Upgrade to Pynac-0.7.10

[rwst]

In the new version:

• remove static PyObjects; (Upgrade to Pynac-0.7.8 #23134)
• fix segmentation fault with coefficients() (Doctest: segmentation fault with coefficients() on symbolic expressions #23545)
• fix compile error --with-giac=yes
• fix tgamma/lgamma return types
• (real^m)^(1/n) --> abs(real)^(m/n), m even, m/n integer (Doctest: Immediate simplifications of symbolic powers #14305)
• fix add::conjugate() (Doctest: Conjugate does not distribute over a sum #23135)
• fix is_real(zeta(real))
• negative symbolic domain from assume(sym<0) (Doctest: x.is_negative() when assuming x < 0 #21973)
• add missing calls to set_domain in symbol constructors (Cache assumptions and only send to Maxima when needed #23138)
• implement add.info(negative)
• exact comparison of overall_coefficients
• internal LONG numeric; nice speedup in some parts
• fast internal in-place arithmetic operators
• obsolete some internal usages of Python

https://github.com/pynac/pynac/releases/download/pynac-0.7.10/pynac-0.7.10.tar.bz2

Depends on #23329

CC: @kiwifb

Component: packages: standard

Author: Ralf Stephan

Branch/Commit: 5387ba5

Reviewer: Jeroen Demeyer

Issue created by migration from https://trac.sagemath.org/ticket/23325

[rwst]

Branch: u/rws/upgrade_to_pynac_0_7_9

[rwst]

New commits:

1d1aeb8	23325: pkg version/chksum, remove obsolete patch
cf62180	23325: fix py_get_parent_char()
f976b8c	23325: fix doctests

[rwst]

Author: Ralf Stephan

[rwst]

Commit: f976b8c

[jdemeyer]

comment:4

I don't agree with the change to py_get_parent_char: why assume characteristic zero if the parent cannot decide?

[jdemeyer]

Reviewer: Jeroen Demeyer

[jdemeyer]

comment:5

If you revert the change to py_get_parent_char and all doctests pass, you can set this to positive review.

[rwst]

comment:6

That's a no, because this then needs investigation (doctest fail at src/sage/manifolds/differentiable/diff_form.py:796):

sage: M = Manifold(3, 'R3', '\RR^3', start_index=1)
sage: c_cart.<x,y,z> = M.chart()
sage: eps = M.diff_form(3, 'epsilon', r'\epsilon')
sage: eps[1,2,3] = 1
sage: a = M.one_form('A')
sage: a[:] = (x*y*z, -z*x, y*z)
sage: b = M.one_form('B')
sage: b[:] = (cos(z), sin(x), cos(y))
sage: ab = a.wedge(b)
sage: dab = ab.exterior_derivative()
sage: dab[[1,2,3]]/eps[[1,2,3]]
...
/home/ralf/sage/src/sage/structure/element.pyx in sage.structure.element.RingElement._div_ (build/cythonized/sage/structure/element.c:17655)()
   2453         return l
   2454 
-> 2455     cpdef _div_(self, other):
   2456         """
   2457         Default implementation of division using the fraction field.

/home/ralf/sage/local/lib/python2.7/site-packages/sage/manifolds/coord_func_symb.pyc in _div_(self, other)
    947         if other._express.is_zero():
    948             raise ZeroDivisionError("division of a coordinate function by zero")
--> 949         res = self._simplify(self._express / SR(other))
    950         if res.is_trivial_zero():  # NB: "if res == 0" would be too
    951                                    # expensive (cf. #22859)

/home/ralf/sage/src/sage/structure/element.pyx in sage.structure.element.Element.__div__ (build/cythonized/sage/structure/element.c:12950)()
   1638         cdef int cl = classify_elements(left, right)
   1639         if HAVE_SAME_PARENT(cl):
-> 1640             return (<Element>left)._div_(right)
   1641         if BOTH_ARE_ELEMENT(cl):
   1642             return coercion_model.bin_op(left, right, div)

/home/ralf/sage/src/sage/symbolic/expression.pyx in sage.symbolic.expression.Expression._div_ (build/cythonized/sage/symbolic/expression.cpp:24795)()
   3445                 raise ZeroDivisionError("Symbolic division by zero")
   3446             else:
-> 3447                 raise
   3448         finally:
   3449             sig_off()

/home/ralf/sage/src/sage/symbolic/expression.pyx in sage.symbolic.expression.Expression._div_ (build/cythonized/sage/symbolic/expression.cpp:24684)()
   3437                                o)
   3438             else:
-> 3439                 x = left._gobj / _right._gobj
   3440             return new_Expression_from_GEx(left._parent, x)
   3441         except Exception as msg:

/home/ralf/sage/src/sage/libs/pynac/pynac.pyx in sage.libs.pynac.pynac.py_get_parent_char (build/cythonized/sage/libs/pynac/pynac.cpp:9942)()
    818         return 0
    819 
--> 820     c = (<Element>o)._parent.characteristic()
    821 
    822     # Pynac only differentiates between

/home/ralf/sage/local/lib/python2.7/site-packages/sage/categories/rings.pyc in characteristic(self)
    461             from sage.rings.infinity import infinity
    462             from sage.rings.integer_ring import ZZ
--> 463             order_1 = self.one().additive_order()
    464             return ZZ.zero() if order_1 is infinity else order_1
    465 

/home/ralf/sage/src/sage/structure/element.pyx in sage.structure.element.RingElement.additive_order (build/cythonized/sage/structure/element.c:18049)()
   2470         Return the additive order of ``self``.
   2471         """
-> 2472         raise NotImplementedError
   2473 
   2474     def multiplicative_order(self):

NotImplementedError: 

sage: dab[[1,2,3]]
Scalar field on the 3-dimensional differentiable manifold R3
sage: type(_)
<class 'sage.manifolds.differentiable.scalarfield_algebra.DiffScalarFieldAlgebra_with_category.element_class'>
sage: eps[[1,2,3]]
Scalar field on the 3-dimensional differentiable manifold R3
sage: type(_)
<class 'sage.manifolds.differentiable.scalarfield_algebra.DiffScalarFieldAlgebra_with_category.element_class'>

sage: parent(dab[[1,2,3]])
Algebra of differentiable scalar fields on the 3-dimensional differentiable manifold R3
sage: parent(eps[[1,2,3]])
Algebra of differentiable scalar fields on the 3-dimensional differentiable manifold R3

While this is triggered by changes in Pynac that should be addressed it's not clear to me why the division of two scalar fields must go through SR at all.

[jdemeyer]

comment:7

I will have a look.

[rwst]

comment:8

The reason why this is now failing is that the quotient here, which is 1 but not integer, is now recognized as is_one and triggers the ...pos_char call.

https://github.com/pynac/pynac/blob/master/ginac/mul.cpp#L702

Removing the call altogether in preliminary testing only fails one doctest involving Mod and, frankly, I could care less. Full testing now.

[jdemeyer]

comment:9

I think the best solution here is simply to implement characteric for the "Ring of coordinate functions".

[jdemeyer]

Dependencies: #23329

[sagetrac-git]

Changed commit from f976b8c to fb52b8b

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

fb52b8b

23325: revert libs/pynac commit

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

1a369cb	Merge branch 'develop' into t/23325/upgrade_to_pynac_0_7_9
1fa0f69	Merge branch 'develop' into t/23325/upgrade_to_pynac_0_7_9
725db22	Merge branch 'develop' into t/23325/upgrade_to_pynac_0_7_9
3b7db8b	pynac-2.7.10 doctest fixes
f5682bf	necessary code change to make pynac-2.7.10 work

[sagetrac-git]

Changed commit from fb52b8b to f5682bf

[rwst]

comment:13

Correct is 0.7.10 not 2.7.10.

[sagetrac-git]

Changed commit from f5682bf to 0879761

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

bafd41a	Merge branch 'develop' into t/23325/upgrade_to_pynac_0_7_9
a90ce6a	23582: Robustify doctest in hyperbolic_geodesic.py
0879761	Merge branch 'u/rws/robustify_doctest_in_hyperbolic_geodesic_py' of git://trac.sagemath.org/sage into t/23325/upgrade_to_pynac_0_7_9

[rwst]

Changed dependencies from #23329 to #23329, #23582

[rwst]

Changed dependencies from #23329, #23582 to #23329, #23582, #23587

[jdemeyer]

New commits:

b54f51b

Doc formatting

[jdemeyer]

Changed commit from 62cebba to b54f51b

[vbraun]

Changed branch from u/jdemeyer/23325-1 to b54f51b

[vbraun]

comment:37

Fails on 32-bit Linux

**********************************************************************
File "src/doc/de/thematische_anleitungen/sage_gymnasium.rst", line 191, in doc.de.thematische_anleitungen.sage_gymnasium
Failed example:
    sqrt(18)
Expected:
    3*sqrt(2)
Got:
    sqrt(18)
**********************************************************************
1 item had failures:
   1 of 294 in doc.de.thematische_anleitungen.sage_gymnasium
    [207 tests, 1 failure, 5.39 s]
**********************************************************************
File "src/sage/functions/orthogonal_polys.py", line 1668, in sage.functions.orthogonal_polys.Func_assoc_legendre_Q._eval_
Failed example:
    gen_legendre_Q(2,1,3)
Expected:
    -1/4*sqrt(-2)*(-36*I*pi + 36*log(4) - 36*log(2) - 25)
Got:
    -1/8*sqrt(-8)*(-36*I*pi + 36*log(4) - 36*log(2) - 25)
**********************************************************************
1 item had failures:
   1 of   2 in sage.functions.orthogonal_polys.Func_assoc_legendre_Q._eval_
    [378 tests, 1 failure, 7.79 s]
**********************************************************************
File "src/sage/rings/number_field/number_field_base.pyx", line 219, in sage.rings.number_field.number_field_base.NumberField.minkowski_bound
Failed example:
    B = K.minkowski_bound(); B
Expected:
    16/3*sqrt(3)/pi
Got:
    8/9*sqrt(108)/pi
**********************************************************************
File "src/sage/rings/number_field/number_field_base.pyx", line 230, in sage.rings.number_field.number_field_base.NumberField.minkowski_bound
Failed example:
    B = K.minkowski_bound(); B
Expected:
    sqrt(10)
Got:
    1/2*sqrt(40)
**********************************************************************
1 item had failures:
   2 of  19 in sage.rings.number_field.number_field_base.NumberField.minkowski_bound
    [74 tests, 2 failures, 2.09 s]
**********************************************************************
File "src/sage/rings/real_mpfr.pyx", line 3961, in sage.rings.real_mpfr.RealNumber.sqrt
Failed example:
    r.sqrt()
Expected:
    2*sqrt(1086)
Got:
    sqrt(4344)
**********************************************************************
1 item had failures:
   1 of  13 in sage.rings.real_mpfr.RealNumber.sqrt
    [1000 tests, 1 failure, 3.14 s]

[vbraun]

Changed commit from b54f51b to none

[rwst]

comment:38

Okay, I'm installing virtualization (a first) and Ubuntu 32-bit to get the ability to test on 32-bit.

[rwst]

Changed branch from b54f51b to u/rws/b54f51bab33a602448c1b3e2f719fb375661aac3

[rwst]

Changed branch from u/rws/b54f51bab33a602448c1b3e2f719fb375661aac3 to b54f51b

[rwst]

comment:41

STDERR: error: Server does not allow request for unadvertised object b54f51bab33a602448c1b3e2f719fb375661aac3

So I'll push to my previous branch u/rws/23325-1 (including Jeroen's fix) in the hope you can pick up its last commit, which contains a last-minute fix.

[rwst]

Changed branch from b54f51b to u/rws/23325-1

[rwst]

New commits:

a887a8b	23325: chksum,version
98bab37	23325: remove obsolete patch
fe100f7	23325: explicitly look for sage-python23
8fe77a7	23325: code change to make use of new pynac
62cebba	23325: doctest fixes
5a2da58	23325: doc formatting
5387ba5	23325: last-minute 32-bit fix

[rwst]

Commit: 5387ba5

[kiwifb]

comment:44

I think it can just be put back to positive review. Especially if the last fix is the stuff for 32bits problems.

[vbraun]

Changed branch from u/rws/23325-1 to 5387ba5