Merge stable-1.6 into main

.VERSION

@@ -1 +1 @@
-1.6.2
+1.6.3

.codespellrc

@@ -0,0 +1,3 @@
+[codespell]
+skip = ./.git,./tmp,./data,./extern,./tst,./bin,./libtool,configure,configure~,./gh-pages,./autom4te.cache,./cnf,aclocal.m4,./m4,./doc/*.log,./doc/*.html,./doc/*.txt,./doc/*.six,./doc/*.js,./doc/*.bbl,./doc/*.tex,./doc/*.bib
+ignore-words-list=ist,manuel,MIS,mis

.github/workflows/codespell.yml

@@ -0,0 +1,14 @@
+name: codespell
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+      - stable-*.*
+jobs:
+  codespell:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: codespell-project/actions-codespell@v2

.github/workflows/gap.yml

@@ -3,6 +3,9 @@ on:
   workflow_dispatch:
   pull_request:
   push:
+    branches:
+      - main
+      - stable-*.*
   schedule:
     # Every day at 3:30 AM UTC
     - cron: '30 3 * * *'
@@ -14,8 +17,6 @@ jobs:
   test-unix:
     name: "${{ matrix.os }}${{ matrix.ABI }} / GAP ${{ matrix.gap-branch }}"
     runs-on: "${{ matrix.os }}-latest"
-    # Don't run this twice for PRs from branches in the same repository
-    if: ${{ !(github.event_name == 'pull_request' && github.event.pull_request.head.repo.full_name == github.repository) }}
     strategy:
       fail-fast: false
       matrix:
@@ -61,34 +62,27 @@ jobs:
           curl --retry 5 -L -O "https://digraphs.github.io/Digraphs/${{ env.DIGRAPHS_LIB }}.tar.gz"
           tar xf "${{ env.DIGRAPHS_LIB }}.tar.gz"
       - name: "Run DigraphsTestInstall"
-        if: ${{ always() }}
         uses: gap-actions/run-pkg-tests@v2
         with:
           GAP_TESTFILE: "tst/github_actions/install.g"
       - name: "Run DigraphsTestStandard"
-        if: ${{ always() }}
         uses: gap-actions/run-pkg-tests@v2
         with:
           GAP_TESTFILE: "tst/github_actions/standard.g"
       - name: "Run DigraphsTestManualExamples"
-        if: ${{ always() }}
         uses: gap-actions/run-pkg-tests@v2
         with:
           GAP_TESTFILE: "tst/github_actions/examples.g"
       - name: "Run DigraphsTestExtreme"
-        if: ${{ always() }}
         uses: gap-actions/run-pkg-tests@v2
         with:
           GAP_TESTFILE: "tst/github_actions/extreme.g"
       - uses: gap-actions/process-coverage@v2
-        if: ${{ always() }}
       - uses: codecov/codecov-action@v3
-        if: ${{ always() }}
 
   test-cygwin:
     name: "cygwin / GAP master"
     runs-on: windows-2019
-    if: ${{ !(github.event_name == 'pull_request' && github.event.pull_request.head.repo.full_name == github.repository) }}
     env:
       CHERE_INVOKING: 1
     steps:

.github/workflows/lint.yml

@@ -3,6 +3,9 @@ on:
   workflow_dispatch:
   pull_request:
   push:
+    branches:
+      - main
+      - stable-*.*
   schedule:
     # Every day at 3:30 AM UTC
     - cron: '30 3 * * *'
@@ -11,8 +14,6 @@ jobs:
   lint:
     name: "${{ matrix.linter }}"
     runs-on: ubuntu-latest
-    # Don't run this twice for PRs from branches in the same repository
-    if: ${{ !(github.event_name == 'pull_request' && github.event.pull_request.head.repo.full_name == github.repository) }}
     strategy:
       fail-fast: false
       matrix:

.github/workflows/manual.yml

@@ -3,6 +3,9 @@ on:
   workflow_dispatch:
   pull_request:
   push:
+    branches:
+      - main
+      - stable-*.*
   schedule:
     # Every day at 3:20 AM UTC
     - cron: '20 3 * * *'
@@ -11,8 +14,6 @@ jobs:
   manual:
     name: "compile and upload manual"
     runs-on: ubuntu-latest
-    # Don't run this twice for PRs from branches in the same repository
-    if: ${{ !(github.event_name == 'pull_request' && github.event.pull_request.head.repo.full_name == github.repository) }}
     steps:
       - uses: actions/checkout@v3
       - name: "Install TeX Live"

CHANGELOG.md

@@ -4,6 +4,21 @@ Wilf A. Wilson, Michael Young et al.
 
 Licensing information can be found in the `LICENSE` file.
 
+## Version 1.6.3 (released 13/09/2023)
+
+This is a minor release with some bug fixes, and other issues resolved:
+
+* There was a minor bug in the `RandomDigraph` method for `IsEulerianDigraph`,
+  resolved by @mtorpey
+* Joe Edwards and Maria Tsalakou were incorrectly listed as authors resolved
+  partially by @james-d-mitchell in https://github.com/digraphs/Digraphs/pull/576
+* Standardise the way that `UndirectedSpanningForest` works in relation to
+  mutability by @wilfwilson in https://github.com/digraphs/Digraphs/pull/582
+* Add immediate methods for connected and strongly connected digraphs by
+  @mtorpey
+* There was a minor memory leak in the kernel extension resolved by
+  @james-d-mitchell
+
 ## Version 1.6.2 (released 05/04/2023)
 
 * PackageInfo.g: link to Mathjax manual by default by @fingolfin in

PackageInfo.g

@@ -9,7 +9,7 @@
 ##
 
 ##  <#GAPDoc Label="PKGVERSIONDATA">
-##  <!ENTITY VERSION                  "1.6.2">
+##  <!ENTITY VERSION                  "1.6.3">
 ##  <!ENTITY GAPVERS                  "4.10.0">
 ##  <!ENTITY GRAPEVERS                "4.8.1">
 ##  <!ENTITY IOVERS                   "4.5.1">
@@ -28,8 +28,8 @@ _STANDREWSCS := Concatenation(["Jack Cole Building, North Haugh, ",
 SetPackageInfo(rec(
 PackageName := "Digraphs",
 Subtitle := "Graphs, digraphs, and multidigraphs in GAP",
-Version := "1.6.2",
-Date := "05/04/2023",  # dd/mm/yyyy format
+Version := "1.6.3",
+Date := "13/09/2023",  # dd/mm/yyyy format
 License := "GPL-3.0-or-later",
 ArchiveFormats := ".tar.gz",
 
@@ -122,7 +122,7 @@ Persons := [
   rec(
     LastName      := "Edwards",
     FirstNames    := "Joe",
-    IsAuthor      := true,
+    IsAuthor      := false,
     IsMaintainer  := false,
     Email         := "je53@st-andrews.ac.uk",
     PostalAddress := _STANDREWSMATHS,
@@ -304,7 +304,7 @@ Persons := [
   rec(
     LastName      := "Tsalakou",
     FirstNames    := "Maria",
-    IsAuthor      := true,
+    IsAuthor      := false,
     IsMaintainer  := false,
     Email         := "mt200@st-andrews.ac.uk",
     WWWHome       := "https://mariatsalakou.github.io/",

VERSIONS

@@ -8,6 +8,7 @@
 #############################################################################
 ##
 
+release 1.6.3 - 13/09/2023
 release 1.6.2 - 05/04/2023
 release 1.6.1 - 06/12/2022
 release 1.6.0 - 08/09/2022

ci/coverage.py

@@ -38,7 +38,7 @@ def warn_exit(msg):
 QUIT_GAP(0);
 '''
 
-_RUN_GAP = '../../bin/gap.sh -A -q -m 1g -o 2g -T --cover ' + _DIR + '/profile.gz -c "' + _COMMANDS.replace('"', '\\"') + '"'
+_RUN_GAP = '../../gap -A -q -m 1g -o 2g -T --cover ' + _DIR + '/profile.gz -c "' + _COMMANDS.replace('"', '\\"') + '"'
 
 try:
     pro = subprocess.Popen(_RUN_GAP, shell=True)

ci/docker-test.sh

@@ -58,7 +58,7 @@ env | grep -v "^LS_COLORS"
 # Common curl settings
 CURL="curl --connect-timeout 5 --max-time 40 --retry 5 --retry-delay 0  -L"
 TESTLOG="$GAP_HOME/testlog.txt"
-GAPSH="$GAP_HOME/bin/gap.sh"
+GAPSH="$GAP_HOME/gap"
 DIG_DIR="$GAP_HOME/pkg/digraphs"
 
 ################################################################################

doc/main.xml

@@ -41,7 +41,7 @@
   <#Include SYSTEM="z-chap0.xml"> <!-- intro -->
   <#Include SYSTEM="z-chap1.xml"> <!-- installing -->
   <#Include SYSTEM="z-chap2.xml"> <!-- creating -->
-  <#Include SYSTEM="z-chap3.xml"> <!-- operators/hashs -->
+  <#Include SYSTEM="z-chap3.xml"> <!-- operators/hashes -->
   <#Include SYSTEM="z-chap4.xml"> <!-- attributes, operations -->
   <#Include SYSTEM="z-chap5.xml"> <!-- properties -->
   <#Include SYSTEM="z-chap6.xml"> <!-- homomorphisms -->

doc/z-chap9.xml

@@ -50,7 +50,7 @@
       <Item>
 	<E>DiSparse6</E> is a new format based on <E> Sparse6 </E>, but
 	designed for digraphs. In this format the list of edges is
-	partitioned into inceasing and decreasing edges, depending whether the
+	partitioned into increasing and decreasing edges, depending whether the
 	edge has its source bigger than the range. Then both sets of edges are
 	written separately in <E> Sparse6 </E> format with a separation symbol
 	in between.

etc/tst-local-vars.py

@@ -0,0 +1,40 @@
+#!/usr/bin/env python3
+"""
+This simple script adds the local variables used in a GAP tst file to the top
+of the file.
+"""
+import os
+import re
+import sys
+import textwrap
+
+import yaml
+from bs4 import BeautifulSoup
+
+
+def main():
+    if sys.version_info[0] < 3:
+        raise Exception("Python 3 is required")
+    args = sys.argv[1:]
+    pattern1 = re.compile(r"(\w+)\s*:=")
+    pattern2 = re.compile(r"for (\w+) in")
+    for fname in args:
+        lvars = []
+        with open(fname, "r") as f:
+            lines = f.read()
+            lvars.extend([x.group(1) for x in re.finditer(pattern1, lines)])
+            lvars.extend([x.group(1) for x in re.finditer(pattern2, lines)])
+        lvars = ", ".join(sorted([*{*lvars}]))
+        lvars = [x if x[-1] != "," else x[:-1] for x in textwrap.wrap(lvars, width=72)]
+        lvars = [""] + ["#@local " + x for x in lvars]
+        lines = lines.split("\n")
+        pos = next(i for i in range(len(lines)) if "START_TEST" in lines[i])
+        lines = lines[:pos] + lvars + lines[pos:]
+        lines = "\n".join(lines)
+        with open(fname, "w") as f:
+            print(f"Writing local variables to {fname}...")
+            f.write(lines)
+
+
+if __name__ == "__main__":
+    main()

etc/tst-unbind-local-vars.py

@@ -0,0 +1,49 @@
+#!/usr/bin/env python3
+"""
+This simple script adds the "Unbind" statements to the end of a GAP tst file.
+"""
+import os
+import re
+import sys
+import textwrap
+
+import yaml
+from bs4 import BeautifulSoup
+
+
+def main():
+    if sys.version_info[0] < 3:
+        raise Exception("Python 3 is required")
+    args = sys.argv[1:]
+    pattern1 = re.compile(r"(\w+)\s*:=")
+    pattern2 = re.compile(r"for (\w+) in")
+    for fname in args:
+        lvars = []
+        with open(fname, "r") as f:
+            lines = f.read()
+            lvars.extend([x.group(1) for x in re.finditer(pattern1, lines)])
+            lvars.extend([x.group(1) for x in re.finditer(pattern2, lines)])
+        lvars = sorted([*{*lvars}])
+        lvars = [
+            "# Unbind local variables, auto-generated by etc/tst-unbind-local-vars.py"
+        ] + [f"gap> Unbind({lvar});" for lvar in lvars]
+        lvars.append("")
+        lines = lines.split("\n")
+        pos1 = next(i for i in range(len(lines)) if "STOP_TEST" in lines[i]) - 1
+        try:
+            pos0 = next(
+                i
+                for i in range(len(lines))
+                if "etc/tst-unbind-local-vars.py" in lines[i]
+            )
+        except StopIteration:
+            pos0 = pos1
+        lines = lines[:pos0] + lvars + lines[pos1:]
+        lines = "\n".join(lines)
+        with open(fname, "w") as f:
+            print(f"Writing local variables to {fname}...")
+            f.write(lines)
+
+
+if __name__ == "__main__":
+    main()

gap/attr.gi

@@ -2341,36 +2341,38 @@ InstallMethod(DigraphReflexiveTransitiveReductionAttr,
 "for an immutable digraph",
 [IsImmutableDigraph], DigraphReflexiveTransitiveReduction);
 
-InstallMethod(UndirectedSpanningForest, "for a digraph by out-neighbours",
-[IsDigraphByOutNeighboursRep],
+InstallMethod(UndirectedSpanningForest,
+"for a mutable digraph by out-neighbours",
+[IsMutableDigraph and IsDigraphByOutNeighboursRep],
 function(D)
-  local C;
   if DigraphHasNoVertices(D) then
     return fail;
   fi;
-  C := MaximalSymmetricSubdigraph(D)!.OutNeighbours;
-  C := DIGRAPH_SYMMETRIC_SPANNING_FOREST(C);
-  if IsMutableDigraph(D) then
-    D!.OutNeighbours := C;
-    ClearDigraphEdgeLabels(D);
-    return D;
+  MaximalSymmetricSubdigraph(D);
+  D!.OutNeighbours := DIGRAPH_SYMMETRIC_SPANNING_FOREST(D!.OutNeighbours);
+  ClearDigraphEdgeLabels(D);
+  return D;
+end);
+
+InstallMethod(UndirectedSpanningForest, "for an immutable digraph",
+[IsImmutableDigraph], UndirectedSpanningForestAttr);
+
+InstallMethod(UndirectedSpanningForestAttr, "for an immutable digraph",
+[IsImmutableDigraph and IsDigraphByOutNeighboursRep],
+function(D)
+  local C;
+  if DigraphHasNoVertices(D) then
+    return fail;
   fi;
+  C := MaximalSymmetricSubdigraph(D);
+  C := DIGRAPH_SYMMETRIC_SPANNING_FOREST(C!.OutNeighbours);
   C := ConvertToImmutableDigraphNC(C);
-  SetUndirectedSpanningForestAttr(D, C);
   SetIsUndirectedForest(C, true);
   SetIsMultiDigraph(C, false);
   SetDigraphHasLoops(C, false);
   return C;
 end);
 
-InstallMethod(UndirectedSpanningForest,
-"for a digraph with known undirected spanning forest",
-[IsDigraph and HasUndirectedSpanningForestAttr], SUM_FLAGS,
-UndirectedSpanningForestAttr);
-
-InstallMethod(UndirectedSpanningForestAttr, "for an immutable digraph",
-[IsImmutableDigraph], UndirectedSpanningForest);
-
 InstallMethod(UndirectedSpanningTree, "for a mutable digraph",
 [IsMutableDigraph],
 function(D)

gap/labels.gi

@@ -57,7 +57,7 @@ InstallMethod(SetDigraphVertexLabels, "for a digraph and list",
 [IsDigraph, IsList],
 function(D, names)
   if Length(names) <> DigraphNrVertices(D) then
-    ErrorNoReturn("the 2nd arument <names> must be a list with length equal ",
+    ErrorNoReturn("the 2nd argument <names> must be a list with length equal ",
                   "to the number of vertices of the digraph <D> that is the ",
                   "1st argument,");
   fi;

scripts/check-code-coverage.sh

@@ -58,7 +58,7 @@ printf "\033[1m";
 printf "Running Test(\"$1\"); in GAP . . .\n"; 
 printf "\033[0m"; 
 printf "\033[2m";
-~/gap/bin/gap.sh -A -m 1g -T <<< "Test(\"$1\"); quit;";
+~/gap/gap -A -m 1g -T <<< "Test(\"$1\"); quit;";
 printf "\033[0m"; 
 
 printf "\033[1m";

src/schreier-sims.c

@@ -25,7 +25,7 @@ uint16_t PERM_DEGREE = 0;
 
 // Schreier-Sims set up
 
-SchreierSims* new_schreier_sims() {
+SchreierSims* new_schreier_sims(void) {
   SchreierSims* ss = malloc(sizeof(SchreierSims));
   ss->tmp_perm     = new_perm(MAXVERTS);
   for (uint16_t i = 0; i < MAXVERTS; ++i) {