upgrade normaliz to 3.7.2, pynormaliz to 2.5

[mkoeppe]

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

1. Go to the Sage source tree and pull the branch associated to this ticket

2. Get the tarballs and put them in the upstream repository

$ wget -P upstream https://github.com/Normaliz/Normaliz/releases/download/v3.7.2/normaliz-3.7.2.tar.gz
$ wget -P upstream https://files.pythonhosted.org/packages/31/8f/a1e8e489150a570c81b427d351a29b868df57015f13c12e8e6d2d2d55c45/PyNormaliz-2.5.tar.gz

3. Compile and install everything

$ sage -i pynormaliz

4. Run make

$ make build

Depends on #27782

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

Component: packages: optional

Author: Matthias Koeppe

Branch: 0a8c6f8

Reviewer: Vincent Delecroix

Issue created by migration from https://trac.sagemath.org/ticket/27731

[mkoeppe]

Dependencies: #27682

[mkoeppe]

Branch: public/27731

[mkoeppe]

New commits:

eaa4584	package e-antic 0.1.3b0
e5c669d	upgrade normaliz
14d6c83	Update normaliz to 3.7.1, pynormaliz to 2.1
64f1f19	fix doctest in backend_normaliz.py
3d949a2	Upgrade normaliz to 3.7.2, pynormaliz to 2.2

[mkoeppe]

Commit: 3d949a2

[videlec]

comment:4

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 e-antic which is not nice either.

[mkoeppe]

comment:5

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.

[videlec]

comment:6

PyNormaliz provides a test suite, there should be a spkg-check.

[sagetrac-git]

Changed commit from 3d949a2 to b488911

[sagetrac-git]

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

b488911

Add build/pkgs/pynormaliz/spkg-check

[mkoeppe]

comment:8

PyNormaliz test suite currently fails with the e-antic bug-fix release 0.1.3b0 that we have in #27682.

[sagetrac-git]

Changed commit from b488911 to 5d01388

[sagetrac-git]

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

5d01388

Upgrade pynormaliz to 2.4

[sagetrac-git]

Changed commit from 5d01388 to a4e5977

[sagetrac-git]

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

292e01f	backend_normaliz: py3 fix
d44a00d	backend_normaliz: Canonicalize sort order of fields in normaliz files

[sagetrac-git]

Changed commit from a4e5977 to d44a00d

[mkoeppe]

comment:18

(The canonicalization of the output files is a good idea anyway and takes care of differences in dictionary orders between py2 and py3.)

[jplab]

comment:19

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!
----------------------------------------------------------------------

[jplab]

comment:20

Merge conflict with the new beta.

[sagetrac-git]

Changed commit from d44a00d to dd9a81b

[sagetrac-git]

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

dd9a81b

Merge tag '8.8.beta4' into t/27731/public/27731

[sagetrac-git]

Changed commit from dd9a81b to 0a8c6f8

[sagetrac-git]

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

9b3a5ba	Fix error message in doctest for new pynormaliz version
0a8c6f8	Merge branch 't/27782/1_pynormaliz_doctest_failing_in_src_sage_geometry_polyhedron_backend_normaliz_py' into t/27731/public/27731

[mkoeppe]

Changed dependencies from #27682 to #27782

[mkoeppe]

comment:24

Needs review again!

[vbraun]

Changed branch from public/27731 to 0a8c6f8

[seblabbe]

comment:27

As I reported on sage-release for 8.8.beta6, I get troubles installing pynormaliz.

Is this normal doctor?

[seblabbe]

Changed commit from 0a8c6f8 to none

[videlec]

comment:28

Replying to @seblabbe:

As I reported on sage-release 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/pynormaliz-2.5

and if so attach it.

[seblabbe]

comment:29

No config.log:

$ ls /home/slabbe/GitBox/sage/local/var/tmp/sage/build/pynormaliz-2.5
checksums.ini  package-version.txt  spkg-install  src
dependencies   spkg-check           SPKG.txt      type

[mkoeppe]

comment:30

It would of course be in the src subdirectory.

[seblabbe]

comment:31

The complete pynormaliz-2.5.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?

[seblabbe]

comment:32

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/pynormaliz-2.5/src
$ ls
config.py.in  doc       m4                  PyNormaliz.py  setup.py
configure     examples  NormalizModule.cpp  Readme.md      tests
COPYING       GPLv2     PKG-INFO            setup.cfg
$ cat config.py.in 
# Configuration variables
ENFNORMALIZ=@ENFNORMALIZ@

[videlec]

comment:33

Replying to @seblabbe:

The complete pynormaliz-2.5.log file is pasted on framabin here

I noticed. And this is not what I asked for.

[videlec]

comment:34

Replying to @seblabbe:

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/pynormaliz-2.5/src
$ ls
config.py.in  doc       m4                  PyNormaliz.py  setup.py
configure     examples  NormalizModule.cpp  Readme.md      tests
COPYING       GPLv2     PKG-INFO            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 pynormaliz-2.5.log already mentioned).

Do you have sh installed?

BTW: we should not discuss this on this close ticket... could you open a thread on sage-devel or so.

[seblabbe]

comment:35

BTW: we should not discuss this on this close ticket... could you open a thread on sage-devel or so.

OK, let's continue here: https://groups.google.com/d/msg/sage-devel/2virhaHdt1k/nK-AtlByBAAJ

[mkoeppe]

comment:36

Follow-up in #27920.