Metadata-Version: 2.1
Name: phlorest
Version: 0.2.0
Summary: A cldfbench plugin to curate language phylogenies
Home-page: https://github.com/phlorest/phlorest
Author: Simon Greenhill and Robert Forkel
Author-email: dlce.rdm@eva.mpg.de
License: Apache 2.0
Project-URL: Bug Tracker, https://github.com/phlorest/phlorest/issues
Description: # 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
        ```
        
        
        ### Implementng 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
        ```
        
Keywords: cldf
Platform: any
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: License :: OSI Approved :: Apache Software License
Requires-Python: >=3.7
Description-Content-Type: text/markdown
Provides-Extra: dev
Provides-Extra: test
