rename the R phylo related subs

Make them consistent snake case. And no need to append json to the name.
shawnlaffan · Sep 15, 2023 · 5006825 · 5006825
1 parent d07f88d
commit 5006825
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Showing 4 changed files with 7 additions and 7 deletions.
diff --git a/lib/Biodiverse/ReadNexus.pm b/lib/Biodiverse/ReadNexus.pm
@@ -102,13 +102,13 @@ sub import_data {
     $self->set_param (USE_ELEMENT_PROPERTIES => $use_element_properties);
 
     #  no import_newick here as import_phylip handles such files
-    my @import_methods = qw/import_nexus import_phylip import_R_phylo_json import_tabular_tree/;
+    my @import_methods = qw/import_nexus import_phylip import_R_phylo import_tabular_tree/;
     # promote most likely method to front of the list
     if (defined $args{file} && $args{file} =~ /(txt|csv)$/) {  #  dirty hack
         unshift @import_methods, 'import_tabular_tree';
     }
     elsif (is_ref ($args{data})) {  #  also a dirty hack
-        unshift @import_methods, 'import_R_phylo_json';
+        unshift @import_methods, 'import_R_phylo';
     }
     else {
         my $method = $self->probe_file_type (%args);
@@ -631,7 +631,7 @@ sub get_csv_object_for_tabular_tree_import {
 }
 
 
-sub import_R_phylo_json {
+sub import_R_phylo {
     my $self = shift;
     my %args = @_;
 

diff --git a/lib/Biodiverse/TreeNode.pm b/lib/Biodiverse/TreeNode.pm
@@ -2311,7 +2311,7 @@ sub to_newick {   #  convert the tree to a newick format.  Based on the NEXUS li
 
 #  convert the tree to the same structure as used by the R phylo system
 #  this cannot be a recursive function
-sub to_Rphylo {
+sub to_R_phylo {
     my $self = shift;
     my %args = (use_internal_names => 1, @_);
     my $remap = $args{remap} || {};

diff --git a/t/13-Tree.t b/t/13-Tree.t
@@ -950,10 +950,10 @@ sub test_export_Rphylo {
     my $i;
     foreach my $tree ($tree1, $tree2) {
         $i++;
-        my $result = $tree->to_Rphylo;
+        my $result = $tree->to_R_phylo;
         #  round trip it
         $rn = Biodiverse::ReadNexus->new;
-        $rn->import_R_phylo_json(data => $result);
+        $rn->import_R_phylo(data => $result);
         @trees = $rn->get_tree_array;
         my $roundtripper = shift @trees;
         ok($tree->trees_are_same(comparison => $roundtripper),

diff --git a/t/21-ReadNexus.t b/t/21-ReadNexus.t
@@ -429,7 +429,7 @@ sub test_read_R_phylo_json_data {
         my $readnex = Biodiverse::ReadNexus->new;
         #diag $baddata;
         $result = eval {
-            $readnex->import_R_phylo_json (data => $baddata);
+            $readnex->import_R_phylo (data => $baddata);
         };
         is $@,
           'JSON data is not an R phylo structure',