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Merged
AndersonTorres merged 4 commits into from
May 12, 2021
Merged

sage: 9.3rc4 -> 9.3 #122592

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2a95fe1
gap: 4.11.0 -> 4.11.1
collares May 5, 2021
391028e
pynac: add more patches, link to sage trac
collares May 5, 2021
f206ba8
singular: replace local patches by upstream ones
collares May 5, 2021
b413d35
sage: 9.3.rc4 -> 9.3
collares May 5, 2021
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26 changes: 4 additions & 22 deletions pkgs/applications/science/math/gap/default.nix
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@@ -1,7 +1,6 @@
{ stdenv
, lib
, fetchurl
, fetchpatch
, makeWrapper
, readline
, gmp
Expand Down Expand Up @@ -35,7 +34,7 @@ let
"autpgrp-*"
"alnuth-*"
"crisp-*"
"ctbllib"
"ctbllib-*"
"FactInt-*"
"fga"
"irredsol-*"
Expand All @@ -62,11 +61,11 @@ in
stdenv.mkDerivation rec {
pname = "gap";
# https://www.gap-system.org/Releases/
version = "4.11.0";
version = "4.11.1";

src = fetchurl {
url = "https://files.gap-system.org/gap-${lib.versions.major version}.${lib.versions.minor version}/tar.bz2/gap-${version}.tar.bz2";
sha256 = "sha256-vwcKENwqxgWT/mXfD4c9ctTWdQHobrJipva9SPyGhgI=";
url = "https://github.com/gap-system/gap/releases/download/v${version}/gap-${version}.tar.gz";
sha256 = "sha256-ZjXF2n2CdV+DOUhrnKwzdm9YcS8pfoI0+6QIGJAuowQ=";
};

# remove all non-essential packages (which take up a lot of space)
Expand All @@ -84,23 +83,6 @@ stdenv.mkDerivation rec {
makeWrapper
];

patches = [
# Fix for locale specific tests causing issues. Already upstream.
# Backport of https://github.com/gap-system/gap/pull/4022
(fetchpatch {
name = "remove-locale-specific-tests.patch";
url = "https://github.com/gap-system/gap/commit/c18b0c4215b5212a2cc4f305e2d5b94ba716bee8.patch";
sha256 = "sha256-De+T9Y7ewRT6plJrj2VR8axRvD/JCTYKOBWB7Bw0oq0=";
})

# fixes aarch64 gc crashes: https://github.com/gap-system/gap/pull/3965
(fetchpatch {
name = "mark-genstackfuncbags-as-noinline.patch";
url = "https://github.com/gap-system/gap/commit/f0a8f49ff8dad0a5fa77253d45457c6f40f96778.patch";
sha256 = "sha256-GU9tOP1stX2vn8m8kXOBupEpxIYArA76ibKL8eLn0MY=";
})
];

# "teststandard" is a superset of testinstall. It takes ~1h instead of ~1min.
# tests are run twice, once with all packages loaded and once without
# checkTarget = "teststandard";
Expand Down
13 changes: 0 additions & 13 deletions pkgs/applications/science/math/gap/mark-genstackfuncbags-as-noinline.patch
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This file was deleted.

35 changes: 28 additions & 7 deletions pkgs/applications/science/math/pynac/default.nix
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Expand Up @@ -22,23 +22,44 @@ stdenv.mkDerivation rec {
};

patches = [
(fetchpatch {
name = "handle_factor.patch";
url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/handle_factor.patch?h=9.3.rc3";
sha256 = "sha256-U1lb5qwBqZZgklfDMhBX4K5u8bz5x42O4w7hyNy2YVw=";
})
# the five patches below are included with sage 9.3. since pynac
# is a self-described "Sage Math support library", we include them
# here.

# https://trac.sagemath.org/ticket/30688
(fetchpatch {
name = "power_inf_loop.patch";
url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/power_inf_loop.patch?h=9.3.rc3";
url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/power_inf_loop.patch?h=9.3";
sha256 = "sha256-VYeaJl8u2wl7FQ/6xnpZv1KpdNYEmJoPhuMrBADyTRs=";
})

# https://trac.sagemath.org/ticket/31479
(fetchpatch {
name = "disable_poly_mul_expand.patch";
url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/disable_poly_mul_expand.patch?h=9.3";
sha256 = "sha256-gRjoltU9Tzj7fjNyE25fY+iyDxERzSTOMigzxFpUqPo=";
})

# https://trac.sagemath.org/ticket/31530
(fetchpatch {
name = "too_much_sub.patch";
url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/too_much_sub.patch?h=9.3.rc3";
url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/too_much_sub.patch?h=9.3";
sha256 = "sha256-lw7xSQ/l+rzPu+ghWF4omYF0mKksGGPuuHJTktvbdis=";
})

# https://trac.sagemath.org/ticket/31554
(fetchpatch {
name = "handle_factor.patch";
url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/handle_factor.patch?h=9.3";
sha256 = "sha256-U1lb5qwBqZZgklfDMhBX4K5u8bz5x42O4w7hyNy2YVw=";
})

# https://trac.sagemath.org/ticket/31645
(fetchpatch {
name = "seriesbug.patch";
url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/seriesbug.patch?h=9.3";
sha256 = "sha256-b3//oirN7JHDYqrvE+tDYcnKpSYQJ08yBzcNlII2Dts=";
})
];

buildInputs = [
Expand Down
4 changes: 2 additions & 2 deletions pkgs/applications/science/math/sage/sage-src.nix
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Expand Up @@ -24,14 +24,14 @@ let
);
in
stdenv.mkDerivation rec {
version = "9.3.rc4";
version = "9.3";
pname = "sage-src";

src = fetchFromGitHub {
owner = "sagemath";
repo = "sage";
rev = version;
sha256 = "sha256-LDY07By2j6JagkgT9zeDJ93+m2/oXXEnDRTDzmR8ftk=";
sha256 = "sha256-l9DX8jcDdKA7GJ6xU+nBsmlZxrcZ9ZUAJju621ooBEo=";
};

# Patches needed because of particularities of nix or the way this is packaged.
Expand Down
29 changes: 19 additions & 10 deletions pkgs/applications/science/math/singular/default.nix
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Expand Up @@ -31,11 +31,9 @@ stdenv.mkDerivation rec {
owner = "Singular";
repo = "Singular";

# 4.2.0p2 is not tagged, but the tarball matches commit
# 6f68939ddf612d96e3caaaaa8275f77613ac1da8. the commit below has
# two extra fixes.
rev = "3cda50c00a849455efa2502e56596955491a353a";
sha256 = "sha256-OizPhGE6L2LTOrKfeDdDB6BSdvYkDVXvbbYjV14hnHM=";
# 4.2.0p2 is not tagged, but the tarball matches the commit below.
rev = "6f68939ddf612d96e3caaaaa8275f77613ac1da8";
sha256 = "sha256-BJNzYylzDqD/5YjzjxPRb/c96tYiuGy9Y+A7qf3ZSG8=";

# if a release is tagged it will be in the format below.
# rev = "Release${lib.replaceStrings ["."] ["-"] version}";
Expand All @@ -60,13 +58,27 @@ stdenv.mkDerivation rec {
# https://github.com/alsa-project/alsa-firmware/issues/3 for a
# related issue.
./use-older-ax-prog-cc-for-build.patch

# https://github.com/Singular/Singular/issues/1086
(fetchpatch {
name = "schubert-lib-fails-with-too-many-cpus.patch";
url = "https://github.com/Singular/Singular/commit/3cda50c00a849455efa2502e56596955491a353a.patch";
sha256 = "sha256-fgYd+2vT32w5Ki8kKx6PfZn2e4QSJcYWOwEFXtc+lSA=";
})
] ++ lib.optionals enableDocs [
# singular supports building without 4ti2, bertini, normaliz or
# topcom just fine, but the docbuilding does not skip manual pages
# tagged as depending on those binaries (probably a bug in
# doc2tex.pl::HandleLib, since it seems to ignore "-exclude"
# argumens). skip them manually.
./disable-docs-for-optional-unpackaged-deps.patch

# fix some non-ascii characters in doc/decodegb.doc
(fetchpatch {
name = "decodegb-ascii.patch";
url = "https://github.com/Singular/Singular/commit/36966d9009de572ee4dbc487f3e5744098fe91be.patch";
sha256 = "sha256-9WcEov/oOQRC584ag6WVHFwY2aCjbM75HWyvZoEwppw=";
})
];

configureFlags = [
Expand All @@ -83,9 +95,6 @@ stdenv.mkDerivation rec {
substituteInPlace Tst/regress.cmd --replace 'mysystem_catch("hostname")' 'nix_test_runner'

patchShebangs .
'' + lib.optionalString enableDocs ''
# work around encoding problem
sed -i -e 's/\xb7/@cdot{}/g' doc/decodegb.doc
'';

# For reference (last checked on commit 75f460d):
Expand Down Expand Up @@ -149,7 +158,7 @@ stdenv.mkDerivation rec {

# singular tests are a bit complicated, see
# https://github.com/Singular/Singular/tree/spielwiese/Tst
# https://www.singular.uni-kl.de/forum/viewtopic.php&t=2773
# https://www.singular.uni-kl.de/forum/viewtopic.php?f=10&t=2773
testsToRun = [
"Old/universal.lst"
"Buch/buch.lst"
Expand Down Expand Up @@ -181,7 +190,7 @@ stdenv.mkDerivation rec {
2>"$TMPDIR/out-err.log"

# unfortunately regress.cmd always returns exit code 0, so check stderr
# https://www.singular.uni-kl.de/forum/viewtopic.php&t=2773
# https://www.singular.uni-kl.de/forum/viewtopic.php?f=10&t=2773
if [[ -s "$TMPDIR/out-err.log" ]]; then
cat "$TMPDIR/out-err.log"
exit 1
Expand Down
4 changes: 1 addition & 3 deletions pkgs/data/misc/graphs/default.nix
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Expand Up @@ -7,9 +7,7 @@ stdenv.mkDerivation rec {
version = "20210214";

src = fetchurl {
url = "https://mirrors.mit.edu/sage/spkg/upstream/${pname}/${pname}-${version}.tar.bz2";
# TODO: switch to the url below once Sage 9.3 is released
# url = "mirror://sageupstream/${pname}/${pname}-${version}.tar.bz2";
url = "mirror://sageupstream/${pname}/${pname}-${version}.tar.bz2";
sha256 = "sha256-ByN8DZhTYRUFw4n9e7klAMh0P1YxurtND0Xf2DMvN0E=";
};

Expand Down