sagemathgh-38804: GAP 4.13.1

    
Follow-up to:

* sagemath#37884
* sagemath#38169

With the four additional work items I mentioned in a comment on the
latter:

1. Everything has been rebased
2. There's a new feature to detect the polenta GAP package
3. The three failing simplicial sets tests have been marked `# needs
gap_package_polenta`
4. I backported gap-system/gap#5796 to the GAP
spkg so that the optional GRAPE tests will pass (untested).

Let's see what the CI has to say...
    
URL: sagemath#38804
Reported by: Michael Orlitzky
Reviewer(s): Dima Pasechnik, Enrique Manuel Artal Bartolo

.ci/write-dockerfile.sh

@@ -326,7 +326,7 @@ ARG NUMPROC=8
 ENV MAKE="make -j\${NUMPROC}"
 ARG USE_MAKEFLAGS="-k V=0"
 ENV SAGE_CHECK=warn
-ENV SAGE_CHECK_PACKAGES="!cython,!r,!python3,!gap,!cysignals,!linbox,!git,!ppl,!cmake,!rpy2,!sage_sws2rst"
+ENV SAGE_CHECK_PACKAGES="!cython,!python3,!cysignals,!linbox,!ppl,!cmake,!rpy2,!sage_sws2rst"
 #:toolchain:
 $RUN$CHECK_STATUS_THEN make \${USE_MAKEFLAGS} base-toolchain$ENDRUN$THEN_SAVE_STATUS
 
@@ -335,7 +335,7 @@ ARG NUMPROC=8
 ENV MAKE="make -j\${NUMPROC}"
 ARG USE_MAKEFLAGS="-k V=0"
 ENV SAGE_CHECK=warn
-ENV SAGE_CHECK_PACKAGES="!cython,!r,!python3,!gap,!cysignals,!linbox,!git,!ppl,!cmake,!rpy2,!sage_sws2rst"
+ENV SAGE_CHECK_PACKAGES="!cython,!python3,!cysignals,!linbox,!ppl,!cmake,!rpy2,!sage_sws2rst"
 #:make:
 ARG TARGETS_PRE="all-sage-local"
 $RUN$CHECK_STATUS_THEN make SAGE_SPKG="sage-spkg -y -o" \${USE_MAKEFLAGS} \${TARGETS_PRE}$ENDRUN$THEN_SAVE_STATUS
@@ -345,7 +345,7 @@ ARG NUMPROC=8
 ENV MAKE="make -j\${NUMPROC}"
 ARG USE_MAKEFLAGS="-k V=0"
 ENV SAGE_CHECK=warn
-ENV SAGE_CHECK_PACKAGES="!cython,!r,!python3,!gap,!cysignals,!linbox,!git,!ppl,!cmake,!rpy2,!sage_sws2rst"
+ENV SAGE_CHECK_PACKAGES="!cython,!python3,!cysignals,!linbox,!ppl,!cmake,!rpy2,!sage_sws2rst"
 $ADD .gitignore /new/.gitignore
 $ADD src /new/src
 RUN cd /new && rm -rf .git && \\
@@ -366,7 +366,7 @@ ARG NUMPROC=8
 ENV MAKE="make -j\${NUMPROC}"
 ARG USE_MAKEFLAGS="-k V=0"
 ENV SAGE_CHECK=warn
-ENV SAGE_CHECK_PACKAGES="!cython,!r,!python3,!gap,!cysignals,!linbox,!git,!ppl,!cmake,!rpy2,!sage_sws2rst"
+ENV SAGE_CHECK_PACKAGES="!cython,!python3,!cysignals,!linbox,!ppl,!cmake,!rpy2,!sage_sws2rst"
 ARG TARGETS_OPTIONAL="ptest"
 $RUN$CHECK_STATUS_THEN make SAGE_SPKG="sage-spkg -y -o" \${USE_MAKEFLAGS} \${TARGETS_OPTIONAL} || echo "(error ignored)"$ENDRUN$THEN_SAVE_STATUS
 

build/pkgs/gap/SPKG.rst

@@ -25,26 +25,3 @@ Upstream Contact
 https://www.gap-system.org
 
 Mailing list at https://mail.gap-system.org/mailman/listinfo/gap
-
-Special Update/Build Instructions
----------------------------------
-
-This is a stripped-down version of GAP. The downloading of the sources
-and removal of unneeded parts is done by the script spkg-src. When you
-update GAP, please also update and use the spkg-src script.
-
--  Do we really want to copy everything from the build directory???
-
-   You need the full GAP tree to compile/install many GAP packages.
-
--  There's apparently a command missing (in ``spkg-install``) building
-   the
-   (HTML?) documentation. Earlier changelog entries as well as the
-   description
-   above state the documentation was removed from the upstream
-   sources...
-   Since the (pre-)built HTML documentation is currently included, I've
-   commented out some lines in that part of ``spkg-install``. -leif
-
-Patches
-~~~~~~~

build/pkgs/gap/checksums.ini

@@ -1,4 +1,4 @@
 tarball=gap-VERSION.tar.gz
-sha1=a6e36f3f874a2c46f51561402634497eab705cca
-sha256=672308745eb78a222494ee8dd6786edd5bc331456fcc6456ac064bdb28d587a8
+sha1=cf91834954849dbaeae17079a4c4565bc28d03a8
+sha256=9794dbdba6fb998e0a2d0aa8ce21fc8848ad3d3f9cc9993b0b8e20be7e1dbeba
 upstream_url=https://github.com/gap-system/gap/releases/download/vVERSION/gap-VERSION.tar.gz

build/pkgs/gap/distros/conda.txt

@@ -1 +1 @@
-gap-defaults>=4.12.2,<4.13.0
+gap-defaults

build/pkgs/gap/distros/gentoo.txt

@@ -0,0 +1 @@
+sci-mathematics/gap

build/pkgs/gap/package-version.txt

@@ -1 +1 @@
-4.12.2
+4.13.1

build/pkgs/gap/patches/0001-Makefile.rules-Darwin-Remove-use-of-single_module-ob.patch

@@ -0,0 +1,29 @@
+From 89b95994807970d90671e1e02cc03ddca4cf0a10 Mon Sep 17 00:00:00 2001
+From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
+Date: Sat, 8 Jun 2024 14:01:16 -0700
+Subject: [PATCH] Makefile.rules [Darwin]: Remove use of '-single_module'
+ (obsolete), activate '-install_name'
+
+---
+ Makefile.rules | 5 +----
+ 1 file changed, 1 insertion(+), 4 deletions(-)
+
+diff --git a/Makefile.rules b/Makefile.rules
+index 8bfd3dba0..adfed731f 100644
+--- a/Makefile.rules
++++ b/Makefile.rules
+@@ -446,10 +446,7 @@ else ifneq (,$(findstring darwin,$(host_os)))
+   LINK_SHLIB_FLAGS = -dynamiclib
+   LINK_SHLIB_FLAGS += -compatibility_version $(LIBGAP_COMPAT_VER)
+   LINK_SHLIB_FLAGS += -current_version $(LIBGAP_CURRENT_VER)
+-  LINK_SHLIB_FLAGS += -Wl,-single_module
+-
+-  # TODO: set install_name, at least for installed version of the lib?
+-  #LINK_SHLIB_FLAGS += -install_name $(libdir)/$(LIBGAP_FULL)
++  LINK_SHLIB_FLAGS += -install_name $(libdir)/$(LIBGAP_FULL)
+
+   GAP_CPPFLAGS += -DPIC
+   GAP_CFLAGS += -fno-common
+-- 
+2.42.0
+

build/pkgs/gap/patches/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);

build/pkgs/gap/spkg-check.in

@@ -10,7 +10,8 @@ cd pkg/io
 make
 cd ../..
 
-make testinstall
+# This is the same as 'dev/ci.sh testinstall' (but dev/ci.sh is not part of the GAP tarball)
+./gap tst/testinstall.g
 if [[ $? -ne 0 ]]; then
     exit 1
 fi

build/pkgs/gap/spkg-configure.m4

@@ -2,8 +2,8 @@ SAGE_SPKG_CONFIGURE([gap], [
   # Default to installing the SPKG, if the check is run at all.
   sage_spkg_install_gap=yes
 
-  m4_pushdef([GAP_MINVER],["4.12.2"])
-  m4_pushdef([GAP_LTVER],["4.13.0"])
+  m4_pushdef([GAP_MINVER],["4.13.0"])
+  m4_pushdef([GAP_LTVER],["5.0.0"])
 
   SAGE_SPKG_DEPCHECK([ncurses readline zlib], [
     AC_PATH_PROG(GAP, gap)

src/sage/algebras/fusion_rings/fusion_double.py

@@ -133,7 +133,7 @@ class FusionDouble(CombinatorialFreeModule):
         sage: G = SmallPermutationGroup(16,9)
         sage: F = FusionDouble(G, prefix='b', inject_variables=True)
         sage: b13^2 # long time (4s)
-        b0 + b2 + b4 + b15 + b16 + b17 + b18 + b24 + b26 + b27
+        b0 + b3 + b4
     """
     @staticmethod
     def __classcall_private__(cls, G, prefix='s', inject_variables=False):