phlorest

A cldfbench plugin to curate language phylogenies.

Install

pip install phlorest

Usage

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.

Running

cldfbench new --template phlorest 

will create a dataset skeleton looking as follows

$ tree testtree/
testtree/
├── cldf
│   └── README.md
├── cldfbench_testtree.py
├── etc
│   ├── characters.csv
│   └── taxa.csv
├── metadata.json
├── raw
│   └── README.md
├── setup.cfg
├── setup.py
└── test.py

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

    args.writer.add_summary(
        self.raw_dir.read_tree(...),
        self.metadata,
        args.log)

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

pytest

Release workflow

cldfbench makecldf --glottolog-version v4.8 --with-cldfreadme cldfbench_<id>.py
pytest
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

Dependencies

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 https://beast.community/index.html