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A cldfbench plugin to curate language phylogenies

Project description


A cldfbench plugin to curate language phylogenies.


pip install phlorest


Bootstrapping a phlorest-curated dataset

phlorest provides a cldfbench dataset template to create the skeleton of files and directories for a phlorest-curated dataset, to be run with cldfbench new.


cldfbench new --template phlorest 

will create a dataset skeleton looking as follows

$ tree testtree/
├── cldf
│   └──
├── etc
│   ├── characters.csv
│   └── taxa.csv
├── metadata.json
├── raw
│   └──
├── setup.cfg

Implementing CLDF creation

Implementing CLDF creation means - as for any other cldfbench-curated dataset - filling in the cmd_makecldf method of the Dataset subclass in cldfbench_<id>.py.

The CLDF writer which can be accessed as args.writer within cmd_makecldf is an instance of phlorest.CLDFWriter, which has convenience methods to add summary- or posterior trees to the CLDF dataset. At least a summary is needed to make a dataset valid. Adding one looks as follows


Running CLDF creation

With cmd_makecldf implemented, CLDF creation can be triggered running

cldfbench makecldf cldfbench_<id>.py

The resulting CLDF dataset can be validated running


Release workflow

cldfbench makecldf --glottolog-version v4.8 --with-cldfreadme cldfbench_<id>.py
cldfbench zenodo --communities phlorest cldfbench_<id>.py
cldfbench readme cldfbench_<id>.py
phlorest check --with-R cldfbench_<id>.py
git commit -a -m"release vX.Y"
git push origin
phlorest release cldfbench_<id>.py vX.Y


The run_treeannotator method of Dataset requires the treeannotator command from BEAST to be installed. For details on how to install treeannotator (and BEAST), see

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