Merge pull request #876 from shawnlaffan/issue_853_pt1

Replace Path::Class and File::Spec with Path::Tiny
shawnlaffan · Aug 12, 2023 · 9d2b3b0 · 9d2b3b0
2 parents c4bad7d + dd085f7
commit 9d2b3b0
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Showing 21 changed files with 67 additions and 81 deletions.
diff --git a/Makefile.PL b/Makefile.PL
@@ -9,7 +9,6 @@ my %common_reqs = (
     "Class::Inspector" => 0,
     "Clone" => "0.35",
     "Cpanel::JSON::XS" => "3",
-    "DBD::XBase" => 0,
     "Data::Structure::Util" => 0,
     "Data::Compare" => 0,
     "Exception::Class" => 0,
@@ -28,7 +27,6 @@ my %common_reqs = (
     "List::Util" => "1.54",
     "Math::Polygon" => 0,
     "Math::Random::MT::Auto" => "6.21",
-    "Path::Class" => 0,
     "Readonly" => 0,
     "Ref::Util" => 0,
     "Ref::Util::XS" => 0,

diff --git a/bin/load_and_randomise.pl b/bin/load_and_randomise.pl
@@ -6,10 +6,8 @@
 use FindBin qw { $Bin };
 use Carp;
 use English qw { -no_match_vars };
-use Path::Class;
 use Scalar::Util qw /blessed/;
 
-#use lib Path::Class::dir ( $Bin, '..', 'lib')->stringify;
 use rlib;
 
 local $| = 1;

diff --git a/bin/load_and_randomise_wrapper.pl b/bin/load_and_randomise_wrapper.pl
@@ -8,11 +8,8 @@
 use FindBin qw { $Bin };
 use English qw { -no_match_vars };
 use Carp;
-use File::Spec;
+Path::Tiny qw /path/;
 
-use Path::Class;
-
-#use lib Path::Class::dir ( $Bin, '..', 'lib')->stringify;
 use rlib;
 
 our $VERSION = '4.99_001';
@@ -54,7 +51,7 @@
 
 
 my $script_name = 'load_and_randomise.pl';
-my $script = File::Spec -> catfile ($FindBin::Bin, $script_name);
+my $script = path($FindBin::Bin, $script_name)->stringify;
 
 #  need to get it from the perlapp bindings?
 if ($perl_app_tool eq 'PerlApp') {

diff --git a/cpanfile b/cpanfile
@@ -1,7 +1,6 @@
 requires "Class::Inspector";
 requires "Clone", "0.35";
 requires "Cpanel::JSON::XS", "3";
-requires "DBD::XBase";
 requires "Data::Structure::Util";
 requires "Data::Compare";
 #requires "Data::DumpXML";
@@ -22,7 +21,6 @@ requires "List::Unique::DeterministicOrder", "0.003";
 requires "List::Util", "1.54";
 requires "Math::Polygon";
 requires "Math::Random::MT::Auto", "6.21";
-requires "Path::Class";
 requires "Readonly";
 requires "Ref::Util";
 requires "Ref::Util::XS";

diff --git a/lib/Biodiverse/BaseData.pm b/lib/Biodiverse/BaseData.pm
@@ -16,7 +16,6 @@ use POSIX qw {fmod floor};
 use Scalar::Util qw /looks_like_number blessed/;
 use List::Util 1.45 qw /max min sum pairs uniq/;
 use List::MoreUtils qw /first_index/;
-use Path::Class;
 use Path::Tiny qw /path/;
 use Geo::Converter::dms2dd qw {dms2dd};
 use Regexp::Common qw /number/;

diff --git a/lib/Biodiverse/BaseData/Import.pm b/lib/Biodiverse/BaseData/Import.pm
@@ -15,8 +15,7 @@ use POSIX qw {fmod floor ceil log2};
 use Scalar::Util qw /looks_like_number blessed reftype/;
 use List::Util 1.45 qw /max min sum any all none notall pairs uniq/;
 use List::MoreUtils qw /first_index/;
-use Path::Class;
-#use Path::Tiny qw /path/;
+use Path::Tiny qw /path/;
 use Geo::Converter::dms2dd qw {dms2dd};
 use Regexp::Common qw /number/;
 use Data::Compare ();
@@ -316,7 +315,7 @@ sub import_data {
 
 #print "[BASEDATA] Input files to load are ", join (" ", @{$args{input_files}}), "\n";
     foreach my $file ( @{ $args{input_files} } ) {
-        $file = Path::Class::file($file)->absolute;
+        $file = path($file)->absolute;
         say "[BASEDATA] INPUT FILE: $file";
         my $file_base = $file->basename;
 
@@ -705,8 +704,8 @@ sub import_data_raster {
             );
         }
 
-        $file = Path::Class::file($file)->absolute;
-        my $file_base = Path::Class::File->new($file)->basename();
+        $file = path($file)->absolute;
+        my $file_base = $file->basename;
         say "[BASEDATA] INPUT FILE: $file";
 
         croak "[BASEDATA] $file DOES NOT EXIST OR CANNOT BE READ "
@@ -1048,7 +1047,7 @@ sub import_data_shapefile {
     my $file_num = 0;
     foreach my $file ( @input_files ) {
         $file_num++;
-        $file = Path::Class::file($file)->absolute->stringify;
+        $file = path($file)->absolute->stringify;
         say "[BASEDATA] INPUT FILE: $file";
 
         if ($file_progress) {
@@ -1092,7 +1091,7 @@ sub import_data_shapefile {
             my $shape_x_index = first_index {$_ eq ':shape_x'} @group_field_names;
             my $shape_y_index = first_index {$_ eq ':shape_y'} @group_field_names;
 
-            if (-w Path::Class::file($fnamebase)->dir->stringify
+            if (-w path($fnamebase)->parent->stringify
                 && -w $fnamebase) {
                 #  only works for shapefiles
                 eval {
@@ -1751,7 +1750,7 @@ sub import_data_spreadsheet {
           if !defined $book;    # assuming undef on fail
 
         if ( blessed $book || !ref $book ) {    #  we have a file name
-            my $file = Path::Class::file($book)->absolute;
+            my $file = path($book)->absolute;
             say "[BASEDATA] INPUT FILE: $file";
 
             $book = $self->get_book_struct_from_spreadsheet_file (

diff --git a/lib/Biodiverse/BaseStruct.pm b/lib/Biodiverse/BaseStruct.pm
@@ -17,8 +17,6 @@ use English ( -no_match_vars );
 use Scalar::Util qw /looks_like_number reftype/;
 use List::Util qw /min max sum any/;
 use List::MoreUtils qw /first_index/;
-use File::Basename;
-use Path::Class;
 use POSIX qw /fmod floor/;
 use Time::localtime;
 use Ref::Util qw { :all };

diff --git a/lib/Biodiverse/BaseStruct/Export.pm b/lib/Biodiverse/BaseStruct/Export.pm
@@ -12,7 +12,7 @@ use Scalar::Util qw /looks_like_number reftype/;
 use List::Util qw /min max sum any/;
 use List::MoreUtils qw /first_index/;
 use File::Basename;
-use Path::Class;
+use Path::Tiny qw /path/;
 use POSIX qw /fmod floor/;
 use Time::localtime;
 use Ref::Util qw { :all };
@@ -876,7 +876,7 @@ sub write_table {
     my $data = $args{data} || croak "data argument not specified\n";
     is_arrayref($data) || croak "data arg must be an array ref\n";
 
-    $args{file} = Path::Class::file($args{file})->absolute;
+    $args{file} = path($args{file})->absolute;
 
     return;
 }
@@ -1436,7 +1436,7 @@ sub write_table_asciigrid {
     is_arrayref($data) || croak "data arg must be an array ref\n";
 
     my $file = $args{file} || croak "file arg not specified\n";
-    my ($name, $path, $suffix) = fileparse (Path::Class::file($file)->absolute, qr/\.asc/, qr/\.txt/);
+    my ($name, $path, $suffix) = fileparse (path($file)->absolute, qr/\.asc/, qr/\.txt/);
     my $file_list_ref = $args{filelist} || [];
 
     if (! defined $suffix || $suffix eq q{}) {  #  clear off the trailing .asc and store it
@@ -1468,7 +1468,7 @@ sub write_table_asciigrid {
         my $this_file = $name . "_" . $header->[$i];
         $this_file = $self->escape_filename (string => $this_file);
 
-        my $filename    = Path::Class::file($path, $this_file)->stringify;
+        my $filename    = path($path, $this_file)->stringify;
         $filename      .= $suffix;
         $file_names[$i] = $filename;
         push @$file_list_ref, $filename; # record file in list
@@ -1535,7 +1535,7 @@ sub write_table_floatgrid {
     is_arrayref($data) || croak "data arg must be an array ref\n";
 
     my $file = $args{file} || croak "file arg not specified\n";
-    my ($name, $path, $suffix) = fileparse (Path::Class::file($file)->absolute, qr/\.flt/);
+    my ($name, $path, $suffix) = fileparse (path($file)->absolute, qr/\.flt/);
     if (! defined $suffix || $suffix eq q{}) {  #  clear off the trailing .flt and store it
         $suffix = '.flt';
     }
@@ -1568,7 +1568,7 @@ sub write_table_floatgrid {
         my $this_file = $name . "_" . $header->[$i];
         $this_file = $self->escape_filename (string => $this_file);
 
-        my $filename = Path::Class::file($path, $this_file)->stringify;
+        my $filename = path($path, $this_file)->stringify;
         $filename .= $suffix;
         $file_names[$i] = $filename;
 
@@ -1638,7 +1638,7 @@ sub write_table_divagis {
     is_arrayref($data) || croak "data arg must be an array ref\n";
 
     my $file = $args{file} || croak "file arg not specified\n";
-    my ($name, $path, $suffix) = fileparse (Path::Class::file($file)->stringify, qr'\.gri');
+    my ($name, $path, $suffix) = fileparse (path($file)->stringify, qr'\.gri');
     if (! defined $suffix || $suffix eq q{}) {  #  clear off the trailing .gri and store it
         $suffix = '.gri';
     }
@@ -1667,7 +1667,7 @@ sub write_table_divagis {
         my $this_file = $name . "_" . $header->[$i];
         $this_file = $self->escape_filename (string => $this_file);
 
-        my $filename = Path::Class::file($path, $this_file)->stringify;
+        my $filename = path($path, $this_file)->stringify;
         $filename .= $suffix;
         $file_names[$i] = $filename;
 
@@ -1773,7 +1773,7 @@ sub write_table_geotiff {
     is_arrayref($data) || croak "data arg must be an array ref\n";
 
     my $file = $args{file} || croak "file arg not specified\n";
-    my ($name, $path, $suffix) = fileparse (Path::Class::file($file)->absolute, qr/\.tif{1,2}/);
+    my ($name, $path, $suffix) = fileparse (path($file)->absolute, qr/\.tif{1,2}/);
     if (! defined $suffix || $suffix eq q{}) {  #  clear off the trailing .tif and store it
         $suffix = '.tif';
     }
@@ -1819,7 +1819,7 @@ sub write_table_geotiff {
         my $this_file = $name . "_" . $header->[$i];
         $this_file = $self->escape_filename (string => $this_file);
 
-        my $filename = Path::Class::file($path, $this_file)->stringify;
+        my $filename = path($path, $this_file)->stringify;
         $filename   .= $suffix;
         $file_names[$i] = $filename;
         $index_fname_hash{$header->[$i]} = $filename;
@@ -1881,7 +1881,7 @@ sub write_rgb_geotiff {
     my %args = @_;
 
     my $file = $args{file} || croak "file arg not specified\n";
-    my ($name, $path, $suffix) = fileparse (Path::Class::file($file)->absolute, qr/\.tif{1,2}/);
+    my ($name, $path, $suffix) = fileparse (path($file)->absolute, qr/\.tif{1,2}/);
     if (! defined $suffix || $suffix eq q{}) {  #  clear off the trailing .tif and store it
         $suffix = '.tif';
     }
@@ -1903,7 +1903,7 @@ sub write_rgb_geotiff {
         my $this_file = "${name}_${index}_rgb";
         $this_file = $self->escape_filename (string => $this_file);
 
-        my $f_name = Path::Class::file($path, $this_file)->stringify;
+        my $f_name = path($path, $this_file)->stringify;
         $f_name   .= $suffix;
 
         #  we really should cache using a basestruct        
@@ -2004,7 +2004,7 @@ sub write_table_ers {
     my $file = $args{file} || croak "file arg not specified\n";
 
     my ($name, $path, $suffix)
-        = fileparse (Path::Class::file($file)->absolute, qr/\.ers/);
+        = fileparse (path($file)->absolute, qr/\.ers/);
 
     #  add suffix if not specified
     if (!defined $suffix || $suffix eq q{}) {
@@ -2030,7 +2030,7 @@ sub write_table_ers {
 
     #my %stats;
 
-    my $data_file = Path::Class::file($path, $name)->stringify;
+    my $data_file = path($path, $name)->stringify;
     my $ofh = $self->get_file_handle (
         file_name => $data_file,
         mode      => '>',
@@ -2134,7 +2134,7 @@ END_OF_ERS_HEADER_START
         "DatasetHeader End"
     );
 
-    my $header_file = Path::Class::file($path, $name)->stringify . $suffix;
+    my $header_file = path($path, $name)->stringify . $suffix;
     my $header_fh = $self->get_file_handle (
         file_name => $header_file,
         mode      => '>:utf8',

diff --git a/lib/Biodiverse/Cluster.pm b/lib/Biodiverse/Cluster.pm
@@ -19,6 +19,7 @@ use Scalar::Util qw /looks_like_number/;
 use Time::HiRes qw /time/;
 use Sort::Key qw /rnkeysort/;
 use Sort::Key::Natural qw /natsort/;
+use Path::Tiny qw /path/;
 
 
 use experimental qw /declared_refs/;
@@ -294,7 +295,7 @@ sub export_matrices {
         $suffix = ".$suffix";
     }
 
-    $file = Path::Class::file($path, $name)->absolute;
+    $file = path($path, $name)->absolute;
 
     foreach my $matrix (@$matrices) {
         next if ! defined $matrix;  #  allow for absent shadow matrix

diff --git a/lib/Biodiverse/Common.pm b/lib/Biodiverse/Common.pm
@@ -24,7 +24,7 @@ use List::MoreUtils qw /none/;
 use List::Util qw /first/;
 use Storable qw /nstore retrieve dclone/;
 use File::Basename;
-use Path::Class;
+use Path::Tiny qw /path/;
 use POSIX ();
 use HTML::QuickTable;
 #use XBase;
@@ -166,7 +166,7 @@ sub load_sereal_file {
         // eval {$self->get_file_suffix}
         // $EMPTY_STRING;
 
-    my $file = Path::Class::file($args{file})->absolute;
+    my $file = path($args{file})->absolute;
     croak "[BASEDATA] File $file does not exist\n"
       if !$self->file_exists_aa ($file);
 
@@ -231,7 +231,7 @@ sub load_storable_file {
 
     my $suffix = $args{suffix} || $self->get_param('OUTSUFFIX') || $EMPTY_STRING;
 
-    my $file = Path::Class::file($args{file})->absolute;
+    my $file = path($args{file})->absolute;
 
     croak "Unicode file names not supported for Storable format,"
         . "please rename $file and try again\n"
@@ -813,9 +813,9 @@ sub save_to_sereal {
     my $file = $args{filename};
     if (! defined $file) {
         my $prefix = $args{OUTPFX} || $self->get_param('OUTPFX') || $self->get_param('NAME') || caller();
-        $file = Path::Class::file($file || ($prefix . '.' . $self->get_param('OUTSUFFIX')));
+        $file = path($file || ($prefix . '.' . $self->get_param('OUTSUFFIX')));
     }
-    $file = Path::Class::file($file)->absolute;
+    $file = path($file)->absolute;
 
     say "[COMMON] WRITING TO SEREAL FORMAT FILE $file";
 
@@ -851,9 +851,9 @@ sub save_to_storable {
     my $file = $args{filename};
     if (! defined $file) {
         my $prefix = $args{OUTPFX} || $self->get_param('OUTPFX') || $self->get_param('NAME') || caller();
-        $file = Path::Class::file($file || ($prefix . '.' . $self->get_param('OUTSUFFIX')));
+        $file = path($file || ($prefix . '.' . $self->get_param('OUTSUFFIX')));
     }
-    $file = Path::Class::file($file)->absolute;
+    $file = path($file)->absolute;
 
     print "[COMMON] WRITING TO STORABLE FORMAT FILE $file\n";
 
@@ -876,9 +876,9 @@ sub save_to_yaml {
     my $file = $args{filename};
     if (! defined $file) {
         my $prefix = $args{OUTPFX} || $self->get_param('OUTPFX') || $self->get_param('NAME') || caller();
-        $file = Path::Class::file($file || ($prefix . "." . $self->get_param('OUTSUFFIX_YAML')));
+        $file = path($file || ($prefix . "." . $self->get_param('OUTSUFFIX_YAML')));
     }
-    $file = Path::Class::file($file)->absolute;
+    $file = path($file)->absolute;
 
     print "[COMMON] WRITING TO YAML FORMAT FILE $file\n";
 
@@ -896,9 +896,9 @@ sub save_to_data_dumper {
     if (! defined $file) {
         my $prefix = $args{OUTPFX} || $self->get_param('OUTPFX') || $self->get_param('NAME') || caller();
         my $suffix = $self->get_param('OUTSUFFIX') || 'data_dumper';
-        $file = Path::Class::file($file || ($prefix . '.' . $suffix));
+        $file = path($file || ($prefix . '.' . $suffix));
     }
-    $file = Path::Class::file($file)->absolute;
+    $file = path($file)->absolute;
 
     print "[COMMON] WRITING TO DATA DUMPER FORMAT FILE $file\n";
 
@@ -919,7 +919,7 @@ sub dump_to_yaml {
     my $data = $args{data};
 
     if (defined $args{filename}) {
-        my $file = Path::Class::file($args{filename})->absolute;
+        my $file = path($args{filename})->absolute;
         say "WRITING TO YAML FORMAT FILE $file";
         YAML::Syck::DumpFile ($file, $data);
     }
@@ -942,7 +942,7 @@ sub dump_to_json {
     my $data = $args{data};
 
     if (defined $args{filename}) {
-        my $file = Path::Class::file($args{filename})->absolute;
+        my $file = path($args{filename})->absolute;
         say "WRITING TO JSON FILE $file";
         open (my $fh, '>', $file)
           or croak "Cannot open $file to write to, $!\n";
@@ -1038,7 +1038,7 @@ sub write_table {
     my $data = $args{data} || croak "data argument not specified\n";
     is_arrayref($data) || croak "data arg must be an array ref\n";
 
-    $args{file} = Path::Class::file($args{file})->absolute;
+    $args{file} = path($args{file})->absolute;
 
     #  now do stuff depending on what format was chosen, based on the suffix
     my (undef, $suffix) = lc ($args{file}) =~ /(.*?)\.(.*?)$/;