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* [PR PATCH] [RFC] New package: sagelib-9.5
@ 2022-02-01  4:05 tornaria
  2022-02-01  9:21 ` dkwo
                   ` (17 more replies)
  0 siblings, 18 replies; 19+ messages in thread
From: tornaria @ 2022-02-01  4:05 UTC (permalink / raw)
  To: ml

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There is a new pull request by tornaria against master on the void-packages repository

https://github.com/tornaria/void-packages sagelib
https://github.com/void-linux/void-packages/pull/35339

[RFC] New package: sagelib-9.5
This is a different approach for a sagemath package than #34030.

Here we build the sagelib as a python module and install it in the system site-packages. The scripts are all installed in `/usr/lib/sagemath/bin` to avoid polluting the PATH. A symlink `/usr/bin/sagelib` is provided.

NOTE: for the moment this is set up so it can coexists together with the `sagemath` package; that's why the package name is `sagelib` (instead of `sagemath`) and the binary is `sagelib` (instead of `sage`). The plan is to rename this package to `sagemath` and the binary to `sage` to replace the other since this one is much simpler and should work better.

With this version jupyter notebook should work out of the box without any adjustments. Please let me know if there's anything missing.

Any comments about packaging, package layout, etc, now is the moment. I would like to get this merged soon since everything seems to be in place.

Cc: @dkwo @leahneukirchen 

A patch file from https://github.com/void-linux/void-packages/pull/35339.patch is attached

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From f9002d5ec9cc7dbfa364d1f8cb3ab2f1f4608364 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 31 Jan 2022 12:50:38 -0300
Subject: [PATCH] New package: sagelib-9.5

---
 srcpkgs/sagelib/files/timings2.json           | 398 ++++++++++++++++++
 .../patches/01-dont_link_ratpoints.patch      |  10 +
 ...2-fix_get_shared_lib_path--see_29644.patch |  13 +
 .../patches/03-doctest_have_program.patch     |  20 +
 .../patches/04-doctest_sage_getfile.patch     |  22 +
 .../sagelib/patches/05-fix_sage_getfile.patch |  16 +
 ...6-skip_doctest_giac-1.7.0--see_31563.patch |  16 +
 .../sagelib/patches/07-ignore_warning.patch   |  15 +
 .../08-dont_run_pytest--see_31924.patch       |  27 ++
 ...2ddd4e2dc92469c1590ebf0c40f8f69bf579.patch | 126 ++++++
 .../patches/zzz-skip_doctest_no_threejs.patch |  13 +
 srcpkgs/sagelib/template                      | 131 ++++++
 12 files changed, 807 insertions(+)
 create mode 100644 srcpkgs/sagelib/files/timings2.json
 create mode 100644 srcpkgs/sagelib/patches/01-dont_link_ratpoints.patch
 create mode 100644 srcpkgs/sagelib/patches/02-fix_get_shared_lib_path--see_29644.patch
 create mode 100644 srcpkgs/sagelib/patches/03-doctest_have_program.patch
 create mode 100644 srcpkgs/sagelib/patches/04-doctest_sage_getfile.patch
 create mode 100644 srcpkgs/sagelib/patches/05-fix_sage_getfile.patch
 create mode 100644 srcpkgs/sagelib/patches/06-skip_doctest_giac-1.7.0--see_31563.patch
 create mode 100644 srcpkgs/sagelib/patches/07-ignore_warning.patch
 create mode 100644 srcpkgs/sagelib/patches/08-dont_run_pytest--see_31924.patch
 create mode 100644 srcpkgs/sagelib/patches/trac-33189-fix_doctests_for_arb_2.22-53532ddd4e2dc92469c1590ebf0c40f8f69bf579.patch
 create mode 100644 srcpkgs/sagelib/patches/zzz-skip_doctest_no_threejs.patch
 create mode 100644 srcpkgs/sagelib/template

diff --git a/srcpkgs/sagelib/files/timings2.json b/srcpkgs/sagelib/files/timings2.json
new file mode 100644
index 000000000000..71a9aa84ce58
--- /dev/null
+++ b/srcpkgs/sagelib/files/timings2.json
@@ -0,0 +1,398 @@
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+  "sage.plot.plot3d.implicit_surface": {"walltime": 8},
+  "sage.plot.plot3d.parametric_plot3d": {"walltime": 8},
+  "sage.plot.plot3d.parametric_surface": {"walltime": 8},
+  "sage.plot.plot3d.plot3d": {"walltime": 16},
+  "sage.plot.plot3d.tachyon": {"walltime": 8},
+  "sage.plot.plot3d.transform": {"walltime": 32},
+  "sage.plot.point": {"walltime": 8},
+  "sage.plot.polygon": {"walltime": 8},
+  "sage.plot.streamline_plot": {"walltime": 8},
+  "sage.quadratic_forms.genera.genus": {"walltime": 16},
+  "sage.quadratic_forms.quadratic_form__automorphisms": {"walltime": 8},
+  "sage.quadratic_forms.quadratic_form__local_representation_conditions": {"walltime": 64},
+  "sage.quadratic_forms.quadratic_form__neighbors": {"walltime": 8},
+  "sage.quadratic_forms.quadratic_form__siegel_product": {"walltime": 8},
+  "sage.repl.ipython_extension": {"walltime": 8},
+  "sage.rings.asymptotic.asymptotic_expansion_generators": {"walltime": 64},
+  "sage.rings.asymptotic.asymptotic_ring": {"walltime": 8},
+  "sage.rings.asymptotic.asymptotics_multivariate_generating_functions": {"walltime": 32},
+  "sage.rings.asymptotic.term_monoid": {"walltime": 8},
+  "sage.rings.continued_fraction": {"walltime": 8},
+  "sage.rings.finite_rings.finite_field_base": {"walltime": 8},
+  "sage.rings.function_field.function_field": {"walltime": 256},
+  "sage.rings.function_field.function_field_valuation": {"walltime": 64},
+  "sage.rings.function_field.ideal": {"walltime": 8},
+  "sage.rings.function_field.place": {"walltime": 8},
+  "sage.rings.integer": {"walltime": 128},
+  "sage.rings.invariants.invariant_theory": {"walltime": 8},
+  "sage.rings.number_field.bdd_height": {"walltime": 8},
+  "sage.rings.number_field.number_field": {"walltime": 64},
+  "sage.rings.number_field.number_field_element": {"walltime": 16},
+  "sage.rings.number_field.splitting_field": {"walltime": 8},
+  "sage.rings.number_field.totallyreal": {"walltime": 16},
+  "sage.rings.number_field.totallyreal_rel": {"walltime": 8},
+  "sage.rings.padics.padic_base_leaves": {"walltime": 64},
+  "sage.rings.padics.padic_extension_leaves": {"walltime": 64},
+  "sage.rings.padics.padic_generic_element": {"walltime": 16},
+  "sage.rings.padics.padic_lattice_element": {"walltime": 32},
+  "sage.rings.padics.relative_extension_leaves": {"walltime": 32},
+  "sage.rings.polynomial.multi_polynomial_ideal": {"walltime": 8},
+  "sage.rings.polynomial.multi_polynomial_sequence": {"walltime": 8},
+  "sage.rings.polynomial.ore_function_element": {"walltime": 8},
+  "sage.rings.polynomial.polynomial_element": {"walltime": 16},
+  "sage.rings.polynomial.polynomial_rational_flint": {"walltime": 8},
+  "sage.rings.polynomial.polynomial_zmod_flint": {"walltime": 512},
+  "sage.rings.qqbar": {"walltime": 16},
+  "sage.rings.tests": {"walltime": 16},
+  "sage.rings.valuation.augmented_valuation": {"walltime": 32},
+  "sage.rings.valuation.mapped_valuation": {"walltime": 64},
+  "sage.rings.valuation.valuation": {"walltime": 8},
+  "sage.sandpiles.sandpile": {"walltime": 16},
+  "sage.schemes.curves.affine_curve": {"walltime": 16},
+  "sage.schemes.curves.closed_point": {"walltime": 8},
+  "sage.schemes.curves.projective_curve": {"walltime": 32},
+  "sage.schemes.cyclic_covers.cycliccover_finite_field": {"walltime": 64},
+  "sage.schemes.elliptic_curves.BSD": {"walltime": 8},
+  "sage.schemes.elliptic_curves.Qcurves": {"walltime": 8},
+  "sage.schemes.elliptic_curves.constructor": {"walltime": 32},
+  "sage.schemes.elliptic_curves.ell_curve_isogeny": {"walltime": 16},
+  "sage.schemes.elliptic_curves.ell_egros": {"walltime": 32},
+  "sage.schemes.elliptic_curves.ell_finite_field": {"walltime": 8},
+  "sage.schemes.elliptic_curves.ell_generic": {"walltime": 8},
+  "sage.schemes.elliptic_curves.ell_modular_symbols": {"walltime": 16},
+  "sage.schemes.elliptic_curves.ell_number_field": {"walltime": 128},
+  "sage.schemes.elliptic_curves.ell_point": {"walltime": 8},
+  "sage.schemes.elliptic_curves.ell_rational_field": {"walltime": 128},
+  "sage.schemes.elliptic_curves.gal_reps_number_field": {"walltime": 32},
+  "sage.schemes.elliptic_curves.gp_simon": {"walltime": 16},
+  "sage.schemes.elliptic_curves.heegner": {"walltime": 32},
+  "sage.schemes.elliptic_curves.height": {"walltime": 64},
+  "sage.schemes.elliptic_curves.isogeny_class": {"walltime": 32},
+  "sage.schemes.elliptic_curves.isogeny_small_degree": {"walltime": 256},
+  "sage.schemes.elliptic_curves.kraus": {"walltime": 16},
+  "sage.schemes.elliptic_curves.mod_sym_num": {"walltime": 8},
+  "sage.schemes.elliptic_curves.padic_lseries": {"walltime": 8},
+  "sage.schemes.elliptic_curves.padics": {"walltime": 16},
+  "sage.schemes.elliptic_curves.saturation": {"walltime": 16},
+  "sage.schemes.elliptic_curves.sha_tate": {"walltime": 32},
+  "sage.schemes.hyperelliptic_curves.hyperelliptic_finite_field": {"walltime": 64},
+  "sage.schemes.hyperelliptic_curves.hyperelliptic_generic": {"walltime": 8},
+  "sage.schemes.hyperelliptic_curves.hyperelliptic_padic_field": {"walltime": 32},
+  "sage.schemes.hyperelliptic_curves.monsky_washnitzer": {"walltime": 8},
+  "sage.schemes.projective.projective_rational_point": {"walltime": 8},
+  "sage.schemes.riemann_surfaces.riemann_surface": {"walltime": 64},
+  "sage.schemes.toric.chow_group": {"walltime": 8},
+  "sage.schemes.toric.sheaf.klyachko": {"walltime": 8},
+  "sage.stats.distributions.discrete_gaussian_integer": {"walltime": 8},
+  "sage.stats.time_series": {"walltime": 8},
+  "sage.structure.coerce_dict": {"walltime": 32},
+  "sage.structure.element": {"walltime": 16},
+  "sage.structure.sage_object": {"walltime": 8},
+  "sage.symbolic.expression": {"walltime": 32},
+  "sage.symbolic.integration.integral": {"walltime": 32},
+  "sage.symbolic.random_tests": {"walltime": 32},
+  "sage.symbolic.relation": {"walltime": 8},
+  "sage.tests.book_schilling_zabrocki_kschur_primer": {"walltime": 32},
+  "sage.tests.book_stein_ent": {"walltime": 16},
+  "sage.tests.books.computational-mathematics-with-sagemath.combinat_doctest": {"walltime": 32},
+  "sage.tests.books.computational-mathematics-with-sagemath.float_doctest": {"walltime": 16},
+  "sage.tests.books.computational-mathematics-with-sagemath.graphique_doctest": {"walltime": 32},
+  "sage.tests.books.computational-mathematics-with-sagemath.graphtheory_doctest": {"walltime": 8},
+  "sage.tests.books.computational-mathematics-with-sagemath.integration_doctest": {"walltime": 32},
+  "sage.tests.books.computational-mathematics-with-sagemath.mpoly_doctest": {"walltime": 8},
+  "sage.tests.books.computational-mathematics-with-sagemath.nonlinear_doctest": {"walltime": 8},
+  "sage.tests.books.computational-mathematics-with-sagemath.recequadiff_doctest": {"walltime": 8},
+  "sage.tests.books.computational-mathematics-with-sagemath.sol.graphique_doctest": {"walltime": 16},
+  "sage.tests.books.computational-mathematics-with-sagemath.sol.numbertheory_doctest": {"walltime": 16},
+  "sage.tests.books.computational-mathematics-with-sagemath.sol.polynomes_doctest": {"walltime": 16},
+  "sage.tests.cmdline": {"walltime": 64},
+  "sage.tests.gosper-sum": {"walltime": 16},
+  "sage.tests.parigp": {"walltime": 8},
+  "sage.topology.simplicial_complex": {"walltime": 8},
+  "sage.topology.simplicial_complex_examples": {"walltime": 16}
+}
diff --git a/srcpkgs/sagelib/patches/01-dont_link_ratpoints.patch b/srcpkgs/sagelib/patches/01-dont_link_ratpoints.patch
new file mode 100644
index 000000000000..e5c3f5776aa2
--- /dev/null
+++ b/srcpkgs/sagelib/patches/01-dont_link_ratpoints.patch
@@ -0,0 +1,10 @@
+ - do not link ratpoints where it's not used
+
+--- a/src/sage/schemes/elliptic_curves/descent_two_isogeny.pyx
++++ b/src/sage/schemes/elliptic_curves/descent_two_isogeny.pyx
+@@ -1,5 +1,3 @@
+-# distutils: libraries = ratpoints
+-
+ r"""
+ Descent on elliptic curves over `\QQ` with a 2-isogeny
+ """
diff --git a/srcpkgs/sagelib/patches/02-fix_get_shared_lib_path--see_29644.patch b/srcpkgs/sagelib/patches/02-fix_get_shared_lib_path--see_29644.patch
new file mode 100644
index 000000000000..d3672b094c1c
--- /dev/null
+++ b/srcpkgs/sagelib/patches/02-fix_get_shared_lib_path--see_29644.patch
@@ -0,0 +1,13 @@
+ - fix _get_shared_lib_path() so we don't need to configure GAP_SO
+
+--- a/src/sage/env.py
++++ b/src/sage/env.py
+@@ -293,7 +293,7 @@ def _get_shared_lib_path(*libnames: str) -> Optional[str]:
+             if sys.platform == 'darwin':
+                 ext = 'dylib'
+             else:
+-                ext = 'so'
++                ext = 'so*'
+ 
+             if SAGE_LOCAL:
+                 search_directories.append(Path(SAGE_LOCAL) / 'lib')
diff --git a/srcpkgs/sagelib/patches/03-doctest_have_program.patch b/srcpkgs/sagelib/patches/03-doctest_have_program.patch
new file mode 100644
index 000000000000..27ba3776470c
--- /dev/null
+++ b/srcpkgs/sagelib/patches/03-doctest_have_program.patch
@@ -0,0 +1,20 @@
+ - we don't know `SAGE_VENV/bin` contains `sage`, but `sys.argv[0]` should
+   be the full path to `sage-ipython` and the same directory should have `sage`
+
+--- a/src/sage/misc/sage_ostools.pyx
++++ b/src/sage/misc/sage_ostools.pyx
+@@ -32,12 +32,11 @@ def have_program(program, path=None):
+         True
+         sage: have_program('there_is_not_a_program_with_this_name')
+         False
+-        sage: from sage.env import SAGE_VENV
+-        sage: have_program('sage', os.path.join(SAGE_VENV, 'bin'))
++        sage: have_program('sage', os.path.dirname(sys.argv[0]))
+         True
+         sage: have_program('sage', '/there_is_not_a_path_with_this_name')
+         False
+-        sage: have_program('there_is_not_a_program_with_this_name', os.path.join(SAGE_VENV, 'bin'))
++        sage: have_program('there_is_not_a_program_with_this_name', "/bin")
+         False
+     """
+     if path is None:
diff --git a/srcpkgs/sagelib/patches/04-doctest_sage_getfile.patch b/srcpkgs/sagelib/patches/04-doctest_sage_getfile.patch
new file mode 100644
index 000000000000..95bce107f854
--- /dev/null
+++ b/srcpkgs/sagelib/patches/04-doctest_sage_getfile.patch
@@ -0,0 +1,22 @@
+ - add one doctest for coverage
+
+--- a/src/sage/misc/sageinspect.py
++++ b/src/sage/misc/sageinspect.py
+@@ -1341,10 +1342,12 @@ def sage_getfile(obj):
+     EXAMPLES::
+ 
+         sage: from sage.misc.sageinspect import sage_getfile
+-        sage: sage_getfile(sage.rings.rational)[-23:]
+-        'sage/rings/rational.pyx'
+-        sage: sage_getfile(Sq)[-42:]
+-        'sage/algebras/steenrod/steenrod_algebra.py'
++        sage: sage_getfile(sage.rings.rational)
++        '...sage/rings/rational.pyx'
++        sage: sage_getfile(Sq)
++        '...sage/algebras/steenrod/steenrod_algebra.py'
++        sage: sage_getfile(x)
++        '...sage/symbolic/expression.pyx'
+ 
+     The following tests against some bugs fixed in :trac:`9976`::
+ 
+
diff --git a/srcpkgs/sagelib/patches/05-fix_sage_getfile.patch b/srcpkgs/sagelib/patches/05-fix_sage_getfile.patch
new file mode 100644
index 000000000000..56c58078f319
--- /dev/null
+++ b/srcpkgs/sagelib/patches/05-fix_sage_getfile.patch
@@ -0,0 +1,16 @@
+ - fix sage_getfile() by checking all possible EXTENSION_SUFFIXES
+
+--- a/src/sage/misc/sageinspect.py
++++ b/src/sage/misc/sageinspect.py
+@@ -1400,8 +1403,9 @@ def sage_getfile(obj):
+         sourcefile = inspect.getabsfile(obj)
+     except TypeError: # this happens for Python builtins
+         return ''
+-    if sourcefile.endswith(loadable_module_extension()):
+-        return sourcefile[:-len(loadable_module_extension())]+os.path.extsep+'pyx'
++    for suffix in import_machinery.EXTENSION_SUFFIXES:
++        if sourcefile.endswith(suffix):
++            return sourcefile[:-len(suffix)]+os.path.extsep+'pyx'
+     return sourcefile
+ 
+ 
diff --git a/srcpkgs/sagelib/patches/06-skip_doctest_giac-1.7.0--see_31563.patch b/srcpkgs/sagelib/patches/06-skip_doctest_giac-1.7.0--see_31563.patch
new file mode 100644
index 000000000000..619e62f928dd
--- /dev/null
+++ b/srcpkgs/sagelib/patches/06-skip_doctest_giac-1.7.0--see_31563.patch
@@ -0,0 +1,16 @@
+ - these are broken in giac 1.7.0, skip
+
+--- a/src/sage/functions/min_max.py
++++ b/src/sage/functions/min_max.py
+@@ -233,9 +233,9 @@ class MaxSymbolic(MinMax_base):
+             sage: f = max_symbolic(sin(x), cos(x))
+             sage: r = integral(f, x, 0, 1)
+             ...
+-            sage: r
++            sage: r             # not tested -- broken with giac 1.7.0
+             sqrt(2) - cos(1)
+-            sage: r.n()
++            sage: r.n()         # not tested -- broken with giac 1.7.0
+             0.873911256504955
+         """
+         return max_symbolic(args)
diff --git a/srcpkgs/sagelib/patches/07-ignore_warning.patch b/srcpkgs/sagelib/patches/07-ignore_warning.patch
new file mode 100644
index 000000000000..69668678a40b
--- /dev/null
+++ b/srcpkgs/sagelib/patches/07-ignore_warning.patch
@@ -0,0 +1,15 @@
+ - this ignores a warning caused by old notebook
+
+--- a/src/sage/all.py
++++ b/src/sage/all.py
+@@ -100,6 +100,9 @@ warnings.filterwarnings('ignore', category=DeprecationWarning,
+                         message='The distutils(.sysconfig module| package) is deprecated',
+                         module='Cython|distutils|numpy|sage.env|sage.features')
+ 
++warnings.filterwarnings('ignore', category=DeprecationWarning,
++                        message=r"invalid escape sequence '\\s'")
++
+ ################ end setup warnings ###############################
+ 
+ 
+
diff --git a/srcpkgs/sagelib/patches/08-dont_run_pytest--see_31924.patch b/srcpkgs/sagelib/patches/08-dont_run_pytest--see_31924.patch
new file mode 100644
index 000000000000..06bd2ccae6fb
--- /dev/null
+++ b/srcpkgs/sagelib/patches/08-dont_run_pytest--see_31924.patch
@@ -0,0 +1,27 @@
+ - using pytest is broken, see #31924
+
+--- a/src/bin/sage-runtests
++++ b/src/bin/sage-runtests
+@@ -154,21 +154,4 @@ if __name__ == "__main__":
+     DC = DocTestController(args, args.filenames)
+     err = DC.run()
+ 
+-    try:
+-        exit_code_pytest = 0
+-        import pytest
+-        pytest_options = ["--import-mode", "importlib"]
+-        if args.verbose:
+-            pytest_options.append("-v")
+-        exit_code_pytest = pytest.main(pytest_options + args.filenames)
+-        if exit_code_pytest == 5:
+-            # Exit code 5 means there were no test files, pass in this case
+-            exit_code_pytest = 0
+-
+-    except ModuleNotFoundError:
+-        print("Pytest is not installed, skip checking tests that rely on it.")
+-
+-    if err == 0:
+-        sys.exit(exit_code_pytest)
+-    else:
+-        sys.exit(err)
++    sys.exit(err)
diff --git a/srcpkgs/sagelib/patches/trac-33189-fix_doctests_for_arb_2.22-53532ddd4e2dc92469c1590ebf0c40f8f69bf579.patch b/srcpkgs/sagelib/patches/trac-33189-fix_doctests_for_arb_2.22-53532ddd4e2dc92469c1590ebf0c40f8f69bf579.patch
new file mode 100644
index 000000000000..b861af7ec982
--- /dev/null
+++ b/srcpkgs/sagelib/patches/trac-33189-fix_doctests_for_arb_2.22-53532ddd4e2dc92469c1590ebf0c40f8f69bf579.patch
@@ -0,0 +1,126 @@
+From 24cc94b1988a90f3bd22a2368ec30c086283af13 Mon Sep 17 00:00:00 2001
+From: Antonio Rojas <arojas@archlinux.org>
+Date: Sun, 16 Jan 2022 11:55:04 +0100
+Subject: Add abs tol to some arb tests
+
+---
+ src/sage/functions/error.py    |  2 +-
+ src/sage/rings/complex_arb.pyx |  6 +++---
+ src/sage/rings/real_arb.pyx    | 10 +++++-----
+ 3 files changed, 9 insertions(+), 9 deletions(-)
+
+diff --git a/src/sage/functions/error.py b/src/sage/functions/error.py
+index f48d04f..06f0b24 100644
+--- a/src/sage/functions/error.py
++++ b/src/sage/functions/error.py
+@@ -267,7 +267,7 @@ class Function_erf(BuiltinFunction):
+ 
+         Check that real ball evaluation is fixed :trac:`28061`::
+ 
+-            sage: RealBallField(128)(erf(5))
++            sage: RealBallField(128)(erf(5)) # abs tol 1e-38
+             [0.99999999999846254020557196514981165651 +/- 7.33e-39]
+         """
+         R = parent or s_parent(x)
+diff --git a/src/sage/rings/complex_arb.pyx b/src/sage/rings/complex_arb.pyx
+index f986970..93ff565 100644
+--- a/src/sage/rings/complex_arb.pyx
++++ b/src/sage/rings/complex_arb.pyx
+@@ -3974,8 +3974,8 @@ cdef class ComplexBall(RingElement):
+ 
+         EXAMPLES::
+ 
+-            sage: CBF(20).erfc()
+-            [5.39586561160790e-176 +/- ...e-191]
++            sage: CBF(20).erfc() # abs tol 1e-190
++            [5.39586561160790e-176 +/- 6.73e-191]
+             sage: CBF(100, 100).erfc()
+             [0.00065234366376858 +/- ...e-18] + [-0.00393572636292141 +/- ...e-18]*I
+         """
+@@ -4280,7 +4280,7 @@ cdef class ComplexBall(RingElement):
+ 
+         TESTS:
+ 
+-            sage: CBF(Shi(I))
++            sage: CBF(Shi(I)) # abs tol 1e-15
+             [0.946083070367183 +/- 9.22e-16]*I
+         """
+         cdef ComplexBall result = self._new()
+diff --git a/src/sage/rings/real_arb.pyx b/src/sage/rings/real_arb.pyx
+index 4a81784..292bfea 100644
+--- a/src/sage/rings/real_arb.pyx
++++ b/src/sage/rings/real_arb.pyx
+@@ -3506,7 +3506,7 @@ cdef class RealBall(RingElement):
+ 
+         EXAMPLES::
+ 
+-            sage: RBF(1/2).erf()
++            sage: RBF(1/2).erf() # abs tol 1e-16
+             [0.520499877813047 +/- 6.10e-16]
+         """
+         cdef RealBall res = self._new()
+@@ -3556,12 +3556,12 @@ cdef class RealBall(RingElement):
+ 
+         EXAMPLES::
+ 
+-            sage: RBF(1).Si()
++            sage: RBF(1).Si() # abs tol 1e-15
+             [0.946083070367183 +/- 9.22e-16]
+ 
+         TESTS::
+ 
+-            sage: RBF(Si(1))
++            sage: RBF(Si(1)) # abs tol 1e-15
+             [0.946083070367183 +/- 9.22e-16]
+         """
+         cdef RealBall res = self._new()
+@@ -3578,12 +3578,12 @@ cdef class RealBall(RingElement):
+ 
+         EXAMPLES::
+ 
+-            sage: RBF(1).Ci()  # abs tol 1e-16
++            sage: RBF(1).Ci()  # abs tol 1e-15
+             [0.337403922900968 +/- 3.25e-16]
+ 
+         TESTS::
+ 
+-            sage: RBF(Ci(1))  # abs tol 1e-16
++            sage: RBF(Ci(1))  # abs tol 1e-15
+             [0.337403922900968 +/- 3.25e-16]
+         """
+         cdef RealBall res = self._new()
+-- 
+cgit v1.0-1-gd88e
+
+
+From 53532ddd4e2dc92469c1590ebf0c40f8f69bf579 Mon Sep 17 00:00:00 2001
+From: Antonio Rojas <arojas@archlinux.org>
+Date: Sun, 16 Jan 2022 14:16:53 +0100
+Subject: Decrease abs tol
+
+---
+ src/sage/rings/real_arb.pyx | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/src/sage/rings/real_arb.pyx b/src/sage/rings/real_arb.pyx
+index 292bfea..eb30f7f 100644
+--- a/src/sage/rings/real_arb.pyx
++++ b/src/sage/rings/real_arb.pyx
+@@ -3578,12 +3578,12 @@ cdef class RealBall(RingElement):
+ 
+         EXAMPLES::
+ 
+-            sage: RBF(1).Ci()  # abs tol 1e-15
++            sage: RBF(1).Ci()  # abs tol 5e-16
+             [0.337403922900968 +/- 3.25e-16]
+ 
+         TESTS::
+ 
+-            sage: RBF(Ci(1))  # abs tol 1e-15
++            sage: RBF(Ci(1))  # abs tol 5e-16
+             [0.337403922900968 +/- 3.25e-16]
+         """
+         cdef RealBall res = self._new()
+-- 
+cgit v1.0-1-gd88e
+
diff --git a/srcpkgs/sagelib/patches/zzz-skip_doctest_no_threejs.patch b/srcpkgs/sagelib/patches/zzz-skip_doctest_no_threejs.patch
new file mode 100644
index 000000000000..5cb62f56e902
--- /dev/null
+++ b/srcpkgs/sagelib/patches/zzz-skip_doctest_no_threejs.patch
@@ -0,0 +1,13 @@
+ - we don't have threejs in void
+
+--- a/src/sage/repl/ipython_kernel/install.py
++++ b/src/sage/repl/ipython_kernel/install.py
+@@ -124,7 +124,7 @@ class SageKernelSpec(object):
+             sage: spec = SageKernelSpec(prefix=tmp_dir())
+             sage: spec.use_local_threejs()
+             sage: threejs = os.path.join(spec.nbextensions_dir, 'threejs-sage')
+-            sage: os.path.isdir(threejs)
++            sage: os.path.isdir(threejs)    # optional - threejs
+             True
+         """
+         src = THREEJS_DIR
diff --git a/srcpkgs/sagelib/template b/srcpkgs/sagelib/template
new file mode 100644
index 000000000000..90bdbf56960f
--- /dev/null
+++ b/srcpkgs/sagelib/template
@@ -0,0 +1,131 @@
+# Template file for 'sagelib'
+pkgname=sagelib
+version=9.5
+revision=1
+wrksrc=sage-$version
+build_wrksrc=pkgs/sagemath-standard
+build_style=python3-module
+_bindir=/usr/lib/sagemath/bin
+make_install_args="--install-scripts=$_bindir"
+hostmakedepends="m4 pkg-config python3-Cython python3-Jinja2 python3-pkgconfig
+ python3-setuptools"
+makedepends="arb-devel boost-devel brial-devel cliquer-devel ecl eclib-devel
+ ecm-devel fflas-ffpack flintlib-devel gap-devel gd-devel giac-devel glpk-devel
+ gsl-devel iml-devel lcalc-devel libbraiding-devel libhomfly-devel libmpc-devel
+ libpng-devel linbox-devel lrcalc-devel m4ri-devel m4rie-devel mpfi-devel
+ mpfr-devel ntl-devel openblas-devel pari-devel planarity-devel python3-cypari2
+ python3-cysignals python3-devel python3-gmpy2 python3-memory_allocator
+ python3-numpy rankwidth-devel singular symmetrica-devel zn_poly"
+depends="FlintQS eclib-devel fflas-ffpack flintlib-devel gcc-fortran gd-devel
+ gfan giac gsl-devel gzip libpng-devel linbox-devel m4ri-devel maxima-ecl
+ mpfr-devel nauty ntl-devel palp pari-devel pari-elldata-small pari-galdata
+ pari-galpol-small pari-seadata-small pkg-config python3-Cython python3-cypari2
+ python3-cysignals python3-devel python3-fpylll python3-ipython
+ python3-ipython_ipykernel python3-jupyter_ipywidgets python3-matplotlib
+ python3-memory_allocator python3-networkx python3-pip python3-pkgconfig
+ python3-pplpy python3-primecountpy python3-requests python3-scipy
+ python3-sympy python3-traitlets sage-data-combinatorial_designs
+ sage-data-conway_polynomials sage-data-elliptic_curves sage-data-graphs
+ sage-data-polytopes_db sympow tachyon"
+checkdepends="$depends"
+short_desc="Open source mathematics software"
+maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
+license="GPL-2.0-or-later"
+homepage="http://sagemath.org/"
+distfiles="https://github.com/sagemath/sage/archive/refs/tags/$version.tar.gz"
+checksum=8d70a3b26080802c5b2e33dda4c23795d494d8216a0c2ecfcd608ebab0e64ff6
+
+post_patch() {
+	# these are unused and nothing else uses ratpoints
+	rm sage/libs/ratpoints.{pyx,pxd}
+
+	pushd $wrksrc/build/pkgs/sagelib
+	PATH=../../bin:$PATH BOOTSTRAP_QUIET=no ./bootstrap
+	popd
+}
+
+do_configure() {
+	# set variables in sage.env since we do not install sage_conf
+	cat >> sage/env.py <<-EOF
+	CONWAY_POLYNOMIALS_DATA_DIR = "/usr/share/sagemath/conway_polynomials"
+	GRAPHS_DATA_DIR = "/usr/share/sagemath/graphs"
+	ELLCURVE_DATA_DIR = "/usr/share/sagemath/ellcurves"
+	POLYTOPE_DATA_DIR = "/usr/share/sagemath/reflexive_polytopes"
+	COMBINATORIAL_DESIGN_DATA_DIR = "/usr/share/sagemath/combinatorial_designs"
+	CREMONA_MINI_DATA_DIR = "/usr/share/sagemath/cremona"
+	CREMONA_LARGE_DATA_DIR = "/usr/share/sagemath/cremona"
+	EOF
+}
+
+pre_build() {
+	export PYTHONPATH=../sage-setup
+	export PYTHONDONTWRITEBYTECODE=yes
+	export SAGE_NUM_THREADS="$XBPS_MAKEJOBS"
+}
+
+post_build() {
+	_scripts=$(cd build/scripts* && pwd)
+	cat >> $_scripts/sage-env-config <<-'EOF'
+	# sage-venv-config sets SAGE_VENV=/usr (sys.prefix)
+	# then sage-env prepends "$SAGE_VENV/bin" to PATH
+	# we don't want that to happen so we unset SAGE_VENV here
+	unset SAGE_VENV
+	PATH=$(dirname $SELF):$PATH
+	EOF
+}
+
+pre_install() {
+	export PYTHONPATH=../sage-setup
+	export PYTHONDONTWRITEBYTECODE=yes
+	export SAGE_NUM_THREADS="$XBPS_MAKEJOBS"
+}
+
+post_install() {
+	# fix jupyter kernel spec
+	vsed -i -e 's|"/usr/bin/sage", "--python"|"/usr/bin/python"|' \
+		${DESTDIR}/usr/share/jupyter/kernels/sagemath/kernel.json
+	# replace broken symlinks by good copies (sagemath logo images)
+	for file in $(ls sage/ext_data/notebook-ipython); do
+		rm ${DESTDIR}/usr/share/jupyter/kernels/sagemath/$file
+		cp -a sage/ext_data/notebook-ipython/$file \
+			${DESTDIR}/usr/share/jupyter/kernels/sagemath
+	done
+	# we don't have docs here
+	rm ${DESTDIR}/usr/share/jupyter/kernels/sagemath/doc
+	# we don't have threejs in void
+	rm ${DESTDIR}/usr/share/jupyter/nbextensions/threejs-sage
+
+	# symlink main binary
+	vmkdir usr/bin
+	ln -s $_bindir/sage ${DESTDIR}/usr/bin/sagelib-${version}
+	ln -s sagelib-${version} ${DESTDIR}/usr/bin/sagelib
+}
+
+do_check() {
+	_scripts=$(cd build/scripts* && pwd)
+	export PYTHONPATH=$(cd build/lib* && pwd)
+	export PYTHONDONTWRITEBYTECODE=yes
+
+	# get out of $build_wrksrc, otherwise python picks the wrong sage module
+	cd $(mktemp -dp build)
+
+	if [ -f ${XBPS_DISTDIR}/sagemath-check ] ; then
+		_sed='s|#.*||;/^\s*$/d;s|[^ ]*/sage/|'$PYTHONPATH'/sage/|g' \
+		_test_files=$(sed -e "$_sed" ${XBPS_DISTDIR}/sagemath-check)
+	fi
+	if [ -z "$_test_files" ]; then
+		_test_files=--all
+	fi
+	cp ${FILESDIR}/timings2.json .
+	_test_args="--stats_path=timings2.json"
+	if [ "$XBPS_CHECK_PKGS" = full ]; then
+		_test_args+=" --long --warn-long 60.0"
+	else
+		_test_args+=" --warn-long 30.0"
+	fi
+	if [ "$XBPS_BUILD_ENVIRONMENT" = "void-packages-ci" ]; then
+		# for CI use a predictable random seed
+		_test_args+=" --random-seed=0"
+	fi
+	$_scripts/sage -tp ${XBPS_MAKEJOBS} ${_test_args} ${_test_files}
+}

^ permalink raw reply	[flat|nested] 19+ messages in thread
end of thread, other threads:[~2022-02-02 21:06 UTC | newest]

Thread overview: 19+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2022-02-01  4:05 [PR PATCH] [RFC] New package: sagelib-9.5 tornaria
2022-02-01  9:21 ` dkwo
2022-02-01 10:10 ` dkwo
2022-02-01 10:12 ` dkwo
2022-02-01 10:13 ` dkwo
2022-02-01 12:17 ` tornaria
2022-02-01 12:58 ` tornaria
2022-02-01 13:32 ` dkwo
2022-02-01 13:32 ` dkwo
2022-02-01 13:32 ` tornaria
2022-02-01 13:32 ` dkwo
2022-02-01 13:39 ` dkwo
2022-02-01 13:55 ` dkwo
2022-02-01 15:14 ` leahneukirchen
2022-02-01 15:25 ` [PR PATCH] [Updated] " tornaria
2022-02-01 15:51 ` tornaria
2022-02-01 21:40 ` leahneukirchen
2022-02-02 21:06 ` tornaria
2022-02-02 21:06 ` [PR PATCH] [Closed]: " tornaria

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