sci-mathematics/gap: revbump with an upstream patch

Backport https://github.com/gap-system/gap/pull/5796 because it's
causing failures in the SageMath test suite when dev-gap/grape also
happens to be installed.

Thanks to Dima Pasechnik for the pointer.

Signed-off-by: Michael Orlitzky <mjo@gentoo.org>

2 files changed, 318 insertions, 0 deletions

diff --git a/sci-mathematics/gap/files/gap-4.13.1-hash-fixes.patch b/sci-mathematics/gap/files/gap-4.13.1-hash-fixes.patch
new file mode 100644
index 000000000000..c99b39ab91c6
--- /dev/null
+++ b/sci-mathematics/gap/files/gap-4.13.1-hash-fixes.patch
@@ -0,0 +1,178 @@
+diff --git a/lib/dicthf.gi b/lib/dicthf.gi
+index 5ee7341..e4349ac 100644
+--- a/lib/dicthf.gi
++++ b/lib/dicthf.gi
+@@ -152,16 +152,37 @@ end);
+ ##
+ InstallMethod(SparseIntKey,"for bounded tuples",true,
+     [ IsList,IsList and IsCyclotomicCollection ], 0,
+-function(m,v)
+-local c;
+-  if Length(m)<>3 or m[1]<>"BoundedTuples" then
++function(m, v)
++  if Length(m)<> 3 or m[1]<>"BoundedTuples" then
+     TryNextMethod();
+   fi;
+-  c:=[1,Maximum(m[2])+1];
+-  return function(a)
+-    return a*c;
++  # Due to the way BoundedTuples are presently implemented we expect the input
++  # to the hash function to always be a list of positive immediate integers. This means
++  # that using HashKeyWholeBag should be safe.
++  return function(x)
++    Assert(1, IsPositionsList(x));
++    if not IsPlistRep(x) then
++      x := AsPlist(x);
++    fi;
++    return HashKeyWholeBag(x, 1);
+   end;
+ 
++  # alternative code w/o HashKeyBag
++  ## build a weight vector to distinguish lists. Make entries large while staying clearly within
++  ## immediate int (2^55 replacing 2^60, since we take subsequent primes).
++  #step:=NextPrimeInt(QuoInt(2^55,Maximum(m[2])*m[3]));
++  #weights:=[1];
++  #len:=Length(v);
++  ## up to 56 full, then increasingly reduce
++  #len:=Minimum(len,8*RootInt(len));
++  #while Length(weights)<len do
++  #  Add(weights,weights[Length(weights)]+step);
++  #  step:=NextPrimeInt(step);
++  #od;
++  #return function(a)
++  #  return a*weights;
++  #end;
++
+ end);
+ 
+ BindGlobal( "SparseIntKeyVecListAndMatrix", function(d,m)
+diff --git a/lib/oprt.gi b/lib/oprt.gi
+index c1def0b..00e2953 100644
+--- a/lib/oprt.gi
++++ b/lib/oprt.gi
+@@ -3565,6 +3565,7 @@ InstallMethod(DomainForAction,"permutations on lists of integers",true,
+ function(pnt,acts,act)
+   local m;
+   if not (Length(pnt)>0 and ForAll(pnt,IsPosInt) and
++    ForAll(acts,IsPerm) and
+     (act=OnSets or act=OnPoints or act=OnRight or act=\^)) then
+     TryNextMethod();
+   fi;
+diff --git a/lib/vecmat.gi b/lib/vecmat.gi
+index 017c3c6..93ba828 100644
+--- a/lib/vecmat.gi
++++ b/lib/vecmat.gi
+@@ -2142,7 +2142,8 @@ InstallMethod(DomainForAction,"matrix/matrix",IsElmsCollsX,
+ function(pnt,acts,act)
+ local l,f;
+   if (not ForAll(acts,IsMatrix)) or
+-    (act<>OnPoints and act<>OnSubspacesByCanonicalBasis and act<>OnRight) then
++    (act<>OnPoints and act<>OnSubspacesByCanonicalBasis and act<>OnRight and act<>OnSets and
++    act<>OnTuples) then
+     TryNextMethod(); # strange operation, might extend the domain
+   fi;
+   l:=NaturalActedSpace(acts,pnt);
+diff --git a/tst/testbugfix/2024-09-14-actdomain.tst b/tst/testbugfix/2024-09-14-actdomain.tst
+new file mode 100644
+index 0000000..84f8b50
+--- /dev/null
++++ b/tst/testbugfix/2024-09-14-actdomain.tst
+@@ -0,0 +1,85 @@
++# Fix #5786 and error reported by Len Soicher in support list
++gap>   gg:=SpecialUnitaryGroup(4,2);;
++gap>    hl:=Z(2)*[
++>                 [0,0,1,0],
++>                 [1,1,0,0],
++>                 [0,1,0,1],
++>                 [0,1,1,0],
++>                 [1,1,0,1]];;
++gap> o:=Orbit(gg,Set(hl),OnSets);;
++gap> Length(o);
++216
++gap> set:=[ 1,10,15,24,29,33,38,40,44,59, 60, 63, 69, 74, 77,79,85, 86, 90,
++>   95, 99, 103, 105, 110, 122, 125, 143, 148, 149, 153, 162, 165, 174, 182,
++>   185, 191, 197, 198, 202, 218, 223, 227, 228, 235, 236, 240, 243, 248,
++>   254,
++>   256, 259, 270, 275, 288, 291, 295, 298, 302, 305, 310, 312, 315, 325,
++>   329,
++>   333, 340, 341, 350, 356, 366, 369, 381, 385, 390, 397, 402, 412, 414,
++>   419,
++>   421, 425, 428, 433, 436, 445, 447, 451, 452, 453, 454, 461, 466, 474,
++>   479,
++>   481, 489, 490, 493, 497, 507, 509, 512, 513, 519, 521 ];;
++gap> gp:=Group(
++> (  1,340,124,306,216,492,100, 25,108,270,220,332)(  2,138, 54,161,132,159,198,
++>  336,439,269, 89,419)(  3,467,177,404,505,437,379,312,481,271,223,135)
++> (  4,510, 79,504,259,234,378,251,272,268,360,303)(  5,278,176,191,231,275,263,
++>  190,230,146,265,192)(  6,486,126,523,490,448,375,237,288,400,243,329)
++> (  7,131,123,516, 48,392,350,333,418, 16,139,175)(  8,289,125,386,241, 29,376,
++>  334,242,417,442,331)(  9,430, 32, 59,446,367,377,335,411,416,515,330)
++> ( 10,391, 56,407,475,414,200,328,165,473, 86,119)( 11,368, 35,390,522,408,199,
++>  415,440,326, 87,503)( 12,412, 55,457,399,245,201, 33,438,431, 88,317)
++> ( 13,471, 40,348,452,292, 43,346,373, 77, 41,347)( 14,137,174,162, 60, 69,321,
++>  487, 61,158,322,370)( 15,101,114,109,130,160,488,489,352,351,420, 17)
++> ( 18,339,167,290,202,385, 99, 22, 90,323,217,129)( 19, 26, 93,304, 96,342)
++> ( 20,338,166,305,215,141, 97, 24, 51,150,219,507)( 21,337, 63,186,214,424, 98,
++>  23,107,382,218,349)( 27, 91,445,451,525, 67,519,239,144,203,155,353)
++> ( 28,324,444,128, 70,428,496,238,286,300,283, 64)( 30,236,287,441,387,354)
++> ( 31,345,366,517, 45,344,413,521, 46,248,244,121)( 34,314,394,402,222,447, 81,
++>  282,262,173,246,435)( 36,482,178,364,148,495,179,363,140,102,113,111)
++> ( 37,253,273,168,294,302,226,183, 72,480,154,233)( 38,483,520,393,403,465,362,
++>  298,143,356,153,369)( 39,157,320,472)( 42,228,277,264)( 44,343,147,501)
++> ( 47, 73,308,380,184,389,310,327,163,295,151,425)( 49,221,456, 80,474,260,405,
++>  325,164,524,152,449)( 50,479,365,477,461,459,497,169,296,247,134,117)
++> ( 52,361,299,285,355,188,423,464,434,453,133,118)( 53,257,509, 68,511,458,293,
++>  204,384,374, 75, 82)( 57,116,112,149,514,396,470,485,493,249,421,120)
++> ( 58,500,266,250,429,122)( 62,156,319,311)( 65,187,225,357,127, 71,388,235,
++>  460,252,274,371)( 66,106,462,291,205,383,372, 76, 92,410,280,498)
++> ( 74,401,381,476,409,281,171,104,297,307,426,182)( 78, 84,261,256,180,436,512,
++>  313,181,491,224,499)( 83,466,255,508,506,395,469,422,142,103,115,110)
++> ( 85,468,258,502,267,136)( 94,341)( 95,211)(105,478,195,432,518,316,197,484,
++>  494,455,196,170)(145,513,359,232,227,254)(172,209,398,207,279,206)
++> (185,194,309,443)(189,406,463,318,450,427,433,454,315,301,284,358)
++> (193,229,276,240)(208,397)(210,213,212)
++> ,(  1,379,148, 48,128,430,416)(  2, 34,338, 35,235,131,521)(  3,512,352, 47,
++>  318,289,237)(  4,272,506, 49,434,486,282)(  5,524,485, 10,483,340, 55)
++> (  6,458, 36,487, 60,121, 16)(  7,313,140,336,127,435,270)(  8, 85,147,489,
++>   98,201,417)(  9,469, 94,488,129,329,400)( 11,291, 26, 54,234,473,169)
++> ( 12,207,339, 56,233,503,515)( 13,426,337, 40,232,295,500)( 14, 32,414, 27,
++>  167,130,472)( 15, 33,188, 38,382,109,501)( 17, 31,459, 37,496,132,517)
++> ( 18,263,294,446,451,134,497)( 19,198,525,241,441,244,470)( 20,100,199,490,
++>  242,429,413)( 21,378,403,216,523,421, 58)( 22,124,159, 77, 63,123,292)
++> ( 23,176,275,431,168, 86,293)( 24,177,492,326,104,151,290)( 25, 79,437,269,
++>  163,152,144)( 28,462,150,162, 62,120,415)( 29,239, 83,311, 61,117,260)
++> ( 30,452,149,370, 39,122,389)( 41,468, 73,254,277,432,371)( 42,210,319,502,
++>  373,205,283)( 43,387,194,212,320,508, 99)( 44,396,349,331,399,250,420)
++> ( 45,411,461,375,475,377,418)( 46,344,409,519,522,477,419)( 50,253,278,433,
++>  231, 88,422)( 51,482,138,358,229,463,381)( 52, 91,467,221,230,518,484)
++> ( 53,390,510,494,228,454, 92)( 57,310,460,118,259,367,363)( 59,281,227,274,
++>  505,402,215)( 64,125,245, 76, 93,160,471)( 65,126,408, 75,166, 69,264)
++> ( 66,302,186,116,257,424,327)( 67,187,297,479,217,425,171)( 68,303,296,345,
++>  280,226,273)( 70,240,359,366,364, 97,200)( 71,265,360,394,393,133,423)
++> ( 72,251,146,164,268, 87,312)( 74,252,276,406,513, 89,181)( 78,395,158,185,
++>  315,287,333)( 80,136,351,156,316,286,334)( 81,511,350,184,317,288,335)
++> ( 82,261,392,183,105,309,238)( 84,224,439,182,284,193,236)( 90,466,391,357,
++>  443,170,465)( 95,321,509,353,203,243,197)( 96,516,498,354,300,246,401)
++> (101,405,453,464,154,112,341)(102,139,450,208,388,365,111)(103,440,520,285,
++>  192,266,343)(106,308,218,119,262,448,298)(107,219,368,356,442,301,209)
++> (108,514,412,355,376,474,222)(110,495,137,478,361,444,380)(113,255,342,175,
++>  173,247,305)(114,256,141,328,153,307,304)(115,258,385,325,172,214,306)
++> (135,493,157,455,362,445,407)(142,346,189,398,323,161,499)(143,190,145,436,
++>  271,165,314)(155,195,211,174,404,374,204)(178,507,332,330,248,249,179)
++> (180,372,202,386,196,213,322)(191,267,491,384,438,279,225)(206,428,299,369,
++>  480,220,449)(223,481,383,427,397,324,504)(347,457,447,410,348,456,476));;
++gap> Length(Orbit(gp,set,OnSets));
++241920
+diff --git a/tst/teststandard/hash2.tst b/tst/teststandard/hash2.tst
+index 6bfa4d3..d47452e 100644
+--- a/tst/teststandard/hash2.tst
++++ b/tst/teststandard/hash2.tst
+@@ -32,4 +32,8 @@ gap> Length(Orbit(h,h.1[1],OnRight));
+ 2079
+ gap> Length(Orbit(h,h.2^5,OnPoints));
+ 693
++gap> Length(Orbit(SymmetricGroup(14), [1 .. 7], OnSets));
++3432
++gap> Length(Orbit(SymmetricGroup(16), [1 .. 8], OnSets));
++12870
+ gap> STOP_TEST( "hash2.tst", 1);
diff --git a/sci-mathematics/gap/gap-4.13.1-r1.ebuild b/sci-mathematics/gap/gap-4.13.1-r1.ebuild
new file mode 100644
index 000000000000..45cb0c98749e
--- /dev/null
+++ b/sci-mathematics/gap/gap-4.13.1-r1.ebuild
@@ -0,0 +1,140 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit estack
+
+DESCRIPTION="System for computational discrete algebra. Core functionality."
+HOMEPAGE="https://www.gap-system.org/"
+SRC_URI="https://github.com/gap-system/gap/releases/download/v${PV/_/-}/${P/_/-}-core.tar.gz"
+
+S="${WORKDIR}/${P/_/-}"
+
+LICENSE="GPL-2+"
+SLOT="0/9" # soname
+KEYWORDS="~amd64 ~riscv"
+IUSE="cpu_flags_x86_popcnt debug memcheck minimal readline test valgrind"
+REQUIRED_USE="?? ( memcheck valgrind )"
+
+RESTRICT="!test? ( test )"
+
+# The minimum set of packages needed for basic GAP operation. You can
+# actually start gap without these by passing "--bare" to it on the CLI,
+# but don't expect anything to work.
+REQUIRED_PKGS="
+	dev-gap/gapdoc
+	dev-gap/primgrp
+	dev-gap/smallgrp
+	dev-gap/transgrp"
+
+# The packages aren't really required, but GAP tries to load them
+# automatically, and will complain to the user if they fail to load.
+# The list of automatically-loaded packages is a user preference, called
+# AutoloadPackages, and the upstream default can be found in
+# lib/package.gi within the GAP source tree. Passing "-A" to GAP on the
+# CLI (or setting that user preference) will suppress the autoload
+# behavior and allow GAP to start without these, which is why we allow
+# the user to skip them with USE=minimal if he knows what he is doing.
+AUTOLOADED_PKGS="
+	dev-gap/autpgrp
+	dev-gap/alnuth
+	dev-gap/crisp
+	dev-gap/ctbllib
+	dev-gap/factint
+	dev-gap/fga
+	dev-gap/irredsol
+	dev-gap/laguna
+	dev-gap/polenta
+	dev-gap/polycyclic
+	dev-gap/resclasses
+	dev-gap/sophus
+	dev-gap/tomlib"
+
+# The test suite will fail without the "required" subset.
+BDEPEND="test? ( ${REQUIRED_PKGS} )"
+
+DEPEND="dev-libs/gmp:=
+	sys-libs/zlib
+	valgrind? ( dev-debug/valgrind )
+	readline? ( sys-libs/readline:= )"
+
+RDEPEND="${DEPEND}"
+
+# If you _really_ want to install GAP without the set of required
+# packages, use package.provided.
+PDEPEND="${REQUIRED_PKGS} !minimal? ( ${AUTOLOADED_PKGS} )"
+
+PATCHES=( "${FILESDIR}/gap-4.13.1-hash-fixes.patch" )
+
+pkg_setup() {
+	if use valgrind; then
+		elog "If you enable the use of valgrind during building"
+		elog "be sure that you have enabled the proper flags"
+		elog "in gcc to support it:"
+		elog "https://wiki.gentoo.org/wiki/Debugging#Valgrind"
+	fi
+}
+
+src_prepare() {
+	# Remove these to be extra sure we don't use bundled libraries.
+	rm -r extern || die
+	rm -r hpcgap/extern || die
+
+	# The Makefile just tells you to run ./configure, which then
+	# produces a GNUmakefile.
+	rm Makefile || die
+
+	default
+}
+
+src_configure() {
+	# We unset $ABI because GAP uses it internally for something else.
+	# --without-gmp and --without-zlib both trigger an AC_MSG_ERROR
+	local myeconfargs=(
+		ABI=""
+		--with-gmp
+		--with-zlib
+		$(use_enable cpu_flags_x86_popcnt popcnt)
+		$(use_enable memcheck memory-checking)
+		$(use_enable valgrind)
+		$(use_with readline)
+		$(use_enable debug)
+	)
+	econf "${myeconfargs[@]}"
+}
+
+src_compile() {
+	# Without this, the default is a quiet build.
+	emake V=1
+}
+
+src_test() {
+	# We need to specify additional root paths because otherwise the
+	# recently-built GAP doesn't know where to look for the "required"
+	# packages (which must already be installed). The two paths we
+	# append to $S are where those packages wind up.
+	local gaproots="${S}/;"
+	gaproots+="${EPREFIX}/usr/$(get_libdir)/gap/;"
+	gaproots+="${EPREFIX}/usr/share/gap/"
+
+	# GAPARGS is a Makefile variable that exists for this purpose. We
+	# use "-A" to hide the warnings about missing autoloaded-but-not-
+	# required packages. The tee/pipefail works around a glitch in
+	# dev-gap/browse that can clobber your terminal.
+	eshopts_push -o pipefail
+	emake GAPARGS="-A -l '${gaproots}'" check | tee test-suite.log \
+		|| die "test suite failed, see test-suite.log"
+	eshopts_pop
+}
+
+src_install() {
+	default
+
+	# Manually install Makefile.gappkg
+	insinto usr/share/gap/etc
+	doins etc/Makefile.gappkg
+
+	# la files removal
+	find "${ED}" -type f -name '*.la' -delete || die
+}