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Merge pull request #130396 from collares/sage-9.4

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sage: 9.3 -> 9.4
This commit is contained in:
Sandro 2021-08-22 21:26:12 +02:00 committed by GitHub
commit 00f31216e0
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GPG Key ID: 4AEE18F83AFDEB23
8 changed files with 56 additions and 93 deletions
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4
pkgs/applications/science/math/maxima/default.nix
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@ -4,7 +4,7 @@
let
name = "maxima";
version = "5.44.0";
version = "5.45.0";
lisp-compiler = if ecl-fasl then ecl else sbcl;
@ -18,7 +18,7 @@ stdenv.mkDerivation ({
src = fetchurl {
url = "mirror://sourceforge/${name}/${name}-${version}.tar.gz";
sha256 = "1v6jr5s6hhj6r18gfk6hgxk2qd6z1dxkrjq9ss2z1y6sqi45wgyr";
sha256 = "sha256-x2MfMmRIBc67e6/vOrUzHEus0sJ+OE/YgyO1A5pg0Ng=";
};
nativeBuildInputs = [

11
pkgs/applications/science/math/pynac/default.nix
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@ -1,4 +1,5 @@
{ lib, stdenv
, fetchpatch
, fetchFromGitHub
, autoreconfHook
, pkg-config
@ -20,6 +21,16 @@ stdenv.mkDerivation rec {
sha256 = "sha256-ocR7emXtKs+Xe2f6dh4xEDAacgiolY8mtlLnWnNBS8A=";
};
patches = [
# the patch below is included in sage 9.4 and should be included
# in a future pynac release. see https://trac.sagemath.org/ticket/28357
(fetchpatch {
name = "realpartloop.patch";
url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/realpartloop.patch?h=9.4.beta5";
sha256 = "sha256-1nj0xtlFN5fZKEiRLD+tiW/ZtxMQre1ziEGA0OVUGE4=";
})
];
buildInputs = [
flint
gmp

18
pkgs/applications/science/math/sage/patches/do-not-test-find-library.patch
View File

@ -1,8 +1,8 @@
diff --git a/src/sage/env.py b/src/sage/env.py
index 2908f5d04f..81dfd75c0d 100644
index 95980cc2df..37107a30e1 100644
--- a/src/sage/env.py
+++ b/src/sage/env.py
@@ -218,93 +218,12 @@ NTL_LIBDIR = var("NTL_LIBDIR")
@@ -227,93 +227,12 @@ OPENMP_CXXFLAGS = var("OPENMP_CXXFLAGS", "")
SAGE_BANNER = var("SAGE_BANNER", "")
SAGE_IMPORTALL = var("SAGE_IMPORTALL", "yes")
@ -51,10 +51,9 @@ index 2908f5d04f..81dfd75c0d 100644
- if sys.platform == 'cygwin':
- # Later down we take the first matching DLL found, so search
- # SAGE_LOCAL first so that it takes precedence
- search_directories = [
- Path(SAGE_LOCAL) / 'bin',
- Path(sysconfig.get_config_var('BINDIR')),
- ]
- if SAGE_LOCAL:
- search_directories.append(Path(SAGE_LOCAL) / 'bin')
- search_directories.append(Path(sysconfig.get_config_var('BINDIR')))
- # Note: The following is not very robust, since if there are multible
- # versions for the same library this just selects one more or less
- # at arbitrary. However, practically speaking, on Cygwin, there
@ -66,14 +65,15 @@ index 2908f5d04f..81dfd75c0d 100644
- else:
- ext = 'so'
-
- search_directories = [Path(SAGE_LOCAL) / 'lib']
- if SAGE_LOCAL:
- search_directories.append(Path(SAGE_LOCAL) / 'lib')
- libdir = sysconfig.get_config_var('LIBDIR')
- if libdir is not None:
- libdir = Path(libdir)
- search_directories.append(libdir)
-
- multiarchlib = sysconfig.get_config_var('MULTIARCH')
- if multiarchlib is not None:
- if multiarchlib is not None:
- search_directories.append(libdir / multiarchlib),
-
- patterns = [f'lib{libname}.{ext}']
@ -97,4 +97,4 @@ index 2908f5d04f..81dfd75c0d 100644
+GAP_SO = var("GAP_SO", '/default')
# post process
if ' ' in DOT_SAGE:
if DOT_SAGE is not None and ' ' in DOT_SAGE:

24
pkgs/applications/science/math/sage/patches/ignore-cmp-deprecation.patch
View File

@ -1,24 +0,0 @@
diff --git a/src/sage/tests/cmdline.py b/src/sage/tests/cmdline.py
index 6e034dcb5a..8ec60ec72b 100644
--- a/src/sage/tests/cmdline.py
+++ b/src/sage/tests/cmdline.py
@@ -660,8 +660,8 @@ def test_executable(args, input="", timeout=100.0, pydebug_ignore_warnings=False
sage: with open(input, 'w') as F:
....: _ = F.write(s)
sage: L = ["sage", "--rst2ipynb", input, output]
- sage: test_executable(L) # optional - rst2ipynb
- ('', '', 0)
+ sage: test_executable(L)[2] # optional - rst2ipynb
+ 0
sage: import json # optional - rst2ipynb
sage: d = json.load(open(output,'r')) # optional - rst2ipynb
sage: type(d) # optional - rst2ipynb
@@ -757,8 +757,6 @@ def test_executable(args, input="", timeout=100.0, pydebug_ignore_warnings=False
///
4
}}}
- sage: err # py2 # optional -- sagenb
- ''
sage: ret # py2 # optional -- sagenb
0

61
pkgs/applications/science/math/sage/sage-src.nix
View File

@ -29,14 +29,14 @@ let
);
in
stdenv.mkDerivation rec {
version = "9.3";
version = "9.4";
pname = "sage-src";
src = fetchFromGitHub {
owner = "sagemath";
repo = "sage";
rev = version;
sha256 = "sha256-l9DX8jcDdKA7GJ6xU+nBsmlZxrcZ9ZUAJju621ooBEo=";
sha256 = "sha256-jqkr4meG02KbTCMsGvyr1UbosS4ZuUJhPXU/InuS+9A=";
};
# Patches needed because of particularities of nix or the way this is packaged.
@ -77,64 +77,9 @@ stdenv.mkDerivation rec {
# be empty since dependencies update all the time.
packageUpgradePatches = [
# After updating smypow to (https://trac.sagemath.org/ticket/3360) we can
# now set the cache dir to be withing the .sage directory. This is not
# now set the cache dir to be within the .sage directory. This is not
# strictly necessary, but keeps us from littering in the user's HOME.
./patches/sympow-cache.patch
# ignore a deprecation warning for usage of `cmp` in the attrs library in the doctests
./patches/ignore-cmp-deprecation.patch
# remove use of matplotlib function deprecated in 3.4
# https://trac.sagemath.org/ticket/31827
(fetchSageDiff {
base = "9.3";
name = "remove-matplotlib-deprecated-function.patch";
rev = "32b2bcaefddc4fa3d2aee6fa690ce1466cbb5948";
sha256 = "sha256-SXcUGBMOoE9HpuBzgKC3P6cUmM5MiktXbe/7dVdrfWo=";
})
# pari 2.13 update
# https://trac.sagemath.org/ticket/30801
#
# the last commit in that ticket is
# c78b1470fccd915e2fa93f95f2fefba6220fb1f7, but commits after
# 10a4531721d2700fd717e2b3a1364508ffd971c3 only deal with 32-bit
# and post-26635 breakage, none of which is relevant to us. since
# there are post-9.4.beta0 rebases after that, we just skip later
# commits.
(fetchSageDiff {
base = "9.3";
name = "pari-2.13.1.patch";
rev = "10a4531721d2700fd717e2b3a1364508ffd971c3";
sha256 = "sha256-gffWKK9CMREaNOb5zb63iZUgON4FvsPrMQNqe+5ZU9E=";
})
# sympy 1.8 update
# https://trac.sagemath.org/ticket/31647
(fetchSageDiff {
base = "9.4.beta0";
name = "sympy-1.8.patch";
rev = "fa864b36e15696450c36d54215b1e68183b29d25";
sha256 = "sha256-fj/9QEZlVF0fw9NpWflkTuBSKpGjCE6b96ECBgdn77o=";
})
# sphinx 4 update
# https://trac.sagemath.org/ticket/31696
(fetchSageDiff {
base = "9.4.beta3";
name = "sphinx-4.patch";
rev = "bc84af8c795b7da433d2000afc3626ee65ba28b8";
sha256 = "sha256-5Kvs9jarC8xRIU1rdmvIWxQLC25ehiTLJpg5skh8WNM=";
})
# eclib 20210625 update
# https://trac.sagemath.org/ticket/31443
(fetchSageDiff {
base = "9.4.beta3";
name = "eclib-20210625.patch";
rev = "789550ca04c94acfb1e803251538996a34962038";
sha256 = "sha256-VlyEn5hg3joG8t/GwiRfq9TzJ54AoHxLolsNQ3shc2c=";
})
];
patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches;

2
pkgs/applications/science/math/sage/sagelib.nix
View File

@ -27,6 +27,7 @@
, linbox
, m4ri
, m4rie
, memory-allocator
, libmpc
, mpfi
, ntl
@ -107,6 +108,7 @@ buildPythonPackage rec {
lrcalc
m4ri
m4rie
memory-allocator
mpfi
ntl
blas

27
pkgs/development/python-modules/memory-allocator/default.nix Normal file
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@ -0,0 +1,27 @@
{ lib
, fetchPypi
, buildPythonPackage
, cython
}:
buildPythonPackage rec {
pname = "memory-allocator";
version = "0.1.0";
src = fetchPypi {
inherit version;
pname = "memory_allocator";
sha256 = "sha256-UUcR71e3eAQIQpmWM+AVQxVtgHvrNjaIlHo5pURUln0=";
};
propagatedBuildInputs = [ cython ];
pythonImportsCheck = [ "memory_allocator" ];
meta = with lib; {
description = "An extension class to allocate memory easily with cython";
homepage = "https://github.com/sagemath/memory_allocator/";
maintainers = teams.sage.members;
license = licenses.lgpl3Plus;
};
}

2
pkgs/top-level/python-packages.nix
View File

@ -4471,6 +4471,8 @@ in {
memcached = callPackage ../development/python-modules/memcached { };
memory-allocator = callPackage ../development/python-modules/memory-allocator { };
memory_profiler = callPackage ../development/python-modules/memory_profiler { };
mercantile = callPackage ../development/python-modules/mercantile { };