From dc757b90e2d26797293c75bd64f50277eee20901 Mon Sep 17 00:00:00 2001
From: Wout Bittremieux <wout@bittremieux.be>
Date: Mon, 25 Dec 2023 12:48:11 +0100
Subject: [PATCH] Update `output` command-line description

Fixes #241.
---
 CHANGELOG.md         |  4 ++++
 casanovo/casanovo.py | 15 ++++++++++-----
 2 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index bbc9284e..4d2e54ab 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,10 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ## [Unreleased]
 
+### Changed
+
+- Update description of the `output` command-line argument to reflect that this is the root of the output (mzTab, log) files.
+
 ## [4.0.0] - 2023-12-22
 
 ### Added
diff --git a/casanovo/casanovo.py b/casanovo/casanovo.py
index 0a1c3618..1fa53f6b 100644
--- a/casanovo/casanovo.py
+++ b/casanovo/casanovo.py
@@ -58,14 +58,17 @@ def __init__(self, *args, **kwargs) -> None:
             click.Option(
                 ("-m", "--model"),
                 help="""
-                The model weights (.ckpt file). If not provided, Casanovo
-                will try to download the latest release.
+                The model weights (.ckpt file). If not provided, Casanovo will
+                try to download the latest release (during sequencing).
                 """,
                 type=click.Path(exists=True, dir_okay=False),
             ),
             click.Option(
                 ("-o", "--output"),
-                help="The mzTab file to which results will be written.",
+                help="The root file name to which results (i.e. the mzTab file "
+                     "during sequencing, as well as the log file during all "
+                     "modes) will be written. If not specified, a default "
+                     "timestamped file name will be used.",
                 type=click.Path(dir_okay=False),
             ),
             click.Option(
@@ -139,7 +142,7 @@ def sequence(
         for peak_file in peak_path:
             logger.info("  %s", peak_file)
 
-        runner.predict(peak_path, output)
+        runner.predict(peak_path, str(output))
 
     logger.info("DONE!")
 
@@ -328,7 +331,7 @@ def setup_model(
     config: Optional[str],
     output: Optional[Path],
     is_train: bool,
-) -> Config:
+) -> Tuple[Config, str]:
     """Setup Casanovo for most commands.
 
     Parameters
@@ -347,6 +350,8 @@ def setup_model(
     ------
     config : Config
         The parsed configuration
+    model : str
+        The name of the model weights.
     """
     # Read parameters from the config file.
     config = Config(config)