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Merge pull request #114881 from collares/sage-dependencies

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sage dependency updates
This commit is contained in:
Guillaume Girol 2021-03-11 17:52:16 +00:00 committed by GitHub
parent 902a479225 3a093544b2
commit a72148f3bc
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GPG key ID: 4AEE18F83AFDEB23
12 changed files with 165 additions and 174 deletions
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43
pkgs/applications/science/math/giac/default.nix
View file

@ -2,32 +2,44 @@
, gmp, mpfr, pari, ntl, gsl, mpfi, ecm, glpk, nauty
, readline, gettext, libpng, libao, gfortran, perl
, enableGUI ? false, libGL, libGLU, xorg, fltk
, enableMicroPy ? false, python3
}:
assert (!blas.isILP64) && (!lapack.isILP64);
stdenv.mkDerivation rec {
pname = "giac${lib.optionalString enableGUI "-with-xcas"}";
version = "1.5.0-87"; # TODO try to remove preCheck phase on upgrade
version = "1.6.0-47"; # TODO try to remove preCheck phase on upgrade
src = fetchurl {
url = "https://www-fourier.ujf-grenoble.fr/~parisse/debian/dists/stable/main/source/giac_${version}.tar.gz";
sha256 = "1d0h1yb7qvh9x7wwv9yrzmcp712f49w1iljkxp4y6g9pzsmg1mmv";
sha256 = "sha256-c5A9/I6L/o3Y3dxEPoTKpw/fJqYMr6euLldaQ1HWT5c=";
};
patches = lib.optionals (!enableGUI) [
# when enableGui is false, giac is compiled without fltk. That means some
# outputs differ in the make check. Patch around this:
patches = [
(fetchpatch {
url = "https://git.sagemath.org/sage.git/plain/build/pkgs/giac/patches/nofltk-check.patch?id=7553a3c8dfa7bcec07241a07e6a4e7dcf5bb4f26";
name = "pari_2_11.patch";
url = "https://git.sagemath.org/sage.git/plain/build/pkgs/giac/patches/pari_2_11.patch?id=21ba7540d385a9864b44850d6987893dfa16bfc0";
sha256 = "sha256-vEo/5MNzMdYRPWgLFPsDcMT1W80Qzj4EPBjx/B8j68k=";
})
] ++ lib.optionals (!enableGUI) [
# when enableGui is false, giac is compiled without fltk. That
# means some outputs differ in the make check. Patch around this:
(fetchpatch {
name = "nofltk-check.patch";
url = "https://git.sagemath.org/sage.git/plain/build/pkgs/giac/patches/nofltk-check.patch?id=7553a3c8dfa7bcec07241a07e6a4e7dcf5bb4f26";
sha256 = "0xkmfc028vg5w6va04gp2x2iv31n8v4shd6vbyvk4blzgfmpj2cw";
})
];
postPatch = ''
for i in doc/*/Makefile*; do
for i in doc/*/Makefile* micropython*/xcas/Makefile*; do
substituteInPlace "$i" --replace "/bin/cp" "cp";
done;
'' +
# workaround for 1.6.0-47, should not be necessary in future versions
lib.optionalString (!enableMicroPy) ''
sed -i -e 's/micropython-[0-9.]* //' Makefile*
'';
nativeBuildInputs = [
@ -44,7 +56,7 @@ stdenv.mkDerivation rec {
lapack blas
] ++ lib.optionals enableGUI [
libGL libGLU fltk xorg.libX11
];
] ++ lib.optional enableMicroPy python3;
/* fixes:
configure:16211: checking for main in -lntl
@ -58,13 +70,12 @@ stdenv.mkDerivation rec {
outputs = [ "out" ] ++ lib.optional (!enableGUI) "doc";
doCheck = true;
preCheck = ''
# One test in this file fails. That test just tests a part of the pari
# interface that isn't actually used in giac. Of course it would be better
# to only remove that one test, but that would require a patch.
# Removing the whole test set should be good enough for now.
# Upstream report: https://xcas.univ-grenoble-alpes.fr/forum/viewtopic.php?f=4&t=2102#p10326
echo > check/chk_fhan11
preCheck = lib.optionalString (!enableGUI) ''
# even with the nofltk patch, some changes in src/misc.cc (grep
# for HAVE_LIBFLTK) made it so that giac behaves differently
# when fltk is disabled. disable these tests for now.
echo > check/chk_fhan2
echo > check/chk_fhan9
'';
enableParallelBuilding = true;
@ -75,7 +86,7 @@ stdenv.mkDerivation rec {
"--enable-ao" "--enable-ecm" "--enable-glpk"
] ++ lib.optionals enableGUI [
"--enable-gui" "--with-x"
];
] ++ lib.optional (!enableMicroPy) "--disable-micropy";
postInstall = ''
# example Makefiles contain the full path to some commands

6
pkgs/applications/science/math/palp/default.nix
View file

@ -10,11 +10,11 @@ let
in
stdenv.mkDerivation rec {
pname = "palp";
version = "2.11";
version = "2.20";
src = fetchurl {
url = "http://hep.itp.tuwien.ac.at/~kreuzer/CY/palp/palp-${version}.tar.gz";
sha256 = "00jpm73fw9jjq58z6rysr1mwv489j6rpfqqlhm9ab0dln4kyhh05";
url = "http://hep.itp.tuwien.ac.at/~kreuzer/CY/palp/${pname}-${version}.tar.gz";
sha256 = "1q1cl3vpdir16szy0jcadysydcrjp48hqxyx42kr8g9digkqjgkj";
};
hardeningDisable = [

29
pkgs/applications/science/math/sage/patches/disable-pexpect-intermittent-failure.patch
View file

@ -1,29 +0,0 @@
diff --git a/src/sage/interfaces/singular.py b/src/sage/interfaces/singular.py
index 88a33b0349..b3321f0bec 100644
--- a/src/sage/interfaces/singular.py
+++ b/src/sage/interfaces/singular.py
@@ -495,24 +495,6 @@ class Singular(ExtraTabCompletion, Expect):
"""
Send an interrupt to Singular. If needed, additional
semi-colons are sent until we get back at the prompt.
-
- TESTS:
-
- The following works without restarting Singular::
-
- sage: a = singular(1)
- sage: _ = singular._expect.sendline('1+') # unfinished input
- sage: try:
- ....: alarm(0.5)
- ....: singular._expect_expr('>') # interrupt this
- ....: except KeyboardInterrupt:
- ....: pass
- Control-C pressed. Interrupting Singular. Please wait a few seconds...
-
- We can still access a::
-
- sage: 2*a
- 2
"""
# Work around for Singular bug
# http://www.singular.uni-kl.de:8002/trac/ticket/727

39
pkgs/applications/science/math/sage/patches/pillow-update.patch
View file

@ -1,39 +0,0 @@
diff --git a/src/sage/repl/image.py b/src/sage/repl/image.py
index d7d00b0..cd1607a 100644
--- a/src/sage/repl/image.py
+++ b/src/sage/repl/image.py
@@ -77,7 +77,7 @@ class Image(SageObject):
- ``size`` -- 2-tuple, containing (width, height) in pixels.
- - ``color`` -- string or tuple of numeric. What colour to use
+ - ``color`` -- string, numeric or tuple of numeric. What colour to use
for the image. Default is black. If given, this should be a
a tuple with one value per band. When creating RGB images,
you can also use colour strings as supported by the
@@ -91,9 +91,15 @@ class Image(SageObject):
EXAMPLES::
sage: from sage.repl.image import Image
- sage: Image('P', (16, 16), (13,))
+ sage: Image('P', (16, 16), 13)
16x16px 8-bit Color image
"""
+ # pillow does not support Sage integers as color
+ from sage.rings.integer import Integer
+ if isinstance(color, Integer):
+ color = int(color)
+ elif isinstance(color, tuple):
+ color = tuple(int(i) if isinstance(i, Integer) else i for i in color)
self._pil = PIL.Image.new(mode, size, color)
@property
@@ -233,7 +239,7 @@ class Image(SageObject):
EXAMPLES::
sage: from sage.repl.image import Image
- sage: img = Image('P', (12, 34), (13,))
+ sage: img = Image('P', (12, 34), 13)
sage: filename = tmp_filename(ext='.png')
sage: img.save(filename)
sage: with open(filename, 'rb') as f:

36
pkgs/applications/science/math/sage/patches/register-pretty-printer-earlier.patch
View file

@ -1,36 +0,0 @@
diff --git a/src/sage/doctest/forker.py b/src/sage/doctest/forker.py
index cb3667659e..867f547d71 100644
--- a/src/sage/doctest/forker.py
+++ b/src/sage/doctest/forker.py
@@ -200,6 +200,15 @@ def init_sage(controller=None):
from sage.cpython._py2_random import Random
sage.misc.randstate.DEFAULT_PYTHON_RANDOM = Random
+ # IPython's pretty printer sorts the repr of dicts by their keys by default
+ # (or their keys' str() if they are not otherwise orderable). However, it
+ # disables this for CPython 3.6+ opting to instead display dicts' "natural"
+ # insertion order, which is preserved in those versions).
+ # However, this order is random in some instances.
+ # Also modifications of code may affect the order.
+ # So here we fore sorted dict printing.
+ IPython.lib.pretty.for_type(dict, _sorted_dict_pprinter_factory('{', '}'))
+
if controller is None:
import sage.repl.ipython_kernel.all_jupyter
else:
@@ -222,15 +231,6 @@ def init_sage(controller=None):
from sage.repl.rich_output.backend_doctest import BackendDoctest
dm.switch_backend(BackendDoctest())
- # IPython's pretty printer sorts the repr of dicts by their keys by default
- # (or their keys' str() if they are not otherwise orderable). However, it
- # disables this for CPython 3.6+ opting to instead display dicts' "natural"
- # insertion order, which is preserved in those versions).
- # However, this order is random in some instances.
- # Also modifications of code may affect the order.
- # So here we fore sorted dict printing.
- IPython.lib.pretty.for_type(dict, _sorted_dict_pprinter_factory('{', '}'))
-
# Switch on extra debugging
from sage.structure.debug_options import debug
debug.refine_category_hash_check = True

13
pkgs/applications/science/math/sage/patches/sagespawn-implicit-casting.patch
View file

@ -1,13 +0,0 @@
diff --git a/src/sage/interfaces/sagespawn.pyx b/src/sage/interfaces/sagespawn.pyx
index 9041238f1d..469befbc66 100644
--- a/src/sage/interfaces/sagespawn.pyx
+++ b/src/sage/interfaces/sagespawn.pyx
@@ -228,7 +228,7 @@ class SagePtyProcess(PtyProcess):
Check that the process eventually dies after calling
``terminate_async``::
- sage: s.ptyproc.terminate_async(interval=0.2)
+ sage: s.ptyproc.terminate_async(interval=float(0.2))
sage: while True:
....: try:
....: os.kill(s.pid, 0)

102
pkgs/applications/science/math/sage/sage-src.nix
View file

@ -9,6 +9,20 @@
# This is done because multiple derivations rely on these sources and they should
# all get the same sources with the same patches applied.
let
# Fetch a diff between `base` and `rev` on sage's git server.
# Used to fetch trac tickets by setting the `base` to the last release and the
# `rev` to the last commit of the ticket.
fetchSageDiff = { base, name, rev, sha256, ...}@args: (
fetchpatch ({
inherit name sha256;
url = "https://git.sagemath.org/sage.git/patch?id2=${base}&id=${rev}";
# We don't care about sage's own build system (which builds all its dependencies).
# Exclude build system changes to avoid conflicts.
excludes = [ "build/*" ];
} // builtins.removeAttrs args [ "rev" "base" "sha256" ])
);
in
stdenv.mkDerivation rec {
version = "9.2";
pname = "sage-src";
@ -40,17 +54,13 @@ stdenv.mkDerivation rec {
# https://groups.google.com/forum/#!topic/sage-packaging/YGOm8tkADrE
./patches/sphinx-docbuild-subprocesses.patch
# Sage's workaround to pretty print dicts (in
# src/sage/doctest/forker.py:init_sage) runs too late (after
# controller.load_environment(), which imports sage.all.*) to to
# affect sage.sandpiles.Sandpile{Config,Divisor}'s pretty printer.
# Due to the sandpiles module being lazily loaded, this only
# affects the first run (subsequent runs read from an import cache
# at ~/.sage/cache and are not affected), which is probably why
# other distributions don't hit this bug. This breaks two sandpile
# tests, so do the workaround a little bit earlier.
# https://trac.sagemath.org/ticket/31053
./patches/register-pretty-printer-earlier.patch
# Register sorted dict pprinter earlier (https://trac.sagemath.org/ticket/31053)
(fetchSageDiff {
base = "9.3.beta4";
name = "register-pretty-printer-earlier.patch";
rev = "d658230ce06ca19f4a3b3a4576297ee82f2d2151";
sha256 = "sha256-9mPUV7K5PoLDH2vVaYaOfvDLDpmxU0Aj7m/eaXYotDs=";
})
];
# Since sage unfortunately does not release bugfix releases, packagers must
@ -63,17 +73,20 @@ stdenv.mkDerivation rec {
# fix intermittent errors in Sage 9.2's psage.py (this patch is
# already included in Sage 9.3): https://trac.sagemath.org/ticket/30730
(fetchpatch {
(fetchSageDiff {
base = "9.2.rc2";
name = "fix-psage-is-locked.patch";
url = "https://git.sagemath.org/sage.git/patch/?id=75df605f216ddc7b6ca719be942d666b241520e9";
rev = "75df605f216ddc7b6ca719be942d666b241520e9";
sha256 = "0g9pl1wbb3sgs26d3bvv70cpa77sfskylv4kd255y1794f1fgk4q";
})
# fix intermittent errors in sagespawn.pyx: https://trac.sagemath.org/ticket/31052
./patches/sagespawn-implicit-casting.patch
# disable pexpect interrupt test (see https://trac.sagemath.org/ticket/30945)
./patches/disable-pexpect-intermittent-failure.patch
(fetchSageDiff {
base = "9.2";
name = "sagespawn-implicit-casting.patch";
rev = "2959ac792ebd6107fe87c9af1541083de5ba02d6";
sha256 = "sha256-bWIpEGir9Kawak5CJegBMNcHm/CqhWmdru+emeSsvO0=";
})
];
# Patches needed because of package updates. We could just pin the versions of
@ -82,20 +95,7 @@ stdenv.mkDerivation rec {
# compatible with never dependency versions when possible. All these changes
# should come from or be proposed to upstream. This list will probably never
# be empty since dependencies update all the time.
packageUpgradePatches = let
# Fetch a diff between `base` and `rev` on sage's git server.
# Used to fetch trac tickets by setting the `base` to the last release and the
# `rev` to the last commit of the ticket.
fetchSageDiff = { base, rev, name ? "sage-diff-${base}-${rev}.patch", ...}@args: (
fetchpatch ({
inherit name;
url = "https://git.sagemath.org/sage.git/patch?id2=${base}&id=${rev}";
# We don't care about sage's own build system (which builds all its dependencies).
# Exclude build system changes to avoid conflicts.
excludes = [ "build/*" ];
} // builtins.removeAttrs args [ "rev" "base" ])
);
in [
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
# strictly necessary, but keeps us from littering in the user's HOME.
@ -105,7 +105,20 @@ stdenv.mkDerivation rec {
./patches/ignore-cmp-deprecation.patch
# adapt sage's Image class to pillow 8.0.1 (https://trac.sagemath.org/ticket/30971)
./patches/pillow-update.patch
(fetchSageDiff {
base = "9.3.beta2";
name = "pillow-8.0.1-update.patch";
rev = "f05f2d0aac9c4b5abe68105cee2cc7f2c8461847";
sha256 = "sha256-uY2UlgSd5hhOUUukB4Xc3Gjy0/e7p/qyq9jdvz10IOs=";
})
# don't use deprecated numpy type aliases (https://trac.sagemath.org/ticket/31364)
(fetchSageDiff {
base = "9.3.beta7";
name = "dont-use-deprecated-numpy-type-aliases.patch";
rev = "dfdef60515d4a4269e82d91280f76a7fdf10bf97";
sha256 = "sha256-77/3LkT5J7DQN8IPlGJKB6ZcJPaF7xwje06JNns+0AE=";
})
# fix test output with sympy 1.7 (https://trac.sagemath.org/ticket/30985)
./patches/sympy-1.7-update.patch
@ -115,6 +128,31 @@ stdenv.mkDerivation rec {
# updated eclib output has punctuation changes and tidier whitespace
./patches/eclib-20210223-test-formatting.patch
# upgrade arb to 2.18.1 (https://trac.sagemath.org/ticket/28623)
(fetchSageDiff {
base = "9.3.beta3";
name = "arb-2.18.1-update.patch";
rev = "0c9c4ed35c2eaf34ae0d19387c07b7f460e4abce";
sha256 = "sha256-CjOJIsyyVCziAfvE6pWSihPO35IZMcY2/taXAsqhPLY=";
})
# giac 1.6.0-47 update (https://trac.sagemath.org/ticket/30537)
(fetchSageDiff {
base = "9.3.beta7";
name = "giac-1.6.0-47-update.patch";
rev = "f05720bf63dfaf33a4e3b6d3ed2c2c0ec46b5d31";
sha256 = "sha256-gDUq+84eXd5GxLBWUSI61GMJpBF2KX4LBVOt3mS1NF8=";
})
# Make gcd/lcm interact better with pari and gmpy2 (https://trac.sagemath.org/ticket/30849)
# needed for pari 2.13.1 update, which we will do in the future
(fetchSageDiff {
base = "9.3.beta0";
name = "make-gcd-lcm-interact-better-with-pari-and-gmpy2.patch";
rev = "75c1516f0abb9e6f8c335e38e4031f6ef674ed30";
sha256 = "sha256-RukkieIZcXNrju904H2oyGKdtpdE+9vNzvyjN2IBNg0=";
})
];
patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches;

13
pkgs/development/libraries/arb/default.nix
View file

@ -1,14 +1,21 @@
{ lib, stdenv, fetchFromGitHub, mpir, gmp, mpfr, flint }:
{ lib
, stdenv
, fetchFromGitHub
, mpir
, gmp
, mpfr
, flint
}:
stdenv.mkDerivation rec {
pname = "arb";
version = "2.17.0";
version = "2.19.0";
src = fetchFromGitHub {
owner = "fredrik-johansson";
repo = pname;
rev = version;
sha256 = "05lpy3hkl5f8ik19aw40cqydrb932xaf2n8hbq9ib5dnk7f010p1";
sha256 = "sha256-J/LQVZ8gmssazE7ru89EtvW6cVjaLEHgUHuwjW1nuOE=";
};
buildInputs = [ mpir gmp mpfr flint ];

6
pkgs/development/libraries/science/math/rankwidth/default.nix
View file

@ -4,18 +4,18 @@
stdenv.mkDerivation rec {
pname = "rankwidth";
version = "0.7";
version = "0.9";
src = fetchurl {
url = "mirror://sageupstream/rw/rw-${version}.tar.gz";
sha256 = "1rv2v42x2506x7f10349m1wpmmfxrv9l032bkminni2gbip9cjg0";
sha256 = "sha256-weA1Bv4lzfy0KMBR/Fay0q/7Wwb7o/LOdWYxRmvvtEE=";
};
configureFlags = [
"--enable-executable=no" # no igraph dependency
];
# check phase is empty for now (as of version 0.7)
# check phase is empty for now (as of version 0.9)
doCheck = true;
meta = with lib; {

39
pkgs/development/libraries/science/math/sympow/clean-extra-logfile-output-from-pari.patch Normal file
View file

@ -0,0 +1,39 @@
commit 433a8b99da9d71e96434bd421c2468cbda29d37c
Author: Mauricio Collares <mauricio@collares.org>
Date: Tue Mar 2 22:07:11 2021 -0300
trim logfile information from pari 2.13 output
Pari (since commit 609fb01faf827d91dfa9136849a647a3bbfe8036) prints
extra logfile information such as
[logfile is "/tmp/nix-shell.2BquN9/home/.sympow/datafiles/P02HM.txt"]
which messes up sympow's parsing. This commit reuses the same trimming
mechanism already in sympow to trim this new message.
diff --git a/Configure b/Configure
index 1ef9756..776bec2 100755
--- a/Configure
+++ b/Configure
@@ -322,7 +322,7 @@ echo "datafiles/param_data: \$(OTHERb)" >> $FILE
echo " \$(MKDIR) -p datafiles" >> $FILE
echo " \$(TOUCH) datafiles/param_data" >> $FILE
echo " \$(SH) armd.sh" >> $FILE
-echo " \$(SED) -i -e '/logfile =/d' datafiles/*.txt" >> $FILE
+echo " \$(SED) -i -e '/logfile /d' datafiles/*.txt" >> $FILE
echo "sympow.1: sympow" >> $FILE
echo " \$(HELP2MAN) \$(H2MFLAGS) -s 1 -n \"SYMPOW program\" -I sympow.h2m -o \$@ ./\$<" >> $FILE
echo "clean:" >> $FILE
diff --git a/generate.c b/generate.c
index dbb811f..783320c 100644
--- a/generate.c
+++ b/generate.c
@@ -148,6 +148,7 @@ static void trimit(char *A)
" -e '"
"/^\?/d" ";"
"/^(/d" ";"
+ "/logfile /d" ";"
"/Warning:/d" ";"
"/^About to find TOO_BIG/d" ";"
"/^Now working backwards/d" ";"

2
pkgs/development/libraries/science/math/sympow/default.nix
View file

@ -20,6 +20,8 @@ stdenv.mkDerivation rec {
sha256 = "132l0xv00ld1svvv9wh99wfra4zzjv2885h2sq0dsl98wiyvi5zl";
};
patches = [ ./clean-extra-logfile-output-from-pari.patch ];
postUnpack = ''
patchShebangs .
'';

11
pkgs/development/python-modules/cysignals/default.nix
View file

@ -1,4 +1,5 @@
{ lib
, fetchpatch
, fetchPypi
, buildPythonPackage
, cython
@ -16,6 +17,16 @@ buildPythonPackage rec {
sha256 = "1ckxzch3wk5cg80mppky5jib5z4fzslny3001r5zg4ar1ixbc1w1";
};
patches = [
# fixes intermittent crashes in Sage tests (including in interfaces/singular.py)
# will be included in cysignals 1.10.3: https://github.com/sagemath/cysignals/pull/127
(fetchpatch {
name = "fix-verify_exc_value.patch";
url = "https://github.com/sagemath/cysignals/commit/49a7eee4bba3ab8f340cf56c371fa4f5ed702dcc.patch";
sha256 = "sha256-Pfc5tL9VDSP6ftDoHoIb+MDi5rjYqr0PRfIajFuuYVs=";
})
];
# explicit check:
# build/src/cysignals/implementation.c:27:2: error: #error "cysignals must be compiled without _FORTIFY_SOURCE"
hardeningDisable = [