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.