.zenodo.json MANIFEST.in setup.cfg setup.py src/lingpy/__init__.py src/lingpy/__main__.py src/lingpy/_settings.py src/lingpy/algorithm/__init__.py src/lingpy/algorithm/_tree.py src/lingpy/algorithm/cluster_util.py src/lingpy/algorithm/clustering.py src/lingpy/algorithm/cython/__init__.py src/lingpy/algorithm/cython/_calign.py src/lingpy/algorithm/cython/_cluster.py src/lingpy/algorithm/cython/_malign.py src/lingpy/algorithm/cython/_misc.py src/lingpy/algorithm/cython/_talign.py src/lingpy/algorithm/extra.py src/lingpy/align/__init__.py src/lingpy/align/_align/__init__.py src/lingpy/align/_align/confidence.py src/lingpy/align/multiple.py src/lingpy/align/pairwise.py src/lingpy/align/sca.py src/lingpy/basic/__init__.py src/lingpy/basic/ops.py src/lingpy/basic/parser.py src/lingpy/basic/tree.py src/lingpy/basic/wordlist.py src/lingpy/basictypes.py src/lingpy/cache.py src/lingpy/cli.py src/lingpy/compare/__init__.py src/lingpy/compare/_phylogeny/__init__.py src/lingpy/compare/_phylogeny/_settings.py src/lingpy/compare/_phylogeny/convex_hull.py src/lingpy/compare/_phylogeny/polygon.py src/lingpy/compare/_phylogeny/utils.py src/lingpy/compare/_structure.py src/lingpy/compare/lexstat.py src/lingpy/compare/partial.py src/lingpy/compare/phylogeny.py src/lingpy/compare/sanity.py src/lingpy/compare/strings.py src/lingpy/compare/util.py src/lingpy/config.py src/lingpy/convert/__init__.py src/lingpy/convert/cldf.py src/lingpy/convert/graph.py src/lingpy/convert/html.py src/lingpy/convert/plot.py src/lingpy/convert/strings.py src/lingpy/convert/tree.py src/lingpy/data/__init__.py src/lingpy/data/conf/dictionary.rc src/lingpy/data/conf/qlc.rc src/lingpy/data/conf/swadesh.rc src/lingpy/data/conf/wordlist.rc src/lingpy/data/derive.py src/lingpy/data/ipa/__init__.py src/lingpy/data/ipa/sampa.py src/lingpy/data/model.py src/lingpy/data/models/art/INFO src/lingpy/data/models/art/converter src/lingpy/data/models/art_el/INFO src/lingpy/data/models/art_el/converter src/lingpy/data/models/asjp/INFO src/lingpy/data/models/asjp/asjp.py src/lingpy/data/models/asjp/cons_score src/lingpy/data/models/asjp/converter src/lingpy/data/models/asjp/matrix src/lingpy/data/models/asjp/score src/lingpy/data/models/asjp/vows_score src/lingpy/data/models/asjp_el/INFO src/lingpy/data/models/asjp_el/converter src/lingpy/data/models/asjp_el/matrix src/lingpy/data/models/burmish/converter src/lingpy/data/models/color/INFO src/lingpy/data/models/color/converter src/lingpy/data/models/color_el/INFO src/lingpy/data/models/color_el/converter src/lingpy/data/models/cv/INFO src/lingpy/data/models/cv/converter src/lingpy/data/models/cv/matrix src/lingpy/data/models/diss/INFO src/lingpy/data/models/diss/converter src/lingpy/data/models/diss/makediss.py src/lingpy/data/models/diss/scorer src/lingpy/data/models/dolgo/INFO src/lingpy/data/models/dolgo/converter src/lingpy/data/models/dolgo/matrix src/lingpy/data/models/dolgo/scorer src/lingpy/data/models/dolgo_el/INFO src/lingpy/data/models/dolgo_el/converter src/lingpy/data/models/dolgo_el/matrix src/lingpy/data/models/dolgo_el/scorer src/lingpy/data/models/dvt/diacritics src/lingpy/data/models/dvt/tones src/lingpy/data/models/dvt/vowels src/lingpy/data/models/dvt_el/diacritics src/lingpy/data/models/dvt_el/tones src/lingpy/data/models/dvt_el/vowels src/lingpy/data/models/gamb_el/converter src/lingpy/data/models/internal_asjp/INFO src/lingpy/data/models/internal_asjp/converter src/lingpy/data/models/jaeger/INFO src/lingpy/data/models/jaeger/converter src/lingpy/data/models/jaeger/matrix src/lingpy/data/models/jaeger_el/INFO src/lingpy/data/models/jaeger_el/converter src/lingpy/data/models/jaeger_el/matrix src/lingpy/data/models/sca/INFO src/lingpy/data/models/sca/converter src/lingpy/data/models/sca/matrix src/lingpy/data/models/sca/scorer src/lingpy/data/models/sca_el/INFO src/lingpy/data/models/sca_el/converter src/lingpy/data/models/sca_el/matrix src/lingpy/data/models/sca_el/scorer src/lingpy/data/templates/alm.css src/lingpy/data/templates/alm.js src/lingpy/data/templates/beast.nex src/lingpy/data/templates/jcov.css src/lingpy/data/templates/jcov.dighl.js src/lingpy/data/templates/jcov.js src/lingpy/data/templates/jcov.vendor.js src/lingpy/data/templates/mrbayes.nex src/lingpy/data/templates/msa.css src/lingpy/data/templates/msa.js src/lingpy/data/templates/msa.tex src/lingpy/data/templates/psa.css src/lingpy/data/templates/splitstree.nex src/lingpy/evaluate/__init__.py src/lingpy/evaluate/acd.py src/lingpy/evaluate/alr.py src/lingpy/evaluate/apa.py src/lingpy/log.py src/lingpy/meaning/__init__.py src/lingpy/meaning/colexification.py src/lingpy/read/__init__.py src/lingpy/read/csv.py src/lingpy/read/phylip.py src/lingpy/read/qlc.py src/lingpy/read/starling.py src/lingpy/sequence/__init__.py src/lingpy/sequence/generate.py src/lingpy/sequence/ngrams.py src/lingpy/sequence/profile.py src/lingpy/sequence/smoothing.py src/lingpy/sequence/sound_classes.py src/lingpy/settings.py src/lingpy/thirdparty/__init__.py src/lingpy/thirdparty/cogent/__init__.py src/lingpy/thirdparty/cogent/newick.py src/lingpy/thirdparty/cogent/tree.py src/lingpy/thirdparty/linkcomm/__init__.py src/lingpy/thirdparty/linkcomm/link_clustering.py src/lingpy/util.py tests/algorithm/test__tree.py tests/algorithm/test_cluster_util.py tests/algorithm/test_clustering.py tests/algorithm/test_cython.py tests/algorithm/test_extra.py tests/align/test_multiple.py tests/align/test_pairwise.py tests/align/test_sca.py tests/basic/test_ops.py tests/basic/test_parser.py tests/basic/test_tree.py tests/basic/test_wordlist.py tests/compare/test__phylogeny.py tests/compare/test__structure.py tests/compare/test_compare_strings.py tests/compare/test_lexstat.py tests/compare/test_partial.py tests/compare/test_phylogeny.py tests/compare/test_sanity.py tests/conftest.py tests/convert/test_cldf.py tests/convert/test_cldf_methods.py tests/convert/test_convert_tree.py tests/convert/test_graph.py tests/convert/test_html.py tests/convert/test_plot.py tests/convert/test_strings.py tests/data/test_derive.py tests/data/test_sound_class_models.py tests/evaluate/test_acd.py tests/evaluate/test_alr.py tests/evaluate/test_apa.py tests/meaning/test_colexification.py tests/read/test_csv.py tests/read/test_phylip.py tests/read/test_qlc.py tests/read/test_starling.py tests/sequence/test_generate.py tests/sequence/test_ngrams.py tests/sequence/test_profile.py tests/sequence/test_smoothing.py tests/sequence/test_sound_classes.py tests/test_basictypes.py tests/test_cache.py tests/test_cli.py tests/test_config.py tests/test_data/GER.tsv tests/test_data/Haspelmath-2009-1460.tsv tests/test_data/Jachontov-1991-100.tsv tests/test_data/KSL.bscorer.json tests/test_data/KSL.pairs.json tests/test_data/KSL.qlc tests/test_data/KSL.rscorer.json tests/test_data/KSL2.qlc tests/test_data/KSL3.qlc tests/test_data/KSL4.qlc tests/test_data/KSL5.qlc tests/test_data/KSL6.qlc tests/test_data/Ringe-2002-421.tsv tests/test_data/alm.alm tests/test_data/asjp_test_list.tsv tests/test_data/bad_file.tsv tests/test_data/bad_file2.tsv tests/test_data/cldf/non-wordlist-metadata.json tests/test_data/cldf/sources.bib tests/test_data/cldf/test-metadata.json tests/test_data/colexification.tsv tests/test_data/dolgo.matrix tests/test_data/dolgo.scorer tests/test_data/good_file.tsv tests/test_data/harry.msa tests/test_data/harry.msq tests/test_data/harry_potter.psa tests/test_data/harry_potter.psq tests/test_data/harry_potter_bad.psa tests/test_data/harry_potter_misaligned.psa tests/test_data/harry_unnormal.msa tests/test_data/harry_with_ids.msa tests/test_data/harryp.msa tests/test_data/listA.tsv tests/test_data/listB.tsv tests/test_data/partial_cognates-scored.tsv tests/test_data/partial_cognates.tsv tests/test_data/phybo-r-3 tests/test_data/phybo-r-3.gls tests/test_data/phybo-t-3 tests/test_data/phybo-t-3.gls tests/test_data/phybo-w-1-1 tests/test_data/phybo-w-1-1.gls tests/test_data/phybo.qlc tests/test_data/phybo.tre tests/test_data/phybo2.qlc tests/test_data/phylip_basic.dst tests/test_data/phylip_tabstop.dst tests/test_data/phylogeny.taxa tests/test_data/phylogeny.tre tests/test_data/read_qlc.qlc tests/test_data/rom.starling.tsv tests/test_data/target_list_ringe.tsv tests/test_data/test-partial-alignments.tsv tests/test_data/test_reduce.msa tests/test_data/test_tokenization.tsv tests/test_data/test_tokenization_mv.tsv tests/test_data/test_tokenization_nasals.tsv tests/test_data/tokens.test tests/test_data/tokentestjs tests/test_data/tutorial.qlc tests/test_log.py tests/test_misc.py tests/test_settings.py tests/test_util.py tests/thirdparty/test_cogent.py tests/thirdparty/test_linkcomm.py tox.ini <<<<<< network # path=./coverage.xml /home/runner/work/lingpy/lingpy/tests <<<<<< EOF