Fix issue with Perl>5.36 (#509)

* add dockerfile for AGAT with perl version 536

* replace export_to_level(2,@_) in each module called by AGAT::AGAT by AGAT::Module->export_to_level(1,@_) from AGAT::AGAT. This fix issiue related to replace export_to_level(2,@_) introduced in perl 5.36. Fix #416 #392

* add test for perl>5.36

* remove indentation in shebang

* add missing semicolon

* run make test for first job

.github/workflows/main.yml

@@ -12,13 +12,51 @@ concurrency:
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:  
-  # This workflow contains a single job called "build"
-  build:
+
+  # This workflow contains a second job called "build2"
+  build_perl536:
+    # avoid to run twice push and PR
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+
+    # The type of runner that the job will run on
+    runs-on: ubuntu-22.04
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      - name: Install libdb-dev
+        run: sudo apt-get -y install libdb-dev
+      - name: Install R
+        run: sudo apt-get -y install r-base
+
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      #- name: Checkout AGAT
+      - uses: actions/checkout@v2
+      - name: Setup Perl
+        uses: shogo82148/actions-setup-perl@v1
+        with:
+            perl-version: '5.36'
+            install-modules-with: cpanm
+            install-modules-args: --notest --force
+            install-modules: File::ShareDir::Install
+      - uses: webiny/action-post-run@2.0.1
+        id: post-run-command
+        if: ${{ failure() }}
+        with:
+          run: cat /home/runner/.cpanm/build.log
+      - name: install AGAT deps
+        run: cpanm --installdeps --notest --force .
+      - name: test
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: make test
+
+  # This workflow contains a first job called "build"
+  build_perl530:
     # avoid to run twice push and PR
     if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
 
     # The type of runner that the job will run on
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
 
     #container:
     #  image: perl:5.30
@@ -51,4 +89,4 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           DEVEL_COVER_OPTIONS: "+ignore,^local/"
-        run: cover -test -report Coveralls
+        run: cover -test -report Coveralls

bin/agat_sp_load_function_from_protein_align.pl

@@ -840,10 +840,10 @@ sub check_gene_overlap_gffAlign{
   my  ($hash_omniscient, $prot_omniscient, $gene_id, $gene_id2, $prot_tag)=@_;
 
 #  my $overlap12=undef;
-  my $overlap12_abs=undef
+  my $overlap12_abs=undef;
 
 #  my $w_overlap12=undef;
-  my $w_overlap12_abs=undef
+  my $w_overlap12_abs=undef;
 
 #  my $overlap21=undef;
   my $overlap21_abs=undef;

docker/dockerfile_perl536

@@ -0,0 +1,9 @@
+From perl:5.36
+
+RUN cpanm install BioPerl Graph::Directed LWP::UserAgent Carp Sort::Naturally File::Share File::ShareDir::Install Moose YAML LWP::Protocol::https Term::ProgressBar
+RUN git clone https://github.com/NBISweden/AGAT.git
+WORKDIR /usr/src/app/AGAT
+RUN perl Makefile.PL
+RUN make
+RUN make test
+RUN make install

lib/AGAT/AGAT.pm

@@ -20,7 +20,15 @@ our $VERSION     = "v1.4.1";
 our @ISA         = qw(Exporter);
 our @EXPORT      = qw(get_agat_header print_agat_version get_agat_config handle_levels);
 sub import {
-  AGAT::AGAT->export_to_level(1, @_); # to be able to load the EXPORT functions when direct call; (normal case)
+    AGAT::AGAT->export_to_level(1, @_); # to be able to load the EXPORT functions when direct call; (normal case)
+    AGAT::OmniscientI->export_to_level(1, @_);
+    AGAT::OmniscientO->export_to_level(1, @_);
+    AGAT::OmniscientTool->export_to_level(1, @_);
+    AGAT::Config->export_to_level(1, @_);
+    AGAT::Levels->export_to_level(1, @_);
+    AGAT::OmniscientStat->export_to_level(1, @_);
+    AGAT::Utilities->export_to_level(1, @_);
+    AGAT::PlotR->export_to_level(1, @_);
 }
 
 =head1 SYNOPSIS

lib/AGAT/Config.pm

@@ -14,10 +14,6 @@ use Exporter;
 
 our @ISA = qw(Exporter);
 our @EXPORT = qw( load_config expose_config_file check_config get_config expose_config_hash );
-sub import {
-  AGAT::Config->export_to_level(1, @_); # to be able to load the EXPORT functions when direct call; (normal case)
-  AGAT::Config->export_to_level(2, @_); # to be able to load the EXPORT functions when called from one level up;
-}
 
 =head1 SYNOPSIS
 

lib/AGAT/Levels.pm

@@ -14,10 +14,6 @@ use Exporter;
 
 our @ISA = qw(Exporter);
 our @EXPORT = qw( get_levels_info load_levels expose_levels get_feature_type_by_agat_value );
-sub import {
-  AGAT::Levels->export_to_level(1, @_); # to be able to load the EXPORT functions when direct call; (normal case)
-  AGAT::Levels->export_to_level(2, @_); # to be able to load the EXPORT functions when called from one level up;
-}
 
 =head1 SYNOPSIS
 

lib/AGAT/OmniscientI.pm

@@ -26,10 +26,6 @@ our @ISA = qw(Exporter);
 our @EXPORT = qw(get_level select_gff_format
 							modelate_utr_and_cds_features_from_exon_features_and_cds_start_stop
 							slurp_gff3_file_JD);
-sub import {
-	AGAT::OmniscientI->export_to_level(1, @_); # to be able to load the EXPORT functions when direct call; (normal case)
-	AGAT::OmniscientI->export_to_level(2, @_); # to be able to load the EXPORT functions when called from one level up;
-}
 
 =head1 SYNOPSIS
 

lib/AGAT/OmniscientO.pm

@@ -1,4 +1,4 @@
-	#!/usr/bin/perl -w
+#!/usr/bin/perl -w
 
 package AGAT::OmniscientO;
 
@@ -18,11 +18,6 @@ our @EXPORT = qw(print_ref_list_feature print_omniscient print_omniscient_as_mat
 print_omniscient_from_level1_id_list webapollo_compliant embl_compliant
 convert_omniscient_to_ensembl_style write_top_features prepare_gffout prepare_fileout);
 
-sub import {
-  AGAT::OmniscientO->export_to_level(1, @_); # to be able to load the EXPORT functions when direct call; (normal case)
-  AGAT::OmniscientO->export_to_level(2, @_); # to be able to load the EXPORT functions when called from one level up;
-}
-
 =head1 SYNOPSIS
 
   This is the code to output data store in Omniscient.

lib/AGAT/OmniscientStat.pm

@@ -17,11 +17,6 @@ use Exporter;
 our @ISA = qw(Exporter);
 our @EXPORT = qw( print_omniscient_statistics );
 
-sub import {
-  AGAT::OmniscientStat->export_to_level(1, @_); # to be able to load the EXPORT functions when direct call; (normal case)
-  AGAT::OmniscientStat->export_to_level(2, @_); # to be able to load the EXPORT functions when called from one level up;
-}
-
 =head1 SYNOPSIS
 
 This is the code to perform statisctis of data store in Omniscient.

lib/AGAT/OmniscientToGTF.pm

@@ -16,11 +16,6 @@ use Exporter;
 our @ISA = qw(Exporter);
 our @EXPORT = qw(print_omniscient_as_gtf);
 
-sub import {
-  AGAT::OmniscientToGTF->export_to_level(1, @_); # to be able to load the EXPORT functions when direct call; (normal case)
-  AGAT::OmniscientToGTF->export_to_level(2, @_); # to be able to load the EXPORT functions when called from one level up;
-}
-
 # --------------------------- INFO ---------------------------
 # Set GTF version definitions
 #my @GTF3 = ("gene", "transcript", "exon", "CDS", "Selenocysteine", "start_codon", "stop_codon", "three_prime_utr", "five_prime_utr");

lib/AGAT/OmniscientTool.pm

@@ -33,11 +33,6 @@ remove_l1_and_relatives remove_l2_and_relatives remove_l3_and_relatives get_long
 check_mrna_positions check_features_overlap initialize_omni_from clean_clone
 create_omniscient get_cds_from_l2 merge_overlap_loci get_uniq_id );
 
-sub import {
-  AGAT::OmniscientTool->export_to_level(1, @_); # to be able to load the EXPORT functions when direct call; (normal case)
-  AGAT::OmniscientTool->export_to_level(2, @_); # to be able to load the EXPORT functions when called from one level up;
-}
-
 =head1 SYNOPSIS
 
 This is the code to handle data store in Omniscient.

lib/AGAT/PlotR.pm

@@ -15,10 +15,6 @@ use AGAT::Utilities;
 
 our @ISA         = qw(Exporter);
 our @EXPORT   = qw(execute_R_command rcc_density_one_row_per_file rcc_plot_from_list may_i_plot);
-sub import {
-  AGAT::PlotR->export_to_level(1, @_); # to be able to load the EXPORT functions when direct call; (normal case)
-  AGAT::PlotR->export_to_level(2, @_); # to be able to load the EXPORT functions when called from one level up;
-}
 
 =head1 SYNOPSIS
 

lib/AGAT/Utilities.pm

@@ -13,11 +13,6 @@ our @EXPORT = qw(exists_keys exists_undef_value get_proper_codon_table surround_
 sizedPrint activate_warning_limit print_time dual_print file_text_line print_wrap_text
 string_sep_to_hash);
 
-sub import {
-  AGAT::Utilities->export_to_level(1, @_); # to be able to load the EXPORT functions when direct call; (normal case)
-  AGAT::Utilities->export_to_level(2, @_); # to be able to load the EXPORT functions when called from one level up;
-}
-
 =head1 SYNOPSIS
 
  package containing utility tools