Merge remote-tracking branch 'upstream/master'

shawnlaffan · Apr 24, 2016 · 5b21ebf · 5b21ebf
2 parents 99d7879 + 903cf42
commit 5b21ebf
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Showing 7 changed files with 13 additions and 10 deletions.
diff --git a/etc/site_pair_sampler/bin/sample_parameters_phylo.txt b/etc/site_pair_sampler/bin/sample_parameters_phylo.txt
@@ -17,7 +17,7 @@
 #  Blank lines are also ignored.                                               #
 #                                                                              #
 #  Help is available at:                                                       #
-#    https://code.google.com/p/biodiverse/wiki/SitePairSampler                 #
+#    https://purl.org/biodiverse/wiki/SitePairSampler                 #
 #                                                                              #
 #  Dan Rosauer	August 2013 to May 2014  	                               #
 ################################################################################

diff --git a/etc/site_pair_sampler/bin/sample_parameters_simplest.txt b/etc/site_pair_sampler/bin/sample_parameters_simplest.txt
@@ -17,7 +17,7 @@
 #  Blank lines are also ignored.                                               #
 #                                                                              #
 #  Help is available at:                                                       #
-#    https://code.google.com/p/biodiverse/wiki/SitePairSampler                 #
+#    https://purl.org/biodiverse/wiki/SitePairSampler                 #
 #                                                                              #
 #  Dan Rosauer	August 2013 to May 2014 	                               #
 ################################################################################

diff --git a/etc/site_pair_sampler/bin/sample_parameters_species.txt b/etc/site_pair_sampler/bin/sample_parameters_species.txt
@@ -17,7 +17,7 @@
 #  Blank lines are also ignored.                                               #
 #                                                                              #
 #  Help is available at:                                                       #
-#    https://code.google.com/p/biodiverse/wiki/SitePairSampler                 #
+#    https://purl.org/biodiverse/wiki/SitePairSampler                 #
 #                                                                              #
 #  Dan Rosauer	August 2013 and March 2014	                               #
 ################################################################################

diff --git a/lib/Biodiverse/BaseData.pm b/lib/Biodiverse/BaseData.pm
@@ -22,10 +22,10 @@ use Spreadsheet::Read 0.60;
 #  these are here for PAR purposes to ensure they get packed
 #  Spreadsheet::Read calls them as needed
 #  (not sure we need all of them, though)
-use Spreadsheet::ReadSXC qw //;
-use Spreadsheet::ParseExcel qw //;
-use Spreadsheet::ParseXLSX qw //;
-use Spreadsheet::XLSX qw //;
+require Spreadsheet::ReadSXC;
+require Spreadsheet::ParseExcel;
+require Spreadsheet::ParseXLSX;
+require Spreadsheet::XLSX;
 
 use English qw { -no_match_vars };
 

diff --git a/lib/Biodiverse/Metadata/Export.pm b/lib/Biodiverse/Metadata/Export.pm
@@ -4,7 +4,6 @@ use warnings;
 
 use 5.016;
 use Carp;
-use Readonly;
 use Scalar::Util qw /reftype/;
 use Readonly;
 
@@ -51,6 +50,9 @@ sub get_sub_name_from_format {
     no autovivification;
 
     my $check_name = $args{format_label} // $args{format};
+    croak "neither 'format_label' nor 'format' argument is not defined\n"
+      if !defined $check_name;
+
     my $check_sub_name = "export_$check_name";
 
     my $format_labels = $self->get_format_labels;

diff --git a/lib/Biodiverse/ReadNexus.pm b/lib/Biodiverse/ReadNexus.pm
@@ -598,6 +598,7 @@ sub parse_newick {
     my $node_count      = $args{node_count} // croak 'node_count arg not passed (must be scalar ref)';
     my $translate_hash  = $args{translate_hash}
                         || $self->get_param ('TRANSLATE_HASH');
+    #  clunky that we need to do this - was convenient once, but not now
     my $use_element_properties = $self->get_param ('USE_ELEMENT_PROPERTIES');
     my $element_properties     = $use_element_properties
       ? ($args{element_properties} || $self->get_param ('ELEMENT_PROPERTIES'))
@@ -613,7 +614,7 @@ sub parse_newick {
 
     my $progress_bar = $args{progress_bar};
     if (!$progress_bar) {
-        $est_node_count = $string =~ tr/,(//;  #  tr shortcuts to count items matching /(,/
+        $est_node_count = $string =~ tr/,(//;  #  tr shortcuts to count items matching /,(/
         $est_node_count ||= 1;
         #say "Estimated node count is $est_node_count";
         $tree->set_cached_value (ESTIMATED_NODE_COUNT => $est_node_count);

diff --git a/lib/Biodiverse/SpatialConditions.pm b/lib/Biodiverse/SpatialConditions.pm
@@ -2581,7 +2581,7 @@ sub get_polygons_from_shapefile {
 
     my $field_val = $args{field_val};
 
-    my $cache_name = join ':', 'SHAPEPOLYS', $file, ($field || $NULL_STRING), (defined $field_val ? $field_val : $NULL_STRING);
+    my $cache_name = join ':', 'SHAPEPOLYS', $file, ($field // $NULL_STRING), ($field_val // $NULL_STRING);
     my $cached     = $self->get_cached_value($cache_name);
 
     return (wantarray ? @$cached : $cached) if $cached;