Merge branch 'main' into better-nambooripad

.VERSION

@@ -1 +1 @@
-5.3.7
+5.4.0

.clang-format

@@ -45,7 +45,6 @@ ConstructorInitializerIndentWidth: 4
 ContinuationIndentWidth: 4
 Cpp11BracedListStyle: true
 DerivePointerAlignment: false
-PointerAlignment: PAS_Left
 DisableFormat:   false
 ExperimentalAutoDetectBinPacking: false
 FixNamespaceComments: true

.github/workflows/ci.yml

@@ -57,6 +57,7 @@ jobs:
           # removed in the fullness of time.
           LDFLAGS: "-pthread"
         with:
+          GAP_PKGS_TO_CLONE: digraphs/digraphs
           GAP_PKGS_TO_BUILD: "digraphs io orb datastructures profiling"
           GAPBRANCH: ${{ matrix.gap-branch }}
           ABI: ${{ matrix.ABI }}

.github/workflows/codespell.yml

@@ -5,4 +5,4 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - uses: codespell-project/actions-codespell@v2.0
+    - uses: codespell-project/actions-codespell@v2.1

.github/workflows/config-options.yml

@@ -10,7 +10,6 @@ jobs:
   enable-debug:
     runs-on: "ubuntu-latest"
     env:
-      GAPBRANCH: "stable-4.12"
       ABI: 64
     steps:
       - uses: actions/checkout@v4
@@ -44,7 +43,6 @@ jobs:
         uses: gap-actions/setup-gap@v2
         with:
           GAP_PKGS_TO_BUILD: "digraphs io orb datastructures profiling"
-          GAPBRANCH: stable-4.12
           ABI: 64
       - name: "Build Semigroups"
         uses: gap-actions/build-pkg@v1
@@ -62,7 +60,6 @@ jobs:
   with-external-libsemigroups:
     runs-on: "ubuntu-latest"
     env:
-      GAPBRANCH: "stable-4.12"
       ABI: 64
       PKG_CONFIG_PATH: "/home/runner/micromamba/envs/libsemigroups/lib/pkgconfig:/home/runner/micromamba/envs/libsemigroups/share/pkgconfig/"
       LD_LIBRARY_PATH: "/home/runner/micromamba/envs/libsemigroups/lib"
@@ -73,7 +70,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: "Install conda environment from environment.yml . . ."
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
             environment-file: environment.yml
             cache-environment: true

.github/workflows/lint.yml

@@ -16,7 +16,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: "Install dependencies . . ."
-        run: sudo pip install gaplint==1.1.3
+        run: sudo pip install gaplint==1.3.2
       - name: "Run gaplint . . ."
         run: bash etc/gaplint.sh
 

.github/workflows/release.yml

@@ -32,7 +32,7 @@ jobs:
       - uses: actions/checkout@v4
       - name: "Install dependencies (macOS only!)"
         if: ${{ runner.os == 'macOS' }}
-        run: brew install automake
+        run: brew install automake autoconf zlib gmp pkg-config libtool
       # Setup ccache, to speed up repeated compilation of the same binaries
       # (i.e., GAP and the packages)
       - name: "Setup ccache"

.mailmap

@@ -1,3 +1,4 @@
+Marina Anagnostopoulou-Merkouri <marina.anagnostopoulou-merkouri@bristol.ac.uk> Marina Anagnostopoulou-Merkouri <mam49@st-andrews.ac.uk>
 Stuart Burrell <stuartburrell1994@gmail.com> <stuartburrell@users.noreply.github.com>
 Stuart Burrell <stuartburrell1994@gmail.com> stuartburrell <unknown>
 Reinis Cirpons <rc234@st-andrews.ac.uk> Reinis Cirpons <43414125+reiniscirpons@users.noreply.github.com>
@@ -8,8 +9,10 @@ Joseph Edwards <jde1@st-andrews.ac.uk> Joe Edwards <80713360+Joseph-Edwards@user
 Joseph Edwards <jde1@st-andrews.ac.uk> Joseph Edwards <josephdavidedwards@gmail.com>
 Luke Elliott <le27@st-andrews.ac.uk> le27 <le27@st-andrews.ac.uk>
 Fernando Flores Brito <ffloresbrito@gmail.com> Fernando Flores Brito <ffb3@st-andrews.ac.uk>
+Tillman Froehlich <trf1@st-andrews.ac.uk> <47321884+awesometillman@users.noreply.github.com>
 Nick Ham <nicholas.charles.ham@gmail.com>
-Robert Hancock <hancock@informatik.uni-heidelberg.de> Robert Hancock <unknown>
+Robert Hancock <robert.hancock@maths.ox.ac.uk> Robert Hancock <hancock@informatik.uni-heidelberg.de>
+Robert Hancock <robert.hancock@maths.ox.ac.uk> Robert Hancock <unknown>
 Max Horn <horn@mathematik.uni-kl.de> Max Horn <max@quendi.de>
 Chris Jefferson <caj21@st-andrews.ac.uk> Chris Jefferson <chris@bubblescope.net>
 Julius Jonusas <j.jonusas@gmail.com> Julius <jj252@st-andrews.ac.uk>
@@ -19,6 +22,7 @@ Olexandr Konovalov <obk1@st-andrews.ac.uk> Alexander Konovalov <alex-konovalov@u
 Olexandr Konovalov <obk1@st-andrews.ac.uk> Alexander Konovalov <alexk@mcs.st-andrews.ac.uk>
 Olexandr Konovalov <obk1@st-andrews.ac.uk> Olexandr Konovalov <5751387+olexandr-konovalov@users.noreply.github.com>
 Artemis Konstantinidi <ak316@st-andrews.ac.uk> artemiskonst <97620468+artemiskonst@users.noreply.github.com>
+Hyeokjun Kwon <hk78@st-andrews.ac.uk> Hyeokjun Kwon <rnjsgurwns27@gmail.com>
 James Mitchell <jdm3@st-andrews.ac.uk> <jdm3@st-and.ac.uk>
 James Mitchell <jdm3@st-andrews.ac.uk> <jdm3@st-andrews.ac.uk>
 James Mitchell <jdm3@st-andrews.ac.uk> <jenkyfunds@gmail.com>
@@ -39,6 +43,7 @@ Chris Wensley <cdwensley.maths@btinternet.com> cdwensley <cdwensley.maths@btinte
 Murray Whyte <mw231@st-andrews.ac.uk> Murray Whyte <42549861+MTWhyte@users.noreply.github.com>
 Wilf Wilson <gap@wilf-wilson.net> Wilf Wilson <wilf@wilf-wilson.net>
 Wilf Wilson <gap@wilf-wilson.net> wilfwilson <wilf@wilf-wilson.net>
+Tianrun Yang <ty39@st-andrews.ac.uk> Tianrun Yang <117233646+Tianrun-Y@users.noreply.github.com>
 Michael Young <mct25@st-andrews.ac.uk> <mct25@st-andrews.ac.uk>
 Michael Young <mct25@st-andrews.ac.uk> <mtorpey@mtorpey-debtest>
 Michael Young <mct25@st-andrews.ac.uk> mct25 <unknown>

CHANGELOG.md

@@ -3,6 +3,23 @@ Copyright © 2011-2024 [James D. Mitchell][] et al.
 
 Licensing information can be found in the `LICENSE` file.
 
+## Version 5.4.0 (released 19/10/2024)
+
+## What's Changed
+
+* Improved IsIsomorphicSemigroup Method by @awesometillman in https://github.com/semigroups/Semigroups/pull/1023
+* fix typo in nambooripad partial order documentation by @Tianrun-Y in https://github.com/semigroups/Semigroups/pull/1030
+* Better kernel module checking by @Joseph-Edwards in https://github.com/semigroups/Semigroups/pull/1032
+* Fix ChooseHashFunction rank issue. by @reiniscirpons in https://github.com/semigroups/Semigroups/pull/1035
+* kernel: Semigroups can be used in GAP on julia by @james-d-mitchell in https://github.com/semigroups/Semigroups/pull/1036
+* Use LoadKernelExtension for gapbind_demo by @fingolfin in https://github.com/semigroups/Semigroups/pull/1039
+
+## New Contributors
+* @awesometillman made their first contribution in https://github.com/semigroups/Semigroups/pull/1023
+* @Tianrun-Y made their first contribution in https://github.com/semigroups/Semigroups/pull/1030
+
+**Full Changelog**: https://github.com/semigroups/Semigroups/compare/v5.3.7...v5.4.0
+
 ## Version 5.3.7 (released 11/03/2024)
 
 This is a minor release with some changes for compatibility with GAP.

GNUmakefile.in

@@ -101,7 +101,7 @@ lint:
 	etc/cpplint.sh
 
 format:
-	clang-format -i src/*.[hc]
+	clang-format -i src/*.*pp
 
 .PHONY: lint format
 

PackageInfo.g

@@ -34,8 +34,8 @@ _STANDREWSCS := Concatenation(["Jack Cole Building, North Haugh, ",
 SetPackageInfo(rec(
 PackageName := "Semigroups",
 Subtitle := "A package for semigroups and monoids",
-Version := "5.3.7",
-Date := "11/03/2024",  # dd/mm/yyyy format
+Version := "5.4.0",
+Date := "19/10/2024",  # dd/mm/yyyy format
 License := "GPL-3.0-or-later",
 
 ArchiveFormats := ".tar.gz",
@@ -71,11 +71,10 @@ Persons := [
     FirstNames    := "Marina",
     IsAuthor      := true,
     IsMaintainer  := false,
-    Email         := "mam49@st-andrews.ac.uk",
-    PostalAddress := _STANDREWSMATHS,
-    Place         := "St Andrews",
-    Institution   := "University of St Andrews",
-    WWWHome       := "https://github.com/marinaanagno"),
+    Email         := "marina.anagnostopoulou-merkouri@bristol.ac.uk",
+    Place         := "Bristol",
+    Institution   := "University of Bristol",
+    WWWHome       := "https://marinaanagno.github.io"),
 
   rec(
     LastName      := "Breuer",
@@ -149,8 +148,14 @@ Persons := [
     FirstNames    := "Fernando",
     IsAuthor      := true,
     IsMaintainer  := false,
-    Email         := "ffloresbrito@gmail.com",
-    WWWHome       := "https://github.com/ffloresbrito"),
+    Email         := "ffloresbrito@gmail.com"),
+
+  rec(
+    LastName      := "Froehlich",
+    FirstNames    := "Tillman",
+    IsAuthor      := true,
+    IsMaintainer  := false,
+    Email         := "trf1@st-andrews.ac.uk"),
 
   rec(
     LastName      := "Ham",
@@ -167,7 +172,7 @@ Persons := [
     FirstNames    := "Robert",
     IsAuthor      := true,
     IsMaintainer  := false,
-    Email         := "hancock@informatik.uni-heidelberg.de",
+    Email         := "robert.hancock@maths.ox.ac.uk",
     WWWHome       := "https://sites.google.com/view/robert-hancock/"),
 
   rec(
@@ -210,11 +215,7 @@ Persons := [
     LastName      := "Nagpal",
     FirstNames    := "Chinmaya",
     IsAuthor      := true,
-    IsMaintainer  := false,
-    Email         := "chinmaya1011@gmail.com",
-    PostalAddress := _STANDREWSMATHS,
-    Place         := "St Andrews",
-    Institution   := "University of St Andrews"),
+    IsMaintainer  := false),
 
   rec(
     LastName      := "Konovalov",
@@ -231,11 +232,13 @@ Persons := [
     LastName      := "Konstantinidi",
     FirstNames    := "Artemis",
     IsAuthor      := true,
-    IsMaintainer  := false,
-    Email         := "ak316@st-andrews.ac.uk",
-    PostalAddress := _STANDREWSMATHS,
-    Place         := "St Andrews",
-    Institution   := "University of St Andrews"),
+    IsMaintainer  := false),
+
+  rec(
+    LastName      := "Kwon",
+    FirstNames    := "Hyeokjun",
+    IsAuthor      := true,
+    IsMaintainer  := false),
 
   rec(
     LastName      := "Pasechnik",
@@ -257,7 +260,7 @@ Persons := [
     IsAuthor      := true,
     IsMaintainer  := false,
     Email         := "markus.pfeiffer@morphism.de",
-    WWWHome       := "https://www.morphism.de/~markusp/"),
+    WWWHome       := "https://markusp.morphism.de/"),
 
   rec(
     LastName      := "Russell",
@@ -295,8 +298,7 @@ Persons := [
     LastName      := "Spiers",
     FirstNames    := "Ben",
     IsAuthor      := true,
-    IsMaintainer  := false,
-    Email         := "bspiers972@outlook.com"),
+    IsMaintainer  := false),
 
   rec(
     LastName      := "Thiéry",
@@ -344,6 +346,12 @@ Persons := [
      Email         := "gap@wilf-wilson.net",
      WWWHome       := "https://wilf.me"),
 
+   rec(
+     LastName      := "Yang",
+     FirstNames    := "Tianrun",
+     IsAuthor      := true,
+     IsMaintainer  := false),
+
    rec(
      LastName      := "Young",
      FirstNames    := "Michael",
@@ -375,7 +383,7 @@ PackageDoc := rec(
 ),
 
 Dependencies := rec(
-  GAP := ">=4.12.0",
+  GAP := ">=4.12.1",
   NeededOtherPackages := [["datastructures", ">=0.2.5"],
                           ["digraphs", ">=1.6.2"],
                           ["genss", ">=1.6.5"],
@@ -406,13 +414,10 @@ BannerString := Concatenation(
   "------\n"),
 
 AvailabilityTest := function()
-  local semigroups_so;
-  semigroups_so := Filename(DirectoriesPackagePrograms("semigroups"),
-                            "semigroups.so");
-  if (not "semigroups" in SHOW_STAT()) and semigroups_so = fail then
+  if not IsKernelExtensionAvailable("semigroups") then
     LogPackageLoadingMessage(PACKAGE_WARNING,
-                             "the kernel module is not compiled, ",
-                             "the package cannot be loaded.");
+                             ["the kernel module is not compiled, ",
+                              "the package cannot be loaded."]);
     return fail;
   fi;
   return true;

VERSIONS

@@ -9,6 +9,7 @@
 ##
 ##
 
+release 5.4.0  - 19/10/2024
 release 5.3.7  - 11/03/2024
 release 5.3.6  - 19/02/2024
 release 5.3.5  - 14/02/2024

doc/attr.xml

@@ -1292,7 +1292,7 @@ true]]></Example>
 
     <C>NambooripadPartialOrder</C> returns the Nambooripad partial order on the
     regular semigroup <A>S</A> as a list of sets of positive integers where
-    entry <C>i</C> in <C>NaturalPartialOrder(<A>S</A>)</C> is the set of
+    entry <C>i</C> in <C>NambooripadPartialOrder(<A>S</A>)</C> is the set of
     positions in <C>Elements(<A>S</A>)</C> of elements which are less than
     <C>Elements(<A>S</A>)[i]</C>. See also <Ref
       Func="NambooripadLeqRegularSemigroup"/>.

etc/code-coverage-test-gap.py

@@ -64,19 +64,29 @@
 _DIR = tempfile.mkdtemp()
 print(f"{_INFO_PREFIX}Using temporary directory: {_DIR}\033[0m")
 
-_COMMANDS = 'echo "'
-_COMMANDS += "".join(rf"Test(\"{f}\");;\n" for f in _ARGS.tstfiles)
-_COMMANDS += rf"""UncoverageLineByLine();;
-LoadPackage(\"profiling\", false);;
-filesdir := \"{getcwd()}{_PROFILE_DIR}\";;\n"""
-
-_COMMANDS += rf"outdir := \"{_DIR}\";;\n"
-_COMMANDS += rf"x := ReadLineByLineProfile(\"{_DIR}/profile.gz\");;\n"
-_COMMANDS += 'OutputAnnotatedCodeCoverageFiles(x, filesdir, outdir);"'
+# Raw strings are used to correctly escape quotes " for input in another
+# process, i.e. we explicitly need the string to contain \" instead of just "
+# for each quote.
+_GAP_COMMANDS = [rf"Test(\"{f}\");;" for f in _ARGS.tstfiles]
+_GAP_COMMANDS.extend(
+    [
+        "UncoverageLineByLine();;",
+        rf"LoadPackage(\"profiling\", false);;",
+        rf"filesdir := \"{getcwd()}{_PROFILE_DIR}\";;",
+        rf"outdir := \"{_DIR}\";;",
+        rf"x := ReadLineByLineProfile(\"{_DIR}/profile.gz\");;",
+        "OutputAnnotatedCodeCoverageFiles(x, filesdir, outdir);",
+    ]
+)
 
 _RUN_GAP = f"{_ARGS.gap_root}/gap -A -m 1g -T --cover {_DIR}/profile.gz"
 
-with subprocess.Popen(_COMMANDS, stdout=subprocess.PIPE, shell=True) as pro1:
+# Commands are stored in a list and then joined with "\n" since including
+# newlines directly in raw strings cause issues when piping into GAP on some
+# platforms.
+with subprocess.Popen(
+    'echo "' + "\n".join(_GAP_COMMANDS) + '"', stdout=subprocess.PIPE, shell=True
+) as pro1:
     try:
         with subprocess.Popen(_RUN_GAP, stdin=pro1.stdout, shell=True) as pro2:
             pro2.wait()

etc/cpplint.sh

@@ -1,4 +1,4 @@
 #!/bin/bash
 set -e
 
-cpplint src/*.hpp src/*.h src/*.cpp
+cpplint src/*.*pp

gap/attributes/properties.gd

@@ -44,7 +44,7 @@ DeclareOperation("IsNormalInverseSubsemigroup",
                  [IsInverseSemigroup, IsInverseSemigroup]);
 
 if not IsBoundGlobal("IsSelfDualSemigroup") then
-  DeclareProperty("IsSelfDualSemigroup", IsSemigroup and CanUseFroidurePin);
+  DeclareProperty("IsSelfDualSemigroup", IsSemigroup);
 fi;
 
 DeclareSynonymAttr("IsRectangularGroup",

gap/attributes/rms-translat.gi

@@ -736,7 +736,7 @@ function(T)
   od;
 
   for a in group_gens do
-    fa := function(x)
+    fa := function(x)  # gaplint: disable=W047
       if x = 1 then
         return a;
       fi;

gap/elements/maxplusmat.gi

@@ -196,18 +196,9 @@ end);
 InstallMethod(UnweightedPrecedenceDigraph, "for a max-plus matrix",
 [IsMaxPlusMatrix],
 function(mat)
-  local adj;
-  # Auxiliary function used to compute the adjacency matrix of the precedence
-  # digraph
-  adj := function(i, j)
-    if mat[i][j] = -infinity then
-      return false;
-    else
-      return true;
-    fi;
-  end;
   # Generate and return digraph object
-  return Digraph([1 .. DimensionOfMatrixOverSemiring(mat)], adj);
+  return Digraph([1 .. DimensionOfMatrixOverSemiring(mat)],
+                 {i, j} -> mat[i][j] <> -infinity);
 end);
 
 ## Method from lemma 19, page 36, of:

gap/libsemigroups/cong.gi

@@ -417,7 +417,7 @@ function(cong, elm)
   elif IsFpSemigroup(Range(cong))
       or (HasIsFreeSemigroup(Range(cong)) and IsFreeSemigroup(Range(cong)))
       or IsFpMonoid(Range(cong))
-      or (HasIsFreeSemigroup(Range(cong)) and IsFreeMonoid(Range(cong)))
+      or (HasIsFreeMonoid(Range(cong)) and IsFreeMonoid(Range(cong)))
       or IsQuotientSemigroup(Range(cong)) then
     part := EquivalenceRelationPartition(cong);
     pos := PositionProperty(part, l -> [elm, l[1]] in cong);