From e140f5fc801e6a273633611a22f3a47ea6a7b51a Mon Sep 17 00:00:00 2001
From: Chunyu Ma <machunyu4402@hotmail.com>
Date: Mon, 18 Mar 2024 21:33:45 -0400
Subject: [PATCH] add better instruction when entering the command

---
 yacht/__init__.py                         | 50 +++++++++++++++++++++--
 yacht/download_default_ref_db.py          |  3 +-
 yacht/download_demofiles.py               |  3 +-
 yacht/download_pretrained_ref_db.py       |  3 +-
 yacht/make_training_data_from_sketches.py |  3 --
 yacht/run_YACHT.py                        |  3 --
 yacht/sketch_ref_genomes.py               |  2 -
 yacht/sketch_sample.py                    |  2 -
 yacht/standardize_yacht_output.py         |  3 +-
 9 files changed, 51 insertions(+), 21 deletions(-)

diff --git a/yacht/__init__.py b/yacht/__init__.py
index 328dda8..68a1b27 100644
--- a/yacht/__init__.py
+++ b/yacht/__init__.py
@@ -1,4 +1,5 @@
 import argparse
+import sys
 
 from . import (
     download_default_ref_db,
@@ -12,10 +13,48 @@
 )
 from .utils import __version__
 
+# Custom help action
+class CustomHelpAction(argparse.Action):
+    def __init__(self, option_strings, dest, **kwargs):
+        super(CustomHelpAction, self).__init__(option_strings=option_strings, dest=dest, nargs=0, **kwargs)
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        print_custom_help_exit()
+
+def print_version():
+    print(f"== This is YACHT version {utils.__version__} ==")
+    print("== Please cite https://doi.org/10.1093/bioinformatics/btae047. ==")
+
+def print_custom_help_exit():
+    print_version()
+    print("""
+YACHT is a mathematically rigorous hypothesis test for the presence or absence of organisms 
+in a metagenomic sample, based on average nucleotide identity (ANI).
+
+Usage instructions:
+    yacht download demo -h download YACHT demo files
+    yacht download default_ref_db -h download default raw reference databases
+    yacht download pretrained_ref_db -h download pretrained databases
+
+    yacht sketch ref -h sketch reference genomes
+    yacht sketch sample -h sketch metagenomics samples
+        
+    yacht train -h pre-process the reference genomes
+    
+    yacht run -h run the YACHT algorithm
+    
+    yacht convert -h convert YACHT result to other popular output formats
+
+Options:
+  -h, --help     show this help message and exit
+  -v, --version  show program's version number and exit
+""")
+    sys.exit()
 
 def main():
-    parser = argparse.ArgumentParser(prog="yacht")
-    parser.add_argument("--version", action="version", version=f"YACHT {utils.__version__}")
+    parser = argparse.ArgumentParser(prog="yacht", add_help=False)
+    parser.add_argument("-v", "--version", action="store_true", help="show program's version number and exit")
+    parser.add_argument("-h", "--help", action=CustomHelpAction, help="show this help message and exit")
     subparsers = parser.add_subparsers(dest="command")
 
     # Train command
@@ -86,10 +125,15 @@ def main():
     sketch_sample_parser.set_defaults(func=sketch_sample.main)
 
     args = parser.parse_args()
+    
+    if args.version:
+        print_version()
+        sys.exit()
+    
     if "func" in args:
         args.func(args)
     else:
-        parser.print_help()
+        print_custom_help_exit()
 
 
 if __name__ == "__main__":
diff --git a/yacht/download_default_ref_db.py b/yacht/download_default_ref_db.py
index 8d4edbc..ee038fd 100644
--- a/yacht/download_default_ref_db.py
+++ b/yacht/download_default_ref_db.py
@@ -6,7 +6,7 @@
 import os
 from .utils import create_output_folder, check_download_args
 # Import global variables
-from .utils import BASE_URL, __version__
+from .utils import BASE_URL
 
 # Configure Loguru logger
 logger.remove()
@@ -16,7 +16,6 @@
 
 
 def add_arguments(parser):
-    parser.add_argument("--version", action="version", version=f"YACHT {__version__}")
     parser.add_argument("--database", choices=["genbank", "gtdb"], required=True)
     parser.add_argument(
         "--db_version",
diff --git a/yacht/download_demofiles.py b/yacht/download_demofiles.py
index 0e89e44..a0551d0 100644
--- a/yacht/download_demofiles.py
+++ b/yacht/download_demofiles.py
@@ -5,7 +5,7 @@
 import argparse
 from loguru import logger
 # Import global variables
-from .utils import GITHUB_API_URL, GITHUB_RAW_URL, __version__
+from .utils import GITHUB_API_URL, GITHUB_RAW_URL
 
 # Configure Loguru logger
 logger.remove()
@@ -17,7 +17,6 @@
 
 
 def add_arguments(parser):
-    parser.add_argument("--version", action="version", version=f"YACHT {__version__}")
     parser.add_argument("--outfolder", help="Output folder.", default="demo")
 
 
diff --git a/yacht/download_pretrained_ref_db.py b/yacht/download_pretrained_ref_db.py
index 8aeab71..43fd9b4 100644
--- a/yacht/download_pretrained_ref_db.py
+++ b/yacht/download_pretrained_ref_db.py
@@ -8,7 +8,7 @@
 import zipfile
 from .utils import create_output_folder, check_download_args
 # Import global variables
-from .utils import ZENODO_COMMUNITY_URL, __version__
+from .utils import ZENODO_COMMUNITY_URL
 
 # Configure Loguru logger
 logger.remove()
@@ -20,7 +20,6 @@
 
 
 def add_arguments(parser):
-    parser.add_argument("--version", action="version", version=f"YACHT {__version__}")
     parser.add_argument("--database", choices=["genbank", "gtdb"], required=True)
     parser.add_argument(
         "--db_version", choices=["genbank-2022.03", "rs214"], required=True
diff --git a/yacht/make_training_data_from_sketches.py b/yacht/make_training_data_from_sketches.py
index 9a0830f..ffbdb93 100644
--- a/yacht/make_training_data_from_sketches.py
+++ b/yacht/make_training_data_from_sketches.py
@@ -17,9 +17,6 @@
 
 
 def add_arguments(parser):
-    parser.add_argument(
-        "--version", action="version", version=f"YACHT {utils.__version__}"
-    )
     parser.add_argument(
         "--ref_file",
         help="Location of the Sourmash signature database file. "
diff --git a/yacht/run_YACHT.py b/yacht/run_YACHT.py
index 9d5e5d0..50b888d 100644
--- a/yacht/run_YACHT.py
+++ b/yacht/run_YACHT.py
@@ -21,9 +21,6 @@
 
 
 def add_arguments(parser):
-    parser.add_argument(
-        "--version", action="version", version=f"YACHT {utils.__version__}"
-    )
     parser.add_argument(
         "--json",
         type=str,
diff --git a/yacht/sketch_ref_genomes.py b/yacht/sketch_ref_genomes.py
index a97c397..b20bde0 100644
--- a/yacht/sketch_ref_genomes.py
+++ b/yacht/sketch_ref_genomes.py
@@ -6,7 +6,6 @@
 from pathlib import Path
 from loguru import logger
 # Import global variables
-from .utils import __version__
 
 # Configure Loguru logger
 logger.remove()
@@ -16,7 +15,6 @@
 
 
 def add_arguments(parser):
-    parser.add_argument("--version", action="version", version=f"YACHT {__version__}")
     parser.add_argument("--infile", help="Input file or folder path.", required=True)
     parser.add_argument("--kmer", type=int, help="K-mer size.", default=31)
     parser.add_argument("--scaled", type=int, help="Scaled factor.", default=1000)
diff --git a/yacht/sketch_sample.py b/yacht/sketch_sample.py
index a59c8c2..1b26fb8 100644
--- a/yacht/sketch_sample.py
+++ b/yacht/sketch_sample.py
@@ -7,7 +7,6 @@
 from loguru import logger
 
 # Import global variables
-from .utils import __version__
 
 # Configure Loguru logger
 logger.remove()
@@ -18,7 +17,6 @@
 
 
 def add_arguments(parser):
-    parser.add_argument("--version", action="version", version=f"YACHT {__version__}")
     parser.add_argument(
         "--infile",
         nargs="+",
diff --git a/yacht/standardize_yacht_output.py b/yacht/standardize_yacht_output.py
index f168c38..8fdac04 100644
--- a/yacht/standardize_yacht_output.py
+++ b/yacht/standardize_yacht_output.py
@@ -11,7 +11,7 @@
 import biom
 import argparse
 from biom.util import biom_open
-from .utils import get_cami_profile, __version__
+from .utils import get_cami_profile
 from collections import OrderedDict
 from loguru import logger
 
@@ -23,7 +23,6 @@
 
 
 def add_arguments(parser):
-    parser.add_argument("--version", action="version", version=f"YACHT {__version__}")
     parser.add_argument(
         "--yacht_output",
         type=str,