Merge pull request #105 from monarch-initiative/develop

QoL updates

Makefile

@@ -27,6 +27,10 @@ build:
 test: install
 	poetry run python -m pytest
 
+.PHONY: docs
+docs: install
+	poetry run typer src/koza/main.py utils docs --name koza --output docs/Usage/CLI.md
+
 .PHONY: clean
 clean:
 	rm -rf `find . -name __pycache__`

README.md

@@ -1,7 +1,12 @@
-# Koza - a data transformation framework [![Pyversions](https://img.shields.io/pypi/pyversions/koza.svg)](https://pypi.python.org/pypi/koza) ![](https://github.com/monarch-initiative/koza/actions/workflows/build.yml/badge.svg) [![PyPi](https://img.shields.io/pypi/v/koza.svg)](https://pypi.python.org/pypi/koza)
+# Koza - a data transformation framework  
+
+[![Pyversions](https://img.shields.io/pypi/pyversions/koza.svg)](https://pypi.python.org/pypi/koza)
+[![PyPi](https://img.shields.io/pypi/v/koza.svg)](https://pypi.python.org/pypi/koza)
+![Github Action](https://github.com/monarch-initiative/koza/actions/workflows/build.yml/badge.svg)
+
 ![pupa](docs/img/pupa.png)  
 
-**Documentation**: https://koza.monarchinitiative.org/  
+[**Documentation**](https://koza.monarchinitiative.org/  )
 
 _Disclaimer_: Koza is in beta; we are looking for beta testers
 
@@ -14,9 +19,9 @@ _Disclaimer_: Koza is in beta; we are looking for beta testers
   - Create and use translation tables to map between source and target vocabularies
 
 ### Installation
-Koza is available on PyPi and can be installed via pip:
+Koza is available on PyPi and can be installed via pip/pipx:
 ```
-pip install koza
+[pip|pipx] install koza
 ```
 
 ### Usage

docs/Usage/CLI.md

@@ -0,0 +1,63 @@
+# `koza`
+
+**Usage**:
+
+```console
+$ koza [OPTIONS] COMMAND [ARGS]...
+```
+
+**Options**:
+
+* `--install-completion`: Install completion for the current shell.
+* `--show-completion`: Show completion for the current shell, to copy it or customize the installation.
+* `--help`: Show this message and exit.
+
+**Commands**:
+
+* `transform`: Transform a source file
+* `validate`: Validate a source file
+
+## `koza transform`
+
+Transform a source file
+
+**Usage**:
+
+```console
+$ koza transform [OPTIONS]
+```
+
+**Options**:
+
+* `--source TEXT`: Source metadata file  [required]
+* `--output-dir TEXT`: Path to output directory  [default: ./output]
+* `--output-format [tsv|jsonl|kgx]`: Output format  [default: tsv]
+* `--global-table TEXT`: Path to global translation table
+* `--local-table TEXT`: Path to local translation table
+* `--schema TEXT`: Path to schema YAML for validation in writer
+* `--row-limit INTEGER`: Number of rows to process (if skipped, processes entire source file)
+* `--debug / --quiet`
+* `--log / --no-log`: Optional log mode - set true to save output to ./logs  [default: no-log]
+* `--help`: Show this message and exit.
+
+## `koza validate`
+
+Validate a source file
+
+Given a file and configuration checks that the file is valid, ie
+format is as expected (tsv, json), required columns/fields are there
+
+**Usage**:
+
+```console
+$ koza validate [OPTIONS]
+```
+
+**Options**:
+
+* `--file TEXT`: Path or url to the source file  [required]
+* `--format [csv|jsonl|json|yaml|xml]`: [default: FormatType.csv]
+* `--delimiter TEXT`: [default: ,]
+* `--header-delimiter TEXT`
+* `--skip-blank-lines / --no-skip-blank-lines`: [default: skip-blank-lines]
+* `--help`: Show this message and exit.