Modularization of sagelib: Break out a separate package sagemath-polyhedra #32432

mkoeppe · 2021-08-28T17:49:41Z

We define a superset of the distribution sagemath-categories (from #29865), called https://pypi.org/project/sagemath-polyhedra/, which is large enough to work with rational polyhedra, including running most doctests

In:

ZZ, QQ, RDF
enough of sage.modules, sage.matrix to do linear algebra over these rings
install_requires on pplpy

Out:

real fields other than RDF
number fields (we conditionalize out doctests that use them - sage.geometry.polyhedron: Mark doctests # optional - sage.rings.number_field #32652)
sage.symbolic
most of sage.combinat (we conditionalize out doctests that use combinatorial examples such as associahedra)
sage.graphs
sage.plot

To test:

$ ./bootstrap && ./sage -sh -c '(cd pkgs/sagemath-polyhedra && SAGE_NUM_THREADS=16 tox -v -v -v)'

To run more of the testsuite afterwards:

$ . pkgs/sagemath-polyhedra/.tox/python/bin/activate
(python) $ (cd $(python -c "from sage.env import SAGE_SRC; print(SAGE_SRC)") && sage -tp --environment=sage.all__sagemath_polyhedra sage/geometry)
...
(python) $ deactivate

Follow-up steps:

redo as distribution with dependency on sagemath-categories
wheels for this distribution, for pplpy and PyNormaliz
native Windows port

Depends on #32779
Depends on #34855
Depends on #34849
Depends on #32709
Depends on #34849
Depends on #34931
Depends on #34941

CC: @kliem @tscrim @anneschilling

Component: refactoring

Work Issues: git blame -b --first-parent 32432-base.. src/sage/geometry/polyhedron/base.py

Author: Matthias Koeppe

Issue created by migration from https://trac.sagemath.org/ticket/32432

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

mkoeppe · 2021-08-28T18:56:09Z

Branch: u/mkoeppe/modularization_of_sagelib__break_out_a_separate_package_sagemath_polyhedra

mkoeppe · 2021-08-28T18:57:53Z

Commit: 8ea1332

mkoeppe · 2021-08-28T18:57:53Z

comment:3

Initial draft. Needs more work to get integers/rationals to work, and need to include vectors/matrices

Last 10 new commits:

`08084b3`	`sage.libs.pari.convert_sage: Move set_integer_from_gen here from sage.rings.integer (set_from_pari_gen)`
`9986723`	`remove compile time dependency of Integer and Rational on cypari2`
`c08a8b5`	`remove compile-time dependency on flint from integer`
`b0ba835`	`Merge #30022`
`d3479c7`	`remove some of symbolics from sage.geometry`
`2991f8d`	`Merge #32416`
`0101366`	`pkgs/sagemath-polyhedra, src/sage/all__sagemath_polyhedra.py: New`
`bb708f3`	`#29865: Rename all__sage_objects.py, all__sage_categories.py to all__sagemath_objects.py, all__sagemath_categories.py`
`a301f70`	`build/pkgs/sagemath_polyhedra: New`
`8ea1332`	`pkgs/sagemath-polyhedra/MANIFEST.in.m4: Include more`

sagetrac-git · 2021-08-28T19:34:59Z

Changed commit from 8ea1332 to 4085b62

sagetrac-git · 2021-08-28T19:34:59Z

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

`4085b62`	`pkgs/sagemath-polyhedra/MANIFEST.in.m4: Add what we can from sage.matrix`

sagetrac-git · 2021-08-28T19:55:58Z

Changed commit from 4085b62 to 1d7f906

sagetrac-git · 2021-08-28T19:55:58Z

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

`1d7f906`	`pkgs/sagemath-polyhedra/MANIFEST.in.m4: Add what we can from sage.modules`

mkoeppe · 2021-08-31T19:31:55Z

Changed dependencies from #29865, #30022, #32416 to #29865, #30022, #32416, #32441

mkoeppe · 2021-09-02T19:55:28Z

Changed dependencies from #29865, #30022, #32416, #32441 to #29865, #30022, #32416, #32441, #32455

mkoeppe · 2021-09-03T20:44:09Z

comment:8

One of the next issues is use of Matrix_integer_dense in combinatorial_polyhedron.list_of_faces etc.

mkoeppe · 2021-09-19T00:38:34Z

Changed dependencies from #29865, #30022, #32416, #32441, #32455 to #29865, #32416, #32441, #32455

sagetrac-git · 2021-09-19T00:46:25Z

Changed commit from 1d7f906 to f0dd43d

sagetrac-git · 2021-09-19T00:46:25Z

Branch pushed to git repo; I updated commit sha1. This was a forced push. Last 10 new commits:

`41df930`	`fix function signatures`
`90b6f3d`	`Merge #32441`
`13f9003`	`move pari type detection to convert_sage`
`e925042`	`Merge #32455`
`ccbde78`	`pkgs/sagemath-polyhedra, src/sage/all__sagemath_polyhedra.py: New`
`8baebcf`	`build/pkgs/sagemath_polyhedra: New`
`039f66b`	`pkgs/sagemath-polyhedra/MANIFEST.in.m4: Include more`
`3dfac9f`	`pkgs/sagemath-polyhedra/MANIFEST.in.m4: Add what we can from sage.matrix`
`23a49b9`	`pkgs/sagemath-polyhedra/MANIFEST.in.m4: Add what we can from sage.modules`
`f0dd43d`	`pkgs/sagemath-polyhedra/MANIFEST.in.m4: WIP`

sagetrac-git · 2021-09-19T01:58:58Z

Changed commit from f0dd43d to 8159516

sagetrac-git · 2021-09-19T01:58:58Z

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

`3983ce5`	`pkgs/sagemath-polyhedra/MANIFEST.in.m4: More&less`
`5adceb1`	`src/sage/geometry/polyhedron/combinatorial_polyhedron/base.pyx: Avoid imports from .all`
`8159516`	`src/sage/geometry/polyhedron/combinatorial_polyhedron/base.pyx: Experimental: Remove cimport of Matrix_integer_dense`

sagetrac-git · 2021-09-19T02:10:28Z

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

`685c1fa`	`src/sage/geometry/polyhedron/combinatorial_polyhedron/: Experimental: Remove cimport of Matrix_integer_dense`

sagetrac-git · 2021-09-19T02:10:28Z

Changed commit from 8159516 to 685c1fa

sagetrac-git · 2021-09-19T02:21:10Z

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

`64a8ec1`	`pkgs/sagemath-polyhedra/MANIFEST.in.m4: fixup`

sagetrac-git · 2021-09-19T02:21:10Z

Changed commit from 685c1fa to 64a8ec1

mkoeppe · 2021-09-19T02:23:40Z

comment:14

This version compiles now (I had to butcher combinatorial_polyhedron a bit)
and is able to run (but not pass) doctests

sagetrac-git · 2021-09-19T05:22:24Z

Changed commit from 64a8ec1 to 4f76ecf

sagetrac-git · 2021-09-19T05:22:24Z

Branch pushed to git repo; I updated commit sha1. Last 10 new commits:

`7955111`	`git grep -l 'all import latex' src/sage \| xargs sed -i.bak 's/sage[.]misc[.]all import latex *$/sage.misc.latex import latex/'`
`b693d89`	`git grep -l 'all import vector' src/sage \| xargs sed -i.bak 's/sage[.]modules[.]all import vector *$/sage.modules.free_module_element import vector/'`
`8e357e1`	`git grep -l 'all import matrix' src/sage \| xargs sed -i.bak 's/sage[.]matrix[.]all import matrix *$/sage.matrix.constructor import matrix/'`
`d070bff`	`git grep -l 'all import RDF' src/sage \| xargs sed -i.bak 's/sage[.]rings[.]all import RDF *$/sage.rings.real_double import RDF/'`
`2344514`	`git grep -l 'all import SR' src/sage \| xargs sed -i.bak 's/sage.[.]all import SR $/sage.symbolic.ring import SR/'`
`c254b74`	`Merge #32534`
`d98d3cc`	`src/sage/rings/rational.pyx: Move import of mathml into method`
`49659b9`	`pkgs/sagemath-polyhedra/MANIFEST.in.m4: Add sage/rings/number_field/number_field_base`
`459c5e0`	`pkgs/sagemath-polyhedra/MANIFEST.in.m4: Add sage.rings.infinity`
`4f76ecf`	`src/sage/rings/all__sagemath_polyhedra.py: Change order of imports`

mkoeppe · 2021-09-19T05:22:49Z

comment:16

    from .rational import Rational
  File "sage/rings/rational.pyx", line 1, in init sage.rings.rational (build/cythonized/sage/rings/rational.cpp:39909)
  File "sage/rings/integer.pyx", line 182, in init sage.rings.integer (build/cythonized/sage/rings/integer.c:53606)
  File "/Users/mkoeppe/s/sage/sage-rebasing/worktree-rebase/pkgs/sagemath-polyhedra/.tox/python/lib/python3.9/site-packages/sage/rings/infinity.py", line 226, in <module>
    import sage.rings.integer_ring
  File "sage/rings/integer_ring.pyx", line 57, in init sage.rings.integer_ring (build/cythonized/sage/rings/integer_ring.c:18098)
ModuleNotFoundError: No module named 'sage.libs.pari'

mkoeppe · 2021-09-19T05:23:04Z

Changed dependencies from #29865, #32416, #32441, #32455 to #29865, #32416, #32441, #32455, #32534

sagetrac-git · 2021-09-19T07:16:19Z

Changed commit from 4f76ecf to 5372b70

sagetrac-git · 2022-12-19T05:35:19Z

Branch pushed to git repo; I updated commit sha1. Last 10 new commits:

`00deebe`	`pkgs/sagemath-objects/setup.py: Run finder also for sdist, egg_info, dist_info`
`39bd748`	`src/sage/dynamics/arithmetic_dynamics/projective_ds.py: Remove unused import of typing_extensions`
`e229436`	`Merge #34859`
`2b39b3d`	`Merge #34858`
`c59622a`	`build/pkgs/sagemath*/spkg-src: Use build`
`7fc93d0`	`build/pkgs/sagemath*/spkg-src: Use --skip-dependency-check`
`4940db4`	`build/make/Makefile.in: Add targets SPKG-src for script packages`
`573fcfd`	`build/make/Makefile.in: Move targets pypi-sdists, wheel, pypi-wheels here; use SPKG-sdist targets`
`0bd13ac`	`build/make/Makefile.in: Remove duplicate setting of PYPI_WHEEL_PACKAGES`
`6bf44ec`	`Merge #34855`

sagetrac-git · 2022-12-19T05:35:19Z

Changed commit from 4bcb10f to 6bf44ec

sagetrac-git · 2022-12-19T05:46:52Z

Changed commit from 6bf44ec to 702ee8d

sagetrac-git · 2022-12-19T05:46:52Z

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

`702ee8d`	`build/pkgs/sagemath*/spkg-src: Use build`

mkoeppe · 2023-01-23T02:48:21Z

Changed dependencies from #32779, #34195, #33011, #34804, #34855 to #32779, #34855, #34849, #32709

sagetrac-git · 2023-01-23T07:26:08Z

Branch pushed to git repo; I updated commit sha1. Last 10 new commits:

`449b56b`	`pkgs/sagemath*/tox.ini: Fix for tox 4`
`4a27a3d`	`Merge #34839`
`95fe89a`	`build/pkgs/tox/spkg-configure.m4: Check for good tox 3, tox 4 versions separately`
`cc7196a`	`src/tox.ini: More allowlist_externals for tox 4`
`1999bd6`	`src/tox.ini: Quoting fix for tox 4`
`071c113`	`Merge tag '9.8.beta6' into t/34849/more_fixes_to_support_tox_4`
`6b8c666`	`Merge #34839`
`a2eb816`	`tox.ini: Require tox >= 4.2.7`
`516798a`	`Merge #34849`
`d857fa0`	`pkgs/sagemath-categories: Add parts of sage.rings.polynomial`

sagetrac-git · 2023-01-23T07:26:08Z

Changed commit from 702ee8d to d857fa0

sagetrac-git · 2023-01-23T08:30:44Z

Changed commit from d857fa0 to 10d3767

sagetrac-git · 2023-01-23T08:30:44Z

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

`7f279d1`	`pkgs/sagemath-polyhedra/tox.ini: Change to allowlist_externals`
`10d3767`	`pkgs/sagemath-categories/setup.cfg.m4: Add to package_data`

sagetrac-git · 2023-01-24T04:00:44Z

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

`c28996d`	`pkgs/sagemath-categories: Add parts of sage.sets`

sagetrac-git · 2023-01-24T04:00:44Z

Changed commit from 10d3767 to c28996d

sagetrac-git · 2023-01-24T08:03:55Z

Changed commit from c28996d to 62da507

sagetrac-git · 2023-01-24T08:03:55Z

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

`7b02fb2`	`sage.structure.element.NumberFieldElement: New ABC`
`a9dacbe`	`is_NumberFieldElement: Deprecate, replace uses by isinstance`
`81e875b`	`Merge #34931`
`1cc09cc`	`Replace some imports of NumberFieldElement classes by ABC`
`4dfefbf`	`src/sage/rings/number_field/number_field_element.pyx: Update doctest with deprecation warning`
`62da507`	`Merge #34931`

sagetrac-git · 2023-01-24T21:37:26Z

Changed commit from 62da507 to f084629

sagetrac-git · 2023-01-24T21:37:26Z

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

`f084629`	`pkgs/sagemath-polyhedra/setup.cfg.m4: Allow python 3.11`

sagetrac-git · 2023-01-25T08:27:09Z

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

`ba246ff`	`src/sage/combinat/all__sagemath_polyhedra.py: New`
`58f7767`	`Use try..except when importing polynomial implementation classes`

sagetrac-git · 2023-01-25T08:27:09Z

Changed commit from f084629 to 58f7767

mkoeppe · 2023-01-27T06:25:24Z

Changed dependencies from #32779, #34855, #34849, #32709 to #32779, #34855, #34849, #32709, #34849, #34931, #34941

sagetrac-git · 2023-01-27T07:27:15Z

Changed commit from 58f7767 to 8270697

sagetrac-git · 2023-01-27T07:27:15Z

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

`c9afec2`	`src/sage/rings/integer.pyx: Mark doctests # optional - sage.libs.pari, sage.rings.number_field, sage.symbolic`
`a4f7955`	`pkgs/sagemath-categories/MANIFEST.in.m4: Add sage.rings.finite_rings.integer_mod, sage.rings.factorint`
`e46b5d5`	`src/sage/rings/polynomial/polynomial_element_generic.py: Use try...except for an unpickle_override import`
`f4730da`	`pkgs/sagemath-categories/MANIFEST.in.m4: Add sage.rings.finite_rings.integer_mod_ring`
`86f2f74`	`src/sage/geometry/polyhedron: Add # optional - sage.combinat, sage.groups, sage.plot, sage.rings.number_field, sage.symbolic`
`9b6cb96`	`pkgs/sagemath-polyhedra: Add sage.numerical.mip etc`
`ad6a466`	`pkgs/sagemath-polyhedra/tox.ini: Add more passing files`
`131e3be`	`pkgs/sagemath-polyhedra: Add sage.numerical.mip etc (fixup)`
`25f84e3`	`src/sage/numerical/backends/scip_backend.pyx: Remove unused imports`
`8270697`	`Merge #34941`

mkoeppe · 2023-02-12T18:40:31Z

Removed the branch from the issue description; replaced by #35095

…trix_integer_dense`  ### 📚 Description   This is for the distribution sagemath-polyhedra (#32432) so that it does not have to depend on the flint library.  ### 📝 Checklist    - [x] I have made sure that the title is self-explanatory and the description concisely explains the PR. - [ ] I have linked an issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### ⌛ Dependencies   URL: #35135 Reported by: Matthias Köppe Reviewer(s): Jonathan Kliem, Matthias Köppe

mkoeppe added this to the sage-9.5 milestone Aug 28, 2021

mkoeppe added t: refactoring labels Aug 28, 2021

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mkoeppe modified the milestones: sage-9.8, sage-9.9 Jan 7, 2023

mkoeppe removed the s: needs work label Feb 12, 2023

mkoeppe self-assigned this Feb 12, 2023

mkoeppe modified the milestones: sage-10.0, sage-10.1 Apr 30, 2023

mkoeppe removed this from the sage-10.1 milestone Aug 7, 2023

orlitzky mentioned this issue Jan 2, 2024

Meta-ticket: Create upstream repositories, pip-installable packages for database packages #30914

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Modularization of sagelib: Break out a separate package sagemath-polyhedra #32432

Modularization of sagelib: Break out a separate package sagemath-polyhedra #32432

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