Improve installation documentation and add optional dependency instructions

package/README.md

@@ -16,15 +16,14 @@ A Python package for generating methods sections and reports for ASL (Arterial S
 
 ### Prerequisites
 
-- Python 3.7 or higher
+- Python 3.8 or higher
 - pip
 
-### Install from Source
+### Clone the Repository
 
 ```bash
-# Clone the repository
-git clone <repository-url>
-cd ASL\ Generator/package
+git clone https://github.com/OSIPI/Method-section-generator.git
+cd Method-section-generator/package
 
 # Install in development mode
 pip install -e .

package/src/pyaslreport/tests/test_package.py

@@ -1,9 +1,18 @@
 import pytest
 from unittest.mock import patch, MagicMock
-from .main import get_bids_metadata
+from pyaslreport.main import get_bids_metadata
 
-# filepath: /home/ibrahim/MyPc/Projects/GSoC/ASL-Parameter-Generator/package/src/pyaslreport/test_main.py
+# Test missing keys safely
+def test_missing_key_returns_none():
+    data = {"dicom_dir": "/fake/path", "modality": None}
+    with patch("pyaslreport.main.get_dicom_header", return_value=None), \
+         patch("pyaslreport.main.get_sequence", return_value=None):
+        import pytest
+        with pytest.raises(ValueError) as exc:
+            get_bids_metadata(data)
+        assert "No matching sequence found" in str(exc.value)
 
+# Test: normal successful run
 def test_get_bids_metadata_success():
     data = {"modality": "asl", "dicom_dir": "/fake/dir"}
     fake_header = MagicMock()
@@ -15,11 +24,13 @@ def test_get_bids_metadata_success():
         assert result == ("meta", "context")
         fake_sequence.extract_bids_metadata.assert_called_once()
 
+# Test: no dicom_dir raises TypeError
 def test_get_bids_metadata_no_dicom_dir():
     data = {"modality": "asl"}
     with pytest.raises(TypeError):
         get_bids_metadata(data)
 
+# Test: no sequence raises ValueError
 def test_get_bids_metadata_no_sequence():
     data = {"modality": "asl", "dicom_dir": "/fake/dir"}
     fake_header = MagicMock()
@@ -29,6 +40,7 @@ def test_get_bids_metadata_no_sequence():
             get_bids_metadata(data)
         assert "No matching sequence found" in str(exc.value)
 
+# Test: invalid modality raises ValueError
 def test_get_bids_metadata_invalid_modality():
     data = {"modality": None, "dicom_dir": "/fake/dir"}
     fake_header = MagicMock()

pytest.ini

@@ -0,0 +1,3 @@
+[pytest] 
+testpaths = package/src/pyaslreport/tests 
+addopts = -m "not backend"