cli: fix and add make cmd

src/raman_fitting/interfaces/argparse_cli.py

@@ -29,7 +29,7 @@ def main():
 
     parser.add_argument(
         "-sIDs",
-        "--sample_IDs",
+        "--sample_ids",
         nargs="+",
         default=[],
         help="Selection of names of SampleIDs from index to run over.",
@@ -52,10 +52,8 @@ def main():
 
     parser.add_argument(
         "--version",
-        # action=print(_version_text),
         action="version",
         version="%(prog)s {}".format(get_package_version()),
-        # const=_version_text,
         help="Prints out the current version of the raman_fitting distribution, via importlib.metadata.version",
     )
 
@@ -66,16 +64,7 @@ def main():
     import raman_fitting as rf
 
     extra_kwargs = {}
-    if args.run_mode == "normal":
-        pass
-        # _org_index = OrganizeRamanFiles()
-        # RL = RamanLoop(_org_index, run_mode ='normal')
-    elif args.run_mode.lower() == "debug":
-        pass
-        # IDEA Add a FAST TRACK for DEBUG
-    elif args.run_mode == "testing":
-        pass
-    elif args.run_mode == RunModes.EXAMPLES:
+    if args.run_mode == RunModes.EXAMPLES:
         extra_kwargs.update(
             {"fit_model_specific_names": ["2peaks", "3peaks", "4peaks"]}
         )

src/raman_fitting/interfaces/typer_cli.py

@@ -1,13 +1,12 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 from typing import List, Optional
 from typing_extensions import Annotated
 
-
+from pathlib import Path
 from enum import StrEnum, auto
 from loguru import logger
 from raman_fitting.config.path_settings import RunModes
 from raman_fitting.delegating.main_delegator import MainDelegator
+from raman_fitting.imports.files.file_indexer import initialize_index_from_source_files
 from .utils import get_package_version
 
 import typer
@@ -16,6 +15,7 @@
 class MakeTypes(StrEnum):
     INDEX = auto()
     CONFIG = auto()
+    EXAMPLE = auto()
 
 
 __version__ = "0.1.0"
@@ -64,24 +64,31 @@ def run(
     ],
     run_mode: Annotated[RunModes, typer.Argument()] = RunModes.NORMAL,
 ):
+    if run_mode is None:
+        print("No make run mode passed")
+        raise typer.Exit()
     kwargs = {"run_mode": run_mode}
-    if run_mode == RunModes.NORMAL:
-        pass
-        # _org_index = OrganizeRamanFiles()
-        # RL = RamanLoop(_org_index, run_mode ='normal')
-    elif run_mode.lower() == RunModes.DEBUG:
-        pass
-        # IDEA Add a FAST TRACK for DEBUG
-    elif run_mode == RunModes.EXAMPLES:
+    if run_mode == RunModes.EXAMPLES:
         kwargs.update({"fit_model_specific_names": ["2peaks", "3peaks", "4peaks"]})
     logger.info(f"Starting raman_fitting with CLI args:\n{run_mode}")
     _main_run = MainDelegator(**kwargs)
 
 
 @app.command()
-def make(make_type: Annotated[MakeTypes, typer.Argument()]):
+def make(
+    source_files: Annotated[List[Path], typer.Option()],
+    index_file: Annotated[List[Path], typer.Option()],
+    force_reindex: Annotated[bool, typer.Option("--force-reindex")] = False,
+    make_type: Annotated[MakeTypes, typer.Option()] = None,
+):
+    if make_type is None:
+        print("No make type args passed")
+        raise typer.Exit()
+
     if make_type == MakeTypes.INDEX:
-        pass  # make index
+        initialize_index_from_source_files(
+            files=source_files, index_file=index_file, force_reindex=force_reindex
+        )
 
     elif make_type == MakeTypes.CONFIG:
         pass  # make config