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Description:

phlorest 1.6.1

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