyx_t_6 == ((int)-1))) __PYX_ERR(0, 
>> 917, __pyx_L1_error)
>> [sagelib-9.3.beta5]  
>> 
>> ~^
>> [sagelib-9.3.beta5] 
>> build/cythonized/sage/graphs/base/sparse_graph.cpp:6280:155: note:   
>> initializing argument 1 of ‘int 
>> __pyx_f_4sage_6graphs_4base_12sparse_graph_11SparseGraph_add_arc_label_unsafe(__pyx_obj_4sage_6graphs_4base_12sparse_graph_SparseGraph*,
>>  
>> int, int, int)’
>> [sagelib-9.3.beta5]  static int 
>> __pyx_f_4sage_6graphs_4base_12sparse_graph_11SparseGraph_add_arc_label_unsafe(struct
>>  
>> __pyx_obj_4sage_6graphs_4base_12sparse_graph_SparseGraph *__pyx_v_self, int 
>> __pyx_v_u, int __pyx_v_v, int __pyx_v_l) {
>> [sagelib-9.3.beta5]  
>>  
>> ~^~~~
>> [sagelib-9.3.beta5] build/cythonized/sage/graphs/base/sparse_graph.cpp: 
>> In function ‘PyObject* 
>> __pyx_pf_4sage_6graphs_4base_12sparse_graph_18SparseGraphBackend_4has_edge(__pyx_obj_4sage_6graphs_4base_12sparse_graph_SparseGraphBackend*,
>>  
>> PyObject*, PyObject*, PyObject*)’:
>> [sagelib-9.3.beta5] 
>> build/cythonized/sage/graphs/base/sparse_graph.cpp:10771:105: error: cannot 
>> convert ‘__pyx_obj_4sage_6graphs_4base_7c_graph_CGraphBackend*’ to 
>> ‘__pyx_obj_4sage_6graphs_4base_12sparse_graph_SparseGraphBackend*’
>> [sagelib-9.3.beta5]__pyx_t_2 = 
>> __pyx_f_4sage_6graphs_4base_12sparse_graph_18SparseGraphBackend__has_labeled_edge_unsafe(((struct
>>  
>> __pyx_obj_4sage_6graphs_4base_7c_graph_CGraphBackend *)__pyx_v_self), 
>> __pyx_v_u_int, __pyx_v_v_int, __pyx_v_l); if (unlikely(__pyx_t_2 == 
>> ((int)-1))) __PYX_ERR(0, 1348, __pyx_L1_error)
>> [sagelib-9.3.beta5]  
>>
>> ~^~~~
>> [sagelib-9.3.beta5] 
>> build/cythonized/sage/graphs/base/sparse_graph.cpp:2013:173: note:   
>> initializing argument 1 of ‘int 
>> __pyx_f_4sage_6graphs_4base_12sparse_graph_18SparseGraphBackend__has_labeled_edge_unsafe(__pyx_obj_4sage_6graphs_4base_12sparse_graph_SparseGraphBackend*,
>>  
>> int, int, PyObject*)’
>> 

Re: [sage-devel] error while installing python_igraph on fedora 32 - missing texttable

[David Coudert]

Thank you !

+1 to make it default, in particular since it's the last place it tries to 
download from.

Le mercredi 9 décembre 2020 à 12:21:13 UTC+1, dim...@gmail.com a écrit :

> On Wed, Dec 9, 2020 at 11:16 AM David Coudert  wrote:
> >
> > I just installed sagemath on a new desktop running fedora 32 and I'm now 
> trying to install python_igraph.
> >
> > Command 'sage -I python_igraph' failed because it is unable to download 
> dependency texttable-1.6.3.tar.gz (log file attached)
> > It tries to download it from mirrors (where it is not present) and not 
> from the upstream url that is indicated in 
> build/pkgs/texttable/checksums.ini
> > ===
> > tarball=texttable-VERSION.tar.gz
> > sha1=0b345a86669730f204804916e439820d06321223
> > md5=68e6b31d36f5c20221da7d5db3eca772
> > cksum=3865027881 <(386)%20502-7881>
> > upstream_url=
> https://pypi.io/packages/source/t/texttable/texttable-VERSION.tar.gz
> > ===
> >
> > I can download it manually from upstream url. I don't know how to fix 
> that.
>
> ./configure --enable-download-from-upstream-url
>
> (I don't see why we should not make this option default, at least for
> development work.)
>
> >
> >
> >
> >
> >
> >
> > --
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> an email to sage-devel+...@googlegroups.com.
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> .
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[sage-devel] error while installing python_igraph on fedora 32 - missing texttable

[David Coudert]

I just installed sagemath on a new desktop running fedora 32 and I'm now 
trying to install python_igraph.

Command 'sage -I python_igraph' failed because it is unable to download 
dependency texttable-1.6.3.tar.gz (log file attached)
It tries to download it from mirrors (where it is not present) and not from 
the upstream url that is indicated in build/pkgs/texttable/checksums.ini
===
tarball=texttable-VERSION.tar.gz
sha1=0b345a86669730f204804916e439820d06321223
md5=68e6b31d36f5c20221da7d5db3eca772
cksum=3865027881
upstream_url=https://pypi.io/packages/source/t/texttable/texttable-VERSION.tar.gz
===

I can download it manually from upstream url. I don't know how to fix that.






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Found local metadata for texttable-1.6.3
Attempting to download package texttable-1.6.3.tar.gz from mirrors
http://www-ftp.lip6.fr/pub/math/sagemath/spkg/upstream/texttable/texttable-1.6.3.tar.gz
[xx]
ERROR [transfer|run:135]: [Errno socket error] [Errno 404] Not Found: 
'//www-ftp.lip6.fr/pub/math/sagemath/spkg/upstream/texttable/texttable-1.6.3.tar.gz'
http://www.mirrorservice.org/sites/www.sagemath.org/spkg/upstream/texttable/texttable-1.6.3.tar.gz
[xx]
ERROR [transfer|run:135]: [Errno socket error] [Errno 404] Not Found: 
'//www.mirrorservice.org/sites/www.sagemath.org/spkg/upstream/texttable/texttable-1.6.3.tar.gz'
http://ftp.rediris.es/mirror/sagemath/spkg/upstream/texttable/texttable-1.6.3.tar.gz
[xx]
ERROR [transfer|run:135]: [Errno socket error] [Errno 404] Not Found: 
'//ftp.rediris.es/mirror/sagemath/spkg/upstream/texttable/texttable-1.6.3.tar.gz'
https://mirror.dogado.de/sage/spkg/upstream/texttable/texttable-1.6.3.tar.gz
[xx]
ERROR [transfer|run:135]: [Errno socket error] [Errno 404] Not Found: 
'//mirror.dogado.de/sage/spkg/upstream/texttable/texttable-1.6.3.tar.gz'
http://mirror.yandex.ru/mirrors/sage.math.washington.edu/spkg/upstream/texttable/texttable-1.6.3.tar.gz
[xx]
ERROR [transfer|run:135]: [Errno socket error] [Errno 404] Not Found: 
'//mirror.yandex.ru/mirrors/sage.math.washington.edu/spkg/upstream/texttable/texttable-1.6.3.tar.gz'
https://mirrors.up.pt/pub/sage/spkg/upstream/texttable/texttable-1.6.3.tar.gz
[xx]
ERROR [transfer|run:135]: [Errno socket error] [Errno 404] Not Found: 
'//mirrors.up.pt/pub/sage/spkg/upstream/texttable/texttable-1.6.3.tar.gz'
http://mirrors.mit.edu/sage/spkg/upstream/texttable/texttable-1.6.3.tar.gz
[xx]
ERROR [transfer|run:135]: [Errno socket error] [Errno 404] Not Found: 
'//mirrors.mit.edu/sage/spkg/upstream/texttable/texttable-1.6.3.tar.gz'
https://mirror.lyrahosting.com/sagemath/spkg/upstream/texttable/texttable-1.6.3.tar.gz
[xx]
ERROR [transfer|run:135]: [Errno socket error] [Errno 404] Not Found: 
'//mirror.lyrahosting.com/sagemath/spkg/upstream/texttable/texttable-1.6.3.tar.gz'
http://sage.mirror.garr.it/mirrors/sage/spkg/upstream/texttable/texttable-1.6.3.tar.gz
[xx]
ERROR [transfer|run:135]: [Errno socket error] [Errno 404] Not Found: 
'//sage.mirror.garr.it/mirrors/sage/spkg/upstream/texttable/texttable-1.6.3.tar.gz'
http://files.sagemath.org/spkg/upstream/texttable/texttable-1.6.3.tar.gz
[xx]
ERROR [transfer|run:135]: [Errno socket error] [Errno 404] Not Found: 
'//files.sagemath.org/spkg/upstream/texttable/texttable-1.6.3.tar.gz'
https://mirror.koddos.net/sagemath/spkg/upstream/texttable/texttable-1.6.3.tar.gz
[xx]
ERROR [transfer|run:135]: [Errno socket error] [Errno 404] Not Found: 
'//mirror.koddos.net/sagemath/spkg/upstream/texttable/texttable-1.6.3.tar.gz'
https://mirror.marwan.ma/sage/spkg/upstream/texttable/texttable-1.6.3.tar.gz
[xx]
ERROR [transfer|run:135]: [Errno socket error] [Errno 404] Not Found: 
'//mirror.marwan.ma/sage/spkg/upstream/texttable/texttable-1.6.3.tar.gz'
http://sagemath.mirror.ac.za/spkg/upstream/texttable/texttable-1.6.3.tar.gz

Re: [sage-devel] Changes to bitset.pxi

[David Coudert]

Most of the bitsets used in the graph backend are to record sets of seen or 
active vertices. These sets are not sparse.
But I think we have several places in the graph module where we use sets 
instead of bitsets for small number of vertices. Sparse bitsets could be 
useful in this case if effectively faster.


Le mercredi 23 septembre 2020 à 08:46:33 UTC+2, jonatha...@googlemail.com a 
écrit :

> Thanks. I still can only guess, if people care about large bitsets like 
> this.
>
> I can try to make it available with the same syntax and then however likes 
> it, can just use it.
>
> Sébastien Labbé schrieb am Dienstag, 22. September 2020 um 16:07:15 UTC+2:
>
>> Am I the only one using larger bitsets?
>>>
>>
>> Doing the following from SAGE_ROOT:
>>
>> git grep --name-only bitset
>>
>> shows that modules in sage using bitset are mostly graphs but also 
>> matroid, groups, combinat, data_structures, but also crypto, coding, misc 
>> and quivers. I don't know if those usage are for larger bitsets or not.
>>
>

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[sage-devel] Re: LOTS of tickets waiting for review

[David Coudert]

Anyone able to review #11736? It's a truly linear time implementation of 
Lex BFS.
I spent some time on the original paper to fully understand the algorithm 
(not well described) and find the issues in the original code. 

Le lundi 31 août 2020 à 19:05:13 UTC+2, Matthias Koeppe a écrit :

> On Saturday, August 15, 2020 at 3:11:18 PM UTC-7, Matthias Koeppe wrote:
>>
>> On Friday, August 14, 2020 at 6:49:44 AM UTC-7, Sébastien Labbé wrote:
>>>
>>> I made the size of list go from 130 to 120 this afternoon. Who can do 
>>> better?
>>>
>>
>> Thanks to everyone who helped bring this down to 100.
>>
>>
> 78 now.
>
>

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Re: [sage-devel] Need help in English, French, German, Japanese and Portuguese for 30212

[David Coudert]

anyone around you able to do the Japanese translation ? it's 2 lines...

Le lundi 31 août 2020 à 12:41:37 UTC+2, hel...@potuz.net a écrit :

>
>
> On August 31, 2020 7:10:35 AM GMT-03:00, David Coudert <
> david@gmail.com> wrote:
> >Ticket https://trac.sagemath.org/ticket/30212 touches tutorials in
> >English, 
> >French, German, Japanese, Portuguese.
> >We need reviewers for each of these languages.
> >I did tentative translations in German and Portuguese, but not in
> >Japanese.
> >
> >Thank you,
> >David.
> Portuguese is fine.
>
> R
>
> -- 
> Sent from my Android device with K-9 Mail. Please excuse my brevity.
>

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[sage-devel] Need help in English, French, German, Japanese and Portuguese for 30212

[David Coudert]

Ticket https://trac.sagemath.org/ticket/30212 touches tutorials in English, 
French, German, Japanese, Portuguese.
We need reviewers for each of these languages.
I did tentative translations in German and Portuguese, but not in Japanese.

Thank you,
David.

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[sage-devel] Re: Cplex installation (for beginners)

[David Coudert]

Perfect. Thank you.

Le jeudi 27 août 2020 à 17:00:14 UTC+2, Matthias Koeppe a écrit :

> On Thursday, August 27, 2020 at 4:44:07 AM UTC-7, David Coudert wrote:
>>
>> "sage -i sage_numerical_backends_cplex" is working well. Thank you.
>>
>> May be we should say that in the documentation of 
>> https://github.com/mkoeppe/sage-numerical-backends-cplex.
>>
>>
> I have already updated the README there - please take a look  
>

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[sage-devel] Re: Cplex installation (for beginners)

[David Coudert]

"sage -i sage_numerical_backends_cplex" is working well. Thank you.

May be we should say that in the documentation of 
https://github.com/mkoeppe/sage-numerical-backends-cplex.

Best,
David.

Le jeudi 27 août 2020 à 00:25:28 UTC+2, Matthias Koeppe a écrit :

> This package is also prepared as an optional sage package.
> "sage -i sage_numerical_backends_cplex" suffices. See 
> https://doc.sagemath.org/html/en/thematic_tutorials/linear_programming.html#solvers-backends
>
>
> On Wednesday, August 26, 2020 at 9:10:33 AM UTC-7, David Coudert wrote:
>>
>> Hello,
>>
>> I'm posting this here as it may help improving the documentation of sage 
>> math and the install guide of Cplex.
>>
>> A colleague (with very little system knowledge) just installed sagemath 
>> on his new macOS laptop using the  precompiled 
>> binary sage-9.1-OSX_10.15.4-x86_64.app.dmg.
>> He also installed Cplex Studio 12.10.
>> Then he followed the install guide of Cplex from 
>> https://github.com/mkoeppe/sage-numerical-backends-cplex and got the 
>> following error.
>> I don't know how to solve this issue.
>>
>> Any help is more than welcome :))
>>
>> Best,
>> David.
>>
>> =
>> aioli:~ nnisse$ sage -python -m pip install sage-numerical-backends-cplex
>> pip is configured with locations that require TLS/SSL, however the ssl 
>> module in Python is not available.
>> Collecting sage-numerical-backends-cplex
>>   Retrying (Retry(total=4, connect=None, read=None, redirect=None, 
>> status=None)) after connection broken by 'SSLError("Can't connect to HTTPS 
>> URL because the SSL module is not available.")': 
>> /simple/sage-numerical-backends-cplex/
>>   Retrying (Retry(total=3, connect=None, read=None, redirect=None, 
>> status=None)) after connection broken by 'SSLError("Can't connect to HTTPS 
>> URL because the SSL module is not available.")': 
>> /simple/sage-numerical-backends-cplex/
>>   Retrying (Retry(total=2, connect=None, read=None, redirect=None, 
>> status=None)) after connection broken by 'SSLError("Can't connect to HTTPS 
>> URL because the SSL module is not available.")': 
>> /simple/sage-numerical-backends-cplex/
>>   Retrying (Retry(total=1, connect=None, read=None, redirect=None, 
>> status=None)) after connection broken by 'SSLError("Can't connect to HTTPS 
>> URL because the SSL module is not available.")': 
>> /simple/sage-numerical-backends-cplex/
>>   Retrying (Retry(total=0, connect=None, read=None, redirect=None, 
>> status=None)) after connection broken by 'SSLError("Can't connect to HTTPS 
>> URL because the SSL module is not available.")': 
>> /simple/sage-numerical-backends-cplex/
>>   Could not fetch URL 
>> https://pypi.org/simple/sage-numerical-backends-cplex/: There was a 
>> problem confirming the ssl certificate: HTTPSConnectionPool(host='
>> pypi.org', port=443): Max retries exceeded with url: 
>> /simple/sage-numerical-backends-cplex/ (Caused by SSLError("Can't connect 
>> to HTTPS URL because the SSL module is not available.")) - skipping
>>   Could not find a version that satisfies the requirement 
>> sage-numerical-backends-cplex (from versions: )
>> No matching distribution found for sage-numerical-backends-cplex
>> pip is configured with locations that require TLS/SSL, however the ssl 
>> module in Python is not available.
>> Could not fetch URL https://pypi.org/simple/pip/: There was a problem 
>> confirming the ssl certificate: HTTPSConnectionPool(host='pypi.org', 
>> port=443): Max retries exceeded with url: /simple/pip/ (Caused by 
>> SSLError("Can't connect to HTTPS URL because the SSL module is not 
>> available.")) - skipping
>> =
>>
>

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Re: [sage-devel] Cplex installation (for beginners)

[David Coudert]

Xcode and home-brew are installed on that machine
We'll try tomorrow and tell you the result.
Thanks.

Le mercredi 26 août 2020 à 22:58:36 UTC+2, dim...@gmail.com a écrit :

>
>
> On Wed, 26 Aug 2020, 21:49 Zachary Scherr,  wrote:
>
>> I think you need to run:
>>
>> sage -i openssl
>> sage -f python3
>>
>> and then you should be able to add packages through pip. 
>>
>
> I would be surprised if this works on 
> a machine without Xcode installed.
>
>
>> On Wednesday, August 26, 2020 at 12:23:20 PM UTC-4 dim...@gmail.com 
>> wrote:
>>
>>> On Wed, Aug 26, 2020 at 5:10 PM David Coudert  
>>> wrote: 
>>> > 
>>> > Hello, 
>>> > 
>>> > I'm posting this here as it may help improving the documentation of 
>>> sage math and the install guide of Cplex. 
>>> > 
>>> > A colleague (with very little system knowledge) just installed 
>>> sagemath on his new macOS laptop using the precompiled binary 
>>> sage-9.1-OSX_10.15.4-x86_64.app.dmg. 
>>> > He also installed Cplex Studio 12.10. 
>>> > Then he followed the install guide of Cplex from 
>>> https://github.com/mkoeppe/sage-numerical-backends-cplex and got the 
>>> following error. 
>>> > I don't know how to solve this issue. 
>>> > 
>>> > Any help is more than welcome :)) 
>>> > 
>>> > Best, 
>>> > David. 
>>> > 
>>> > = 
>>> > aioli:~ nnisse$ sage -python -m pip install 
>>> sage-numerical-backends-cplex 
>>> > pip is configured with locations that require TLS/SSL, however the ssl 
>>> module in Python is not available. 
>>> 
>>>  
>>>
>>>
>>> this is the 1st problem to fix, by doing 
>>> "sage -i openssl pyopenssl" 
>>> and crossing your fingers... 
>>>
>>>
>>>
>>>
>>> > Collecting sage-numerical-backends-cplex 
>>> > Retrying (Retry(total=4, connect=None, read=None, redirect=None, 
>>> status=None)) after connection broken by 'SSLError("Can't connect to HTTPS 
>>> URL because the SSL module is not available.")': 
>>> /simple/sage-numerical-backends-cplex/ 
>>> > Retrying (Retry(total=3, connect=None, read=None, redirect=None, 
>>> status=None)) after connection broken by 'SSLError("Can't connect to HTTPS 
>>> URL because the SSL module is not available.")': 
>>> /simple/sage-numerical-backends-cplex/ 
>>> > Retrying (Retry(total=2, connect=None, read=None, redirect=None, 
>>> status=None)) after connection broken by 'SSLError("Can't connect to HTTPS 
>>> URL because the SSL module is not available.")': 
>>> /simple/sage-numerical-backends-cplex/ 
>>> > Retrying (Retry(total=1, connect=None, read=None, redirect=None, 
>>> status=None)) after connection broken by 'SSLError("Can't connect to HTTPS 
>>> URL because the SSL module is not available.")': 
>>> /simple/sage-numerical-backends-cplex/ 
>>> > Retrying (Retry(total=0, connect=None, read=None, redirect=None, 
>>> status=None)) after connection broken by 'SSLError("Can't connect to HTTPS 
>>> URL because the SSL module is not available.")': 
>>> /simple/sage-numerical-backends-cplex/ 
>>> > Could not fetch URL 
>>> https://pypi.org/simple/sage-numerical-backends-cplex/: There was a 
>>> problem confirming the ssl certificate: HTTPSConnectionPool(host='
>>> pypi.org', port=443): Max retries exceeded with url: 
>>> /simple/sage-numerical-backends-cplex/ (Caused by SSLError("Can't connect 
>>> to HTTPS URL because the SSL module is not available.")) - skipping 
>>> > Could not find a version that satisfies the requirement 
>>> sage-numerical-backends-cplex (from versions: ) 
>>> > No matching distribution found for sage-numerical-backends-cplex 
>>> > pip is configured with locations that require TLS/SSL, however the ssl 
>>> module in Python is not available. 
>>> > Could not fetch URL https://pypi.org/simple/pip/: There was a problem 
>>> confirming the ssl certificate: HTTPSConnectionPool(host='pypi.org', 
>>> port=443): Max retries exceeded with url: /simple/pip/ (Caused by 
>>> SSLError("Can't connect to HTTPS URL because the SSL module is not 
>>> available.")) - skipping 
>>> > = 
>

[sage-devel] Cplex installation (for beginners)

[David Coudert]

Hello,

I'm posting this here as it may help improving the documentation of sage 
math and the install guide of Cplex.

A colleague (with very little system knowledge) just installed sagemath on 
his new macOS laptop using the  precompiled 
binary sage-9.1-OSX_10.15.4-x86_64.app.dmg.
He also installed Cplex Studio 12.10.
Then he followed the install guide of Cplex 
from https://github.com/mkoeppe/sage-numerical-backends-cplex and got the 
following error.
I don't know how to solve this issue.

Any help is more than welcome :))

Best,
David.

=
aioli:~ nnisse$ sage -python -m pip install sage-numerical-backends-cplex
pip is configured with locations that require TLS/SSL, however the ssl 
module in Python is not available.
Collecting sage-numerical-backends-cplex
  Retrying (Retry(total=4, connect=None, read=None, redirect=None, 
status=None)) after connection broken by 'SSLError("Can't connect to HTTPS 
URL because the SSL module is not available.")': 
/simple/sage-numerical-backends-cplex/
  Retrying (Retry(total=3, connect=None, read=None, redirect=None, 
status=None)) after connection broken by 'SSLError("Can't connect to HTTPS 
URL because the SSL module is not available.")': 
/simple/sage-numerical-backends-cplex/
  Retrying (Retry(total=2, connect=None, read=None, redirect=None, 
status=None)) after connection broken by 'SSLError("Can't connect to HTTPS 
URL because the SSL module is not available.")': 
/simple/sage-numerical-backends-cplex/
  Retrying (Retry(total=1, connect=None, read=None, redirect=None, 
status=None)) after connection broken by 'SSLError("Can't connect to HTTPS 
URL because the SSL module is not available.")': 
/simple/sage-numerical-backends-cplex/
  Retrying (Retry(total=0, connect=None, read=None, redirect=None, 
status=None)) after connection broken by 'SSLError("Can't connect to HTTPS 
URL because the SSL module is not available.")': 
/simple/sage-numerical-backends-cplex/
  Could not fetch URL 
https://pypi.org/simple/sage-numerical-backends-cplex/: There was a problem 
confirming the ssl certificate: HTTPSConnectionPool(host='pypi.org', 
port=443): Max retries exceeded with url: 
/simple/sage-numerical-backends-cplex/ (Caused by SSLError("Can't connect 
to HTTPS URL because the SSL module is not available.")) - skipping
  Could not find a version that satisfies the requirement 
sage-numerical-backends-cplex (from versions: )
No matching distribution found for sage-numerical-backends-cplex
pip is configured with locations that require TLS/SSL, however the ssl 
module in Python is not available.
Could not fetch URL https://pypi.org/simple/pip/: There was a problem 
confirming the ssl certificate: HTTPSConnectionPool(host='pypi.org', 
port=443): Max retries exceeded with url: /simple/pip/ (Caused by 
SSLError("Can't connect to HTTPS URL because the SSL module is not 
available.")) - skipping
=

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[sage-devel] 2 issues with 9.2.beta3

[David Coudert]

Hello,

1) To be able to compile the documentation of 9.2.beta2, I had to "export 
LANG=C.UTF-8 "
See discussion here 
https://groups.google.com/forum/#!topic/sage-release/7wBxNRbJaaU 

But after "git pull" on develop branch to get 9.2.beta3, "make" fails 
quickly.
It indicates that language related variables were not properly sets.
So I started a new shell without  "export LANG=C.UTF-8 " and was able to 
complete "make build".
However, I'm unable to compile documentation. To compile it, I certainly 
need to "export LANG=C.UTF-8" as for 9.2.beta2.

I don't know how to get something consistent here.


2) With this working 9.2.beta3, I found 2 doctests errors in 
sage/graphs/connectivity.pyx (see below).
I can reproduce the errors inside the sage console.

Then I realized that I forgot to "source .homebrew-build-env" before "make 
build".
So I "source .homebrew-build-env" and now all tests pass (without extra 
"make build").


Let's hope we can fix these issues in a forthcoming release.

Best,
David.


sage -t src/sage/graphs/connectivity.pyx

**

File "src/sage/graphs/connectivity.pyx", line 2671, in 
sage.graphs.connectivity._Component.__init__

Failed example:

cython(os.linesep.join(cython_code))

Exception raised:

Traceback (most recent call last):

  File 
"/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/unixccompiler.py",
 
line 118, in _compile

extra_postargs)

  File 
"/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/ccompiler.py",
 
line 910, in spawn

spawn(cmd, dry_run=self.dry_run)

  File 
"/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/spawn.py",
 
line 36, in spawn

_spawn_posix(cmd, search_path, dry_run=dry_run)

  File 
"/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/spawn.py",
 
line 159, in _spawn_posix

% (cmd, exit_status))

distutils.errors.DistutilsExecError: command 'gcc' failed with exit 
status 1


During handling of the above exception, another exception occurred:


Traceback (most recent call last):

  File 
"/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage/misc/cython.py", 
line 371, in cython

dist.run_command("build")

  File 
"/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/dist.py",
 
line 985, in run_command

cmd_obj.run()

  File 
"/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/command/build.py",
 
line 135, in run

self.run_command(cmd_name)

  File 
"/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/cmd.py",
 
line 313, in run_command

self.distribution.run_command(command)

  File 
"/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/dist.py",
 
line 985, in run_command

cmd_obj.run()

  File 
"/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/command/build_ext.py",
 
line 340, in run

self.build_extensions()

  File 
"/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/command/build_ext.py",
 
line 449, in build_extensions

self._build_extensions_serial()

  File 
"/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/command/build_ext.py",
 
line 474, in _build_extensions_serial

self.build_extension(ext)

  File 
"/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/command/build_ext.py",
 
line 534, in build_extension

depends=ext.depends)

  File 
"/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/ccompiler.py",
 
line 574, in compile

self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)

  File 
"/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/unixccompiler.py",
 
line 120, in _compile

raise CompileError(msg)

distutils.errors.CompileError: command 'gcc' failed with exit status 1


During handling of the above exception, another exception occurred:


Traceback (most recent call last):

  File 
"/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py",
 
line 707, in _run

self.compile_and_execute(example, compiler, test.globs)

  File 
"/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py",
 
line 1131, in compile_and_execute

exec(compiled, globs)

  File "", 
line 1, in 

cython(os.linesep.join(cython_code))

  File 

Re: [sage-devel] Re: Error with Pynac when building sage9.2.beta1

[David Coudert]

it’s working. Thank you !

Let’s hope it’s the only issue ;)
David.

> Le 16 juin 2020 à 13:24, Matthias Koeppe  a écrit :
> 
> Try again after
> 
> source /Users/dcoudert/sage/.homebrew-build-env 
> 
> 
> 
> On Tuesday, June 16, 2020 at 12:32:14 AM UTC-7 david@inria.fr wrote:
> I have a compilation error with Pynac when trying building sage9.2.beta1 
> after a `make distclean`. See attached log file.
> 
> It's on macOS mojave 10.14.6, and I have gmp installed by homebrew.
> 
> Help is more than welcome ;)
> Thanks.
> David.
> 
> 
> 
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David Coudert
Equipe-Projet COATI
Centre de Recherche INRIA Sophia Antipolis - Méditerranée
Université Côte d’Azur, Inria, CNRS, I3S, France
http://www-sop.inria.fr/members/David.Coudert

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[sage-devel] Error with Pynac when building sage9.2.beta1

[David Coudert]

I have a compilation error with Pynac when trying building sage9.2.beta1 
after a `make distclean`. See attached log file.

It's on macOS mojave 10.14.6, and I have gmp installed by homebrew.

Help is more than welcome ;)
Thanks.
David.


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Found local metadata for pynac-0.7.26.sage-2020-04-03
Attempting to download package pynac-0.7.26.sage-2020-04-03.tar.bz2 from mirrors
http://ftp.ntua.gr/pub/sagemath/spkg/upstream/pynac/pynac-0.7.26.sage-2020-04-03.tar.bz2
[..]
pynac-0.7.26.sage-2020-04-03

Setting up build directory for pynac-0.7.26.sage-2020-04-03
Finished extraction
No patch files found in ../patches

Host system:
Darwin confetti 18.7.0 Darwin Kernel Version 18.7.0: Thu Jun 20 18:42:21 PDT 
2019; root:xnu-4903.270.47~4/RELEASE_X86_64 x86_64

C compiler: gcc
C compiler version:
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr 
--with-gxx-include-dir=/usr/include/c++/4.2.1
Apple clang version 11.0.0 (clang-1100.0.33.17)
Target: x86_64-apple-darwin18.7.0
Thread model: posix
InstalledDir: 
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

Package 'pynac' is currently not installed
No legacy uninstaller found for 'pynac'; nothing to do
Starting build...
Running build_pynac...
Configuring pynac-0.7.26.sage-2020-04-03
configure: WARNING: unrecognized options: --disable-maintainer-mode
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether sage-python23 version is >= 2.7... yes
checking for sage-python23 version... 3.7
checking for sage-python23 platform... darwin
checking for sage-python23 script directory... 
${prefix}/lib/python3.7/site-packages
checking for sage-python23 extension module directory... 
${exec_prefix}/lib/python3.7/site-packages
checking for Python preprocessor flags... 
-I/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m
 
-I/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m
 -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic 
-DNDEBUG -g -fwrapv -O3 -Wall -isysroot 
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk 
-I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include 
-I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers
checking for Python library flags... -bundle -undefined dynamic_lookup 
-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk 
-L/Users/dcoudert/sage/local/lib -Wl,-rpath,/Users/dcoudert/sage/local/lib
checking build system type... x86_64-apple-darwin18.7.0
checking host system type... x86_64-apple-darwin18.7.0
checking for Cygwin... 
checking whether make supports nested variables... (cached) yes
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++11 accepts -g... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of g++ -std=gnu++11... none
checking how to run the C++ preprocessor... g++ -std=gnu++11 -E
checking how to print strings... printf
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... rm: conftest.dSYM: is a 
directory
yes
checking dependency style of gcc... none
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... 
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld
checking if the linker 

[sage-devel] Bug in is_line_graph()

[David Coudert]

Bernard Lidicky reported me the following issue with method is_line_graph.
I don't know how to fix that and I opened ticket 
https://trac.sagemath.org/ticket/29740

sage: g = Graph('O{e[{}^~z`MDZBZBkXzE^')

sage: g.is_line_graph()

---

Exception Traceback (most recent call last)

 in ()

> 1 g.is_line_graph()


/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage/graphs/
line_graph.pyx in sage.graphs.line_graph.is_line_graph (build/cythonized/
sage/graphs/line_graph.c:2286)()

*220* if g.is_connected():

*221* try:

--> 222 R, isom = root_graph(g)

*223* if certificate:

*224* return True, R, isom

/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage/graphs/
line_graph.pyx in sage.graphs.line_graph.root_graph (build/cythonized/sage/
graphs/line_graph.c:7147)()

*621*

*622* if not is_isom:

--> 623 raise Exception(error_message)

*624*

*625* return R, isom

Exception: It looks like there is a problem somewhere. Youfound a bug here ! 
Please report it on sage-devel,our google group !


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Re: [sage-devel] Re: A possible defect in hypergraph generator of Graph module

[David Coudert]

there is another issue with `vertices = range(nverts)`. Should be `vertices 
= list(range(nverts))` as vertices is used twice.

Have you already opened a ticket ?

Le mercredi 22 avril 2020 07:11:00 UTC+2, Dima Pasechnik a écrit :
>
> On Wed, Apr 22, 2020 at 10:59 AM John H Palmieri  > wrote: 
> > 
> > 
> > 
> > On Tuesday, April 21, 2020 at 5:26:00 PM UTC-7, Dima Pasechnik wrote: 
> >> 
> >> On Wed, Apr 22, 2020 at 2:56 AM k2wagle  wrote: 
> >> > 
> >> > Tried this just now, getting the same error. Open a ticket please. 
> >> 
> >> This error is already in Sage 9.0 - and this is an example from the 
> manual! 
> >> 
> >> It's quite alarming that our doctests let it through, as it never 
> >> showed in doctests, and 
> >> indeed if I do 
> >> 
> >> ./sage -tp --verbose src/sage/graphs/hypergraph_generators.py 
> >> 
> >> I see in particular 
> >> --- 
> >> Trying (line 218):H = hypergraphs.UniformRandomUniform(52, 3, 17) 
> >> Expecting nothing 
> >> ok [0.01 s] 
> >> Trying (line 219):H 
> >> Expecting: 
> >> Incidence structure with 52 points and 17 blocks 
> >> ok [0.00 s] 
> >> - 
> >> 
> >> as if it works. 
> > 
> > 
> > Maybe it is working: maybe there is something in the doctesting 
> framework that makes it work somehow. If I put obviously failing doctests 
> in that file immediately before and after these lines, those failures are 
> caught. It's very strange. 
> > 
> > To fix this particular problem, do something like: 
> > 
> > diff --git a/src/sage/graphs/hypergraph_generators.py 
> b/src/sage/graphs/hypergraph_generators.py 
> > index aa3d5e3988..679ddea5ce 100644 
> > --- a/src/sage/graphs/hypergraph_generators.py 
> > +++ b/src/sage/graphs/hypergraph_generators.py 
> > @@ -262,7 +262,7 @@ class HypergraphGenerators(): 
> >  raise ValueError("the uniformity should be an integer") 
> >  all_edges = Subsets(vertices, uniformity) 
> >  try: 
> > -edges = sample(all_edges, m) 
> > +edges = sample(set(all_edges), m) 
>
> this is very inefficient for large all_edges. 
> all_edges is a kind of iterator, so there is really no need to build 
> this list fully. 
> Something like 
>
> edges=list(map(lambda t: all_edges[t], sample(range(len(all_edges)),m))) 
>
> is much more optimal. 
>
>
> >  except OverflowError: 
> >  raise OverflowError("binomial({}, {}) too large to be 
> treated".format(n, k)) 
> >  except ValueError: 
> > 
> > 
> >> 
> >> 
> >> 
> >> 
> >> > 
> >> > On Tuesday, 21 April 2020 23:56:45 UTC+5:30, Vipul Gupta wrote: 
> >> >> 
> >> >> On running the example given here in the documentation of 
> `UniformRandomUniform` method. 
> >> >> It is raising the following error. 
> >> >> 
> >> >> sage: H = hypergraphs.UniformRandomUniform(52, 3, 17) 
> >> >> 
> --- 
> >> >> TypeError Traceback (most recent 
> call last) 
> >> >>  in () 
> >> >> > 1 H = hypergraphs.UniformRandomUniform(Integer(52), 
> Integer(3), Integer(17)) 
> >> >> 
> >> >> 
> /home/vipul/sage/local/lib/python3.7/site-packages/sage/graphs/hypergraph_generators.py
>  
> in UniformRandomUniform(self, n, k, m) 
> >> >> 263 all_edges = Subsets(vertices, uniformity) 
> >> >> 264 try: 
> >> >> --> 265 edges = sample(all_edges, m) 
> >> >> 266 except OverflowError: 
> >> >> 267 raise OverflowError("binomial({}, {}) too large 
> to be treated".format(n, k)) 
> >> >> 
> >> >> 
> /home/vipul/sage/local/lib/python3.7/site-packages/sage/misc/prandom.py in 
> sample(population, k) 
> >> >> 178 [357009070, 558990255, 196187132, 752551188, 
> 85926697, 954621491, 624802848] 
> >> >> 179 """ 
> >> >> --> 180 return _pyrand().sample(population, k) 
> >> >> 181 
> >> >> 182 def random(): 
> >> >> 
> >> >> /home/vipul/sage/local/lib/python3.7/random.py in sample(self, 
> population, k) 
> >> >> 315 population = tuple(population) 
> >> >> 316 if not isinstance(population, _Sequence): 
> >> >> --> 317 raise TypeError("Population must be a sequence 
> or set.  For dicts, use list(d).") 
> >> >> 318 randbelow = self._randbelow 
> >> >> 319 n = len(population) 
> >> >> 
> >> >> TypeError: Population must be a sequence or set.  For dicts, use 
> list(d). 
> >> >> 
> >> >> 
> >> >> 
> >> >> Can somebody please point out if I am doing something wrong. 
> >> >> Or Should I open a ticket on trac server regarding this, so that 
> this defect can be solved. 
> >> >> 
> >> >> Regards 
> >> >> Vipul Gupta 
> >> >> 
> >> >> 
> >> >> 
> >> > -- 
> >> > You received this message because you are subscribed to the Google 
> Groups "sage-devel" group. 
> >> > To unsubscribe from this group and stop receiving emails from it, 
> send an email to 

Re: [sage-devel] Re: archlinux: some system package not recognized

[David Coudert]

> Le 15 avr. 2020 à 16:41, Dima Pasechnik  a écrit :
> 
> You need to copy/symlink all these m4 files.
> Spicifically, you seems to have forgotten lib-link.m4, which contains
> the definition of AC_LIB_RPATH
> you see the error about.

Right. thank you. 

This way it’s much better and after .configure, I get

config.status: creating directory local/var/lib/sage/installed
configure: notice: the following SPKGs did not find equivalent system packages: 
flintqs gf2x gp2c libsemigroups nauty pari_elldata pari_galpol pari_nftables 
pari_seadata perl_term_readline_gnu
checking for the package system in use... homebrew
configure: No equivalent system packages for homebrew are known to Sage


The last part is curious...

I will follow #29504 <https://trac.sagemath.org/ticket/29504> 

> 
> On Wed, Apr 15, 2020 at 10:19 PM David Coudert  wrote:
>> 
>> 
>> 
>> Le 15 avr. 2020 à 15:50, Dima Pasechnik  a écrit :
>> 
>> On Wed, Apr 15, 2020 at 7:13 PM David Coudert  wrote:
>> 
>> 
>> 
>> 
>> Le 15 avr. 2020 à 12:40, Dima Pasechnik  a écrit :
>> 
>> On Wed, Apr 15, 2020 at 6:22 PM David Coudert  wrote:
>> 
>> 
>> I tried that already, but:
>> 
>> confetti:sage dcoudert$ brew install gettext
>> Warning: gettext 0.20.1 is already installed and up-to-date
>> To reinstall 0.20.1, run `brew reinstall gettext`
>> confetti:sage dcoudert$ brew link --force gettext
>> Warning: Refusing to link macOS provided/shadowed software: gettext
>> If you need to have gettext first in your PATH run:
>> echo 'export PATH="/usr/local/opt/gettext/bin:$PATH"' >> ~/.bash_profile
>> 
>> For compilers to find gettext you may need to set:
>> export LDFLAGS="-L/usr/local/opt/gettext/lib"
>> export CPPFLAGS="-I/usr/local/opt/gettext/include"
>> 
>> 
>> this is not enough, as you need m4 macros that come with gettext, in
>> particular iconv.m4
>> I am not sure where brew installes them exactly, but probably
>> somewhere under /usr/local/opt/gettext/
>> Probably /usr/local/opt/gettext/share/aclocal
>> but you can find it by running
>> 
>> find /usr/local/opt/ -name iconv.m4
>> 
>> and then
>> 
>> export M4PATH=$M4PATH:/usr/local/opt/gettext/share/aclocal # (or
>> whatever the correct value of the directory is)
>> ./bootstrap
>> 
>> PS. Homebrew should get a bug report on this, I gather…
>> 
>> 
>> not working :((
>> 
>> confetti:sage dcoudert$ ll /usr/local/opt/gettext/share/aclocal/
>> total 280
>> -rw-r--r--  1 dcoudert  staff  14483 12 mai  2019 gettext.m4
>> -rw-r--r--  1 dcoudert  staff  21489 12 mai  2019 host-cpu-c-abi.m4
>> -rw-r--r--  1 dcoudert  staff   9731 12 mai  2019 iconv.m4
>> -rw-r--r--  1 dcoudert  staff   3321 12 mai  2019 intlmacosx.m4
>> -rw-r--r--  1 dcoudert  staff   5370 12 mai  2019 lib-ld.m4
>> -rw-r--r--  1 dcoudert  staff  32772 15 avr 09:35 lib-link.m4
>> -rw-r--r--  1 dcoudert  staff   9680 15 avr 09:35 lib-prefix.m4
>> -rw-r--r--  1 dcoudert  staff   1229 12 mai  2019 nls.m4
>> -rw-r--r--  1 dcoudert  staff  18831 12 mai  2019 po.m4
>> -rw-r--r--  1 dcoudert  staff   3092 12 mai  2019 progtest.m4
>> confetti:sage dcoudert$ export 
>> M4PATH=$M4PATH:/usr/local/opt/gettext/share/aclocal/
>> 
>> 
>> maybe it should not have / at the end?
>> 
>> Anyway, I presume you can just copy or symlink these files to
>> /usr/local/share/aclocal
>> and try ./bootstrap again
>> 
>> 
>> 
>> I tried that and it’s not better
>> 
>> confetti:sage dcoudert$ ./bootstrap
>> rm -rf config configure build/make/Makefile-auto.in
>> rm -f src/doc/en/installation/*.txt
>> src/doc/bootstrap:48: installing src/doc/en/installation/arch.txt and 
>> src/doc/en/installation/arch-optional.txt
>> src/doc/bootstrap:48: installing src/doc/en/installation/debian.txt and 
>> src/doc/en/installation/debian-optional.txt
>> src/doc/bootstrap:48: installing src/doc/en/installation/fedora.txt and 
>> src/doc/en/installation/fedora-optional.txt
>> src/doc/bootstrap:48: installing src/doc/en/installation/cygwin.txt and 
>> src/doc/en/installation/cygwin-optional.txt
>> bootstrap:69: installing 'config/config.rpath'
>> m4/sage_spkg_configures.m4:103: warning: AC_LIB_RPATH is m4_require'd but 
>> not m4_defun'd
>> /usr/local/share/aclocal/iconv.m4:19: AM_ICONV_LINKFLAGS_BODY is expanded 
>> from...
>> /usr/local/share/aclocal/iconv.m4:226: AM_ICONV_LINK is expanded from...
>> ../../lib/m4sugar/m4sh.m4:643: AS_IF is expanded from...
>> ../../lib

Re: [sage-devel] Re: archlinux: some system package not recognized

[David Coudert]

> Le 15 avr. 2020 à 15:50, Dima Pasechnik  a écrit :
> 
> On Wed, Apr 15, 2020 at 7:13 PM David Coudert  <mailto:david.coud...@inria.fr>> wrote:
>> 
>> 
>> 
>> Le 15 avr. 2020 à 12:40, Dima Pasechnik  a écrit :
>> 
>> On Wed, Apr 15, 2020 at 6:22 PM David Coudert  wrote:
>> 
>> 
>> I tried that already, but:
>> 
>> confetti:sage dcoudert$ brew install gettext
>> Warning: gettext 0.20.1 is already installed and up-to-date
>> To reinstall 0.20.1, run `brew reinstall gettext`
>> confetti:sage dcoudert$ brew link --force gettext
>> Warning: Refusing to link macOS provided/shadowed software: gettext
>> If you need to have gettext first in your PATH run:
>> echo 'export PATH="/usr/local/opt/gettext/bin:$PATH"' >> ~/.bash_profile
>> 
>> For compilers to find gettext you may need to set:
>> export LDFLAGS="-L/usr/local/opt/gettext/lib"
>> export CPPFLAGS="-I/usr/local/opt/gettext/include"
>> 
>> 
>> this is not enough, as you need m4 macros that come with gettext, in
>> particular iconv.m4
>> I am not sure where brew installes them exactly, but probably
>> somewhere under /usr/local/opt/gettext/
>> Probably /usr/local/opt/gettext/share/aclocal
>> but you can find it by running
>> 
>> find /usr/local/opt/ -name iconv.m4
>> 
>> and then
>> 
>> export M4PATH=$M4PATH:/usr/local/opt/gettext/share/aclocal # (or
>> whatever the correct value of the directory is)
>> ./bootstrap
>> 
>> PS. Homebrew should get a bug report on this, I gather…
>> 
>> 
>> not working :((
>> 
>> confetti:sage dcoudert$ ll /usr/local/opt/gettext/share/aclocal/
>> total 280
>> -rw-r--r--  1 dcoudert  staff  14483 12 mai  2019 gettext.m4
>> -rw-r--r--  1 dcoudert  staff  21489 12 mai  2019 host-cpu-c-abi.m4
>> -rw-r--r--  1 dcoudert  staff   9731 12 mai  2019 iconv.m4
>> -rw-r--r--  1 dcoudert  staff   3321 12 mai  2019 intlmacosx.m4
>> -rw-r--r--  1 dcoudert  staff   5370 12 mai  2019 lib-ld.m4
>> -rw-r--r--  1 dcoudert  staff  32772 15 avr 09:35 lib-link.m4
>> -rw-r--r--  1 dcoudert  staff   9680 15 avr 09:35 lib-prefix.m4
>> -rw-r--r--  1 dcoudert  staff   1229 12 mai  2019 nls.m4
>> -rw-r--r--  1 dcoudert  staff  18831 12 mai  2019 po.m4
>> -rw-r--r--  1 dcoudert  staff   3092 12 mai  2019 progtest.m4
>> confetti:sage dcoudert$ export 
>> M4PATH=$M4PATH:/usr/local/opt/gettext/share/aclocal/
> 
> maybe it should not have / at the end?
> 
> Anyway, I presume you can just copy or symlink these files to
> /usr/local/share/aclocal
> and try ./bootstrap again
> 


I tried that and it’s not better

confetti:sage dcoudert$ ./bootstrap 
rm -rf config configure build/make/Makefile-auto.in
rm -f src/doc/en/installation/*.txt
src/doc/bootstrap:48: installing src/doc/en/installation/arch.txt and 
src/doc/en/installation/arch-optional.txt
src/doc/bootstrap:48: installing src/doc/en/installation/debian.txt and 
src/doc/en/installation/debian-optional.txt
src/doc/bootstrap:48: installing src/doc/en/installation/fedora.txt and 
src/doc/en/installation/fedora-optional.txt
src/doc/bootstrap:48: installing src/doc/en/installation/cygwin.txt and 
src/doc/en/installation/cygwin-optional.txt
bootstrap:69: installing 'config/config.rpath'
m4/sage_spkg_configures.m4:103: warning: AC_LIB_RPATH is m4_require'd but not 
m4_defun'd
/usr/local/share/aclocal/iconv.m4:19: AM_ICONV_LINKFLAGS_BODY is expanded 
from...
/usr/local/share/aclocal/iconv.m4:226: AM_ICONV_LINK is expanded from...
../../lib/m4sugar/m4sh.m4:643: AS_IF is expanded from...
../../lib/m4sugar/m4sh.m4:643: AS_IF is expanded from...
../../lib/m4sugar/m4sh.m4:643: AS_IF is expanded from...
m4/sage_spkg_collect.m4:310: SAGE_SPKG_COLLECT is expanded from...
m4/sage_spkg_configures.m4:103: the top level
m4/sage_spkg_configures.m4:103: warning: AC_LIB_RPATH is m4_require'd but not 
m4_defun'd
/usr/local/share/aclocal/iconv.m4:19: AM_ICONV_LINKFLAGS_BODY is expanded 
from...
/usr/local/share/aclocal/iconv.m4:226: AM_ICONV_LINK is expanded from...
../../lib/m4sugar/m4sh.m4:643: AS_IF is expanded from...
../../lib/m4sugar/m4sh.m4:643: AS_IF is expanded from...
../../lib/m4sugar/m4sh.m4:643: AS_IF is expanded from...
m4/sage_spkg_collect.m4:310: SAGE_SPKG_COLLECT is expanded from...
m4/sage_spkg_configures.m4:103: the top level
m4/sage_spkg_configures.m4:103: warning: AC_LIB_RPATH is m4_require'd but not 
m4_defun'd
aclocal.m4:41: AM_ICONV_LINKFLAGS_BODY is expanded from...
aclocal.m4:248: AM_ICONV_LINK is expanded from...
../../lib/m4sugar/m4sh.m4:643: AS_IF is expanded from...
../../lib/m4sugar/m4sh.m4:643: AS_IF is expanded from...
../../lib/m4sugar/m4sh.m4:643: AS_IF is expanded from...
m4/s

Re: [sage-devel] Re: archlinux: some system package not recognized

[David Coudert]

> Le 15 avr. 2020 à 12:40, Dima Pasechnik  a écrit :
> 
> On Wed, Apr 15, 2020 at 6:22 PM David Coudert  <mailto:david.coud...@inria.fr>> wrote:
>> 
>> I tried that already, but:
>> 
>> confetti:sage dcoudert$ brew install gettext
>> Warning: gettext 0.20.1 is already installed and up-to-date
>> To reinstall 0.20.1, run `brew reinstall gettext`
>> confetti:sage dcoudert$ brew link --force gettext
>> Warning: Refusing to link macOS provided/shadowed software: gettext
>> If you need to have gettext first in your PATH run:
>>  echo 'export PATH="/usr/local/opt/gettext/bin:$PATH"' >> ~/.bash_profile
>> 
>> For compilers to find gettext you may need to set:
>>  export LDFLAGS="-L/usr/local/opt/gettext/lib"
>>  export CPPFLAGS="-I/usr/local/opt/gettext/include"
> 
> this is not enough, as you need m4 macros that come with gettext, in
> particular iconv.m4
> I am not sure where brew installes them exactly, but probably
> somewhere under /usr/local/opt/gettext/
> Probably /usr/local/opt/gettext/share/aclocal
> but you can find it by running
> 
> find /usr/local/opt/ -name iconv.m4
> 
> and then
> 
> export M4PATH=$M4PATH:/usr/local/opt/gettext/share/aclocal # (or
> whatever the correct value of the directory is)
> ./bootstrap
> 
> PS. Homebrew should get a bug report on this, I gather…

not working :((

confetti:sage dcoudert$ ll /usr/local/opt/gettext/share/aclocal/
total 280
-rw-r--r--  1 dcoudert  staff  14483 12 mai  2019 gettext.m4
-rw-r--r--  1 dcoudert  staff  21489 12 mai  2019 host-cpu-c-abi.m4
-rw-r--r--  1 dcoudert  staff   9731 12 mai  2019 iconv.m4
-rw-r--r--  1 dcoudert  staff   3321 12 mai  2019 intlmacosx.m4
-rw-r--r--  1 dcoudert  staff   5370 12 mai  2019 lib-ld.m4
-rw-r--r--  1 dcoudert  staff  32772 15 avr 09:35 lib-link.m4
-rw-r--r--  1 dcoudert  staff   9680 15 avr 09:35 lib-prefix.m4
-rw-r--r--  1 dcoudert  staff   1229 12 mai  2019 nls.m4
-rw-r--r--  1 dcoudert  staff  18831 12 mai  2019 po.m4
-rw-r--r--  1 dcoudert  staff   3092 12 mai  2019 progtest.m4
confetti:sage dcoudert$ export 
M4PATH=$M4PATH:/usr/local/opt/gettext/share/aclocal/
confetti:sage dcoudert$ ./bootstrap 
rm -rf config configure build/make/Makefile-auto.in
rm -f src/doc/en/installation/*.txt
src/doc/bootstrap:48: installing src/doc/en/installation/arch.txt and 
src/doc/en/installation/arch-optional.txt
src/doc/bootstrap:48: installing src/doc/en/installation/debian.txt and 
src/doc/en/installation/debian-optional.txt
src/doc/bootstrap:48: installing src/doc/en/installation/fedora.txt and 
src/doc/en/installation/fedora-optional.txt
src/doc/bootstrap:48: installing src/doc/en/installation/cygwin.txt and 
src/doc/en/installation/cygwin-optional.txt
bootstrap:69: installing 'config/config.rpath'
build/pkgs/iconv/spkg-configure.m4:2: warning: macro 'AM_ICONV' not found in 
library
configure.ac:336: installing 'config/compile'
configure.ac:113: installing 'config/config.guess'
configure.ac:113: installing 'config/config.sub'
configure.ac:68: installing 'config/install-sh'
configure.ac:68: installing 'config/missing'
configure:20606: error: possibly undefined macro: AM_ICONV
  If this token and others are legitimate, please use m4_pattern_allow.
  See the Autoconf documentation.







> 
>> 
>> 
>> 
>> even setting the LDFLAGS and CPPFLAGS, I still get
>> Checking whether SageMath should install SPKG iconv...
>> ./configure: line 20606: AM_ICONV: command not found
>> configure: no suitable system package found for SPKG iconv
>> 
>> 
>> I can work with that for now.
>> 
>> Best,
>> David.
>> 
>> 
>> Le 15 avr. 2020 à 12:00, Dima Pasechnik  a écrit :
>> 
>> On Wed, Apr 15, 2020 at 5:33 PM David Coudert  wrote:
>> 
>> 
>> it gives the following. Not clear to me.
>> 
>> confetti:sage dcoudert$ ./bootstrap
>> rm -rf config configure build/make/Makefile-auto.in
>> rm -f src/doc/en/installation/*.txt
>> src/doc/bootstrap:48: installing src/doc/en/installation/arch.txt and 
>> src/doc/en/installation/arch-optional.txt
>> src/doc/bootstrap:48: installing src/doc/en/installation/debian.txt and 
>> src/doc/en/installation/debian-optional.txt
>> src/doc/bootstrap:48: installing src/doc/en/installation/fedora.txt and 
>> src/doc/en/installation/fedora-optional.txt
>> src/doc/bootstrap:48: installing src/doc/en/installation/cygwin.txt and 
>> src/doc/en/installation/cygwin-optional.txt
>> bootstrap:69: installing 'config/config.rpath'
>> build/pkgs/iconv/spkg-configure.m4:2: warning: macro 'AM_ICONV' not found in 
>> library
>> configure.ac:336: installing 'config/compile'
>> configure.ac:113: installing 'config/co

Re: [sage-devel] Re: archlinux: some system package not recognized

[David Coudert]

I tried that already, but:

confetti:sage dcoudert$ brew install gettext
Warning: gettext 0.20.1 is already installed and up-to-date
To reinstall 0.20.1, run `brew reinstall gettext`
confetti:sage dcoudert$ brew link --force gettext
Warning: Refusing to link macOS provided/shadowed software: gettext
If you need to have gettext first in your PATH run:
  echo 'export PATH="/usr/local/opt/gettext/bin:$PATH"' >> ~/.bash_profile

For compilers to find gettext you may need to set:
  export LDFLAGS="-L/usr/local/opt/gettext/lib"
  export CPPFLAGS="-I/usr/local/opt/gettext/include"



even setting the LDFLAGS and CPPFLAGS, I still get
Checking whether SageMath should install SPKG iconv...
./configure: line 20606: AM_ICONV: command not found
configure: no suitable system package found for SPKG iconv


I can work with that for now.

Best,
David.


> Le 15 avr. 2020 à 12:00, Dima Pasechnik  a écrit :
> 
> On Wed, Apr 15, 2020 at 5:33 PM David Coudert  <mailto:david.coud...@inria.fr>> wrote:
>> 
>> it gives the following. Not clear to me.
>> 
>> confetti:sage dcoudert$ ./bootstrap
>> rm -rf config configure build/make/Makefile-auto.in
>> rm -f src/doc/en/installation/*.txt
>> src/doc/bootstrap:48: installing src/doc/en/installation/arch.txt and 
>> src/doc/en/installation/arch-optional.txt
>> src/doc/bootstrap:48: installing src/doc/en/installation/debian.txt and 
>> src/doc/en/installation/debian-optional.txt
>> src/doc/bootstrap:48: installing src/doc/en/installation/fedora.txt and 
>> src/doc/en/installation/fedora-optional.txt
>> src/doc/bootstrap:48: installing src/doc/en/installation/cygwin.txt and 
>> src/doc/en/installation/cygwin-optional.txt
>> bootstrap:69: installing 'config/config.rpath'
>> build/pkgs/iconv/spkg-configure.m4:2: warning: macro 'AM_ICONV' not found in 
>> library
>> configure.ac:336: installing 'config/compile'
>> configure.ac:113: installing 'config/config.guess'
>> configure.ac:113: installing 'config/config.sub'
>> configure.ac:68: installing 'config/install-sh'
>> configure.ac:68: installing 'config/missing'
>> configure:20606: error: possibly undefined macro: AM_ICONV
>>  If this token and others are legitimate, please use m4_pattern_allow.
>>  See the Autoconf documentation.
> 
> internet says that you need
> 
> brew Install gettext
> brew link --force gettext
> 
> 
> 
>> confetti:sage dcoudert$
>> 
>> 
>> Le 15 avr. 2020 à 11:26, David Coudert  a écrit :
>> 
>> no. I will try that.
>> David.
>> 
>> Le 15 avr. 2020 à 11:24, Dima Pasechnik  a écrit :
>> 
>> On Wed, Apr 15, 2020 at 4:58 PM David Coudert  wrote:
>> 
>> 
>> unfortunately not.
>> I installed gettext with brew some time ago now and added 
>> /usr/local/opt/gettext/bin to my PATH, but it’s not working.
>> 
>> did you re-run
>> 
>> ./bootstrap
>> 
>> ?
>> 
>> Checking whether SageMath should install SPKG iconv...
>> ./configure: line 20606: AM_ICONV: command not found
>> configure: no suitable system package found for SPKG iconv
>> 
>> 
>> 
>> Le 15 avr. 2020 à 03:06, Dima Pasechnik  a écrit :
>> 
>> On Wed, Apr 15, 2020 at 2:22 AM David Coudert  wrote:
>> 
>> 
>> 
>> 
>> Le 14 avr. 2020 à 18:15, John H Palmieri  a écrit :
>> 
>> I would suggest two things:
>> 
>>  $ brew install pkg-config
>> 
>> and then before building Sage, while in SAGE_ROOT:
>> 
>>  $ source .homebrew-build-env
>> 
>> Then try ./configure to see what it says at the end about system packages.
>> 
>> 
>> 
>> I installed some more packages and did what you proposed.
>> I still get issues with pari / flint and so all related packages.
>> 
>> configure: notice: the following SPKGs did not find equivalent system 
>> packages: arb brial cddlib cliquer eclib ecm fflas_ffpack flint flintqs 
>> fplll gf2x givaro gp2c iconv lcalc libatomic_ops libbraiding libsemigroups 
>> lrcalc m4rie nauty pari pari_elldata pari_galdata pari_galpol pari_nftables 
>> pari_seadata pari_seadata_small perl_term_readline_gnu planarity r rw 
>> symmetrica tachyon
>> checking for the package system in use... homebrew
>> configure: hint: installing the following system packages is recommended and 
>> may avoid building some of the above SPKGs from source:
>> configure:   $ brew install r
>> 
>> I also have an issue with AM_ICONV, although I have gettext (with path in 
>> $PATH), readline (recognized) and libiconv.
>> Checking whether SageMath should 

Re: [sage-devel] Re: archlinux: some system package not recognized

[David Coudert]

it gives the following. Not clear to me.

confetti:sage dcoudert$ ./bootstrap 
rm -rf config configure build/make/Makefile-auto.in
rm -f src/doc/en/installation/*.txt
src/doc/bootstrap:48: installing src/doc/en/installation/arch.txt and 
src/doc/en/installation/arch-optional.txt
src/doc/bootstrap:48: installing src/doc/en/installation/debian.txt and 
src/doc/en/installation/debian-optional.txt
src/doc/bootstrap:48: installing src/doc/en/installation/fedora.txt and 
src/doc/en/installation/fedora-optional.txt
src/doc/bootstrap:48: installing src/doc/en/installation/cygwin.txt and 
src/doc/en/installation/cygwin-optional.txt
bootstrap:69: installing 'config/config.rpath'
build/pkgs/iconv/spkg-configure.m4:2: warning: macro 'AM_ICONV' not found in 
library
configure.ac:336: installing 'config/compile'
configure.ac:113: installing 'config/config.guess'
configure.ac:113: installing 'config/config.sub'
configure.ac:68: installing 'config/install-sh'
configure.ac:68: installing 'config/missing'
configure:20606: error: possibly undefined macro: AM_ICONV
  If this token and others are legitimate, please use m4_pattern_allow.
  See the Autoconf documentation.
confetti:sage dcoudert$ 


> Le 15 avr. 2020 à 11:26, David Coudert  a écrit :
> 
> no. I will try that.
> David.
> 
>> Le 15 avr. 2020 à 11:24, Dima Pasechnik > <mailto:dimp...@gmail.com>> a écrit :
>> 
>> On Wed, Apr 15, 2020 at 4:58 PM David Coudert > <mailto:david.coud...@inria.fr>> wrote:
>>> 
>>> unfortunately not.
>>> I installed gettext with brew some time ago now and added 
>>> /usr/local/opt/gettext/bin to my PATH, but it’s not working.
>>> 
>> did you re-run
>> 
>> ./bootstrap
>> 
>> ?
>>> Checking whether SageMath should install SPKG iconv...
>>> ./configure: line 20606: AM_ICONV: command not found
>>> configure: no suitable system package found for SPKG iconv
>>> 
>>> 
>>> 
>>> Le 15 avr. 2020 à 03:06, Dima Pasechnik >> <mailto:dimp...@gmail.com>> a écrit :
>>> 
>>> On Wed, Apr 15, 2020 at 2:22 AM David Coudert >> <mailto:david.coud...@inria.fr>> wrote:
>>> 
>>> 
>>> 
>>> 
>>> Le 14 avr. 2020 à 18:15, John H Palmieri >> <mailto:jhpalmier...@gmail.com>> a écrit :
>>> 
>>> I would suggest two things:
>>> 
>>>   $ brew install pkg-config
>>> 
>>> and then before building Sage, while in SAGE_ROOT:
>>> 
>>>   $ source .homebrew-build-env
>>> 
>>> Then try ./configure to see what it says at the end about system packages.
>>> 
>>> 
>>> 
>>> I installed some more packages and did what you proposed.
>>> I still get issues with pari / flint and so all related packages.
>>> 
>>> configure: notice: the following SPKGs did not find equivalent system 
>>> packages: arb brial cddlib cliquer eclib ecm fflas_ffpack flint flintqs 
>>> fplll gf2x givaro gp2c iconv lcalc libatomic_ops libbraiding libsemigroups 
>>> lrcalc m4rie nauty pari pari_elldata pari_galdata pari_galpol pari_nftables 
>>> pari_seadata pari_seadata_small perl_term_readline_gnu planarity r rw 
>>> symmetrica tachyon
>>> checking for the package system in use... homebrew
>>> configure: hint: installing the following system packages is recommended 
>>> and may avoid building some of the above SPKGs from source:
>>> configure:   $ brew install r
>>> 
>>> I also have an issue with AM_ICONV, although I have gettext (with path in 
>>> $PATH), readline (recognized) and libiconv.
>>> Checking whether SageMath should install SPKG iconv...
>>> ./configure: line 20606: AM_ICONV: command not found
>>> configure: no suitable system package found for SPKG iconv
>>> 
>>> 
>>> AM_ICONV is a part of gettext
>>> 
>>> brew install gettext
>>> 
>>> should fix it.
>>> 
>>> 
>>> Don’t know how to fix that.
>>> I think it’s currently why r is not accepted.
>>> 
>>> Best,
>>> David.
>>> 
>>> 
>>> 
>>> On Tuesday, April 14, 2020 at 6:21:40 AM UTC-7, David Coudert wrote:
>>> 
>>> 
>>> I assume there is nothing simple I can do to fix this.
>>> Thanks,
>>> David.
>>> 
>>> Le 14 avr. 2020 à 15:09, Dima Pasechnik >> <http://gmail.com/>> a écrit :
>>> 
>>> On Tue, Apr 14, 2020 at 8:41 PM David Coudert >> <http://inria.fr/>> wrote:
>>> 
>>> 
>

Re: [sage-devel] Re: archlinux: some system package not recognized

[David Coudert]

no. I will try that.
David.

> Le 15 avr. 2020 à 11:24, Dima Pasechnik  a écrit :
> 
> On Wed, Apr 15, 2020 at 4:58 PM David Coudert  <mailto:david.coud...@inria.fr>> wrote:
>> 
>> unfortunately not.
>> I installed gettext with brew some time ago now and added 
>> /usr/local/opt/gettext/bin to my PATH, but it’s not working.
>> 
> did you re-run
> 
> ./bootstrap
> 
> ?
>> Checking whether SageMath should install SPKG iconv...
>> ./configure: line 20606: AM_ICONV: command not found
>> configure: no suitable system package found for SPKG iconv
>> 
>> 
>> 
>> Le 15 avr. 2020 à 03:06, Dima Pasechnik  a écrit :
>> 
>> On Wed, Apr 15, 2020 at 2:22 AM David Coudert  wrote:
>> 
>> 
>> 
>> 
>> Le 14 avr. 2020 à 18:15, John H Palmieri  a écrit :
>> 
>> I would suggest two things:
>> 
>>   $ brew install pkg-config
>> 
>> and then before building Sage, while in SAGE_ROOT:
>> 
>>   $ source .homebrew-build-env
>> 
>> Then try ./configure to see what it says at the end about system packages.
>> 
>> 
>> 
>> I installed some more packages and did what you proposed.
>> I still get issues with pari / flint and so all related packages.
>> 
>> configure: notice: the following SPKGs did not find equivalent system 
>> packages: arb brial cddlib cliquer eclib ecm fflas_ffpack flint flintqs 
>> fplll gf2x givaro gp2c iconv lcalc libatomic_ops libbraiding libsemigroups 
>> lrcalc m4rie nauty pari pari_elldata pari_galdata pari_galpol pari_nftables 
>> pari_seadata pari_seadata_small perl_term_readline_gnu planarity r rw 
>> symmetrica tachyon
>> checking for the package system in use... homebrew
>> configure: hint: installing the following system packages is recommended and 
>> may avoid building some of the above SPKGs from source:
>> configure:   $ brew install r
>> 
>> I also have an issue with AM_ICONV, although I have gettext (with path in 
>> $PATH), readline (recognized) and libiconv.
>> Checking whether SageMath should install SPKG iconv...
>> ./configure: line 20606: AM_ICONV: command not found
>> configure: no suitable system package found for SPKG iconv
>> 
>> 
>> AM_ICONV is a part of gettext
>> 
>> brew install gettext
>> 
>> should fix it.
>> 
>> 
>> Don’t know how to fix that.
>> I think it’s currently why r is not accepted.
>> 
>> Best,
>> David.
>> 
>> 
>> 
>> On Tuesday, April 14, 2020 at 6:21:40 AM UTC-7, David Coudert wrote:
>> 
>> 
>> I assume there is nothing simple I can do to fix this.
>> Thanks,
>> David.
>> 
>> Le 14 avr. 2020 à 15:09, Dima Pasechnik  a écrit :
>> 
>> On Tue, Apr 14, 2020 at 8:41 PM David Coudert  wrote:
>> 
>> 
>> I have similar issues on osx.
>> 
>> I installed several packages using brew. Some of them are recognized, but 
>> not some others.
>> I suspect that I'm missing some dependencies, and possibly some environment 
>> variables.
>> 
>> For instance, I installed amp, mpfr, mpir, ntl and flint, and flint is the 
>> only one not accepted. Why ?
>> 
>> I have also an issue with readline. I'm unable to tell sage that it has been 
>> installed with brew :(
>> 
>> Any advise is more than welcome.
>> Best,
>> David.
>> 
>> -
>> 
>> Checking whether SageMath should install SPKG mpfr...
>> 
>> checking installing gmp/mpir? ... no
>> 
>> checking mpfr.h usability... yes
>> 
>> checking mpfr.h presence... yes
>> 
>> checking for mpfr.h... yes
>> 
>> checking for library containing mpfr_free_pool... -lmpfr
>> 
>> configure: will use system package and not install SPKG mpfr
>> 
>> using mpfr library from the system
>> 
>> -
>> 
>> Checking whether SageMath should install SPKG ntl...
>> 
>> checking installing gmp/mpir? ... no
>> 
>> checking NTL/ZZ.h usability... yes
>> 
>> checking NTL/ZZ.h presence... yes
>> 
>> checking for NTL/ZZ.h... yes
>> 
>> checking whether we can link a program using NTL... yes
>> 
>> checking NTL version >= 10.3... 11.4.3
>> 
>> configure: will use system package and not install SPKG ntl
>> 
>> using ntl library from the system
>> 
>> --

Re: [sage-devel] Re: archlinux: some system package not recognized

[David Coudert]

unfortunately not. 
I installed gettext with brew some time ago now and added 
/usr/local/opt/gettext/bin to my PATH, but it’s not working.

Checking whether SageMath should install SPKG iconv...
./configure: line 20606: AM_ICONV: command not found
configure: no suitable system package found for SPKG iconv



> Le 15 avr. 2020 à 03:06, Dima Pasechnik  a écrit :
> 
> On Wed, Apr 15, 2020 at 2:22 AM David Coudert  <mailto:david.coud...@inria.fr>> wrote:
>> 
>> 
>> 
>> Le 14 avr. 2020 à 18:15, John H Palmieri  a écrit :
>> 
>> I would suggest two things:
>> 
>>$ brew install pkg-config
>> 
>> and then before building Sage, while in SAGE_ROOT:
>> 
>>$ source .homebrew-build-env
>> 
>> Then try ./configure to see what it says at the end about system packages.
>> 
>> 
>> 
>> I installed some more packages and did what you proposed.
>> I still get issues with pari / flint and so all related packages.
>> 
>> configure: notice: the following SPKGs did not find equivalent system 
>> packages: arb brial cddlib cliquer eclib ecm fflas_ffpack flint flintqs 
>> fplll gf2x givaro gp2c iconv lcalc libatomic_ops libbraiding libsemigroups 
>> lrcalc m4rie nauty pari pari_elldata pari_galdata pari_galpol pari_nftables 
>> pari_seadata pari_seadata_small perl_term_readline_gnu planarity r rw 
>> symmetrica tachyon
>> checking for the package system in use... homebrew
>> configure: hint: installing the following system packages is recommended and 
>> may avoid building some of the above SPKGs from source:
>> configure:   $ brew install r
>> 
>> I also have an issue with AM_ICONV, although I have gettext (with path in 
>> $PATH), readline (recognized) and libiconv.
>> Checking whether SageMath should install SPKG iconv...
>> ./configure: line 20606: AM_ICONV: command not found
>> configure: no suitable system package found for SPKG iconv
> 
> AM_ICONV is a part of gettext
> 
> brew install gettext
> 
> should fix it.
> 
>> 
>> Don’t know how to fix that.
>> I think it’s currently why r is not accepted.
>> 
>> Best,
>> David.
>> 
>> 
>> 
>> On Tuesday, April 14, 2020 at 6:21:40 AM UTC-7, David Coudert wrote:
>>> 
>>> I assume there is nothing simple I can do to fix this.
>>> Thanks,
>>> David.
>>> 
>>> Le 14 avr. 2020 à 15:09, Dima Pasechnik  a écrit :
>>> 
>>> On Tue, Apr 14, 2020 at 8:41 PM David Coudert  wrote:
>>> 
>>> 
>>> I have similar issues on osx.
>>> 
>>> I installed several packages using brew. Some of them are recognized, but 
>>> not some others.
>>> I suspect that I'm missing some dependencies, and possibly some environment 
>>> variables.
>>> 
>>> For instance, I installed amp, mpfr, mpir, ntl and flint, and flint is the 
>>> only one not accepted. Why ?
>>> 
>>> I have also an issue with readline. I'm unable to tell sage that it has 
>>> been installed with brew :(
>>> 
>>> Any advise is more than welcome.
>>> Best,
>>> David.
>>> 
>>> -
>>> 
>>> Checking whether SageMath should install SPKG mpfr...
>>> 
>>> checking installing gmp/mpir? ... no
>>> 
>>> checking mpfr.h usability... yes
>>> 
>>> checking mpfr.h presence... yes
>>> 
>>> checking for mpfr.h... yes
>>> 
>>> checking for library containing mpfr_free_pool... -lmpfr
>>> 
>>> configure: will use system package and not install SPKG mpfr
>>> 
>>> using mpfr library from the system
>>> 
>>> -
>>> 
>>> Checking whether SageMath should install SPKG ntl...
>>> 
>>> checking installing gmp/mpir? ... no
>>> 
>>> checking NTL/ZZ.h usability... yes
>>> 
>>> checking NTL/ZZ.h presence... yes
>>> 
>>> checking for NTL/ZZ.h... yes
>>> 
>>> checking whether we can link a program using NTL... yes
>>> 
>>> checking NTL version >= 10.3... 11.4.3
>>> 
>>> configure: will use system package and not install SPKG ntl
>>> 
>>> using ntl library from the system
>>> 
>>> -
>>> 
>>> Checking whether SageMath should install

Re: [sage-devel] Re: archlinux: some system package not recognized

[David Coudert]

> Le 14 avr. 2020 à 18:15, John H Palmieri  a écrit :
> 
> I would suggest two things:
> 
> $ brew install pkg-config
> 
> and then before building Sage, while in SAGE_ROOT:
> 
> $ source .homebrew-build-env
> 
> Then try ./configure to see what it says at the end about system packages.


I installed some more packages and did what you proposed.
I still get issues with pari / flint and so all related packages.

configure: notice: the following SPKGs did not find equivalent system packages: 
arb brial cddlib cliquer eclib ecm fflas_ffpack flint flintqs fplll gf2x givaro 
gp2c iconv lcalc libatomic_ops libbraiding libsemigroups lrcalc m4rie nauty 
pari pari_elldata pari_galdata pari_galpol pari_nftables pari_seadata 
pari_seadata_small perl_term_readline_gnu planarity r rw symmetrica tachyon
checking for the package system in use... homebrew
configure: hint: installing the following system packages is recommended and 
may avoid building some of the above SPKGs from source:
configure:   $ brew install r

I also have an issue with AM_ICONV, although I have gettext (with path in 
$PATH), readline (recognized) and libiconv.
Checking whether SageMath should install SPKG iconv...
./configure: line 20606: AM_ICONV: command not found
configure: no suitable system package found for SPKG iconv

Don’t know how to fix that. 
I think it’s currently why r is not accepted.

Best,
David.

> 
> 
> On Tuesday, April 14, 2020 at 6:21:40 AM UTC-7, David Coudert wrote:
> I assume there is nothing simple I can do to fix this.
> Thanks,
> David.
> 
>> Le 14 avr. 2020 à 15:09, Dima Pasechnik > a écrit :
>> 
>> On Tue, Apr 14, 2020 at 8:41 PM David Coudert > wrote:
>>> 
>>> I have similar issues on osx.
>>> 
>>> I installed several packages using brew. Some of them are recognized, but 
>>> not some others.
>>> I suspect that I'm missing some dependencies, and possibly some environment 
>>> variables.
>>> 
>>> For instance, I installed amp, mpfr, mpir, ntl and flint, and flint is the 
>>> only one not accepted. Why ?
>>> 
>>> I have also an issue with readline. I'm unable to tell sage that it has 
>>> been installed with brew :(
>>> 
>>> Any advise is more than welcome.
>>> Best,
>>> David.
>>> 
>>> -
>>> 
>>> Checking whether SageMath should install SPKG mpfr...
>>> 
>>> checking installing gmp/mpir? ... no
>>> 
>>> checking mpfr.h usability... yes
>>> 
>>> checking mpfr.h presence... yes
>>> 
>>> checking for mpfr.h... yes
>>> 
>>> checking for library containing mpfr_free_pool... -lmpfr
>>> 
>>> configure: will use system package and not install SPKG mpfr
>>> 
>>> using mpfr library from the system
>>> 
>>> -
>>> 
>>> Checking whether SageMath should install SPKG ntl...
>>> 
>>> checking installing gmp/mpir? ... no
>>> 
>>> checking NTL/ZZ.h usability... yes
>>> 
>>> checking NTL/ZZ.h presence... yes
>>> 
>>> checking for NTL/ZZ.h... yes
>>> 
>>> checking whether we can link a program using NTL... yes
>>> 
>>> checking NTL version >= 10.3... 11.4.3
>>> 
>>> configure: will use system package and not install SPKG ntl
>>> 
>>> using ntl library from the system
>>> 
>>> -
>>> 
>>> Checking whether SageMath should install SPKG flint...
>>> 
>>> checking installing mpfr or ntl? ... checking flint/flint.h usability... yes
>>> 
>>> checking flint/flint.h presence... yes
>>> 
>>> checking for flint/flint.h... yes
>>> 
>>> checking for library containing fmpz_mat_is_hadamard... -lflint
>>> 
>>> checking for library containing fmpz_poly_get_ZZX... no
>>> 
>>> configure: no suitable system package found for SPKG flint
>>> 
>>> using Sage's flint SPKG
>>> 
>> 
>> Apparently in your Arch Flint is not linked with NTL, while this is a
>> requirement for it to be
>> in useful in Sage.
>> 
>> E.g. that's on Debian:
>> 
>> dimpase@penguin:~/sage$ ldd /usr/lib/x86_64-linux-gnu/libflint-arb.so
>> linux-vdso.so.1 (0x7fff6a5fe000)
>> libflint-2.5.2.so <http://libflint-2.5.2.so/> => /usr/lib/libflint-2.5.

Re: [sage-devel] Re: archlinux: some system package not recognized

[David Coudert]

I assume there is nothing simple I can do to fix this.
Thanks,
David.

> Le 14 avr. 2020 à 15:09, Dima Pasechnik  a écrit :
> 
> On Tue, Apr 14, 2020 at 8:41 PM David Coudert  wrote:
>> 
>> I have similar issues on osx.
>> 
>> I installed several packages using brew. Some of them are recognized, but 
>> not some others.
>> I suspect that I'm missing some dependencies, and possibly some environment 
>> variables.
>> 
>> For instance, I installed amp, mpfr, mpir, ntl and flint, and flint is the 
>> only one not accepted. Why ?
>> 
>> I have also an issue with readline. I'm unable to tell sage that it has been 
>> installed with brew :(
>> 
>> Any advise is more than welcome.
>> Best,
>> David.
>> 
>> -
>> 
>> Checking whether SageMath should install SPKG mpfr...
>> 
>> checking installing gmp/mpir? ... no
>> 
>> checking mpfr.h usability... yes
>> 
>> checking mpfr.h presence... yes
>> 
>> checking for mpfr.h... yes
>> 
>> checking for library containing mpfr_free_pool... -lmpfr
>> 
>> configure: will use system package and not install SPKG mpfr
>> 
>> using mpfr library from the system
>> 
>> -
>> 
>> Checking whether SageMath should install SPKG ntl...
>> 
>> checking installing gmp/mpir? ... no
>> 
>> checking NTL/ZZ.h usability... yes
>> 
>> checking NTL/ZZ.h presence... yes
>> 
>> checking for NTL/ZZ.h... yes
>> 
>> checking whether we can link a program using NTL... yes
>> 
>> checking NTL version >= 10.3... 11.4.3
>> 
>> configure: will use system package and not install SPKG ntl
>> 
>> using ntl library from the system
>> 
>> -
>> 
>> Checking whether SageMath should install SPKG flint...
>> 
>> checking installing mpfr or ntl? ... checking flint/flint.h usability... yes
>> 
>> checking flint/flint.h presence... yes
>> 
>> checking for flint/flint.h... yes
>> 
>> checking for library containing fmpz_mat_is_hadamard... -lflint
>> 
>> checking for library containing fmpz_poly_get_ZZX... no
>> 
>> configure: no suitable system package found for SPKG flint
>> 
>> using Sage's flint SPKG
>> 
> 
> Apparently in your Arch Flint is not linked with NTL, while this is a
> requirement for it to be
> in useful in Sage.
> 
> E.g. that's on Debian:
> 
> dimpase@penguin:~/sage$ ldd /usr/lib/x86_64-linux-gnu/libflint-arb.so
> linux-vdso.so.1 (0x7fff6a5fe000)
> libflint-2.5.2.so => /usr/lib/libflint-2.5.2.so (0x7d084386d000)
> libmpfr.so.6 => /usr/lib/x86_64-linux-gnu/libmpfr.so.6 (0x7d08437eb000)
> libgmp.so.10 => /usr/lib/x86_64-linux-gnu/libgmp.so.10 (0x7d0843768000)
> libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x7d08435e5000)
> libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x7d08435c4000)
> libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x7d0843403000)
> /lib64/ld-linux-x86-64.so.2 (0x7d0843e39000)
> libntl.so.35 => /usr/lib/libntl.so.35 (0x7d0842fd2000)
> libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 
> (0x7d0842e4e000)
> libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x7d0842e34000)
> libgf2x.so.1 => /usr/lib/x86_64-linux-gnu/libgf2x.so.1 (0x7d0842c26000)
> 
> So you see libntl there.
> 
> 
> 
> 
>> -
>> 
>> 
>> 
>> 
>> 
>> 
>> Le jeudi 19 mars 2020 14:52:46 UTC+1, vdelecroix a écrit :
>>> 
>>> Dear all,
>>> 
>>> Thanks to hard work it is now possible to use some package from
>>> the system! That is great! But on my archlinux computer that also
>>> has sage installed from the package manager the following
>>> packages are still detected has "to be installed"
>>> 
>>> * eclib-20190909
>>> * givaro-4.1.1
>>> * lcalc-1.23.p19
>>> * pari-2.11.2
>>> * pari_galdata-20080411.p0
>>> * pari_seadata_small-20090618.p0
>>> 
>>> The relevant package in archlinux I have are
>>> 
>>> * community/eclib 20190909-8
>>> * community/givaro 4.1.1-1
>>> * community/lcalc 1.23-19
>>> * community/pari 2.11.3-2
>>> * community/pari-galdata 2008

[sage-devel] Re: archlinux: some system package not recognized

[David Coudert]

I have similar issues on osx.

I installed several packages using brew. Some of them are recognized, but 
not some others.
I suspect that I'm missing some dependencies, and possibly some environment 
variables.

For instance, I installed amp, mpfr, mpir, ntl and flint, and flint is the 
only one not accepted. Why ?

I have also an issue with readline. I'm unable to tell sage that it has 
been installed with brew :(

Any advise is more than welcome.
Best,
David.

-

Checking whether SageMath should install SPKG mpfr...

checking installing gmp/mpir? ... no

checking mpfr.h usability... yes

checking mpfr.h presence... yes

checking for mpfr.h... yes

checking for library containing mpfr_free_pool... -lmpfr

configure: will use system package and not install SPKG mpfr

using mpfr library from the system

-

Checking whether SageMath should install SPKG ntl...

checking installing gmp/mpir? ... no

checking NTL/ZZ.h usability... yes

checking NTL/ZZ.h presence... yes

checking for NTL/ZZ.h... yes

checking whether we can link a program using NTL... yes

checking NTL version >= 10.3... 11.4.3

configure: will use system package and not install SPKG ntl

using ntl library from the system

-

Checking whether SageMath should install SPKG flint...

checking installing mpfr or ntl? ... checking flint/flint.h usability... yes

checking flint/flint.h presence... yes

checking for flint/flint.h... yes

checking for library containing fmpz_mat_is_hadamard... -lflint

checking for library containing fmpz_poly_get_ZZX... no

configure: no suitable system package found for SPKG flint

using Sage's flint SPKG

-





Le jeudi 19 mars 2020 14:52:46 UTC+1, vdelecroix a écrit :
>
> Dear all, 
>
> Thanks to hard work it is now possible to use some package from 
> the system! That is great! But on my archlinux computer that also 
> has sage installed from the package manager the following 
> packages are still detected has "to be installed" 
>
> * eclib-20190909 
> * givaro-4.1.1 
> * lcalc-1.23.p19 
> * pari-2.11.2 
> * pari_galdata-20080411.p0 
> * pari_seadata_small-20090618.p0 
>
> The relevant package in archlinux I have are 
>
> * community/eclib 20190909-8 
> * community/givaro 4.1.1-1 
> * community/lcalc 1.23-19 
> * community/pari 2.11.3-2 
> * community/pari-galdata 20080411-2 
> * community/pari-seadata-small 20090618-2 
>
> Should I suspect that something is wrong with the Sage 
> configure scripts? Or that something is wrong with the packages 
> from archlinux? 
>
> Best 
> Vincent 
>

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Re: [sage-devel] 9.1.beta0: issue with sage-numerical-backends-gurobi

[David Coudert]

Done. This is now issue #1

Le samedi 11 janvier 2020 11:19:23 UTC+1, Dima Pasechnik a écrit :
>
>
>
> On Sat, 11 Jan 2020, 10:14 David Coudert,  > wrote:
>
>> I have an error when trying to install the gurobi backend that is now a 
>> separate optional package.
>> I followed the instructions for installing the gurobi backend with sage 
>> 9.1.beta0 and macOS Mojave 10.14.6.
>> I have gurobi 8.11 and gurobi.sh is in my path (so no need to set 
>> GUROBI_HOME).
>> (note that I successfully installed the cplex backend).
>>
>> Should I report this issue directly on 
>> https://github.com/mkoeppe/sage-numerical-backends-gurobi ?
>>
>
> it would help if you copied this report there too.
>
>>
>> confetti:sage dcoudert$ ./sage -python -m pip install 
>> sage-numerical-backends-gurobi
>>
>> Collecting sage-numerical-backends-gurobi
>>
>>   Downloading 
>> https://files.pythonhosted.org/packages/2c/5c/e1532bb6cde28cf86ebffd408ccb500d7b846bc29bbd1c5e479a2f18acb6/sage_numerical_backends_gurobi-9.0b12.tar.gz
>>
>> Requirement already satisfied: sphinx in 
>> ./local/lib/python3.7/site-packages (from sage-numerical-backends-gurobi) 
>> (1.8.5)
>>
>> Requirement already satisfied: six>=1.5 in 
>> ./local/lib/python3.7/site-packages (from 
>> sphinx->sage-numerical-backends-gurobi) (1.12.0)
>>
>> Requirement already satisfied: Jinja2>=2.3 in 
>> ./local/lib/python3.7/site-packages (from 
>> sphinx->sage-numerical-backends-gurobi) (2.10)
>>
>> Requirement already satisfied: Pygments>=2.0 in 
>> ./local/lib/python3.7/site-packages (from 
>> sphinx->sage-numerical-backends-gurobi) (2.3.1)
>>
>> Requirement already satisfied: docutils>=0.11 in 
>> ./local/lib/python3.7/site-packages (from 
>> sphinx->sage-numerical-backends-gurobi) (0.14)
>>
>> Requirement already satisfied: snowballstemmer>=1.1 in 
>> ./local/lib/python3.7/site-packages (from 
>> sphinx->sage-numerical-backends-gurobi) (1.2.1)
>>
>> Requirement already satisfied: babel!=2.0,>=1.3 in 
>> ./local/lib/python3.7/site-packages (from 
>> sphinx->sage-numerical-backends-gurobi) (2.6.0)
>>
>> Requirement already satisfied: alabaster<0.8,>=0.7 in 
>> ./local/lib/python3.7/site-packages (from 
>> sphinx->sage-numerical-backends-gurobi) (0.7.12)
>>
>> Requirement already satisfied: imagesize in 
>> ./local/lib/python3.7/site-packages (from 
>> sphinx->sage-numerical-backends-gurobi) (1.1.0)
>>
>> Requirement already satisfied: requests>=2.0.0 in 
>> ./local/lib/python3.7/site-packages (from 
>> sphinx->sage-numerical-backends-gurobi) (2.13.0)
>>
>> Requirement already satisfied: setuptools in 
>> ./local/lib/python3.7/site-packages (from 
>> sphinx->sage-numerical-backends-gurobi) (40.6.3)
>>
>> Requirement already satisfied: packaging in 
>> ./local/lib/python3.7/site-packages (from 
>> sphinx->sage-numerical-backends-gurobi) (18.0)
>>
>> Requirement already satisfied: sphinxcontrib-websupport in 
>> ./local/lib/python3.7/site-packages (from 
>> sphinx->sage-numerical-backends-gurobi) (1.1.0)
>>
>> Requirement already satisfied: MarkupSafe>=0.23 in 
>> ./local/lib/python3.7/site-packages (from 
>> Jinja2>=2.3->sphinx->sage-numerical-backends-gurobi) (1.1.0)
>>
>> Requirement already satisfied: pytz>=0a in 
>> ./local/lib/python3.7/site-packages (from 
>> babel!=2.0,>=1.3->sphinx->sage-numerical-backends-gurobi) (2018.7)
>>
>> Requirement already satisfied: pyparsing>=2.0.2 in 
>> ./local/lib/python3.7/site-packages (from 
>> packaging->sphinx->sage-numerical-backends-gurobi) (2.3.0)
>>
>> Installing collected packages: sage-numerical-backends-gurobi
>>
>>   Running setup.py install for sage-numerical-backends-gurobi ... error
>>
>> Complete output from command /Users/dcoudert/sage/local/bin/python3 
>> -u -c "import setuptools, 
>> tokenize;__file__='/private/var/folders/l8/sxf193t11mvdyqq56f4w_6_8gn/T/pip-install-t4k429rc/sage-numerical-backends-gurobi/setup.py';f=getattr(tokenize,
>>  
>> 'open', open)(__file__);code=f.read().replace('\r\n', 
>> '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record 
>> /private/var/folders/l8/sxf193t11mvdyqq56f4w_6_8gn/T/pip-record-sk9om1cp/install-record.txt
>>  
>> --single-version-externally-managed --compile:
>>
>> Using GUROBI_HOME obtained from gurobi.sh:
>>
>>

[sage-devel] 9.1.beta0: issue with sage-numerical-backends-gurobi

[David Coudert]

I have an error when trying to install the gurobi backend that is now a 
separate optional package.
I followed the instructions for installing the gurobi backend with sage 
9.1.beta0 and macOS Mojave 10.14.6.
I have gurobi 8.11 and gurobi.sh is in my path (so no need to set 
GUROBI_HOME).
(note that I successfully installed the cplex backend).

Should I report this issue directly 
on https://github.com/mkoeppe/sage-numerical-backends-gurobi ?

confetti:sage dcoudert$ ./sage -python -m pip install 
sage-numerical-backends-gurobi

Collecting sage-numerical-backends-gurobi

  Downloading 
https://files.pythonhosted.org/packages/2c/5c/e1532bb6cde28cf86ebffd408ccb500d7b846bc29bbd1c5e479a2f18acb6/sage_numerical_backends_gurobi-9.0b12.tar.gz

Requirement already satisfied: sphinx in 
./local/lib/python3.7/site-packages (from sage-numerical-backends-gurobi) 
(1.8.5)

Requirement already satisfied: six>=1.5 in 
./local/lib/python3.7/site-packages (from 
sphinx->sage-numerical-backends-gurobi) (1.12.0)

Requirement already satisfied: Jinja2>=2.3 in 
./local/lib/python3.7/site-packages (from 
sphinx->sage-numerical-backends-gurobi) (2.10)

Requirement already satisfied: Pygments>=2.0 in 
./local/lib/python3.7/site-packages (from 
sphinx->sage-numerical-backends-gurobi) (2.3.1)

Requirement already satisfied: docutils>=0.11 in 
./local/lib/python3.7/site-packages (from 
sphinx->sage-numerical-backends-gurobi) (0.14)

Requirement already satisfied: snowballstemmer>=1.1 in 
./local/lib/python3.7/site-packages (from 
sphinx->sage-numerical-backends-gurobi) (1.2.1)

Requirement already satisfied: babel!=2.0,>=1.3 in 
./local/lib/python3.7/site-packages (from 
sphinx->sage-numerical-backends-gurobi) (2.6.0)

Requirement already satisfied: alabaster<0.8,>=0.7 in 
./local/lib/python3.7/site-packages (from 
sphinx->sage-numerical-backends-gurobi) (0.7.12)

Requirement already satisfied: imagesize in 
./local/lib/python3.7/site-packages (from 
sphinx->sage-numerical-backends-gurobi) (1.1.0)

Requirement already satisfied: requests>=2.0.0 in 
./local/lib/python3.7/site-packages (from 
sphinx->sage-numerical-backends-gurobi) (2.13.0)

Requirement already satisfied: setuptools in 
./local/lib/python3.7/site-packages (from 
sphinx->sage-numerical-backends-gurobi) (40.6.3)

Requirement already satisfied: packaging in 
./local/lib/python3.7/site-packages (from 
sphinx->sage-numerical-backends-gurobi) (18.0)

Requirement already satisfied: sphinxcontrib-websupport in 
./local/lib/python3.7/site-packages (from 
sphinx->sage-numerical-backends-gurobi) (1.1.0)

Requirement already satisfied: MarkupSafe>=0.23 in 
./local/lib/python3.7/site-packages (from 
Jinja2>=2.3->sphinx->sage-numerical-backends-gurobi) (1.1.0)

Requirement already satisfied: pytz>=0a in 
./local/lib/python3.7/site-packages (from 
babel!=2.0,>=1.3->sphinx->sage-numerical-backends-gurobi) (2018.7)

Requirement already satisfied: pyparsing>=2.0.2 in 
./local/lib/python3.7/site-packages (from 
packaging->sphinx->sage-numerical-backends-gurobi) (2.3.0)

Installing collected packages: sage-numerical-backends-gurobi

  Running setup.py install for sage-numerical-backends-gurobi ... error

Complete output from command /Users/dcoudert/sage/local/bin/python3 -u 
-c "import setuptools, 
tokenize;__file__='/private/var/folders/l8/sxf193t11mvdyqq56f4w_6_8gn/T/pip-install-t4k429rc/sage-numerical-backends-gurobi/setup.py';f=getattr(tokenize,
 
'open', open)(__file__);code=f.read().replace('\r\n', 
'\n');f.close();exec(compile(code, __file__, 'exec'))" install --record 
/private/var/folders/l8/sxf193t11mvdyqq56f4w_6_8gn/T/pip-record-sk9om1cp/install-record.txt
 
--single-version-externally-managed --compile:

Using GUROBI_HOME obtained from gurobi.sh:

GUROBI_HOME is not set, or it does not point to a directory with a 
Gurobi installation.  Trying to link against -lgurobi

Checking whether HAVE_SAGE_CPYTHON_STRING...

Checking whether HAVE_ADD_COL_UNTYPED_ARGS...

Using compile_time_env: {'HAVE_SAGE_CPYTHON_STRING': True, 
'HAVE_ADD_COL_UNTYPED_ARGS': True}

running install

running build

running build_py

creating build

creating build/lib.macosx-10.9-x86_64-3.7

creating build/lib.macosx-10.9-x86_64-3.7/sage_numerical_backends_gurobi

copying sage_numerical_backends_gurobi/__init__.py -> 
build/lib.macosx-10.9-x86_64-3.7/sage_numerical_backends_gurobi

copying sage_numerical_backends_gurobi/gurobi_backend.pxd -> 
build/lib.macosx-10.9-x86_64-3.7/sage_numerical_backends_gurobi

running build_ext

building 'sage_numerical_backends_gurobi.gurobi_backend' extension

creating build/temp.macosx-10.9-x86_64-3.7

creating 
build/temp.macosx-10.9-x86_64-3.7/sage_numerical_backends_gurobi

clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g 
-fwrapv -O3 -Wall -Wno-unused 
-I/Users/dcoudert/sage/local/lib/python3.7/site-packages/cysignals 

[sage-devel] Re: Removing reverse graph from CGraph

[David Coudert]

I'm in favor of this change. The code is faster and slightly easier to 
understand.

Extra opinions are more than welcome.
David.

Le mardi 7 janvier 2020 22:42:45 UTC+1, Jonathan Kliem a écrit :
>
> Dear all,
>
> currently the sparse graph backend keeps a reversed copy of the graph.
>
> However, the SparseGraph itself does not have access to it and thus the 
> reversed structure should be moved there for obvious optimizations. See 
> #28904 .
>
> As the sparse graph backend is the only backend actually using the 
> reversed structure, it would make sense to remove this.
>
> However, it is very well possible that people use the unsafe methods of 
> SparseGraph directly and code will break.
> E.g. in graphs/trees.py the undirected trees are generated by manually 
> adding an arc in each direction.
>
> I think, if we remove the reversed graph attribute in CGraph altogether, 
> people are more likely to catch on that something changed.
> But in an undirected graph it can very well happen that they add two edges 
> instead of one (as they used to add one arc for each direction).
>
> Any thoughts?
>
> Jonathan
>

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[sage-devel] Re: [sage-gsoc-mentors] Google GSoC 2020

[David Coudert]

I don’t know if I will participate next year.
This year I somehow supervised 3 students and it was way too much.
Also, I’m not happy as these students disappeared after the end of GSoC. It 
would be much more profitable if GSoC could help us attract or secure long term 
contributors.

It would be nice if others could get involved in this, propose projects and 
mentor students.

Concerning possible projects, clearly the graph module needs work in the 
backends. Some operations are way too slow (add/remove edges, copy, etc.), and 
the backends are extremely complicated. Not sure this can be done with a GSoC 
project.

David.


> Le 12 déc. 2019 à 10:38, Harald Schilly  a écrit :
> 
> Hello everyone, Google's GSOC 2020 is announced. The application period for 
> organizations is  January 14, 2020 - February 5, 2020. In the past, it was me 
> who wrote it, but I'm worn down with that. Is there someone who wants to take 
> over?
> 
> Despite that, is there enough interest to apply? This mainly concerns the few 
> usual mentors, but maybe there is someone else who also likes to mentor a 
> project?
> 
> Timeline: https://summerofcode.withgoogle.com/how-it-works/#timeline 
> <https://summerofcode.withgoogle.com/how-it-works/#timeline>
> 
> Wiki entry: https://wiki.sagemath.org/GSoC/2020 
> <https://wiki.sagemath.org/GSoC/2020>
> 
> -- harald
> 
> 
> -- 
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>  
> <https://groups.google.com/d/msgid/sage-gsoc-mentors/CAGG4CB5cbq5Zn%3DOt5Zr_w6nv1yFHu1_PVSuvHObLcEP6faQ95A%40mail.gmail.com?utm_medium=email_source=footer>.


David Coudert
Equipe-Projet COATI
Centre de Recherche INRIA Sophia Antipolis - Méditerranée
Université Côte d’Azur, Inria, CNRS, I3S, France
http://www-sop.inria.fr/members/David.Coudert

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Re: [sage-devel] Optional and experimental packages

[David Coudert]

File splay.c has changed in nauty (at least in 26r12). The main difference 
is 

- static SPLAYNODE* 
- SPLAY_DELETE(SPLAYNODE **to_root, SPLAYNODE *p)
+ void
+ SPLAY_DELETE(SPLAYNODE **to_root, SPLAYNODE *p)

With this change, I can do gcc -O3 -std=c89 buckygen.c -o buckygen

So upstream must be updated.


Le mardi 29 octobre 2019 11:56:12 UTC+1, nvcleemp a écrit :
>
> OK, the answer is below:
>
> The file splay.c is actually taken from Nauty, so that issue should be 
> resolved there. The most obvious solution is to not compile this as C99, 
> but as C89 since that is what buckygen was written in.
>
> So, I can mail this to Brendan McKay to ask to solve this, but since Nauty 
> is already in Sage the issue should already be resolved in that code, so we 
> could also just take splay.c from there.
>
> Nico
>
> Op di 29 okt. 2019 om 09:31 schreef Nico Van Cleemput <
> nico.va...@gmail.com >:
>
>> Well, upstream sits at another desk in my office, so I will ask when he 
>> gets in.
>>
>> Nico
>>
>> Op di 29 okt. 2019 09:29 schreef Dima Pasechnik > >:
>>
>>> clang is unhappy about C standards violations. E.g. this is what I get
>>> with clang 7:
>>>
>>> cc -O4 buckygen.c -o buckygen
>>> cc: warning: -O4 is equivalent to -O3 [-Wdeprecated]
>>> In file included from buckygen.c:272:
>>> ./splay.c:139:6: warning: implicit declaration of function
>>> 'outputnode' is invalid in C99 [-Wimplicit-function-declaration]
>>> ACTION(p);
>>> ^
>>> buckygen.c:254:19: note: expanded from macro 'ACTION'
>>> #define ACTION(p) outputnode(p)
>>>   ^
>>> In file included from buckygen.c:272:
>>> ./splay.c:263:15: warning: implicit declaration of function
>>> 'comparenodes' is invalid in C99 [-Wimplicit-function-declaration]
>>> cmp = COMPARE(p);
>>>   ^
>>> buckygen.c:260:20: note: expanded from macro 'COMPARE'
>>> #define COMPARE(p) comparenodes(canong, codelength, type, p)
>>>^
>>> In file included from buckygen.c:272:
>>> ./splay.c:328:15: warning: implicit declaration of function
>>> 'comparenodes' is invalid in C99 [-Wimplicit-function-declaration]
>>> cmp = COMPARE(p);
>>>   ^
>>> buckygen.c:260:20: note: expanded from macro 'COMPARE'
>>> #define COMPARE(p) comparenodes(canong, codelength, type, p)
>>>^
>>> In file included from buckygen.c:272:
>>> ./splay.c:352:20: error: non-void function 'splay_delete' should
>>> return a value [-Wreturn-type]
>>> if (p == NULL) return;
>>>^
>>> ./splay.c:366:2: error: non-void function 'splay_delete' should return
>>> a value [-Wreturn-type]
>>> return;
>>> ^
>>> ./splay.c:376:9: error: non-void function 'splay_delete' should return
>>> a value [-Wreturn-type]
>>> return;
>>> ^
>>> buckygen.c:943:1: warning: type specifier missing, defaults to 'int'
>>> [-Wimplicit-int]
>>> outputnode(SPLAYNODE *liste)
>>> ^
>>> 4 warnings and 3 errors generated.
>>> make: *** [makefile:12: buckygen] Error 1
>>>
>>> Easy to fix, I'd say - can this be done upstream?
>>>
>>> On Tue, Oct 29, 2019 at 8:31 AM Nico Van Cleemput
>>> > wrote:
>>> >
>>> > buckygen is a pure C package, so I doubt that this has anything to do 
>>> with the switch to Python 3. Do you have any more information about the 
>>> fail build, because here it built fine.
>>> >
>>> > Nico
>>> >
>>> > Op ma 28 okt. 2019 om 23:02 schreef John H Palmieri <
>>> jhpalm...@gmail.com >:
>>> >>
>>> >> With a Python 3 build of Sage on OS X 10.14.6, I decided to install 
>>> as many optional and experimental packages as I could. The results:
>>> >>
>>> >> Optional:
>>> >>
>>> >> - the following packages failed to build, and the reason wasn't 
>>> completely obvious:
>>> >>
>>> >> awali
>>> >> buckygen
>>> >> cbc
>>> >> gambit
>>> >> gdb
>>> >> mpi4py
>>> >>
>>> >> - the following packages failed because they (or their installation 
>>> scripts) are not compatible with Python 3:
>>> >>
>>> >> beautifulsoup
>>> >> brian
>>> >> guppy
>>> >> mercurial
>>> >> p_group_cohomology (but work is in progress)
>>> >> pyx
>>> >> scons
>>> >> trac
>>> >>
>>> >> - the following packages failed at first, but built after installing 
>>> some prerequisities:
>>> >>
>>> >> deformation — requires installation of mpir
>>> >> dot2tex — requires Graphviz
>>> >> rst2ipynb — requires pandoc
>>> >>
>>> >> - I skipped the following packages:
>>> >>
>>> >> atlas (installation is skipped on OS X)
>>> >> python2 (I wanted to use a pure Python 3 build)
>>> >>
>>> >> - Every other optional package built.
>>> >>
>>> >> Question/Proposal: do we demote the failed packages to experimental? 
>>> (Not deformation, dot2tex, or rst2ipynb, also not p_group_cohomology 
>>> because it is just about ready for py3, but the others.) I plan to do this 
>>> unless there are objections.
>>> >>
>>> >>
>>> >> Experimental:
>>> >>
>>> >> - the following failed to build:
>>> >>
>>> >> autotools
>>> >> cocoalib
>>> >> libtheora

Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

[David Coudert]

Since it’s cleaner, I tried, and after a make distclean and the removal of 
MacOSX10.14.sdk, I was able to build Sage !

Thanks,
David.


> Le 14 oct. 2019 à 01:29, Volker Braun  a écrit :
> 
> I just tried the latest Xcode and gfortran fails to build for me, too...
> 
> 
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David Coudert
Equipe-Projet COATI
Centre de Recherche INRIA Sophia Antipolis - Méditerranée
Université Côte d’Azur, Inria, CNRS, I3S, France
http://www-sop.inria.fr/members/David.Coudert

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Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

[David Coudert]

> Le 13 oct. 2019 à 20:24, Dima Pasechnik  a écrit :
> 
> On Sun, Oct 13, 2019 at 4:57 PM David Coudert  <mailto:david.coud...@inria.fr>> wrote:
>> 
>> It’s working ! I can now complete compilation.
>> 
>> Thanks both of you for the help.
>> 
>> Now I have to remember to remove MacOSX10.14.sdk when it will no longer be 
>> needed, but when…
> 
> 
> 
> hmm, so does this mean that you didn't do a full rebuild of Sage after
> OS upgrade?
> Cause you are on 10.15 now, no?

I had to reformat my hard drive, so I reinstalled / rebuilt everything from 
scratch, including Sagemath.
I’m currently with Mojave 10.14.6. 
However, I did an update Xcode 2-3 days ago (app store said I should update 
Xcode…) but didn’t do full rebuild. Should I ?

D.



>> David.
>> 
>> Le 13 oct. 2019 à 17:32, Isuru Fernando  a écrit :
>> 
>> You have the same issue as https://github.com/sagemath/binary-pkg/issues/19
>> 
>> Can you try downloading 10.14 SDK from 
>> https://github.com/phracker/MacOSX-SDKs/releases/download/10.14-beta4/MacOSX10.14.sdk.tar.xz
>>  extracting it inside 
>> `/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk`
>> 
>> Isuru
>> 
>> On Sun, Oct 13, 2019 at 10:27 AM David Coudert  
>> wrote:
>>> 
>>> No, but MacOSX10.15.sdk
>>> 
>>> confetti:lib dcoudert$ ll 
>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
>>> ls: 
>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk:
>>>  No such file or directory
>>> confetti:lib dcoudert$ ll 
>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/
>>> total 0
>>> drwxr-xr-x  4 root  wheel  128 12 sep 05:13 DriverKit19.0.sdk
>>> drwxr-xr-x  8 root  wheel  256 12 sep 05:13 MacOSX.sdk
>>> lrwxr-xr-x  1 root  wheel   10  8 oct 15:28 MacOSX10.15.sdk -> MacOSX.sdk
>>> 
>>> 
>>> Le 13 oct. 2019 à 17:16, Isuru Fernando  a écrit :
>>> 
>>> Hi,
>>> 
>>> Do you have the folder 
>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
>>>  ?
>>> 
>>> Isuru
>>> 
>>> On Sun, Oct 13, 2019 at 10:14 AM David Coudert  
>>> wrote:
>>>> 
>>>> here it is.
>>>> 
>>>> confetti:lib dcoudert$  /Users/dcoudert/sage3/sage/local/bin/gfortran 
>>>> -print-prog-name=ld
>>>> ld
>>>> confetti:lib dcoudert$  /Users/dcoudert/sage3/sage/local/bin/gfortran -v
>>>> Using built-in specs.
>>>> COLLECT_GCC=/Users/dcoudert/sage3/sage/local/bin/gfortran
>>>> COLLECT_LTO_WRAPPER=/Users/dcoudert/sage3/sage/local/libexec/gcc/x86_64-apple-darwin18.6.0/7.4.0/lto-wrapper
>>>> Target: x86_64-apple-darwin18.6.0
>>>> Configured with: ../src/configure 
>>>> --prefix=/Users/dcoudert/sage3/sage/local 
>>>> --with-local-prefix=/Users/dcoudert/sage3/sage/local 
>>>> --with-gmp=/Users/dcoudert/sage3/sage/local 
>>>> --with-mpfr=/Users/dcoudert/sage3/sage/local 
>>>> --with-mpc=/Users/dcoudert/sage3/sage/local --with-system-zlib 
>>>> --without-isl --disable-multilib --disable-nls --disable-libitm 
>>>> --with-build-config=bootstrap-debug --without-isl --without-cloog 
>>>> --with-sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
>>>>  --disable-bootstrap --enable-languages=fortran
>>>> Thread model: posix
>>>> gcc version 7.4.0 (GCC)
>>>> 
>>>> 
>>>> Le 13 oct. 2019 à 16:47, Isuru Fernando  a écrit :
>>>> 
>>>> Hi,
>>>> 
>>>> This is a problem with gfortran using an incorrect linker.
>>>> 
>>>> Can you post the output of,
>>>> 
>>>> /Users/dcoudert/sage3/sage/local/bin/gfortran -print-prog-name=ld
>>>> 
>>>> /Users/dcoudert/sage3/sage/local/bin/gfortran -v
>>>> 
>>>> Isuru
>>>> 
>>>> 
>>>> On Sun, Oct 13, 2019 at 8:21 AM David Coudert  
>>>> wrote:
>>>>> 
>>>>> confetti:lib dcoudert$ otool -L libfflas.dylib
>>>>> libfflas.dylib:
>>>>> /Users/dcoudert/sage3/sage/local/lib/libfflas.1.dylib (compatibility 
>>>>> version 2.0.0, current version 2.0.0)
&g

Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

[David Coudert]

It’s working ! I can now complete compilation.

Thanks both of you for the help.

Now I have to remember to remove MacOSX10.14.sdk when it will no longer be 
needed, but when…

David.

> Le 13 oct. 2019 à 17:32, Isuru Fernando  a écrit :
> 
> You have the same issue as https://github.com/sagemath/binary-pkg/issues/19 
> <https://github.com/sagemath/binary-pkg/issues/19>
> 
> Can you try downloading 10.14 SDK from 
> https://github.com/phracker/MacOSX-SDKs/releases/download/10.14-beta4/MacOSX10.14.sdk.tar.xz
>  
> <https://github.com/phracker/MacOSX-SDKs/releases/download/10.14-beta4/MacOSX10.14.sdk.tar.xz>
>  extracting it inside 
> `/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk`
> 
> Isuru
> 
> On Sun, Oct 13, 2019 at 10:27 AM David Coudert  <mailto:david.coud...@inria.fr>> wrote:
> No, but MacOSX10.15.sdk
> 
> confetti:lib dcoudert$ ll 
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
>  
> ls: 
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk:
>  No such file or directory
> confetti:lib dcoudert$ ll 
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/
> total 0
> drwxr-xr-x  4 root  wheel  128 12 sep 05:13 DriverKit19.0.sdk
> drwxr-xr-x  8 root  wheel  256 12 sep 05:13 MacOSX.sdk
> lrwxr-xr-x  1 root  wheel   10  8 oct 15:28 MacOSX10.15.sdk -> MacOSX.sdk
> 
> 
>> Le 13 oct. 2019 à 17:16, Isuru Fernando > <mailto:isu...@gmail.com>> a écrit :
>> 
>> Hi,
>> 
>> Do you have the folder 
>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
>>  ?
>> 
>> Isuru
>> 
>> On Sun, Oct 13, 2019 at 10:14 AM David Coudert > <mailto:david.coud...@inria.fr>> wrote:
>> here it is.
>> 
>> confetti:lib dcoudert$  /Users/dcoudert/sage3/sage/local/bin/gfortran 
>> -print-prog-name=ld
>> ld
>> confetti:lib dcoudert$  /Users/dcoudert/sage3/sage/local/bin/gfortran -v
>> Using built-in specs.
>> COLLECT_GCC=/Users/dcoudert/sage3/sage/local/bin/gfortran
>> COLLECT_LTO_WRAPPER=/Users/dcoudert/sage3/sage/local/libexec/gcc/x86_64-apple-darwin18.6.0/7.4.0/lto-wrapper
>> Target: x86_64-apple-darwin18.6.0
>> Configured with: ../src/configure --prefix=/Users/dcoudert/sage3/sage/local 
>> --with-local-prefix=/Users/dcoudert/sage3/sage/local 
>> --with-gmp=/Users/dcoudert/sage3/sage/local 
>> --with-mpfr=/Users/dcoudert/sage3/sage/local 
>> --with-mpc=/Users/dcoudert/sage3/sage/local --with-system-zlib --without-isl 
>> --disable-multilib --disable-nls --disable-libitm 
>> --with-build-config=bootstrap-debug --without-isl --without-cloog 
>> --with-sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
>>  --disable-bootstrap --enable-languages=fortran  
>> Thread model: posix
>> gcc version 7.4.0 (GCC) 
>> 
>> 
>>> Le 13 oct. 2019 à 16:47, Isuru Fernando >> <mailto:isu...@gmail.com>> a écrit :
>>> 
>>> Hi,
>>> 
>>> This is a problem with gfortran using an incorrect linker.
>>> 
>>> Can you post the output of,
>>> 
>>>  /Users/dcoudert/sage3/sage/local/bin/gfortran -print-prog-name=ld
>>> 
>>>  /Users/dcoudert/sage3/sage/local/bin/gfortran -v
>>> 
>>> Isuru
>>> 
>>> On Sun, Oct 13, 2019 at 8:21 AM David Coudert >> <mailto:david.coud...@inria.fr>> wrote:
>>> confetti:lib dcoudert$ otool -L libfflas.dylib
>>> libfflas.dylib:
>>> /Users/dcoudert/sage3/sage/local/lib/libfflas.1.dylib (compatibility 
>>> version 2.0.0, current version 2.0.0)
>>> /Users/dcoudert/sage3/sage/local/lib/libgivaro.9.dylib (compatibility 
>>> version 11.0.0, current version 11.1.0)
>>> /Users/dcoudert/sage3/sage/local/lib/libgmp.23.dylib (compatibility 
>>> version 24.0.0, current version 24.3.0)
>>> /Users/dcoudert/sage3/sage/local/lib/libgmpxx.8.dylib (compatibility 
>>> version 13.0.0, current version 13.3.0)
>>> /Users/dcoudert/sage3/sage/local/lib/libopenblas_haswellp-r0.3.6.dylib 
>>> (compatibility version 0.0.0, current version 0.0.0)
>>> /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 
>>> 400.9.4)
>>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current 
>>> version 1252.250.1)
>>> 
>>> 
>>>> Le 13 oct. 2019 à 15:19, Dima Pasechnik &g

Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

[David Coudert]

No, but MacOSX10.15.sdk

confetti:lib dcoudert$ ll 
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
 
ls: 
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk:
 No such file or directory
confetti:lib dcoudert$ ll 
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/
total 0
drwxr-xr-x  4 root  wheel  128 12 sep 05:13 DriverKit19.0.sdk
drwxr-xr-x  8 root  wheel  256 12 sep 05:13 MacOSX.sdk
lrwxr-xr-x  1 root  wheel   10  8 oct 15:28 MacOSX10.15.sdk -> MacOSX.sdk


> Le 13 oct. 2019 à 17:16, Isuru Fernando  a écrit :
> 
> Hi,
> 
> Do you have the folder 
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
>  ?
> 
> Isuru
> 
> On Sun, Oct 13, 2019 at 10:14 AM David Coudert  <mailto:david.coud...@inria.fr>> wrote:
> here it is.
> 
> confetti:lib dcoudert$  /Users/dcoudert/sage3/sage/local/bin/gfortran 
> -print-prog-name=ld
> ld
> confetti:lib dcoudert$  /Users/dcoudert/sage3/sage/local/bin/gfortran -v
> Using built-in specs.
> COLLECT_GCC=/Users/dcoudert/sage3/sage/local/bin/gfortran
> COLLECT_LTO_WRAPPER=/Users/dcoudert/sage3/sage/local/libexec/gcc/x86_64-apple-darwin18.6.0/7.4.0/lto-wrapper
> Target: x86_64-apple-darwin18.6.0
> Configured with: ../src/configure --prefix=/Users/dcoudert/sage3/sage/local 
> --with-local-prefix=/Users/dcoudert/sage3/sage/local 
> --with-gmp=/Users/dcoudert/sage3/sage/local 
> --with-mpfr=/Users/dcoudert/sage3/sage/local 
> --with-mpc=/Users/dcoudert/sage3/sage/local --with-system-zlib --without-isl 
> --disable-multilib --disable-nls --disable-libitm 
> --with-build-config=bootstrap-debug --without-isl --without-cloog 
> --with-sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
>  --disable-bootstrap --enable-languages=fortran  
> Thread model: posix
> gcc version 7.4.0 (GCC) 
> 
> 
>> Le 13 oct. 2019 à 16:47, Isuru Fernando > <mailto:isu...@gmail.com>> a écrit :
>> 
>> Hi,
>> 
>> This is a problem with gfortran using an incorrect linker.
>> 
>> Can you post the output of,
>> 
>>  /Users/dcoudert/sage3/sage/local/bin/gfortran -print-prog-name=ld
>> 
>>  /Users/dcoudert/sage3/sage/local/bin/gfortran -v
>> 
>> Isuru
>> 
>> On Sun, Oct 13, 2019 at 8:21 AM David Coudert > <mailto:david.coud...@inria.fr>> wrote:
>> confetti:lib dcoudert$ otool -L libfflas.dylib
>> libfflas.dylib:
>>  /Users/dcoudert/sage3/sage/local/lib/libfflas.1.dylib (compatibility 
>> version 2.0.0, current version 2.0.0)
>>  /Users/dcoudert/sage3/sage/local/lib/libgivaro.9.dylib (compatibility 
>> version 11.0.0, current version 11.1.0)
>>  /Users/dcoudert/sage3/sage/local/lib/libgmp.23.dylib (compatibility 
>> version 24.0.0, current version 24.3.0)
>>  /Users/dcoudert/sage3/sage/local/lib/libgmpxx.8.dylib (compatibility 
>> version 13.0.0, current version 13.3.0)
>>  /Users/dcoudert/sage3/sage/local/lib/libopenblas_haswellp-r0.3.6.dylib 
>> (compatibility version 0.0.0, current version 0.0.0)
>>  /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 
>> 400.9.4)
>>  /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current 
>> version 1252.250.1)
>> 
>> 
>>> Le 13 oct. 2019 à 15:19, Dima Pasechnik >> <mailto:dimp...@gmail.com>> a écrit :
>>> 
>>> oops sorry, your gfortran is ok.
>>> how about fflas* package, it is probably broken...
>>> 
>>> On Sun, 13 Oct 2019, 14:17 Dima Pasechnik, >> <mailto:dimp...@gmail.com>> wrote:
>>> are you building gfortran in Sage, or using a prebuilt one?
>>> 
>>> it might be that its libgfortran got broken
>>> 
>>> On Sun, 13 Oct 2019, 13:01 David Coudert, >> <mailto:david.coud...@inria.fr>> wrote:
>>> 
>>> 
>>> confetti:lib dcoudert$ pwd
>>> 
>>> /Users/dcoudert/sage3/sage/local/lib
>>> 
>>> confetti:lib dcoudert$ otool -L libgfortran.dylib 
>>> 
>>> libgfortran.dylib:
>>> 
>>> /Users/dcoudert/sage3/sage/local/lib/libgfortran.4.dylib (compatibility 
>>> version 5.0.0, current version 5.0.0)
>>> 
>>> /Users/dcoudert/sage3/sage/local/lib/libquadmath.0.dylib (compatibility 
>>> version 1.0.0, current version 1.0.0)
>>> 
>>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current 
>>> version 1252.250.1)
>>> 
>>> /Us

Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

[David Coudert]

here it is.

confetti:lib dcoudert$  /Users/dcoudert/sage3/sage/local/bin/gfortran 
-print-prog-name=ld
ld
confetti:lib dcoudert$  /Users/dcoudert/sage3/sage/local/bin/gfortran -v
Using built-in specs.
COLLECT_GCC=/Users/dcoudert/sage3/sage/local/bin/gfortran
COLLECT_LTO_WRAPPER=/Users/dcoudert/sage3/sage/local/libexec/gcc/x86_64-apple-darwin18.6.0/7.4.0/lto-wrapper
Target: x86_64-apple-darwin18.6.0
Configured with: ../src/configure --prefix=/Users/dcoudert/sage3/sage/local 
--with-local-prefix=/Users/dcoudert/sage3/sage/local 
--with-gmp=/Users/dcoudert/sage3/sage/local 
--with-mpfr=/Users/dcoudert/sage3/sage/local 
--with-mpc=/Users/dcoudert/sage3/sage/local --with-system-zlib --without-isl 
--disable-multilib --disable-nls --disable-libitm 
--with-build-config=bootstrap-debug --without-isl --without-cloog 
--with-sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
 --disable-bootstrap --enable-languages=fortran  
Thread model: posix
gcc version 7.4.0 (GCC) 


> Le 13 oct. 2019 à 16:47, Isuru Fernando  a écrit :
> 
> Hi,
> 
> This is a problem with gfortran using an incorrect linker.
> 
> Can you post the output of,
> 
>  /Users/dcoudert/sage3/sage/local/bin/gfortran -print-prog-name=ld
> 
>  /Users/dcoudert/sage3/sage/local/bin/gfortran -v
> 
> Isuru
> 
> On Sun, Oct 13, 2019 at 8:21 AM David Coudert  <mailto:david.coud...@inria.fr>> wrote:
> confetti:lib dcoudert$ otool -L libfflas.dylib
> libfflas.dylib:
>   /Users/dcoudert/sage3/sage/local/lib/libfflas.1.dylib (compatibility 
> version 2.0.0, current version 2.0.0)
>   /Users/dcoudert/sage3/sage/local/lib/libgivaro.9.dylib (compatibility 
> version 11.0.0, current version 11.1.0)
>   /Users/dcoudert/sage3/sage/local/lib/libgmp.23.dylib (compatibility 
> version 24.0.0, current version 24.3.0)
>   /Users/dcoudert/sage3/sage/local/lib/libgmpxx.8.dylib (compatibility 
> version 13.0.0, current version 13.3.0)
>   /Users/dcoudert/sage3/sage/local/lib/libopenblas_haswellp-r0.3.6.dylib 
> (compatibility version 0.0.0, current version 0.0.0)
>   /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 
> 400.9.4)
>   /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current 
> version 1252.250.1)
> 
> 
>> Le 13 oct. 2019 à 15:19, Dima Pasechnik > <mailto:dimp...@gmail.com>> a écrit :
>> 
>> oops sorry, your gfortran is ok.
>> how about fflas* package, it is probably broken...
>> 
>> On Sun, 13 Oct 2019, 14:17 Dima Pasechnik, > <mailto:dimp...@gmail.com>> wrote:
>> are you building gfortran in Sage, or using a prebuilt one?
>> 
>> it might be that its libgfortran got broken
>> 
>> On Sun, 13 Oct 2019, 13:01 David Coudert, > <mailto:david.coud...@inria.fr>> wrote:
>> 
>> 
>> confetti:lib dcoudert$ pwd
>> 
>> /Users/dcoudert/sage3/sage/local/lib
>> 
>> confetti:lib dcoudert$ otool -L libgfortran.dylib 
>> 
>> libgfortran.dylib:
>> 
>>  /Users/dcoudert/sage3/sage/local/lib/libgfortran.4.dylib (compatibility 
>> version 5.0.0, current version 5.0.0)
>> 
>>  /Users/dcoudert/sage3/sage/local/lib/libquadmath.0.dylib (compatibility 
>> version 1.0.0, current version 1.0.0)
>> 
>>  /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current 
>> version 1252.250.1)
>> 
>>  /Users/dcoudert/sage3/sage/local/lib/libgcc_s.1.dylib (compatibility 
>> version 1.0.0, current version 1.0.0)
>> 
>> 
>> 
>> but I don't have the 2 others
>> 
>> confetti:sage dcoudert$ ls -lR | grep ftpack | grep dylib
>> 
>> confetti:sage dcoudert$ pwd
>> 
>> 
>> /Users/dcoudert/sage3/sage
>> 
>> 
>> 
>> 
>> 
>> 
>> Le dimanche 13 octobre 2019 13:48:55 UTC+2, Dima Pasechnik a écrit :
>> I gather that the error comes from one of  -ldfftpack -lfftpack -lgfortran 
>> being incorrectly linked/broken. 
>> 
>> please locate the relevant lib*.dylib files (in SAGE_LOCAL?) and run 
>> "otool -L" on each of them 
>> to see if they are OK. 
>> 
>> 
>> On Sun, Oct 13, 2019 at 12:43 PM David Coudert > 
>> wrote: 
>> > 
>> > it's an incremental build from 9.0.beta0. 
>> > I upgraded my OS in July after a system crash. So I had to reinstall 
>> > everything from scratch. 
>> > 
>> > In case, I have Xcode Version 11.1 (11A1027). 
>> > 
>> > Le dimanche 13 octobre 2019 13:29:21 UTC+2, Dima Pasechnik a écrit : 
>> >> 
>> >> Is this a build from scratch? 
>> >> (after

Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

[David Coudert]

confetti:lib dcoudert$ otool -L libfflas.dylib
libfflas.dylib:
/Users/dcoudert/sage3/sage/local/lib/libfflas.1.dylib (compatibility 
version 2.0.0, current version 2.0.0)
/Users/dcoudert/sage3/sage/local/lib/libgivaro.9.dylib (compatibility 
version 11.0.0, current version 11.1.0)
/Users/dcoudert/sage3/sage/local/lib/libgmp.23.dylib (compatibility 
version 24.0.0, current version 24.3.0)
/Users/dcoudert/sage3/sage/local/lib/libgmpxx.8.dylib (compatibility 
version 13.0.0, current version 13.3.0)
/Users/dcoudert/sage3/sage/local/lib/libopenblas_haswellp-r0.3.6.dylib 
(compatibility version 0.0.0, current version 0.0.0)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 
400.9.4)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current 
version 1252.250.1)


> Le 13 oct. 2019 à 15:19, Dima Pasechnik  a écrit :
> 
> oops sorry, your gfortran is ok.
> how about fflas* package, it is probably broken...
> 
> On Sun, 13 Oct 2019, 14:17 Dima Pasechnik,  <mailto:dimp...@gmail.com>> wrote:
> are you building gfortran in Sage, or using a prebuilt one?
> 
> it might be that its libgfortran got broken
> 
> On Sun, 13 Oct 2019, 13:01 David Coudert,  <mailto:david.coud...@inria.fr>> wrote:
> 
> 
> confetti:lib dcoudert$ pwd
> 
> /Users/dcoudert/sage3/sage/local/lib
> 
> confetti:lib dcoudert$ otool -L libgfortran.dylib 
> 
> libgfortran.dylib:
> 
>   /Users/dcoudert/sage3/sage/local/lib/libgfortran.4.dylib (compatibility 
> version 5.0.0, current version 5.0.0)
> 
>   /Users/dcoudert/sage3/sage/local/lib/libquadmath.0.dylib (compatibility 
> version 1.0.0, current version 1.0.0)
> 
>   /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current 
> version 1252.250.1)
> 
>   /Users/dcoudert/sage3/sage/local/lib/libgcc_s.1.dylib (compatibility 
> version 1.0.0, current version 1.0.0)
> 
> 
> 
> but I don't have the 2 others
> 
> confetti:sage dcoudert$ ls -lR | grep ftpack | grep dylib
> 
> confetti:sage dcoudert$ pwd
> 
> 
> /Users/dcoudert/sage3/sage
> 
> 
> 
> 
> 
> 
> Le dimanche 13 octobre 2019 13:48:55 UTC+2, Dima Pasechnik a écrit :
> I gather that the error comes from one of  -ldfftpack -lfftpack -lgfortran 
> being incorrectly linked/broken. 
> 
> please locate the relevant lib*.dylib files (in SAGE_LOCAL?) and run 
> "otool -L" on each of them 
> to see if they are OK. 
> 
> 
> On Sun, Oct 13, 2019 at 12:43 PM David Coudert > wrote: 
> > 
> > it's an incremental build from 9.0.beta0. 
> > I upgraded my OS in July after a system crash. So I had to reinstall 
> > everything from scratch. 
> > 
> > In case, I have Xcode Version 11.1 (11A1027). 
> > 
> > Le dimanche 13 octobre 2019 13:29:21 UTC+2, Dima Pasechnik a écrit : 
> >> 
> >> Is this a build from scratch? 
> >> (after an OS upgrade, incremental builds may break) 
> >> 
> >> 
> >> On Sun, Oct 13, 2019 at 12:19 PM David Coudert > 
> >> wrote: 
> >> > 
> >> > 
> >> > 
> >> > Le dimanche 13 octobre 2019 12:53:02 UTC+2, Dima Pasechnik a écrit : 
> >> >> 
> >> >> We have already seen that puzzling 
> >> >> 
> >> >> ld: library not found for -lSystem 
> >> >> 
> >> >> error message. 
> >> >> 
> >> >> Is there a /usr/lib/libSystem.dylib present? 
> >> > 
> >> > 
> >> > Yes: 
> >> > 
> >> > 
> >> > confetti:sage dcoudert$ ll /usr/lib/libSystem.dylib 
> >> > 
> >> > lrwxr-xr-x  1 root  wheel  17 19 jul 08:15 /usr/lib/libSystem.dylib -> 
> >> > libSystem.B.dylib 
> >> > 
> >> > 
> >> > 
> >> >> 
> >> >> If yes, then I guess this means a broken dependency of scipy, more 
> >> >> specifically, a broken dylib, built 
> >> >> along the way. 
> >> >> or Xcode that needs to be reinstalled... 
> >> >> 
> >> >> Can you do 
> >> >> ./sage --python 
> >> >> >> import numpy 
> >> >> 
> >> >> without an error? 
> >> > 
> >> > 
> >> > yes too: 
> >> > 
> >> > confetti:sage dcoudert$ ./sage --python 
> >> > 
> >> > Python 3.7.3 (default, Oct 13 2019, 02:06:13) 
> >> > 
> >> > [Clang 11.0.0 (clang-1100.0.33.8)] on darwin 
> >> > 
> >> > Type "help"

Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

[David Coudert]

confetti:lib dcoudert$ pwd

/Users/dcoudert/sage3/sage/local/lib

confetti:lib dcoudert$ otool -L libgfortran.dylib 

libgfortran.dylib:

/Users/dcoudert/sage3/sage/local/lib/libgfortran.4.dylib (compatibility 
version 5.0.0, current version 5.0.0)

/Users/dcoudert/sage3/sage/local/lib/libquadmath.0.dylib (compatibility 
version 1.0.0, current version 1.0.0)

/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 
1252.250.1)

/Users/dcoudert/sage3/sage/local/lib/libgcc_s.1.dylib (compatibility 
version 1.0.0, current version 1.0.0)


but I don't have the 2 others

confetti:sage dcoudert$ ls -lR | grep ftpack | grep dylib

confetti:sage dcoudert$ pwd

/Users/dcoudert/sage3/sage





Le dimanche 13 octobre 2019 13:48:55 UTC+2, Dima Pasechnik a écrit :
>
> I gather that the error comes from one of  -ldfftpack -lfftpack -lgfortran 
> being incorrectly linked/broken. 
>
> please locate the relevant lib*.dylib files (in SAGE_LOCAL?) and run 
> "otool -L" on each of them 
> to see if they are OK. 
>
>
> On Sun, Oct 13, 2019 at 12:43 PM David Coudert  > wrote: 
> > 
> > it's an incremental build from 9.0.beta0. 
> > I upgraded my OS in July after a system crash. So I had to reinstall 
> everything from scratch. 
> > 
> > In case, I have Xcode Version 11.1 (11A1027). 
> > 
> > Le dimanche 13 octobre 2019 13:29:21 UTC+2, Dima Pasechnik a écrit : 
> >> 
> >> Is this a build from scratch? 
> >> (after an OS upgrade, incremental builds may break) 
> >> 
> >> 
> >> On Sun, Oct 13, 2019 at 12:19 PM David Coudert  
> wrote: 
> >> > 
> >> > 
> >> > 
> >> > Le dimanche 13 octobre 2019 12:53:02 UTC+2, Dima Pasechnik a écrit : 
> >> >> 
> >> >> We have already seen that puzzling 
> >> >> 
> >> >> ld: library not found for -lSystem 
> >> >> 
> >> >> error message. 
> >> >> 
> >> >> Is there a /usr/lib/libSystem.dylib present? 
> >> > 
> >> > 
> >> > Yes: 
> >> > 
> >> > 
> >> > confetti:sage dcoudert$ ll /usr/lib/libSystem.dylib 
> >> > 
> >> > lrwxr-xr-x  1 root  wheel  17 19 jul 08:15 /usr/lib/libSystem.dylib 
> -> libSystem.B.dylib 
> >> > 
> >> > 
> >> > 
> >> >> 
> >> >> If yes, then I guess this means a broken dependency of scipy, more 
> >> >> specifically, a broken dylib, built 
> >> >> along the way. 
> >> >> or Xcode that needs to be reinstalled... 
> >> >> 
> >> >> Can you do 
> >> >> ./sage --python 
> >> >> >> import numpy 
> >> >> 
> >> >> without an error? 
> >> > 
> >> > 
> >> > yes too: 
> >> > 
> >> > confetti:sage dcoudert$ ./sage --python 
> >> > 
> >> > Python 3.7.3 (default, Oct 13 2019, 02:06:13) 
> >> > 
> >> > [Clang 11.0.0 (clang-1100.0.33.8)] on darwin 
> >> > 
> >> > Type "help", "copyright", "credits" or "license" for more 
> information. 
> >> > 
> >> > >>> import numpy 
> >> > 
> >> > >>> 
> >> > 
> >> > 
> >> > 
> >> > 
> >> > -- 
> >> > You received this message because you are subscribed to the Google 
> Groups "sage-devel" group. 
> >> > To unsubscribe from this group and stop receiving emails from it, 
> send an email to sage-...@googlegroups.com. 
> >> > To view this discussion on the web visit 
> https://groups.google.com/d/msgid/sage-devel/848357f8-1c79-481a-abb3-e87331775d8a%40googlegroups.com.
>  
>
> > 
> > -- 
> > You received this message because you are subscribed to the Google 
> Groups "sage-devel" group. 
> > To unsubscribe from this group and stop receiving emails from it, send 
> an email to sage-...@googlegroups.com . 
> > To view this discussion on the web visit 
> https://groups.google.com/d/msgid/sage-devel/752fcf51-af9a-4315-b62d-f15dab05f4ea%40googlegroups.com.
>  
>
>

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Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

[David Coudert]

it's an incremental build from 9.0.beta0.
I upgraded my OS in July after a system crash. So I had to reinstall 
everything from scratch.

In case, I have Xcode Version 11.1 (11A1027).

Le dimanche 13 octobre 2019 13:29:21 UTC+2, Dima Pasechnik a écrit :
>
> Is this a build from scratch? 
> (after an OS upgrade, incremental builds may break) 
>
>
> On Sun, Oct 13, 2019 at 12:19 PM David Coudert  > wrote: 
> > 
> > 
> > 
> > Le dimanche 13 octobre 2019 12:53:02 UTC+2, Dima Pasechnik a écrit : 
> >> 
> >> We have already seen that puzzling 
> >> 
> >> ld: library not found for -lSystem 
> >> 
> >> error message. 
> >> 
> >> Is there a /usr/lib/libSystem.dylib present? 
> > 
> > 
> > Yes: 
> > 
> > 
> > confetti:sage dcoudert$ ll /usr/lib/libSystem.dylib 
> > 
> > lrwxr-xr-x  1 root  wheel  17 19 jul 08:15 /usr/lib/libSystem.dylib -> 
> libSystem.B.dylib 
> > 
> > 
> > 
> >> 
> >> If yes, then I guess this means a broken dependency of scipy, more 
> >> specifically, a broken dylib, built 
> >> along the way. 
> >> or Xcode that needs to be reinstalled... 
> >> 
> >> Can you do 
> >> ./sage --python 
> >> >> import numpy 
> >> 
> >> without an error? 
> > 
> > 
> > yes too: 
> > 
> > confetti:sage dcoudert$ ./sage --python 
> > 
> > Python 3.7.3 (default, Oct 13 2019, 02:06:13) 
> > 
> > [Clang 11.0.0 (clang-1100.0.33.8)] on darwin 
> > 
> > Type "help", "copyright", "credits" or "license" for more information. 
> > 
> > >>> import numpy 
> > 
> > >>> 
> > 
> > 
> > 
> > 
> > -- 
> > You received this message because you are subscribed to the Google 
> Groups "sage-devel" group. 
> > To unsubscribe from this group and stop receiving emails from it, send 
> an email to sage-...@googlegroups.com . 
> > To view this discussion on the web visit 
> https://groups.google.com/d/msgid/sage-devel/848357f8-1c79-481a-abb3-e87331775d8a%40googlegroups.com.
>  
>
>

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Re: [sage-devel] Error installing scipy-1.2.0 when compiling sage math 9.0.beta1

[David Coudert]

Le dimanche 13 octobre 2019 12:53:02 UTC+2, Dima Pasechnik a écrit :
>
> We have already seen that puzzling 
>
> ld: library not found for -lSystem 
>
> error message. 
>
> Is there a /usr/lib/libSystem.dylib present? 
>

Yes:


confetti:sage dcoudert$ ll /usr/lib/libSystem.dylib

lrwxr-xr-x  1 root  wheel  17 19 jul 08:15 /usr/lib/libSystem.dylib -> 
libSystem.B.dylib

 

> If yes, then I guess this means a broken dependency of scipy, more 
> specifically, a broken dylib, built 
> along the way. 
> or Xcode that needs to be reinstalled... 
>
> Can you do 
> ./sage --python 
> >> import numpy 
>
> without an error? 
>

yes too:

confetti:sage dcoudert$ ./sage --python

Python 3.7.3 (default, Oct 13 2019, 02:06:13) 

[Clang 11.0.0 (clang-1100.0.33.8)] on darwin

Type "help", "copyright", "credits" or "license" for more information.

>>> import numpy

>>> 

 

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[sage-devel] nauty_geng and subprocess : how to ensure the termination of the subprocess ?

[David Coudert]

While playing with graphs.nauty_geng(...), I noticed that the geng 
subprocess might remain active after a ctrl-C, and even after existing the 
current sagemath session. This is not always the case, but it happens 
frequently.

Try this for instance (I'm using debug mode to quickly get an output):
sage: next(graphs.nauty_geng("-c 30", debug=True))
'>A geng -cd1D29 n=30 e=29-435\n'
sage:
then check your active processes, quit the sage session and continue 
checking for active processes.

Then I tried to handle keyboard interrupt in nauty_geng adding
except KeyboardInterrupt:
sp.kill()
raise KeyboardInterrupt()

and used the following example:
sage: for g in graphs.nauty_geng("-c 30", debug=True):
: print(g)
:
>A geng -cd1D29 n=30 e=29-435

^C
again, most of the time the geng process remains active after ctrl-C even 
if I quit the sage session. I also tried sp.terminate() with the same 
result.

At least, using this code the geng process is always killed after ctrl-C
except KeyboardInterrupt:
while sp.poll() is None:
sp.kill()
raise KeyboardInterrupt()

However, I don't know how to force termination of the process after
sage: next(graphs.nauty_geng("-c 30", debug=True))


What can we do to fix that ?

David.









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[sage-devel] Re: The opportunity of Python 3 migration

[David Coudert]

> A few examples: vertices() and edges() of graphs should not be lists, 
> but keep links to the graph itself. 


For edges, see https://trac.sagemath.org/ticket/27408
 

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Re: [sage-devel] error building 8.9.beta7 on OSX

[David Coudert]

> Le 19 août 2019 à 10:58, Dima Pasechnik  a écrit :
> 
> On Mon, Aug 19, 2019 at 11:20 AM David Coudert  <mailto:david.coud...@inria.fr>> wrote:
>> 
>> but for beta6, I succeeded to compile it without downloading the configure 
>> tarball...
> 
> there were changes in configure  in beta7.
> Or do you mean to say that you used to be able to run ./bootstrap and it
> produced the ./configure script for you?

I was able to use bootstrap to produce the configure script.

I have no configure-* file in upstream/

David.


> 
>> 
>> Le 19 août 2019 à 09:27, Dima Pasechnik  a écrit :
>> 
>> something is funny with your internet connection, and so you cannot
>> download the needed configure tarball.
>> 
>> On Mon, Aug 19, 2019 at 10:20 AM David Coudert  
>> wrote:
>> 
>> 
>> I don't know how to fix this issue with aclocal. Some help is more than 
>> welcome.
>> 
>> confetti:sage dcoudert$ make build
>> 
>> /Applications/Xcode.app/Contents/Developer/usr/bin/make build/make/Makefile 
>> --stop
>> 
>> ./bootstrap -d
>> 
>> rm -rf config configure build/make/Makefile-auto.in
>> 
>> bootstrap:69: installing 'config/config.rpath'
>> 
>> build/pkgs/iconv/spkg-configure.m4:2: warning: macro 'AM_ICONV' not found in 
>> library
>> 
>> Error: could not locate the pkg-config autoconf macros. These are
>> 
>> usually located in /usr/share/aclocal/pkg.m4. If your macros are
>> 
>> in a different location, try setting the environment variable
>> 
>> ACLOCAL="aclocal -I/other/macro/dir" before running ./bootstrap
>> 
>> autom4te: /usr/bin/m4 failed with exit status: 16
>> 
>> aclocal: error: echo failed with exit status: 16
>> 
>> Bootstrap failed, downloading required files instead.
>> 
>> Attempting to download package 
>> configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz from mirrors
>> 
>> Downloading the Sage mirror list
>> 
>> CRITICAL [mirror_list|_refresh:182]: Downloading the mirror list failed, 
>> using cached version
>> 
>> https://mirror.koddos.net/sagemath/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz
>> 
>> [xx]
>> 
>> ERROR [transfer|run:135]: [Errno socket error] [Errno 54] Connection reset 
>> by peer
>> 
>> http://www-ftp.lip6.fr/pub/math/sagemath/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz
>> 
>> [xx]
>> 
>> ERROR [transfer|run:135]: [Errno socket error] [Errno 54] Connection reset 
>> by peer
>> 
>> http://www.mirrorservice.org/sites/www.sagemath.org/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz
>> 
>> [xx]
>> 
>> ERROR [transfer|run:135]: [Errno socket error] [Errno 54] Connection reset 
>> by peer
>> 
>> http://mirrors.mit.edu/sage/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz
>> 
>> [xx]
>> 
>> ERROR [transfer|run:135]: [Errno socket error] [Errno 54] Connection reset 
>> by peer
>> 
>> http://mirror.yandex.ru/mirrors/sage.math.washington.edu/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz
>> 
>> [xx]
>> 
>> ERROR [transfer|run:135]: [Errno socket error] [Errno 54] Connection reset 
>> by peer
>> 
>> https://mirrors.up.pt/pub/sage/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz
>> 
>> [xx]
>> 
>> ERROR [transfer|run:135]: [Errno socket error] [Errno 54] Connection reset 
>> by peer
>> 
>> http://sage.mirror.garr.it/mirrors/sage/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz
>> 
>> [xx]
>> 
>> ERROR [transfer|run:135]: [Errno socket error] [Errno 54] Connection reset 
>> by peer
>> 
>> http://ftp.sun.ac.za/ftp/pub/mirrors/www.sagemath.org/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz
>> 
>> [xx]
>> 
>> ERR

Re: [sage-devel] error building 8.9.beta7 on OSX

[David Coudert]

but for beta6, I succeeded to compile it without downloading the configure 
tarball...

> Le 19 août 2019 à 09:27, Dima Pasechnik  a écrit :
> 
> something is funny with your internet connection, and so you cannot
> download the needed configure tarball.
> 
> On Mon, Aug 19, 2019 at 10:20 AM David Coudert  wrote:
>> 
>> I don't know how to fix this issue with aclocal. Some help is more than 
>> welcome.
>> 
>> confetti:sage dcoudert$ make build
>> 
>> /Applications/Xcode.app/Contents/Developer/usr/bin/make build/make/Makefile 
>> --stop
>> 
>> ./bootstrap -d
>> 
>> rm -rf config configure build/make/Makefile-auto.in
>> 
>> bootstrap:69: installing 'config/config.rpath'
>> 
>> build/pkgs/iconv/spkg-configure.m4:2: warning: macro 'AM_ICONV' not found in 
>> library
>> 
>> Error: could not locate the pkg-config autoconf macros. These are
>> 
>> usually located in /usr/share/aclocal/pkg.m4. If your macros are
>> 
>> in a different location, try setting the environment variable
>> 
>> ACLOCAL="aclocal -I/other/macro/dir" before running ./bootstrap
>> 
>> autom4te: /usr/bin/m4 failed with exit status: 16
>> 
>> aclocal: error: echo failed with exit status: 16
>> 
>> Bootstrap failed, downloading required files instead.
>> 
>> Attempting to download package 
>> configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz from mirrors
>> 
>> Downloading the Sage mirror list
>> 
>> CRITICAL [mirror_list|_refresh:182]: Downloading the mirror list failed, 
>> using cached version
>> 
>> https://mirror.koddos.net/sagemath/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz
>> 
>> [xx]
>> 
>> ERROR [transfer|run:135]: [Errno socket error] [Errno 54] Connection reset 
>> by peer
>> 
>> http://www-ftp.lip6.fr/pub/math/sagemath/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz
>> 
>> [xx]
>> 
>> ERROR [transfer|run:135]: [Errno socket error] [Errno 54] Connection reset 
>> by peer
>> 
>> http://www.mirrorservice.org/sites/www.sagemath.org/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz
>> 
>> [xx]
>> 
>> ERROR [transfer|run:135]: [Errno socket error] [Errno 54] Connection reset 
>> by peer
>> 
>> http://mirrors.mit.edu/sage/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz
>> 
>> [xx]
>> 
>> ERROR [transfer|run:135]: [Errno socket error] [Errno 54] Connection reset 
>> by peer
>> 
>> http://mirror.yandex.ru/mirrors/sage.math.washington.edu/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz
>> 
>> [xx]
>> 
>> ERROR [transfer|run:135]: [Errno socket error] [Errno 54] Connection reset 
>> by peer
>> 
>> https://mirrors.up.pt/pub/sage/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz
>> 
>> [xx]
>> 
>> ERROR [transfer|run:135]: [Errno socket error] [Errno 54] Connection reset 
>> by peer
>> 
>> http://sage.mirror.garr.it/mirrors/sage/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz
>> 
>> [xx]
>> 
>> ERROR [transfer|run:135]: [Errno socket error] [Errno 54] Connection reset 
>> by peer
>> 
>> http://ftp.sun.ac.za/ftp/pub/mirrors/www.sagemath.org/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz
>> 
>> [xx]
>> 
>> ERROR [transfer|run:135]: [Errno socket error] [Errno 54] Connection reset 
>> by peer
>> 
>> http://files.sagemath.org/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz
>> 
>> [xx]
>> 
>> ERROR [transfer|run:135]: [Errno socket error] [Errno 54] Connection reset 
>> by peer
>> 
>> http://ftp.ntua.gr/pub/sagemath/spkg/upstream/confi

[sage-devel] error building 8.9.beta7 on OSX

[David Coudert]

I don't know how to fix this issue with aclocal. Some help is more than 
welcome.

confetti:sage dcoudert$ make build

/Applications/Xcode.app/Contents/Developer/usr/bin/make build/make/Makefile 
--stop

./bootstrap -d

rm -rf config configure build/make/Makefile-auto.in

bootstrap:69: installing 'config/config.rpath'

build/pkgs/iconv/spkg-configure.m4:2: warning: macro 'AM_ICONV' not found 
in library

Error: could not locate the pkg-config autoconf macros. These are

usually located in /usr/share/aclocal/pkg.m4. If your macros are

in a different location, try setting the environment variable

ACLOCAL="aclocal -I/other/macro/dir" before running ./bootstrap

autom4te: /usr/bin/m4 failed with exit status: 16

aclocal: error: echo failed with exit status: 16

Bootstrap failed, downloading required files instead.

Attempting to download package 
configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz from mirrors

Downloading the Sage mirror list

CRITICAL [mirror_list|_refresh:182]: Downloading the mirror list failed, 
using cached version

https://mirror.koddos.net/sagemath/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz

[xx]

ERROR [transfer|run:135]: [Errno socket error] [Errno 54] Connection reset 
by peer

http://www-ftp.lip6.fr/pub/math/sagemath/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz

[xx]

ERROR [transfer|run:135]: [Errno socket error] [Errno 54] Connection reset 
by peer

http://www.mirrorservice.org/sites/www.sagemath.org/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz

[xx]

ERROR [transfer|run:135]: [Errno socket error] [Errno 54] Connection reset 
by peer

http://mirrors.mit.edu/sage/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz

[xx]

ERROR [transfer|run:135]: [Errno socket error] [Errno 54] Connection reset 
by peer

http://mirror.yandex.ru/mirrors/sage.math.washington.edu/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz

[xx]

ERROR [transfer|run:135]: [Errno socket error] [Errno 54] Connection reset 
by peer

https://mirrors.up.pt/pub/sage/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz

[xx]

ERROR [transfer|run:135]: [Errno socket error] [Errno 54] Connection reset 
by peer

http://sage.mirror.garr.it/mirrors/sage/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz

[xx]

ERROR [transfer|run:135]: [Errno socket error] [Errno 54] Connection reset 
by peer

http://ftp.sun.ac.za/ftp/pub/mirrors/www.sagemath.org/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz

[xx]

ERROR [transfer|run:135]: [Errno socket error] [Errno 54] Connection reset 
by peer

http://files.sagemath.org/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz

[xx]

ERROR [transfer|run:135]: [Errno socket error] [Errno 54] Connection reset 
by peer

http://ftp.ntua.gr/pub/sagemath/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz

[xx]

ERROR [transfer|run:135]: [Errno socket error] [Errno 54] Connection reset 
by peer

http://linorg.usp.br/sage/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz

[xx]

ERROR [transfer|run:135]: [Errno socket error] [Errno 54] Connection reset 
by peer

http://ftp.rediris.es/mirror/sagemath/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz

[xx]

ERROR [transfer|run:135]: [Errno socket error] [Errno 54] Connection reset 
by peer

http://mirrors.xmission.com/sage/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz

[xx]

ERROR [transfer|run:135]: [Errno socket error] [Errno 54] Connection reset 
by peer

http://sagemath.mirror.ac.za/spkg/upstream/configure/configure-8c985712aebdb887c2e66308af1d29907a6fc242.tar.gz

[xx]

ERROR [transfer|run:135]: [Errno socket error] [Errno 54] Connection reset 
by peer

[sage-devel] Re: Failure to build SageMath

[David Coudert]

This is the same issue than 
https://groups.google.com/forum/#!topic/sage-devel/cdw793St6cE

So try to remove local/share/gap/ and local/lib/gap by hand and then build 
again. 


Le dimanche 4 août 2019 21:11:15 UTC+2, Georgios Giapitzakis Tzintanos a 
écrit :
>
> Hello,
>
> I am new here so please excuse my ignorance. When I updated Sage to the 
> latest beta (Sage 8.9.beta5) and ran make I got an error when building 
> package gap-4.10.2.p0. I am attaching the log file. The main error 
> message I am getting is this:
>
> [gap-4.10.2.p0] cp: cannot overwrite directory 
>> /Users/giorgosgiapis/Desktop/sage/local/./share/gap/bin/x86_64-apple-darwin18.5.0-default64-kv3/src
>>  
>> with non-directory 
>> /Users/giorgosgiapis/Desktop/sage/local/var/tmp/sage/build/gap-4.10.2.p0/inst/Users/giorgosgiapis/Desktop/sage/local/./share/gap/bin/x86_64-apple-darwin18.5.0-default64-kv3/src
>>
>> [gap-4.10.2.p0] 
>> 
>>
>> [gap-4.10.2.p0] Error copying files for gap-4.10.2.p0.
>>
>> [gap-4.10.2.p0] 
>> 
>>
>
> Thank you.
>

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Re: [sage-devel] Error building the documentation with 8.8.beta5

[David Coudert]

Working ! Thank you. 
D.

> you need to install full JDK, not just JRE, if you need java/javac. 
>
>

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Re: [sage-devel] Error building the documentation with 8.8.beta5

[David Coudert]

I had to fully reinstall my laptop (with reformat). So I updated my system 
to OSX Mojave, installed last Xcode, command tools, etc., and made a fresh 
install of 8.9.beta3, but I still have the same issue :(

I have installed Java 8 update 221 (last version)

But when I try:

MacBook-Air-de-David:sage dcoudert$ java --version

No Java runtime present, requesting install.

MacBook-Air-de-David:sage dcoudert$ javac --version

No Java runtime present, requesting install.

There is something wrong here, but what ?
Also, I don't understand why this problem appears only with 8.8.beta5...

Thanks for your help.
David.

Le mercredi 22 mai 2019 11:45:42 UTC-4, David Coudert a écrit :
>
> Let us know if you find a way to fix that. All my attempts failed (make 
> doc-clean, dist-clean)
> David.
>
> Le mardi 21 mai 2019 10:35:38 UTC+2, Nicolas M. Thiéry a écrit :
>>
>>
>> Just for the record: same error here on Balthazar's laptop, sage 
>> 8.8.beta5, fresh Ubuntu 18.04. 
>>
>> Cheers, 
>> Nicolas 
>>
>

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Re: [sage-devel] issues with gurobi

[David Coudert]

Right, linking libgurobi81.dylib as libgurobi.so works.

We will certainly have to update the documentation of 
http://doc.sagemath.org/html/en/thematic_tutorials/linear_programming.html 
<http://doc.sagemath.org/html/en/thematic_tutorials/linear_programming.html>
I can do a ticket but would not be able to check if the documentation builds 
well…

Thanks.



> Le 16 juil. 2019 à 17:28, Dima Pasechnik  a écrit :
> 
> 
> 
> On Tue, 16 Jul 2019 at 16:24, David Coudert  <mailto:david.coud...@inria.fr>> wrote:
> I recently installed gurobi 8.0.1 and identified py3 issues. See ticket 
> 28206. <https://trac.sagemath.org/ticket/28206>
> 
> I also installed the last version of gurobi, 8.1.1, for OSX, but I cannot use 
> it with Sagemath as I don't find something like libgurobi81.so
> 
> Does anyone know what to do ?
> 
> I suppose you can use libgurobi81.dylib
> 
> 
> Below is what we have in the respective lib/ directories of 8.0.1 and 8.1.1.
> 
> confetti:~ dcoudert$ ll /Library/gurobi801/mac64/lib/
> total 24088
> -rwxrwxr-x  1 root  admin   147992 21 jui  2018 gurobi-javadoc.jar
> -rwxrwxr-x  1 root  admin78688 21 jui  2018 gurobi.jar
> -rwxrwxr-x  1 root  admin  773 21 jui  2018 gurobi.py
> -rwxrwxr-x  1 root  admin   125952 21 jui  2018 gurobi80.netstandard20.dll
> -rwxrwxr-x  1 root  admin   394543 21 jui  2018 gurobi80.netstandard20.xml
> drwxrwxr-x  4 root  admin  136 21 jui  2018 gurobipy
> -rwxrwxr-x  1 root  admin65692 21 jui  2018 libGurobiJni80.jnilib
> -rwxrwxr-x  1 root  admin  5563260 21 jui  2018 libgurobi80.so
> -rwxrwxr-x  1 root  admin  5161864 21 jui  2018 libgurobi80_light.so
> lrwxr-xr-x  1 root  admin   20 21 jui  2018 libgurobi_c++.a -> 
> ./libgurobi_g++4.2.a
> -rwxrwxr-x  1 root  admin   385920 21 jui  2018 libgurobi_g++4.2.a
> -rwxrwxr-x  1 root  admin   369600 21 jui  2018 libgurobi_stdc++.a
> drwxrwxr-x  3 root  admin  102 21 jui  2018 python2.7
> drwxrwxr-x  3 root  admin  102 21 jui  2018 python3.5
> drwxrwxr-x  3 root  admin  102 21 jui  2018 python3.6
> -rwxrwxr-x  1 root  admin 1215 21 jui  2018 rootcert.pem
> 
> 
> confetti:~ dcoudert$ ll /Library/gurobi811/mac64/lib/
> total 24352
> -rwxrwxr-x  1 root  admin   148246 22 mar 05:09 gurobi-javadoc.jar
> -rwxrwxr-x  1 root  admin78891 22 mar 05:09 gurobi.jar
> -rwxrwxr-x  1 root  admin  773 22 mar 05:09 gurobi.py
> -rwxrwxr-x  1 root  admin   126464 22 mar 05:09 gurobi81.netstandard20.dll
> -rwxrwxr-x  1 root  admin   396172 22 mar 05:09 gurobi81.netstandard20.xml
> drwxrwxr-x  4 root  admin  136 22 mar 05:09 gurobipy
> -rwxrwxr-x  1 root  admin65852 22 mar 05:09 libGurobiJni81.jnilib
> -rwxrwxr-x  1 root  admin  5634452 22 mar 05:09 libgurobi81.dylib
> -rwxrwxr-x  1 root  admin  5228544 22 mar 05:09 libgurobi81_light.dylib
> lrwxr-xr-x  1 root  admin   20 22 mar 05:09 libgurobi_c++.a -> 
> ./libgurobi_g++4.2.a
> -rwxrwxr-x  1 root  admin   386712 22 mar 05:09 libgurobi_g++4.2.a
> -rwxrwxr-x  1 root  admin   370376 22 mar 05:09 libgurobi_stdc++.a
> drwxrwxr-x  3 root  admin  102 22 mar 05:09 python2.7
> drwxrwxr-x  3 root  admin  102 22 mar 05:09 python3.5
> drwxrwxr-x  3 root  admin  102 22 mar 05:09 python3.6
> drwxrwxr-x  3 root  admin  102 22 mar 05:09 python3.7
> -rwxrwxr-x  1 root  admin 1215 22 mar 05:09 rootcert.pem
> 
> 
> 
> 
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[sage-devel] issues with gurobi

[David Coudert]

I recently installed gurobi 8.0.1 and identified py3 issues. See ticket 
28206. 

I also installed the last version of gurobi, 8.1.1, for OSX, but I cannot 
use it with Sagemath as I don't find something like libgurobi81.so

Does anyone know what to do ?

Below is what we have in the respective lib/ directories of 8.0.1 and 8.1.1.

confetti:~ dcoudert$ ll /Library/gurobi801/mac64/lib/
total 24088
-rwxrwxr-x  1 root  admin   147992 21 jui  2018 gurobi-javadoc.jar
-rwxrwxr-x  1 root  admin78688 21 jui  2018 gurobi.jar
-rwxrwxr-x  1 root  admin  773 21 jui  2018 gurobi.py
-rwxrwxr-x  1 root  admin   125952 21 jui  2018 gurobi80.netstandard20.dll
-rwxrwxr-x  1 root  admin   394543 21 jui  2018 gurobi80.netstandard20.xml
drwxrwxr-x  4 root  admin  136 21 jui  2018 gurobipy
-rwxrwxr-x  1 root  admin65692 21 jui  2018 libGurobiJni80.jnilib
-rwxrwxr-x  1 root  admin  5563260 21 jui  2018 libgurobi80.so
-rwxrwxr-x  1 root  admin  5161864 21 jui  2018 libgurobi80_light.so
lrwxr-xr-x  1 root  admin   20 21 jui  2018 libgurobi_c++.a -> 
./libgurobi_g++4.2.a
-rwxrwxr-x  1 root  admin   385920 21 jui  2018 libgurobi_g++4.2.a
-rwxrwxr-x  1 root  admin   369600 21 jui  2018 libgurobi_stdc++.a
drwxrwxr-x  3 root  admin  102 21 jui  2018 python2.7
drwxrwxr-x  3 root  admin  102 21 jui  2018 python3.5
drwxrwxr-x  3 root  admin  102 21 jui  2018 python3.6
-rwxrwxr-x  1 root  admin 1215 21 jui  2018 rootcert.pem


confetti:~ dcoudert$ ll /Library/gurobi811/mac64/lib/
total 24352
-rwxrwxr-x  1 root  admin   148246 22 mar 05:09 gurobi-javadoc.jar
-rwxrwxr-x  1 root  admin78891 22 mar 05:09 gurobi.jar
-rwxrwxr-x  1 root  admin  773 22 mar 05:09 gurobi.py
-rwxrwxr-x  1 root  admin   126464 22 mar 05:09 gurobi81.netstandard20.dll
-rwxrwxr-x  1 root  admin   396172 22 mar 05:09 gurobi81.netstandard20.xml
drwxrwxr-x  4 root  admin  136 22 mar 05:09 gurobipy
-rwxrwxr-x  1 root  admin65852 22 mar 05:09 libGurobiJni81.jnilib
-rwxrwxr-x  1 root  admin  5634452 22 mar 05:09 libgurobi81.dylib
-rwxrwxr-x  1 root  admin  5228544 22 mar 05:09 libgurobi81_light.dylib
lrwxr-xr-x  1 root  admin   20 22 mar 05:09 libgurobi_c++.a -> 
./libgurobi_g++4.2.a
-rwxrwxr-x  1 root  admin   386712 22 mar 05:09 libgurobi_g++4.2.a
-rwxrwxr-x  1 root  admin   370376 22 mar 05:09 libgurobi_stdc++.a
drwxrwxr-x  3 root  admin  102 22 mar 05:09 python2.7
drwxrwxr-x  3 root  admin  102 22 mar 05:09 python3.5
drwxrwxr-x  3 root  admin  102 22 mar 05:09 python3.6
drwxrwxr-x  3 root  admin  102 22 mar 05:09 python3.7
-rwxrwxr-x  1 root  admin 1215 22 mar 05:09 rootcert.pem


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[sage-devel] Re: python3 report (may of the last python2 year)

[David Coudert]

> * There are some remaining hard problems in graphs, under current scrutiny 
> I think.
>

The main remaining issues in the graph module are related to isomorphisms, 
automorphisms, and related methods.

1) #27571: align behaviors of algorithm 'sage' and 'bliss' in 
`automorphism_group` and fix a doctest in 
MathonPseudocyclicStronglyRegularGraph generator.

When finalized, we will have to fix bugs with `automorphism_group`, 
`PermutationGroupElement`, and possibly other methods.

2) fix `is_isomorphic` for graphs with edge labels. 
A first attempt is done in #27232 , 
but this proposal is certainly not satisfactory. One issue is that we can 
sort lists of unhashable objects (of different types).

3) #27435 deal with a failing doctest in graph_database.py with 
interactive_query 

Help is more than welcome !!

David.

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Re: [sage-devel] Error building the documentation with 8.8.beta5

[David Coudert]

Let us know if you find a way to fix that. All my attempts failed (make 
doc-clean, dist-clean)
David.

Le mardi 21 mai 2019 10:35:38 UTC+2, Nicolas M. Thiéry a écrit :
>
>
> Just for the record: same error here on Balthazar's laptop, sage 
> 8.8.beta5, fresh Ubuntu 18.04. 
>
> Cheers, 
> Nicolas 
>

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Re: [sage-devel] Error building the documentation with 8.8.beta5

[David Coudert]

And what can I do to fix that ?
Until recently I was able to build the doc and I have not touched 
environment variables by myself.

In case, I tested some instructions from 
https://ask.sagemath.org/question/39422/sage-on-mac-unable-to-use-plot3d-due-to-javajmol-issues/


sage: import subprocess
sage: print subprocess.check_output(['java', '-version'], 
stderr=subprocess.STDOUT)
java version "1.6.0_65"
Java(TM) SE Runtime Environment (build 1.6.0_65-b14-466.1-11M4716)
Java HotSpot(TM) 64-Bit Server VM (build 20.65-b04-466.1, mixed mode)

sage: from sage.interfaces.jmoldata import JmolData
sage: jdata = JmolData()
sage: jdata.is_jvm_available()
False



Le lundi 13 mai 2019 21:30:22 UTC+2, François Bissey a écrit :
>
> It looks like you are using tachyon instead of jmol for rendering some 
> 3D plots. I think that's what is causing the issues. Your jmol install 
> may be broken and tachyon is used as the fallback. 
>

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[sage-devel] Error building the documentation with 8.8.beta5

[David Coudert]

I already had issues building the doc with 8.8.beta4, so after upgrading to 
8.8.beta5, I did make doc-clean but it's not enough.

Attached is the log file.

I have not tried a dist-clean, and I hope I can avoid it...

Best,
David.

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Building reference manual, first pass.

[manifolds] chargement de l'environnement sérialisé...fait
[manifolds] building [inventory]: targets for 63 source files that are out of 
date
[manifolds] updating environment: 63 added, 0 changed, 0 removed
[manifolds] 
/Users/dcoudert/sage/src/sage_setup/docbuild/ext/sage_autodoc.py:1170: 
RemovedInSphinx20Warning: formatargspec() is now deprecated.  Please use 
sphinx.util.inspect.Signature instead.
[manifolds]   return formatargspec(initmeth, *argspec)
[manifolds] 
/Users/dcoudert/sage/src/sage_setup/docbuild/ext/sage_autodoc.py:1406: 
RemovedInSphinx20Warning: formatargspec() is now deprecated.  Please use 
sphinx.util.inspect.Signature instead.
[manifolds]   args = formatargspec(self.object, *argspec)
[manifolds] 
/Users/dcoudert/sage/src/sage_setup/docbuild/ext/sage_autodoc.py:1072: 
RemovedInSphinx20Warning: formatargspec() is now deprecated.  Please use 
sphinx.util.inspect.Signature instead.
[manifolds]   args = formatargspec(self.object, *argspec)
[manifolds] 
/Users/dcoudert/sage/local/lib/python2.7/site-packages/sage/manifolds/differentiable/integrated_curve.py:docstring
 of 
sage.manifolds.differentiable.integrated_curve.IntegratedAutoparallelCurve:309: 
WARNING: Exception occurred in plotting integrated_curve-3
[manifolds]  from 
/Users/dcoudert/sage/src/doc/en/reference/manifolds/sage/manifolds/differentiable/integrated_curve.rst:
[manifolds] Traceback (most recent call last):
[manifolds]   File 
"/Users/dcoudert/sage/local/lib/python2.7/site-packages/matplotlib/sphinxext/plot_directive.py",
 line 524, in run_code
[manifolds] six.exec_(code, ns)
[manifolds]   File 
"/Users/dcoudert/sage/local/lib/python2.7/site-packages/six.py", line 709, in 
exec_
[manifolds] exec("""exec _code_ in _globs_, _locs_""")
[manifolds]   File "", line 1, in 
[manifolds]   File "", line 34, in 
[manifolds]   File "", line 68, in sphinx_plot
[manifolds]   File "sage/plot/plot3d/base.pyx", line 1621, in 
sage.plot.plot3d.base.Graphics3d.save 
(build/cythonized/sage/plot/plot3d/base.c:20977)
[manifolds] self.save_image(filename, **kwds)
[manifolds]   File "sage/plot/plot3d/base.pyx", line 1550, in 
sage.plot.plot3d.base.Graphics3d.save_image 
(build/cythonized/sage/plot/plot3d/base.c:20535)
[manifolds] self._save_image_png(filename, **kwds)
[manifolds]   File "sage/plot/plot3d/base.pyx", line 1512, in 
sage.plot.plot3d.base.Graphics3d._save_image_png 
(build/cythonized/sage/plot/plot3d/base.c:20172)
[manifolds] scene = self._rich_repr_jmol(**opts)
[manifolds]   File "sage/plot/plot3d/base.pyx", line 264, in 
sage.plot.plot3d.base.Graphics3d._rich_repr_jmol 
(build/cythonized/sage/plot/plot3d/base.c:7182)
[manifolds] tachyon = self._rich_repr_tachyon(OutputImagePng, **opts)
[manifolds]   File "sage/plot/plot3d/base.pyx", line 208, in 
sage.plot.plot3d.base.Graphics3d._rich_repr_tachyon 
(build/cythonized/sage/plot/plot3d/base.c:6180)
[manifolds] tachyon_rt(T.tachyon(), filename, opts['verbosity'],
[manifolds]   File 
"/Users/dcoudert/sage/local/lib/python2.7/site-packages/sage/interfaces/tachyon.py",
 line 162, in __call__
[manifolds] raise RuntimeError(out)
[manifolds] RuntimeError: Tachyon Parallel/Multiprocessor Ray Tracer   Version 
0.98.9
[manifolds] Copyright 1994-2010,John E. Stone 
[manifolds] 
[manifolds] Parse Error:
[manifolds]Encountered a syntax error in file 
/Users/dcoudert/.sage/temp/confetti.inria.fr/82937/tmp_feQXWm.dat
[manifolds]Expected to find V1
[manifolds]Actually found: ,61208
[manifolds]Error occured at or prior to file offset 11659, line 368
[manifolds]Error position is only approximate, but should be close
[manifolds] Parse Error:
[manifolds]Encountered a syntax error in file 
/Users/dcoudert/.sage/temp/confetti.inria.fr/82937/tmp_feQXWm.dat
[manifolds]Expected to find V2
[manifolds]Actually found: ,412589
[manifolds]Error occured at or prior to file offset 11669, line 368
[manifolds]Error position is only approximate, but should be close
[manifolds] Undefined texture ',716998', using default.
[manifolds] Parser failed due to an input file 

[sage-devel] Re: k-choosability and k-degeneracy of graphs on SageMath

[David Coudert]

 At least we have a method to compute the cores of a graph. You can 
certainly use it to get the degeneracy.

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[sage-devel] Re: Error while building sage 8.8 due to igraph

[David Coudert]

The problem has been fixed. The packages were missing in the repository. Of 
course, it takes time to update all the mirrors.

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[sage-devel] Re: Add centroid decomposition of tree

[David Coudert]

The original paper of Jordan (1869) can be found at e.g. 
https://www.degruyter.com/view/j/crll.1869.issue-70/crll.1869.70.185/crll.1869.70.185.xml
 
or https://eudml.org/doc/148084
But it is written in French in a German journal.

See the lecture notes of Erik Demaine 
https://courses.csail.mit.edu/6.897/spring05/lec.html  (Lecture 16 in 
particular).


Le lundi 25 mars 2019 10:56:44 UTC+1, Abhay Pratap Singh a écrit :
>
> Centroid decomposition is a divide and conquer approach which helps in 
> making distance queries on large trees in an efficient way. \\
> For example, using centroid decomposition on tree(n vertices), we can find 
> the number of nodes at distance of x from vertex v in O(log^2^ n) time and 
> O(n log (n)) memory. Due to low memory requirements, it can be used on 
> large graphs.\\
> I wish to submit a patch on this if idea is fine and nothing of this sort 
> is implemented till now.
> Currently, I am not able to find any paper explaining algorithms, though 
> there are some blogs which describe this approach. If anyone wishes, I can 
> link some blogs regarding the technique or write it myself.
>

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Re: [sage-devel] Suggestion to speed up nauty_geng()?

[David Coudert]

Our interface to nauty geng is in Python, but the difficulty is not here.

   - It takes time to build graphs from graph6 strings, and also to build 
   Sandpiles (12 for each graph)
   - The number of biconnected graphs with 12 nodes is huge:  153.620.333.545  
   See https://oeis.org/A002218
   
Some parallelism could certainly help here, but there will be no miracle. A 
faster method for the tests on Sandpile is needed.


Le jeudi 21 mars 2019 19:47:37 UTC+1, Dima Pasechnik a écrit :
>
>
>
> On Thu, 21 Mar 2019 18:42 Ai Bo, > wrote:
>
>> I found it. Thank you.
>> I also tried the command listed above.
>> I am confused. Where is this "I]~~w"?
>>
>
> This is a particular way to encode graph as a string of characters (8 bits 
> per character).
> Read Sage docs on Graph for details.
>
> Is it a file? How did Graph load this?
>>
>> In my program, my code looks like this:
>> i=12
>> for G in graphs.nauty_geng(str(i) + " -C"): 
>> q = True
>> for j in range (0,i):
>> S = Sandpile(G,j)
>> if S.identity() != S.max_stable():
>> q = False
>> break
>>
>>
>>
>> If I use geng to generate graphs, how should I load them in my for loop 
>> so I can check with Sandpile?
>>
>
> Ideally one should create a fast interface from Python to geng, probably 
> using Cython, if it is not already done.
>
>
>> On Thursday, March 21, 2019 at 8:46:56 AM UTC-7, Dima Pasechnik wrote:
>>>
>>> On Thu, Mar 21, 2019 at 3:03 PM Ai Bo  wrote: 
>>>
>>> > is this "nauty26r7/geng" a program available? 
>>>
>>> geng is installed in local/bin/ sub-directory of your Sage 
>>> installation, as a part of Sage's standard package nauty. 
>>>
>>> > Also, as Python is slow, any part of the nautygen can be written in 
>>> other language, such as C/C++? 
>>>
>>> it is written in C, so it's quite fast in this sense. 
>>>
>>> > 
>>> > Thanks, 
>>> > Laura 
>>> > 
>>> > On Wednesday, March 20, 2019 at 11:48:38 PM UTC-7, Jori Mäntysalo 
>>> (TAU) wrote: 
>>> >> 
>>> >> On Thu, 21 Mar 2019, Ai Bo wrote: 
>>> >> 
>>> >> > Is there a way to "random access"? For example, access the nth 
>>> element 
>>> >> > in the "generator", instead of one by one? 
>>> >> 
>>> >> Kind of. As a most time is propably spent by creating Python data 
>>> >> structures for SageMath, you can use nautygen directly to generate 
>>> huge 
>>> >> number of graphs. 
>>> >> 
>>> >> As an example, it takes below 5 seconds to generate all biconnected 
>>> graphs 
>>> >> on 10 vertices, and I took third last one: 
>>> >> 
>>> >> $ nauty26r7/geng 10 -C | tail -3 | head -1 
>>> >> >A /home/jm58660/lat-koe/nauty26r7/geng -Cd2D9 n=10 e=10-45 
>>> >> >Z 9743542 graphs generated in 4.59 sec 
>>> >> I]~~w 
>>> >> 
>>> >> and now 
>>> >> 
>>> >> sage: g = Graph('I]~~w', format='graph6') 
>>> >> sage: g.is_biconnected() 
>>> >> True 
>>> >> 
>>> >> 
>>> >> -- 
>>> >> Jori Mäntysalo 
>>> >> 
>>> >> Tampereen yliopisto - Ihminen ratkaisee 
>>> > 
>>> > -- 
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[sage-devel] Re: Graph.show with js sometimes messes up labels

[David . Coudert]

Unfortunately, this is not a good idea.

We are working hard on making Sagemath compatible with Python 3.
With Python 3 you cannot sort objects of different types. For instance 
sorted([1, 'a']) will raise an error.
Currently, in the graph module, vertices can be any hashable objects, so we 
try to avoid sorting as much as possible.
We should certainly change the way vertex ids are handled, but there is a 
long road ahead...

David.

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[sage-devel] Re: Enhancement of Kruskal Algorithmn

[David . Coudert]

Given a (di)graph, you can easily assign random edge weights using for 
instance `G.set_edge_lable(u, v, randint(1, 100))`.

Le lundi 11 mars 2019 17:53:05 UTC+1, hy...@iitbbs.ac.in a écrit :
>
>  Is there a way to generate Random directed weighted Graph, I have read 
> the module for Random Graph generator but couldn't find one for weighted.
> Is there a program to generate Random directed weighted Graph there ?
>
>

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[sage-devel] Re: Graph.show with js sometimes messes up labels

[David . Coudert]

 Thank you for reporting this issue.

The order of the vertices given to d3.js was incorrect. This is fixed in 
https://trac.sagemath.org/ticket/27460

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Re: [sage-devel] Re: python3 status report

[David Coudert]

Le mardi 29 janvier 2019 23:19:12 UTC+1, Thierry (sage-googlesucks@xxx) a 
écrit :
>
> Hi, 
>
> On Sun, Jan 27, 2019 at 11:21:21AM -0800, David Coudert wrote: 
> [...] 
> > The most complicated issue is certainly edges of Graph: we sort the 
> > vertices of an edge before returning it... I have no solution for this 
> > issue. We can decide to stop ordering the vertices, but then we will 
> have 
> > to update a very large number of algorithms. We could also design a 
> method 
> > to compare object of different types. 
> > In fact, the main issue is that we use and compare vertices by id 
> instead 
> > of mapping vertices to integer and work only with these integers. That 
> > would ease our life, but it's not easy to change that. 
>
> We discussed the difference between mathematical and algorithmic level 
> various times (for equality, comparison, etc). 
>
> Here, at the "algorithmic" level, the vertices are of course comparable, 
> and most algorithms in graph theory rely on this (starting by the most 
> fundamental such as DFS, BFS, etc). Trying to avoid comparison of 
> vertices would be suicidary, and trying to do that with Sage will just 
> lead to unreadable artificially complicated code. 
>
> If you want an integer label for each vertex, why not just ask to the 
> backend: 
>
> sage: G = graphs.WorldMap() 
> sage: G 
> World Map: Graph on 251 vertices 
> sage: G.vertices()[0] 
> 'Afghanistan' 
>
> sage: GG = G._backend.c_graph()[0] 
> sage: GG 
>  
> sage: GG.verts()[0] 
> 0 
>
> So, somehow, you do not have to map Sage objects back to integers, since 
> we already have a map from integers to Sage objects. 
>
> I did not check the implementations, but though it is kind of too late 
> given the size of Sage, i would advocate to have two explicit layers for 
> combinatorial objects such as words, graphs, permutations, etc, one 
> "algorithmic" where the atoms are integers, with all the good 
> properties, and a "label" dictionary, where we could attach any Sage 
> object to them for "mathematical" questions. And it would be amazing if 
> they were an specified way to do that uniformly. 
>

In fact we already have methods to do that, but changing the code to use 
these methods is not an easy task...

sage: G = graphs.PetersenGraph()
sage: G.set_vertex(0, 'abc')
sage: G.set_vertex(1, graphs.CycleGraph(3))
sage: print(G.get_vertices())
{0: 'abc', 1: Cycle graph: Graph on 3 vertices, 2: None, 3: None, 4: None, 
5: None, 6: None, 7: None, 8: None, 9: None}


That said, regarding the .edges() method, i think that returning a list 
> of pairs is a very wrong approach (though this is what is done for 
> years). Indeed, a list is not only an iterator, but also a container. In 
> particular: 
>
> (a,b) in G.edges() 
>
> is a syntaxially correct statement, but it is far from equivalent to: 
>
> G.has_edge(a,b) 
>
> Which is extremely misleading and can lead to silent mistakes 
> (personally, i used lot of hand-made reorderings in my pyograms before i 
> discovered has_edge). 
>
> Here i would advocate that G.edges() returns a *view* on G, with a 
> dedicated __iter__ method corresponding to the edge_iterator method and 
> a __contains__ method corresponding to the has_edge method. By having a 
> view, you will save a lot of time and memory, and have the benefit that 
> it will follow the graph's mutations. 
>
>
This is an interesting idea, although I'm not sure how to implement that 
efficiently.

David.

PS: when all currently in "needs review" tickets will be closed, the number 
of py3 failing doctests in the graph module will be small (HELP welcome 
here to review tickets and fix remaining doctests). It will then become 
easier to see the effect of changes like not sorting end vertices of edges 
(we could try that), implement a *view* on G, etc.



 

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[sage-devel] Re: py3: issue with round

[David Coudert]

Thanks, it's working well.

Le jeudi 31 janvier 2019 08:45:37 UTC+1, Frédéric Chapoton a écrit :
>
> You could add (at the price of some speed)
>
> from sage.misc.functional import round
>
>>
>>

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[sage-devel] py3: issue with round

[David Coudert]

Does anyone know a suitable way to fix the following issue with round in 
Python3 ?

sage: G = Graph([(0, 1)])
sage: f = g._build_flow_graph({(0, 1): 1}, True)
---
TypeError Traceback (most recent call last)
 in ()
> 1 f = g._build_flow_graph({(Integer(0), Integer(1)): Integer(1)}, 
True)

/Users/dcoudert/sage3/sage/local/lib/python3.6/site-packages/sage/graphs/generic_graph.py
 
in _build_flow_graph(self, flow, integer)
   9094 g.delete_edge(u, v)
   9095 else:
-> 9096 g.set_edge_label(u, v, int(round(l)))
   9097 
   9098 # returning a graph with the same embedding, the 
corresponding name, etc ...

TypeError: type sage.rings.integer.Integer doesn't define __round__ method
sage:
sage: f = g._build_flow_graph({(0, 1): 1.0}, True)
---
TypeError Traceback (most recent call last)
 in ()
> 1 f = g._build_flow_graph({(Integer(0), Integer(1)): 
RealNumber('1.0')}, True)

/Users/dcoudert/sage3/sage/local/lib/python3.6/site-packages/sage/graphs/generic_graph.py
 
in _build_flow_graph(self, flow, integer)
   9094 g.delete_edge(u, v)
   9095 else:
-> 9096 g.set_edge_label(u, v, int(round(l)))
   9097 
   9098 # returning a graph with the same embedding, the 
corresponding name, etc ...

TypeError: type sage.rings.real_mpfr.RealLiteral doesn't define __round__ 
method

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[sage-devel] Re: python3 status report

[David Coudert]

> Is there an apparent common reason for most of these failing tests? Such 
> as code that makes assumptions on sorting (which, IIRC, is different in 
> Python 2 and Python 3)? 
>

Many many methods were relying on sorted list of vertices and edges. We 
have done significant progresses to reduce that.

Another source of problems is that the order of keys of dictionary, i.e., 
list(mydict.keys()) or list(myset), might be different in py2 and py3. This 
breaks many doctests, but may be more complicated, it changes the order in 
which the neighbors of a vertex are visited (check 
G._backend.iterator_nbrs??). Consequently, the returned solution of some 
algorithms might be differents (but still correct). A solution is to tag 
doctests with py2 and py3.

The most complicated issue is certainly edges of Graph: we sort the 
vertices of an edge before returning it... I have no solution for this 
issue. We can decide to stop ordering the vertices, but then we will have 
to update a very large number of algorithms. We could also design a method 
to compare object of different types. 
In fact, the main issue is that we use and compare vertices by id instead 
of mapping vertices to integer and work only with these integers. That 
would ease our life, but it's not easy to change that.

David.

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[sage-devel] Re: GSoC 2019?

[David Coudert]

I'm ready to help mentoring and writing the application.

Le mardi 15 janvier 2019 21:28:16 UTC+1, Harald Schilly a écrit :
>
> Hi everyone. This years Google Summer of Code 2019 just started. Should we 
> write an application? Who is motivated to be a mentor? Everyone from last 
> year still on board?
>
> Here is the timeline, such that everyone can orient:
> https://developers.google.com/open-source/gsoc/timeline
>
> For our application, Feb 6th is the first important date!
>
> -- Harald
>
>

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Re: [sage-devel] Error compiling 8.5.beta3 - gsl-2.5

[David Coudert]

It's working !
Thank you.
David.

Le lundi 12 novembre 2018 10:35:06 UTC+1, Erik Bray a écrit :
>
> I have an idea of what might cause this and will submit a fix, but 
> just manually delete the existing file and try again. 
> On Mon, Nov 12, 2018 at 8:23 AM David Coudert  > wrote: 
> > 
> > Hello, 
> > 
> > After git pull to go from 8.5.beta2 to 8.5.beta3, I get a compilation 
> error with gsl-2.5 (see attached log file). 
> > 
> > [gsl-2.5] Copying package files from temporary location 
> /Users/dcoudert/sage/local/var/tmp/sage/build/gsl-2.5/inst to 
> /Users/dcoudert/sage/local 
> > [gsl-2.5] cp: symlink: libgsl.23.dylib: File exists 
> > [gsl-2.5] 
>  
> > [gsl-2.5] Error copying files for gsl-2.5. 
> > 
> > 
> > I'm still on OSX 10.10.5. I agree I should update the system, but I 
> don't think it's the reason for this compilation issue. 
> > 
> > Thank you for your help, 
> > David. 
> > 
> > -- 
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Re: [sage-devel] Re: Py3, sorting vertices of graph

[David Coudert]

Two more:

   - #26284 : deals with comparability.pyx, digraph.py, 
   vertex_separation.pyx, cutwidth.pyx and connectivity.pyx
   - #26285: avoid comparison of vertex labels in MIPs of generic_graph.


Le vendredi 14 septembre 2018 13:43:37 UTC+2, David Coudert a écrit :
>
> I'm working on reducing the number of places where we explicitly compare 
> vertex labels.
> So far I'm focusing on MIPs.
>
>- #26274 : avoid comparison of vertex labels in MIP for file 
>`graph_coloring.py`
>- #26282 : avoid comparison of vertex labels in MIP for file `graph.py`
>
> More to come, and help for reviewing is more than welcome.
>

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Re: [sage-devel] Re: Py3, sorting vertices of graph

[David Coudert]

I'm working on reducing the number of places where we explicitly compare 
vertex labels.
So far I'm focusing on MIPs.

   - #26274 : avoid comparison of vertex labels in MIP for file 
   `graph_coloring.py`
   - #26282 : avoid comparison of vertex labels in MIP for file `graph.py`
   
More to come, and help for reviewing is more than welcome.

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[sage-devel] Re: Py3, sorting vertices of graph

[David Coudert]

Le jeudi 6 septembre 2018 14:16:33 UTC+2, Martin R a écrit :
>
> Would it be hard to separate vertex labels and vertices? In other words, 
> vertices would always be 0,...,n-1, and there would be an additional array 
> containing the vertex labels.
>

Some graph backends do that, like `c_graph`. I'm not sure it's true for all 
backends.
But, there might be situation in which it is useful to compare vertex 
labels.

 

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[sage-devel] Re: Py3, sorting vertices of graph

[David Coudert]

Comparisons like u < v are used in many places in the code of graphs. 
We can try to use hash(u) < hash(v) instead, but this is certainly not the 
smartest solution.



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Re: [sage-devel] issue with cos(pi/2) and sin(pi)

[David Coudert]

> Le 14 août 2018 à 20:37, TB  a écrit :
> 
> Because float(pi/2) is not exactly pi/2:
> 
> sage: n(pi/2 - float(pi/2), 53)
> 0.000
> sage: n(pi/2 - float(pi/2), 54) # also for perc > 54 of course
> 1.11022302462516e-16

and what’s the advantage of numerical_approx(v, digits=10) over round(v, 
digits=10) ?


> This does mean that:
> 
> sage: float(cos(pi/2))
> 0.0
> sage: float(sin(pi))
> 0.0

This is not what I get when I use float(sin(pi)) or float(cos(pi/2)) inside the 
code. 

When I add a `print(sin, cos)`  in some method (and then recompile), I get
, 

I will use round. It’s apparently the easiest solution.

Best,

> 
> Regards,
> TB


David Coudert
Equipe-Projet COATI
Centre de Recherche INRIA Sophia Antipolis - Méditerranée
Université Côte d’Azur, Inria, CNRS, I3S, France
http://www-sop.inria.fr/members/David.Coudert 
<http://www-sop.inria.fr/mascotte/David.Coudert>






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