Refactor Floyd–Warshall C implementation

[mtorpey]

In digraphs.c we have a FLOYD_WARSHALL function that does a generalised version of the Floyd–Warshall algorithm with various options that customise the output. As noted in comments, some of this was rather hacky, with flags for special cases that return a totally different type of object early in the function and so on.

This PR adds a post parameter to FLOYD_WARSHALL, which takes a post-processing function that inspects the state of the distance matrix and produces a final output. So far we have three post functions:

• FW_POST_DIAMETER, used by DIGRAPH_DIAMETER (returns the highest number in the matrix, or fail)
• FW_POST_HAS_CHANGED used by IS_TRANSITIVE_DIGRAPH (returns a bool saying whether the matrix was changed in the main loop)
• FW_POST_DISTANCES, used by the other functions (returns the distance matrix as a GAP object)

and more could be added. This replaces the diameter and copy parameters which previously hard-coded some of this into the function.

There are also some readability improvements, basically changing variable names to describe what they do:

• dist1 and dist2 are now nonEdgeDist and edgeDist
• shortest is now zeroEdgeDist
• copy is now keepCopy, and is now used for nothing but creating a copy of dist.
• adj is now distCopy (it's just a copy of dist)
• out was previously used for two things: out neighbours and function output. This is now split into neighbours and out.

This will be a useful first step towards making the function more configurable, which might be useful for edge-weighted algorithms later.

[mtorpey]

I've run Valgrind on this, but I'm not exactly sure how to read the output. I can at least say that every line that starts ERROR SUMMARY: claims there are 0 errors.

Reveal full output

[16:40:48] ~/.gap/pkg/Digraphs $ echo "DigraphsTestStandard(); quit;" | valgrind --trace-children=yes --leak-check=full gap
==21277== Memcheck, a memory error detector
==21277== Copyright (C) 2002-2022, and GNU GPL'd, by Julian Seward et al.
==21277== Using Valgrind-3.20.0 and LibVEX; rerun with -h for copyright info
==21277== Command: /home/mtorpey/bin/gap
==21277== 
==21278== Memcheck, a memory error detector
==21278== Copyright (C) 2002-2022, and GNU GPL'd, by Julian Seward et al.
==21278== Using Valgrind-3.20.0 and LibVEX; rerun with -h for copyright info
==21278== Command: /home/mtorpey/gap/gap -m 2g
==21278== 
==21278== Warning: set address range perms: large range [0x100000000000, 0x100100001000) (defined)
==21278== Warning: set address range perms: large range [0x100000000000, 0x100080000000) (noaccess)
 ┌───────┐   GAP 4.13.1-1-g09fcf75 built on 2024-06-19 16:28:14+0100
 │  GAP  │   https://www.gap-system.org
 └───────┘   Architecture: x86_64-pc-linux-gnu-default64-kv9
 Configuration:  gmp 6.3.0, GASMAN, readline
 Loading the library and packages ...
 Packages:   datastructures 0.3.0, Digraphs 1.7.1, GAPDoc 1.6.7, IO 4.8.2, 
             orb 4.9.0, PrimGrp 3.4.4, SmallGrp 1.5.3, TransGrp 3.6.5
 Try '??help' for help. See also '?copyright', '?cite' and '?authors'
gap> Architecture: x86_64-pc-linux-gnu-default64-kv9

testing: /home/mtorpey/.gap/pkg/Digraphs/tst/standard/attr.tst
==21278== Warning: set address range perms: large range [0x100000000000, 0x100080000000) (noaccess)
==21281== Memcheck, a memory error detector
==21281== Copyright (C) 2002-2022, and GNU GPL'd, by Julian Seward et al.
==21281== Using Valgrind-3.20.0 and LibVEX; rerun with -h for copyright info
==21281== Command: /usr/bin/gzip -dq
==21281== 
==21281== 
==21281== HEAP SUMMARY:
==21281==     in use at exit: 0 bytes in 0 blocks
==21281==   total heap usage: 3 allocs, 3 frees, 2,608 bytes allocated
==21281== 
==21281== All heap blocks were freed -- no leaks are possible
==21281== 
==21281== For lists of detected and suppressed errors, rerun with: -s
==21281== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)
   76230 ms (8602 ms GC) and 682MB allocated for attr.tst
testing: /home/mtorpey/.gap/pkg/Digraphs/tst/standard/cliques.tst
==21278== Warning: set address range perms: large range [0x100000000000, 0x100080000000) (noaccess)
   17086 ms (12567 ms GC) and 24.4MB allocated for cliques.tst
testing: /home/mtorpey/.gap/pkg/Digraphs/tst/standard/constructors.tst
==21278== Warning: set address range perms: large range [0x100000000000, 0x100080000000) (noaccess)
    8489 ms (7746 ms GC) and 3.60MB allocated for constructors.tst
testing: /home/mtorpey/.gap/pkg/Digraphs/tst/standard/digraph.tst
==21278== Warning: set address range perms: large range [0x100000000000, 0x100080000000) (noaccess)
   38388 ms (7654 ms GC) and 365MB allocated for digraph.tst
testing: /home/mtorpey/.gap/pkg/Digraphs/tst/standard/display.tst
==21278== Warning: set address range perms: large range [0x100000000000, 0x100080000000) (noaccess)
==21283== Memcheck, a memory error detector
==21283== Copyright (C) 2002-2022, and GNU GPL'd, by Julian Seward et al.
==21283== Using Valgrind-3.20.0 and LibVEX; rerun with -h for copyright info
==21283== Command: /usr/bin/sh -c mkdir\ /tmp/gaptempdirbrPDBv/digraphs_temporary_directory
==21283== 
==21284== Memcheck, a memory error detector
==21284== Copyright (C) 2002-2022, and GNU GPL'd, by Julian Seward et al.
==21284== Using Valgrind-3.20.0 and LibVEX; rerun with -h for copyright info
==21284== Command: /usr/bin/mkdir /tmp/gaptempdirbrPDBv/digraphs_temporary_directory
==21284== 
==21284== 
==21284== HEAP SUMMARY:
==21284==     in use at exit: 0 bytes in 0 blocks
==21284==   total heap usage: 33 allocs, 33 frees, 5,609 bytes allocated
==21284== 
==21284== All heap blocks were freed -- no leaks are possible
==21284== 
==21284== For lists of detected and suppressed errors, rerun with: -s
==21284== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)
==21283== 
==21283== HEAP SUMMARY:
==21283==     in use at exit: 1,857 bytes in 54 blocks
==21283==   total heap usage: 56 allocs, 2 frees, 2,009 bytes allocated
==21283== 
==21283== LEAK SUMMARY:
==21283==    definitely lost: 0 bytes in 0 blocks
==21283==    indirectly lost: 0 bytes in 0 blocks
==21283==      possibly lost: 0 bytes in 0 blocks
==21283==    still reachable: 1,857 bytes in 54 blocks
==21283==         suppressed: 0 bytes in 0 blocks
==21283== Reachable blocks (those to which a pointer was found) are not shown.
==21283== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==21283== 
==21283== For lists of detected and suppressed errors, rerun with: -s
==21283== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)
   14547 ms (13865 ms GC) and 2.68MB allocated for display.tst
testing: /home/mtorpey/.gap/pkg/Digraphs/tst/standard/examples.tst
==21278== Warning: set address range perms: large range [0x100000000000, 0x100080000000) (noaccess)
    8851 ms (7712 ms GC) and 5.37MB allocated for examples.tst
testing: /home/mtorpey/.gap/pkg/Digraphs/tst/standard/grahom.tst
==21278== Warning: set address range perms: large range [0x100000000000, 0x100080000000) (noaccess)
   16399 ms (7459 ms GC) and 57.2MB allocated for grahom.tst
testing: /home/mtorpey/.gap/pkg/Digraphs/tst/standard/grape.tst
==21278== Warning: set address range perms: large range [0x100000000000, 0x100080000000) (noaccess)
    8663 ms (8189 ms GC) and 2.79MB allocated for grape.tst
testing: /home/mtorpey/.gap/pkg/Digraphs/tst/standard/io.tst
==21278== Warning: set address range perms: large range [0x100000000000, 0x100080000000) (noaccess)
==21286== Memcheck, a memory error detector
==21286== Copyright (C) 2002-2022, and GNU GPL'd, by Julian Seward et al.
==21286== Using Valgrind-3.20.0 and LibVEX; rerun with -h for copyright info
==21286== Command: /usr/bin/gzip -dq
==21286== 
==21286== 
==21286== HEAP SUMMARY:
==21286==     in use at exit: 0 bytes in 0 blocks
==21286==   total heap usage: 3 allocs, 3 frees, 2,608 bytes allocated
==21286== 
==21286== All heap blocks were freed -- no leaks are possible
==21286== 
==21286== For lists of detected and suppressed errors, rerun with: -s
==21286== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)
==21287== Memcheck, a memory error detector
==21287== Copyright (C) 2002-2022, and GNU GPL'd, by Julian Seward et al.
==21287== Using Valgrind-3.20.0 and LibVEX; rerun with -h for copyright info
==21287== Command: /usr/bin/gzip -dq
==21287== 
==21287== 
==21287== HEAP SUMMARY:
==21287==     in use at exit: 0 bytes in 0 blocks
==21287==   total heap usage: 3 allocs, 3 frees, 2,608 bytes allocated
==21287== 
==21287== All heap blocks were freed -- no leaks are possible
==21287== 
==21287== For lists of detected and suppressed errors, rerun with: -s
==21287== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)
==21288== Memcheck, a memory error detector
==21288== Copyright (C) 2002-2022, and GNU GPL'd, by Julian Seward et al.
==21288== Using Valgrind-3.20.0 and LibVEX; rerun with -h for copyright info
==21288== Command: /usr/bin/gzip -dq
==21288== 
==21288== 
==21288== HEAP SUMMARY:
==21288==     in use at exit: 0 bytes in 0 blocks
==21288==   total heap usage: 3 allocs, 3 frees, 2,608 bytes allocated
==21288== 
==21288== All heap blocks were freed -- no leaks are possible
==21288== 
==21288== For lists of detected and suppressed errors, rerun with: -s
==21288== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)
==21291== Memcheck, a memory error detector
==21291== Copyright (C) 2002-2022, and GNU GPL'd, by Julian Seward et al.
==21291== Using Valgrind-3.20.0 and LibVEX; rerun with -h for copyright info
==21291== Command: /usr/bin/bzip2 -9q
==21291== 
==21291== 
==21291== HEAP SUMMARY:
==21291==     in use at exit: 0 bytes in 0 blocks
==21291==   total heap usage: 9 allocs, 9 frees, 7,531,372 bytes allocated
==21291== 
==21291== All heap blocks were freed -- no leaks are possible
==21291== 
==21291== For lists of detected and suppressed errors, rerun with: -s
==21291== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)
==21292== Memcheck, a memory error detector
==21292== Copyright (C) 2002-2022, and GNU GPL'd, by Julian Seward et al.
==21292== Using Valgrind-3.20.0 and LibVEX; rerun with -h for copyright info
==21292== Command: /usr/bin/bzip2 -dq
==21292== 
==21292== 
==21292== HEAP SUMMARY:
==21292==     in use at exit: 0 bytes in 0 blocks
==21292==   total heap usage: 7 allocs, 7 frees, 3,677,464 bytes allocated
==21292== 
==21292== All heap blocks were freed -- no leaks are possible
==21292== 
==21292== For lists of detected and suppressed errors, rerun with: -s
==21292== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)
==21293== Memcheck, a memory error detector
==21293== Copyright (C) 2002-2022, and GNU GPL'd, by Julian Seward et al.
==21293== Using Valgrind-3.20.0 and LibVEX; rerun with -h for copyright info
==21293== Command: /usr/bin/gzip -9q
==21293== 
==21293== 
==21293== HEAP SUMMARY:
==21293==     in use at exit: 0 bytes in 0 blocks
==21293==   total heap usage: 0 allocs, 0 frees, 0 bytes allocated
==21293== 
==21293== All heap blocks were freed -- no leaks are possible
==21293== 
==21293== For lists of detected and suppressed errors, rerun with: -s
==21293== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)
==21294== Memcheck, a memory error detector
==21294== Copyright (C) 2002-2022, and GNU GPL'd, by Julian Seward et al.
==21294== Using Valgrind-3.20.0 and LibVEX; rerun with -h for copyright info
==21294== Command: /usr/bin/gzip -dq
==21294== 
==21294== 
==21294== HEAP SUMMARY:
==21294==     in use at exit: 0 bytes in 0 blocks
==21294==   total heap usage: 106 allocs, 106 frees, 8,480 bytes allocated
==21294== 
==21294== All heap blocks were freed -- no leaks are possible
==21294== 
==21294== For lists of detected and suppressed errors, rerun with: -s
==21294== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)
==21295== Memcheck, a memory error detector
==21295== Copyright (C) 2002-2022, and GNU GPL'd, by Julian Seward et al.
==21295== Using Valgrind-3.20.0 and LibVEX; rerun with -h for copyright info
==21295== Command: /usr/bin/gzip -9q
==21295== 
==21295== 
==21295== HEAP SUMMARY:
==21295==     in use at exit: 0 bytes in 0 blocks
==21295==   total heap usage: 0 allocs, 0 frees, 0 bytes allocated
==21295== 
==21295== All heap blocks were freed -- no leaks are possible
==21295== 
==21295== For lists of detected and suppressed errors, rerun with: -s
==21295== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)
==21296== Memcheck, a memory error detector
==21296== Copyright (C) 2002-2022, and GNU GPL'd, by Julian Seward et al.
==21296== Using Valgrind-3.20.0 and LibVEX; rerun with -h for copyright info
==21296== Command: /usr/bin/gzip -dq
==21296== 
==21296== 
==21296== HEAP SUMMARY:
==21296==     in use at exit: 0 bytes in 0 blocks
==21296==   total heap usage: 106 allocs, 106 frees, 8,480 bytes allocated
==21296== 
==21296== All heap blocks were freed -- no leaks are possible
==21296== 
==21296== For lists of detected and suppressed errors, rerun with: -s
==21296== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)
==21297== Memcheck, a memory error detector
==21297== Copyright (C) 2002-2022, and GNU GPL'd, by Julian Seward et al.
==21297== Using Valgrind-3.20.0 and LibVEX; rerun with -h for copyright info
==21297== Command: /usr/bin/bzip2 -9q
==21297== 
==21297== 
==21297== HEAP SUMMARY:
==21297==     in use at exit: 0 bytes in 0 blocks
==21297==   total heap usage: 9 allocs, 9 frees, 7,531,372 bytes allocated
==21297== 
==21297== All heap blocks were freed -- no leaks are possible
==21297== 
==21297== For lists of detected and suppressed errors, rerun with: -s
==21297== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)
==21298== Memcheck, a memory error detector
==21298== Copyright (C) 2002-2022, and GNU GPL'd, by Julian Seward et al.
==21298== Using Valgrind-3.20.0 and LibVEX; rerun with -h for copyright info
==21298== Command: /usr/bin/bzip2 -dq
==21298== 
==21298== 
==21298== HEAP SUMMARY:
==21298==     in use at exit: 0 bytes in 0 blocks
==21298==   total heap usage: 7 allocs, 7 frees, 3,677,464 bytes allocated
==21298== 
==21298== All heap blocks were freed -- no leaks are possible
==21298== 
==21298== For lists of detected and suppressed errors, rerun with: -s
==21298== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)
==21299== Memcheck, a memory error detector
==21299== Copyright (C) 2002-2022, and GNU GPL'd, by Julian Seward et al.
==21299== Using Valgrind-3.20.0 and LibVEX; rerun with -h for copyright info
==21299== Command: /usr/bin/gzip -9q
==21299== 
==21299== 
==21299== HEAP SUMMARY:
==21299==     in use at exit: 0 bytes in 0 blocks
==21299==   total heap usage: 0 allocs, 0 frees, 0 bytes allocated
==21299== 
==21299== All heap blocks were freed -- no leaks are possible
==21299== 
==21299== For lists of detected and suppressed errors, rerun with: -s
==21299== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)
==21300== Memcheck, a memory error detector
==21300== Copyright (C) 2002-2022, and GNU GPL'd, by Julian Seward et al.
==21300== Using Valgrind-3.20.0 and LibVEX; rerun with -h for copyright info
==21300== Command: /usr/bin/sh -c rm\ -f\ tmp.gz
==21300== 
==21301== Memcheck, a memory error detector
==21301== Copyright (C) 2002-2022, and GNU GPL'd, by Julian Seward et al.
==21301== Using Valgrind-3.20.0 and LibVEX; rerun with -h for copyright info
==21301== Command: /usr/bin/rm -f tmp.gz
==21301== 
==21301== 
==21301== HEAP SUMMARY:
==21301==     in use at exit: 0 bytes in 0 blocks
==21301==   total heap usage: 37 allocs, 37 frees, 9,329 bytes allocated
==21301== 
==21301== All heap blocks were freed -- no leaks are possible
==21301== 
==21301== For lists of detected and suppressed errors, rerun with: -s
==21301== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)
==21300== 
==21300== HEAP SUMMARY:
==21300==     in use at exit: 1,854 bytes in 54 blocks
==21300==   total heap usage: 56 allocs, 2 frees, 2,006 bytes allocated
==21300== 
==21300== LEAK SUMMARY:
==21300==    definitely lost: 0 bytes in 0 blocks
==21300==    indirectly lost: 0 bytes in 0 blocks
==21300==      possibly lost: 0 bytes in 0 blocks
==21300==    still reachable: 1,854 bytes in 54 blocks
==21300==         suppressed: 0 bytes in 0 blocks
==21300== Reachable blocks (those to which a pointer was found) are not shown.
==21300== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==21300== 
==21300== For lists of detected and suppressed errors, rerun with: -s
==21300== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)
==21302== Memcheck, a memory error detector
==21302== Copyright (C) 2002-2022, and GNU GPL'd, by Julian Seward et al.
==21302== Using Valgrind-3.20.0 and LibVEX; rerun with -h for copyright info
==21302== Command: /usr/bin/gzip -9q
==21302== 
==21302== 
==21302== HEAP SUMMARY:
==21302==     in use at exit: 0 bytes in 0 blocks
==21302==   total heap usage: 0 allocs, 0 frees, 0 bytes allocated
==21302== 
==21302== All heap blocks were freed -- no leaks are possible
==21302== 
==21302== For lists of detected and suppressed errors, rerun with: -s
==21302== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)
   21392 ms (7694 ms GC) and 169MB allocated for io.tst
testing: /home/mtorpey/.gap/pkg/Digraphs/tst/standard/isomorph.tst
==21278== Warning: set address range perms: large range [0x100000000000, 0x100080000000) (noaccess)
   17943 ms (10715 ms GC) and 48.9MB allocated for isomorph.tst
testing: /home/mtorpey/.gap/pkg/Digraphs/tst/standard/labels.tst
==21278== Warning: set address range perms: large range [0x100000000000, 0x100080000000) (noaccess)
    8020 ms (7926 ms GC) and 453KB allocated for labels.tst
testing: /home/mtorpey/.gap/pkg/Digraphs/tst/standard/obsolete.tst
#I  Test: File does not contain any tests!
      22 ms (0 ms GC) and 147KB allocated for obsolete.tst
testing: /home/mtorpey/.gap/pkg/Digraphs/tst/standard/oper.tst
==21278== Warning: set address range perms: large range [0x100000000000, 0x100080000000) (noaccess)
   19996 ms (7400 ms GC) and 127MB allocated for oper.tst
testing: /home/mtorpey/.gap/pkg/Digraphs/tst/standard/orbits.tst
==21278== Warning: set address range perms: large range [0x100000000000, 0x100080000000) (noaccess)
    8859 ms (8821 ms GC) and 243KB allocated for orbits.tst
testing: /home/mtorpey/.gap/pkg/Digraphs/tst/standard/planar.tst
==21278== Warning: set address range perms: large range [0x100000000000, 0x100080000000) (noaccess)
    8165 ms (7368 ms GC) and 8.76MB allocated for planar.tst
testing: /home/mtorpey/.gap/pkg/Digraphs/tst/standard/prop.tst
==21278== Warning: set address range perms: large range [0x100000000000, 0x100080000000) (noaccess)
   34480 ms (7478 ms GC) and 185MB allocated for prop.tst
testing: /home/mtorpey/.gap/pkg/Digraphs/tst/standard/weights.tst
==21278== Warning: set address range perms: large range [0x100000000000, 0x100080000000) (noaccess)
    8969 ms (8913 ms GC) and 352KB allocated for weights.tst
-----------------------------------
total    316499 ms (140109 ms GC) and 1.64GB allocated
              0 failures in 17 files

true
==21278== 
==21278== HEAP SUMMARY:
==21278==     in use at exit: 1,658,131,006 bytes in 3,159,960 blocks
==21278==   total heap usage: 3,760,602 allocs, 600,642 frees, 2,318,259,763 bytes allocated
==21278== 
==21278== LEAK SUMMARY:
==21278==    definitely lost: 0 bytes in 0 blocks
==21278==    indirectly lost: 0 bytes in 0 blocks
==21278==      possibly lost: 0 bytes in 0 blocks
==21278==    still reachable: 1,658,131,006 bytes in 3,159,960 blocks
==21278==         suppressed: 0 bytes in 0 blocks
==21278== Reachable blocks (those to which a pointer was found) are not shown.
==21278== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==21278== 
==21278== For lists of detected and suppressed errors, rerun with: -s
==21278== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)
==21277== 
==21277== HEAP SUMMARY:
==21277==     in use at exit: 54,778 bytes in 613 blocks
==21277==   total heap usage: 730 allocs, 117 frees, 63,220 bytes allocated
==21277== 
==21277== LEAK SUMMARY:
==21277==    definitely lost: 0 bytes in 0 blocks
==21277==    indirectly lost: 0 bytes in 0 blocks
==21277==      possibly lost: 0 bytes in 0 blocks
==21277==    still reachable: 54,778 bytes in 613 blocks
==21277==         suppressed: 0 bytes in 0 blocks
==21277== Reachable blocks (those to which a pointer was found) are not shown.
==21277== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==21277== 
==21277== For lists of detected and suppressed errors, rerun with: -s
==21277== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)
[16:46:52] ~/.gap/pkg/Digraphs $ 

[james-d-mitchell]

Looks good to me, thanks @mtorpey