# $Id: Build.pm 16197 2009-09-29 15:50:47Z cjfields $
#
# BioPerl module for Bio::Root::Build
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Sendu Bala <bix@sendu.me.uk>
#
# Copyright Sendu Bala
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

Bio::Root::Build - A common Module::Build subclass base for BioPerl distributions

=head1 SYNOPSIS

  ...TO BE ADDED

=head1 DESCRIPTION

This is a subclass of Module::Build so we can override certain methods and do
fancy stuff

It was first written against Module::Build::Base v0.2805. Many of the methods
here are copy/pasted from there in their entirety just to change one or two
minor things, since for the most part Module::Build::Base code is hard to
cleanly override.

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Support 

Please direct usage questions or support issues to the mailing list:

I<bioperl-l@bioperl.org>

rather than to the module maintainer directly. Many experienced and 
reponsive experts will be able look at the problem and quickly 
address it. Please include a thorough description of the problem 
with code and data examples if at all possible.

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:

  http://bugzilla.open-bio.org/

=head1 AUTHOR - Sendu Bala

Email bix@sendu.me.uk

=head1 APPENDIX

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _

=cut

package Bio::Root::Build;

BEGIN {
    # we really need Module::Build to be installed
    eval "use base Module::Build; 1" or die "This package requires Module::Build v0.2805 or greater to install itself.\n$@";
    
    # ensure we'll be able to reload this module later by adding its path to inc
    use Cwd;
    use lib Cwd::cwd();
}

use strict;
use warnings;

our $VERSION = '1.006001';
our @extra_types = qw(options excludes_os feature_requires test); # test must always be last in the list!
our $checking_types = "requires|conflicts|".join("|", @extra_types);


# our modules are in Bio, not lib
sub find_pm_files {
    my $self = shift;
    foreach my $pm (@{$self->rscan_dir('Bio', qr/\.pm$/)}) {
        $self->{properties}{pm_files}->{$pm} = File::Spec->catfile('lib', $pm);
    }
    
    $self->_find_file_by_type('pm', 'lib');
}

# ask what scripts to install (this method is unique to bioperl)
sub choose_scripts {
    my $self = shift;
    my $accept = shift;
    
    # we can offer interactive installation by groups only if we have subdirs
    # in scripts and no .PLS files there
    opendir(my $scripts_dir, 'scripts') or die "Can't open directory 'scripts': $!\n";
    my $int_ok = 0;
    my @group_dirs;
    while (my $thing = readdir($scripts_dir)) {
        next if $thing =~ /^\./;
        next if $thing eq 'CVS';
        if ($thing =~ /PLS$|pl$/) {
            $int_ok = 0;
            last;
        }
        $thing = File::Spec->catfile('scripts', $thing);
        if (-d $thing) {
            $int_ok = 1;
            push(@group_dirs, $thing);
        }
    }
    closedir($scripts_dir);
    my $question = $int_ok ? "Install [a]ll BioPerl scripts, [n]one, or choose groups [i]nteractively?" : "Install [a]ll BioPerl scripts or [n]one?";
    
    my $prompt = $accept ? 'a' : $self->prompt($question, 'a');
    
    if ($prompt =~ /^[aA]/) {
        $self->log_info("  - will install all scripts\n");
        $self->notes(chosen_scripts => 'all');
    }
    elsif ($prompt =~ /^[iI]/) {
        $self->log_info("  - will install interactively:\n");
        
        my @chosen_scripts;
        foreach my $group_dir (@group_dirs) {
            my $group = File::Basename::basename($group_dir);
            print "    * group '$group' has:\n";
            
            my @script_files = @{$self->rscan_dir($group_dir, qr/\.PLS$|\.pl$/)};
            foreach my $script_file (@script_files) {
                my $script = File::Basename::basename($script_file);
                print "      $script\n";
            }
            
            my $result = $self->prompt("    Install scripts for group '$group'? [y]es [n]o [q]uit", 'n');
            die if $result =~ /^[qQ]/;
            if ($result =~ /^[yY]/) {
                $self->log_info("      + will install group '$group'\n");
                push(@chosen_scripts, @script_files);
            }
            else {
                $self->log_info("      - will not install group '$group'\n");
            }
        }
        
        my $chosen_scripts = @chosen_scripts ? join("|", @chosen_scripts) : 'none';
        
        $self->notes(chosen_scripts => $chosen_scripts);
    }
    else {
        $self->log_info("  - won't install any scripts\n");
        $self->notes(chosen_scripts => 'none');
    }
    
    print "\n";
}

# our version of script_files doesn't take args but just installs those scripts
# requested by the user after choose_scripts() is called. If it wasn't called,
# installs all scripts in scripts directory
sub script_files {
    my $self = shift;
    
    unless (-d 'scripts') {
        return {};
    }
    
    my $chosen_scripts = $self->notes('chosen_scripts');
    if ($chosen_scripts) {
        return if $chosen_scripts eq 'none';
        return { map {$_, 1} split(/\|/, $chosen_scripts) } unless $chosen_scripts eq 'all';
    }
    
    return $_ = { map {$_,1} @{$self->rscan_dir('scripts', qr/\.PLS$|\.pl$/)} };
}

# process scripts normally, except that we change name from *.PLS to bp_*.pl
sub process_script_files {
    my $self = shift;
    my $files = $self->find_script_files;
    return unless keys %$files;
  
    my $script_dir = File::Spec->catdir($self->blib, 'script');
    File::Path::mkpath( $script_dir );
    
    foreach my $file (keys %$files) {
        my $result = $self->copy_if_modified($file, $script_dir, 'flatten') or next;
        $self->fix_shebang_line($result) unless $self->os_type eq 'VMS';
        $self->make_executable($result);
        
        my $final = File::Basename::basename($result);
        $final =~ s/\.PLS$/\.pl/;                  # change from .PLS to .pl
        $final =~ s/^/bp_/ unless $final =~ /^bp/; # add the "bp" prefix
        $final = File::Spec->catfile($script_dir, $final);
        $self->log_info("$result -> $final\n");
        if (-e $final) {
            unlink $final || warn "[WARNING] Deleting '$final' failed!\n";
        }
        File::Copy::move($result, $final) or die "Can't rename '$result' to '$final': $!";
    }
}

# extended to handle extra checking types
sub features {
    my $self = shift;
    my $ph = $self->{phash};
    
    if (@_) {
        my $key = shift;
        if ($ph->{features}->exists($key)) {
            return $ph->{features}->access($key, @_);
        }
        
        if (my $info = $ph->{auto_features}->access($key)) {
            my $failures = $self->prereq_failures($info);
            my $disabled = grep( /^(?:\w+_)?(?:$checking_types)$/, keys %$failures ) ? 1 : 0;
            return !$disabled;
        }
        
        return $ph->{features}->access($key, @_);
    }
  
    # No args - get the auto_features & overlay the regular features
    my %features;
    my %auto_features = $ph->{auto_features}->access();
    while (my ($name, $info) = each %auto_features) {
        my $failures = $self->prereq_failures($info);
        my $disabled = grep( /^(?:\w+_)?(?:$checking_types)$/, keys %$failures ) ? 1 : 0;
        $features{$name} = $disabled ? 0 : 1;
    }
    %features = (%features, $ph->{features}->access());
  
    return wantarray ? %features : \%features;
}
*feature = \&features;

# overridden to fix a stupid bug in Module::Build and extended to handle extra
# checking types
sub check_autofeatures {
    my ($self) = @_;
    my $features = $self->auto_features;
    
    return unless %$features;
    
    $self->log_info("Checking features:\n");
    
    my $max_name_len = 0; # this wasn't set to 0 in Module::Build, causing warning in next line
    $max_name_len = ( length($_) > $max_name_len ) ? length($_) : $max_name_len for keys %$features;
    
    while (my ($name, $info) = each %$features) {
        $self->log_info("  $name" . '.' x ($max_name_len - length($name) + 4));
        if ($name eq 'PL_files') {
            print "got $name => $info\n";
            print "info has:\n";
            while (my ($key, $val) = each %$info) {
                print "  $key => $val\n";
            }
        }
        
        if ( my $failures = $self->prereq_failures($info) ) {
            my $disabled = grep( /^(?:\w+_)?(?:$checking_types)$/, keys %$failures ) ? 1 : 0;
            $self->log_info( $disabled ? "disabled\n" : "enabled\n" );
            
            my $log_text;
            while (my ($type, $prereqs) = each %$failures) {
                while (my ($module, $status) = each %$prereqs) {
                    my $required = ($type =~ /^(?:\w+_)?(?:requires|conflicts)$/) ? 1 : 0;
                    my $prefix = ($required) ? '-' : '*';
                    $log_text .= "    $prefix $status->{message}\n";
                }
            }
            $self->log_warn($log_text) if $log_text && ! $self->quiet;
        }
        else {
            $self->log_info("enabled\n");
        }
    }
    
    $self->log_info("\n");
}

# overriden just to hide pointless ugly warnings
sub check_installed_status {
    my $self = shift;
    open (my $olderr, ">&", \*STDERR);
    open(STDERR, "/dev/null");
    my $return = $self->SUPER::check_installed_status(@_);
    open(STDERR, ">&", $olderr);
    return $return;
}

# extend to handle option checking (which takes an array ref) and code test
# checking (which takes a code ref and must return a message only on failure)
# and excludes_os (which takes an array ref of regexps).
# also handles more informative output of recommends section
sub prereq_failures {
    my ($self, $info) = @_;
    
    my @types = (@{ $self->prereq_action_types }, @extra_types);
    $info ||= {map {$_, $self->$_()} @types};
    
    my $out = {};
    foreach my $type (@types) {
        my $prereqs = $info->{$type} || next;
        
        my $status = {};
        if ($type eq 'test') {
            unless (keys %$out) {
                if (ref($prereqs) eq 'CODE') {
                    $status->{message} = &{$prereqs};
                    
                    # drop the code-ref to avoid Module::Build trying to store
                    # it with Data::Dumper, generating warnings. (And also, may
                    # be expensive to run the sub multiple times.)
                    $info->{$type} = $status->{message};
                }
                else {
                    $status->{message} = $prereqs;
                }
                $out->{$type}{'test'} = $status if $status->{message};
            }
        }
        elsif ($type eq 'options') {
            my @not_ok;
            foreach my $wanted_option (@{$prereqs}) {
                unless ($self->args($wanted_option)) {
                    push(@not_ok, $wanted_option);
                }
            }
            
            if (@not_ok > 0) {
                $status->{message} = "Command line option(s) '@not_ok' not supplied";
                $out->{$type}{'options'} = $status;
            }
        }
        elsif ($type eq 'excludes_os') {
            foreach my $os (@{$prereqs}) {
                if ($^O =~ /$os/i) {
                    $status->{message} = "This feature isn't supported under your OS ($os)";
                    $out->{$type}{'excludes_os'} = $status;
                    last;
                }
            }
        }
        else {
            while ( my ($modname, $spec) = each %$prereqs ) {
                $status = $self->check_installed_status($modname, $spec);
                
                if ($type =~ /^(?:\w+_)?conflicts$/) {
                    next if !$status->{ok};
                    $status->{conflicts} = delete $status->{need};
                    $status->{message} = "$modname ($status->{have}) conflicts with this distribution";
                }
                elsif ($type =~ /^(?:\w+_)?recommends$/) {
                    next if $status->{ok};
                    
                    my ($preferred_version, $why, $by_what) = split("/", $spec);
                    $by_what = join(", ", split(",", $by_what));
                    $by_what =~ s/, (\S+)$/ and $1/;
                    
                    $status->{message} = (!ref($status->{have}) && $status->{have} eq '<none>'
                                  ? "Optional prerequisite $modname is not installed"
                                  : "$modname ($status->{have}) is installed, but we prefer to have $preferred_version");
                    
                    $status->{message} .= "\n   (wanted for $why, used by $by_what)";
                    
                    if ($by_what =~ /\[circular dependency!\]/) {
                        $preferred_version = -1;
                    }
                    
                    my $installed = $self->install_optional($modname, $preferred_version, $status->{message});
                    next if $installed eq 'ok';
                    $status->{message} = $installed unless $installed eq 'skip';
                }
                elsif ($type =~ /^feature_requires/) {
                    next if $status->{ok};
                    
                    # if there is a test code-ref, drop it to avoid
                    # Module::Build trying to store it with Data::Dumper,
                    # generating warnings.
                    delete $info->{test};
                }
                else {
                    next if $status->{ok};
                    
                    my $installed = $self->install_required($modname, $spec, $status->{message});
                    next if $installed eq 'ok';
                    $status->{message} = $installed;
                }
                
                $out->{$type}{$modname} = $status;
            }
        }
    }
    
    return keys %{$out} ? $out : return;
}

# install an external module using CPAN prior to testing and installation
# should only be called by install_required or install_optional
sub install_prereq {
    my ($self, $desired, $version, $required) = @_;
    
    if ($self->under_cpan) {
        # Just add to the required hash, which CPAN >= 1.81 will check prior
        # to install
        $self->{properties}{requires}->{$desired} = $version;
        $self->log_info("   I'll get CPAN to prepend the installation of this\n");
        return 'ok';
    }
    else {
        my $question = $required ?  "$desired is absolutely required prior to installation: shall I install it now using a CPAN shell?" :
                                    "To install $desired I'll need to open a CPAN shell right now; is that OK?";
        my $do_install = $self->y_n($question.' y/n', 'y');
        
        if ($do_install) {
            # Here we use CPAN to actually install the desired module, the benefit
            # being we continue even if installation fails, and that this works
            # even when not using CPAN to install.
            require Cwd;
            require CPAN;
            
            # Save this because CPAN will chdir all over the place.
            my $cwd = Cwd::cwd();
            
            CPAN::Shell->install($desired);
            my $msg;
            my $expanded = CPAN::Shell->expand("Module", $desired);
            if ($expanded && $expanded->uptodate) {
                $self->log_info("\n\n*** (back in BioPerl Build.PL) ***\n * You chose to install $desired and it installed fine\n");
                $msg = 'ok';
            }
            else {
                $self->log_info("\n\n*** (back in BioPerl Build.PL) ***\n");
                $msg = "You chose to install $desired but it failed to install";
            }
            
            chdir $cwd or die "Cannot chdir() back to $cwd: $!";
            return $msg;
        }
        else {
            return $required ? "You chose not to install the REQUIRED module $desired: you'd better install it yourself manually!" :
                               "Even though you wanted the optional module $desired, you chose not to actually install it: do it yourself manually.";
        }
    }
}

# install required modules listed in 'requires' or 'build_requires' arg to
# new that weren't already installed. Should only be called by prereq_failures
sub install_required {
    my ($self, $desired, $version, $msg) = @_;
    
    $self->log_info(" - ERROR: $msg\n");
    
    return $self->install_prereq($desired, $version, 1);
}

# install optional modules listed in 'recommends' arg to new that weren't
# already installed. Should only be called by prereq_failures
sub install_optional {
    my ($self, $desired, $version, $msg) = @_;
    
    unless (defined $self->{ask_optional}) {
        $self->{ask_optional} = $self->args->{accept}
                              ? 'n' : $self->prompt("Install [a]ll optional external modules, [n]one, or choose [i]nteractively?", 'n');
    }
    return 'skip' if $self->{ask_optional} =~ /^n/i;
    
    my $install;
    if ($self->{ask_optional} =~ /^a/i) {
        $self->log_info(" * $msg\n");
        $install = 1;
    }
    else {
        $install = $self->y_n(" * $msg\n   Do you want to install it? y/n", 'n');
    }
    
    my $orig_version = $version;
    $version = 0 if $version == -1;
    if ($install && ! ($self->{ask_optional} =~ /^a/i && $orig_version == -1)) {
        return $self->install_prereq($desired, $version);
    }
    else {
        my $circular = ($self->{ask_optional} =~ /^a/i && $orig_version == -1) ? " - this is a circular dependency so doesn't get installed when installing 'all' modules. If you really want it, choose modules interactively." : '';
        $self->log_info(" * You chose not to install $desired$circular\n");
        return 'ok';
    }
}

# there's no official way to discover if being run by CPAN, we take an approach
# similar to that of Module::AutoInstall
sub under_cpan {
    my $self = shift;
    
    unless (defined $self->{under_cpan}) {
        ## modified from Module::AutoInstall
        
        my $cpan_env = $ENV{PERl5_CPAN_IS_RUNNING};
        if ($ENV{PERL5_CPANPLUS_IS_RUNNING}) {
            $self->{under_cpan} = $cpan_env ? 'CPAN' : 'CPANPLUS';
        }
        
        require CPAN;
        
        unless (defined $self->{under_cpan}) {
            if ($CPAN::VERSION > '1.89') {
                if ($cpan_env) {
                    $self->{under_cpan} = 'CPAN';
                }
                else {
                    $self->{under_cpan} = 0;
                }
            }
        }
        
        unless (defined $self->{under_cpan}) {
            # load cpan config
            if ($CPAN::HandleConfig::VERSION) {
                # Newer versions of CPAN have a HandleConfig module
                CPAN::HandleConfig->load;
            }
            else {
                # Older versions had the load method in Config directly
                CPAN::Config->load;
            }
            
            # Find the CPAN lock-file
            my $lock = File::Spec->catfile($CPAN::Config->{cpan_home}, '.lock');
            if (-f $lock) {
                # Module::AutoInstall now goes on to open the lock file and compare
                # its pid to ours, but we're not in a situation where we expect
                # the pids to match, so we take the windows approach for all OSes:
                # find out if we're in cpan_home
                my $cwd  = File::Spec->canonpath(Cwd::cwd());
                my $cpan = File::Spec->canonpath($CPAN::Config->{cpan_home});
                
                $self->{under_cpan} = index($cwd, $cpan) > -1;
            }
        }
        
        if ($self->{under_cpan}) {
            $self->log_info("(I think I'm being run by CPAN/CPANPLUS, so will rely on it to handle prerequisite installation)\n");
        }
        else {
            $self->log_info("(I think you ran Build.PL directly, so will use CPAN to install prerequisites on demand)\n");
            $self->{under_cpan} = 0;
        }
    }
    
    return $self->{under_cpan};
}

# overridden simply to not print the default answer if chosen by hitting return
sub prompt {
    my $self = shift;
    my $mess = shift or die "prompt() called without a prompt message";
    
    my $def;
    if ( $self->_is_unattended && !@_ ) {
        die <<EOF;
ERROR: This build seems to be unattended, but there is no default value
for this question.  Aborting.
EOF
    }
    $def = shift if @_;
    ($def, my $dispdef) = defined $def ? ($def, "[$def] ") : ('', ' ');
    
    local $|=1;
    print "$mess $dispdef";
  
    my $ans = $self->_readline();
  
    if ( !defined($ans)        # Ctrl-D or unattended
         or !length($ans) ) {  # User hit return
        #print "$def\n"; didn't like this!
        $ans = $def;
    }
    
    return $ans;
}

# like the Module::Build version, except that we always get version from
# dist_version
sub find_dist_packages {
    my $self = shift;
    
    # Only packages in .pm files are candidates for inclusion here.
    # Only include things in the MANIFEST, not things in developer's
    # private stock.
    
    my $manifest = $self->_read_manifest('MANIFEST') or die "Can't find dist packages without a MANIFEST file - run 'manifest' action first";
    
    # Localize
    my %dist_files = map { $self->localize_file_path($_) => $_ } keys %$manifest;
    
    my @pm_files = grep {exists $dist_files{$_}} keys %{ $self->find_pm_files };
    
    my $actual_version = $self->dist_version;
    
    # First, we enumerate all packages & versions,
    # seperating into primary & alternative candidates
    my( %prime, %alt );
    foreach my $file (@pm_files) {
        next if $dist_files{$file} =~ m{^t/};  # Skip things in t/
        
        my @path = split( /\//, $dist_files{$file} );
        (my $prime_package = join( '::', @path[1..$#path] )) =~ s/\.pm$//;
        
        my $pm_info = Module::Build::ModuleInfo->new_from_file( $file );
        
        foreach my $package ( $pm_info->packages_inside ) {
            next if $package eq 'main';  # main can appear numerous times, ignore
            next if grep /^_/, split( /::/, $package ); # private package, ignore
            
            my $version = $pm_info->version( $package );
            if ($version && $version != $actual_version) {
                $self->log_warn("Package $package had version $version!\n");
            }
            $version = $actual_version;
            
            if ( $package eq $prime_package ) {
                if ( exists( $prime{$package} ) ) {
                    # M::B::ModuleInfo will handle this conflict
                    die "Unexpected conflict in '$package'; multiple versions found.\n";
                }
                else {
                    $prime{$package}{file} = $dist_files{$file};
                    $prime{$package}{version} = $version if defined( $version );
                }
            }
            else {
                push( @{$alt{$package}}, { file => $dist_files{$file}, version => $version } );
            }
        }
    }
    
    # Then we iterate over all the packages found above, identifying conflicts
    # and selecting the "best" candidate for recording the file & version
    # for each package.
    foreach my $package ( keys( %alt ) ) {
        my $result = $self->_resolve_module_versions( $alt{$package} );
        
        if ( exists( $prime{$package} ) ) { # primary package selected
            if ( $result->{err} ) {
                # Use the selected primary package, but there are conflicting
                 # errors amoung multiple alternative packages that need to be
                 # reported
                 $self->log_warn("Found conflicting versions for package '$package'\n" .
                                 "  $prime{$package}{file} ($prime{$package}{version})\n" . $result->{err});
            }
            elsif ( defined( $result->{version} ) ) {
                # There is a primary package selected, and exactly one
                # alternative package
                
                if ( exists( $prime{$package}{version} ) && defined( $prime{$package}{version} ) ) {
                    # Unless the version of the primary package agrees with the
                    # version of the alternative package, report a conflict
                    if ( $self->compare_versions( $prime{$package}{version}, '!=', $result->{version} ) ) {
                        $self->log_warn("Found conflicting versions for package '$package'\n" .
                                        "  $prime{$package}{file} ($prime{$package}{version})\n" .
                                        "  $result->{file} ($result->{version})\n");
                    }
                }
                else {
                  # The prime package selected has no version so, we choose to
                  # use any alternative package that does have a version
                  $prime{$package}{file}    = $result->{file};
                  $prime{$package}{version} = $result->{version};
                }
            }
            else {
                # no alt package found with a version, but we have a prime
                # package so we use it whether it has a version or not
            }
        }
        else { # No primary package was selected, use the best alternative
            if ( $result->{err} ) {
                $self->log_warn("Found conflicting versions for package '$package'\n" . $result->{err});
            }
            
            # Despite possible conflicting versions, we choose to record
            # something rather than nothing
            $prime{$package}{file}    = $result->{file};
            $prime{$package}{version} = $result->{version} if defined( $result->{version} );
        }
    }
  
    # Stringify versions
    for (grep exists $_->{version}, values %prime) {
        $_->{version} = $_->{version}->stringify if ref($_->{version});
    }
  
    return \%prime;
}

# our recommends syntax contains extra info that needs to be ignored at this
# stage
sub _parse_conditions {
    my ($self, $spec) = @_;
    
    ($spec) = split("/", $spec);
    
    if ($spec =~ /^\s*([\w.]+)\s*$/) { # A plain number, maybe with dots, letters, and underscores
        return (">= $spec");
    }
    else {
        return split /\s*,\s*/, $spec;
    }
}

# when generating META.yml, we output optional_features syntax (instead of
# recommends syntax). Note that as of CPAN v1.9402 nothing useful is done
# with this information, which is why we implement our own request to install
# the optional modules in install_optional().
# Also note that CPAN PLUS complains with an [ERROR] when it sees this META.yml,
# but it isn't fatal and installation continues fine.

# 'recommends' groups broken up now into separate modules and grouping the
# 'requires' instead of lumping modules together (quotes were choking YAML
# parsing). Now passes Parse::CPAN::Meta w/o errors.
# -cjfields 9-17-09

sub prepare_metadata {
    my ($self, $node, $keys) = @_;
    my $p = $self->{properties};
    
    # A little helper sub
    my $add_node = sub {
        my ($name, $val) = @_;
        $node->{$name} = $val;
        push @$keys, $name if $keys;
    };
    
    foreach (qw(dist_name dist_version dist_author dist_abstract license)) {
        (my $name = $_) =~ s/^dist_//;
        $add_node->($name, $self->$_());
        die "ERROR: Missing required field '$_' for META.yml\n" unless defined($node->{$name}) && length($node->{$name});
    }
    $node->{version} = '' . $node->{version}; # Stringify version objects
    
    if (defined( $self->license ) && defined( my $url = $self->valid_licenses->{ $self->license } )) {
        $node->{resources}{license} = $url;
    }
    
    foreach ( @{$self->prereq_action_types} ) {
        if (exists $p->{$_} and keys %{ $p->{$_} }) {
            if ($_ eq 'recommends') {
                my $hash;
                while (my ($req, $val) = each %{ $p->{$_} }) {
                    my ($ver, $why, $mods) = split("/", $val);
                    for my $used_by (split ',',$mods) {
                        $used_by =~ s{^(\S+)\s.*$}{$1};
                        if (exists $hash->{$used_by}) {
                            push @{$hash->{$used_by}->{requires}}, {$req => $ver};
                        } else {
                            $hash->{$used_by} = {description => $why,
                                    requires    => [{$req => $ver}]};
                        }
                    }
                }
                $add_node->('optional_features', $hash);
            }
            else {
                $add_node->($_, $p->{$_});
            }
        }
    }
    
    if (exists $p->{dynamic_config}) {
        $add_node->('dynamic_config', $p->{dynamic_config});
    }
    my $pkgs = eval { $self->find_dist_packages };
    if ($@) {
        $self->log_warn("$@\nWARNING: Possible missing or corrupt 'MANIFEST' file.\n" . "Nothing to enter for 'provides' field in META.yml\n");
    }
    else {
        $node->{provides} = $pkgs if %$pkgs;
    };
    
    if (exists $p->{no_index}) {
        $add_node->('no_index', $p->{no_index});
    }
    
    $add_node->('generated_by', "Module::Build version $Module::Build::VERSION");
    
    $add_node->('meta-spec', 
            {version => '1.2',
             url     => 'http://module-build.sourceforge.net/META-spec-v1.2.html',
            });
    
    while (my($k, $v) = each %{$self->meta_add}) {
        $add_node->($k, $v);
    }
    
    while (my($k, $v) = each %{$self->meta_merge}) {
        $self->_hash_merge($node, $k, $v);
    }
    
    return $node;
}

# let us store extra things persistently in _build
sub _construct {
    my $self = shift;
    
    # calling SUPER::_construct will dump some of the input to this sub out
    # with Data::Dumper, which will complain about code refs. So we replace
    # any code refs with dummies first, then put them back afterwards
    my %in_hash = @_;
    my $auto_features = $in_hash{auto_features} if defined $in_hash{auto_features};
    my %code_refs;
    if ($auto_features) {
        while (my ($key, $hash) = each %{$auto_features}) {
            while (my ($sub_key, $val) = each %{$hash}) {
                if (ref($val) && ref($val) eq 'CODE') {
                    $hash->{$sub_key} = 'CODE_ref';
                    $code_refs{$key}->{$sub_key} = $val;
                }
            }
        }
    }
    
    $self = $self->SUPER::_construct(@_);
    
    my ($p, $ph) = ($self->{properties}, $self->{phash});
    
    if (keys %code_refs) {
        while (my ($key, $hash) = each %{$auto_features}) {
            if (defined $code_refs{$key}) {
                while (my ($sub_key, $code_ref) = each %{$code_refs{$key}}) {
                    $hash->{$sub_key} = $code_ref;
                }
                $ph->{auto_features}->{$key} = $hash;
            }
        }
    }
    
    foreach (qw(manifest_skip post_install_scripts)) {
        my $file = File::Spec->catfile($self->config_dir, $_);
        $ph->{$_} = Module::Build::Notes->new(file => $file);
        $ph->{$_}->restore if -e $file;
    }
    
    return $self;
}
sub write_config {
    my $self = shift;
    $self->SUPER::write_config;
    
    # write extra things
    $self->{phash}{$_}->write() foreach qw(manifest_skip post_install_scripts);
    
    # be even more certain we can reload ourselves during a resume by copying
    # ourselves to _build\lib
    # this is only possible for the core distribution where we are actually
    # present in the distribution
    my $self_filename = File::Spec->catfile('Bio', 'Root', 'Build.pm');
    -e $self_filename || return;
    
    my $filename = File::Spec->catfile($self->{properties}{config_dir}, 'lib', 'Bio', 'Root', 'Build.pm');
    my $filedir  = File::Basename::dirname($filename);
    
    File::Path::mkpath($filedir);
    warn "Can't create directory $filedir: $!" unless -d $filedir;
    
    File::Copy::copy($self_filename, $filename);
    warn "Unable to copy 'Bio/Root/Build.pm' to '$filename'\n" unless -e $filename;
}

# add a file to the default MANIFEST.SKIP
sub add_to_manifest_skip {
    my $self = shift;
    my %files = map {$self->localize_file_path($_), 1} @_;
    $self->{phash}{manifest_skip}->write(\%files);
}

# we always generate a new MANIFEST and MANIFEST.SKIP here, instead of allowing
# existing files to remain
sub ACTION_manifest {
    my ($self) = @_;
    
    my $maniskip = 'MANIFEST.SKIP';
    if ( -e 'MANIFEST' || -e $maniskip ) {
        $self->log_warn("MANIFEST files already exist, will overwrite them\n");
        unlink('MANIFEST');
        unlink($maniskip);
    }
    $self->_write_default_maniskip($maniskip);
    
    require ExtUtils::Manifest;  # ExtUtils::Manifest is not warnings clean.
    local ($^W, $ExtUtils::Manifest::Quiet) = (0,1);
    ExtUtils::Manifest::mkmanifest();
}

# extended to add extra things to the default MANIFEST.SKIP
sub _write_default_maniskip {
    my $self = shift;
    $self->SUPER::_write_default_maniskip;
    
    my @extra = keys %{$self->{phash}{manifest_skip}->read};
    if (@extra) {
        open(my $fh, '>>', 'MANIFEST.SKIP') or die "Could not open MANIFEST.SKIP file\n";
        print $fh "\n# Avoid additional run-time generated things\n";
        foreach my $line (@extra) {
            print $fh $line, "\n";
        }
        close($fh);
    }
}

# extended to run scripts post-installation
sub ACTION_install {
  my ($self) = @_;
  require ExtUtils::Install;
  $self->depends_on('build');
  ExtUtils::Install::install($self->install_map, !$self->quiet, 0, $self->{args}{uninst}||0);
  $self->run_post_install_scripts;
}
sub add_post_install_script {
    my $self = shift;
    my %files = map {$self->localize_file_path($_), 1} @_;
    $self->{phash}{post_install_scripts}->write(\%files);
}
sub run_post_install_scripts {
    my $self = shift;
    my @scripts = keys %{$self->{phash}{post_install_scripts}->read};
    foreach my $script (@scripts) {
        $self->run_perl_script($script);
    }
}

# for use with auto_features, which should require LWP::UserAgent as one of
# its reqs
sub test_internet {
    eval {require LWP::UserAgent;};
    if ($@) {
        # ideally this won't happen because auto_feature already specified
        # LWP::UserAgent, so this sub wouldn't get called if LWP not installed
        return "LWP::UserAgent not installed";
    }
    my $ua = LWP::UserAgent->new;
    $ua->timeout(10);
    $ua->env_proxy;
    my $response = $ua->get('http://search.cpan.org/');
    unless ($response->is_success) {
        return "Could not connect to the internet (http://search.cpan.org/)";
    }
    return;
}

# nice directory names for dist-related actions
sub dist_dir {
    my ($self) = @_;
    my $version = $self->dist_version;
    if ($version =~ /^\d\.\d{6}\d$/) {
        # 1.x.x.100 returned as 1.x.x.1
        $version .= '00';
    }
    $version =~ s/00(\d)/$1./g;
    $version =~ s/\.$//;
    
    if (my ($minor, $rev) = $version =~ /^\d\.(\d)\.\d\.(\d+)$/) {
        my $dev = ! ($minor % 2 == 0);
        if ($rev == 100) {
            my $replace = $dev ? "_$rev" : '';
            $version =~ s/\.\d+$/$replace/;
        }
        elsif ($rev < 100) {
            $rev = sprintf("%03d", $rev);
            $version =~ s/\.\d+$/_$rev-RC/;
        }
        else {
            $rev -= 100 unless $dev;
            my $replace = $dev ? "_$rev" : ".$rev";
            $version =~ s/\.\d+$/$replace/;
        }
    }
    
    return "$self->{properties}{dist_name}-$version";
}
sub ppm_name {
    my $self = shift;
    return $self->dist_dir.'-ppm';
}

# generate complete ppd4 version file
sub ACTION_ppd {
    my $self = shift;
    
    my $file = $self->make_ppd(%{$self->{args}});
    $self->add_to_cleanup($file);
    $self->add_to_manifest_skip($file);
}

# add pod2htm temp files to MANIFEST.SKIP, generated during ppmdist most likely
sub htmlify_pods {
    my $self = shift;
    $self->SUPER::htmlify_pods(@_);
    $self->add_to_manifest_skip('pod2htm*');
}

# don't copy across man3 docs since they're of little use under Windows and
# have bad filenames
sub ACTION_ppmdist {
    my $self = shift;
    my @types = $self->install_types(1);
    $self->SUPER::ACTION_ppmdist(@_);
    $self->install_types(0);
}

# when supplied a true value, pretends libdoc doesn't exist (preventing man3
# installation for ppmdist). when supplied false, they exist again
sub install_types {
    my ($self, $no_libdoc) = @_;
    $self->{no_libdoc} = $no_libdoc if defined $no_libdoc;
    my @types = $self->SUPER::install_types;
    if ($self->{no_libdoc}) {
        my @altered_types;
        foreach my $type (@types) {
            push(@altered_types, $type) unless $type eq 'libdoc';
        }
        return @altered_types;
    }
    return @types;
}

# overridden from Module::Build::PPMMaker for ppd4 compatability
sub make_ppd {
    my ($self, %args) = @_;
    
    require Module::Build::PPMMaker;
    my $mbp = Module::Build::PPMMaker->new();
    
    my %dist;
    foreach my $info (qw(name author abstract version)) {
        my $method = "dist_$info";
        $dist{$info} = $self->$method() or die "Can't determine distribution's $info\n";
    }
    $dist{codebase} = $self->ppm_name.'.tar.gz';
    $mbp->_simple_xml_escape($_) foreach $dist{abstract}, $dist{codebase}, @{$dist{author}};
    
    my (undef, undef, undef, $mday, $mon, $year) = localtime();
    $year += 1900;
    $mon++;
    my $date = "$year-$mon-$mday";
    
    my $softpkg_version = $self->dist_dir;
    $softpkg_version =~ s/^$dist{name}-//;
    
    # to avoid a ppm bug, instead of including the requires in the softpackage
    # for the distribution we're making, we'll make a seperate Bundle::
    # softpackage that contains all the requires, and require only the Bundle in
    # the real softpackage
    my ($bundle_name) = $dist{name} =~ /^.+-(.+)/;
    $bundle_name ||= 'core';
    $bundle_name =~ s/^(\w)/\U$1/;
    my $bundle_dir = "Bundle-BioPerl-$bundle_name-$softpkg_version-ppm";
    my $bundle_file = "$bundle_dir.tar.gz";
    my $bundle_softpkg_name = "Bundle-BioPerl-$bundle_name";
    $bundle_name = "Bundle::BioPerl::$bundle_name";
    
    # header
    my $ppd = <<"PPD";
    <SOFTPKG NAME=\"$dist{name}\" VERSION=\"$softpkg_version\" DATE=\"$date\">
        <TITLE>$dist{name}</TITLE>
        <ABSTRACT>$dist{abstract}</ABSTRACT>
@{[ join "\n", map "        <AUTHOR>$_</AUTHOR>", @{$dist{author}} ]}
        <PROVIDE NAME=\"$dist{name}::\" VERSION=\"$dist{version}\"/>
PPD
    
    # provide section
    foreach my $pm (@{$self->rscan_dir('Bio', qr/\.pm$/)}) {
        # convert these filepaths to Module names
        $pm =~ s/\//::/g;
        $pm =~ s/\.pm//;
        
        $ppd .= sprintf(<<'EOF', $pm, $dist{version});
        <PROVIDE NAME="%s" VERSION="%s"/>
EOF
    }
    
    # rest of softpkg
    $ppd .= <<"PPD";
        <IMPLEMENTATION>
            <ARCHITECTURE NAME=\"MSWin32-x86-multi-thread-5.8\"/>
            <CODEBASE HREF=\"$dist{codebase}\"/>
            <REQUIRE NAME=\"$bundle_name\" VERSION=\"$dist{version}\"/>
        </IMPLEMENTATION>
    </SOFTPKG>
PPD
    
    # now a new softpkg for the bundle
    $ppd .= <<"PPD";
    
    <SOFTPKG NAME=\"$bundle_softpkg_name\" VERSION=\"$softpkg_version\" DATE=\"$date\">
        <TITLE>$bundle_name</TITLE>
        <ABSTRACT>Bundle of pre-requisites for $dist{name}</ABSTRACT>
@{[ join "\n", map "        <AUTHOR>$_</AUTHOR>", @{$dist{author}} ]}
        <PROVIDE NAME=\"$bundle_name\" VERSION=\"$dist{version}\"/>
        <IMPLEMENTATION>
            <ARCHITECTURE NAME=\"MSWin32-x86-multi-thread-5.8\"/>
            <CODEBASE HREF=\"$bundle_file\"/>
PPD
    
    # required section
    # we do both requires and recommends to make installation on Windows as
    # easy (mindless) as possible
    for my $type ('requires', 'recommends') {
        my $prereq = $self->$type;
        while (my ($modname, $version) = each %$prereq) {
            next if $modname eq 'perl';
            ($version) = split("/", $version) if $version =~ /\//;
            
            # Module names must have at least one ::
            unless ($modname =~ /::/) {
                $modname .= '::';
            }
            
            # Bio::Root::Version number comes out as triplet number like 1.5.2;
            # convert to our own version
            if ($modname eq 'Bio::Root::Version') {
                $version = $dist{version};
            }
            
            $ppd .= sprintf(<<'EOF', $modname, $version || '');
            <REQUIRE NAME="%s" VERSION="%s"/>
EOF
        }
    }
    
    # footer
    $ppd .= <<'EOF';
        </IMPLEMENTATION>
    </SOFTPKG>
EOF
    
    my $ppd_file = "$dist{name}.ppd";
    my $fh = IO::File->new(">$ppd_file") or die "Cannot write to $ppd_file: $!";
    print $fh $ppd;
    close $fh;
    
    $self->delete_filetree($bundle_dir);
    mkdir($bundle_dir) or die "Cannot create '$bundle_dir': $!";
    $self->make_tarball($bundle_dir);
    $self->delete_filetree($bundle_dir);
    $self->add_to_cleanup($bundle_file);
    $self->add_to_manifest_skip($bundle_file);
    
    return $ppd_file;
}

# we make all archive formats we want, not just .tar.gz
# we also auto-run manifest action, since we always want to re-create
# MANIFEST and MANIFEST.SKIP just-in-time
sub ACTION_dist {
    my ($self) = @_;
    
    $self->depends_on('manifest');
    $self->depends_on('distdir');
    
    my $dist_dir = $self->dist_dir;
    
    $self->make_zip($dist_dir);
    $self->make_tarball($dist_dir);
    $self->delete_filetree($dist_dir);
}

# makes zip file for windows users and bzip2 files as well
sub make_zip {
    my ($self, $dir, $file) = @_;
    $file ||= $dir;
    
    $self->log_info("Creating $file.zip\n");
    my $zip_flags = $self->verbose ? '-r' : '-rq';
    $self->do_system($self->split_like_shell("zip"), $zip_flags, "$file.zip", $dir);
    
    $self->log_info("Creating $file.bz2\n");
    require Archive::Tar;
    # Archive::Tar versions >= 1.09 use the following to enable a compatibility
    # hack so that the resulting archive is compatible with older clients.
    $Archive::Tar::DO_NOT_USE_PREFIX = 0;
    my $files = $self->rscan_dir($dir);
    Archive::Tar->create_archive("$file.tar", 0, @$files);
    $self->do_system($self->split_like_shell("bzip2"), "-k", "$file.tar");
}

# a method that can be called in a Build.PL script to ask the user if they want
# internet tests.
# Should only be called if you have tested for yourself that
# $build->feature('Network') is true
sub prompt_for_network {
    my ($self, $accept) = @_;

    my $proceed = $accept ? 0 : $self->y_n("Do you want to run tests that require connection to servers across the internet\n(likely to cause some failures)? y/n", 'n');
    
    if ($proceed) {
        $self->notes(network => 1);
        $self->log_info("  - will run internet-requiring tests\n");
    }
    else {
        $self->notes(network => 0);
        $self->log_info("  - will not run internet-requiring tests\n");
    }
}

1;
