Update new version:2.5 ChangeLog please see: https://github.com/lingpy/lingpy/issues

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: Update new version:2.5 ChangeLog please see: https://github.com/lingpy/lingpy/issues
From: K.I.A.Derouiche <kamel.derouiche%gmail.com@localhost>
Date: Fri, 07 Oct 2016 11:19:15 +0000
Module Name:	pkgsrc-wip
Committed By:	K.I.A.Derouiche <kamel.derouiche%gmail.com@localhost>
Pushed By:	jihbed
Date:		Fri Oct 7 11:19:15 2016 +0000
Changeset:	0b4da7b246c4dedd9949e1aecb4af7d7c7353a36

Modified Files:
	py-lingpy/Makefile
	py-lingpy/PLIST
	py-lingpy/distinfo

Log Message:
Update new version:2.5
ChangeLog please see: https://github.com/lingpy/lingpy/issues

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=0b4da7b246c4dedd9949e1aecb4af7d7c7353a36

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 py-lingpy/Makefile |  15 +-
 py-lingpy/PLIST    | 740 ++++++++++++++++++++++++++++++-----------------------
 py-lingpy/distinfo |   7 +-
 3 files changed, 428 insertions(+), 334 deletions(-)

diffs:
diff --git a/py-lingpy/Makefile b/py-lingpy/Makefile
index 9407d68..ea5b819 100644
--- a/py-lingpy/Makefile
+++ b/py-lingpy/Makefile
@@ -1,19 +1,20 @@
-# $NetBSD: Makefile,v 1.4 2014/06/01 12:49:43 thomasklausner Exp $
+# $NetBSD$
 
-DISTNAME=	lingpy-2.0
+DISTNAME=	lingpy-2.5
 PKGNAME=	${PYPKGPREFIX}-${DISTNAME}
-CATEGORIES=	devel
+CATEGORIES=	textproc
 MASTER_SITES=	${MASTER_SITE_PYPI:=l/lingpy/}
 
+
 MAINTAINER=	jihbed.research%gmail.com@localhost
 HOMEPAGE=	https://files.pythonhosted.org/packages/source/l/lingpy/
 COMMENT=	Python library for automatic tasks in historical linguistics
 LICENSE=	gnu-gpl-v3
 
-BROKEN=		Needs py-distribute which conflicts with py-setuptools which is pulled in by dependencies
-
-DEPENDS+=	${PYPKGPREFIX}-networkx>=1.7:../../math/py-networkx
-DEPENDS+=	${PYPKGPREFIX}-regex-[0-9]*:../../wip/py-regex
+DEPENDS+=	${PYPKGPREFIX}-six>=1.10.0:../../lang/py-six
+DEPENDS+=	${PYPKGPREFIX}-networkx>=1.11:../../math/py-networkx
+DEPENDS+=	${PYPKGPREFIX}-appdirs>=1.4.0:../../wip/py-appdirs
+DEPENDS+=	${PYPKGPREFIX}-pathlib>=1.0.1:../../wip/py-pathlib
 
 .include "../../lang/python/egg.mk"
 .include "../../math/py-numpy/buildlink3.mk"
diff --git a/py-lingpy/PLIST b/py-lingpy/PLIST
index d3f266e..babfc0e 100644
--- a/py-lingpy/PLIST
+++ b/py-lingpy/PLIST
@@ -1,13 +1,29 @@
-@comment $NetBSD: PLIST,v 1.1 2014/01/17 20:55:33 jihbed Exp $
+@comment $NetBSD$
+bin/lingpy
+${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
+${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
+${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
+${PYSITELIB}/${EGG_INFODIR}/entry_points.txt
+${PYSITELIB}/${EGG_INFODIR}/requires.txt
+${PYSITELIB}/${EGG_INFODIR}/top_level.txt
 ${PYSITELIB}/lingpy/__init__.py
 ${PYSITELIB}/lingpy/__init__.pyc
 ${PYSITELIB}/lingpy/__init__.pyo
+${PYSITELIB}/lingpy/__main__.py
+${PYSITELIB}/lingpy/__main__.pyc
+${PYSITELIB}/lingpy/__main__.pyo
 ${PYSITELIB}/lingpy/_settings.py
 ${PYSITELIB}/lingpy/_settings.pyc
 ${PYSITELIB}/lingpy/_settings.pyo
 ${PYSITELIB}/lingpy/algorithm/__init__.py
 ${PYSITELIB}/lingpy/algorithm/__init__.pyc
 ${PYSITELIB}/lingpy/algorithm/__init__.pyo
+${PYSITELIB}/lingpy/algorithm/_tree.py
+${PYSITELIB}/lingpy/algorithm/_tree.pyc
+${PYSITELIB}/lingpy/algorithm/_tree.pyo
+${PYSITELIB}/lingpy/algorithm/clustering.py
+${PYSITELIB}/lingpy/algorithm/clustering.pyc
+${PYSITELIB}/lingpy/algorithm/clustering.pyo
 ${PYSITELIB}/lingpy/algorithm/cython/__init__.py
 ${PYSITELIB}/lingpy/algorithm/cython/__init__.pyc
 ${PYSITELIB}/lingpy/algorithm/cython/__init__.pyo
@@ -29,12 +45,18 @@ ${PYSITELIB}/lingpy/algorithm/cython/_talign.pyo
 ${PYSITELIB}/lingpy/algorithm/cython/compilePYX.py
 ${PYSITELIB}/lingpy/algorithm/cython/compilePYX.pyc
 ${PYSITELIB}/lingpy/algorithm/cython/compilePYX.pyo
-${PYSITELIB}/lingpy/algorithm/distance.py
-${PYSITELIB}/lingpy/algorithm/distance.pyc
-${PYSITELIB}/lingpy/algorithm/distance.pyo
+${PYSITELIB}/lingpy/algorithm/extra.py
+${PYSITELIB}/lingpy/algorithm/extra.pyc
+${PYSITELIB}/lingpy/algorithm/extra.pyo
 ${PYSITELIB}/lingpy/align/__init__.py
 ${PYSITELIB}/lingpy/align/__init__.pyc
 ${PYSITELIB}/lingpy/align/__init__.pyo
+${PYSITELIB}/lingpy/align/_align/__init__.py
+${PYSITELIB}/lingpy/align/_align/__init__.pyc
+${PYSITELIB}/lingpy/align/_align/__init__.pyo
+${PYSITELIB}/lingpy/align/_align/confidence.py
+${PYSITELIB}/lingpy/align/_align/confidence.pyc
+${PYSITELIB}/lingpy/align/_align/confidence.pyo
 ${PYSITELIB}/lingpy/align/multiple.py
 ${PYSITELIB}/lingpy/align/multiple.pyc
 ${PYSITELIB}/lingpy/align/multiple.pyo
@@ -47,102 +69,218 @@ ${PYSITELIB}/lingpy/align/sca.pyo
 ${PYSITELIB}/lingpy/basic/__init__.py
 ${PYSITELIB}/lingpy/basic/__init__.pyc
 ${PYSITELIB}/lingpy/basic/__init__.pyo
-${PYSITELIB}/lingpy/basic/spreadsheet.py
-${PYSITELIB}/lingpy/basic/spreadsheet.pyc
-${PYSITELIB}/lingpy/basic/spreadsheet.pyo
+${PYSITELIB}/lingpy/basic/ops.py
+${PYSITELIB}/lingpy/basic/ops.pyc
+${PYSITELIB}/lingpy/basic/ops.pyo
+${PYSITELIB}/lingpy/basic/parser.py
+${PYSITELIB}/lingpy/basic/parser.pyc
+${PYSITELIB}/lingpy/basic/parser.pyo
+${PYSITELIB}/lingpy/basic/tree.py
+${PYSITELIB}/lingpy/basic/tree.pyc
+${PYSITELIB}/lingpy/basic/tree.pyo
 ${PYSITELIB}/lingpy/basic/wordlist.py
 ${PYSITELIB}/lingpy/basic/wordlist.pyc
 ${PYSITELIB}/lingpy/basic/wordlist.pyo
+${PYSITELIB}/lingpy/basic/workflow.py
+${PYSITELIB}/lingpy/basic/workflow.pyc
+${PYSITELIB}/lingpy/basic/workflow.pyo
+${PYSITELIB}/lingpy/cache.py
+${PYSITELIB}/lingpy/cache.pyc
+${PYSITELIB}/lingpy/cache.pyo
+${PYSITELIB}/lingpy/cli.py
+${PYSITELIB}/lingpy/cli.pyc
+${PYSITELIB}/lingpy/cli.pyo
 ${PYSITELIB}/lingpy/compare/__init__.py
 ${PYSITELIB}/lingpy/compare/__init__.pyc
 ${PYSITELIB}/lingpy/compare/__init__.pyo
-${PYSITELIB}/lingpy/compare/borrowing/__init__.py
-${PYSITELIB}/lingpy/compare/borrowing/__init__.pyc
-${PYSITELIB}/lingpy/compare/borrowing/__init__.pyo
-${PYSITELIB}/lingpy/compare/borrowing/_settings.py
-${PYSITELIB}/lingpy/compare/borrowing/_settings.pyc
-${PYSITELIB}/lingpy/compare/borrowing/_settings.pyo
-${PYSITELIB}/lingpy/compare/borrowing/convex_hull.py
-${PYSITELIB}/lingpy/compare/borrowing/convex_hull.pyc
-${PYSITELIB}/lingpy/compare/borrowing/convex_hull.pyo
-${PYSITELIB}/lingpy/compare/borrowing/polygon.py
-${PYSITELIB}/lingpy/compare/borrowing/polygon.pyc
-${PYSITELIB}/lingpy/compare/borrowing/polygon.pyo
-${PYSITELIB}/lingpy/compare/borrowing/trebor.py
-${PYSITELIB}/lingpy/compare/borrowing/trebor.pyc
-${PYSITELIB}/lingpy/compare/borrowing/trebor.pyo
+${PYSITELIB}/lingpy/compare/_phylogeny/__init__.py
+${PYSITELIB}/lingpy/compare/_phylogeny/__init__.pyc
+${PYSITELIB}/lingpy/compare/_phylogeny/__init__.pyo
+${PYSITELIB}/lingpy/compare/_phylogeny/_settings.py
+${PYSITELIB}/lingpy/compare/_phylogeny/_settings.pyc
+${PYSITELIB}/lingpy/compare/_phylogeny/_settings.pyo
+${PYSITELIB}/lingpy/compare/_phylogeny/convex_hull.py
+${PYSITELIB}/lingpy/compare/_phylogeny/convex_hull.pyc
+${PYSITELIB}/lingpy/compare/_phylogeny/convex_hull.pyo
+${PYSITELIB}/lingpy/compare/_phylogeny/polygon.py
+${PYSITELIB}/lingpy/compare/_phylogeny/polygon.pyc
+${PYSITELIB}/lingpy/compare/_phylogeny/polygon.pyo
+${PYSITELIB}/lingpy/compare/_phylogeny/utils.py
+${PYSITELIB}/lingpy/compare/_phylogeny/utils.pyc
+${PYSITELIB}/lingpy/compare/_phylogeny/utils.pyo
 ${PYSITELIB}/lingpy/compare/lexstat.py
 ${PYSITELIB}/lingpy/compare/lexstat.pyc
 ${PYSITELIB}/lingpy/compare/lexstat.pyo
-${PYSITELIB}/lingpy/compare/matrix.py
-${PYSITELIB}/lingpy/compare/matrix.pyc
-${PYSITELIB}/lingpy/compare/matrix.pyo
+${PYSITELIB}/lingpy/compare/partial.py
+${PYSITELIB}/lingpy/compare/partial.pyc
+${PYSITELIB}/lingpy/compare/partial.pyo
+${PYSITELIB}/lingpy/compare/phylogeny.py
+${PYSITELIB}/lingpy/compare/phylogeny.pyc
+${PYSITELIB}/lingpy/compare/phylogeny.pyo
+${PYSITELIB}/lingpy/compare/strings.py
+${PYSITELIB}/lingpy/compare/strings.pyc
+${PYSITELIB}/lingpy/compare/strings.pyo
+${PYSITELIB}/lingpy/compat.py
+${PYSITELIB}/lingpy/compat.pyc
+${PYSITELIB}/lingpy/compat.pyo
+${PYSITELIB}/lingpy/config.py
+${PYSITELIB}/lingpy/config.pyc
+${PYSITELIB}/lingpy/config.pyo
 ${PYSITELIB}/lingpy/convert/__init__.py
 ${PYSITELIB}/lingpy/convert/__init__.pyc
 ${PYSITELIB}/lingpy/convert/__init__.pyo
-${PYSITELIB}/lingpy/convert/csv.py
-${PYSITELIB}/lingpy/convert/csv.pyc
-${PYSITELIB}/lingpy/convert/csv.pyo
-${PYSITELIB}/lingpy/convert/gml.py
-${PYSITELIB}/lingpy/convert/gml.pyc
-${PYSITELIB}/lingpy/convert/gml.pyo
-${PYSITELIB}/lingpy/convert/misc.py
-${PYSITELIB}/lingpy/convert/misc.pyc
-${PYSITELIB}/lingpy/convert/misc.pyo
-${PYSITELIB}/lingpy/convert/newick.py
-${PYSITELIB}/lingpy/convert/newick.pyc
-${PYSITELIB}/lingpy/convert/newick.pyo
-${PYSITELIB}/lingpy/convert/nexus.py
-${PYSITELIB}/lingpy/convert/nexus.pyc
-${PYSITELIB}/lingpy/convert/nexus.pyo
-${PYSITELIB}/lingpy/convert/phylip.py
-${PYSITELIB}/lingpy/convert/phylip.pyc
-${PYSITELIB}/lingpy/convert/phylip.pyo
+${PYSITELIB}/lingpy/convert/graph.py
+${PYSITELIB}/lingpy/convert/graph.pyc
+${PYSITELIB}/lingpy/convert/graph.pyo
+${PYSITELIB}/lingpy/convert/html.py
+${PYSITELIB}/lingpy/convert/html.pyc
+${PYSITELIB}/lingpy/convert/html.pyo
 ${PYSITELIB}/lingpy/convert/plot.py
 ${PYSITELIB}/lingpy/convert/plot.pyc
 ${PYSITELIB}/lingpy/convert/plot.pyo
-${PYSITELIB}/lingpy/convert/utils.py
-${PYSITELIB}/lingpy/convert/utils.pyc
-${PYSITELIB}/lingpy/convert/utils.pyo
+${PYSITELIB}/lingpy/convert/strings.py
+${PYSITELIB}/lingpy/convert/strings.pyc
+${PYSITELIB}/lingpy/convert/strings.pyo
+${PYSITELIB}/lingpy/convert/tree.py
+${PYSITELIB}/lingpy/convert/tree.pyc
+${PYSITELIB}/lingpy/convert/tree.pyo
 ${PYSITELIB}/lingpy/data/__init__.py
 ${PYSITELIB}/lingpy/data/__init__.pyc
 ${PYSITELIB}/lingpy/data/__init__.pyo
+${PYSITELIB}/lingpy/data/conceptlists/alpher1999_151.tsv
+${PYSITELIB}/lingpy/data/conceptlists/concepticon.tsv
+${PYSITELIB}/lingpy/data/conceptlists/dolgopolsky1964_15.tsv
+${PYSITELIB}/lingpy/data/conceptlists/dunn2012_wiktionary200.tsv
+${PYSITELIB}/lingpy/data/conceptlists/greenhill2008_210.tsv
+${PYSITELIB}/lingpy/data/conceptlists/hamed2006_200.tsv
+${PYSITELIB}/lingpy/data/conceptlists/haspelmath2009_WOLD.tsv
+${PYSITELIB}/lingpy/data/conceptlists/holman2008_ASJP-40.tsv
+${PYSITELIB}/lingpy/data/conceptlists/hou2004_180.tsv
+${PYSITELIB}/lingpy/data/conceptlists/huber1992_374.tsv
+${PYSITELIB}/lingpy/data/conceptlists/kraft1981.tsv
+${PYSITELIB}/lingpy/data/conceptlists/matisoff2000_CALMSEA-200.tsv
+${PYSITELIB}/lingpy/data/conceptlists/starostin1991_TOB-110.tsv
+${PYSITELIB}/lingpy/data/conceptlists/starostin1991_jachontov-100.tsv
+${PYSITELIB}/lingpy/data/conceptlists/starostin1991_jachontov-35.tsv
+${PYSITELIB}/lingpy/data/conceptlists/starostin1991_jachontov-65.tsv
+${PYSITELIB}/lingpy/data/conceptlists/swadesh1952_200.tsv
+${PYSITELIB}/lingpy/data/conceptlists/tadmor2009_LeipzigJakarta-100.tsv
+${PYSITELIB}/lingpy/data/conceptlists/zgraggen1980_380.tsv
+${PYSITELIB}/lingpy/data/conf/dictionary.rc
+${PYSITELIB}/lingpy/data/conf/qlc.rc
+${PYSITELIB}/lingpy/data/conf/swadesh.rc
+${PYSITELIB}/lingpy/data/conf/wordlist.rc
 ${PYSITELIB}/lingpy/data/derive.py
 ${PYSITELIB}/lingpy/data/derive.pyc
 ${PYSITELIB}/lingpy/data/derive.pyo
 ${PYSITELIB}/lingpy/data/ipa/__init__.py
 ${PYSITELIB}/lingpy/data/ipa/__init__.pyc
 ${PYSITELIB}/lingpy/data/ipa/__init__.pyo
+${PYSITELIB}/lingpy/data/ipa/sampa.csv
 ${PYSITELIB}/lingpy/data/ipa/sampa.py
 ${PYSITELIB}/lingpy/data/ipa/sampa.pyc
 ${PYSITELIB}/lingpy/data/ipa/sampa.pyo
 ${PYSITELIB}/lingpy/data/model.py
 ${PYSITELIB}/lingpy/data/model.pyc
 ${PYSITELIB}/lingpy/data/model.pyo
-${PYSITELIB}/lingpy/data/moreunicodedata.py
-${PYSITELIB}/lingpy/data/moreunicodedata.pyc
-${PYSITELIB}/lingpy/data/moreunicodedata.pyo
-${PYSITELIB}/lingpy/data/names/__init__.py
-${PYSITELIB}/lingpy/data/names/__init__.pyc
-${PYSITELIB}/lingpy/data/names/__init__.pyo
-${PYSITELIB}/lingpy/data/names/evolaemp.py
-${PYSITELIB}/lingpy/data/names/evolaemp.pyc
-${PYSITELIB}/lingpy/data/names/evolaemp.pyo
-${PYSITELIB}/lingpy/data/names/qlc.py
-${PYSITELIB}/lingpy/data/names/qlc.pyc
-${PYSITELIB}/lingpy/data/names/qlc.pyo
+${PYSITELIB}/lingpy/data/models/art/INFO
+${PYSITELIB}/lingpy/data/models/art/converter
+${PYSITELIB}/lingpy/data/models/art_el/INFO
+${PYSITELIB}/lingpy/data/models/art_el/converter
+${PYSITELIB}/lingpy/data/models/asjp/INFO
+${PYSITELIB}/lingpy/data/models/asjp/converter
+${PYSITELIB}/lingpy/data/models/asjp/matrix
+${PYSITELIB}/lingpy/data/models/asjp_el/INFO
+${PYSITELIB}/lingpy/data/models/asjp_el/converter
+${PYSITELIB}/lingpy/data/models/asjp_el/matrix
+${PYSITELIB}/lingpy/data/models/burmish/converter
+${PYSITELIB}/lingpy/data/models/color/INFO
+${PYSITELIB}/lingpy/data/models/color/converter
+${PYSITELIB}/lingpy/data/models/color_el/INFO
+${PYSITELIB}/lingpy/data/models/color_el/converter
+${PYSITELIB}/lingpy/data/models/cv/INFO
+${PYSITELIB}/lingpy/data/models/cv/converter
+${PYSITELIB}/lingpy/data/models/diss/INFO
+${PYSITELIB}/lingpy/data/models/diss/converter
+${PYSITELIB}/lingpy/data/models/diss/scorer
+${PYSITELIB}/lingpy/data/models/dolgo/INFO
+${PYSITELIB}/lingpy/data/models/dolgo/converter
+${PYSITELIB}/lingpy/data/models/dolgo/matrix
+${PYSITELIB}/lingpy/data/models/dolgo/scorer
+${PYSITELIB}/lingpy/data/models/dolgo_el/INFO
+${PYSITELIB}/lingpy/data/models/dolgo_el/converter
+${PYSITELIB}/lingpy/data/models/dolgo_el/matrix
+${PYSITELIB}/lingpy/data/models/dolgo_el/scorer
+${PYSITELIB}/lingpy/data/models/dvt/diacritics
+${PYSITELIB}/lingpy/data/models/dvt/tones
+${PYSITELIB}/lingpy/data/models/dvt/vowels
+${PYSITELIB}/lingpy/data/models/dvt_el/diacritics
+${PYSITELIB}/lingpy/data/models/dvt_el/tones
+${PYSITELIB}/lingpy/data/models/dvt_el/vowels
+${PYSITELIB}/lingpy/data/models/gamb_el/converter
+${PYSITELIB}/lingpy/data/models/internal_asjp/INFO
+${PYSITELIB}/lingpy/data/models/internal_asjp/converter
+${PYSITELIB}/lingpy/data/models/jaeger/INFO
+${PYSITELIB}/lingpy/data/models/jaeger/converter
+${PYSITELIB}/lingpy/data/models/jaeger/matrix
+${PYSITELIB}/lingpy/data/models/jaeger_el/INFO
+${PYSITELIB}/lingpy/data/models/jaeger_el/converter
+${PYSITELIB}/lingpy/data/models/jaeger_el/matrix
+${PYSITELIB}/lingpy/data/models/sca/INFO
+${PYSITELIB}/lingpy/data/models/sca/converter
+${PYSITELIB}/lingpy/data/models/sca/matrix
+${PYSITELIB}/lingpy/data/models/sca/scorer
+${PYSITELIB}/lingpy/data/models/sca_el/INFO
+${PYSITELIB}/lingpy/data/models/sca_el/converter
+${PYSITELIB}/lingpy/data/models/sca_el/matrix
+${PYSITELIB}/lingpy/data/models/sca_el/scorer
+${PYSITELIB}/lingpy/data/orthography_profiles/asjp.prf
+${PYSITELIB}/lingpy/data/swadesh/swadesh.qlc
+${PYSITELIB}/lingpy/data/templates/alm.css
+${PYSITELIB}/lingpy/data/templates/alm.js
+${PYSITELIB}/lingpy/data/templates/alm2html.html
+${PYSITELIB}/lingpy/data/templates/alm2html.table.html
+${PYSITELIB}/lingpy/data/templates/alm2html.table.js.html
+${PYSITELIB}/lingpy/data/templates/jcov.css
+${PYSITELIB}/lingpy/data/templates/jcov.dighl.js
+${PYSITELIB}/lingpy/data/templates/jcov.direct.html
+${PYSITELIB}/lingpy/data/templates/jcov.js
+${PYSITELIB}/lingpy/data/templates/jcov.remote.html
+${PYSITELIB}/lingpy/data/templates/jcov.vendor.js
+${PYSITELIB}/lingpy/data/templates/msa.css
+${PYSITELIB}/lingpy/data/templates/msa.js
+${PYSITELIB}/lingpy/data/templates/msa.tex
+${PYSITELIB}/lingpy/data/templates/msa2html.html
+${PYSITELIB}/lingpy/data/templates/msa2html.js.html
+${PYSITELIB}/lingpy/data/templates/psa.css
+${PYSITELIB}/lingpy/data/templates/psa.html
 ${PYSITELIB}/lingpy/evaluate/__init__.py
 ${PYSITELIB}/lingpy/evaluate/__init__.pyc
 ${PYSITELIB}/lingpy/evaluate/__init__.pyo
 ${PYSITELIB}/lingpy/evaluate/acd.py
 ${PYSITELIB}/lingpy/evaluate/acd.pyc
 ${PYSITELIB}/lingpy/evaluate/acd.pyo
+${PYSITELIB}/lingpy/evaluate/alr.py
+${PYSITELIB}/lingpy/evaluate/alr.pyc
+${PYSITELIB}/lingpy/evaluate/alr.pyo
 ${PYSITELIB}/lingpy/evaluate/apa.py
 ${PYSITELIB}/lingpy/evaluate/apa.pyc
 ${PYSITELIB}/lingpy/evaluate/apa.pyo
+${PYSITELIB}/lingpy/log.py
+${PYSITELIB}/lingpy/log.pyc
+${PYSITELIB}/lingpy/log.pyo
 ${PYSITELIB}/lingpy/meaning/__init__.py
 ${PYSITELIB}/lingpy/meaning/__init__.pyc
 ${PYSITELIB}/lingpy/meaning/__init__.pyo
+${PYSITELIB}/lingpy/meaning/basvoc.py
+${PYSITELIB}/lingpy/meaning/basvoc.pyc
+${PYSITELIB}/lingpy/meaning/basvoc.pyo
+${PYSITELIB}/lingpy/meaning/colexification.py
+${PYSITELIB}/lingpy/meaning/colexification.pyc
+${PYSITELIB}/lingpy/meaning/colexification.pyo
+${PYSITELIB}/lingpy/meaning/glosses.py
+${PYSITELIB}/lingpy/meaning/glosses.pyc
+${PYSITELIB}/lingpy/meaning/glosses.pyo
 ${PYSITELIB}/lingpy/read/__init__.py
 ${PYSITELIB}/lingpy/read/__init__.pyc
 ${PYSITELIB}/lingpy/read/__init__.pyo
@@ -155,27 +293,229 @@ ${PYSITELIB}/lingpy/read/phylip.pyo
 ${PYSITELIB}/lingpy/read/qlc.py
 ${PYSITELIB}/lingpy/read/qlc.pyc
 ${PYSITELIB}/lingpy/read/qlc.pyo
+${PYSITELIB}/lingpy/read/starling.py
+${PYSITELIB}/lingpy/read/starling.pyc
+${PYSITELIB}/lingpy/read/starling.pyo
 ${PYSITELIB}/lingpy/sequence/__init__.py
 ${PYSITELIB}/lingpy/sequence/__init__.pyc
 ${PYSITELIB}/lingpy/sequence/__init__.pyo
 ${PYSITELIB}/lingpy/sequence/generate.py
 ${PYSITELIB}/lingpy/sequence/generate.pyc
 ${PYSITELIB}/lingpy/sequence/generate.pyo
-${PYSITELIB}/lingpy/sequence/ngram.py
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-${PYSITELIB}/lingpy2/data/ipa/__init__.pyc
-${PYSITELIB}/lingpy2/data/ipa/__init__.pyo
-${PYSITELIB}/lingpy2/data/ipa/sampa.csv
-${PYSITELIB}/lingpy2/data/ipa/sampa.py
-${PYSITELIB}/lingpy2/data/ipa/sampa.pyc
-${PYSITELIB}/lingpy2/data/ipa/sampa.pyo
-${PYSITELIB}/lingpy2/data/model.py
-${PYSITELIB}/lingpy2/data/model.pyc
-${PYSITELIB}/lingpy2/data/model.pyo
-${PYSITELIB}/lingpy2/data/models/art/INFO
-${PYSITELIB}/lingpy2/data/models/art/converter
-${PYSITELIB}/lingpy2/data/models/art/converter.bin
-${PYSITELIB}/lingpy2/data/models/art_el/INFO
-${PYSITELIB}/lingpy2/data/models/art_el/converter
-${PYSITELIB}/lingpy2/data/models/asjp/INFO
-${PYSITELIB}/lingpy2/data/models/asjp/asjp_score_dict.csv
-${PYSITELIB}/lingpy2/data/models/asjp/cons_score
-${PYSITELIB}/lingpy2/data/models/asjp/converter
-${PYSITELIB}/lingpy2/data/models/asjp/converter.bin
-${PYSITELIB}/lingpy2/data/models/asjp/score
-${PYSITELIB}/lingpy2/data/models/asjp/scorer.bin
-${PYSITELIB}/lingpy2/data/models/asjp/vows_score
-${PYSITELIB}/lingpy2/data/models/asjp_el/INFO
-${PYSITELIB}/lingpy2/data/models/asjp_el/converter
-${PYSITELIB}/lingpy2/data/models/color/INFO
-${PYSITELIB}/lingpy2/data/models/color/converter
-${PYSITELIB}/lingpy2/data/models/color/converter.bin
-${PYSITELIB}/lingpy2/data/models/color_el/INFO
-${PYSITELIB}/lingpy2/data/models/color_el/converter
-${PYSITELIB}/lingpy2/data/models/diss/INFO
-${PYSITELIB}/lingpy2/data/models/diss/converter
-${PYSITELIB}/lingpy2/data/models/diss/scorer
-${PYSITELIB}/lingpy2/data/models/dolgo/INFO
-${PYSITELIB}/lingpy2/data/models/dolgo/converter
-${PYSITELIB}/lingpy2/data/models/dolgo/converter.bin
-${PYSITELIB}/lingpy2/data/models/dolgo/scorer
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-${PYSITELIB}/lingpy2/data/models/dolgo_el/scorer
-${PYSITELIB}/lingpy2/data/models/dvt/diacritics
-${PYSITELIB}/lingpy2/data/models/dvt/dvt.bin
-${PYSITELIB}/lingpy2/data/models/dvt/tones
-${PYSITELIB}/lingpy2/data/models/dvt/vowels
-${PYSITELIB}/lingpy2/data/models/dvt_el/diacritics
-${PYSITELIB}/lingpy2/data/models/dvt_el/tones
-${PYSITELIB}/lingpy2/data/models/dvt_el/vowels
-${PYSITELIB}/lingpy2/data/models/internal_asjp/INFO
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-${PYSITELIB}/lingpy2/data/models/sca/INFO
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-${PYSITELIB}/lingpy2/data/models/sca/converter.bin
-${PYSITELIB}/lingpy2/data/models/sca/scorer
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-${PYSITELIB}/lingpy2/data/models/sca_el/INFO
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-${PYSITELIB}/lingpy2/data/models/sca_el/scorer
-${PYSITELIB}/lingpy2/data/moreunicodedata.py
-${PYSITELIB}/lingpy2/data/moreunicodedata.pyc
-${PYSITELIB}/lingpy2/data/moreunicodedata.pyo
-${PYSITELIB}/lingpy2/data/names/__init__.py
-${PYSITELIB}/lingpy2/data/names/__init__.pyc
-${PYSITELIB}/lingpy2/data/names/__init__.pyo
-${PYSITELIB}/lingpy2/data/names/evolaemp.py
-${PYSITELIB}/lingpy2/data/names/evolaemp.pyc
-${PYSITELIB}/lingpy2/data/names/evolaemp.pyo
-${PYSITELIB}/lingpy2/data/names/qlc.py
-${PYSITELIB}/lingpy2/data/names/qlc.pyc
-${PYSITELIB}/lingpy2/data/names/qlc.pyo
-${PYSITELIB}/lingpy2/evaluate/__init__.py
-${PYSITELIB}/lingpy2/evaluate/__init__.pyc
-${PYSITELIB}/lingpy2/evaluate/__init__.pyo
-${PYSITELIB}/lingpy2/evaluate/acd.py
-${PYSITELIB}/lingpy2/evaluate/acd.pyc
-${PYSITELIB}/lingpy2/evaluate/acd.pyo
-${PYSITELIB}/lingpy2/evaluate/apa.py
-${PYSITELIB}/lingpy2/evaluate/apa.pyc
-${PYSITELIB}/lingpy2/evaluate/apa.pyo
-${PYSITELIB}/lingpy2/meaning/__init__.py
-${PYSITELIB}/lingpy2/meaning/__init__.pyc
-${PYSITELIB}/lingpy2/meaning/__init__.pyo
-${PYSITELIB}/lingpy2/read/__init__.py
-${PYSITELIB}/lingpy2/read/__init__.pyc
-${PYSITELIB}/lingpy2/read/__init__.pyo
-${PYSITELIB}/lingpy2/read/csv.py
-${PYSITELIB}/lingpy2/read/csv.pyc
-${PYSITELIB}/lingpy2/read/csv.pyo
-${PYSITELIB}/lingpy2/read/phylip.py
-${PYSITELIB}/lingpy2/read/phylip.pyc
-${PYSITELIB}/lingpy2/read/phylip.pyo
-${PYSITELIB}/lingpy2/read/qlc.py
-${PYSITELIB}/lingpy2/read/qlc.pyc
-${PYSITELIB}/lingpy2/read/qlc.pyo
-${PYSITELIB}/lingpy2/sequence/__init__.py
-${PYSITELIB}/lingpy2/sequence/__init__.pyc
-${PYSITELIB}/lingpy2/sequence/__init__.pyo
-${PYSITELIB}/lingpy2/sequence/generate.py
-${PYSITELIB}/lingpy2/sequence/generate.pyc
-${PYSITELIB}/lingpy2/sequence/generate.pyo
-${PYSITELIB}/lingpy2/sequence/ngram.py
-${PYSITELIB}/lingpy2/sequence/ngram.pyc
-${PYSITELIB}/lingpy2/sequence/ngram.pyo
-${PYSITELIB}/lingpy2/sequence/orthography.py
-${PYSITELIB}/lingpy2/sequence/orthography.pyc
-${PYSITELIB}/lingpy2/sequence/orthography.pyo
-${PYSITELIB}/lingpy2/sequence/sound_classes.py
-${PYSITELIB}/lingpy2/sequence/sound_classes.pyc
-${PYSITELIB}/lingpy2/sequence/sound_classes.pyo
-${PYSITELIB}/lingpy2/sequence/tokenizer.py
-${PYSITELIB}/lingpy2/sequence/tokenizer.pyc
-${PYSITELIB}/lingpy2/sequence/tokenizer.pyo
-${PYSITELIB}/lingpy2/settings.py
-${PYSITELIB}/lingpy2/settings.pyc
-${PYSITELIB}/lingpy2/settings.pyo
-${PYSITELIB}/lingpy2/thirdparty/__init__.py
-${PYSITELIB}/lingpy2/thirdparty/__init__.pyc
-${PYSITELIB}/lingpy2/thirdparty/__init__.pyo
-${PYSITELIB}/lingpy2/thirdparty/cogent/__init__.py
-${PYSITELIB}/lingpy2/thirdparty/cogent/__init__.pyc
-${PYSITELIB}/lingpy2/thirdparty/cogent/__init__.pyo
-${PYSITELIB}/lingpy2/thirdparty/cogent/newick.py
-${PYSITELIB}/lingpy2/thirdparty/cogent/newick.pyc
-${PYSITELIB}/lingpy2/thirdparty/cogent/newick.pyo
-${PYSITELIB}/lingpy2/thirdparty/cogent/tree.py
-${PYSITELIB}/lingpy2/thirdparty/cogent/tree.pyc
-${PYSITELIB}/lingpy2/thirdparty/cogent/tree.pyo
+${PYSITELIB}/lingpy/thirdparty/linkcomm/__init__.py
+${PYSITELIB}/lingpy/thirdparty/linkcomm/__init__.pyc
+${PYSITELIB}/lingpy/thirdparty/linkcomm/__init__.pyo
+${PYSITELIB}/lingpy/thirdparty/linkcomm/link_clustering.py
+${PYSITELIB}/lingpy/thirdparty/linkcomm/link_clustering.pyc
+${PYSITELIB}/lingpy/thirdparty/linkcomm/link_clustering.pyo
+${PYSITELIB}/lingpy/util.py
+${PYSITELIB}/lingpy/util.pyc
+${PYSITELIB}/lingpy/util.pyo
diff --git a/py-lingpy/distinfo b/py-lingpy/distinfo
index 230067c..89ad5ff 100644
--- a/py-lingpy/distinfo
+++ b/py-lingpy/distinfo
@@ -1,5 +1,6 @@
 $NetBSD: distinfo,v 1.1 2014/01/17 20:55:33 jihbed Exp $
 
-SHA1 (lingpy-2.0.tar.gz) = a0132df54a8f6fc746910efa26d400b89e33989a
-RMD160 (lingpy-2.0.tar.gz) = 3bf9b71d75b34abab797428c2216c7a77126b143
-Size (lingpy-2.0.tar.gz) = 8358117 bytes
+SHA1 (lingpy-2.5.tar.gz) = 3ad1c6668194c87b52b18cb339762865e8e367a6
+RMD160 (lingpy-2.5.tar.gz) = 325b793edea41b8a37f401215a0066c662095f07
+SHA512 (lingpy-2.5.tar.gz) = 16bbfab8f64b6ab5e99f42233a363029c6e10e8129ee188556f667afe4cb1c14818cb17bd8f7cc03dddeddd3c4f6b0a161ec13a73b8327fcaeaf67bc09e9d22f
+Size (lingpy-2.5.tar.gz) = 9291752 bytes
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