Better dot

.github/workflows/ci.yml

@@ -50,9 +50,17 @@ jobs:
           # removed in the fullness of time.
           LDFLAGS: "-pthread"
         with:
-          GAP_PKGS_TO_BUILD: "digraphs io orb datastructures profiling"
+          GAP_PKGS_TO_BUILD: "Digraphs io orb datastructures profiling"
+          # TODO remove the following when graphviz is released
+          GAP_PKGS_TO_CLONE: "james-d-mitchell/Digraphs digraphs/graphviz"
           GAPBRANCH: ${{ matrix.gap-branch }}
           ABI: ${{ matrix.ABI }}
+      - name: "Checkout digraphs graphviz branch (TMP REMOVE)!"
+        run: |
+            cd $HOME/gap/pkg/Digraphs
+            git remote -v
+            git fetch origin graphviz --depth 1
+            git checkout graphviz
       - name: "Build Semigroups"
         uses: gap-actions/build-pkg@v1
         with:

PackageInfo.g

@@ -379,6 +379,7 @@ Dependencies := rec(
   NeededOtherPackages := [["datastructures", ">=0.2.5"],
                           ["digraphs", ">=1.6.2"],
                           ["genss", ">=1.6.5"],
+                          ["graphviz", ">=0.0.0"],
                           ["images", ">=1.3.1"],
                           ["IO", ">=4.5.1"],
                           ["orb", ">=4.8.2"]],

doc/display.xml

@@ -265,13 +265,15 @@ gap> FileString("t3.dot", DotString(S));
 gap> S := DualSymmetricInverseMonoid(4);
 <inverse block bijection monoid of degree 4 with 3 generators>
 gap> DotSemilatticeOfIdempotents(S);
-"//dot\ngraph graphname {\n  node [shape=point]\nranksep=2;\nsubgraph \
-cluster_1{\n15 \n}\nsubgraph cluster_2{\n5 11 14 12 13 8 \n}\nsubgraph\
- cluster_3{\n2 10 6 3 4 9 7 \n}\nsubgraph cluster_4{\n1 \n}\n2 -- 1\n3\
- -- 1\n4 -- 1\n5 -- 2\n5 -- 3\n5 -- 4\n6 -- 1\n7 -- 1\n8 -- 2\n8 -- 6\
-\n8 -- 7\n9 -- 1\n10 -- 1\n11 -- 2\n11 -- 9\n11 -- 10\n12 -- 3\n12 -- \
-6\n12 -- 9\n13 -- 3\n13 -- 7\n13 -- 10\n14 -- 4\n14 -- 6\n14 -- 10\n15\
- -- 5\n15 -- 8\n15 -- 11\n15 -- 12\n15 -- 13\n15 -- 14\n }"]]></Example>
+"//dot\ngraph semilattice {\n\tnode[shape=point] ranksep=2 \nsubgraph \
+cluster_1 {\n\t15\n}\nsubgraph cluster_2 {\n\t5\n\t11\n\t14\n\t12\n\t1\
+3\n\t8\n}\nsubgraph cluster_3 {\n\t2\n\t10\n\t6\n\t3\n\t4\n\t9\n\t7\n}\
+\nsubgraph cluster_4 {\n\t1\n}\n\t2 -- 1\n\t3 -- 1\n\t4 -- 1\n\t5 -- 2\
+\n\t5 -- 3\n\t5 -- 4\n\t6 -- 1\n\t7 -- 1\n\t8 -- 2\n\t8 -- 6\n\t8 -- 7\
+\n\t9 -- 1\n\t10 -- 1\n\t11 -- 2\n\t11 -- 9\n\t11 -- 10\n\t12 -- 3\n\t\
+12 -- 6\n\t12 -- 9\n\t13 -- 3\n\t13 -- 7\n\t13 -- 10\n\t14 -- 4\n\t14 \
+-- 6\n\t14 -- 10\n\t15 -- 5\n\t15 -- 8\n\t15 -- 11\n\t15 -- 12\n\t15 -\
+- 13\n\t15 -- 14\n}\n"]]></Example>
     </Description>
   </ManSection>
 <#/GAPDoc>

doc/semicons.xml

@@ -147,6 +147,61 @@ true]]></Example>
   </ManSection>
 <#/GAPDoc>
 
+<#GAPDoc Label="FreeSemilattice">
+  <ManSection>
+    <Func Name="FreeSemilattice" Arg="[filt, ] n"/>
+    <Returns>
+      A free semilattice with <A>n</A> generators.
+    </Returns>
+    <Description>
+      If <A>n</A> is a positive integer, then this function returns a free
+      semilattice with <A>n</A> generators in the representation given by the
+      filter <A>filt</A>.
+
+      The optional argument <A>filt</A> may be one of the following:
+      <List>
+        <Item><C>IsTransformationSemigroup</C>
+          (the default, if <A>filt</A> is not specified),</Item>
+        <Item><C>IsTransformationMonoid</C>,</Item>
+        <Item><C>IsPartialPermSemigroup</C>,</Item>
+        <Item><C>IsPartialPermMonoid</C>,</Item>
+        <Item><C>IsFpSemigroup</C>,</Item>
+        <Item><C>IsFpMonoid</C>,</Item>
+        <Item><C>IsBipartitionSemigroup</C>,</Item>
+        <Item><C>IsBipartitionMonoid</C>,</Item>
+        <Item><C>IsPBRSemigroup</C>,</Item>
+        <Item><C>IsPBRMonoid</C>,</Item>
+        <Item><C>IsBooleanMatSemigroup</C>,</Item>
+        <Item><C>IsBooleanMatMonoid</C>,</Item>
+        <Item><C>IsNTPMatrixSemigroup</C>,</Item>
+        <Item><C>IsNTPMatrixMonoid</C>,</Item>
+        <Item><C>IsMaxPlusMatrixSemigroup</C>,</Item>
+        <Item><C>IsMaxPlusMatrixMonoid</C>,</Item>
+        <Item><C>IsMinPlusMatrixSemigroup</C>,</Item>
+        <Item><C>IsMinPlusMatrixMonoid</C>,</Item>
+        <Item><C>IsTropicalMaxPlusMatrixSemigroup</C>,</Item>
+        <Item><C>IsTropicalMaxPlusMatrixMonoid</C>,</Item>
+        <Item><C>IsTropicalMinPlusMatrixSemigroup</C>,</Item>
+        <Item><C>IsTropicalMinPlusMatrixMonoid</C>,</Item>
+        <Item><C>IsProjectiveMaxPlusMatrixSemigroup</C>,</Item>
+        <Item><C>IsProjectiveMaxPlusMatrixMonoid</C>,</Item>
+        <Item><C>IsIntegerMatrixSemigroup.</C></Item>
+        <Item><C>IsIntegerMatrixMonoid.</C></Item>
+      </List>
+
+      <Example><![CDATA[
+gap> S := FreeSemilattice(IsTransformationSemigroup, 5);
+<inverse transformation semigroup of size 31, degree 6 with 5 
+ generators>
+gap> T := FreeSemilattice(IsPartialPermSemigroup, 3);
+<inverse partial perm semigroup of size 7, rank 3 with 3 generators>
+gap> U := FreeSemilattice(IsBooleanMatSemigroup, 4);
+<inverse semigroup of size 15, 5x5 boolean matrices with 4 generators>
+]]></Example>
+    </Description>
+  </ManSection>
+<#/GAPDoc>
+
 <#GAPDoc Label="ZeroSemigroup">
   <ManSection>
     <Func Name="ZeroSemigroup" Arg="[filt, ]n"/>

doc/z-chap07.xml

@@ -155,6 +155,7 @@
     <#Include Label = "TrivialSemigroup">
     <#Include Label = "MonogenicSemigroup">
     <#Include Label = "RectangularBand">
+    <#Include Label = "FreeSemilattice">
     <#Include Label = "ZeroSemigroup">
     <#Include Label = "LeftZeroSemigroup">
     <#Include Label = "BrandtSemigroup">

etc/code-coverage-test-gap.py

@@ -0,0 +1,117 @@
+#!/usr/bin/env python3
+"""
+"""
+
+import argparse, tempfile, subprocess, re, sys, os, webbrowser
+from os.path import exists, isdir, isfile
+
+_ERR_PREFIX = "\033[31mcode-coverage-test-gap.py: error: "
+_INFO_PREFIX = "\033[40;38;5;82m"
+
+_PARSER = argparse.ArgumentParser(
+    prog="code-coverage-test-gap.py", usage="%(prog)s [options]"
+)
+_PARSER.add_argument(
+    "tstfiles",
+    nargs="+",
+    type=str,
+    help="the test files you want to check code coverage for"
+    + "(must be at least one)",
+)
+_PARSER.add_argument(
+    "--gap-root",
+    nargs="?",
+    type=str,
+    help="the gap root directory (default: ~/gap)",
+    default="~/gap/",
+)
+_PARSER.add_argument(
+    "--open",
+    nargs="?",
+    type=str,
+    help=("open the html page for this file " + "(default: None)"),
+    default=None,
+)
+
+_ARGS = _PARSER.parse_args()
+if not _ARGS.gap_root[-1] == "/":
+    _ARGS.gap_root += "/"
+
+if exists("gap") and isdir("gap"):
+    _PROFILE_DIR = "/gap/"
+elif exists("lib") and isdir("lib"):
+    _PROFILE_DIR = "/lib/"
+else:
+    sys.exit(_ERR_PREFIX + "no directory gap or lib to profile!\033[0m")
+
+_ARGS.gap_root = os.path.expanduser(_ARGS.gap_root)
+if not (exists(_ARGS.gap_root) and isdir(_ARGS.gap_root)):
+    sys.exit(_ERR_PREFIX + "can't find GAP root directory!\033[0m")
+
+for f in _ARGS.tstfiles:
+    if not (exists(f) and isfile(f)):
+        sys.exit(_ERR_PREFIX + f + " does not exist!\033[0m")
+
+_DIR = tempfile.mkdtemp()
+print(f"{_INFO_PREFIX}Using temporary directory: {_DIR}\033[0m")
+
+_COMMANDS = 'echo "'
+for f in _ARGS.tstfiles:
+    _COMMANDS += f'Test(\\"{f}\\");;\n'
+_COMMANDS += (
+    '''UncoverageLineByLine();;
+LoadPackage(\\"profiling\\", false);;
+filesdir := \\"'''
+    + os.getcwd()
+    + _PROFILE_DIR
+    + """\\";;\n"""
+)
+_COMMANDS += 'outdir := \\"' + _DIR + '\\";;\n'
+_COMMANDS += 'x := ReadLineByLineProfile(\\"' + _DIR + '/profile.gz\\");;\n'
+_COMMANDS += 'OutputAnnotatedCodeCoverageFiles(x, filesdir, outdir);"'
+
+pro1 = subprocess.Popen(_COMMANDS, stdout=subprocess.PIPE, shell=True)
+_RUN_GAP = _ARGS.gap_root + "gap -A -m 1g -T --cover " + _DIR + "/profile.gz"
+
+try:
+    pro2 = subprocess.Popen(_RUN_GAP, stdin=pro1.stdout, shell=True)
+    pro2.wait()
+except KeyboardInterrupt:
+    pro1.terminate()
+    pro1.wait()
+    pro2.terminate()
+    pro2.wait()
+    sys.exit("\033[31mKilled!\033[0m")
+except (subprocess.CalledProcessError, IOError, OSError):
+    sys.exit(_ERR_PREFIX + "Something went wrong calling GAP!\033[0m")
+
+suffix = ""
+if _ARGS.open:
+    filename = (
+        _DIR
+        + "/"
+        + os.getcwd().replace("/", "_")
+        + "_"
+        + _ARGS.open.replace("/", "_")
+        + ".html"
+    )
+    p = re.compile(r"<tr class='missed'><td><a name=\"line(\d+)\">")
+    with open(filename, "r") as f:
+        m = p.search(f.read())
+        if m:
+            suffix += f"#line{m.group(1)}"
+else:
+    filename = _DIR + "/index.html"
+
+if exists(filename) and isfile(filename):
+    if _ARGS.open:
+        filename += suffix
+    try:
+        webbrowser.get("safari").open(f"file://{filename}", new=2)
+    except Exception:
+        webbrowser.open(f"file://{filename}", new=2)
+else:
+    sys.exit(f"\n{_ERR_PREFIX}Failed to open file://{filename}\033[0m")
+
+print(f"\n{_INFO_PREFIX}SUCCESS!\033[0m")
+sys.exit(0)

gap/attributes/factor.gd

@@ -15,3 +15,8 @@ DeclareOperation("NonTrivialFactorization",
 DeclareOperation("Factorization", [IsLambdaOrb, IsPosInt, IsPerm]);
 DeclareOperation("Factorization", [IsSemigroup, IsMultiplicativeElement]);
 DeclareOperation("TraceSchreierTreeForward", [IsSemigroupData, IsPosInt]);
+
+DeclareOperation("MonoidFactorization",
+                 [IsMonoid, IsMultiplicativeElementWithOne]);
+DeclareOperation("MinimalMonoidFactorization",
+                 [IsMonoid, IsMultiplicativeElementWithOne]);

gap/attributes/factor.gi

@@ -451,3 +451,34 @@ function(S, x)
 
   return word1;
 end);
+
+SEMIGROUPS._MonoidFactorization := function(M, word)
+  local pos, i;
+
+  pos := Position(GeneratorsOfSemigroup(M), One(M));
+  if pos = fail then
+    return word;
+  fi;
+  # Words are in terms of GeneratorsOfSemigroup(S) but we want it in terms of
+  # GeneratorsOfMonoid(S), so we have to normalise
+  i := 1;
+  while i <= Length(word) do
+    if word[i] = pos then
+      Remove(word, i);
+    else
+      if word[i] > pos then
+        word[i] := word[i] - 1;
+      fi;
+      i := i + 1;
+    fi;
+  od;
+  return word;
+end;
+
+InstallMethod(MonoidFactorization, "for a monoid and element-with-one",
+[IsMonoid, IsMultiplicativeElementWithOne],
+{M, x} -> SEMIGROUPS._MonoidFactorization(M, Factorization(M, x)));
+
+InstallMethod(MinimalMonoidFactorization, "for a monoid and element-with-one",
+[IsMonoid, IsMultiplicativeElementWithOne],
+{M, x} -> SEMIGROUPS._MonoidFactorization(M, MinimalFactorization(M, x)));

gap/congruences/congwordgraph.gi

@@ -10,6 +10,7 @@
 ## This file contains implementation for left, right, and two-sided
 ## congruences that are defined in terms of a IsWordGraph.
 
+# TODO promote this to a proper operation
 BindGlobal("_MonoidFactorization", function(M, x)
   local word, pos, i;
 

gap/semigroups/semicons.gd

@@ -12,6 +12,8 @@ DeclareGlobalFunction("TrivialSemigroup");
 DeclareConstructor("TrivialSemigroupCons", [IsSemigroup, IsInt]);
 DeclareGlobalFunction("RectangularBand");
 DeclareConstructor("RectangularBandCons", [IsSemigroup, IsPosInt, IsPosInt]);
+DeclareGlobalFunction("FreeSemilattice");
+DeclareConstructor("FreeSemilatticeCons", [IsSemigroup, IsPosInt]);
 DeclareGlobalFunction("MonogenicSemigroup");
 DeclareConstructor("MonogenicSemigroupCons", [IsSemigroup, IsPosInt, IsPosInt]);
 DeclareGlobalFunction("ZeroSemigroup");