Updates to mathematical software

[Jerry James]

Hello everyone.  Months ago, I started working on updates to a couple of
our mathematical packages.  But they, in turn, required other packages to
be updated, and those updates required other packages to be updated, and
the whole thing kind of snowballed.  I believe that I have finally reached
a point of closure, where I can update the whole pile and have everything
still work afterwards.

I propose to do the following updates and builds in Rawhide in about a
week.  If maintainers of any of these packages object, please let me know
the nature of your objection.

The only explicit soname bump in these updates is libntl.so.35 to
libntl.so.36.  However, there are a few other libraries that changed ABI
without a corresponding soname bump (typically with an soname of
libfoo.so.0, sigh), so I will rebuild all consumers.

Changes:

   - arb: update from 2.11.1 to 2.13.0
   - brial: update from 0.8.5 to 1.2.3.  Build for both python 2 and 3.
   Add a %check script.
   - cbmc: rebuild for glpk 4.65
   - coin-or-lemon: rebuild for glpk 4.65
   - eclib: update from 20170815 to 20171002
   - fflas-ffpack: update from 2.2.2 to 2.3.2.  Drop all patches.
   - flint: rebuild for ntl 11.0.0.  Attempt to work around bz 1555151 on
   arm.
   - gap-pkg-float: rebuild for libfplll 5.2.1 and mpfi 1.5.3
   - gfan: build libgfan as a shared library and distribute it in a new
   subpackage, which obsoletes the erroneous gfanlib subpackage of Singular.
   - giac: rebuild for libfplll 5.2.1 and mpfi 1.5.3
   - givaro: update from 4.0.2 to 4.0.4
   - glpk: update from 4.61 to 4.65.  Add a patch slated for 4.66, needed
   by sagemath.  Build with ODBC and MariaDB support.
   - latte-integrale: rebuild for ntl 11.0.0 and glpk 4.65
   - libfplll: update from 5.1.0 to 5.2.1.  Drop the rounding patch, fixed
   upstream.
   - libgap: require the GAP default packages (silences startup warnings
   about missing packages).
   - linbox: update from 1.4.2 to 1.5.2.  Drop upstreamed fplll patch.  Add
   gcc8 patch as recommended by upstream to fix a C++ issue.
   - Macaulay2: update from 1.9.2 to 1.11.  Drop upstreamed verbose_build,
   givaro, pari, and endian patches.
   - mpfi: update from 1.5.1 to 1.5.3.  Drop the aarch64 patch, fixed
   upstream.
   - normaliz: update from 3.4.0 to 3.5.4.  Drop all patches.
   - ntl: update from 10.5.0 to 11.0.0
   - octave: rebuild for glpk 4.65
   - openms: rebuild for glpk 4.65
   - pari: backport ellratpoints and hyperellratpoints from pari 2.10
   alpha, needed by sagemath.  The alternative is to update pari to an alpha
   version, which makes me very uncomfortable.
   - polymake: update from 3.1 to 3.2r3.  Drop upstreamed gcc7 patch.
   - ppl: rebuild for glpk 4.65
   - pynac: update from 0.7.8 to 0.7.16.  Drop arch conditionals for giac,
   which is now available on all supported arches.
   - python-cvxopt: update from 1.1.9 to 1.2.0
   - python-cypari2: update from 1.1.3 to 1.1.4.  Drop upstreamed offbyone
   patch.
   - python-cysignals: update from 1.6.4 to 1.7.1
   - python-flask-autoindex: update from 0.4.1 to 0.6.  Drop upstreamed
   tests patch.  Build for both python 2 and 3.  Build and package the
   documentation.
   - python-flask-silk: update from 0.1.2 to 0.2.  Do not bundle
   flask-sphinx-themes.  Build for both python 2 and 3.  Build and package the
   documentation.  Add a %check script.
   - python-fpylll: update from 0.2.4dev to 0.4.0dev for libfplll 5.2.1.
   - python-gmpy2: update from 2.0.8 to 2.1.0a2.  The alpha version has
   some functions required by the latest sagemath.  Since the only consumers
   of this package currently in Fedora are sagemath and sympy, which is
   consumed by sagemath, I figure that if the sagemath team is going to
   require an alpha version, they are only hurting themselves if something
   goes wrong.
   - sagemath: update from 8.0 to 8.2.  Numerous changes were necessary to
   make this work.
   - shogun: rebuild for glpk 4.65.  Add two patches to fix FTBFS.  The
   sources use some deprecated json-c macros, which are no longer defined by
   default; the first patch includes the relevant header.  The second patch
   works around a bug in pybtex, which has already been reported to upstream
   pybtex and fixed in git.  If a new pybtex release is made soon, I will
   build it and drop this patch.
   - Singular: drop the mistakenly exposed gfanlib package; build with
   libgfan instead.  Rebuild for ntl 11.0.0 and polymake 3.2r2.  Drop the
   sequence-point patch, which patches the libgfan sources.

NOTE ON MPFR: There is an update to mpfr 4 in the works:
https://fedoraproject.org/wiki/Changes/mpfr-4.0.0.  The above updates help
that effort in the following ways:

   - The mpfi update brings in a version that is compatible with both mpfr
   3 and 4, so when the time comes, simply rebuilding against mpfr 4 will work.
   - The sagemath update brings in a version that wants mpfr 4.  For now, I
   will patch it to use the old mpfr 3 interface.  Once we have mpfr 4
   available, all we have to do is remove that patch and rebuild.

Let me know of any concerns you might have about this pile of updates.  As
usual with this particular set of packages, some builds take many hours, so
the rebuilds will probably span multiple days.  Expect broken deps reports
out of Rawhide while in the middle.  They will disappear once the entire
stack has been built.

Regards,
-- 
Jerry James
http://www.jamezone.org/

[Rex Dieter]

Jerry James wrote:

>  Hello everyone.  Months ago, I started working on updates to a couple
> of
>  our mathematical packages.  
...
>  I believe that I have finally reached
>  a point of closure, where I can update the whole pile and have everything
>  still work afterwards. 
Thanks for your heroic efforts, much appreciated!

-- Rex

[Paul Howarth]

Hi Jerry,

On Fri, 25 May 2018 22:27:38 -0600
Jerry James <loganjerry(a)gmail.com&gt; wrote:
>     - pari: backport ellratpoints and hyperellratpoints from pari
> 2.10
>     alpha, needed by sagemath.  The alternative is to update pari to
>  an alpha version, which makes me very uncomfortable. 
Do what you need to for pari; your maths stack is the main (only?)
consumer of pari in Fedora. I originally took pari as I needed it for
perl-Math-Pari but that's dead upstream and stuck using the libpari23
compat package now.

In fact, I'd be happy to hand pari maintainership over to you if that
would help you at all, but I'm fine with keeping it if you don't want
the additional burden.

Cheers, Paul.

[Jerry James]

On Sun, May 27, 2018 at 8:18 AM, Paul Howarth <paul(a)city-fan.org&gt; wrote:

>  Do what you need to for pari; your maths stack is the main (only?)
>  consumer of pari in Fedora. I originally took pari as I needed it for
>  perl-Math-Pari but that's dead upstream and stuck using the libpari23
>  compat package now.
>
>  In fact, I'd be happy to hand pari maintainership over to you if that
>  would help you at all, but I'm fine with keeping it if you don't want
>  the additional burden.
>  
It looks like the giac, Macaulay2, and sagemath stacks are the only pari
consumers.  There is also a pending update to clisp that will bring its
pari integration back; that has been missing for a few years.  And sure
enough, I've got my fingers in all of those pies. :-)  I'm happy to take
pari off of your hands if you want to hand it over.

Regards,
-- 
Jerry James
http://www.jamezone.org/

[Paul Howarth]

On Mon, 28 May 2018 21:03:34 -0600
Jerry James <loganjerry(a)gmail.com&gt; wrote:

>  On Sun, May 27, 2018 at 8:18 AM, Paul Howarth
> <paul(a)city-fan.org&gt;
>  wrote:
>  
>  > Do what you need to for pari; your maths stack is the main (only?)
>  > consumer of pari in Fedora. I originally took pari as I needed it
>  > for perl-Math-Pari but that's dead upstream and stuck using the
>  > libpari23 compat package now.
>  >
>  > In fact, I'd be happy to hand pari maintainership over to you if
>  > that would help you at all, but I'm fine with keeping it if you
>  > don't want the additional burden.
>  >  
>  
>  It looks like the giac, Macaulay2, and sagemath stacks are the only
>  pari consumers.  There is also a pending update to clisp that will
>  bring its pari integration back; that has been missing for a few
>  years.  And sure enough, I've got my fingers in all of those
>  pies. :-)  I'm happy to take pari off of your hands if you want to
>  hand it over. 
OK, done. Have fun!

Cheers, Paul.

[Jerry James]

Paul,

On Tue, May 29, 2018 at 4:36 AM Paul Howarth <paul(a)city-fan.org&gt; wrote:
>  On Mon, 28 May 2018 21:03:34 -0600
>  Jerry James <loganjerry(a)gmail.com&gt; wrote:
>  > It looks like the giac, Macaulay2, and sagemath stacks are the only
>  > pari consumers.  There is also a pending update to clisp that will
>  > bring its pari integration back; that has been missing for a few
>  > years.  And sure enough, I've got my fingers in all of those
>  > pies. :-)  I'm happy to take pari off of your hands if you want to
>  > hand it over.
>
>  OK, done. Have fun! 
Are you also the maintainer of the pari-elldata, pari-galdata,
pari-galpol, and pari-seadata packages?  If so, I might as well take
those, too.  An update to pari-galpol is needed for the latest version
of pari.

Regards,
-- 
Jerry James
http://www.jamezone.org/

[Paul Howarth]

Hi Jerry,

On Tue, 31 Jul 2018 19:09:02 -0600
Jerry James <loganjerry(a)gmail.com&gt; wrote:

>  On Tue, May 29, 2018 at 4:36 AM Paul Howarth
> <paul(a)city-fan.org&gt;
>  wrote:
>  > On Mon, 28 May 2018 21:03:34 -0600
>  > Jerry James <loganjerry(a)gmail.com&gt; wrote:  
>  > > It looks like the giac, Macaulay2, and sagemath stacks are the
>  > > only pari consumers.  There is also a pending update to clisp
>  > > that will bring its pari integration back; that has been missing
>  > > for a few years.  And sure enough, I've got my fingers in all of
>  > > those pies. :-)  I'm happy to take pari off of your hands if you
>  > > want to hand it over.  
>  >
>  > OK, done. Have fun!  
>  
>  Are you also the maintainer of the pari-elldata, pari-galdata,
>  pari-galpol, and pari-seadata packages?  If so, I might as well take
>  those, too.  An update to pari-galpol is needed for the latest version
>  of pari. 
I've now given these to you too. Enjoy :-)

Paul.

[Vascom]

Hi Jerry,
You're doing a good job. Thanks.

Are you plan update Octave to 4.4.0?

--
Best regards,
Vasiliy Glazov

ср, 1 авг. 2018 г. в 12:25, Paul Howarth <paul(a)city-fan.org&gt;:

>  Hi Jerry,
>
>  On Tue, 31 Jul 2018 19:09:02 -0600
>  Jerry James <loganjerry(a)gmail.com&gt; wrote:
>
>  > On Tue, May 29, 2018 at 4:36 AM Paul Howarth <paul(a)city-fan.org&gt;
>  > wrote:
>  > > On Mon, 28 May 2018 21:03:34 -0600
>  > > Jerry James <loganjerry(a)gmail.com&gt; wrote:
>  > > > It looks like the giac, Macaulay2, and sagemath stacks are the
>  > > > only pari consumers.  There is also a pending update to clisp
>  > > > that will bring its pari integration back; that has been missing
>  > > > for a few years.  And sure enough, I've got my fingers in all of
>  > > > those pies. :-)  I'm happy to take pari off of your hands if you
>  > > > want to hand it over.
>  > >
>  > > OK, done. Have fun!
>  >
>  > Are you also the maintainer of the pari-elldata, pari-galdata,
>  > pari-galpol, and pari-seadata packages?  If so, I might as well take
>  > those, too.  An update to pari-galpol is needed for the latest version
>  > of pari.
>
>  I've now given these to you too. Enjoy :-)
>
>  Paul.
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[José Abílio Matos]

On Tuesday, 7 August 2018 07.29.24 WEST Vascom wrote:
>  Hi Jerry,
>  You're doing a good job. Thanks.
>  
>  Are you plan update Octave to 4.4.0?
>  
>  --
>  Best regards,
>  Vasiliy Glazov 
Actually it is Orion who usually does that, also 4.4.1 should be out soon. After there are
a 
batch of updates for octave packages to fix some issues with 4.4 compatibility.

It would be nice to have octave 4.4 in Fedora 29.

The next stable release will be 5.1 (octave changed to the gcc version scheme).

-- 
José Abílio

[Jerry James]

On Fri, May 25, 2018 at 10:27 PM Jerry James <loganjerry(a)gmail.com&gt; wrote:

>  Hello everyone.  Months ago, I started working on updates to a couple
> of
>  our mathematical packages.  But they, in turn, required other packages to
>  be updated, and those updates required other packages to be updated, and
>  the whole thing kind of snowballed.  I believe that I have finally reached
>  a point of closure, where I can update the whole pile and have everything
>  still work afterwards.
>  
I encountered a few problems while doing those builds, mostly on non-x86_64
architectures, but the builds are now all done.  If you notice problems
with any of this software, please let me know.

Regards,
-- 
Jerry James
http://www.jamezone.org/