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Demote brial (= polybori) from standard to optional, add distribution sagemath-brial, enlarge sagemath-objects, sagemath-categories #36380

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@mkoeppe mkoeppe commented Oct 1, 2023

as proposed in https://groups.google.com/g/sage-devel/c/ewHP20bmskQ, because (among other things):
It has been dropped from Debian testing (debian-trixie) and ubuntu-noble, where it seems to block SageMath upgrades (Sage is stuck at 9.5 in Debian/Ubuntu). See https://repology.org/project/brial/versions

The new distribution builds on top of enlarged distributions sagemath-objects, sagemath-categories. This is a major update of these distributions, which makes them much more useful.

Also includes style changes to all*.py files cherry-picked from #37900.

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dimpase commented Oct 2, 2023

docs don't build. I think one can't build boolean polynomials' docs without brial installed, so this has to be moved out:

--- a/src/doc/en/reference/polynomial_rings/index.rst
+++ b/src/doc/en/reference/polynomial_rings/index.rst
@@ -62,12 +62,4 @@ Infinite Polynomial Rings
    sage/rings/polynomial/symmetric_ideal
    sage/rings/polynomial/symmetric_reduction
 
-Boolean Polynomials
--------------------
-
-.. toctree::
-   :maxdepth: 1
-
-   sage/rings/polynomial/pbori/pbori
-
 .. include:: ../footer.txt

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mkoeppe commented Oct 2, 2023

Right. We will need to find a solution for this more general problem of building the manual with optional parts...

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dimpase commented Oct 2, 2023

also:

src/sage/features/sagemath.py:867: UserWarning: Feature sage.rings.polynomial.pbori is declared standard, but it is provided by sagemath_brial, which is declared experimental in SAGE_ROOT/build/pkgs
  JoinFeature.__init__(self, 'sage.rings.polynomial.pbori',

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dimpase commented Oct 3, 2023

there are several unconditional imports of BooleanPolynomials left, e.g. in
src/sage/rings/polynomial/multi_polynomial_libsingular.pyx

Should it go via an abstract class, etc, to achieve modularity ?

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mkoeppe commented Oct 3, 2023

there are several unconditional imports of BooleanPolynomials left, e.g. in src/sage/rings/polynomial/multi_polynomial_libsingular.pyx

Should it go via an abstract class, etc, to achieve modularity ?

I think I have already done all necessary changes of this kind in #35095. I'll cherry-pick them to this branch later today.

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mkoeppe commented Oct 3, 2023

Actually I created the ABC BooleanPolynomialRing_base for the parent, but not for the element class. So if you have chance, a modularizing fix here would be welcome

Edit: Done already in f5c6196

.gitignore Outdated
@@ -215,6 +217,7 @@ build/bin/sage-build-env-config
/pkgs/sagemath-categories/requirements.txt
/pkgs/sagemath-environment/requirements.txt
/pkgs/sagemath-repl/requirements.txt
/pkgs/sagemath-brial/requirements*.txt
/pkgs/sagemath-categories/MANIFEST.in

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OK for now. But I think this block of lines should be sorted out by distribution names...

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kwankyu commented Oct 18, 2023

I get

$ ./sage -sh -c '(cd pkgs/sagemath-brial && tox -v -v -v -e sagepython)'
...
      
            cypari2/closure.pyx:139:4: 'sig_on' is not a constant, variable or function identifier
      
            Error compiling Cython file:
            ------------------------------------------------------------
            ...
      
            cdef int _pari_init_closure() except -1:
                sig_on()
                global ep_call_python
                ep_call_python = install(<void*>call_python, "call_python", 'DGDGDGDGDGD5,U,U')
                sig_off()
                ^
            ------------------------------------------------------------
      
            cypari2/closure.pyx:142:4: 'sig_off' is not a constant, variable or function identifier
      
            Error compiling Cython file:
            ------------------------------------------------------------
            ...
                # Only 5 arguments are supported for now...
                if nargs > 5:
                    nargs = 5
      
                # Fill in default arguments of PARI function
                sig_on()
                ^
            ------------------------------------------------------------
      
            cypari2/closure.pyx:230:4: 'sig_on' is not a constant, variable or function identifier
            Traceback (most recent call last):
...
              File "/private/var/folders/td/fw1q9ljs311ggyph77rs53_40000gn/T/pip-install-h6yasewl/cypari2_0d737fa76b3f479ea5e1b6ab73dffe77/.eggs/Cython-3.0.4-py3.11.egg/Cython/Build/Dependencies.py", line 1321, in cythonize_one
                raise CompileError(None, pyx_file)
            Cython.Compiler.Errors.CompileError: cypari2/closure.pyx
            [end of output]
      
        note: This error originates from a subprocess, and is likely not a problem with pip.
      error: legacy-install-failure
      
      × Encountered error while trying to install package.
      ╰─> cypari2
      
      note: This is an issue with the package mentioned above, not pip.
      hint: See above for output from the failure.
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.
sagepython: 67309 C exit 1 (66.94 seconds) /Users/kwankyu/GitHub/sage-dev/pkgs/sagemath-brial> python -I -m pip install -r requirements.txt pid=54141 [tox/execute/api.py:275]
  sagepython: FAIL code 1 (66.95 seconds)
  evaluation failed :( (67.15 seconds)

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kwankyu commented Oct 18, 2023

This src/sage_setup/__init__.py seems new (or copied from somewhere?) What is the intention? Should this

sage: sage_setup.sage_setup(['sagemath-modules'])

work? There's no doc for it...

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Documentation preview for this PR (built with commit 876fa67; changes) is ready! 🎉
This preview will update shortly after each push to this PR.

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As requested in
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cherry-picked from there.

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… pattern

    
As requested in
sagemath#36380 (comment) and
cherry-picked from there.

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mkoeppe commented Sep 26, 2024

"Disputed" was set 3 weeks ago.

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Needs rebasing

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mkoeppe commented Sep 27, 2024

Needs rebasing

No, it's up to date

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Could you please explain why this file is needed and where the name of the file comes from? What does taylor have to do with categories?

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sagemath-categories per definition in its README provides "Sage categories, basic rings, polynomials, functions".

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In general, the all__*.py define the top-level interactive environment that is used for running the doctests.

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Concretely, the imports from sage.calculus.functional are global functions that dispatch to like-named methods. They are usable with polynomials, for example, which are provided by the enlarged sagemath-categories.

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Yes, but expand, simplify and taylor are not in "Sage categories, basic rings, polynomials, functions".

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factor is not provided by sagemath_categories, is it?

Well, the class Factorization is provided already by sagemath-objects (dependency of sagemath-categories).

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In what way are simplify, expand and taylor usable with polynomials?

simplify and expand are no-ops with polynomials. taylor works with polynomials as it does with symbolic expressions.

Note that the current implementation of some of these methods goes through SR. That's a typical modularization obstacle that should be addressed eventually in a follow-up PR.

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OK, but what do these function have to do with sagemath_categories? I thought that this should be a rather minimal subset of sage, and simplify is something that I would certainly not expect to use on polynomials (as: elements of an exact polynomial ring with zero test).

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Consider that there may be a wide range of expectations among Sage users. I'd say it's unwise to generalize from your specific expectations.

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"Minimality" is not a goal for sagemath-categories, except regarding its dependencies.

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There are many optional tags missing in doctests. With brial uninstalled (so sage__rings__polynomial__pbori().is_present() is False), I get all these failures:

sage -t --long /usr/lib/python3.12/site-packages/sage/crypto/mq/sr.py  # 1 doctest failed
sage -t --long /usr/lib/python3.12/site-packages/sage/groups/matrix_gps/finitely_generated_gap.py  # 1 doctest failed
sage -t --long /usr/lib/python3.12/site-packages/sage/libs/singular/function.pyx  # 1 doctest failed
sage -t --long /usr/lib/python3.12/site-packages/sage/misc/citation.pyx  # 1 doctest failed
sage -t --long /usr/lib/python3.12/site-packages/sage/misc/cython.py  # 4 doctests failed
sage -t --long /usr/lib/python3.12/site-packages/sage/rings/qqbar_decorators.py  # 4 doctests failed
sage -t --long /usr/lib/python3.12/site-packages/sage/rings/polynomial/infinite_polynomial_element.py  # 1 doctest failed
sage -t --long /usr/lib/python3.12/site-packages/sage/rings/polynomial/multi_polynomial_ideal.py  # 5 doctests failed
sage -t --long /usr/lib/python3.12/site-packages/sage/rings/polynomial/multi_polynomial_libsingular.pyx  # 2 doctests failed
sage -t --long /usr/lib/python3.12/site-packages/sage/rings/polynomial/multi_polynomial_sequence.py  # 41 doctests failed
sage -t --long /usr/lib/python3.12/site-packages/sage/rings/polynomial/toy_buchberger.py  # 2 doctests failed
sage -t --long /usr/lib/python3.12/site-packages/sage/rings/polynomial/pbori/PyPolyBoRi.py  # 28 doctests failed
sage -t --long /usr/lib/python3.12/site-packages/sage/rings/polynomial/pbori/blocks.py  # 2 doctests failed
sage -t --long /usr/lib/python3.12/site-packages/sage/rings/polynomial/pbori/cnf.py  # 46 doctests failed
sage -t --long /usr/lib/python3.12/site-packages/sage/rings/polynomial/pbori/easy_polynomials.py  # 10 doctests failed
sage -t --long /usr/lib/python3.12/site-packages/sage/rings/polynomial/pbori/fglm.py  # 29 doctests failed
sage -t --long /usr/lib/python3.12/site-packages/sage/rings/polynomial/pbori/frontend.py  # 12 doctests failed
sage -t --long /usr/lib/python3.12/site-packages/sage/rings/polynomial/pbori/gbcore.py  # 18 doctests failed
sage -t --long /usr/lib/python3.12/site-packages/sage/rings/polynomial/pbori/ll.py  # 33 doctests failed
sage -t --long /usr/lib/python3.12/site-packages/sage/rings/polynomial/pbori/nf.py  # 8 doctests failed
sage -t --long /usr/lib/python3.12/site-packages/sage/rings/polynomial/pbori/parallel.py  # 31 doctests failed
sage -t --long /usr/lib/python3.12/site-packages/sage/rings/polynomial/pbori/pbori.pyx  # Timed out
sage -t --long /usr/lib/python3.12/site-packages/sage/rings/polynomial/pbori/randompoly.py  # 11 doctests failed

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mkoeppe commented Sep 28, 2024

@antonio-rojas Thanks for testing!

Note that files such as sage/rings/polynomial/pbori/cnf.py should no longer be installed as part of sagemath-standard as they are shipped by a different distribution now.

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mkoeppe commented Sep 28, 2024

(I'll look into the failures in the other files.)

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@antonio-rojas Thanks for testing!

Note that files such as sage/rings/polynomial/pbori/cnf.py should no longer be installed as part of sagemath-standard as they are shipped by a different distribution now.

I understard. So far on Arch I've been shipping sagemath-standard together with all optional distributions in a single distro package. Optional extensions are then enabled by installing the respective shared libraries. Since sage features test for modules being importable (not just present) this works nicely as long as doctest are properly tagged.

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mkoeppe commented Sep 28, 2024

OK, I have added the doctest tags for the files in sage/rings/polynomial/pbori to make this easier.

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mkoeppe commented Sep 29, 2024

@antonio-rojas Tests should be better now

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@antonio-rojas Tests should be better now

Thanks, looks good now

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