Merge branch 'main' of https://github.com/phlorest/bowern_and_atkinso…

…n2012

.zenodo.json

@@ -1,5 +1,5 @@
 {
-    "title": "Phlorest phylogeny derived from Bowern & Atkinson 2012 'Pama-Nyungen (Bowern and Atkinson 2012)'",
+    "title": "Phlorest phylogeny derived from Bowern & Atkinson 2012 'Computational phylogenetics and the internal structure of Pama-Nyungan'",
     "access_right": "open",
     "keywords": [
         "cldf:Generic",

README.md

@@ -1,4 +1,4 @@
-# Phlorest phylogeny derived from Bowern & Atkinson 2012 'Pama-Nyungen (Bowern and Atkinson 2012)'
+# Phlorest phylogeny derived from Bowern & Atkinson 2012 'Computational phylogenetics and the internal structure of Pama-Nyungan'
 
 [![CLDF validation](https://github.com/phlorest/bowern_and_atkinson2012/workflows/CLDF-validation/badge.svg)](https://github.com/phlorest/bowern_and_atkinson2012/actions?query=workflow%3ACLDF-validation)
 
@@ -11,10 +11,12 @@ If you use these data please cite
 
 ## Description
 
+A [Phlorest phylogeny](https://github.com/phlorest) of the Pama-Nyungan language family computed from a bayesian analysis scaled by years.
+
 
 This dataset is licensed under a https://creativecommons.org/licenses/by/2.0/ license
 
-Available online at https://doi.org/10.1353/lan.2012.0081
+Source available online at https://doi.org/10.1353/lan.2012.0081
 
 
 ## CLDF Datasets
@@ -25,4 +27,4 @@ The following CLDF datasets are available in [cldf](cldf):
 
 ## Summary Tree
 
-![summary](./summary_tree.svg)
+![summary](https://raw.githubusercontent.com/phlorest/bowern_and_atkinson2012/main/summary_tree.svg)

cldf/Generic-metadata.json

@@ -15,7 +15,7 @@
         "analysis": "bayesian",
         "scaling": "years"
     },
-    "dc:title": "Phlorest phylogeny derived from Bowern & Atkinson 2012 'Pama-Nyungen (Bowern and Atkinson 2012)'",
+    "dc:title": "Phlorest phylogeny derived from Bowern & Atkinson 2012 'Computational phylogenetics and the internal structure of Pama-Nyungan'",
     "dcat:accessURL": "https://github.com/phlorest/bowern_and_atkinson2012",
     "prov:wasDerivedFrom": [
         {
@@ -27,7 +27,7 @@
         {
             "rdf:about": "https://github.com/phlorest/bowern_and_atkinson2012",
             "rdf:type": "prov:Entity",
-            "dc:created": "a709a12",
+            "dc:created": "196725f",
             "dc:title": "Repository"
         },
         {

cldf/README.md

@@ -1,6 +1,6 @@
 <a name="ds-genericmetadatajson"> </a>
 
-# Generic Phlorest phylogeny derived from Bowern & Atkinson 2012 'Pama-Nyungen (Bowern and Atkinson 2012)'
+# Generic Phlorest phylogeny derived from Bowern & Atkinson 2012 'Computational phylogenetics and the internal structure of Pama-Nyungan'
 
 **CLDF Metadata**: [Generic-metadata.json](./Generic-metadata.json)
 
@@ -14,7 +14,7 @@ property | value
 [dc:license](http://purl.org/dc/terms/license) | https://creativecommons.org/licenses/by/2.0/
 [dc:subject](http://purl.org/dc/terms/subject) | <dl><dt>family</dt><dd>Pama-Nyungan</dd><dt>analysis</dt><dd>bayesian</dd><dt>scaling</dt><dd>years</dd></dl>
 [dcat:accessURL](http://www.w3.org/ns/dcat#accessURL) | https://github.com/phlorest/bowern_and_atkinson2012
-[prov:wasDerivedFrom](http://www.w3.org/ns/prov#wasDerivedFrom) | <ol><li><a href="https://doi.org/10.5281/zenodo.1312841">https://doi.org/10.5281/zenodo.1312841 </a></li><li><a href="https://github.com/phlorest/bowern_and_atkinson2012/tree/a709a12">phlorest/bowern_and_atkinson2012 a709a12</a></li><li><a href="https://github.com/glottolog/glottolog/tree/v4.8">Glottolog v4.8</a></li></ol>
+[prov:wasDerivedFrom](http://www.w3.org/ns/prov#wasDerivedFrom) | <ol><li><a href="https://doi.org/10.5281/zenodo.1312841">https://doi.org/10.5281/zenodo.1312841 </a></li><li><a href="https://github.com/phlorest/bowern_and_atkinson2012/tree/196725f">phlorest/bowern_and_atkinson2012 196725f</a></li><li><a href="https://github.com/glottolog/glottolog/tree/v4.8">Glottolog v4.8</a></li></ol>
 [prov:wasGeneratedBy](http://www.w3.org/ns/prov#wasGeneratedBy) | <ol><li><strong>python</strong>: 3.10.6</li><li><strong>python-packages</strong>: <a href="./requirements.txt">requirements.txt</a></li></ol>
 [rdf:ID](http://www.w3.org/1999/02/22-rdf-syntax-ns#ID) | bowern_and_atkinson2012
 [rdf:type](http://www.w3.org/1999/02/22-rdf-syntax-ns#type) | http://www.w3.org/ns/dcat#Distribution

cldf/requirements.txt

@@ -6,8 +6,8 @@ certifi==2022.12.7
 cffi==1.15.1
 chardet==5.1.0
 cldfbench==1.13.0
--e git+https://github.com/phlorest/atkinson2006.git@d0e5048954a747e7b5274fd424f3ca2b3ac7b44f#egg=cldfbench_atkinson2006
--e git+https://github.com/phlorest/michael_et_al2015@c68f51edd9a7f23e65618dd84163011c9e038f61#egg=cldfbench_michael_et_al2015
+-e git+https://github.com/phlorest/atkinson2006.git@b0458e4fabc3aec7f156fc75da16b32932c3a5a1#egg=cldfbench_atkinson2006
+-e git+https://github.com/phlorest/michael_et_al2015@b481dd8011cafaac72339694a065b37bdd683646#egg=cldfbench_michael_et_al2015
 cldfcatalog==1.5.1
 cldfviz==0.10.0
 cldfzenodo==1.1.0
@@ -38,7 +38,7 @@ nameparser==1.1.2
 newick==1.9.0
 numpy==1.24.1
 packaging==23.1
-phlorest==1.1.0
+-e git+https://github.com/phlorest/phlorest@b62b8b6447f7fe20c97780bcae349a6f7fd8af48#egg=phlorest
 pluggy==1.2.0
 purl==1.6
 pybtex==0.24.0

metadata.json

@@ -3,7 +3,7 @@
     "license": "https://creativecommons.org/licenses/by/2.0/",
     "url": "https://doi.org/10.1353/lan.2012.0081",
     "citation": "Bowern C & Atkinson QD. 2012. Computational phylogenetics and the internal structure of Pama-Nyungan. Language, 88(4), 817-845.",
-    "name": "Pama-Nyungen (Bowern and Atkinson 2012)",
+    "name": "Computational phylogenetics and the internal structure of Pama-Nyungan",
     "author": "Bowern & Atkinson",
     "year": 2012,
     "scaling": "years",