GAP (changes) - Chapter 3: Changes between GAP 4.7 and GAP 4.8

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3 Changes between GAP 4.7 and GAP 4.8
3.1 GAP 4.8.2 (February 2016)
3.1-1 Changes in the core GAP system introduced in GAP 4.8
3.1-2 New and updated packages since GAP 4.7.8
3.2 GAP 4.8.3 (March 2016)
3.2-1 Changes in the core GAP system introduced in GAP 4.8.3
3.3 GAP 4.8.4 (June 2016)
3.3-1 Changes in the core GAP system introduced in GAP 4.8.4
3.4 GAP 4.8.5 (September 2016)
3.4-1 Changes in the core GAP system introduced in GAP 4.8.5
3.5 GAP 4.8.6 (November 2016)
3.5-1 Changes in the core GAP system introduced in GAP 4.8.6
3.6 GAP 4.8.7 (March 2017)
3.6-1 Changes in the core GAP system introduced in GAP 4.8.7
3.6-2 New and updated packages since GAP 4.8.6
3.7 GAP 4.8.8 (August 2017)
3.7-1 Changes in the core GAP system introduced in GAP 4.8.8
3.7-2 New and updated packages since GAP 4.8.7

### 3 Changes between GAP 4.7 and GAP 4.8

This chapter contains an overview of the most important changes introduced in GAP 4.8.2 release (the 1st public release of GAP 4.8). Later it will also contain information about subsequent update releases for GAP 4.8. First of all, the GAP development repository is now hosted on GitHub at https://github.com/gap-system/gap, and GAP 4.8 is the first major GAP release made from this repository. The public issue tracker for the core GAP system is located at https://github.com/gap-system/gap/issues, and you may use appropriate milestones from https://github.com/gap-system/gap/milestones to see all changes that were introduced in corresponding GAP releases. An overview of the most significant ones is provided below.

#### 3.1 GAP 4.8.2 (February 2016)

##### 3.1-1 Changes in the core GAP system introduced in GAP 4.8

New features:

- Added support for profiling which tracks how much time in spent on each line of GAP code. This can be used to show where code is spending a long time and also check which lines of code are even executed. See the documentation for `ProfileLineByLine` (Reference: ProfileLineByLine) and `CoverageLineByLine` (Reference: CoverageLineByLine) for details on generating profiles, and the Profiling package for transforming these profiles into a human-readable form.

- Added ability to install (in the library or packages) methods for accessing lists using multiple indices and indexing into lists using indices other than positive small integers. Such methods could allow, for example, to support expressions like

      m[1,2];
      m[1,2,3] := x;
      IsBound(m["a","b",Z(7)]);
      Unbind(m[1][2,3])

- Added support for partially variadic functions to allow function expressions like

      function( a, b, c, x... ) ... end;

  which would require at least three arguments and assign the first three to a, b and c and then a list containing any remaining ones to x.

  The former special meaning of the argument arg is still supported and is now equivalent to `function( arg... )`, so no changes in the existing code are required.

- Introduced `CallWithTimeout` and `CallWithTimeoutList` to call a function with a limit on the CPU time it can consume. This functionality may not be available on all systems and you should check `GAPInfo.TimeoutsSupported` before using this functionality. (These functions were withdrawn in GAP 4.9.)

- GAP now displays the filename and line numbers of statements in backtraces when entering the break loop.

- Introduced `TestDirectory` (Reference: TestDirectory) function to find (recursively) all `.tst` files from a given directory or a list of directories and run them using `Test` (Reference: Test).

Improved and extended functionality:

- Method tracing shows the filename and line of function during tracing.

- `TraceAllMethods` (Reference: TraceAllMethods) and `UntraceAllMethods` (Reference: UntraceAllMethods) to turn on and off tracing all methods in GAP. Also, for the uniform approach `UntraceImmediateMethods` (Reference: UntraceImmediateMethods) has been added as an equivalent of `TraceImmediateMethods(false)`.

- The most common cases of `AddDictionary` (Reference: AddDictionary) on three arguments now bypass method selection, avoiding the cost of determining homogeneity for plain lists of mutable objects.

- Improved methods for symmetric and alternating groups in the "natural" representations and removed some duplicated code.

- Package authors may optionally specify the source code repository, issue tracker and support email address for their package using new components in the `PackageInfo.g` file, which will be used to create hyperlinks from the package overview page (see `PackageInfo.g` from the Example package which you may use as a template).

Changed functionality:

- As a preparation for the future developments to support multithreading, some language extensions from the HPC-GAP project were backported to the GAP library to help to unify the codebase of both GAP 4 and HPC-GAP. The only change which is not backwards compatible is that `atomic`, `readonly` and `readwrite` are now keywords, and thus are no longer valid identifiers. So if you have any variables or functions using that name, you will have to change it in GAP 4.8.

- There was inconsistent use of the following properties of semigroups: `IsGroupAsSemigroup`, `IsMonoidAsSemigroup`, and `IsSemilatticeAsSemigroup`. `IsGroupAsSemigroup` was true for semigroups that mathematically defined a group, and for semigroups in the category `IsGroup` (Reference: IsGroup); `IsMonoidAsSemigroup` was only true for semigroups that mathematically defined monoids, but did not belong to the category `IsMonoid` (Reference: IsMonoid); and `IsSemilatticeAsSemigroup` was simply a property of semigroups, as there is no category `IsSemilattice`.

  From version 4.8 onwards, `IsSemilatticeAsSemigroup` is renamed to `IsSemilattice`, and `IsMonoidAsSemigroup` returns true for semigroups in the category `IsMonoid` (Reference: IsMonoid).

  This way all of the properties of the type `IsXAsSemigroup` are consistent. It should be noted that the only methods installed for `IsMonoidAsSemigroup` belong to the Semigroups and Smallsemi packages.

- `ReadTest` became obsolete and for backwards compatibility is replaced by `Test` (Reference: Test) with the option to compare the output up to whitespaces.

- The function `ErrorMayQuit`, which differs from `Error` (Reference: Error) by not allowing execution to continue, has been renamed to `ErrorNoReturn` (Reference: ErrorNoReturn).

Fixed bugs:

- A combination of two bugs could lead to a segfault. First off, `NullMat` (Reference: NullMat) (and various other GAP functions), when asked to produce matrix over a small field, called `ConvertToMatrixRep` (Reference: ConvertToMatrixRep for a list (and a field)). After this, if the user tried to change one of the entries to a value from a larger extension field, this resulted in an error. (This is now fixed).

  Unfortunately, the C code catching this error had a bug and allowed users to type "return" to continue while ignoring the conversion error. This was a bad idea, as the C code would be in an inconsistent state at this point, subsequently leading to a crash.

  This, too, has been fixed, by not allowing the user to ignore the error by entering "return".

- The Fitting-free code and code inheriting PCGS is now using `IndicesEANormalSteps` (Reference: IndicesEANormalSteps) instead of `IndicesNormalSteps` (Reference: IndicesNormalSteps), as these indices are neither guaranteed, nor required to be maximally refined when restricting to subgroups.

- A bug that caused a break loop in the computation of the Hall subgroup for groups having a trivial Fitting subgroup.

- Including a `break` or `continue` statement in a function body but not in a loop now gives a syntax error instead of failing at run time.

- `GroupGeneralMappingByImages` (Reference: GroupGeneralMappingByImages) now verifies that that image of a mapping is contained in its range.

- Fixed a bug in caching the degree of transformation that could lead to a non-identity transformation accidentally changing its value to the identity transformation.

- Fixed the problem with using Windows default browser as a help viewer using `SetHelpViewer("browser");`.

##### 3.1-2 New and updated packages since GAP 4.7.8

At the time of the release of GAP 4.7.8 there were 119 packages redistributed with GAP. New packages that have been added to the redistribution since the release of GAP 4.7.8 are:

- CAP (Categories, Algorithms, Programming) package by Sebastian Gutsche, Sebastian Posur and Øystein Skartsæterhagen, together with three associated packages GeneralizedMorphismsForCAP, LinearAlgebraForCAP and ModulePresentationsForCAP (all three - by Sebastian Gutsche and Sebastian Posur).

- Digraphs package by Jan De Beule, Julius Jonušas, James Mitchell, Michael Torpey and Wilf Wilson, which provides functionality to work with graphs, digraphs, and multidigraphs.

- FinInG package by John Bamberg, Anton Betten, Philippe Cara, Jan De Beule, Michel Lavrauw and Max Neunhöffer for computation in Finite Incidence Geometry.

- HeLP package by Andreas Bächle and Leo Margolis, which computes constraints on partial augmentations of torsion units in integral group rings using a method developed by Luthar, Passi and Hertweck. The package can be employed to verify the Zassenhaus Conjecture and the Prime Graph Question for finite groups, once their characters are known. It uses an interface to the software package 4ti2 to solve integral linear inequalities.

- matgrp package by Alexander Hulpke, which provides an interface to the solvable radical functionality for matrix groups, building on constructive recognition.

- NormalizInterface package by Sebastian Gutsche, Max Horn and Christof Söger, which provides a GAP interface to Normaliz, enabling direct access to the complete functionality of Normaliz, such as computations in affine monoids, vector configurations, lattice polytopes, and rational cones.

- profiling package by Christopher Jefferson for transforming profiles produced by `ProfileLineByLine` (Reference: ProfileLineByLine) and `CoverageLineByLine` (Reference: CoverageLineByLine) into a human-readable form.

- Utils package by Sebastian Gutsche, Stefan Kohl and Christopher Wensley, which provides a collection of utility functions gleaned from many packages.

- XModAlg package by Zekeriya Arvasi and Alper Odabas, which provides a collection of functions for computing with crossed modules and Cat1-algebras and morphisms of these structures.

#### 3.2 GAP 4.8.3 (March 2016)

##### 3.2-1 Changes in the core GAP system introduced in GAP 4.8.3

New features:

- New function `TestPackage` (Reference: TestPackage) to run standard tests (if available) for a single package in the current GAP session (also callable via `make testpackage PKGNAME=pkgname` to run package tests in the same settings that are used for testing GAP releases).

Improved and extended functionality:

- `TestDirectory` (Reference: TestDirectory) now prints a special status message to indicate the outcome of the test (this is convenient for automated testing). If necessary, this message may be suppressed by using the option `suppressStatusMessage`

- Improved output of tracing methods (which may be invoked, for example, with `TraceAllMethods` (Reference: TraceAllMethods)) by displaying filename and line number in some more cases.

Changed functionality:

- Fixed some inconsistencies in the usage of `IsGeneratorsOfSemigroup` (Reference: IsGeneratorsOfSemigroup).

Fixed bugs that could lead to incorrect results:

- Fallback methods for conjugacy classes, that were never intended for infinite groups, now use `IsFinite` (Reference: IsFinite) filter to prevent them being called for infinite groups. [Reported by Gabor Horvath]

Fixed bugs that could lead to break loops:

- Calculating stabiliser for the alternating group caused a break loop in the case when it defers to the corresponding symmetric group.

- It was not possible to use `DotFileLatticeSubgroups` (Reference: DotFileLatticeSubgroups) for a trivial group. [Reported by Sergio Siccha]

- A break loop while computing `AutomorphismGroup` (Reference: AutomorphismGroup) for `TransitiveGroup(12,269)`. [Reported by Ignat Soroko]

- A break loop while computing conjugacy classes of `PSL(6,4)`. [Reported by Martin Macaj]

Other fixed bugs:

- Fix for using Firefox as a default help viewer with `SetHelpViewer` (Reference: SetHelpViewer). [Reported by Tom McDonough]

#### 3.3 GAP 4.8.4 (June 2016)

##### 3.3-1 Changes in the core GAP system introduced in GAP 4.8.4

New features:

- The GAP distribution now includes `bin/BuildPackages.sh`, a script which can be started from the `pkg` directory via `../bin/BuildPackages.sh` and will attempt to build as many packages as possible. It replaces the `InstPackages.sh` 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 `./configure; make` build procedure.

Improved and extended functionality:

- `SimpleGroup` (Reference: SimpleGroup) now produces more informative error message in the case when `AtlasGroup` (AtlasRep: AtlasGroup) could not load the requested group.

- An info message with the suggestion to use `InfoPackageLoading` (Reference: InfoPackageLoading) will now be displayed when `LoadPackage` (Reference: LoadPackage) returns `fail` (unless GAP is started with `-b` option).

- The build system will now enable C++ support in GMP only if a working C++ compiler is detected.

- More checks were added when embedding coefficient rings or rational numbers into polynomial rings in order to forbid adding polynomials in different characteristic.

Fixed bugs that could lead to crashes:

- Fixed the crash in `--cover` mode when reading files with more than 65,536 lines.

Fixed bugs that could lead to incorrect results:

- Fixed an error in the code for partial permutations that occurred on big-endian systems. [Reported by Bill Allombert]

- Fixed the kernel method for `Remove` (Reference: Remove) with one argument, which failed to reduce the length of a list to the position of the last bound entry. [Reported by Peter Schauenburg]

Fixed bugs that could lead to break loops:

- Fixed the break loop while using `Factorization` (Reference: factorization) on permutation groups by removing some old code that relied on further caching in `Factorization`. [Reported by Grahame Erskine]

- Fixed a problem with computation of maximal subgroups in an almost simple group. [Reported by Ramon Esteban Romero]

- Added missing methods for `Intersection2` (Reference: Intersection2) when one of the arguments is an empty list. [Reported by Wilf Wilson]

Other fixed bugs:

- Fixed several bugs in `RandomPrimitivePolynomial` (Reference: RandomPrimitivePolynomial). [Reported by Nusa Zidaric]

- Fixed several problems with `Random` (Reference: Random) on long lists in 64-bit GAP installations.

#### 3.4 GAP 4.8.5 (September 2016)

##### 3.4-1 Changes in the core GAP system introduced in GAP 4.8.5

Improved and extended functionality:

- The error messages produced when an unexpected `fail` is returned were made more clear by explicitly telling that the result should not be boolean or `fail` (before it only said "not a boolean").

- For consistency, both `NrTransitiveGroups` (transgrp: NrTransitiveGroups) and `TransitiveGroup` (transgrp: TransitiveGroup) now disallow the transitive group of degree 1.

Fixed bugs that could lead to incorrect results:

- A bug in the code for algebraic field extensions over non-prime fields that may cause, for example, a list of all elements of the extension not being a duplicate-free. [Reported by Huta Gana]

- So far, `FileString` (GAPDoc: FileString) only wrote files of sizes less than 2G and did not indicate an error in case of larger strings. Now strings of any length can be written, and in the case of a failure the corresponding system error is shown.

Fixed bugs that could lead to break loops:

- `NaturalHomomorphismByIdeal` (Reference: NaturalHomomorphismByIdeal) was not reducing monomials before forming a quotient ring, causing a break loop on some inputs. [Reported by Dmytro Savchuk]

- A bug in `DefaultInfoHandler` (Reference: DefaultInfoHandler) caused a break loop on startup with the setting `SetUserPreference( "InfoPackageLoadingLevel", 4 )``. [Reported by Mathieu Dutour]

- The `Iterator` (Reference: Iterator) for permutation groups was broken when the `StabChainMutable` (Reference: StabChainMutable for a group) of the group was not reduced, which can reasonably happen as the result of various algorithms.

#### 3.5 GAP 4.8.6 (November 2016)

##### 3.5-1 Changes in the core GAP system introduced in GAP 4.8.6

Fixed bugs that could lead to break loops:

- Fixed regression in the GAP kernel code introduced in GAP 4.8.5 and breaking `StringFile` (GAPDoc: StringFile) ability to work with compressed files. [Reported by Bill Allombert]

#### 3.6 GAP 4.8.7 (March 2017)

##### 3.6-1 Changes in the core GAP system introduced in GAP 4.8.7

Fixed bugs that could lead to incorrect results:

- Fixed a regression from GAP 4.7.6 when reading compressed files after a workspace is loaded. Before the fix, if GAP is started with the `-L` option (load workspace), using `ReadLine` (Reference: ReadLine) on the input stream for a compressed file returned by `InputTextFile` (Reference: InputTextFile) only returned the first character. [Reported by Bill Allombert]

Other fixed bugs:

- Fixed compiler warning occurring when GAP is compiled with gcc 6.2.0. [Reported by Bill Allombert]

##### 3.6-2 New and updated packages since GAP 4.8.6

This release contains updated versions of 19 packages from GAP 4.8.6 distribution. Additionally, the following package has been added for the redistribution with GAP:

- lpres package (author: René Hartung, maintainer: Laurent Bartholdi) to work with L-presented groups, namely groups given by a finite generating set and a possibly infinite set of relations given as iterates of finitely many seed relations by a finite set of endomorphisms. The package implements nilpotent quotient, Todd-Coxeter and Reidemeister-Schreier algorithms for such groups.

#### 3.7 GAP 4.8.8 (August 2017)

##### 3.7-1 Changes in the core GAP system introduced in GAP 4.8.8

Fixed bugs that could lead to incorrect results:

- Fixed a bug in `RepresentativeAction` (Reference: RepresentativeAction) producing incorrect answers for both symmetric and alternating groups, with both `OnTuples` (Reference: OnTuples) and `OnSets` (Reference: OnSets), by producing elements outside the group. [Reported by Mun See Chang]

Fixed bugs that could lead to break loops:

- Fixed a bug in `RepresentativeAction` (Reference: RepresentativeAction) for S_n and A_n acting on non-standard domains.

Other fixed bugs:

- Fixed a problem with checking the path to a file when using the default browser as a help viewer on Windows. [Reported by Jack Saunders]

##### 3.7-2 New and updated packages since GAP 4.8.7

This release contains updated versions of 29 packages from GAP 4.8.7 distribution. Additionally, the Gpd package (author: Chris Wensley) has been renamed to Groupoids.

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