Merge pull request #1 from gap-system/master

Get updates from parent repository

.travis.yml

@@ -2,29 +2,37 @@ language: c
 matrix:
   include:
     - os: linux
-      env: TEST_SUITE=testtravis
+      env: TEST_SUITE=testinstall CFLAGS="-fprofile-arcs -ftest-coverage" LDFLAGS="-fprofile-arcs"
       compiler: gcc
       addons:
         apt_packages:
           - libgmp-dev
-    - os: osx
-      env: TEST_SUITE=testtravis
-      compiler: clang
-      addons:
-        apt_packages:
-         - libgmp-dev
+      after_success:
+          - bash <(curl -s https://codecov.io/bash)
     - os: linux
-      env: TEST_SUITE=testinstall
+      env: TEST_SUITE=testtravis CFLAGS="-fprofile-arcs -ftest-coverage" LDFLAGS="-fprofile-arcs"
       compiler: gcc
+      addons:
+        apt_packages:
+          - libgmp-dev
+      after_success:
+          - bash <(curl -s https://codecov.io/bash)
+    - os: osx
+      env: TEST_SUITE=testtravis CFLAGS="-fprofile-arcs -ftest-coverage" LDFLAGS="-fprofile-arcs"
+      compiler: clang
       addons:
         apt_packages:
          - libgmp-dev
+      after_success:
+          - bash <(curl -s https://codecov.io/bash)
     - os: linux
-      env: TEST_SUITE=testbugfix
+      env: TEST_SUITE=testbugfix  CFLAGS="-fprofile-arcs -ftest-coverage" LDFLAGS="-fprofile-arcs"
       compiler: gcc
       addons:
         apt_packages:
          - libgmp-dev
+      after_success:
+          - bash <(curl -s https://codecov.io/bash)
     - os: linux
       env: TEST_SUITE=makemanuals
       compiler: gcc
@@ -44,18 +52,16 @@ matrix:
         apt_packages:
           - libgmp-dev:i386
           - gcc-multilib
-    - os: linux
-      env: TEST_SUITE=testinstall ABI=32
-      compiler: gcc
-      addons: 
-        apt_packages:
-          - libgmp-dev:i386
-          - gcc-multilib
-
+      after_success:
+          - bash <(curl -s https://codecov.io/bash)
 
 script:
   - ./configure --with-gmp=system
   - make
   - make bootstrap-pkg-full
-  - if [ $TEST_SUITE = 'makemanuals' ]; then if [ $TRAVIS_OS_NAME = 'linux' ]; then make manuals ; cat doc/*/make_manuals.out ; if [ `cat doc/*/make_manuals.out | grep -c "manual.lab written"` != '3' ]; then echo "Build failed"; exit 1; fi; fi; fi
-  - if [ $TEST_SUITE != 'makemanuals' ]; then echo "Read(\"tst/${TEST_SUITE}.g\"); quit;" | sh bin/gap.sh | tee testlog.txt | grep --colour=always -E "########> Diff|$"; cat testlog.txt | tail -n 2 | grep "total"; ( ! grep "########> Diff" testlog.txt ); fi
+  - if [[ x"$ABI" != "x32" ]] ; then cd pkg/io* ; ./configure ; make ; cd ../.. ; cd pkg/profiling* ; ./configure ; make ; cd ../.. ; fi
+  - if [[ $TEST_SUITE = 'makemanuals' && $TRAVIS_OS_NAME = 'linux' ]]; then make manuals ; cat doc/*/make_manuals.out ; if [ `cat doc/*/make_manuals.out | grep -c "manual.lab written"` != '3' ]; then echo "Build failed"; exit 1; fi; fi
+  - if [[ $TEST_SUITE != 'makemanuals' && x"$ABI" != "x32" ]]; then echo "Read(\"tst/${TEST_SUITE}.g\"); quit;" | sh bin/gap.sh --cover coverage | tee testlog.txt | grep --colour=always -E "########> Diff|$" ; echo "CoverToJson(\"coverage\", \"coverage.json\"); quit;" | sh bin/gap.sh etc/cover2json.g ; cd bin/x86* ; gcov -o . ../../src/* ; cd ../.. ; cat testlog.txt | tail -n 2 | grep "total"; ( ! grep "########> Diff" testlog.txt ) ; fi
+  - if [[ $TEST_SUITE != 'makemanuals' && x"$ABI" = "x32" ]]; then echo "Read(\"tst/${TEST_SUITE}.g\"); quit;" | sh bin/gap.sh | tee testlog.txt | grep --colour=always -E "########> Diff|$" ; cat testlog.txt | tail -n 2 | grep "total"; ( ! grep "########> Diff" testlog.txt ) ; fi
+
+

README.md

@@ -1,4 +1,4 @@
-[![Build Status](https://travis-ci.org/gap-system/gap.svg?branch=master)](https://travis-ci.org/gap-system/gap)
+[![Build Status](https://travis-ci.org/gap-system/gap.svg?branch=master)](https://travis-ci.org/gap-system/gap) [![Code Coverage](https://codecov.io/github/gap-system/gap/coverage.svg?branch=master&token=)](https://codecov.io/gh/gap-system/gap)
 
 # What is GAP?
 

bin/BuildPackages.sh

@@ -78,23 +78,16 @@ build_carat() {
 # this out until a user complains.
 # It is not possible to move around compiled binaries because these have the
 # path to some data files burned in.
-tar xzpf carat-2.1b1.tgz
-rm -f bin
+zcat carat-2.1b1.tgz | tar pxf -
 ln -s carat-2.1b1/bin bin
-cd carat-2.1b1/functions
-# Install the include Gmp first.
-# (If you have already Gmp on your system, you can delete the file
-# gmp-*.tar.gz and delete the target 'Gmp' from the target 'ALL' in
-# carat-2.1b1/Makefile.)
-tar xzpf gmp-*.tar.gz
-cd ..
-$MAKE TOPDIR=`pwd` Links
-# Note that Gmp may use processor specific code, so this step may not be ok
-# for a network installation if you want to use the package on older computers
-# as well.
-$MAKE TOPDIR=`pwd` Gmp
-# And now the actual Carat programs.
-$MAKE TOPDIR=`pwd` CFLAGS='-O2'
+cd carat-2.1b1
+make TOPDIR=`pwd`
+chmod -R a+rX .
+cd bin
+aa=`./config.guess`
+for x in "`ls -d1 $GAPDIR/bin/${aa}*`"; do
+ ln -s "$aa" "`basename $x`"
+done
 )
 }
 

cnf/gac.in

@@ -129,6 +129,7 @@ OBJECTS="\
     plist.o \
     pperm.o \
     precord.o \
+    profile.o \
     range.o \
     rational.o \
     read.o \

codecov.yml

@@ -0,0 +1,21 @@
+coverage:
+  precision: 2
+  round: down
+  range: "70...100"
+
+  status:
+    project:
+      default:
+        target: auto
+        if_no_uploads: error
+
+    patch:
+      default:
+        if_no_uploads: error
+
+    changes: true
+
+
+comment:
+  layout: "header, diff, changes, suggestions"
+  behavior: default

doc/changes/changes48.xml

@@ -362,6 +362,117 @@ Fix for using Firefox as a default help viewer with
 </Subsection>
 </Section>
 
+<Section Label="gap484">
+<Heading>&GAP; 4.8.4 (June 2016)</Heading>
+
+<Subsection Label="Changes in the core GAP system introduced in GAP 4.8.4">
+<Heading>Changes in the core &GAP; system introduced in &GAP; 4.8.4</Heading>
+
+New features:
+<List>
+<Item>
+<!-- #737 -->
+The &GAP; distribution now includes <F>bin/BuildPackages.sh</F>, a script which
+can be started from the <F>pkg</F> directory via <C>../bin/BuildPackages.sh</C>
+and will attempt to build as many packages as possible. It replaces the
+<F>InstPackages.sh</F> script which was not a part of the &GAP; distribution
+and had to be downloaded separately from the &GAP; website. The new script is
+more robust and simplifies adding new packages with binaries, as it requires no
+adjustments if the new package supports the standard <C>./configure; make</C>
+build procedure.
+</Item>
+</List>
+
+Improved and extended functionality:
+<List>
+<Item>
+<!-- #678 -->
+<Ref Func="SimpleGroup" BookName="ref"/> now produces more informative error
+message in the case when <Ref Func="AtlasGroup" BookName="AtlasRep"/> could
+not load the requested group.
+</Item>
+<Item>
+<!-- #610 -->
+An info message with the suggestion to use
+<Ref InfoClass="InfoPackageLoading" BookName="ref"/> will now be displayed
+when <Ref Func="LoadPackage" BookName="ref"/> returns <K>fail</K>
+(unless &GAP; is started with <C>-b</C> option).
+</Item>
+<Item>
+<!-- #728 -->
+The build system will now enable C++ support in GMP
+only if a working C++ compiler is detected.
+</Item>
+<Item>
+<!-- #757 -->
+More checks were added when embedding coefficient rings or rational numbers
+into polynomial rings in order to forbid adding polynomials in different
+characteristic.
+</Item>
+</List>
+
+Fixed bugs that could lead to crashes:
+<List>
+<Item>
+<!-- #685 -->
+Fixed the crash in <C>--cover</C> mode when reading files
+with more than 65,536 lines.
+</Item>
+</List>
+
+Fixed bugs that could lead to incorrect results:
+<List>
+<Item>
+<!-- #741 -->
+Fixed an error in the code for partial permutations that
+occurred on big-endian systems. [Reported by Bill Allombert]
+</Item>
+<Item>
+<!-- #766 -->
+Fixed the kernel method for <Ref Oper="Remove" BookName="ref"/> with
+one argument, which failed to reduce the length of a list to the
+position of the last bound entry. [Reported by Peter Schauenburg]
+</Item>
+</List>
+
+Fixed bugs that could lead to break loops:
+<List>
+<Item>
+<!-- #679 -->
+Fixed the break loop while using <Ref Oper="Factorization" BookName="ref"/>
+on permutation groups by removing some old code that relied on further caching
+in <C>Factorization</C>. [Reported by Grahame Erskine]
+</Item>
+<Item>
+<!-- #681 -->
+Fixed a problem with computation of maximal subgroups in an almost
+simple group. [Reported by Ramon Esteban Romero]
+</Item>
+<Item>
+<!-- #773 -->
+Added missing methods for <Ref Oper="Intersection2" BookName="ref"/>
+when one of the arguments is an empty list. [Reported by Wilf Wilson]
+</Item>
+</List>
+
+Other fixed bugs:
+<List>
+<Item>
+<!-- #770 -->
+Fixed several bugs in <Ref Func="RandomPrimitivePolynomial" BookName="ref"/>.
+[Reported by Nusa Zidaric]
+</Item>
+<Item>
+<!-- #781 -->
+Fixed several problems with <Ref Oper="Random" BookName="ref"/>
+on long lists in 64-bit GAP installations.
+</Item>
+</List>
+
+</Subsection>
+
+</Section>
+
 </Chapter>
 
 

doc/manualbib.xml

@@ -1470,6 +1470,30 @@
   <other type="pages">xx+1028</other>
 </book></entry>
 
+<entry id="CRDQ11"><article>
+  <author>
+    <name><first>Hannah J.</first><last>Coutts</last></name>
+  </author>
+  <author>
+    <name><first>Colva M.</first><last>Roney-Dougal</last></name>
+  </author>
+  <author>
+    <name><first>Martyn</first><last>Quick</last></name>
+  </author>
+  <title>The primitive permutation groups of degree less than 4096</title>
+  <journal><value key="comma2"/></journal>
+  <year>2011</year>
+  <volume>39</volume>
+  <number>10</number>
+  <pages>3526&ndash;3546</pages>
+  <issn>0092-7872</issn>
+  <mrnumber>2845584</mrnumber>
+  <mrclass>20B15</mrclass>
+  <mrreviewer>Thomas Michael Keller</mrreviewer>
+  <other type="coden">COALDM</other>
+  <other type="fjournal">Communications in Algebra</other>
+</article></entry>
+
 <entry id="coxlittleoshea"><book>
   <author>
     <name><first>David</first><last>Cox</last></name>

doc/ref/grplib.xml

@@ -702,7 +702,7 @@ together with a serial number if this is necessary to make it unique.
 
 <Description>
 In <Cite Key="DixonMortimer88"/> the primitive groups are sorted in
-<Q>cohorts</Q> according to their socle. For each degree, the variable
+<Q>cohorts</Q> according to their socle. For each degree less than 2500, the variable
 <Ref Var="COHORTS_PRIMITIVE_GROUPS"/> contains a list of the cohorts
 for the primitive groups of this degree. Each cohort is represented by a
 list of length 2, the first entry specifies the socle type (see

doc/ref/testconsistency.g

@@ -101,13 +101,20 @@ for elt in x do
     else
       obj := EvalString( name );
       man := ManSectionType( obj );
-      # we allow to use "Meth" for "Oper" but probably should issue a warning
-      # if there is no at least one "Oper" for any "Meth"
+      # we allow to use "Meth" for "Oper", "Attr", "Prop" but issue a warning
+      # if there is no at least one "Oper", "Attr" or "Prop" for any "Meth"
       if ( man <> elt.name ) and not ( man in ["Attr","Prop","Oper"] and elt.name="Meth") then
         pos:=OriginalPositionDocument(doc[2],elt.start);
         Print( pos[1], ":", pos[2], " : ", name, " uses ", elt.name, " instead of ", man, "\n");
         errcount:=errcount+1;
       fi;
+      if elt.name="Meth" then
+        if Length( Filtered( x, t -> t.attributes.Name=name and t.name in ["Attr","Prop","Oper"] ) ) = 0 then
+          pos:=OriginalPositionDocument(doc[2],elt.start);
+          Print( pos[1], ":", pos[2], " : ", name, " uses Meth with no matching Oper/Attr/Prop\n" );
+          errcount:=errcount+1;
+        fi;
+      fi;
     fi;
   fi;
 od;

doc/tut/group.xml

@@ -697,8 +697,9 @@ Actually there  is a third  block system of <C>a8_56</C>  that gives rise to a
 third subgroup.
 <P/>
 <Example><![CDATA[
-gap> blocks := Blocks( a8_56, [1..56], [1,13] );;
-gap> u28_56 := Stabilizer( a8_56, [1,13], OnSets );;
+gap> seed:=First(AllBlocks(a8_56),x->Length(x)=2);;
+gap> blocks := Blocks( a8_56, [1..56], seed);;
+gap> u28_56 := Stabilizer( a8_56, seed, OnSets );;
 gap> u28 := PreImages( h56, u28_56 );;
 gap> Index( a8, u28 );
 28
@@ -831,9 +832,9 @@ usual way we now look for the subgroups above <C>u105</C>.
 gap> blocks := Blocks( a8, orb );; Length( blocks );
 15
 gap> blocks[1];
-[ (1,2)(3,4)(5,6)(7,8), (1,3)(2,4)(5,7)(6,8), (1,4)(2,3)(5,8)(6,7), 
-  (1,5)(2,6)(3,7)(4,8), (1,6)(2,5)(3,8)(4,7), (1,7)(2,8)(3,5)(4,6), 
-  (1,8)(2,7)(3,6)(4,5) ]
+[ (1,2)(3,4)(5,6)(7,8), (1,3)(2,4)(5,8)(6,7), (1,4)(2,3)(5,7)(6,8), 
+  (1,5)(2,6)(3,8)(4,7), (1,6)(2,5)(3,7)(4,8), (1,7)(2,8)(3,6)(4,5), 
+  (1,8)(2,7)(3,5)(4,6) ]
 ]]></Example>
 <P/>
 To find the subgroup of index 15 we  again use closure. Now  we must be a
@@ -1174,7 +1175,7 @@ gap> niceaut := NiceObject( aut );
 Group([ (1,4,2,3), (1,5,4)(2,6,3), (1,2)(3,4), (3,4)(5,6) ])
 gap> IsomorphismGroups( niceaut, SymmetricGroup( 4 ) );
 [ (1,4,2,3), (1,5,4)(2,6,3), (1,2)(3,4), (3,4)(5,6) ] -> 
-[ (1,2,4,3), (1,2,3), (1,4)(2,3), (1,2)(3,4) ]
+[ (1,4,3,2), (1,4,2), (1,3)(2,4), (1,4)(2,3) ]
 ]]></Example>
 <P/>
 The range of  a nice monomorphism is  in most cases a permutation  group,