use for_list feature, require perl 5.36

.github/workflows/linux_de_locale.yml

@@ -23,7 +23,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: shogo82148/actions-setup-perl@v1
         with:
@@ -65,7 +65,7 @@ jobs:
           ls -l perlversion.txt
 
       - name: Cache CPAN modules
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/perl5
           key: ${{ runner.os }}-build-${{ hashFiles('perlversion.txt') }}

.github/workflows/macos.yml

@@ -20,7 +20,7 @@ jobs:
     runs-on: macOS-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Perl
         run: |
@@ -47,7 +47,7 @@ jobs:
           ls -l perlversion.txt
 
       - name: Cache CPAN modules
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/perl5
           key: ${{ runner.os }}-build-${{ hashFiles('perlversion.txt') }}

.github/workflows/windows.yml

@@ -9,130 +9,24 @@ on:
   pull_request:
 
 env:
-  PERL5LIB: c:\cx\lib\perl5
-  PERL_LOCAL_LIB_ROOT: c:/cx
-  PERL_MB_OPT: --install_base C:/cx
-  PERL_MM_OPT: INSTALL_BASE=C:/cx
-  #ALIEN_BUILD_PRELOAD: Fetch::Cache
   AUTOMATED_TESTING: 1
 
 jobs:
   perl:
     runs-on: windows-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - name: Set up Perl
-        run: |
-          choco install strawberryperl
-          echo "C:\strawberry\c\bin;C:\strawberry\perl\site\bin;C:\strawberry\perl\bin" | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
-          ##echo $env:PATH
-
-      #- name: Check path
-      #  run: |
-      #    echo $env:PATH
-      #    echo "glargglarg"
-      #    echo $GITHUB_PATH
-      #    echo "zogzogzog"
-      #    $env:PATH = "C:\strawberry\c\bin;C:\strawberry\perl\site\bin;C:\strawberry\perl\bin;$env:PATH"
-      #    echo $env:PATH
-      #    echo "zigzig"
-      #    echo "C:\strawberry\c\bin;C:\strawberry\perl\site\bin;C:\strawberry\perl\bin;$env:PATH" > $GITHUB_PATH
-      #    echo $GITHUB_PATH
-
-      - name: perl -V
-        run: perl -V
-
-      - name: Prepare for CPAN cache
-        run: |
-          perl -V > perlversion.txt
-          echo "20220920" >> perlversion.txt
-          dir perlversion.txt
-
-      - name: Cache CPAN modules
-        uses: actions/cache@v3
-        with:
-          path: c:\cx
-          key: ${{ runner.os }}-build-${{ hashFiles('perlversion.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-build-${{ hashFiles('perlversion.txt') }}
-
-      - name: Prepare for Alien cache
-        run: |
-          perl -V > aliencache.txt
-          echo 'aliens' >> aliencache.txt
-          dir aliencache.txt
-
-      - name: Cache Alien downloads
-        uses: actions/cache@v3
+      - uses: shogo82148/actions-setup-perl@v1
         with:
-          path: $HOMEPATH\.alienbuild
-          key: ${{ runner.os }}-build-${{ hashFiles('aliencache.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-build-${{ hashFiles('aliencache.txt') }}
-
-      #- name: Install Dependencies
-      #  run: curl -sL https://git.io/cpm | perl - install -g --show-build-log-on-failure
-
-
-      #- name: Install dependencies 1
-      #  run: |
-      #    #cpanm --notest local::lib
-      #    #eval "$(perl -Mlocal::lib=${PWD}/perl_modules)"
-      #    cpanm --quiet --notest Alien::Build
-      #    cpanm --quiet --notest Alien::Build::MM
-      #    cpanm --quiet --notest Sort::Versions
-      #    cpanm --quiet --notest PkgConfig
-      #    cpanm --quiet --notest Alien::Build::Plugin::Cleanse::BuildDir
-      #    cpanm --quiet --notest File::Find::Rule
-      #    cpanm --quiet --notest Alien::Build::Plugin::Fetch::Cache
-      #    cpanm --quiet --notest Env::ShellWords
-      #    cpanm --quiet --notest Test2::Suite
+          perl-version: "5.38"
+          distribution: strawberry
+          install-modules-with: cpanm
+          install-modules-args: --with-develop --with-configure --verbose
 
-      - name: Install dependencies Alien::MSYS
-        run: |
-          cpanm Alien::Build::Plugin::Fetch::Cache
-          cpanm --notest Alien::MSYS
-
-      - name: Install dependencies Alien::sqlite
-        run: |
-          echo $env:PATH
-          cpanm --notest --installdeps Alien::sqlite
-          cpanm -v Alien::sqlite~1.05
-
-      - name: Install dependencies Alien::proj
-        run: |
-          #cpanm -v --notest https://github.com/shawnlaffan/perl-alien-proj.git
-          cpanm --notest --installdeps Alien::proj
-          cpanm -v --notest Alien::proj
-
-      - name: Install dependencies Alien::geos::af
-        run: |
-          cpanm --notest --installdeps Alien::geos::af
-          cpanm -v Alien::geos::af
-
-      - name: Install dependencies Alien::gdal
-        run: |
-          cpanm --notest --installdeps Alien::gdal
-          echo "ALIEN_GDAL_CONFIG_ARGS=--with-hide_internal_symbols" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append
-          #  qhull issues on gdal 3.5, maybe fixed in 3.6
-          $env:ALIEN_GDAL_CONFIG_ARGS = "--with-hide-internal-symbols=yes --without-gnm --without-qhull"
-          Get-PSDrive C | Select-Object Used,Free
-          #  clunky path override
-          #  $env:PATH = "C:\strawberry\c\bin;C:\strawberry\perl\site\bin;C:\strawberry\perl\bin;$env:PATH"
-          cpanm -v Alien::gdal
-          Get-PSDrive C | Select-Object Used,Free
-
-      - name: Install task deps
-        run: |
-          #cpanm --notest Task::Biodiverse::NoGUI
-          cpanm --notest --no-man-pages PDL
-          cpanm --notest --installdeps .
-          cpanm --installdeps .
-
-      # Runs a set of commands using the runners shell
-      - name: Run tests
+      - name: run tests
         run: |
-          prove 
-
+          #echo 1
+          perl -E'say join q{ }, @INC'
+          prove -l t

Makefile.PL

@@ -1,6 +1,6 @@
 use strict;
 use warnings;
-use 5.010;
+use 5.036;
 use ExtUtils::MakeMaker;
 
 #  these are from the cpanfile
@@ -13,7 +13,7 @@ my %common_reqs = (
     "Data::Compare"         => 0,
     "Exception::Class"      => 0,
     "Exporter::Easy"        => 0,
-    "Faster::Maths"         => 0,
+    #"Faster::Maths"         => 0,
     "File::BOM" => 0,
     "File::Find::Rule" => 0,
     "Geo::Converter::dms2dd" => "0.05",
@@ -76,6 +76,7 @@ my %WriteMakefileArgs = (
     "AUTHOR"   => 'Shawn Laffan <shawnlaffan@gmail.com>',
     "NAME"     => "Biodiverse",
     "VERSION_FROM" => "lib/App/Biodiverse.pm",
+    MIN_PERL_VERSION => '5.036',
     "CONFIGURE_REQUIRES" => {
         %common_reqs,
     },

appveyor.yml

@@ -4,13 +4,15 @@ branches:
 skip_tags: true
 
 cache:
-  - C:\Strawberry
+  - C:\Strawberry538
   #- C:\Strawberry -> appveyor.yml
 
 install:
-  - if not exist "C:\strawberry" appveyor-retry choco install strawberryperl --version 5.30.2.1
-  #- appveyor-retry choco upgrade strawberryperl --version 5.28.1.1
-  - set ST=C:\Strawberry
+  - set ST=C:\Strawberry538
+  - if exist %ST% del /Q %ST%
+  - if not exist %ST% appveyor-retry choco install strawberryperl --version 5.38.0 --install-arguments="INSTALLDIR=""C:\Strawberry538"""
+#  - appveyor-retry choco upgrade strawberryperl --version 5.38.0
+  - refreshenv
   - set PATH=%ST%\perl\bin;%ST%\perl\site\bin;%ST%\c\bin;%PATH%
   - path
   - cd C:\projects\%APPVEYOR_PROJECT_NAME%
@@ -31,14 +33,14 @@ install:
   - cpanm -v Alien::libtiff
   - cpanm -v Alien::proj
 
-  - set ALIEN_GDAL_CONFIG_ARGS=--without-spatialite --without-gnm --without-qhull
+#  - set ALIEN_GDAL_CONFIG_ARGS=--without-spatialite --without-gnm --without-qhull
   - cpanm -v Alien::gdal
-  
+
   - cpanm --notest --installdeps .
   - cpanm --installdeps .
 
 
 build_script:
   - prove -l
-  #- perl -e "1"
+#  - perl -e "1"
 

bin/BiodiverseGUI.pl

@@ -2,7 +2,7 @@
 use warnings;
 use Carp;
 
-use 5.022;
+use 5.036;
 
 #use File::Basename;
 use Cwd;

cpanfile

@@ -8,7 +8,7 @@ requires "Excel::ValueReader::XLSX";
 requires "Exception::Class";
 requires "Exporter::Easy";
 #requires "FFI::Platypus::Declare";
-requires "Faster::Maths";
+#  requires "Faster::Maths";  #  disabled for now
 requires "File::BOM";
 requires "File::Find::Rule";
 requires "Geo::Converter::dms2dd", "0.05";

lib/App/Biodiverse.pm

@@ -3,6 +3,8 @@ package App::Biodiverse;
 use strict;
 use warnings;
 
+use 5.036;
+
 our $VERSION = '4.99_002';
 
 1;

lib/Biodiverse/BaseData.pm

@@ -25,7 +25,7 @@ use Ref::Util qw { :all };
 use Sort::Key::Natural qw /natkeysort/;
 
 
-use experimental qw /refaliasing declared_refs/;
+use experimental qw /refaliasing declared_refs for_list/;
 
 
 use English qw { -no_match_vars };
@@ -1967,8 +1967,7 @@ sub delete_sub_elements_collated_by_group {
 
     my %labels_processed;
 
-    foreach my $group ( keys %$gp_lb_hash ) {
-        my $label_subhash = $gp_lb_hash->{$group};
+    foreach my ($group, $label_subhash) ( %$gp_lb_hash ) {
         foreach my $label ( keys %$label_subhash ) {
             $labels_processed{$label}++;
             $labels_ref->delete_sub_element_aa( $label, $group );

lib/Biodiverse/BaseStruct.pm

@@ -11,6 +11,8 @@ use warnings;
 use Carp;
 use 5.010;
 
+use experimental 'for_list';
+
 use English ( -no_match_vars );
 
 #use Data::Dumper ();
@@ -1131,8 +1133,8 @@ sub add_to_lists {  #  add to a list, create if not already there.
     my $use_ref = delete $args{use_ref};  
     #  should it be in its own sub?
 
-    foreach my $list_name (keys %args) {
-        my $list_values = $args{$list_name};
+    foreach my ($list_name, $list_values) (%args) {
+        # my $list_values = $args{$list_name};
         if ($use_ref) {
             $self->{ELEMENTS}{$element}{$list_name} = $list_values;
         }

lib/Biodiverse/Cluster.pm

@@ -22,7 +22,7 @@ use Sort::Key::Natural qw /natsort/;
 use Path::Tiny qw /path/;
 
 
-use experimental qw /declared_refs/;
+use experimental qw /declared_refs for_list/;
 
 use Geo::GDAL::FFI;
 #  silence some used-once warnings - very clunky
@@ -1640,8 +1640,7 @@ sub get_most_similar_pair {
     my $csv = $self->get_csv_object;
     my @pairs;
     my $pair_key_cache = $self->get_cached_value_dor_set_default_aa ('TIE_BREAKER_STRINGIFIED_PAIR_KEYS', {});
-    foreach my $name1 (keys %$keys_ref) {
-        my $ref = $keys_ref->{$name1};
+    foreach my ($name1, $ref) (%$keys_ref) {
         foreach my $name2 (keys %$ref) {
             my $stringified
                 = $pair_key_cache->{$name1}{$name2}
@@ -1941,8 +1940,7 @@ sub get_outputs_with_same_index_and_spatial_conditions {
         no_regexp => 1,
     );
     my %required;
-    foreach my $calc (keys %required_args) {
-        my $r = $required_args{$calc};
+    foreach my ($calc, $r) (%required_args) {
         @required{keys %$r} = values %$r;
     }
 
@@ -2855,12 +2853,11 @@ sub sp_calc {
             current_node_details => $current_node_details,
         );
 
-        foreach my $key (keys %sp_calc_values) {
-            if (is_arrayref($sp_calc_values{$key}) 
-                || is_hashref($sp_calc_values{$key})) {
+        foreach my ($key, $ref) (%sp_calc_values) {
+            if (is_arrayref($ref) || is_hashref($ref)) {
 
                 $node->add_to_lists (
-                    $key    => $sp_calc_values{$key},
+                    $key    => $ref,
                     use_ref => 1,
                 );
                 delete $sp_calc_values{$key};