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Cubic Lattice Knot generation, identification, topological manipulation, and analysis suite.

License: GNU General Public License v3.0

CMake 0.27% Makefile 15.73% Shell 4.69% M4 0.04% C++ 70.65% C 8.09% Python 0.53%

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recombo_public's Issues

Project does not build with g++

Make failed for g++ on Ubuntu 16.04. g++ (Ubuntu 5.4.0-6ubuntu1~16.04.12) 5.4.0 20160609

Admittedly this is an old version of g++, but project is supposed to build using c++11.

$ make
depbase=`echo src/bfacfProbabilitiesFromZFixed.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I.    -g -fpermissive -std=c++11 -g -O2 -MT src/bfacfProbabilitiesFromZFixed.o -MD -MP -MF $depbase.Tpo -c -o src/bfacfProbabilitiesFromZFixed.o src/bfacfProbabilitiesFromZFixed.cpp &&\
mv -f $depbase.Tpo $depbase.Po
In file included from src/bfacfProbabilitiesFromZFixed.cpp:9:0:
src/clkConformationBfacf3.h:201:10: error: ‘vector’ in namespace ‘std’ does not name a template type
     std::vector<threevector<int> > getChosenSite(int n);
          ^
Makefile:811: recipe for target 'src/bfacfProbabilitiesFromZFixed.o' failed
make: *** [src/bfacfProbabilitiesFromZFixed.o] Error 1

make test

It seems that the test target is just a stub. It should probably run recomboTests

$ make test
Would it not be nice if we knew that this worked?

[mmc] arclength criteria specification

Currently specified for standard and virtual recombination through the -recomboParas argument. We are promoting virtual recombination to an undocumented feature, and therefore should remove descriptions of that functionality from the documentation.

Steps are:

remove -recomboParas from the documentation
re-introduce the -minarc and -maxarc arguments for specifying recombination criteria in f and r modes.

homfly not building with clang

I really thought I had tried this within the last year. Must have been longer, though.

$ make homfly 
depbase=`echo src/cross.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
	gcc -DHAVE_CONFIG_H -I.     -g -O2 -MT src/cross.o -MD -MP -MF $depbase.Tpo -c -o src/cross.o src/cross.c &&\
	mv -f $depbase.Tpo $depbase.Po
src/cross.c:525:7: error: implicitly declaring library function 'strlen' with type 'unsigned long (const char *)' [-Werror,-Wimplicit-function-declaration]
  l = strlen(chaine);
      ^
src/cross.c:525:7: note: include the header <string.h> or explicitly provide a declaration for 'strlen'
src/cross.c:540:43: warning: too few arguments in call to 'creerCroisement'
      if((debut = creerCroisement(DEBUT,-1))==NULL){
                  ~~~~~~~~~~~~~~~         ^
src/cross.c:722:43: warning: too few arguments in call to 'creerCroisement'
      if((debut = creerCroisement(DEBUT,-1))==NULL){
                  ~~~~~~~~~~~~~~~         ^
2 warnings and 1 error generated.
make: *** [src/cross.o] Error 1

Apple clang version 13.0.0 (clang-1300.0.29.3)

Old Makefiles

After I got the autotool build working, I have not removed the old Makefiles from the src directories. Do we intend to keep those? If so, we currently have no description in the readme file.

need to test BFCACF probs with scale factor q > 1

Check that results match literature

testParallelRecombination

In order to get test to build, I had to comment out line 73 from src/tests/recomboCriteriaTests.cpp

    // TODO: RB had to comment out next line to build tests
    // sites=rctc.preConformation.countRecomboSites(18,22,orientation);

It seems that at some point, the signature for countRecomboSites had changed. More generally, the test testParallelRecombination contains significantly many commented lines it is no longer apparent what the intention was for the test.

After commenting out that line from that particular test, the tests built and ran, but with a seg fault. Hence, I further had to comment out line 42 from src/tests/unitTestMain.cpp

	// TODO: RB had to comment next line because of Segmentation fault 11
	// suite.add_test(testParallelRecombination, "Recombination between unknots");

Strictly speaking, we should consider the build to be broken at this point.

test repro running mmc

License

I want to solicit license suggestions to make sure this project is under an appropriate license. Currently it is under GPL 3, but I don't think that license is actually appropriate for a project that uses C++ STL. Also the licensing for the homfly source code is ambiguous. Thoughts?

Tests do not build

recomboCriteriaTests.cpp:72:32: error: no matching member function for call to
      'countRecomboSites'
    sites=rctc.preConformation.countRecomboSites(18,22,orientation);
          ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
../clkConformationBfacf3.h:171:8: note: candidate function not viable: requires 2
      arguments, but 3 were provided
   int countRecomboSites(int minarclength, int maxarclength);
       ^
../clkConformationBfacf3.h:170:8: note: candidate function not viable: requires 8
      arguments, but 3 were provided
   int countRecomboSites(int minarclength, int maxarclength, int Sequence...
       ^

[MMC] Recombo mode issue

Not all the recombo modes work in mmc as described in the manual. Need test coverage for this functionality to move towards a fix.

What are the bugs in clkConformationBfacf3::impl::searchForRecomboSitesOneComp(int minarclength, int maxarclength)?

There is a comment claiming that searchForRecomboSitesOneComp(int minarclength, int maxarclength) is used only in runRecombo and that there are bugs. Unfortunately, the comment does not elaborate. Is this function any longer needed, or is it safe to delete?