iGraphMatch 2.0.5

More changes for igraph 2.0.x to avoid warnings due to use of deprecated functions.
Changes to address https://github.com/dpmcsuss/iGraphMatch/issues/67. init_start and other functions with start = 'rds_perm_bari' and start = 'rds_from_sim_start' will now work correctly.
Updates to documentation on value returned by gm to better explain the list elements that are components of graphMatch class.

iGraphMatch 2.0.4

Updates for igraph 2.0.x.
- Use igraph::upgrade_graph on the Enron and C.Elegans data.
- Explicitly cast nnodes to integer in identity_match function.

All graph_match_ functions have been consolidated into one function called gm that takes a method argument indicating which of the methods to use. This will break pretty much any code but was instituted to improve flexibility and extensibility going forward. The returned values for these functions should be relatively consistent with the older values except that they’ll have a lot more functionality through the graphMatch class.
get_perm is now called get_perm_mat and is more flexible, taking a graph match object.
Removed match_report, edge_match_info, match_plot_igraph, match_plot_matrix, matched_adjs. Instead use methods associated with graphMatch class such as summary, plot, %*% etc.
sample_correlated_rdpg is now sample_correlated_rdpg_pair.
lapjv and lapmod functions are now accessed solely through do_lap.
Most start functions are removed and can be accessed through init_start.
row_cor, row_diff, row_perm_stat have been removed and are now accessed through best_matches.
sample_*_with_junk functions are removed. Instead use the normal sample_* functions with the ncore parameter.
gm_expand_when_stuck is removed and can be accessed by specifying ExpandWhenStuck = TRUE when calling gm with method = "percolation".

bari_start, edge_match_info, get_perm, gm_indefinite, graph_match_ExpandWhenStuck, graph_match_FW, graph_match_IsoRank, graph_match_PATH, graph_match_Umeyama, graph_match_convex, graph_match_percolation, lapjv, lapmod, match_plot_igraph, match_plot_matrix, match_report, matched_adjs, rds_from_sim_start, rds_perm_bari_start, rds_sinkhorn_start, row_cor, row_diff, row_perm_stat, rperm, sample_correlated_gnp_pair_w_junk,sample_correlated_sbm_pair_w_junk,

Implemented graphMatch class for inspecting and using matches.
as.graphMatch can convert data.frames and matrices to the graphMatch class.
The method argument in gm can also take a function so that you can leverage the graph_match class and error checking of gm.
best_matches will compute precision at k if given the true labels.

Lots of small fixes.
Convenience function largest_cc for finding largest connected component.
Improved documentation
The check_graph function is now exported to prepare graphs outside of gm functions.
matrix_lists can now be named lists.