# phlorest
A [cldfbench](https://github.com/cldf/cldfbench) plugin to curate language phylogenies.
## Install
```shell
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](https://github.com/cldf/cldfbench/#creating-a-skeleton-for-a-new-dataset-directory).
Running
```shell
cldfbench new --template phlorest
```
will create a dataset skeleton looking as follows
```shell
$ 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
```python
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
```shell
cldfbench makecldf cldfbench_<id>.py
```
The resulting CLDF dataset can be validated running
```shell
pytest
```
### Release workflow
```shell
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
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