Dear Szabolcs,

Thank You for Your previous help. My last question is the following: How should we cite the IGraph/M package in our paper?

Thank You in advance.

Alright, thank You very much! :)

P.S. For importing undirected graphs, you can also use the built-in Import["...", "Graph6"]. However, IGImport will be noticeably faster for a large number of graphs.

Unfortunately, the tool I mentioned doesn't come with pre-compiled binaries. Indeed you must compile it yourself. Generally, that can be done by running

./configure
make

in the source directory. I would expect this to work with either Cygwin or MSYS2, but I do not use Windows myself, so I couldn't try.

One compilation finishes, you should see several programs appear in that directory, including geng.exe.

so at first I used Cygwin to compile and install these tools, however it did not work on my computer

What exactly happened?

You may need to copy cygwin.dll next to the executables before they will work outside of the cygwin shell.

And I also find out in your documentation that in your examples we assume that the gtools programs are in a directory that is on the operating system’s PATH environment variable. Unfortunatelly I could not figure out how exactly these environments work in Mathematica, but maybe this cause the problem

It is actually not necessary to put them on the path. It is sufficient to call them with the full path. For example, on my system, these tools are installed in /opt/local/bin, so I call them using

IGImport["!/opt/local/bin/geng 3", "Graph6"]

Don't forget the ! at the beginning.

Regarding the errors that IGImport showed: this is a small bug in IGImport. It doesn't handle it well when the path to the file to be imported is incorrect or the file does not exist. I already fixed this and the fix will be released with the next version shortly. The bug only surfaces when the input to IGImport is incorrect, otherwise it imports things fine.

Dear Szabolcs Horvát,

First of all, thank you for your reply and help! I really appreciate it. Based on the examples you presented above this tool is just perfect for me, but unfortunately I could not manage to make it work.

I downloaded the recommended Nauty and Traces, but I use Windows 10 instead of Mac, so at first I used Cygwin to compile and install these tools, however it did not work on my computer. Then I tried to use another computer with Linux to compile and install, and then just copied the files back to the original computer, but I am not convinced that this method solved the entire problem. And I also find out in your documentation that in your examples we assume that the gtools programs are in a directory that is on the operating system’s PATH environment variable. Unfortunatelly I could not figure out how exactly these environments work in Mathematica, but maybe this cause the problem. I do not know, but I get the following warning messages after using the first example you wrote:

-Counts: The argument IGImport[IGDiameter[!geng -d3 -D3 -c 12],IGDiameter[Nauty]] is not a list.

-KeySort: The argument Counts[IGImport[IGDiameter[!geng -d3 -D3 -c 12],IGDiameter[Nauty]]] is not a valid Association or a list of rules.

I also tried the following:

Import["!geng -d3 -D3 12", "Graph6"]

But I got another error, which says 'Import: Cannot import data as Graph6 format.'

Do you have any ideas what could cause the problem? I think I need exactly this tool, so I would be really happy if I could make it work. Thank you for your help!

Also, I do not really know the rules and features of this forum, but I suppose only English is allowed. However if there is a private message option, then maybe it would be easier to discuss the problem there, because based on your name we both speak Hungarian... :)

Thank you for everything!