update tests

binette/io_manager.py

@@ -1,6 +1,6 @@
 import logging
 import pyfastx
-from typing import Iterable, List, Dict, Tuple
+from typing import Iterable, List, Dict, Tuple, Set
 import csv
 
 from binette.bin_manager import Bin
@@ -195,3 +195,25 @@ def check_resume_file(faa_file: Path, diamond_result_file: Path) -> None:
         raise FileNotFoundError(error_msg)
 
 
+def write_original_bin_metrics(bin_set_name_to_bins: Dict[str, Set[Bin]], original_bin_report_dir: Path):
+    """
+    Write metrics of original input bins to a specified directory.
+
+    This function takes a dictionary mapping bin set names to sets of bins and writes
+    the metrics for each bin set to a TSV file in the specified directory. Each bin set
+    will have its own TSV file named according to its set name.
+
+    :param bin_set_name_to_bins: A dictionary where the keys are bin set names (str) and 
+                                 the values are sets of Bin objects representing bins.
+    :param original_bin_report_dir: The directory path (Path) where the bin metrics will be saved.
+    """
+
+    original_bin_report_dir.mkdir(parents=True, exist_ok=True)
+
+    for i, (set_name, bins) in enumerate(sorted(bin_set_name_to_bins.items())):
+        bins_metric_file = original_bin_report_dir / f"input_bins_{i + 1}.{set_name.replace('/', '_')}.tsv"
+
+        logging.debug(f"Writing metrics for bin set '{set_name}' to file: {bins_metric_file}")
+        write_bin_info(bins, bins_metric_file)
+
+    logging.debug("Completed writing all original input bin metrics.")

binette/main.py

@@ -345,23 +345,6 @@ def log_selected_bin_info(selected_bins: List[bin_manager.Bin], hq_min_completen
     thresholds = f"(completeness >= {hq_min_completeness} and contamination <= {hq_max_conta})"
     logging.info(f"{hq_bins}/{len(selected_bins)} selected bins have a high quality {thresholds}.")
 
-def write_original_bin_metrics(bin_set_name_to_bins:Dict[str, Set[bin_manager.Bin]], original_bin_report_dir:Path):
-    """
-    
-    """
-
-    logging.info(f"Writing original input bins metrics in {original_bin_report_dir}")
-
-
-    original_bin_report_dir.mkdir(parents=True, exist_ok=True)
-
-    for i, (set_name, bins) in enumerate(sorted(bin_set_name_to_bins.items())):
-        bins_metric_file = original_bin_report_dir / f"input_bins_{i+1}.{set_name.replace('/', '_')}.tsv"
-
-        logging.info(f"Writing bin_set {set_name} input bins metrics in {bins_metric_file}")
-        io.write_bin_info(bins, bins_metric_file)
-
-
 
 def main():
     "Orchestrate the execution of the program"
@@ -416,7 +399,10 @@ def main():
     logging.info("Add size and assess quality of input bins")
     bin_quality.add_bin_metrics(original_bins, contig_metadat, args.contamination_weight, args.threads)
 
-    write_original_bin_metrics(bin_set_name_to_bins, original_bin_report_dir)
+
+
+    logging.info(f"Writting original input bin metrics to directory: {original_bin_report_dir}")
+    io.write_original_bin_metrics(bin_set_name_to_bins, original_bin_report_dir)
 
 
     logging.info("Create intermediate bins:")

tests/bin_manager_test.py

@@ -9,6 +9,7 @@
 import networkx as nx
 
 import logging
+from pathlib import Path
 
 def test_get_all_possible_combinations():
     input_list = ["2", "3", "4"]
@@ -524,14 +525,14 @@ def create_temp_bin_directories(tmpdir, create_temp_bin_files):
     bin2 = bin_dir2.join("binA.fasta")
     bin2.write(">contig3\nTTAG\n>contig4\nCGAT\n>contig5\nCGGC")
 
-    return {"set1": str(bin_dir1), "set2": str(bin_dir2)}
+    return {"set1": Path(bin_dir1), "set2": Path(bin_dir2)}
 
 
 def test_get_bins_from_directory(create_temp_bin_files):
     bin_dir = create_temp_bin_files
     set_name = "TestSet"
 
-    bins = bin_manager.get_bins_from_directory(str(bin_dir), set_name, fasta_extensions={'.fasta'})
+    bins = bin_manager.get_bins_from_directory(Path(bin_dir), set_name, fasta_extensions={'.fasta'})
 
     assert len(bins) == 2  # Ensure that the correct number of Bin objects is returned
 
@@ -546,15 +547,15 @@ def test_get_bins_from_directory(create_temp_bin_files):
     assert bins[0].name in ["bin2.fasta", "bin1.fasta"]
 
 def test_get_bins_from_directory_no_files(tmpdir):
-    bin_dir = str(tmpdir.mkdir("empty_bins"))
+    bin_dir = Path(tmpdir.mkdir("empty_bins"))
     set_name = "EmptySet"
 
     bins = bin_manager.get_bins_from_directory(bin_dir, set_name, fasta_extensions={'.fasta'})
 
     assert len(bins) == 0  # Ensure that no Bin objects are returned for an empty directory
 
 def test_get_bins_from_directory_no_wrong_extensions(create_temp_bin_files):
-    bin_dir = create_temp_bin_files
+    bin_dir = Path(create_temp_bin_files)
     set_name = "TestSet"
 
     bins = bin_manager.get_bins_from_directory(bin_dir, set_name, fasta_extensions={'.fna'})

tests/io_manager_test.py

@@ -1,15 +1,15 @@
 import pytest
 from binette import io_manager
 from pathlib import Path
-
+from unittest.mock import patch
 
 
 
 
 class Bin:
     def __init__(self, bin_id, origin, name, completeness, contamination, score, length, N50, contigs):
         self.id = bin_id
-        self.origin = origin
+        self.origin = {origin}
         self.name = name
         self.completeness = completeness
         self.contamination = contamination
@@ -65,7 +65,7 @@ def test_infer_bin_name_from_single_path():
     # Check if the output matches the expected dictionary
     assert result == expected_result
 
-    
+
 def test_infer_bin_name_from_bin_table_inputs():
     # Mock input data
     input_bins = [
@@ -283,3 +283,33 @@ def test_check_resume_file_missing_diamond(temp_files, caplog):
         io_manager.check_resume_file(Path(faa_file), Path("nonexistent_diamond_result.txt"))
     assert "Protein file" not in caplog.text
     assert "Diamond result file" in caplog.text
+
+
+@patch('binette.io_manager.write_bin_info')
+def test_write_original_bin_metrics(mock_write_bin_info, bin1,bin2, tmp_path):
+    # Test that `write_original_bin_metrics` correctly writes bin metrics to files
+
+    temp_directory =  tmp_path / "test_output"
+
+    mock_bins = {"set1":{bin1},
+                 "set2":{bin2}}
+    # Call the function with mock data
+    io_manager.write_original_bin_metrics(mock_bins, temp_directory)
+
+    # Check if the output directory was created
+    assert temp_directory.exists(), "Output directory should be created."
+
+    # Check that the correct files are created
+    expected_files = [
+        temp_directory / "input_bins_1.set1.tsv",
+        temp_directory / "input_bins_2.set2.tsv"
+    ]
+
+    assert temp_directory.exists(), f"Expected temp_directory {temp_directory} was not created."
+
+    # Check if `write_bin_info` was called correctly
+    assert mock_write_bin_info.call_count == 2, "write_bin_info should be called once for each bin set."
+
+    # Verify the specific calls to `write_bin_info`
+    mock_write_bin_info.assert_any_call(mock_bins['set1'], expected_files[0])
+    mock_write_bin_info.assert_any_call(mock_bins['set2'], expected_files[1])

tests/main_binette_test.py

@@ -371,6 +371,7 @@ def test_main(monkeypatch):
          patch('binette.bin_quality.add_bin_metrics') as mock_add_bin_metrics, \
          patch('binette.main.log_selected_bin_info') as mock_log_selected_bin_info, \
          patch('binette.contig_manager.make_contig_index') as mock_make_contig_index, \
+         patch('binette.io_manager.write_original_bin_metrics') as mock_write_original_bin_metrics, \
          patch('binette.main.select_bins_and_write_them') as mock_select_bins_and_write_them:
 
         # Set return values for mocked functions if needed
@@ -395,5 +396,7 @@ def test_main(monkeypatch):
 
         mock_log_selected_bin_info.assert_called_once()
         mock_select_bins_and_write_them.assert_called_once()
+        mock_write_original_bin_metrics.assert_called_once()
+
         assert mock_apply_contig_index.call_count == 3
         assert mock_add_bin_metrics.call_count == 2