In `src/setup.py`, we should not run `cythonize()` manually. It would be
better to use a custom `build_ext` command for that.

This is inspired by the `build_ext` from Cython 0.25: https://github.com
/cython/cython/blob/master/Cython/Distutils/build_ext.py
Unfortunately, we cannot really use that since it doesn't allow to pass
options to `cythonize()`.

Due to a [https://github.com/cython/cython/pull/1476 Cython bug], this
warning gets displayed even though the `cache` option is valid:
{{{UserWarning: got unknown compilation option, please remove: cache}}}.

URL: https://trac.sagemath.org/21600
Reported by: jdemeyer
Ticket author(s): Jeroen Demeyer
Reviewer(s): Matthias Koeppe, Erik Bray

Update the spkg to upstream 1.2.2-95

The giac tarball built from spkg-src to put in upstream/ is there:

http://webusers.imj-prg.fr/~frederic.han/xcas/sage/giac-1.2.2.95.tar.bz2

Switch to .bz2 as wished in #18826

add --disable-ao in spkg-install to avoid libao dependency.
remove the --disable-gmpxx in spkg-install. The built seems not broken
anymore.

updtate giacpy to 0.6 doctest fix + change of name to giacpy_sage.
The tarball to put in upstream is:
http://webusers.imj-
prg.fr/~frederic.han/xcas/giacpy/sage/giacpy_sage-0.6.tar.gz

The modifications about giacpy are there:
https://gitlab.math.univ-paris-diderot.fr/han/giacpy-sage

The 1.2.2.85 version of giac should fix a race condition in icas that
could appear during the test suite.

URL: https://trac.sagemath.org/20946
Reported by: frederichan
Ticket author(s): Frederic Han
Reviewer(s): Ralf Stephan

With certain operating systems, certain compilers and certain compiler
flags (in particular Cygwin with `SAGE_DEBUG=yes`), the PARI function
`is_universal_constant()` can be broken. This leads to a `0` return
value for closures returning `gnil`:

{{{
sage: pari("x -> print(x);")("hello")
hello
0
}}}

'''Upstream report''': http://pari.math.u-bordeaux.fr/archives/pari-
dev-1610/msg00006.html

This branch simply adds a patch from upstream.

URL: https://trac.sagemath.org/21637
Reported by: embray
Ticket author(s): Jeroen Demeyer
Reviewer(s): Erik Bray

This ticket is meant to improve support for Linux with
[https://www.kernel.org/doc/Documentation/vm/overcommit-accounting
vm.overcommit = 2].

In Sage, the PARI stack takes a large amount of virtual memory but only
a small part is usually used.

When allocating memory, this memory is "committed" which means that it
is made available as virtual memory. However, as long as a program is
not using that memory, this costs nothing because the kernel does not
need to make available actual memory (physical or swap) for it. This is
different with `vm.overcommit = 2`: then all committed memory is
counted. In that case, even unused virtual memory means that the system
will have less memory available.

This can be solved by using the `PROT_NONE` flag of
[https://linux.die.net/man/2/mmap mmap(2)]. This means that the memory
cannot be read nor written. In this case, the kernel does not commit
this memory (it does show up as virtual memory in `top`). Note that this
is not actually documented anywhere, but that is how it works.

This branch adds a PARI patch which implements this `PROT_NONE` trick.
We first allocate the PARI stack in the usual way (so the maximum stack
size is limited by the available virtual memory, which makes sense) but
then uncommit most of the stack by reallocating it with `PROT_NONE`.

Finally, note that this patch does not functionally affect PARI (but I
did run doctests just in case).

'''Upstream report''': http://pari.math.u-bordeaux.fr/archives/pari-
dev-1609/msg00008.html

'''Release manager''': merge with #21637

URL: https://trac.sagemath.org/21582
Reported by: jdemeyer
Ticket author(s): Jeroen Demeyer
Reviewer(s): Jonathan Bober

{{{
sage: gen_laguerre(n,a,x).diff(a)
-gen_laguerre(n - 1, a + 1, x)
sage: gen_laguerre(n,a,x).diff(x)
-gen_laguerre(n - 1, a + 1, x)

sage: derivative(hermite(n,x),x)
2*n*hermite(n - 1, x)
sage: derivative(hermite(n,x),n)
2*n*hermite(n - 1, x)
}}}
so something is badly wrong with recognizing the diff. parameter. Note
only `hermite` is implemented in Pynac.

URL: https://trac.sagemath.org/21644
Reported by: rws
Ticket author(s): Carlos R. Mafra
Reviewer(s): Ralf Stephan

The option `export` of the command `sage --notebook`, introduced in
#19877, is missing from the output of `sage --advanced`. Besides neither
`export` nor `jupyter` appears in the section ''Command-line options for
Sage'' of the reference manual. The current ticket corrects this. It
also adds an example of use of `export` in the output of `sage
--notebook --help`.

URL: https://trac.sagemath.org/21634
Reported by: egourgoulhon
Ticket author(s): Eric Gourgoulhon
Reviewer(s): Marc Mezzarobba

* compiles with clang (fix by François Bissey)
 * fix `cot(float)` bug; (#21365, fix by Paul Masson)
 * NaN constant; return NaN with atan2(0,0) (#21614)
 * numeric log fixes (#18970)
 * prevent some overflow exceptions in `cot/csc`
 * two-argument log (log to base) (#18970)
 * Support `gegenbauer(n,a,x)` with non-numeric `a` (recurrence by
Carlos R. Mafra)
 * update AUTHORS

https://github.com/pynac/pynac/releases/download/pynac-0.6.91/pynac-0.6.
91.tar.bz2

URL: https://trac.sagemath.org/21623
Reported by: rws
Ticket author(s): Ralf Stephan
Reviewer(s): Paul Masson, Travis Scrimshaw

because sorting using `cmp=` is no longer allowed in py3,
one needs to change the way the complex numbers are sorted for display

URL: https://trac.sagemath.org/21616
Reported by: chapoton
Ticket author(s): Frédéric Chapoton
Reviewer(s): Travis Scrimshaw

This part of `src/setup.py` should be moved inside some distutils
command:
{{{
#########################################################
### Clean
#########################################################

print('Cleaning up stale installed files....')
t = time.time()
from sage_setup.clean import clean_install_dir
output_dirs = SITE_PACKAGES + glob.glob(os.path.join(SAGE_SRC, 'build',
'lib*'))
for output_dir in output_dirs:
    print('- cleaning {0}'.format(output_dir))
    clean_install_dir(output_dir, python_packages, python_modules,
            ext_modules, python_data_files)
print('Finished cleaning, time: %.2f seconds.' % (time.time() - t))
}}}

URL: https://trac.sagemath.org/21604
Reported by: jdemeyer
Ticket author(s): Jeroen Demeyer
Reviewer(s): Matthias Koeppe

Trac #21596: Fix so that Matrix charpoly(algorithm='flint') doesn't destroy the polynomial ring generator

One line fix coming shortly, I hope.

URL: https://trac.sagemath.org/21596
Reported by: bober
Ticket author(s): Jonathan Bober
Reviewer(s): Marc Mezzarobba

The Sage-in-Emacs interface `sage-mode` is broken since IPython 5.0, see
#21227. `sage-shell-mode` by stakemori is a very good alternative. This
is distributed using the Emacs package manager MELPA, which should be
familiar to any Emacs user (in both senses of the word "should"), so
there is no real reason to distribute that with Sage or even have an
spkg for it.

The suggestion is therefore simply to remove `sage-mode` as an optional
package from Sage.

URL: https://trac.sagemath.org/21549
Reported by: jsrn
Ticket author(s): Matthias Koeppe
Reviewer(s): Dima Pasechnik

This patch will add function to check if a lattice is join-distributive.
(And dually, if it is meet-distributive.)

URL: https://trac.sagemath.org/21544
Reported by: jmantysalo
Ticket author(s): Jori Mäntysalo
Reviewer(s): Travis Scrimshaw

Building sage outputs a lot. Especially in highly parallelized builds,
the output is not very useful.

This ticket implements an option to silence the build, using `make`
argument (or environment variable) `V=0`. (This mimics the interface of
[https://www.gnu.org/software/automake/manual/html_node/Automake-Silent-
Rules.html#Automake-Silent-Rules Automake silent rules]; so this is one
step towards #21566):
{{{
$ make -j8 V=0 autotools
make -j8 build/make/Makefile
make[1]: warning: -jN forced in submake: disabling jobserver mode.
make[1]: `build/make/Makefile' is up to date.
*** ALL ENVIRONMENT VARIABLES BEFORE BUILD: ***
... long list of environment variables elided -- this ticket does
nothing about that ...
***********************************************
make[1]: warning: -jN forced in submake: disabling jobserver mode.
Running 'sage-spkg xz-5.2.2', output appears in
/Users/mkoeppe/cvs/sage/logs/pkgs/xz-5.2.2.log...
Running 'sage-spkg xz-5.2.2', output appears in
/Users/mkoeppe/cvs/sage/logs/pkgs/xz-5.2.2.log... done
Running 'sage-spkg autotools-20141105', output appears in
/Users/mkoeppe/cvs/sage/logs/pkgs/autotools-20141105.log...
=========================== WARNING ===========================
You are about to download and install the experimental package
autotools-20141105.  This probably won't work at all for you! There
is no guarantee that it will build correctly, or behave as
expected. Use at your own risk!
===============================================================
Are you sure you want to continue [Y/n]?
OK, installing autotools-20141105 now.
Running 'sage-spkg autotools-20141105', output appears in
/Users/mkoeppe/cvs/sage/logs/pkgs/autotools-20141105.log... exit status
1
make[1]: *** [/Users/mkoeppe/cvs/sage/local/var/lib/sage/installed/autot
ools-20141105] Error 1
}}}

Note that, though all output is redirected, the interactive questions
(#20884, #21082) still go through to the terminal. This is achieved by
using `/dev/tty`.

The patch also unconditionally silences a few make recipe lines
involving `sage-logger`.

Follow-up ticket: #21589

URL: https://trac.sagemath.org/21539
Reported by: mkoeppe
Ticket author(s): Matthias Koeppe
Reviewer(s): John Palmieri

This patch adds a function to check if a lattice is semidistributive,
i.e. both meet- and join-semidistributive.

It is not explicitly said in any paper that a join- (or
meet-)semidistributive lattice with equal number of meet- and join-
irreducible elements is (fully) semidistributive. However, J.B. Nation
forwarded a proof by Kira Adaricheva to me. It uses the fact that a
meet-semidistributive lattice has a kappa function for every join-
irreducible (dually, a dual kappa for meet-semidistributive lattices).
An element that is minimal among those below a meet-irreducible but not
below the upper cover of meet-irreducible is join-irreducible. Following
that we can deduce that kappa and dual-kappa are in 1-to-1 relationship,
and so the lattice is (fully) semidistributive.

URL: https://trac.sagemath.org/21528
Reported by: jmantysalo
Ticket author(s): Jori Mäntysalo
Reviewer(s): Frédéric Chapoton

`notedown` creates jupyter notebooks from markdown. It is a dependency
of `rst_to_ipynb`.

- upstream zipball : https://github.com/aaren/notedown/archive/dfda648b7
6af1d4760652050d47354ce704992af.zip to be renamed `notedown-
dfda648b.zip`
- alternative download : https://lipn.univ-
paris13.fr/~monteil/hebergement/tmp/notedown-dfda648b.zip

URL: https://trac.sagemath.org/21512
Reported by: tmonteil
Ticket author(s): Thierry Monteil
Reviewer(s): Sébastien Labbé

`pandoc_attributes` is a dependency of `notedown`, which is a dependency
of `rst_to_ipynb`.

Tarball can be found at https://github.com/aaren/pandoc-
attributes/archive/8bc82f6d0d1421c7ba84b480748fb89269c6523e.zip and
should be renamed `pandoc_attributes-8bc82f6d.zip`. See also
https://lipn.univ-paris13.fr/~monteil/hebergement/tmp/pandoc_attributes-
8bc82f6d.zip for a direct download.

URL: https://trac.sagemath.org/21490
Reported by: tmonteil
Ticket author(s): Thierry Monteil
Reviewer(s): Sébastien Labbé

The directory `src/sage/symbolic` contains a mixture of modules which
just define the Pynac interface and modules which implement the Sage
symbolics.

This ticket moves all Pynac stuff to `src/sage/libs/pynac`. Also rename
`ginac.pxd` -> `pynac.pxd`.

URL: https://trac.sagemath.org/21372
Reported by: jdemeyer
Ticket author(s): Jeroen Demeyer
Reviewer(s): Travis Scrimshaw

The FriCAS interface is currently very rudimentary.  In particular,
converting the results of a computation into sage types is available
only in very few special cases.

URL: https://trac.sagemath.org/21231
Reported by: mantepse
Ticket author(s): Martin Rubey
Reviewer(s): Bill Page, Emmanuel Charpentier

So that references in sage manuals to pari functions become active
links.

Pari is now able to provide automatic links
to the documentation of every function. Let us use that!

URL: https://trac.sagemath.org/21210
Reported by: chapoton
Ticket author(s): Frédéric Chapoton
Reviewer(s): Travis Scrimshaw

Because `ClonableArray` also takes the parent into consideration of
equality checking, we currently have the following:
{{{
sage: Permutations([1])[0] == Permutation([1])
False
}}}
I propose to have `Permutations(range(n))` be ''identical'' to
`Permutations(n)`.

URL: https://trac.sagemath.org/21069
Reported by: dkrenn
Ticket author(s): Travis Scrimshaw
Reviewer(s): Darij Grinberg

I suggest to upgrade `glpk` to the latest available version (4.60 at the
time of writing). The current version has been superseded in Gentoo and
the formatting of the output has changed.
Here are the tasks for this upgrade:

1. use `spkg-src` instead of patching `configure` directly

2. some part of `have_error.patch` is now upstream, but not every piece
of that patch was accepted

3. clean up `SPKG.txt` and other files so they are reflecting the
current reality more closely without obsolete historical comments

'''Tarball''': http://www.lmona.de/files/sage/glpk-4.60.tar.bz2
(generated with `spkg-src`)

URL: https://trac.sagemath.org/20710
Reported by: fbissey
Ticket author(s): François Bissey
Reviewer(s): Matthias Koeppe, Jeroen Demeyer

In preparation for #20238, take out of `PariInstance` all components
specific to Sage.

URL: https://trac.sagemath.org/20241
Reported by: defeo
Ticket author(s): Luca De Feo
Reviewer(s): Jeroen Demeyer

The eventual goal is to move all references to a central file. This
deals with many of the references, but not all of them. (So far, it
hasn't dealt with the references in `combinat`, `graphs`, `rings`, or
`schemes`.)

URL: https://trac.sagemath.org/21454
Reported by: jhpalmieri
Ticket author(s): John Palmieri, Johan Rosenkilde
Reviewer(s): Johan Rosenkilde, John Palmieri

'''Lots''' of stuff has changed in Singular 4.
This is a big update.

Build system completely changed, and a lot of internal stuff.

Original upstream tarball at `www.mathematik.uni-
kl.de/ftp/pub/Math/Singular/SOURCES/4-0-3/`:  `singular-4.0.3p3`
'''dot''' `tar` '''dot''' `gz`

Modified tarball made with spkg-src at:
* http://www.lmona.de/files/sage/singular-4.0.3p3.tar.bz2

This corresponds to commit a070b84d whose message tells 4.0.3p3 and on
which this branch was based:
* https://github.com/Singular/Sources/commit/a070b84d59be835a2946d1386ed
d3221d80f3fe7

You can also make your own tarball based on this commit or another one
with
{{{
env SINGULAR_GIT_COMMIT=a070b84d ./sage --sh build/pkgs/singular/spkg-
src
./sage --package fix-checksum singular
}}}
This script is loosely based on the `make_tar.sh` script from upstream.

URL: https://trac.sagemath.org/17254
Reported by: jdemeyer
Ticket author(s): Jakob Kroeker, Jean-Pierre Flori, Jeroen Demeyer, John
Perry, François Bissey, Leif Leonhardy, Dima Pasechnik
Reviewer(s): François Bissey, Jeroen Demeyer, Ben Hutz, Leif Leonhardy,
Dima Pasechnik, Travis Scrimshaw

Given an infinite enumerated set `I`, I'd still expect this to work (and
it's very handy):
{{{
sage: Partitions()[:5]
[[], [1], [2], [1, 1], [3]]
}}}

URL: https://trac.sagemath.org/16320
Reported by: tscrim
Ticket author(s): Travis Scrimshaw
Reviewer(s): Nathann Cohen, Darij Grinberg

Lcalc still uses some non-standard "features" of `g++`.

C++ compilers that are pickier than `g++` will not allow this.

GCC 5.x again got stricter and now also needs the second "default
parameter" patch (or once again `-fpermissive`) mentioned below.

----
Current branch fix usage of internal headers and some declarations. More
to be done as I haven't even scratched the issues mentioned in this
ticket - unless they have been fixed by another merged ticket.

URL: https://trac.sagemath.org/12437
Reported by: ohanar
Ticket author(s): François Bissey
Reviewer(s): Travis Scrimshaw

Recently there was a thread on the matplotlib list where someone posted
matplotlib code for a streamline plot.  It looks very nice.  If the code
doesn't get included in matplotlib, we could still ask about including
it in Sage to do streamline plots.

Mailing list message:
http://permalink.gmane.org/gmane.comp.python.matplotlib.general/26362

Mailing list thread:
http://comments.gmane.org/gmane.comp.python.matplotlib.general/26354

Example code: http://web.mit.edu/speth/Public/streamlines.py

Example plot: http://web.mit.edu/speth/Public/streamlines.png

URL: https://trac.sagemath.org/10775
Reported by: jason
Ticket author(s): Paul Masson
Reviewer(s): Travis Scrimshaw

#21670, while fixing `%attach` crashes sage if, for any reason,
`select.select()` is
interrupted once a file has been attached. This happens for example when
resizing windows.

Here is how to reproduce the bug. In a new xterm run

{{{
$ echo "a = 1" > /tmp/test.py
$ sage
┌────────────────────────────────────────────────────────────────────┐
│ SageMath version 7.4.rc2, Release Date: 2016-10-15                 │
│ Type "notebook()" for the browser-based notebook interface.        │
│ Type "help()" for help.                                            │
└────────────────────────────────────────────────────────────────────┘
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Warning: this is a prerelease version, and it may be unstable.     ┃
┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛
sage:
}}}

Now resize the xterm, everything works as it is supposed to.
Now attach /tmp/test.py and again resize the window:
{{{
sage: %attach /tmp/test.py
sage:

**********************************************************************

Oops, Sage crashed. We do our best to make it stable, but...
}}}

URL: https://trac.sagemath.org/21711
Reported by: etn40ff
Ticket author(s): Salvatore Stella
Reviewer(s): Volker Braun

Hopefully part of the solution to restore the broken %attach.

URL: https://trac.sagemath.org/21545
Reported by: chapoton
Ticket author(s): Volker Braun
Reviewer(s): Travis Scrimshaw

SageMath version 7.4.rc2

Merge branch 'public/combinat/permutations_std_set-21069' of git://trac.sagemath.org/sage into public/combinat/permutations_std_set-21069