upgrade lrcalc to 2.1

[sagetrac-tmonteil]

lrcalc 2.1 is out https://bitbucket.org/asbuch/lrcalc/src/master/ChangeLog

Instead of rewriting Sage's Python bindings to support the new API, we replace them with a wrapper around the new upstream provided bindings

Upstream:

lrcalclib-2.1.tar.gz (lrcalc): https://sites.math.rutgers.edu/~asbuch/lrcalc/lrcalc-2.1.tar.gz
lrcalc-2.1.tar.gz (lrcalc_python): https://pypi.io/packages/source/l/lrcalc/lrcalc-2.1.tar.gz

CC: @antonio-rojas @anneschilling @fchapoton @tscrim @thierry-FreeBSD @orlitzky @mkoeppe @kiwifb @asbuch @slel

Component: packages: optional

Keywords: upgrade, lrcalc

Author: Antonio Rojas, Matthias Koeppe

Branch/Commit: de4fe09

Reviewer: Matthias Koeppe, Travis Scrimshaw

Issue created by migration from https://trac.sagemath.org/ticket/31355

[sagetrac-tmonteil]

Branch: u/tmonteil/upgrade_lrcalc_to_2_0

[sagetrac-tmonteil]

Commit: 850f9bc

[sagetrac-tmonteil]

comment:4

I get the following error when doctesting:

ImportError: /opt/sagemath/sage/local/lib/python3.7/site-packages/sage/libs/lrcalc/lrcalc.cpython-37m-x86_64-linux-gnu.so: undefined symbol: st_new

---

New commits:

850f9bc

#31355 : upgrade lrcalc to 2.0

[antonio-rojas]

comment:5

This has major API changes. Large parts of lrcalc.pyx needs to be rewritten because the used functions have been removed or modified.

[sagetrac-tmonteil]

comment:6

I see, any help welcome !

[orlitzky]

comment:8

The existing spkg-configure.m4 needs to be updated to detect v2.0 (once it actually works), too.

[nthiery]

comment:9

Some information from Anders:

I recently put out a new version of my lrcalc program, much of it is
rewritten, and some of the most important functions are close to twice as fast
as before.  Some special cases have also been optimized to run a lot faster.

I have included some (pure) Python3 bindings in the repository, so I think
this update will be easy.  But I don't understand Sage well enough to do it
myself.

For reference, some pointers:

• Sage's lrcalc package: https://github.com/sagemath/sagetrac-mirror/blob/develop/build/pkgs/lrcalc
• Sage's lrcalc bindings: https://github.com/sagemath/sagetrac-mirror/blob/develop/src/sage/libs/lcalc

[asbuch]

comment:10

The Python bindings are only in the repository and a bit raw, so probably only useful as examples. But I expect they are easier to start from than the .h files.

[antonio-rojas]

Changed branch from u/tmonteil/upgrade_lrcalc_to_2_0 to u/arojas/upgrade_lrcalc_to_2_0

[antonio-rojas]

comment:12

Replying to @asbuch:

The Python bindings are only in the repository and a bit raw, so probably only useful as examples. But I expect they are easier to start from than the .h files.

Actually, they are almost equivalent to the current bindings in Sage. The attached branch replaces lrcalc.pyx with a thin wrapper over lrcalc's bindings.

It mostly just translates the output from lrcalc to sage notation. The only function of lrcalc.pyx that isn't straghtforward to port is quantum multiplication: I found no way to recover the q-grading from lrcalc's output, so this is reimplemented in the patch.

The branch needs an update of lrcalc to include python bindings.

---

New commits:

6596bbd

Replace lrcalc.pyx with a wrapper over lrcalc's own Python bindings

[antonio-rojas]

Changed commit from 850f9bc to 6596bbd

[antonio-rojas]

comment:13

Replying to @asbuch:

The Python bindings are only in the repository and a bit raw, so probably only useful as examples. But I expect they are easier to start from than the .h files.

Since you are here and I can not find a bug tracker for lrcalc: the setup.py is missing metadata, so the egg for lrcalc gets installed as UNKNOWN-0.0.0.0

[sagetrac-git]

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

0a9490a	Merge branch 'develop' of git://git.sagemath.org/sage into t/31355/upgrade_lrcalc_to_2_0
26f7f26	Fix oversight in q_degrees formula

[sagetrac-git]

Changed commit from 6596bbd to 26f7f26

[asbuch]

comment:15

If my bindings are used, then that will make it easier to keep things compatible if I make more changes to the C interface. I should be able to keep the Python interface stable, at least up to reordering of output.

Quantum function: I will add a function mult_quantum_pairs that returns a dict from ((partition),d) to integers, you can switch to that if you want.

setup.py: Does the following include the tags you are looking for? Suggestions welcome!

setup(name='lrcalc',
    version='2.0.0',
    description='Littlewood-Richardson Calculator',
    long_description='Littlewood-Richardson Calculator',
    url='https://math.rutgers.edu/~asbuch/lrcalc',
    author='Anders Skovsted Buch',
    license='GPL3',
    ext_modules = cythonize([
        Extension("lrcalc", ["lrcalc.pyx"],
                  libraries=["lrcalc"])
    ])
)

[sagetrac-git]

Changed commit from 26f7f26 to 627192a

[sagetrac-git]

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

627192a

Use Sage integers in results

[antonio-rojas]

comment:17

Replying to @asbuch:

setup.py: Does the following include the tags you are looking for? Suggestions welcome!

setup(name='lrcalc',
    version='2.0.0',
    description='Littlewood-Richardson Calculator',
    long_description='Littlewood-Richardson Calculator',
    url='https://math.rutgers.edu/~asbuch/lrcalc',
    author='Anders Skovsted Buch',
    license='GPL3',
    ext_modules = cythonize([
        Extension("lrcalc", ["lrcalc.pyx"],
                  libraries=["lrcalc"])
    ])
)

That works, thanks. Also, although maybe it is a little bit too late for that, it would be good to bump the soversion of the C shared library since the API changed.

[asbuch]

comment:18

Replying to @antonio-rojas:

Replying to @asbuch:

setup.py: Does the following include the tags you are looking for? Suggestions welcome!

setup(name='lrcalc',
    version='2.0.0',
    description='Littlewood-Richardson Calculator',
    long_description='Littlewood-Richardson Calculator',
    url='https://math.rutgers.edu/~asbuch/lrcalc',
    author='Anders Skovsted Buch',
    license='GPL3',
    ext_modules = cythonize([
        Extension("lrcalc", ["lrcalc.pyx"],
                  libraries=["lrcalc"])
    ])
)

That works, thanks. Also, although maybe it is a little bit too late for that, it would be good to bump the soversion of the C shared library since the API changed.

I changed the version to "2.0.0" and thought that was in line with this page. Please let me know if I am doing something wrong.

[antonio-rojas]

comment:19

Replying to @asbuch:

I changed the version to "2.0.0" and thought that was in line with this page. Please let me know if I am doing something wrong.

You need to change the -version-info in https://bitbucket.org/asbuch/lrcalc/src/master/src/Makefile.am#lines-23

[asbuch]

comment:20

Replying to @antonio-rojas:

Replying to @asbuch:

I changed the version to "2.0.0" and thought that was in line with this page. Please let me know if I am doing something wrong.

You need to change the -version-info in https://bitbucket.org/asbuch/lrcalc/src/master/src/Makefile.am#lines-23

I see, thanks! According to conventions, is that line in Makefile.am independent from this line in configure.am:

AC_INIT([lrcalc],[2.0.0],[asbuch at math rutgers edu])

[sagetrac-git]

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

52c120f

Use new mult_quantum degrees option in lrcalc 2.1 for quantum multiplication

[sagetrac-git]

Changed commit from 627192a to 52c120f

[sagetrac-git]

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

e13f155

Upgrade lrcalc to 2.1 and install python bindings

[antonio-rojas]

comment:95

Ping. Anything else needed here?

[dimpase]

comment:96

What is the minimum lrcalc version required by lrcalc_python?

[antonio-rojas]

comment:97

lrcalc and lrcalc_python come from the same repo, so I suppose the versions need to match.

[dimpase]

comment:98

A number of distrbutions have system-wide lrcalc installations, some still version 1.*, and those can be picked up by Sage.

If these are not compatible they should not be used.

[antonio-rojas]

comment:99

1.* will not be picked up, the ivector.h header was introduced in 2.0. Don't know about 2.0, according to repology only gentoo is shipping that. @kiwifb, any reason it hasn't been updated to 2.1?

[kiwifb]

comment:100

I just have been quite busy. And since @orlitzky has migrated a lot of packages to the main tree, I feel less personal pressure to update. We have 2.0 in the main tree but not 2.1 yet. I will have to see what needs to be done.

[kiwifb]

comment:101

lrcalc_python/SPKG.rst claims it is GPL2+ but https://bitbucket.org/asbuch/lrcalc/src/master/python/ and https://bitbucket.org/asbuch/lrcalc/src/master/python/setup.py make it pretty clear that it is GPL3.

[sagetrac-git]

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

03e0c8f	Fix spkg-configure to use C and only pass for version 2.1
b944aff	Fix license

[sagetrac-git]

Changed commit from 42ecd9a to b944aff

[antonio-rojas]

comment:103

Replying to @dimpase:

A number of distrbutions have system-wide lrcalc installations, some still version 1.*, and those can be picked up by Sage.

If these are not compatible they should not be used.

Actually spkg-configure didn't work at all because it was using C++ instead of C. Fixed it now and added a check for a header only present in 2.1 so it will fail with older versions.

Fixed the license too, should be ready to go now.

[kiwifb]

comment:104

I have opened a PR for getting 2.1 in Gentoo and I have an ebuild ready for the python bindings for the sage-on-gentoo overlay just waiting for the PR inclusion before going live [because of dependencies requirements, cannot go in until lrcalc-2.1 is present].

[sagetrac-git]

Changed commit from b944aff to 5d443b9

[sagetrac-git]

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

5d443b9

Merge remote-tracking branch 'origin/develop' into t/31355/upgrade_lrcalc_to_2_0

[sagetrac-git]

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

ffb08d8

Merge remote-tracking branch 'origin' into t/31355/upgrade_lrcalc_to_2_0

[sagetrac-git]

Changed commit from 5d443b9 to ffb08d8

[antonio-rojas]

comment:108

Ping, hope to get this in 9.6

[tscrim]

Changed branch from u/arojas/upgrade_lrcalc_to_2_0 to u/tscrim/upgrade_lrcalc_2_1-31355

[tscrim]

Changed commit from ffb08d8 to de4fe09

[tscrim]

comment:109

Does Sage's auto-download mechanism automatically rename the tarballs to their appropriate values. I am worried that both tarballs (lib and python) are called lrcalc-2.1.tar.gz on their respective upstream locations.

I made a few other little tweaks and checked the tests. If my changes are good, then it is a positive review.

---

New commits:

e8d0b5b	Merge branch 'u/arojas/upgrade_lrcalc_to_2_0' of git://trac.sagemath.org/sage into u/arojas/upgrade_lrcalc_to_2_0
de4fe09	Some improvements to lrcalc.py.

[tscrim]

Changed reviewer from Matthias Koeppe, ... to Matthias Koeppe, Travis Scrimshaw

[mkoeppe]

comment:110

Replying to @tscrim:

Does Sage's auto-download mechanism automatically rename the tarballs to their appropriate values. I am worried that both tarballs (lib and python) are called lrcalc-2.1.tar.gz on their respective upstream locations.

Yes, it is renamed to the value given in the tarball field of checksums.ini. See comment:80.

[antonio-rojas]

comment:111

Thanks

[vbraun]

Changed branch from u/tscrim/upgrade_lrcalc_2_1-31355 to de4fe09