From: Tara L Andrews <tla@mit.edu>
Date: Thu, 13 Sep 2012 14:40:17 +0000 (+0200)
Subject: split off stemma analysis modules from base Tradition layer
X-Git-Url: http://git.shadowcat.co.uk/gitweb/gitweb.cgi?a=commitdiff_plain;h=951ddfe8781b6111653ed8074488e5ddb65178f7;p=scpubgit%2Fstemmatology.git

split off stemma analysis modules from base Tradition layer
---

diff --git a/.gitignore b/.gitignore
index 484a79c..b00040d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,11 +1,22 @@
 *~
-*.bbprojectd/
-t/var
+*/t/var
 data
-!/t/data
+!*/t/data
 Makefile
 Makefile.old
 META.yml
 blib
 db
 inc
+blib/
+.build/
+_build/
+cover_db/
+inc/
+Build
+Build.bat
+.last_cover_stats
+MANIFEST.bak
+MYMETA.yml
+nytprof.out
+pm_to_blib
diff --git a/MANIFEST.SKIP b/MANIFEST.SKIP
deleted file mode 100644
index 441a8fe..0000000
--- a/MANIFEST.SKIP
+++ /dev/null
@@ -1,11 +0,0 @@
-lib/Text/Tradition/Parser/BaseText.pm
-lib/Text/Tradition/Parser/CollateText.pm
-lib/Text/Tradition/Parser/CTE.pm
-lib/Text/Tradition/Parser/KUL.pm
-lib/Text/Tradition/Analysis.pm
-lib/Text/Tradition/Analysis/Result.pm
-t/analysis.t
-t/text_tradition_analysis.t
-t/text_tradition_analysis_result.t
-.git/
-.gitignore
diff --git a/analysis/Makefile.PL b/analysis/Makefile.PL
new file mode 100644
index 0000000..62d8e49
--- /dev/null
+++ b/analysis/Makefile.PL
@@ -0,0 +1,26 @@
+#!/usr/bin/env perl
+
+use inc::Module::Install;
+author( 'Tara L Andrews <aurum@cpan.org>' );
+license( 'perl' );
+perl_version( '5.012' );
+all_from( 'lib/Text/Tradition/Analysis.pm' );
+requires( 'Algorithm::Diff' );
+requires( 'Bio::Phylo::IO' );
+requires( 'File::chdir' );
+requires( 'File::Which' );
+requires( 'Graph' );
+requires( 'Graph::Reader::Dot' );
+requires( 'IPC::Run' );
+requires( 'JSON' );
+requires( 'LWP::UserAgent' );
+requires( 'Moose' );
+requires( 'Moose::Role' );
+requires( 'Set::Scalar' );
+requires( 'Text::Tradition' );
+requires( 'Text::Tradition::Directory' );
+requires( 'Text::Tradition::Error' );
+requires( 'TryCatch' );
+
+build_requires( 'Test::More::UTF8' );
+&WriteAll;
diff --git a/lib/Text/Tradition/Analysis.pm b/analysis/lib/Text/Tradition/Analysis.pm
similarity index 97%
rename from lib/Text/Tradition/Analysis.pm
rename to analysis/lib/Text/Tradition/Analysis.pm
index e1a69cd..3b76ca1 100644
--- a/lib/Text/Tradition/Analysis.pm
+++ b/analysis/lib/Text/Tradition/Analysis.pm
@@ -14,8 +14,10 @@ use Text::Tradition::Directory;
 use Text::Tradition::Stemma;
 use TryCatch;
 
-use vars qw/ @EXPORT_OK /;
+use vars qw/ @EXPORT_OK $VERSION /;
 @EXPORT_OK = qw/ run_analysis group_variants analyze_variant_location wit_stringify /;
+$VERSION = "1.0";
+
 
 my $SOLVER_URL = 'http://byzantini.st/cgi-bin/graphcalc.cgi';
 my $unsolved_problems = {};
@@ -32,6 +34,7 @@ Text::Tradition::Analysis - functions for stemma analysis of a tradition
     'name' => 'this is a text',
     'input' => 'TEI',
     'file' => '/path/to/tei_parallel_seg_file.xml' );
+  $t->enable_stemmata;
   $t->add_stemma( 'dotfile' => $stemmafile );
 
   my $variant_data = run_analysis( $tradition );
@@ -41,9 +44,18 @@ Text::Tradition::Analysis - functions for stemma analysis of a tradition
 =head1 DESCRIPTION
 
 Text::Tradition is a library for representation and analysis of collated
-texts, particularly medieval ones.  The Collation is the central feature of
-a Tradition, where the text, its sequence of readings, and its relationships
-between readings are actually kept.
+texts, particularly medieval ones.  Where the Collation is the central feature of
+a Tradition, it may also have one or more temmata associated with it, and these stemmata may be analyzed. This package provides the following modules:
+
+=over 4
+
+=item * L<Text::Tradition::HasStemma> - a role that can be composed into Text::Tradition objects, providing the ability for Text::Tradition::Stemma objects to be associated with them.
+
+=item * L<Text::Tradition::Stemma> - an object class that represents stemma hypotheses, both rooted (with a single archetype) and unrooted (e.g. phylogenetic trees).
+
+=item * Text::Tradition::Analysis (this package). Provides functions for the analysis of a given stemma against the collation within a given Tradition.
+
+=back
 
 =head1 SUBROUTINES
 
@@ -75,6 +87,7 @@ my $datafile = 't/data/florilegium_tei_ps.xml';
 my $tradition = Text::Tradition->new( 'input' => 'TEI',
                                       'name' => 'test0',
                                       'file' => $datafile );
+$tradition->enable_stemmata;
 my $s = $tradition->add_stemma( 'dotfile' => 't/data/florilegium.dot' );
 is( ref( $s ), 'Text::Tradition::Stemma', "Added stemma to tradition" );
 
diff --git a/lib/Text/Tradition/Analysis/Result.pm b/analysis/lib/Text/Tradition/Analysis/Result.pm
similarity index 99%
rename from lib/Text/Tradition/Analysis/Result.pm
rename to analysis/lib/Text/Tradition/Analysis/Result.pm
index da1e123..2e920ff 100644
--- a/lib/Text/Tradition/Analysis/Result.pm
+++ b/analysis/lib/Text/Tradition/Analysis/Result.pm
@@ -88,6 +88,7 @@ my $datafile = 't/data/florilegium_tei_ps.xml';
 my $tradition = Text::Tradition->new( 'input' => 'TEI',
                                       'name' => 'flortest',
                                       'file' => $datafile );
+$tradition->enable_stemmata;
 my $s = $tradition->add_stemma( 'dotfile' => 't/data/florilegium.dot' );
 
 my $sets = [ [ qw/ D Q / ], [ qw/ F H / ], [ qw/ A B C P S T / ] ];
diff --git a/analysis/lib/Text/Tradition/HasStemma.pm b/analysis/lib/Text/Tradition/HasStemma.pm
new file mode 100644
index 0000000..c797fab
--- /dev/null
+++ b/analysis/lib/Text/Tradition/HasStemma.pm
@@ -0,0 +1,105 @@
+package Text::Tradition::HasStemma;
+
+use strict;
+use warnings;
+use Moose::Role;
+use Text::Tradition::Stemma;
+
+=head1 NAME
+
+Text::Tradition::HasStemma - add-on to associate stemma hypotheses to Text::Tradition objects
+
+=head1 DESCRIPTION
+
+It is often the case that, for a given text tradition, the order of copying of the witnesses can or should be reconstructed (or at least the attempt should be made.) This class is a role that can be applied to Text::Tradition objects to record stemma hypotheses.  See the documentation for L<Text::Tradition::Stemma> for more information.
+
+=head1 METHODS
+
+=head2 stemmata
+
+Return a list of all stemmata associated with the tradition.
+
+=head2 stemma_count
+
+Return the number of stemma hypotheses defined for this tradition.
+
+=head2 stemma( $idx )
+
+Return the L<Text::Tradition::Stemma> object identified by the given index.
+
+=head2 clear_stemmata
+
+Delete all stemma hypotheses associated with this tradition.
+
+=cut
+
+has 'stemmata' => (
+	traits => ['Array'],
+	isa => 'ArrayRef[Text::Tradition::Stemma]',
+	handles => {
+		stemmata => 'elements',
+		_add_stemma => 'push',
+		stemma => 'get',
+		stemma_count => 'count',
+		clear_stemmata => 'clear',
+	},
+	default => sub { [] },
+	);
+  
+
+=head2 add_stemma( $dotfile )
+
+Initializes a Text::Tradition::Stemma object from the given dotfile,
+and associates it with the tradition.
+
+=begin testing
+
+use Text::Tradition;
+
+my $t = Text::Tradition->new( 
+    'name'  => 'simple test', 
+    'input' => 'Tabular',
+    'file'  => 't/data/simple.txt',
+    );
+$t->enable_stemmata;
+is( $t->stemma_count, 0, "No stemmas added yet" );
+my $s;
+ok( $s = $t->add_stemma( dotfile => 't/data/simple.dot' ), "Added a simple stemma" );
+is( ref( $s ), 'Text::Tradition::Stemma', "Got a stemma object returned" );
+is( $t->stemma_count, 1, "Tradition claims to have a stemma" );
+is( $t->stemma(0), $s, "Tradition hands back the right stemma" );
+
+=end testing
+
+=cut
+
+sub add_stemma {
+	my $self = shift;
+	my %opts = @_;
+	my $stemma_fh;
+	if( $opts{'dotfile'} ) {
+		open $stemma_fh, '<', $opts{'dotfile'}
+			or warn "Could not open file " . $opts{'dotfile'};
+	} elsif( $opts{'dot'} ) {
+		my $str = $opts{'dot'};
+		open $stemma_fh, '<', \$str;
+	}
+	# Assume utf-8
+	binmode $stemma_fh, ':utf8';
+	my $stemma = Text::Tradition::Stemma->new( 
+		'dot' => $stemma_fh );
+	$self->_add_stemma( $stemma ) if $stemma;
+	return $stemma;
+}
+
+1;
+
+=head1 LICENSE
+
+This package is free software and is provided "as is" without express
+or implied warranty.  You can redistribute it and/or modify it under
+the same terms as Perl itself.
+
+=head1 AUTHOR
+
+Tara L Andrews E<lt>aurum@cpan.orgE<gt>
diff --git a/lib/Text/Tradition/Stemma.pm b/analysis/lib/Text/Tradition/Stemma.pm
similarity index 99%
rename from lib/Text/Tradition/Stemma.pm
rename to analysis/lib/Text/Tradition/Stemma.pm
index 765547e..b88226b 100644
--- a/lib/Text/Tradition/Stemma.pm
+++ b/analysis/lib/Text/Tradition/Stemma.pm
@@ -1,6 +1,5 @@
 package Text::Tradition::Stemma;
 
-use Bio::Phylo::IO;
 use Encode qw( decode_utf8 );
 use File::Temp;
 use Graph;
diff --git a/lib/Text/Tradition/StemmaUtil.pm b/analysis/lib/Text/Tradition/StemmaUtil.pm
similarity index 99%
rename from lib/Text/Tradition/StemmaUtil.pm
rename to analysis/lib/Text/Tradition/StemmaUtil.pm
index 5c3f848..1aba28b 100644
--- a/lib/Text/Tradition/StemmaUtil.pm
+++ b/analysis/lib/Text/Tradition/StemmaUtil.pm
@@ -10,7 +10,6 @@ use File::chdir;
 use File::Temp;
 use File::Which;
 use Graph;
-use Graph::Reader::Dot;
 use IPC::Run qw/ run binary /;
 use Text::Tradition::Error;
 use Text::Tradition::Stemma;
diff --git a/t/00dependencies.t b/analysis/t/00dependencies.t
similarity index 100%
copy from t/00dependencies.t
copy to analysis/t/00dependencies.t
diff --git a/t/analysis.t b/analysis/t/analysis.t
similarity index 99%
rename from t/analysis.t
rename to analysis/t/analysis.t
index bc5661f..08ac38f 100755
--- a/t/analysis.t
+++ b/analysis/t/analysis.t
@@ -15,6 +15,7 @@ eval { no warnings; binmode $DB::OUT, ':utf8'; $DB::deep = 1000 };
 my $tradition = Text::Tradition->new(
 	'input' => 'Self',
 	'file' => 't/data/besoin.xml' );
+$tradition->enable_stemmata;
 $tradition->add_stemma( 'dotfile' => 't/data/besoin.dot' );
 
 # Run the analysis of the tradition
diff --git a/t/data/Collatex-16.xml b/analysis/t/data/Collatex-16.xml
similarity index 100%
copy from t/data/Collatex-16.xml
copy to analysis/t/data/Collatex-16.xml
diff --git a/t/data/analysis.db b/analysis/t/data/analysis.db
similarity index 100%
rename from t/data/analysis.db
rename to analysis/t/data/analysis.db
diff --git a/t/data/besoin.dot b/analysis/t/data/besoin.dot
similarity index 100%
rename from t/data/besoin.dot
rename to analysis/t/data/besoin.dot
diff --git a/t/data/besoin.xml b/analysis/t/data/besoin.xml
similarity index 100%
copy from t/data/besoin.xml
copy to analysis/t/data/besoin.xml
diff --git a/t/data/besoin_bad.dot b/analysis/t/data/besoin_bad.dot
similarity index 100%
rename from t/data/besoin_bad.dot
rename to analysis/t/data/besoin_bad.dot
diff --git a/t/data/florilegium.dot b/analysis/t/data/florilegium.dot
similarity index 100%
copy from t/data/florilegium.dot
copy to analysis/t/data/florilegium.dot
diff --git a/t/data/florilegium_tei_ps.xml b/analysis/t/data/florilegium_tei_ps.xml
similarity index 100%
copy from t/data/florilegium_tei_ps.xml
copy to analysis/t/data/florilegium_tei_ps.xml
diff --git a/t/data/simple.dot b/analysis/t/data/simple.dot
similarity index 100%
copy from t/data/simple.dot
copy to analysis/t/data/simple.dot
diff --git a/t/data/simple.txt b/analysis/t/data/simple.txt
similarity index 100%
copy from t/data/simple.txt
copy to analysis/t/data/simple.txt
diff --git a/t/inline2test.conf b/analysis/t/inline2test.conf
similarity index 100%
copy from t/inline2test.conf
copy to analysis/t/inline2test.conf
diff --git a/t/stemma.t b/analysis/t/stemma.t
similarity index 82%
rename from t/stemma.t
rename to analysis/t/stemma.t
index 84193a9..094c30b 100644
--- a/t/stemma.t
+++ b/analysis/t/stemma.t
@@ -6,8 +6,7 @@ use Test::More;
 use lib 'lib';
 use Text::Tradition;
 use Text::Tradition::StemmaUtil qw/ character_input phylip_pars parse_newick /;
-use XML::LibXML;
-use XML::LibXML::XPathContext;
+use TryCatch;
 
 my $datafile = 't/data/Collatex-16.xml'; #TODO need other test data
 
@@ -23,6 +22,7 @@ $c->add_relationship( 'n9', 'n10', { 'type' => 'spelling' } );
 $c->add_relationship( 'n12', 'n13', { 'type' => 'spelling' } );
 $c->calculate_ranks();
 
+$tradition->enable_stemmata;
 my $stemma = $tradition->add_stemma( dotfile => 't/data/simple.dot' );
 
 # Test for object creation
@@ -51,16 +51,16 @@ foreach my $ml ( @mlines ) {
 
 # Test that pars runs
 SKIP: {
-    skip "pars not in path", 3 unless File::Which::which('pars');
-    my $newick = phylip_pars( $mstr );
-    ok( $newick, "pars ran successfully" );
+	skip "pars not in path", 3 unless File::Which::which('pars');
+	my $newick = phylip_pars( $mstr );
+	ok( $newick, "pars ran successfully" );
 
 	my $trees = parse_newick( $newick );
-    # Test that we get a tree
-    is( scalar @$trees, 1, "Got a single tree" );
-    # Test that the tree has all our witnesses
-    my $tree = $trees->[0];
-    is( scalar $tree->witnesses, 3, "All witnesses in the tree" );
+	# Test that we get a tree
+	is( scalar @$trees, 1, "Got a single tree" );
+	# Test that the tree has all our witnesses
+	my $tree = $trees->[0];
+	is( scalar $tree->witnesses, 3, "All witnesses in the tree" );
 }
 
 # Test our dot output
@@ -71,5 +71,4 @@ ok( $display !~ /hypothetical/, "Graph is display rather than edit" );
 my $editable = $stemma->editable();
 ok( $editable =~ /digraph/, "Got a dot edit graph" );
 ok( $editable =~ /hypothetical/, "Graph contains an edit class" );
-
 done_testing();
diff --git a/t/text_tradition_analysis.t b/analysis/t/text_tradition_analysis.t
similarity index 98%
rename from t/text_tradition_analysis.t
rename to analysis/t/text_tradition_analysis.t
index f568b36..1ebf655 100644
--- a/t/text_tradition_analysis.t
+++ b/analysis/t/text_tradition_analysis.t
@@ -15,6 +15,7 @@ my $datafile = 't/data/florilegium_tei_ps.xml';
 my $tradition = Text::Tradition->new( 'input' => 'TEI',
                                       'name' => 'test0',
                                       'file' => $datafile );
+$tradition->enable_stemmata;
 my $s = $tradition->add_stemma( 'dotfile' => 't/data/florilegium.dot' );
 is( ref( $s ), 'Text::Tradition::Stemma', "Added stemma to tradition" );
 
diff --git a/t/text_tradition_analysis_result.t b/analysis/t/text_tradition_analysis_result.t
similarity index 99%
rename from t/text_tradition_analysis_result.t
rename to analysis/t/text_tradition_analysis_result.t
index e3462dc..2997818 100644
--- a/t/text_tradition_analysis_result.t
+++ b/analysis/t/text_tradition_analysis_result.t
@@ -20,6 +20,7 @@ my $datafile = 't/data/florilegium_tei_ps.xml';
 my $tradition = Text::Tradition->new( 'input' => 'TEI',
                                       'name' => 'flortest',
                                       'file' => $datafile );
+$tradition->enable_stemmata;
 my $s = $tradition->add_stemma( 'dotfile' => 't/data/florilegium.dot' );
 
 my $sets = [ [ qw/ D Q / ], [ qw/ F H / ], [ qw/ A B C P S T / ] ];
diff --git a/analysis/t/text_tradition_hasstemma.t b/analysis/t/text_tradition_hasstemma.t
new file mode 100644
index 0000000..ecf253e
--- /dev/null
+++ b/analysis/t/text_tradition_hasstemma.t
@@ -0,0 +1,30 @@
+#!/usr/bin/perl -w
+
+use strict;
+use Test::More 'no_plan';
+$| = 1;
+
+
+
+# =begin testing
+{
+use Text::Tradition;
+
+my $t = Text::Tradition->new( 
+    'name'  => 'simple test', 
+    'input' => 'Tabular',
+    'file'  => 't/data/simple.txt',
+    );
+$t->enable_stemmata;
+is( $t->stemma_count, 0, "No stemmas added yet" );
+my $s;
+ok( $s = $t->add_stemma( dotfile => 't/data/simple.dot' ), "Added a simple stemma" );
+is( ref( $s ), 'Text::Tradition::Stemma', "Got a stemma object returned" );
+is( $t->stemma_count, 1, "Tradition claims to have a stemma" );
+is( $t->stemma(0), $s, "Tradition hands back the right stemma" );
+}
+
+
+
+
+1;
diff --git a/t/text_tradition_stemma.t b/analysis/t/text_tradition_stemma.t
similarity index 100%
rename from t/text_tradition_stemma.t
rename to analysis/t/text_tradition_stemma.t
diff --git a/CHANGES b/base/CHANGES
similarity index 100%
rename from CHANGES
rename to base/CHANGES
diff --git a/base/MANIFEST.SKIP b/base/MANIFEST.SKIP
new file mode 100644
index 0000000..3b31671
--- /dev/null
+++ b/base/MANIFEST.SKIP
@@ -0,0 +1,5 @@
+lib/Text/Tradition/Parser/BaseText.pm
+lib/Text/Tradition/Parser/CollateText.pm
+lib/Text/Tradition/Parser/KUL.pm
+.git/
+.gitignore
diff --git a/Makefile.PL b/base/Makefile.PL
similarity index 96%
rename from Makefile.PL
rename to base/Makefile.PL
index 3aa72f4..c85aaa5 100644
--- a/Makefile.PL
+++ b/base/Makefile.PL
@@ -23,7 +23,9 @@ requires( 'KiokuX::Model' );
 requires( 'KiokuX::User::Util' );
 requires( 'Module::Load' );
 requires( 'Moose' );
+requires( 'Moose::Util' );
 requires( 'Moose::Util::TypeConstraints' );
+requires( 'Safe::Isa' );
 requires( 'Spreadsheet::ParseExcel' );
 requires( 'Spreadsheet::XLSX' );
 requires( 'StackTrace::Auto' );
diff --git a/TODO b/base/TODO
similarity index 100%
rename from TODO
rename to base/TODO
diff --git a/doc/graph_format.txt b/base/doc/graph_format.txt
similarity index 100%
rename from doc/graph_format.txt
rename to base/doc/graph_format.txt
diff --git a/idp_server/graphcalc.cgi b/base/idp_server/graphcalc.cgi
similarity index 100%
rename from idp_server/graphcalc.cgi
rename to base/idp_server/graphcalc.cgi
diff --git a/idp_server/graphcalc_worker.pl b/base/idp_server/graphcalc_worker.pl
similarity index 100%
rename from idp_server/graphcalc_worker.pl
rename to base/idp_server/graphcalc_worker.pl
diff --git a/lib/Text/Tradition.pm b/base/lib/Text/Tradition.pm
similarity index 87%
rename from lib/Text/Tradition.pm
rename to base/lib/Text/Tradition.pm
index 41e14cc..51258dc 100644
--- a/lib/Text/Tradition.pm
+++ b/base/lib/Text/Tradition.pm
@@ -3,10 +3,12 @@ package Text::Tradition;
 use JSON qw / from_json /;
 use Module::Load;
 use Moose;
+use Moose::Util qw/ does_role apply_all_roles /;
 use Text::Tradition::Collation;
-use Text::Tradition::Stemma;
+use Text::Tradition::Error;
 use Text::Tradition::Witness;
 use Text::Tradition::User;
+use TryCatch;
 
 use vars qw( $VERSION );
 $VERSION = "0.5";
@@ -42,19 +44,6 @@ has 'language' => (
 	predicate => 'has_language',
 	);
     
-has 'stemmata' => (
-	traits => ['Array'],
-	isa => 'ArrayRef[Text::Tradition::Stemma]',
-	handles => {
-		stemmata => 'elements',
-		_add_stemma => 'push',
-		stemma => 'get',
-		stemma_count => 'count',
-		clear_stemmata => 'clear',
-	},
-	default => sub { [] },
-	);
-  
 has '_initialized' => (
 	is => 'ro',
 	isa => 'Bool',
@@ -335,49 +324,25 @@ sub add_json_witnesses {
 	}
 }
 
-=head2 add_stemma( $dotfile )
-
-Initializes a Text::Tradition::Stemma object from the given dotfile,
-and associates it with the tradition.
-
-=begin testing
-
-use Text::Tradition;
+=head1 PLUGIN HOOKS
 
-my $t = Text::Tradition->new( 
-    'name'  => 'simple test', 
-    'input' => 'Tabular',
-    'file'  => 't/data/simple.txt',
-    );
-
-is( $t->stemma_count, 0, "No stemmas added yet" );
-my $s;
-ok( $s = $t->add_stemma( dotfile => 't/data/simple.dot' ), "Added a simple stemma" );
-is( ref( $s ), 'Text::Tradition::Stemma', "Got a stemma object returned" );
-is( $t->stemma_count, 1, "Tradition claims to have a stemma" );
-is( $t->stemma(0), $s, "Tradition hands back the right stemma" );
+=head2 enable_stemmata();
 
-=end testing
+If the tradition in question does not have the HasStemma role, make it so. Throws
+an error if the role (ergo, if the Analysis package) is not installed.
 
 =cut
 
-sub add_stemma {
+sub enable_stemmata {
 	my $self = shift;
-	my %opts = @_;
-	my $stemma_fh;
-	if( $opts{'dotfile'} ) {
-		open $stemma_fh, '<', $opts{'dotfile'}
-			or warn "Could not open file " . $opts{'dotfile'};
-	} elsif( $opts{'dot'} ) {
-		my $str = $opts{'dot'};
-		open $stemma_fh, '<', \$str;
+	my $rolename = 'Text::Tradition::HasStemma';
+	return 1 if does_role( $self, $rolename );
+	try {
+		apply_all_roles( $self, $rolename );
+	} catch {
+		throw( "Cannot apply role to enable stemmata; is the Analysis extension installed?" );
 	}
-	# Assume utf-8
-	binmode $stemma_fh, ':utf8';
-	my $stemma = Text::Tradition::Stemma->new( 
-		'dot' => $stemma_fh );
-	$self->_add_stemma( $stemma ) if $stemma;
-	return $stemma;
+	return 1;
 }
 
 sub lemmatize {
@@ -391,6 +356,13 @@ sub lemmatize {
 	$mod->can( 'lemmatize' )->( $self );
 }
 
+sub throw {
+	Text::Tradition::Error->throw( 
+		'ident' => 'Tradition error',
+		'message' => $_[0],
+		);
+}
+
 no Moose;
 __PACKAGE__->meta->make_immutable;
 
diff --git a/lib/Text/Tradition/Collation.pm b/base/lib/Text/Tradition/Collation.pm
similarity index 98%
rename from lib/Text/Tradition/Collation.pm
rename to base/lib/Text/Tradition/Collation.pm
index 022c2bc..d652850 100644
--- a/lib/Text/Tradition/Collation.pm
+++ b/base/lib/Text/Tradition/Collation.pm
@@ -897,6 +897,7 @@ readings.  This is the native transfer format for a tradition.
 =begin testing
 
 use Text::Tradition;
+use TryCatch;
 
 my $READINGS = 311;
 my $PATHS = 361;
@@ -930,11 +931,20 @@ is( scalar $st->collation->paths, $PATHS, "Reparsed collation has all paths" );
 is( scalar $st->collation->relationships, 3, "Reparsed collation has new relationships" );
 
 # Now add a stemma, write to GraphML, and look at the output.
-my $stemma = $tradition->add_stemma( 'dotfile' => 't/data/florilegium.dot' );
-is( ref( $stemma ), 'Text::Tradition::Stemma', "Parsed dotfile into stemma" );
-is( $tradition->stemmata, 1, "Tradition now has the stemma" );
-$graphml = $c->as_graphml;
-like( $graphml, qr/digraph/, "Digraph declaration exists in GraphML" );
+my $SKIP_STEMMA;
+try {
+	$tradition->enable_stemmata;
+} catch {
+	$SKIP_STEMMA = 1;
+}
+SKIP: {
+	skip "Analysis module not present", 3 if $SKIP_STEMMA;
+	my $stemma = $tradition->add_stemma( 'dotfile' => 't/data/florilegium.dot' );
+	is( ref( $stemma ), 'Text::Tradition::Stemma', "Parsed dotfile into stemma" );
+	is( $tradition->stemmata, 1, "Tradition now has the stemma" );
+	$graphml = $c->as_graphml;
+	like( $graphml, qr/digraph/, "Digraph declaration exists in GraphML" );
+}
 
 # Now add a user, write to GraphML, and look at the output.
 unlike( $graphml, qr/testuser/, "Test user name does not exist in GraphML yet" );
@@ -950,6 +960,7 @@ like( $graphml, qr/testuser/, "Test user name now exists in GraphML" );
 
 =cut
 
+## TODO MOVE this to Tradition.pm
 sub as_graphml {
     my( $self, $options ) = @_;
 	$self->calculate_ranks unless $self->_graphcalc_done;
@@ -1013,12 +1024,15 @@ sub as_graphml {
 	}
     # Extra custom keys for complex objects that should be saved in some form.
     # The subroutine should return a string, or undef/empty.
-    $graph_attributes{'stemmata'} = sub { 
-    	my @stemstrs;
-		map { push( @stemstrs, $_->editable( {linesep => ''} ) ) } 
-			$self->tradition->stemmata;
-		join( "\n", @stemstrs );
-	};
+    if( $tmeta->has_method('stemmata') ) {
+		$graph_attributes{'stemmata'} = sub { 
+			my @stemstrs;
+			map { push( @stemstrs, $_->editable( {linesep => ''} ) ) } 
+				$self->tradition->stemmata;
+			join( "\n", @stemstrs );
+		};
+	}
+	
     $graph_attributes{'user'} = sub { 
     	$self->tradition->user ? $self->tradition->user->id : undef 
     };
diff --git a/lib/Text/Tradition/Collation/Data.pm b/base/lib/Text/Tradition/Collation/Data.pm
similarity index 100%
rename from lib/Text/Tradition/Collation/Data.pm
rename to base/lib/Text/Tradition/Collation/Data.pm
diff --git a/lib/Text/Tradition/Collation/Reading.pm b/base/lib/Text/Tradition/Collation/Reading.pm
similarity index 100%
rename from lib/Text/Tradition/Collation/Reading.pm
rename to base/lib/Text/Tradition/Collation/Reading.pm
diff --git a/lib/Text/Tradition/Collation/Reading/Lexeme.pm b/base/lib/Text/Tradition/Collation/Reading/Lexeme.pm
similarity index 100%
rename from lib/Text/Tradition/Collation/Reading/Lexeme.pm
rename to base/lib/Text/Tradition/Collation/Reading/Lexeme.pm
diff --git a/lib/Text/Tradition/Collation/Reading/WordForm.pm b/base/lib/Text/Tradition/Collation/Reading/WordForm.pm
similarity index 100%
rename from lib/Text/Tradition/Collation/Reading/WordForm.pm
rename to base/lib/Text/Tradition/Collation/Reading/WordForm.pm
diff --git a/lib/Text/Tradition/Collation/Relationship.pm b/base/lib/Text/Tradition/Collation/Relationship.pm
similarity index 100%
rename from lib/Text/Tradition/Collation/Relationship.pm
rename to base/lib/Text/Tradition/Collation/Relationship.pm
diff --git a/lib/Text/Tradition/Collation/RelationshipStore.pm b/base/lib/Text/Tradition/Collation/RelationshipStore.pm
similarity index 100%
rename from lib/Text/Tradition/Collation/RelationshipStore.pm
rename to base/lib/Text/Tradition/Collation/RelationshipStore.pm
diff --git a/lib/Text/Tradition/Directory.pm b/base/lib/Text/Tradition/Directory.pm
similarity index 90%
rename from lib/Text/Tradition/Directory.pm
rename to base/lib/Text/Tradition/Directory.pm
index 0734168..542ad4d 100644
--- a/lib/Text/Tradition/Directory.pm
+++ b/base/lib/Text/Tradition/Directory.pm
@@ -8,6 +8,7 @@ use Encode qw/ decode_utf8 /;
 use KiokuDB::GC::Naive;
 use KiokuDB::TypeMap;
 use KiokuDB::TypeMap::Entry::Naive;
+use Safe::Isa;
 use Text::Tradition::Error;
 
 ## users
@@ -31,6 +32,7 @@ Text::Tradition::Directory - a KiokuDB interface for storing and retrieving trad
   );
   
   my $tradition = Text::Tradition->new( @args );
+  $tradition->enable_stemmata;
   my $stemma = $tradition->add_stemma( dotfile => $dotfile ); 
   $d->save_tradition( $tradition );
   
@@ -95,6 +97,7 @@ WARNING!! Garbage collection does not yet work. Use this sparingly.
 
 use TryCatch;
 use File::Temp;
+use Safe::Isa;
 use Text::Tradition;
 use_ok 'Text::Tradition::Directory';
 
@@ -108,26 +111,31 @@ my $t = Text::Tradition->new(
 	'input' => 'Tabular',
 	'file'  => 't/data/simple.txt',
 	);
+my $stemma_enabled;
+eval { $stemma_enabled = $t->enable_stemmata; };
 
 {
 	my $d = Text::Tradition::Directory->new( 'dsn' => $dsn,
 		'extra_args' => { 'create' => 1 } );
-	is( ref $d, 'Text::Tradition::Directory', "Got directory object" );
+	ok( $d->$_isa('Text::Tradition::Directory'), "Got directory object" );
 	
 	my $scope = $d->new_scope;
 	$uuid = $d->save( $t );
 	ok( $uuid, "Saved test tradition" );
 	
-	my $s = $t->add_stemma( dotfile => 't/data/simple.dot' );
-	ok( $d->save( $t ), "Updated tradition with stemma" );
-	is( $d->tradition( $uuid ), $t, "Correct tradition returned for id" );
-	is( $d->tradition( $uuid )->stemma(0), $s, "...and it has the correct stemma" );
-	try {
-		$d->save( $s );
-	} catch( Text::Tradition::Error $e ) {
-		is( $e->ident, 'database error', "Got exception trying to save stemma directly" );
-		like( $e->message, qr/Cannot directly save non-Tradition object/, 
-			"Exception has correct message" );
+	SKIP: {
+		skip "Analysis package not installed", 5 unless $stemma_enabled;
+		my $s = $t->add_stemma( dotfile => 't/data/simple.dot' );
+		ok( $d->save( $t ), "Updated tradition with stemma" );
+		is( $d->tradition( $uuid ), $t, "Correct tradition returned for id" );
+		is( $d->tradition( $uuid )->stemma(0), $s, "...and it has the correct stemma" );
+		try {
+			$d->save( $s );
+		} catch( Text::Tradition::Error $e ) {
+			is( $e->ident, 'database error', "Got exception trying to save stemma directly" );
+			like( $e->message, qr/Cannot directly save non-Tradition object/, 
+				"Exception has correct message" );
+		}
 	}
 }
 my $nt = Text::Tradition->new(
@@ -135,7 +143,7 @@ my $nt = Text::Tradition->new(
 	'input' => 'CollateX',
 	'file' => 't/data/Collatex-16.xml',
 	);
-is( ref( $nt ), 'Text::Tradition', "Made new tradition" );
+ok( $nt->$_isa('Text::Tradition'), "Made new tradition" );
 
 {
 	my $f = Text::Tradition::Directory->new( 'dsn' => $dsn );
@@ -149,24 +157,28 @@ is( ref( $nt ), 'Text::Tradition', "Made new tradition" );
 	my( $tlobj ) = grep { $_->{'id'} eq $uuid } @tlist;
 	is( $tlobj->{'name'}, $tf->name, "Directory index has correct tradition name" );
 	is( $tf->name, $t->name, "Retrieved the tradition from a new directory" );
-	my $sid = $f->object_to_id( $tf->stemma(0) );
-	try {
-		$f->tradition( $sid );
-	} catch( Text::Tradition::Error $e ) {
-		is( $e->ident, 'database error', "Got exception trying to fetch stemma directly" );
-		like( $e->message, qr/not a Text::Tradition/, "Exception has correct message" );
-	}
-	try {
-		$f->delete( $sid );
-	} catch( Text::Tradition::Error $e ) {
-		is( $e->ident, 'database error', "Got exception trying to delete stemma directly" );
-		like( $e->message, qr/Cannot directly delete non-Tradition object/, 
-			"Exception has correct message" );
+	my $sid;
+	SKIP: {
+		skip "Analysis package not installed", 4 unless $stemma_enabled;
+		$sid = $f->object_to_id( $tf->stemma(0) );
+		try {
+			$f->tradition( $sid );
+		} catch( Text::Tradition::Error $e ) {
+			is( $e->ident, 'database error', "Got exception trying to fetch stemma directly" );
+			like( $e->message, qr/not a Text::Tradition/, "Exception has correct message" );
+		}
+		try {
+			$f->delete( $sid );
+		} catch( Text::Tradition::Error $e ) {
+			is( $e->ident, 'database error', "Got exception trying to delete stemma directly" );
+			like( $e->message, qr/Cannot directly delete non-Tradition object/, 
+				"Exception has correct message" );
+		}
 	}
 	
 	$f->delete( $uuid );
 	ok( !$f->exists( $uuid ), "Object is deleted from DB" );
-	ok( !$f->exists( $sid ), "Object stemma also deleted from DB" );
+	ok( !$f->exists( $sid ), "Object stemma also deleted from DB" ) if $stemma_enabled;
 	is( scalar $f->traditionlist, 1, "Object is deleted from index" );
 }
 
@@ -256,12 +268,12 @@ before [ qw/ delete / ] => sub {
 	my $self = shift;
 	my @nontrad;
 	foreach my $obj ( @_ ) {
-		if( ref( $obj ) && ref( $obj ) ne 'Text::Tradition'
-            && ref ($obj) ne 'Text::Tradition::User' ) {
+		if( ref( $obj ) && !$obj->$_isa( 'Text::Tradition' )
+            && !$obj->$_isa('Text::Tradition::User') ) {
 			# Is it an id => Tradition hash?
 			if( ref( $obj ) eq 'HASH' && keys( %$obj ) == 1 ) {
 				my( $k ) = keys %$obj;
-				next if ref( $obj->{$k} ) eq 'Text::Tradition';
+				next if $obj->{$k}->$_isa('Text::Tradition');
 			}
 			push( @nontrad, $obj );
 		}
@@ -297,7 +309,7 @@ sub tradition {
 			}
 		}
 	}
-	if( $obj && ref( $obj ) ne 'Text::Tradition' ) {
+	if( $obj && !$obj->$_isa('Text::Tradition') ) {
 		throw( "Retrieved object is a " . ref( $obj ) . ", not a Text::Tradition" );
 	}
 	return $obj;
diff --git a/lib/Text/Tradition/Error.pm b/base/lib/Text/Tradition/Error.pm
similarity index 100%
rename from lib/Text/Tradition/Error.pm
rename to base/lib/Text/Tradition/Error.pm
diff --git a/lib/Text/Tradition/Language/Armenian.pm b/base/lib/Text/Tradition/Language/Armenian.pm
similarity index 100%
rename from lib/Text/Tradition/Language/Armenian.pm
rename to base/lib/Text/Tradition/Language/Armenian.pm
diff --git a/lib/Text/Tradition/Language/Base.pm b/base/lib/Text/Tradition/Language/Base.pm
similarity index 100%
rename from lib/Text/Tradition/Language/Base.pm
rename to base/lib/Text/Tradition/Language/Base.pm
diff --git a/lib/Text/Tradition/Language/English.pm b/base/lib/Text/Tradition/Language/English.pm
similarity index 100%
rename from lib/Text/Tradition/Language/English.pm
rename to base/lib/Text/Tradition/Language/English.pm
diff --git a/lib/Text/Tradition/Language/French.pm b/base/lib/Text/Tradition/Language/French.pm
similarity index 100%
rename from lib/Text/Tradition/Language/French.pm
rename to base/lib/Text/Tradition/Language/French.pm
diff --git a/lib/Text/Tradition/Language/Greek.pm b/base/lib/Text/Tradition/Language/Greek.pm
similarity index 100%
rename from lib/Text/Tradition/Language/Greek.pm
rename to base/lib/Text/Tradition/Language/Greek.pm
diff --git a/lib/Text/Tradition/Language/Latin.pm b/base/lib/Text/Tradition/Language/Latin.pm
similarity index 100%
rename from lib/Text/Tradition/Language/Latin.pm
rename to base/lib/Text/Tradition/Language/Latin.pm
diff --git a/lib/Text/Tradition/Language/Perseus.pm b/base/lib/Text/Tradition/Language/Perseus.pm
similarity index 100%
rename from lib/Text/Tradition/Language/Perseus.pm
rename to base/lib/Text/Tradition/Language/Perseus.pm
diff --git a/lib/Text/Tradition/Parser/BaseText.pm b/base/lib/Text/Tradition/Parser/BaseText.pm
similarity index 100%
rename from lib/Text/Tradition/Parser/BaseText.pm
rename to base/lib/Text/Tradition/Parser/BaseText.pm
diff --git a/lib/Text/Tradition/Parser/CTE.pm b/base/lib/Text/Tradition/Parser/CTE.pm
similarity index 100%
rename from lib/Text/Tradition/Parser/CTE.pm
rename to base/lib/Text/Tradition/Parser/CTE.pm
diff --git a/lib/Text/Tradition/Parser/CollateText.pm b/base/lib/Text/Tradition/Parser/CollateText.pm
similarity index 100%
rename from lib/Text/Tradition/Parser/CollateText.pm
rename to base/lib/Text/Tradition/Parser/CollateText.pm
diff --git a/lib/Text/Tradition/Parser/CollateX.pm b/base/lib/Text/Tradition/Parser/CollateX.pm
similarity index 100%
rename from lib/Text/Tradition/Parser/CollateX.pm
rename to base/lib/Text/Tradition/Parser/CollateX.pm
diff --git a/lib/Text/Tradition/Parser/GraphML.pm b/base/lib/Text/Tradition/Parser/GraphML.pm
similarity index 100%
rename from lib/Text/Tradition/Parser/GraphML.pm
rename to base/lib/Text/Tradition/Parser/GraphML.pm
diff --git a/lib/Text/Tradition/Parser/JSON.pm b/base/lib/Text/Tradition/Parser/JSON.pm
similarity index 100%
rename from lib/Text/Tradition/Parser/JSON.pm
rename to base/lib/Text/Tradition/Parser/JSON.pm
diff --git a/lib/Text/Tradition/Parser/KUL.pm b/base/lib/Text/Tradition/Parser/KUL.pm
similarity index 100%
rename from lib/Text/Tradition/Parser/KUL.pm
rename to base/lib/Text/Tradition/Parser/KUL.pm
diff --git a/lib/Text/Tradition/Parser/Self.pm b/base/lib/Text/Tradition/Parser/Self.pm
similarity index 89%
rename from lib/Text/Tradition/Parser/Self.pm
rename to base/lib/Text/Tradition/Parser/Self.pm
index 981a855..255f804 100644
--- a/lib/Text/Tradition/Parser/Self.pm
+++ b/base/lib/Text/Tradition/Parser/Self.pm
@@ -97,8 +97,10 @@ source of the XML to be parsed.
 =begin testing
 
 use File::Temp;
+use Safe::Isa;
 use Test::Warn;
 use Text::Tradition;
+use TryCatch;
 binmode STDOUT, ":utf8";
 binmode STDERR, ":utf8";
 eval { no warnings; binmode $DB::OUT, ":utf8"; };
@@ -110,7 +112,7 @@ my $t = Text::Tradition->new(
     'file'  => $tradition,
     );
 
-is( ref( $t ), 'Text::Tradition', "Parsed GraphML version 2" );
+ok( $t->$_isa('Text::Tradition'), "Parsed GraphML version 2" );
 if( $t ) {
     is( scalar $t->collation->readings, 319, "Collation has all readings" );
     is( scalar $t->collation->paths, 376, "Collation has all paths" );
@@ -120,7 +122,15 @@ if( $t ) {
 # TODO add a relationship, add a stemma, write graphml, reparse it, check that 
 # the new data is there
 $t->language('Greek');
-$t->add_stemma( 'dotfile' => 't/data/florilegium.dot' );
+my $stemma_enabled;
+try {
+	$stemma_enabled = $t->enable_stemmata;
+} catch {
+	ok( 1, "Skipping stemma tests without Analysis module" );
+}
+if( $stemma_enabled ) {
+	$t->add_stemma( 'dotfile' => 't/data/florilegium.dot' );
+}
 $t->collation->add_relationship( 'w12', 'w13', 
 	{ 'type' => 'grammatical', 'scope' => 'global', 
 	  'annotation' => 'This is some note' } );
@@ -128,7 +138,7 @@ ok( $t->collation->get_relationship( 'w12', 'w13' ), "Relationship set" );
 my $graphml_str = $t->collation->as_graphml;
 
 my $newt = Text::Tradition->new( 'input' => 'Self', 'string' => $graphml_str );
-is( ref( $newt ), 'Text::Tradition', "Parsed current GraphML version" );
+ok( $newt->$_isa('Text::Tradition'), "Parsed current GraphML version" );
 if( $newt ) {
     is( scalar $newt->collation->readings, 319, "Collation has all readings" );
     is( scalar $newt->collation->paths, 376, "Collation has all paths" );
@@ -138,8 +148,10 @@ if( $newt ) {
     my $rel = $newt->collation->get_relationship( 'w12', 'w13' );
     ok( $rel, "Found set relationship" );
     is( $rel->annotation, 'This is some note', "Relationship has its properties" );
-    is( scalar $newt->stemmata, 1, "Tradition has its stemma" );
-    is( $newt->stemma(0)->witnesses, $t->stemma(0)->witnesses, "Stemma has correct length witness list" );
+    if( $stemma_enabled ) {
+	    is( scalar $newt->stemmata, 1, "Tradition has its stemma" );
+    	is( $newt->stemma(0)->witnesses, $t->stemma(0)->witnesses, "Stemma has correct length witness list" );
+    }
 }
 
 # Test user save / restore
@@ -151,7 +163,7 @@ my $userstore = Text::Tradition::Directory->new( { dsn => $dsn,
 	extra_args => { create => 1 } } );
 my $scope = $userstore->new_scope();
 my $testuser = $userstore->create_user( { url => 'http://example.com' } );
-is( ref( $testuser ), 'Text::Tradition::User', "Created test user via userstore" );
+ok( $testuser->$_isa('Text::Tradition::User'), "Created test user via userstore" );
 $testuser->add_tradition( $newt );
 is( $newt->user->id, $testuser->id, "Assigned tradition to test user" );
 $graphml_str = $newt->collation->as_graphml;
@@ -164,6 +176,14 @@ $usert = Text::Tradition->new( 'input' => 'Self', 'string' => $graphml_str,
 	'userstore' => $userstore );
 is( $usert->user->id, $testuser->id, "Parsed tradition with userstore points to correct user" );
 
+# Test warning if we can
+unless( $stemma_enabled ) {
+	my $nst;
+	warnings_exist {
+		$nst = Text::Tradition->new( 'input' => 'Self', 'file' => 't/data/lexformat.xml' );
+	} [qr/DROPPING stemmata/],
+		"Got expected stemma drop warning on parse";
+}
 
 =end testing
 
@@ -190,9 +210,18 @@ sub parse {
 		if( $gkey eq 'version' ) {
 			$use_version = $val;
 		} elsif( $gkey eq 'stemmata' ) {
+			# Make sure we can handle stemmata
+			my $stemma_enabled;
+			try {
+				$stemma_enabled = $tradition->enable_stemmata;
+			} catch {
+				warn "Analysis module not installed; DROPPING stemmata";
+			}
 			# Parse the stemmata into objects
-			foreach my $dotstr ( split( /\n/, $val ) ) {
-				$tradition->add_stemma( 'dot' => $dotstr );
+			if( $stemma_enabled ) {
+				foreach my $dotstr ( split( /\n/, $val ) ) {
+					$tradition->add_stemma( 'dot' => $dotstr );
+				}
 			}
 		} elsif( $gkey eq 'user' ) {
 			# Assign the tradition to the user if we can
diff --git a/lib/Text/Tradition/Parser/TEI.pm b/base/lib/Text/Tradition/Parser/TEI.pm
similarity index 100%
rename from lib/Text/Tradition/Parser/TEI.pm
rename to base/lib/Text/Tradition/Parser/TEI.pm
diff --git a/lib/Text/Tradition/Parser/Tabular.pm b/base/lib/Text/Tradition/Parser/Tabular.pm
similarity index 100%
rename from lib/Text/Tradition/Parser/Tabular.pm
rename to base/lib/Text/Tradition/Parser/Tabular.pm
diff --git a/lib/Text/Tradition/Parser/Util.pm b/base/lib/Text/Tradition/Parser/Util.pm
similarity index 100%
rename from lib/Text/Tradition/Parser/Util.pm
rename to base/lib/Text/Tradition/Parser/Util.pm
diff --git a/lib/Text/Tradition/Store.pm b/base/lib/Text/Tradition/Store.pm
similarity index 100%
rename from lib/Text/Tradition/Store.pm
rename to base/lib/Text/Tradition/Store.pm
diff --git a/lib/Text/Tradition/TypeMap/Entry.pm b/base/lib/Text/Tradition/TypeMap/Entry.pm
similarity index 100%
rename from lib/Text/Tradition/TypeMap/Entry.pm
rename to base/lib/Text/Tradition/TypeMap/Entry.pm
diff --git a/lib/Text/Tradition/User.pm b/base/lib/Text/Tradition/User.pm
similarity index 100%
rename from lib/Text/Tradition/User.pm
rename to base/lib/Text/Tradition/User.pm
diff --git a/lib/Text/Tradition/UserStore.pm b/base/lib/Text/Tradition/UserStore.pm
similarity index 100%
rename from lib/Text/Tradition/UserStore.pm
rename to base/lib/Text/Tradition/UserStore.pm
diff --git a/lib/Text/Tradition/Witness.pm b/base/lib/Text/Tradition/Witness.pm
similarity index 100%
rename from lib/Text/Tradition/Witness.pm
rename to base/lib/Text/Tradition/Witness.pm
diff --git a/script/admin_users.pl b/base/script/admin_users.pl
similarity index 100%
rename from script/admin_users.pl
rename to base/script/admin_users.pl
diff --git a/script/analyze.pl b/base/script/analyze.pl
similarity index 100%
rename from script/analyze.pl
rename to base/script/analyze.pl
diff --git a/script/dblookup.pl b/base/script/dblookup.pl
similarity index 100%
rename from script/dblookup.pl
rename to base/script/dblookup.pl
diff --git a/script/group_vars.pl b/base/script/group_vars.pl
similarity index 100%
rename from script/group_vars.pl
rename to base/script/group_vars.pl
diff --git a/script/join_readings.pl b/base/script/join_readings.pl
similarity index 100%
rename from script/join_readings.pl
rename to base/script/join_readings.pl
diff --git a/script/majority_text.pl b/base/script/majority_text.pl
similarity index 100%
rename from script/majority_text.pl
rename to base/script/majority_text.pl
diff --git a/script/make_tradition.pl b/base/script/make_tradition.pl
similarity index 100%
rename from script/make_tradition.pl
rename to base/script/make_tradition.pl
diff --git a/script/maketestdb.sh b/base/script/maketestdb.sh
similarity index 100%
rename from script/maketestdb.sh
rename to base/script/maketestdb.sh
diff --git a/script/orth_case_links.pl b/base/script/orth_case_links.pl
similarity index 100%
rename from script/orth_case_links.pl
rename to base/script/orth_case_links.pl
diff --git a/script/poslink.pl b/base/script/poslink.pl
similarity index 100%
rename from script/poslink.pl
rename to base/script/poslink.pl
diff --git a/script/propagate_transitive.pl b/base/script/propagate_transitive.pl
similarity index 100%
rename from script/propagate_transitive.pl
rename to base/script/propagate_transitive.pl
diff --git a/script/statistics.pl b/base/script/statistics.pl
similarity index 100%
rename from script/statistics.pl
rename to base/script/statistics.pl
diff --git a/script/strip_punctuation.pl b/base/script/strip_punctuation.pl
similarity index 100%
rename from script/strip_punctuation.pl
rename to base/script/strip_punctuation.pl
diff --git a/t/00dependencies.t b/base/t/00dependencies.t
similarity index 100%
rename from t/00dependencies.t
rename to base/t/00dependencies.t
diff --git a/t/01app.t b/base/t/01app.t
similarity index 100%
rename from t/01app.t
rename to base/t/01app.t
diff --git a/t/02pod.t b/base/t/02pod.t
similarity index 100%
rename from t/02pod.t
rename to base/t/02pod.t
diff --git a/t/03podcoverage.t b/base/t/03podcoverage.t
similarity index 100%
rename from t/03podcoverage.t
rename to base/t/03podcoverage.t
diff --git a/t/bin/make-load-test.pl b/base/t/bin/make-load-test.pl
similarity index 100%
rename from t/bin/make-load-test.pl
rename to base/t/bin/make-load-test.pl
diff --git a/t/bin/update-load-test.pl b/base/t/bin/update-load-test.pl
similarity index 100%
rename from t/bin/update-load-test.pl
rename to base/t/bin/update-load-test.pl
diff --git a/t/data/Collatex-16.xml b/base/t/data/Collatex-16.xml
similarity index 100%
rename from t/data/Collatex-16.xml
rename to base/t/data/Collatex-16.xml
diff --git a/t/data/armexample.xls b/base/t/data/armexample.xls
similarity index 100%
rename from t/data/armexample.xls
rename to base/t/data/armexample.xls
diff --git a/t/data/armexample.xlsx b/base/t/data/armexample.xlsx
similarity index 100%
rename from t/data/armexample.xlsx
rename to base/t/data/armexample.xlsx
diff --git a/t/data/besoin.xml b/base/t/data/besoin.xml
similarity index 100%
rename from t/data/besoin.xml
rename to base/t/data/besoin.xml
diff --git a/t/data/cx16.json b/base/t/data/cx16.json
similarity index 100%
rename from t/data/cx16.json
rename to base/t/data/cx16.json
diff --git a/t/data/florilegium.csv b/base/t/data/florilegium.csv
similarity index 100%
rename from t/data/florilegium.csv
rename to base/t/data/florilegium.csv
diff --git a/t/data/florilegium.dot b/base/t/data/florilegium.dot
similarity index 100%
rename from t/data/florilegium.dot
rename to base/t/data/florilegium.dot
diff --git a/t/data/florilegium_graphml.xml b/base/t/data/florilegium_graphml.xml
similarity index 100%
rename from t/data/florilegium_graphml.xml
rename to base/t/data/florilegium_graphml.xml
diff --git a/t/data/florilegium_tei_cte.xml b/base/t/data/florilegium_tei_cte.xml
similarity index 100%
rename from t/data/florilegium_tei_cte.xml
rename to base/t/data/florilegium_tei_cte.xml
diff --git a/t/data/florilegium_tei_ps.xml b/base/t/data/florilegium_tei_ps.xml
similarity index 100%
rename from t/data/florilegium_tei_ps.xml
rename to base/t/data/florilegium_tei_ps.xml
diff --git a/t/data/john.xml b/base/t/data/john.xml
similarity index 100%
rename from t/data/john.xml
rename to base/t/data/john.xml
diff --git a/t/data/legendfrag.xml b/base/t/data/legendfrag.xml
similarity index 100%
rename from t/data/legendfrag.xml
rename to base/t/data/legendfrag.xml
diff --git a/t/data/lexformat.xml b/base/t/data/lexformat.xml
similarity index 100%
rename from t/data/lexformat.xml
rename to base/t/data/lexformat.xml
diff --git a/t/data/lf2.xml b/base/t/data/lf2.xml
similarity index 100%
rename from t/data/lf2.xml
rename to base/t/data/lf2.xml
diff --git a/t/data/load-save-benchmark.json b/base/t/data/load-save-benchmark.json
similarity index 100%
rename from t/data/load-save-benchmark.json
rename to base/t/data/load-save-benchmark.json
diff --git a/t/data/simple.dot b/base/t/data/simple.dot
similarity index 100%
rename from t/data/simple.dot
rename to base/t/data/simple.dot
diff --git a/t/data/simple.txt b/base/t/data/simple.txt
similarity index 100%
rename from t/data/simple.txt
rename to base/t/data/simple.txt
diff --git a/t/data/speed_test_load.sql b/base/t/data/speed_test_load.sql
similarity index 100%
rename from t/data/speed_test_load.sql
rename to base/t/data/speed_test_load.sql
diff --git a/t/data/witnesses/group.xml b/base/t/data/witnesses/group.xml
similarity index 100%
rename from t/data/witnesses/group.xml
rename to base/t/data/witnesses/group.xml
diff --git a/t/data/witnesses/teiwit.xml b/base/t/data/witnesses/teiwit.xml
similarity index 100%
rename from t/data/witnesses/teiwit.xml
rename to base/t/data/witnesses/teiwit.xml
diff --git a/t/data/witnesses/testwit.json b/base/t/data/witnesses/testwit.json
similarity index 100%
rename from t/data/witnesses/testwit.json
rename to base/t/data/witnesses/testwit.json
diff --git a/t/graph.t b/base/t/graph.t
similarity index 100%
rename from t/graph.t
rename to base/t/graph.t
diff --git a/t/inline2test.conf b/base/t/inline2test.conf
similarity index 100%
rename from t/inline2test.conf
rename to base/t/inline2test.conf
diff --git a/t/lexeme_serialize.t b/base/t/lexeme_serialize.t
similarity index 85%
rename from t/lexeme_serialize.t
rename to base/t/lexeme_serialize.t
index 7db1bae..401432b 100644
--- a/t/lexeme_serialize.t
+++ b/base/t/lexeme_serialize.t
@@ -1,6 +1,7 @@
 use lib 'lib';
 use strict;
 use warnings;
+use Safe::Isa;
 use Test::More;
 use Text::Tradition;
 
@@ -25,11 +26,11 @@ my $tf2 = Text::Tradition->new(
 	string => $graphmlstr,
 	language => 'French' );
 
-is( ref $tf2, 'Text::Tradition', "Re-parsed tradition with lemmatization" );
+ok( $tf2->$_isa('Text::Tradition'), "Re-parsed tradition with lemmatization" );
 is( $tf->name, $tf2->name, "Traditions have same name" );
 foreach my $r ( $tf->collation->readings ) {
 	my $r2 = $tf2->collation->reading( $r->id );
-	is( ref $r2, 'Text::Tradition::Collation::Reading',
+	ok( $r2->$_isa('Text::Tradition::Collation::Reading'),
 		"Reading $r exists in new tradition" );
 	if( $r2 ) {
 		is( scalar $r->lexemes, scalar $r2->lexemes,
@@ -41,7 +42,7 @@ foreach my $r ( $tf->collation->readings ) {
 my $tf3 = Text::Tradition->new(
 	'input' => 'Self',
 	'file' => 't/data/lexformat.xml' );
-is( ref $tf3, 'Text::Tradition', 
+ok( $tf3->$_isa('Text::Tradition'), 
 	"Successfully parsed tradition with incomplete lexemes" );
 
 done_testing();
diff --git a/t/load-save-speed.t b/base/t/load-save-speed.t
similarity index 98%
rename from t/load-save-speed.t
rename to base/t/load-save-speed.t
index ad4bf53..30837da 100644
--- a/t/load-save-speed.t
+++ b/base/t/load-save-speed.t
@@ -55,7 +55,7 @@ my $tradition = Text::Tradition->new(
 #    'input' => 'Tabular',
 #    'file' => 't/data/simple.txt',
 );
-$tradition->add_stemma(dotfile => "t/data/${test_name}.dot");
+#$tradition->add_stemma(dotfile => "t/data/${test_name}.dot");
 
 #my $fh = File::Temp->new();
 #my $file = $fh->filename;
diff --git a/t/text_tradition.t b/base/t/text_tradition.t
similarity index 74%
rename from t/text_tradition.t
rename to base/t/text_tradition.t
index 2c7be1b..7e1718a 100644
--- a/t/text_tradition.t
+++ b/base/t/text_tradition.t
@@ -47,25 +47,5 @@ is( scalar $s->witnesses, 3, "object has three witnesses again" );
 
 
 
-# =begin testing
-{
-use Text::Tradition;
-
-my $t = Text::Tradition->new( 
-    'name'  => 'simple test', 
-    'input' => 'Tabular',
-    'file'  => 't/data/simple.txt',
-    );
-
-is( $t->stemma_count, 0, "No stemmas added yet" );
-my $s;
-ok( $s = $t->add_stemma( dotfile => 't/data/simple.dot' ), "Added a simple stemma" );
-is( ref( $s ), 'Text::Tradition::Stemma', "Got a stemma object returned" );
-is( $t->stemma_count, 1, "Tradition claims to have a stemma" );
-is( $t->stemma(0), $s, "Tradition hands back the right stemma" );
-}
-
-
-
 
 1;
diff --git a/t/text_tradition_collation.t b/base/t/text_tradition_collation.t
similarity index 91%
rename from t/text_tradition_collation.t
rename to base/t/text_tradition_collation.t
index fc7abe1..f1bcba4 100644
--- a/t/text_tradition_collation.t
+++ b/base/t/text_tradition_collation.t
@@ -53,6 +53,7 @@ is( $c->reading('n21p0')->text, 'unto', "Reading n21p0 merged correctly" );
 # =begin testing
 {
 use Text::Tradition;
+use TryCatch;
 
 my $READINGS = 311;
 my $PATHS = 361;
@@ -86,11 +87,20 @@ is( scalar $st->collation->paths, $PATHS, "Reparsed collation has all paths" );
 is( scalar $st->collation->relationships, 3, "Reparsed collation has new relationships" );
 
 # Now add a stemma, write to GraphML, and look at the output.
-my $stemma = $tradition->add_stemma( 'dotfile' => 't/data/florilegium.dot' );
-is( ref( $stemma ), 'Text::Tradition::Stemma', "Parsed dotfile into stemma" );
-is( $tradition->stemmata, 1, "Tradition now has the stemma" );
-$graphml = $c->as_graphml;
-like( $graphml, qr/digraph/, "Digraph declaration exists in GraphML" );
+my $SKIP_STEMMA;
+try {
+	$tradition->enable_stemmata;
+} catch {
+	$SKIP_STEMMA = 1;
+}
+SKIP: {
+	skip "Analysis module not present", 3 if $SKIP_STEMMA;
+	my $stemma = $tradition->add_stemma( 'dotfile' => 't/data/florilegium.dot' );
+	is( ref( $stemma ), 'Text::Tradition::Stemma', "Parsed dotfile into stemma" );
+	is( $tradition->stemmata, 1, "Tradition now has the stemma" );
+	$graphml = $c->as_graphml;
+	like( $graphml, qr/digraph/, "Digraph declaration exists in GraphML" );
+}
 
 # Now add a user, write to GraphML, and look at the output.
 unlike( $graphml, qr/testuser/, "Test user name does not exist in GraphML yet" );
diff --git a/t/text_tradition_collation_relationshipstore.t b/base/t/text_tradition_collation_relationshipstore.t
similarity index 100%
rename from t/text_tradition_collation_relationshipstore.t
rename to base/t/text_tradition_collation_relationshipstore.t
diff --git a/t/text_tradition_directory.t b/base/t/text_tradition_directory.t
similarity index 55%
rename from t/text_tradition_directory.t
rename to base/t/text_tradition_directory.t
index 8950148..1eaa598 100644
--- a/t/text_tradition_directory.t
+++ b/base/t/text_tradition_directory.t
@@ -10,6 +10,7 @@ $| = 1;
 {
 use TryCatch;
 use File::Temp;
+use Safe::Isa;
 use Text::Tradition;
 use_ok 'Text::Tradition::Directory';
 
@@ -23,26 +24,31 @@ my $t = Text::Tradition->new(
 	'input' => 'Tabular',
 	'file'  => 't/data/simple.txt',
 	);
+my $stemma_enabled;
+eval { $stemma_enabled = $t->enable_stemmata; };
 
 {
 	my $d = Text::Tradition::Directory->new( 'dsn' => $dsn,
 		'extra_args' => { 'create' => 1 } );
-	is( ref $d, 'Text::Tradition::Directory', "Got directory object" );
+	ok( $d->$_isa('Text::Tradition::Directory'), "Got directory object" );
 	
 	my $scope = $d->new_scope;
 	$uuid = $d->save( $t );
 	ok( $uuid, "Saved test tradition" );
 	
-	my $s = $t->add_stemma( dotfile => 't/data/simple.dot' );
-	ok( $d->save( $t ), "Updated tradition with stemma" );
-	is( $d->tradition( $uuid ), $t, "Correct tradition returned for id" );
-	is( $d->tradition( $uuid )->stemma(0), $s, "...and it has the correct stemma" );
-	try {
-		$d->save( $s );
-	} catch( Text::Tradition::Error $e ) {
-		is( $e->ident, 'database error', "Got exception trying to save stemma directly" );
-		like( $e->message, qr/Cannot directly save non-Tradition object/, 
-			"Exception has correct message" );
+	SKIP: {
+		skip "Analysis package not installed", 5 unless $stemma_enabled;
+		my $s = $t->add_stemma( dotfile => 't/data/simple.dot' );
+		ok( $d->save( $t ), "Updated tradition with stemma" );
+		is( $d->tradition( $uuid ), $t, "Correct tradition returned for id" );
+		is( $d->tradition( $uuid )->stemma(0), $s, "...and it has the correct stemma" );
+		try {
+			$d->save( $s );
+		} catch( Text::Tradition::Error $e ) {
+			is( $e->ident, 'database error', "Got exception trying to save stemma directly" );
+			like( $e->message, qr/Cannot directly save non-Tradition object/, 
+				"Exception has correct message" );
+		}
 	}
 }
 my $nt = Text::Tradition->new(
@@ -50,7 +56,7 @@ my $nt = Text::Tradition->new(
 	'input' => 'CollateX',
 	'file' => 't/data/Collatex-16.xml',
 	);
-is( ref( $nt ), 'Text::Tradition', "Made new tradition" );
+ok( $nt->$_isa('Text::Tradition'), "Made new tradition" );
 
 {
 	my $f = Text::Tradition::Directory->new( 'dsn' => $dsn );
@@ -64,24 +70,28 @@ is( ref( $nt ), 'Text::Tradition', "Made new tradition" );
 	my( $tlobj ) = grep { $_->{'id'} eq $uuid } @tlist;
 	is( $tlobj->{'name'}, $tf->name, "Directory index has correct tradition name" );
 	is( $tf->name, $t->name, "Retrieved the tradition from a new directory" );
-	my $sid = $f->object_to_id( $tf->stemma(0) );
-	try {
-		$f->tradition( $sid );
-	} catch( Text::Tradition::Error $e ) {
-		is( $e->ident, 'database error', "Got exception trying to fetch stemma directly" );
-		like( $e->message, qr/not a Text::Tradition/, "Exception has correct message" );
-	}
-	try {
-		$f->delete( $sid );
-	} catch( Text::Tradition::Error $e ) {
-		is( $e->ident, 'database error', "Got exception trying to delete stemma directly" );
-		like( $e->message, qr/Cannot directly delete non-Tradition object/, 
-			"Exception has correct message" );
+	my $sid;
+	SKIP: {
+		skip "Analysis package not installed", 4 unless $stemma_enabled;
+		$sid = $f->object_to_id( $tf->stemma(0) );
+		try {
+			$f->tradition( $sid );
+		} catch( Text::Tradition::Error $e ) {
+			is( $e->ident, 'database error', "Got exception trying to fetch stemma directly" );
+			like( $e->message, qr/not a Text::Tradition/, "Exception has correct message" );
+		}
+		try {
+			$f->delete( $sid );
+		} catch( Text::Tradition::Error $e ) {
+			is( $e->ident, 'database error', "Got exception trying to delete stemma directly" );
+			like( $e->message, qr/Cannot directly delete non-Tradition object/, 
+				"Exception has correct message" );
+		}
 	}
 	
 	$f->delete( $uuid );
 	ok( !$f->exists( $uuid ), "Object is deleted from DB" );
-	ok( !$f->exists( $sid ), "Object stemma also deleted from DB" );
+	ok( !$f->exists( $sid ), "Object stemma also deleted from DB" ) if $stemma_enabled;
 	is( scalar $f->traditionlist, 1, "Object is deleted from index" );
 }
 
diff --git a/t/text_tradition_language_armenian.t b/base/t/text_tradition_language_armenian.t
similarity index 100%
rename from t/text_tradition_language_armenian.t
rename to base/t/text_tradition_language_armenian.t
diff --git a/t/text_tradition_language_english.t b/base/t/text_tradition_language_english.t
similarity index 100%
rename from t/text_tradition_language_english.t
rename to base/t/text_tradition_language_english.t
diff --git a/t/text_tradition_language_french.t b/base/t/text_tradition_language_french.t
similarity index 100%
rename from t/text_tradition_language_french.t
rename to base/t/text_tradition_language_french.t
diff --git a/t/text_tradition_language_greek.t b/base/t/text_tradition_language_greek.t
similarity index 100%
rename from t/text_tradition_language_greek.t
rename to base/t/text_tradition_language_greek.t
diff --git a/t/text_tradition_language_latin.t b/base/t/text_tradition_language_latin.t
similarity index 100%
rename from t/text_tradition_language_latin.t
rename to base/t/text_tradition_language_latin.t
diff --git a/t/text_tradition_parser_collatex.t b/base/t/text_tradition_parser_collatex.t
similarity index 100%
rename from t/text_tradition_parser_collatex.t
rename to base/t/text_tradition_parser_collatex.t
diff --git a/t/text_tradition_parser_json.t b/base/t/text_tradition_parser_json.t
similarity index 100%
rename from t/text_tradition_parser_json.t
rename to base/t/text_tradition_parser_json.t
diff --git a/t/text_tradition_parser_self.t b/base/t/text_tradition_parser_self.t
similarity index 74%
rename from t/text_tradition_parser_self.t
rename to base/t/text_tradition_parser_self.t
index 5583932..35aa695 100644
--- a/t/text_tradition_parser_self.t
+++ b/base/t/text_tradition_parser_self.t
@@ -9,8 +9,10 @@ $| = 1;
 # =begin testing
 {
 use File::Temp;
+use Safe::Isa;
 use Test::Warn;
 use Text::Tradition;
+use TryCatch;
 binmode STDOUT, ":utf8";
 binmode STDERR, ":utf8";
 eval { no warnings; binmode $DB::OUT, ":utf8"; };
@@ -22,7 +24,7 @@ my $t = Text::Tradition->new(
     'file'  => $tradition,
     );
 
-is( ref( $t ), 'Text::Tradition', "Parsed GraphML version 2" );
+ok( $t->$_isa('Text::Tradition'), "Parsed GraphML version 2" );
 if( $t ) {
     is( scalar $t->collation->readings, 319, "Collation has all readings" );
     is( scalar $t->collation->paths, 376, "Collation has all paths" );
@@ -32,7 +34,15 @@ if( $t ) {
 # TODO add a relationship, add a stemma, write graphml, reparse it, check that 
 # the new data is there
 $t->language('Greek');
-$t->add_stemma( 'dotfile' => 't/data/florilegium.dot' );
+my $stemma_enabled;
+try {
+	$stemma_enabled = $t->enable_stemmata;
+} catch {
+	ok( 1, "Skipping stemma tests without Analysis module" );
+}
+if( $stemma_enabled ) {
+	$t->add_stemma( 'dotfile' => 't/data/florilegium.dot' );
+}
 $t->collation->add_relationship( 'w12', 'w13', 
 	{ 'type' => 'grammatical', 'scope' => 'global', 
 	  'annotation' => 'This is some note' } );
@@ -40,7 +50,7 @@ ok( $t->collation->get_relationship( 'w12', 'w13' ), "Relationship set" );
 my $graphml_str = $t->collation->as_graphml;
 
 my $newt = Text::Tradition->new( 'input' => 'Self', 'string' => $graphml_str );
-is( ref( $newt ), 'Text::Tradition', "Parsed current GraphML version" );
+ok( $newt->$_isa('Text::Tradition'), "Parsed current GraphML version" );
 if( $newt ) {
     is( scalar $newt->collation->readings, 319, "Collation has all readings" );
     is( scalar $newt->collation->paths, 376, "Collation has all paths" );
@@ -50,8 +60,10 @@ if( $newt ) {
     my $rel = $newt->collation->get_relationship( 'w12', 'w13' );
     ok( $rel, "Found set relationship" );
     is( $rel->annotation, 'This is some note', "Relationship has its properties" );
-    is( scalar $newt->stemmata, 1, "Tradition has its stemma" );
-    is( $newt->stemma(0)->witnesses, $t->stemma(0)->witnesses, "Stemma has correct length witness list" );
+    if( $stemma_enabled ) {
+	    is( scalar $newt->stemmata, 1, "Tradition has its stemma" );
+    	is( $newt->stemma(0)->witnesses, $t->stemma(0)->witnesses, "Stemma has correct length witness list" );
+    }
 }
 
 # Test user save / restore
@@ -63,7 +75,7 @@ my $userstore = Text::Tradition::Directory->new( { dsn => $dsn,
 	extra_args => { create => 1 } } );
 my $scope = $userstore->new_scope();
 my $testuser = $userstore->create_user( { url => 'http://example.com' } );
-is( ref( $testuser ), 'Text::Tradition::User', "Created test user via userstore" );
+ok( $testuser->$_isa('Text::Tradition::User'), "Created test user via userstore" );
 $testuser->add_tradition( $newt );
 is( $newt->user->id, $testuser->id, "Assigned tradition to test user" );
 $graphml_str = $newt->collation->as_graphml;
@@ -75,6 +87,15 @@ warning_is {
 $usert = Text::Tradition->new( 'input' => 'Self', 'string' => $graphml_str,
 	'userstore' => $userstore );
 is( $usert->user->id, $testuser->id, "Parsed tradition with userstore points to correct user" );
+
+# Test warning if we can
+unless( $stemma_enabled ) {
+	my $nst;
+	warnings_exist {
+		$nst = Text::Tradition->new( 'input' => 'Self', 'file' => 't/data/lexformat.xml' );
+	} [qr/DROPPING stemmata/],
+		"Got expected stemma drop warning on parse";
+}
 }
 
 
diff --git a/t/text_tradition_parser_tabular.t b/base/t/text_tradition_parser_tabular.t
similarity index 100%
rename from t/text_tradition_parser_tabular.t
rename to base/t/text_tradition_parser_tabular.t
diff --git a/t/text_tradition_parser_tei.t b/base/t/text_tradition_parser_tei.t
similarity index 100%
rename from t/text_tradition_parser_tei.t
rename to base/t/text_tradition_parser_tei.t
diff --git a/t/text_tradition_user.t b/base/t/text_tradition_user.t
similarity index 100%
rename from t/text_tradition_user.t
rename to base/t/text_tradition_user.t
diff --git a/t/text_tradition_user_collapse.t b/base/t/text_tradition_user_collapse.t
similarity index 100%
rename from t/text_tradition_user_collapse.t
rename to base/t/text_tradition_user_collapse.t
diff --git a/t/text_tradition_witness.t b/base/t/text_tradition_witness.t
similarity index 100%
rename from t/text_tradition_witness.t
rename to base/t/text_tradition_witness.t