add cli

src/depiction/tools/process_spectra/__main__.py

@@ -0,0 +1,29 @@
+import cyclopts
+import yaml
+from pathlib import Path
+from rich.pretty import pprint
+from depiction.persistence import ImzmlReadFile, ImzmlWriteFile, ImzmlModeEnum
+from depiction.tools.process_spectra.config import ProcessSpectraConfig
+from depiction.tools.process_spectra.process import process_spectra
+
+app = cyclopts.App()
+
+
+@app.command
+def validate(config_file: Path) -> ProcessSpectraConfig:
+    config = ProcessSpectraConfig.model_validate(yaml.safe_load(config_file.read_text()))
+    pprint(config)
+    return config
+
+
+@app.default
+def process(input_imzml_file: Path, output_imzml_file: Path, config_file: Path) -> None:
+    config = validate(config_file)
+    read_file = ImzmlReadFile(input_imzml_file)
+    # TODO in the future we might implement logic to determine when this can still be set to CONTINUOUS
+    write_file = ImzmlWriteFile(output_imzml_file, ImzmlModeEnum.PROCESSED)
+    process_spectra(read_file=read_file, write_file=write_file, config=config)
+
+
+if __name__ == "__main__":
+    app()