Dag io custom format

[davidrich27]

• dagbin
  • Added dag binary file format, as alternative to protobuf.
  • updated input/output file and format options to include dagbin (also, formats can now be inferred by file extension).

• maintenance

  • moved sample_dag.hpp to test_common_dag.hpp, now contains frequently used dag utilities in addition to sample dags.
  • run_larch_usher function added to test_common.hpp.
  • added data/_ignore folder, and redirected all test files to that location.
  • updated all timing to use Benchmark class
  • updated CLI options for larch-usher, merge, dag2dot to be more consistent across tools.
  • updated README to clarify changes to CLI.
  • added options to larch-usher to set random seed and number of threads.

  closes #81

[marybarker]

It would be useful to add an optional argument to larch-usher to enable us to append/write the DAG to the new file format at each sample-optimize-merge loop.

[davidrich27]

@ognian - I did a squash and rebase onto main, but I read your comment about Timer. I removed the class and used Benchmark in those instances.