Upgrade Normaliz version to 3.6.3 and PyNormaliz to 1.19 #25090

mkoeppe · 2018-04-03T17:43:21Z

Upstream:

(cd upstream && wget 'https://github.com/Normaliz/Normaliz/releases/download/v3.6.3/normaliz-3.6.3.tar.gz')

PyNormaliz 1.19:

(cd upstream && wget 'https://files.pythonhosted.org/packages/7f/e9/3c15d1fc8ebba8a2ed17fc0f209804dc1240166a686d2f592305efc9d25e/PyNormaliz-1.19.tar.gz')

Some more helper functions were included to facilitate the interfacing.

Depends on #22984

CC: @jplab @sebasguts @mo271 @videlec @w-bruns @mkoeppe @tscrim

Component: packages: optional

Keywords: IMA-PolyGeom

Author: Matthias Koeppe, Jean-Philippe Labbé

Branch/Commit: 36d5473

Reviewer: Travis Scrimshaw

Issue created by migration from https://trac.sagemath.org/ticket/25090

The text was updated successfully, but these errors were encountered:

mkoeppe · 2018-04-03T17:53:40Z

Branch: u/mkoeppe/pynormaliz2

mkoeppe · 2018-04-03T17:54:55Z

Commit: eaedcc2

mkoeppe · 2018-04-03T17:54:55Z

Last 10 new commits:

`737552d`	`Updating patch with upstream fix for wrong number of lattice points.`
`530302d`	`Merge branch 'u/tscrim/upgrade_noramliz_pynormaliz-22984' of git://trac.sagemath.org/sage into u/tscrim/upgrade_noramliz_pynormaliz-22984`
`57d40b0`	`Upgrade Normaliz to 3.5.2.`
`6ba442d`	`Adding tests from [comment:24](#comment%3A24),25 of #22984.`
`183087a`	`Upgrade PyNormaliz to 1.12`
`7f47ec9`	`Adapted the polyhedron docstring`
`117e428`	`Upgrade normaliz to 3.5.3`
`7057ef4`	`Merge branch to get docstring adaptation`
`b6ae686`	`Merge branch 'develop' of git://trac.sagemath.org/sage into t/25090/pynormaliz2`
`eaedcc2`	`Update PyNormaliz to 1.14`

jplab · 2018-04-03T19:59:13Z

Changed commit from eaedcc2 to 4dbdc7d

jplab · 2018-04-03T19:59:13Z

Changed branch from u/mkoeppe/pynormaliz2 to u/jipilab/pynormaliz2

jplab · 2018-04-03T19:59:13Z

New commits:

`4dbdc7d`	`Updated the Cone calls format`

mkoeppe · 2018-04-04T00:10:21Z

Changed branch from u/jipilab/pynormaliz2 to u/mkoeppe/pynormaliz2

jplab · 2018-04-04T14:31:47Z

Changed branch from u/mkoeppe/pynormaliz2 to public/pynormaliz2

jplab · 2018-04-04T14:31:47Z

New commits:

`1dcef4c`	`_init_from_normaliz_data: New, use it in _init_from_*representation`
`fcd8101`	`Updated pynormaliz to 1.15`

jplab · 2018-04-04T14:31:47Z

Changed commit from 4dbdc7d to fcd8101

sagetrac-git · 2018-04-04T17:40:35Z

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

`19d8539`	`Polyhedron_normaliz: In verbose mode, write out normaliz format files`

sagetrac-git · 2018-04-04T17:40:35Z

Changed commit from fcd8101 to 19d8539

sagetrac-git · 2018-04-04T19:25:04Z

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

`4cfcd14`	`_normaliz_format: Fix last change`

sagetrac-git · 2018-04-04T19:25:04Z

Changed commit from 19d8539 to 4cfcd14

sagetrac-git · 2018-04-04T20:02:10Z

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

`da8ae7a`	`Added data and cone methods to normaliz backend`

sagetrac-git · 2018-04-04T20:02:10Z

Changed commit from 4cfcd14 to da8ae7a

jplab · 2018-04-09T16:25:34Z

comment:11

After a discussion with gh-sebasguts: A new version of pynormaliz will be released in the upcoming days, including extended documentation and latest changes to pynormaliz.

In order not to mix things up too much with #25097 and #25091, it should be put as a priority in the reviewing queue...

jplab · 2018-04-13T15:38:52Z

comment:12

The version numbers are now fixed.

jplab · 2018-04-13T16:01:46Z

Changed branch from public/pynormaliz2 to public/pynormaliz1.16_normaliz3.5.4

jplab · 2018-04-13T16:01:46Z

Changed commit from da8ae7a to 82d7190

jplab · 2018-04-13T16:01:46Z

comment:14

I merged the changes done over the week with a fresh branch on top of sage8.2.rc2.

To be tested!

New commits:

`aa0e2ca`	`Merge branch normaliz3.5.3 and pynormaliz1.12 into sage8.2.rc2`
`2bbd8a6`	`Update normaliz and pynormaliz`
`82d7190`	`Merged old changes with latest versions`

tscrim · 2018-09-16T01:02:44Z

comment:54

LGTM overall, but a few methods are missing doctests:

_init_from_normaliz_data
_make_normaliz_cone

Also, INPUT: items generally do not end with a period.

sagetrac-git · 2018-09-16T01:07:15Z

Changed commit from aa71e25 to 7907f7a

sagetrac-git · 2018-09-16T01:07:15Z

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

`7907f7a`	`Polyhedron_normaliz: Fix: INPUT: items generally do not end with a period`

sagetrac-git · 2018-09-16T01:19:26Z

Changed commit from 7907f7a to 1e20ef2

sagetrac-git · 2018-09-16T01:19:26Z

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

`1e20ef2`	`Polyhedron_normaliz._make_normaliz_cone: Add doctest`

sagetrac-git · 2018-09-16T01:33:54Z

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

`f3d11a3`	`Polyhedron_normaliz._init_from_normaliz_data: Add doctest`

sagetrac-git · 2018-09-16T01:33:54Z

Changed commit from 1e20ef2 to f3d11a3

mkoeppe · 2018-09-16T01:34:08Z

comment:58

Ready for review

tscrim · 2018-09-16T01:45:06Z

Changed work issues from Segfault on empty polyhedron to none

tscrim · 2018-09-16T01:45:06Z

Reviewer: Travis Scrimshaw

tscrim · 2018-09-16T01:45:06Z

comment:59

Thank you. LGTM.

mkoeppe · 2018-09-16T01:45:55Z

comment:60

Thanks for reviewing!

vbraun · 2018-09-16T13:45:26Z

comment:61

sage -t --long src/sage/geometry/polyhedron/backend_normaliz.py
**********************************************************************
File "src/sage/geometry/polyhedron/backend_normaliz.py", line 451, in sage.geometry.polyhedron.backend_normaliz.Polyhedron_normaliz._get_nmzcone_data
Failed example:
    P._get_nmzcone_data()
Exception raised:
    Traceback (most recent call last):
      File "/mnt/disk/home/release/Sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 659, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/mnt/disk/home/release/Sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 1070, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.geometry.polyhedron.backend_normaliz.Polyhedron_normaliz._get_nmzcone_data[1]>", line 1, in <module>
        P._get_nmzcone_data()
      File "/mnt/disk/home/release/Sage/local/lib/python2.7/site-packages/sage/geometry/polyhedron/backend_normaliz.py", line 464, in _get_nmzcone_data
        import PyNormaliz
    ImportError: No module named PyNormaliz
**********************************************************************
File "src/sage/geometry/polyhedron/backend_normaliz.py", line 456, in sage.geometry.polyhedron.backend_normaliz.Polyhedron_normaliz._get_nmzcone_data
Failed example:
    C = Polyhedron(backend='normaliz',rays=[[1,2],[2,1]])
Exception raised:
    Traceback (most recent call last):
      File "/mnt/disk/home/release/Sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 659, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/mnt/disk/home/release/Sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 1070, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.geometry.polyhedron.backend_normaliz.Polyhedron_normaliz._get_nmzcone_data[2]>", line 1, in <module>
        C = Polyhedron(backend='normaliz',rays=[[Integer(1),Integer(2)],[Integer(2),Integer(1)]])
      File "/mnt/disk/home/release/Sage/local/lib/python2.7/site-packages/sage/geometry/polyhedron/constructor.py", line 600, in Polyhedron
        return parent(Vrep, Hrep, convert=convert, verbose=verbose)
      File "sage/structure/parent.pyx", line 923, in sage.structure.parent.Parent.__call__ (build/cythonized/sage/structure/parent.c:9706)
        return mor._call_with_args(x, args, kwds)
      File "sage/structure/coerce_maps.pyx", line 164, in sage.structure.coerce_maps.DefaultConvertMap_unique._call_with_args (build/cythonized/sage/structure/coerce_maps.c:5112)
        raise
      File "sage/structure/coerce_maps.pyx", line 159, in sage.structure.coerce_maps.DefaultConvertMap_unique._call_with_args (build/cythonized/sage/structure/coerce_maps.c:5000)
        return C._element_constructor(x, *args, **kwds)
      File "/mnt/disk/home/release/Sage/local/lib/python2.7/site-packages/sage/geometry/polyhedron/parent.py", line 517, in _element_constructor_
        return self.element_class(self, Vrep, Hrep, **kwds)
      File "/mnt/disk/home/release/Sage/local/lib/python2.7/site-packages/sage/geometry/polyhedron/backend_normaliz.py", line 156, in __init__
        Polyhedron_base.__init__(self, parent, Vrep, Hrep, **kwds)
      File "/mnt/disk/home/release/Sage/local/lib/python2.7/site-packages/sage/geometry/polyhedron/base.py", line 124, in __init__
        self._init_from_Vrepresentation(vertices, rays, lines, **kwds)
      File "/mnt/disk/home/release/Sage/local/lib/python2.7/site-packages/sage/geometry/polyhedron/backend_normaliz.py", line 263, in _init_from_Vrepresentation
        self._init_from_normaliz_data(data, verbose=verbose)
      File "/mnt/disk/home/release/Sage/local/lib/python2.7/site-packages/sage/geometry/polyhedron/backend_normaliz.py", line 192, in _init_from_normaliz_data
        import PyNormaliz
    ImportError: No module named PyNormaliz
**********************************************************************
File "src/sage/geometry/polyhedron/backend_normaliz.py", line 457, in sage.geometry.polyhedron.backend_normaliz.Polyhedron_normaliz._get_nmzcone_data
Failed example:
    C._get_nmzcone_data()
Exception raised:
    Traceback (most recent call last):
      File "/mnt/disk/home/release/Sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 659, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/mnt/disk/home/release/Sage/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 1070, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.geometry.polyhedron.backend_normaliz.Polyhedron_normaliz._get_nmzcone_data[3]>", line 1, in <module>
        C._get_nmzcone_data()
    NameError: name 'C' is not defined
**********************************************************************
1 item had failures:
   3 of   5 in sage.geometry.polyhedron.backend_normaliz.Polyhedron_normaliz._get_nmzcone_data
    [12 tests, 3 failures, 0.14 s]
----------------------------------------------------------------------
sage -t --long src/sage/geometry/polyhedron/backend_normaliz.py  # 3 doctests failed
----------------------------------------------------------------------

sagetrac-git · 2018-09-16T16:31:55Z

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

`36d5473`	`src/sage/geometry/polyhedron/backend_normaliz.py: Add # optional - pynormaliz`

sagetrac-git · 2018-09-16T16:31:55Z

Changed commit from f3d11a3 to 36d5473

tscrim · 2018-09-16T22:32:49Z

comment:64

Whoops, forgot to test on a machine that did not have (py)normaliz installed. Sorry Volker.

vbraun · 2018-09-19T08:09:24Z

Changed branch from public/pynormaliz1.17_normaliz3.6.1 to 36d5473

mkoeppe added this to the sage-8.2 milestone Apr 3, 2018

mkoeppe added c: packages: optional labels Apr 3, 2018

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jplab changed the title ~~Upgrade pynormaliz to 1.14 or higher (2.0?)~~ Upgrade pynormaliz to 1.15 or higher (2.0?) Apr 5, 2018

jplab changed the title ~~Upgrade pynormaliz to 1.15 or higher (2.0?)~~ Upgrade Normaliz version to 3.5.4 and PyNormaliz to 1.16 Apr 13, 2018

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mkoeppe added s: needs review and removed s: needs work labels Sep 16, 2018

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tscrim added s: positive review and removed s: needs review labels Sep 16, 2018

vbraun added s: needs work and removed s: positive review labels Sep 16, 2018

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tscrim added s: positive review and removed s: needs review labels Sep 16, 2018

vbraun removed the s: positive review label Sep 19, 2018

vbraun closed this as completed in 17fdba4 Sep 19, 2018

Upgrade Normaliz version to 3.6.3 and PyNormaliz to 1.19 #25090

Upgrade Normaliz version to 3.6.3 and PyNormaliz to 1.19 #25090

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