Merge pull request #21 from genotoul-bioinfo/dev

Disable multiple arguments and clarify how to ask for help

README.md

@@ -26,6 +26,8 @@ Binette is inspired from the metaWRAP bin-refinement tool but it effectively sol
 <!-- - Bin selection have been improved. It selects the best bins in a more accurate and elegant manner.
 - It is easier to use. -->
 
+A comprehensive documentation of Binette is avalaible here: https://binette.readthedocs.io/
+
 # Installation
 
 ## With Bioconda
@@ -164,12 +166,12 @@ The `final_bins_quality_reports.tsv` file contains the following columns:
 | **N50**             | Displays the N50 of the bin.                                                                                |
 | **contig_count**    | The number of contigs contained within the bin.                                                             |
 
-# Feature requests and bug reporting
+# Help, feature requests and bug reporting
 
-Please submit bug reports and feature requests by opening an [issue](https://github.com/genotoul-bioinfo/Binette/issues). 
+To report bugs, request new features, or seek help and support, please open an [issue](https://github.com/genotoul-bioinfo/Binette/issues). 
 
 
 # Licence
 
-This program is released as an open source software under the terms of [MIT License](https://forgemia.inra.fr/jean.mainguy/binette/-/raw/main/LICENSE).
+This program is released as an open source software under the terms of [MIT License](LICENSE).
 

binette/main.py

@@ -8,7 +8,7 @@
 Portability : POSIX
 """
 
-from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
+from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter, Action, Namespace
 
 import sys
 import logging
@@ -39,6 +39,26 @@ def init_logging(verbose, debug):
         f'command line: {" ".join(sys.argv)}',
     )
 
+class UniqueStore(Action):
+    """
+    Custom argparse action to ensure an argument is provided only once.
+    """
+
+    def __call__(self, parser: ArgumentParser, namespace: Namespace, values: str, option_string: str = None) -> None:
+        """
+        Ensures the argument is only used once. Raises an error if the argument appears multiple times.
+
+        :param parser: The argparse parser instance.
+        :param namespace: The namespace object that will contain the parsed arguments.
+        :param values: The value associated with the argument.
+        :param option_string: The option string that was used to invoke this action.
+        """
+        # Check if the argument has already been set
+        if getattr(namespace, self.dest, self.default) is not self.default:
+            parser.error(f"Error: The argument {option_string} can only be specified once.")
+
+        # Set the argument value
+        setattr(namespace, self.dest, values)
 
 
 def parse_arguments(args):
@@ -57,13 +77,15 @@ def parse_arguments(args):
         "-d",
         "--bin_dirs",
         nargs="+",
+        action=UniqueStore,
         help="List of bin folders containing each bin in a fasta file.",
     )
 
     input_arg.add_argument(
         "-b",
         "--contig2bin_tables",
         nargs="+",
+        action=UniqueStore,
         help="List of contig2bin table with two columns separated\
             with a tabulation: contig, bin",
     )

docs/contributing.md

@@ -1,18 +1,19 @@
 # Contributing
 
-Thank you for your interest in contributing to Binette! This is an open-source project and everyone is welcome to contribute to it. 
+Thank you for your interest in contributing to Binette! This is an open-source project, and we welcome everyone to get involved.
 
-## Reporting a Bug
+## Help or Reporting a Bug
 
-If you have any question, if you found a bug. Please open an issue. 
+If you have a question or found a bug? Please open an issue.
 
-You can check the [Issues](https://github.com/genotoul-bioinfo/Binette/issues) page to see if the bug or question has been already reported.
+Before you do, check the [Issues](https://github.com/genotoul-bioinfo/Binette/issues) page to see if it's already been reported.
 
-If it's not reported, create a new [issue](https://github.com/genotoul-bioinfo/Binette/issues).
+If you don’t see it there, create a new [issue](https://github.com/genotoul-bioinfo/Binette/issues). We appreciate your input!
 
-## Adding a New Feature to Binette
 
-### Starting with an Issue
+## Adding a new feature to Binette
+
+### Starting with an issue
 
 If you have ideas for new features or improvements, initiate a discussion in an issue. This allows us to evaluate and discuss your suggestions together.
 
@@ -28,7 +29,7 @@ For minor changes like fixing typos or making small edits, create a new Pull Req
    Create an environment with all Binette prerequisites installed by following the installation instructions [here](./installation.md#installing-from-source-code-within-a-conda-environnement).
 
 3. **Install in Editable Mode:**
-   To enable seamless code editing and testing of new functionality, install PPanGGOLiN in editable mode using the following command:
+   To enable code editing and testing of new functionality, you can install Binette in editable mode using the following command:
 
    ```bash
    pip install -e .

tests/main_binette_test.py

@@ -1,7 +1,7 @@
 
 import pytest
 import logging
-from binette.main import log_selected_bin_info, select_bins_and_write_them, manage_protein_alignement, parse_input_files, parse_arguments, init_logging, main
+from binette.main import log_selected_bin_info, select_bins_and_write_them, manage_protein_alignement, parse_input_files, parse_arguments, init_logging, main, UniqueStore
 from binette.bin_manager import Bin
 from binette import diamond, contig_manager, cds
 import os
@@ -10,6 +10,8 @@
 
 from collections import Counter
 from tests.bin_manager_test import create_temp_bin_directories, create_temp_bin_files
+from argparse import ArgumentParser
+
 
 @pytest.fixture
 def bins():
@@ -237,6 +239,20 @@ def test_parse_input_files_bin_dirs(create_temp_bin_directories, tmp_path):
     assert len(contig_to_length) == 5
 
 
+def test_argument_used_once():
+    # Test UniqueStore class 
+    parser = ArgumentParser(description='Test parser')
+    parser.add_argument('--example', action=UniqueStore, help='Example argument')
+    args = parser.parse_args(['--example', 'value'])
+    assert args.example == 'value'
+
+def test_argument_used_multiple_times():
+    # Test UniqueStore class 
+    parser = ArgumentParser(description='Test parser')
+    parser.add_argument('--example', action=UniqueStore, help='Example argument')
+    with pytest.raises(SystemExit):
+        parser.parse_args(['--example', 'value', '--example', 'value2'])
+
 
 def test_parse_arguments_required_arguments():
     # Test when only required arguments are provided