Fix cli

README.md

@@ -147,17 +147,17 @@ Once installed, you can call the CLI.
 Example using demo files:
 
 ```bash
-ecoffitter   --input demo_files/censored.txt   --params demo_files/params.txt   --outfile demo_files/output.txt
+ecoff-fitter   --input demo_files/input.txt   --params demo_files/params.txt   --outfile demo_files/output.txt
 ```
 
 Instead of using a parameter file, you can also specify parameters directly.
 
 Usage:
 
 ```bash
-ecoff_fitter [-h] --input INPUT [--params PARAMS]
+ecoff-fitter [-h] --input INPUT [--params PARAMS]
 [--dilution_factor DILUTION_FACTOR]
-[--distributions ] [--boundary_support boundary_support]
+[--distributions DISTRIBUTIONS] [--boundary_support BOUNDARY_SUPPORT]
 [--percentile PERCENTILE] [--outfile OUTFILE] [--verbose]
 ```
 

gui.py

@@ -160,56 +160,41 @@ def run_ecoff(self):
                 individual_results[col] = (fitter, result)
 
 
-            text = "ECOFF RESULTS\n"
-            text += "=====================================\n\n"
+            text = "ECOFF RESULTS\n=====================================\n\n"
 
-            if len(individual_results.keys())>1:
-                text += "GLOBAL FIT\n"
-                text += "-------------------------------------\n"
-                text += f"  ECOFF: {global_result[0]:.4f}\n"
-                text += f"  z-value: {global_result[1]:.4f}\n"
-                for i in range(global_fitter.distributions):
-                    if global_fitter.distributions > 1:
-                        text += f"  Component {i+1}:\n"
-                    text += f"    mu = {dilution_factor**global_fitter.mus_[i]:.4f}\n"
-                    text += f"    sigma (folds) = {dilution_factor**global_fitter.sigmas_[i]:.4f}\n"
-                text += "\n"
-
-                text += "INDIVIDUAL FITS:\n"
-                text += "-------------------------------------\n"
+            global_report = GenerateReport.from_fitter(global_fitter, global_result)
+            if len(individual_results) > 1:
+
+                text += global_report.to_text("GLOBAL FIT")
+                text += "\nINDIVIDUAL FITS:\n-------------------------------------\n"
+
+
+            # Individual fits
+            for name, (fitter, result) in individual_results.items():
+                rep = GenerateReport.from_fitter(fitter, result)
+                text += rep.to_text(label=name)
 
-            for col, (fitter, result) in individual_results.items():
-                text += f"{col}\n"
-                text += f"  ECOFF: {result[0]:.4f}\n"
-                text += f"  z-value: {result[1]:.4f}\n"
-                for i in range(fitter.distributions):
-                    if fitter.distributions>1:
-                        text += f"  Component {i+1}:\n"
-                    text += f"    mu = {dilution_factor**fitter.mus_[i]:.4f}\n"
-                    text += f"    sigma (folds) = {dilution_factor**fitter.sigmas_[i]:.4f}\n"
-                text += "\n"
 
             if outfile:
+                validate_output_path(outfile)
                 if len(individual_results.keys())==1:
-                    validate_output_path(outfile)
-                    report = GenerateReport.from_fitter(global_fitter, global_result)
                     if outfile.endswith(".pdf"):
-                        report.save_pdf(outfile)
+                        global_report.save_pdf(outfile)
                     else:
-                        report.write_out(outfile)
-                    text += f"\nSaved global report to: {outfile}"
+                        global_report.write_out(outfile)
                 elif (len(individual_results.keys()))>1:
                     # Build section reports
-                    global_report = GenerateReport.from_fitter(global_fitter, global_result)
-
                     indiv_reports = {
                         name: GenerateReport.from_fitter(fitter, result)
                         for name, (fitter, result) in individual_results.items()
                     }
 
                     # Build combined PDF
                     combined = CombinedReport(outfile, global_report, indiv_reports)
-                    combined.save_pdf()
+                    if outfile.endswith(".pdf"):
+                        combined.save_pdf()
+                    else:
+                        combined.write_out()
 
 
             for widget in self.plot_frame.winfo_children():

src/ecoff_fitter/cli.py

@@ -9,11 +9,13 @@
 import argparse
 from typing import Any, List, Optional
 from ecoff_fitter import ECOFFitter
-from ecoff_fitter.report import GenerateReport
+from ecoff_fitter.report import GenerateReport, CombinedReport
 from ecoff_fitter.defence import validate_output_path
+from ecoff_fitter.utils import read_multi_obs_input
 from unittest.mock import MagicMock, patch
 
 
+
 def build_parser() -> argparse.ArgumentParser:
     """Create and configure the command-line argument parser."""
     parser = argparse.ArgumentParser(
@@ -27,7 +29,7 @@ def build_parser() -> argparse.ArgumentParser:
         required=True,
         help=(
             "Path to the input MIC dataset (CSV, TSV, XLSX, or XLS) "
-            "with columns 'MIC' and 'observations'."
+            "with columns 'MIC' and assay name."
         ),
     )
     parser.add_argument(
@@ -80,28 +82,74 @@ def main(argv: Optional[List[str]] = None) -> None:
     parser = build_parser()
     args = parser.parse_args(argv)
 
-    fitter = ECOFFitter(
-        input=args.input,
-        params=args.params,
-        dilution_factor=args.dilution_factor,
-        distributions=args.distributions,
-        boundary_support=args.boundary_support,
-    )
-
-    result = fitter.generate(percentile=args.percentile)
-
-    report = GenerateReport.from_fitter(fitter, result)
-
-    report.print_stats(args.verbose)
-
-    if args.outfile:
-
-        validate_output_path(args.outfile)
-
-        if args.outfile.endswith(".pdf"):
-            report.save_pdf(args.outfile)
-        else:
-            report.write_out(args.outfile)
+    try:
+
+        data_dict = read_multi_obs_input(args.input)
+        df_global = data_dict['global']
+        df_individual = data_dict['individual']
+
+        global_fitter = ECOFFitter(
+            input=df_global,
+            params=args.params,
+            distributions=args.distributions,
+            boundary_support=args.boundary_support,
+            dilution_factor=args.dilution_factor
+        )
+
+        global_result = global_fitter.generate(percentile=args.percentile)
+
+        individual_results = {}
+        for col, subdf in df_individual.items():
+
+            fitter = ECOFFitter(
+                input=subdf,
+                params=args.params,
+                dilution_factor=args.dilution_factor,
+                distributions=args.distributions,
+                boundary_support=args.boundary_support,
+            )
+
+            result = fitter.generate(percentile=args.percentile)
+            individual_results[col] = (fitter, result)
+
+        text = "\n\nECOFF RESULTS\n=====================================\n\n"
+
+        global_report = GenerateReport.from_fitter(global_fitter, global_result)
+
+        if len(individual_results) > 1:
+            text += global_report.to_text("GLOBAL FIT")
+            text += "\nINDIVIDUAL FITS:\n-------------------------------------\n"
+
+        # Individual fits
+        for name, (fitter, result) in individual_results.items():
+            rep = GenerateReport.from_fitter(fitter, result)
+            text += rep.to_text(label=name)       
+
+        if args.outfile:
+            validate_output_path(args.outfile)
+            if len(individual_results.keys())==1:
+
+                if args.outfile.endswith(".pdf"):
+                    global_report.save_pdf(args.outfile)
+                else:
+                    global_report.write_out(args.outfile)
+            elif (len(individual_results.keys()))>1:
+                # Build section reports
+                indiv_reports = {
+                    name: GenerateReport.from_fitter(fitter, result)
+                    for name, (fitter, result) in individual_results.items()
+                }
+                # Build combined PDF
+                combined = CombinedReport(args.outfile, global_report, indiv_reports)
+                if args.outfile.endswith(".pdf"):
+                    combined.save_pdf()
+                else:
+                    combined.write_out()
+
+        print (text)
+
+    except Exception as e:
+        print ('Error', str(e))
 
 
 if __name__ == "__main__":