#27731 closed defect (fixed)
upgrade normaliz to 3.7.2, pynormaliz to 2.5
Reported by:  mkoeppe  Owned by:  

Priority:  major  Milestone:  sage8.8 
Component:  packages: optional  Keywords:  
Cc:  Winfried, jipilab, ghsebasguts, mkoeppe, vdelecroix, tscrim  Merged in:  
Authors:  Matthias Koeppe  Reviewers:  Vincent Delecroix 
Report Upstream:  N/A  Work issues:  
Branch:  0a8c6f8 (Commits, GitHub, GitLab)  Commit:  
Dependencies:  #27782  Stopgaps: 
Description (last modified by )
Another update of normaliz, pynormaliz. The upgrade of PyNormaliz from 2.1 to 2.5 fixes a critical data conversion bug (Check overflow for int conversion correctly) that was present in all previous versions.
Tarballs  see wget commands below.
Step by step instructions if you want to try it out
 Go to the Sage source tree and pull the branch associated to this ticket
 Get the tarballs and put them in the
upstream
repository$ wget P upstream https://github.com/Normaliz/Normaliz/releases/download/v3.7.2/normaliz3.7.2.tar.gz $ wget P upstream https://files.pythonhosted.org/packages/31/8f/a1e8e489150a570c81b427d351a29b868df57015f13c12e8e6d2d2d55c45/PyNormaliz2.5.tar.gz
 Compile and install everything
$ sage i pynormaliz
 Run make
$ make build
Change History (36)
comment:1 Changed 2 years ago by
 Dependencies set to #27682
comment:2 Changed 2 years ago by
 Branch set to public/27731
comment:3 Changed 2 years ago by
 Cc tscrim added
 Commit set to 3d949a2219a3a502e3374ba68dd173bfa4acffcb
 Status changed from new to needs_review
comment:4 Changed 2 years ago by
Hi,
What is the point of having several open tickets concerning Normaliz/PyNormaliz? upgrade? You want the job of the release manager to become a nightmare? If Normaliz/PyNormaliz? are not mature you should not have set anything to needs review in the first place. Also, you are shipping a beta version of eantic which is not nice either.
comment:5 Changed 2 years ago by
3.7.1/2.1 are stable and an improvement over the existing versions in sage. The ticket #27682 is positively reviewed already, and per release manager, positively reviewed tickets are not to be modified further.
comment:6 Changed 2 years ago by
 Status changed from needs_review to needs_work
PyNormaliz
provides a test suite, there should be a spkgcheck
.
comment:7 Changed 2 years ago by
 Commit changed from 3d949a2219a3a502e3374ba68dd173bfa4acffcb to b4889111d4478b8dda2e15dac58a4d725cd2f0c0
Branch pushed to git repo; I updated commit sha1. New commits:
b488911  Add build/pkgs/pynormaliz/spkgcheck

comment:8 Changed 2 years ago by
PyNormaliz? test suite currently fails with the eantic bugfix release 0.1.3b0 that we have in #27682.
comment:9 Changed 2 years ago by
 Description modified (diff)
 Summary changed from upgrade normaliz to 3.7.2, pynormaliz to 2.2 to upgrade normaliz to 3.7.2, pynormaliz to 2.4
comment:10 Changed 2 years ago by
 Commit changed from b4889111d4478b8dda2e15dac58a4d725cd2f0c0 to 5d013883725486cee52b7b247b8d0aab6d81f7d7
Branch pushed to git repo; I updated commit sha1. New commits:
5d01388  Upgrade pynormaliz to 2.4

comment:11 Changed 2 years ago by
 Description modified (diff)
 Status changed from needs_work to needs_review
 Type changed from enhancement to defect
comment:12 Changed 2 years ago by
 Description modified (diff)
comment:13 Changed 2 years ago by
 Description modified (diff)
 Summary changed from upgrade normaliz to 3.7.2, pynormaliz to 2.4 to upgrade normaliz to 3.7.2, pynormaliz to 2.5
comment:14 Changed 2 years ago by
 Commit changed from 5d013883725486cee52b7b247b8d0aab6d81f7d7 to a4e597762cf0ed306b81a2ab14aab576aeee85b2
Branch pushed to git repo; I updated commit sha1. New commits:
a4e5977  Upgrade pynormaliz to 2.5

comment:15 Changed 2 years ago by
 Reviewers set to Vincent Delecroix
 Status changed from needs_review to needs_work
With Sage built with Python3
sage t long polyhedron/backend_normaliz.py ********************************************************************** File "polyhedron/backend_normaliz.py", line 497, in sage.geometry.polyhedron.backend_normaliz.Polyhedron_normaliz._normaliz_format Failed example: P = Polyhedron(vertices=[[0, 0], [0, 1], [1, 0]], # indirect doctest; optional  pynormaliz backend='normaliz', verbose=True) Exception raised: Traceback (most recent call last): File "/opt/sage/sagepy3gcc/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 671, in _run self.compile_and_execute(example, compiler, test.globs) File "/opt/sage/sagepy3gcc/local/lib/python3.7/sitepackages/sage/doctest/forker.py", line 1095, in compile_and_execute exec(compiled, globs) File "<doctest sage.geometry.polyhedron.backend_normaliz.Polyhedron_normaliz._normaliz_format[0]>", line 2, in <module> backend='normaliz', verbose=True) File "sage/misc/lazy_import.pyx", line 354, in sage.misc.lazy_import.LazyImport.__call__ (build/cythonized/sage/misc/lazy_import.c:3690) return self.get_object()(*args, **kwds) File "/opt/sage/sagepy3gcc/local/lib/python3.7/sitepackages/sage/geometry/polyhedron/constructor.py", line 604, in Polyhedron return parent(Vrep, Hrep, convert=convert, verbose=verbose) File "sage/structure/parent.pyx", line 902, in sage.structure.parent.Parent.__call__ (build/cythonized/sage/structure/parent.c:9224) return mor._call_with_args(x, args, kwds) File "sage/structure/coerce_maps.pyx", line 181, in sage.structure.coerce_maps.DefaultConvertMap_unique._call_with_args (build/cythonized/sage/structure/coerce_maps.c:5074) raise File "sage/structure/coerce_maps.pyx", line 176, in sage.structure.coerce_maps.DefaultConvertMap_unique._call_with_args (build/cythonized/sage/structure/coerce_maps.c:4962) return C._element_constructor(x, *args, **kwds) File "/opt/sage/sagepy3gcc/local/lib/python3.7/sitepackages/sage/geometry/polyhedron/parent.py", line 517, in _element_constructor_ return self.element_class(self, Vrep, Hrep, **kwds) File "/opt/sage/sagepy3gcc/local/lib/python3.7/sitepackages/sage/geometry/polyhedron/backend_normaliz.py", line 156, in __init__ Polyhedron_base.__init__(self, parent, Vrep, Hrep, **kwds) File "/opt/sage/sagepy3gcc/local/lib/python3.7/sitepackages/sage/geometry/polyhedron/base.py", line 124, in __init__ self._init_from_Vrepresentation(vertices, rays, lines, **kwds) File "/opt/sage/sagepy3gcc/local/lib/python3.7/sitepackages/sage/geometry/polyhedron/backend_normaliz.py", line 263, in _init_from_Vrepresentation self._init_from_normaliz_data(data, verbose=verbose) File "/opt/sage/sagepy3gcc/local/lib/python3.7/sitepackages/sage/geometry/polyhedron/backend_normaliz.py", line 201, in _init_from_normaliz_data print(self._normaliz_format(data), end='') File "/opt/sage/sagepy3gcc/local/lib/python3.7/sitepackages/sage/geometry/polyhedron/backend_normaliz.py", line 511, in _normaliz_format for key, value in data.iteritems(): AttributeError: 'dict' object has no attribute 'iteritems' **********************************************************************
comment:16 Changed 2 years ago by
 Commit changed from a4e597762cf0ed306b81a2ab14aab576aeee85b2 to d44a00d9b3b8b7ee6e4b1d89bf8adbcedebdedf3
comment:17 Changed 2 years ago by
 Status changed from needs_work to needs_review
comment:18 Changed 2 years ago by
(The canonicalization of the output files is a good idea anyway and takes care of differences in dictionary orders between py2 and py3.)
comment:19 Changed 2 years ago by
Compiles cleanly on debian.
Running tests using pynormaliz
in the folder src/sage/geometry/polyhedron
:
$ sage t *.py Using optional=bliss,dochtml,e_antic,gfortran,lrslib,memlimit,mpir,ninja_build,normaliz,pynormaliz,python2,sage,topcom Doctesting 25 files.  All tests passed! 
and without:
$ sage t *.py optional=bliss,dochtml,gfortran,lrslib,memlimit,mpir,ninja_build,python2,sage,topcom Using optional=bliss,dochtml,gfortran,lrslib,memlimit,mpir,ninja_build,python2,sage,topcom Doctesting 25 files.  All tests passed! 
comment:20 Changed 2 years ago by
Merge conflict with the new beta.
comment:21 Changed 2 years ago by
 Commit changed from d44a00d9b3b8b7ee6e4b1d89bf8adbcedebdedf3 to dd9a81bfe6660f52778b4becbc8f848e04f3b07e
Branch pushed to git repo; I updated commit sha1. New commits:
dd9a81b  Merge tag '8.8.beta4' into t/27731/public/27731

comment:22 Changed 2 years ago by
 Commit changed from dd9a81bfe6660f52778b4becbc8f848e04f3b07e to 0a8c6f867f6779020df69e8687f32edf70a778f7
comment:23 Changed 2 years ago by
 Dependencies changed from #27682 to #27782
comment:24 Changed 2 years ago by
Needs review again!
comment:25 Changed 2 years ago by
 Status changed from needs_review to positive_review
comment:26 Changed 2 years ago by
 Branch changed from public/27731 to 0a8c6f867f6779020df69e8687f32edf70a778f7
 Resolution set to fixed
 Status changed from positive_review to closed
comment:27 followup: ↓ 28 Changed 2 years ago by
 Commit 0a8c6f867f6779020df69e8687f32edf70a778f7 deleted
As I reported on sagerelease for 8.8.beta6, I get troubles installing pynormaliz.
Is this normal doctor?
comment:28 in reply to: ↑ 27 Changed 2 years ago by
Replying to slabbe:
As I reported on sagerelease for 8.8.beta6, I get troubles installing pynormaliz.
Is this normal doctor?
Could you check whether there is a config.log in
/home/slabbe/GitBox/sage/local/var/tmp/sage/build/pynormaliz2.5
and if so attach it.
comment:29 Changed 2 years ago by
No config.log:
$ ls /home/slabbe/GitBox/sage/local/var/tmp/sage/build/pynormaliz2.5 checksums.ini packageversion.txt spkginstall src dependencies spkgcheck SPKG.txt type
comment:30 followup: ↓ 32 Changed 2 years ago by
It would of course be in the src subdirectory.
comment:31 followup: ↓ 33 Changed 2 years ago by
The complete pynormaliz2.5.log file is pasted on framabin here
In particular, there is this line:
configure: error: source directory already configured; run "make distclean" there first
Maybe this has to do with the fact that my brother asked me to try to test this ticket one month ago where I installed a previous version of those packages?
comment:32 in reply to: ↑ 30 ; followup: ↓ 34 Changed 2 years ago by
Replying to mkoeppe:
It would of course be in the src subdirectory.
$ cd /home/slabbe/GitBox/sage/local/var/tmp/sage/build/pynormaliz2.5/src $ ls config.py.in doc m4 PyNormaliz.py setup.py configure examples NormalizModule.cpp Readme.md tests COPYING GPLv2 PKGINFO setup.cfg $ cat config.py.in # Configuration variables ENFNORMALIZ=@ENFNORMALIZ@
comment:33 in reply to: ↑ 31 Changed 2 years ago by
Replying to slabbe:
The complete pynormaliz2.5.log file is pasted on framabin here
I noticed. And this is not what I asked for.
comment:34 in reply to: ↑ 32 ; followup: ↓ 35 Changed 2 years ago by
Replying to slabbe:
Replying to mkoeppe:
It would of course be in the src subdirectory.
No config.log file in the src directory, but there is a config.py.in:
$ cd /home/slabbe/GitBox/sage/local/var/tmp/sage/build/pynormaliz2.5/src $ ls config.py.in doc m4 PyNormaliz.py setup.py configure examples NormalizModule.cpp Readme.md tests COPYING GPLv2 PKGINFO setup.cfg $ cat config.py.in # Configuration variables ENFNORMALIZ=@ENFNORMALIZ@
That is to be expected. The setup.py
script calls $ sh configure
that creates the config.py
from the template file config.py.in
. In your situation, the process get stuck at the $ sh configure
call (as you pynormaliz2.5.log
already mentioned).
Do you have sh
installed?
BTW: we should not discuss this on this close ticket... could you open a thread on sagedevel or so.
comment:35 in reply to: ↑ 34 Changed 2 years ago by
BTW: we should not discuss this on this close ticket... could you open a thread on sagedevel or so.
OK, let's continue here: https://groups.google.com/d/msg/sagedevel/2virhaHdt1k/nKAtlByBAAJ
comment:36 Changed 2 years ago by
Followup in #27920.
New commits:
package eantic 0.1.3b0
upgrade normaliz
Update normaliz to 3.7.1, pynormaliz to 2.1
fix doctest in backend_normaliz.py
Upgrade normaliz to 3.7.2, pynormaliz to 2.2