improved cli

README.md

@@ -44,7 +44,23 @@ To install your own code run `pip install -e .` in a terminal
 
 ## Features
 
-Provide examples and explanations of how your project can be used. Include code snippets or screenshots if necessary.
+Run `rlpm -h`
+
+```
+Usage: rlpm [-h] {quickstart,mapping,validate} ...
+
+RareLink Phenopacket Mapper (RLPM) CLI tool.
+
+positional arguments:
+  {quickstart,mapping,validate}
+                        Available commands
+    quickstart          Generate a notebook with sample code.
+    mapping             Execute the mapping.
+    validate            Validate phenopackets.
+
+options:
+  -h, --help            show this help message and exit
+```
 
 ## Contributing
 

pyproject.toml

@@ -51,6 +51,4 @@ version = { attr = "rarelink_phenopacket_mapper.__version__" }
 # The following would provide a command line executable called `sample`
 # which executes the function `main` from this package when invoked.
 [project.scripts]  # Optional
-quickstart = "rarelink_phenopacket_mapper.cli.quickstart:main"
-mapping = "rarelink_phenopacket_mapper.cli.mapping:main"
-validate = "rarelink_phenopacket_mapper.cli.validate:main"
+rlpm = "rarelink_phenopacket_mapper.cli.main:main"

src/rarelink_phenopacket_mapper/cli/main.py

@@ -0,0 +1,46 @@
+import argparse
+from rarelink_phenopacket_mapper.cli.quickstart import main as quickstart_main
+from rarelink_phenopacket_mapper.cli.mapping import main as mapping_main
+from rarelink_phenopacket_mapper.cli.validate import main as validate_main
+
+
+def main():
+    """Main entry point for the rlpm CLI."""
+    parser = argparse.ArgumentParser(
+        prog='rlpm',
+        description='RareLink Phenopacket Mapper (RLPM) CLI tool.'
+    )
+
+    # Define subcommands
+    subparsers = parser.add_subparsers(dest='command', help='Available commands')
+
+    # Quickstart command
+    parser_quickstart = subparsers.add_parser('quickstart', help='Generate a notebook with sample code.')
+    parser_quickstart.add_argument('-p', '--path', type=str, help='Path the notebook should be written to')
+
+    # Mapping command
+    parser_mapping = subparsers.add_parser('mapping', help='Execute the mapping.')
+    parser_mapping.add_argument('-p', '--path', type=str, help='Path to RareLink formatted csv or excel file')
+    parser_mapping.add_argument('-o', '--output', type=str, help='Path to write Phenopackets to')
+    parser_mapping.add_argument('-v', '--validate', action='store_true',
+                                help='Validate phenopackets using phenopacket-tools after creation')
+
+    # Validate command
+    parser_validate = subparsers.add_parser('validate', help='Validate phenopackets.')
+    parser_validate.add_argument('-p', '--path', type=str, help='Path to Phenopackets')
+
+    args = parser.parse_args()
+
+    # Route the command to the appropriate function
+    if args.command == 'quickstart':
+        quickstart_main(args)
+    elif args.command == 'mapping':
+        mapping_main(args)
+    elif args.command == 'validate':
+        validate_main(args)
+    else:
+        parser.print_help()
+
+
+if __name__ == "__main__":
+    main()

src/rarelink_phenopacket_mapper/cli/mapping.py

@@ -4,7 +4,7 @@
 from rarelink_phenopacket_mapper.cli.validate import validate
 
 
-def main():
+def main(args):
     """This method launches the mapping command"""
     arg_parser = argparse.ArgumentParser(
         prog='mapping',

src/rarelink_phenopacket_mapper/cli/quickstart.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 
 
-def main():
+def main(args):
     """This method launches the quickstart command"""
     arg_parser = argparse.ArgumentParser(
         prog='quickstart',

src/rarelink_phenopacket_mapper/cli/validate.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 
 
-def main():
+def main(args):
     """This method launches the validate command"""
     arg_parser = argparse.ArgumentParser(
         prog='validate',