Move filterwarnings calls from sage.all to sage.all__sagemath_repl

[mkoeppe]

📚 Description

We can use sage -t to test with a top-level environment other than sage.all using the parameter --environment=sage.all__sagemath_categories etc.

To make sure that the warnings configuration is also set up in this case, we move the filterwarnings calls from sage.all to sage.all__sagemath_repl. (The doctester loads sage.repl.)

📝 Checklist

• 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

[codecov-commenter]

Codecov Report

Base: 88.60% // Head: 88.58% // Decreases project coverage by -0.02% ⚠️

Coverage data is based on head (a2c64dc) compared to base (8f5bbd2).
Patch coverage: 86.95% of modified lines in pull request are covered.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop   #35160      +/-   ##
===========================================
- Coverage    88.60%   88.58%   -0.02%     
===========================================
  Files         2140     2140              
  Lines       397273   397271       -2     
===========================================
- Hits        352004   351940      -64     
- Misses       45269    45331      +62     

Impacted Files	Coverage Δ
src/sage/all__sagemath_repl.py	89.65% <86.36%> (+89.65%)	⬆️
src/sage/all.py	97.24% <100.00%> (+1.75%)	⬆️
...e/combinat/cluster_algebra_quiver/mutation_type.py	49.76% <0.00%> (-3.21%)	⬇️
src/sage/interfaces/qsieve.py	71.30% <0.00%> (-2.61%)	⬇️
src/sage/modular/local_comp/liftings.py	98.33% <0.00%> (-1.67%)	⬇️
src/sage/cpython/_py2_random.py	75.20% <0.00%> (-1.24%)	⬇️
src/sage/schemes/elliptic_curves/hom_velusqrt.py	94.09% <0.00%> (-1.19%)	⬇️
src/sage/modular/modform/numerical.py	94.19% <0.00%> (-0.65%)	⬇️
...sage/geometry/hyperbolic_space/hyperbolic_model.py	88.95% <0.00%> (-0.62%)	⬇️
src/sage/modular/arithgroup/congroup_gamma0.py	94.41% <0.00%> (-0.56%)	⬇️
... and 21 more

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[github-actions]

Documentation preview for this PR is ready! 🎉
Built with commit: a2c64dc

[tornaria]

I guess this is unrelated to the current PR, I copy it here so it won't get lost.

sage -t --random-seed=46211102795342700483820211214572761418 sage/schemes/elliptic_curves/ell_field.py
**********************************************************************
File "sage/schemes/elliptic_curves/ell_field.py", line 1345, in sage.schemes.elliptic_curves.ell_field.EllipticCurve_field.isogenies_prime_degree
Failed example:
    E.isogenies_prime_degree(max_l=3)
Exception raised:
    Traceback (most recent call last):
      File "sage/structure/category_object.pyx", line 839, in sage.structure.category_object.CategoryObject.getattr_from_category
        return self.__cached_methods[name]
    KeyError: 'point_homset'

    During handling of the above exception, another exception occurred:

    Traceback (most recent call last):
      File "/__w/sage/sage/src/sage/schemes/projective/projective_subscheme.py", line 122, in point
        return self._point(self.point_homset(), v, check=check)
      File "/__w/sage/sage/src/sage/schemes/elliptic_curves/ell_point.py", line 256, in __init__
        point_homset = curve.point_homset()
      File "sage/structure/category_object.pyx", line 833, in sage.structure.category_object.CategoryObject.__getattr__
        return self.getattr_from_category(name)
      File "sage/structure/category_object.pyx", line 848, in sage.structure.category_object.CategoryObject.getattr_from_category
        attr = getattr_from_other_class(self, cls, name)
      File "sage/cpython/getattr.pyx", line 356, in sage.cpython.getattr.getattr_from_other_class
        raise AttributeError(dummy_error_message)
    AttributeError: 'sage.rings.polynomial.polynomial_zz_pex.Polynomial_ZZ_pEX' object has no attribute '__custom_name'

    During handling of the above exception, another exception occurred:

    Traceback (most recent call last):
      File "/__w/sage/sage/src/sage/doctest/forker.py", line 695, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/__w/sage/sage/src/sage/doctest/forker.py", line 1093, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.schemes.elliptic_curves.ell_field.EllipticCurve_field.isogenies_prime_degree[15]>", line 1, in <module>
        E.isogenies_prime_degree(max_l=Integer(3))
      File "/__w/sage/sage/src/sage/schemes/elliptic_curves/ell_field.py", line 1448, in isogenies_prime_degree
        return sum([isogenies_prime_degree(self, d) for d in L], [])
      File "/__w/sage/sage/src/sage/schemes/elliptic_curves/ell_field.py", line 1448, in <listcomp>
        return sum([isogenies_prime_degree(self, d) for d in L], [])
      File "/__w/sage/sage/src/sage/schemes/elliptic_curves/isogeny_small_degree.py", line 2337, in isogenies_prime_degree
        return isogenies_3(E, minimal_models=minimal_models)
      File "/__w/sage/sage/src/sage/schemes/elliptic_curves/isogeny_small_degree.py", line 756, in isogenies_3
        isogs = [E.isogeny(f, model=model) for f in ff]
      File "/__w/sage/sage/src/sage/schemes/elliptic_curves/isogeny_small_degree.py", line 756, in <listcomp>
        isogs = [E.isogeny(f, model=model) for f in ff]
      File "/__w/sage/sage/src/sage/schemes/elliptic_curves/ell_field.py", line 1215, in isogeny
        return EllipticCurveIsogeny(self, kernel, codomain, degree, model, check=check)
      File "/__w/sage/sage/src/sage/schemes/elliptic_curves/ell_curve_isogeny.py", line 974, in __init__
        if not isinstance(kernel, list) and kernel in E:
      File "/__w/sage/sage/src/sage/schemes/elliptic_curves/ell_generic.py", line 442, in __contains__
        P = self(P)
      File "/__w/sage/sage/src/sage/schemes/elliptic_curves/ell_generic.py", line 570, in __call__
        return plane_curve.ProjectivePlaneCurve.__call__(self, *args, **kwds)
      File "/__w/sage/sage/src/sage/schemes/generic/scheme.py", line 266, in __call__
        return self.point(args)
      File "/__w/sage/sage/src/sage/schemes/projective/projective_subscheme.py", line 124, in point
        return self._point(self, v, check=check)
      File "/__w/sage/sage/src/sage/schemes/elliptic_curves/ell_point.py", line 268, in __init__
        raise TypeError("v (=%s) must have %s components" % (v, d))
      File "sage/structure/sage_object.pyx", line 194, in sage.structure.sage_object.SageObject.__repr__
        result = reprfunc()
      File "sage/rings/polynomial/polynomial_element.pyx", line 2696, in sage.rings.polynomial.polynomial_element.Polynomial._repr_
        return self._repr()
      File "sage/rings/polynomial/polynomial_element.pyx", line 2648, in sage.rings.polynomial.polynomial_element.Polynomial._repr
        coeffs = self.list(copy=False)
      File "sage/rings/polynomial/polynomial_zz_pex.pyx", line 201, in sage.rings.polynomial.polynomial_zz_pex.Polynomial_ZZ_pEX.list
        return [K(ZZ_pE_c_to_list(ZZ_pEX_coeff(self.x, i)))
      File "sage/structure/parent.pyx", line 896, in sage.structure.parent.Parent.__call__
        return mor._call_(x)
      File "sage/structure/coerce_maps.pyx", line 161, in sage.structure.coerce_maps.DefaultConvertMap_unique._call_
        raise
      File "sage/structure/coerce_maps.pyx", line 156, in sage.structure.coerce_maps.DefaultConvertMap_unique._call_
        return C._element_constructor(x)
      File "/__w/sage/sage/src/sage/categories/sets_cat.py", line 1010, in _element_constructor_from_element_class
        return self.element_class(self, *args, **keywords)
      File "sage/rings/finite_rings/element_pari_ffelt.pyx", line 335, in sage.rings.finite_rings.element_pari_ffelt.FiniteFieldElement_pari_ffelt.__init__
        self.construct_from(x)
      File "sage/rings/finite_rings/element_pari_ffelt.pyx", line 503, in sage.rings.finite_rings.element_pari_ffelt.FiniteFieldElement_pari_ffelt.construct_from
        self.construct_from(self._parent.polynomial_ring()([Fp(y) for y in x]))
      File "sage/rings/finite_rings/element_pari_ffelt.pyx", line 493, in sage.rings.finite_rings.element_pari_ffelt.FiniteFieldElement_pari_ffelt.construct_from
        self.construct_from(x.substitute(self._parent.gen()))
      File "sage/rings/polynomial/polynomial_element.pyx", line 438, in sage.rings.polynomial.polynomial_element.Polynomial.subs
        return self(*x, **kwds)
      File "sage/rings/polynomial/polynomial_zmod_flint.pyx", line 327, in sage.rings.polynomial.polynomial_zmod_flint.Polynomial_zmod_flint.__call__
        return Polynomial.__call__(self, *x, **kwds)
      File "sage/rings/polynomial/polynomial_element.pyx", line 876, in sage.rings.polynomial.polynomial_element.Polynomial.__call__
        cst, aa = coercion_model.canonical_coercion(cst, a)
      File "sage/structure/coerce.pyx", line 1311, in sage.structure.coerce.CoercionModel.canonical_coercion
        x_elt = (<Map>x_map)._call_(x)
      File "sage/rings/finite_rings/hom_prime_finite_field.pyx", line 94, in sage.rings.finite_rings.hom_prime_finite_field.FiniteFieldHomomorphism_prime._call_
        return self._codomain._element_constructor(x)
      File "/__w/sage/sage/src/sage/categories/sets_cat.py", line 1010, in _element_constructor_from_element_class
        return self.element_class(self, *args, **keywords)
      File "sage/rings/finite_rings/element_pari_ffelt.pyx", line 335, in sage.rings.finite_rings.element_pari_ffelt.FiniteFieldElement_pari_ffelt.__init__
        self.construct_from(x)
      File "sage/rings/finite_rings/element_pari_ffelt.pyx", line 409, in sage.rings.finite_rings.element_pari_ffelt.FiniteFieldElement_pari_ffelt.construct_from
        sig_on()
    SystemError: calling remove_from_pari_stack() inside sig_on()
**********************************************************************
1 item had failures:
   1 of  43 in sage.schemes.elliptic_curves.ell_field.EllipticCurve_field.isogenies_prime_degree
    [323 tests, 1 failure, 7.77 s]

[mkoeppe]

I agree, it's unrelated; just more trouble with PARI

[tornaria]

Works for me, tested in void linux x86_64.

I wonder:;

• what is the process to remove stuff from filterwarnings?
• how can we check which deprecation warnings are being dealt with?

I just worry that we silence deprecation warnings and miss the chance to fix the issues before functionality is removed.

[mkoeppe]

Thank you!

[mkoeppe]

I wonder:

• what is the process to remove stuff from filterwarnings?
• how can we check which deprecation warnings are being dealt with?

I just worry that we silence deprecation warnings and miss the chance to fix the issues before functionality is removed.

It would probably be a good idea to create an Issue whenever such a deprecation warning is silenced.

I think most of the filtered warnings are/were coming from upstream packages that had not been updated yet. Instead of attempting to patch the packages, we'd just add the filter.