Fix issue #5222: [Refactor]: Refactor the evaluation directory (#5223)

Co-authored-by: Engel Nyst <enyst@users.noreply.github.com>

evaluation/benchmarks/biocoder/scripts/setup/copy_changed_code.py

@@ -0,0 +1,45 @@
+import argparse
+
+
+def get_changed_code(target_filepath, line_start, include_signature=False):
+    # copies changed code into /testing_files/
+    # Note that this does NOT copy the function signature
+    selected_lines = []
+    offset = 1 if include_signature else 0
+
+    with open('/testing_files/first_line_after_removed.txt', 'r') as f:
+        first_line_after_removed = f.read()
+    if first_line_after_removed is None:
+        print('First line after removed is None')
+
+    with open(target_filepath, 'r') as f:
+        lines = f.read().split('\n')
+        for i in range(line_start - offset, len(lines)):
+            if lines[i].strip() == first_line_after_removed.strip():
+                break
+            selected_lines.append(lines[i])
+    text = '\n'.join(selected_lines)
+    return text
+
+
+def copy_changed_code(
+    target_filepath, generated_code_filepath, line_start, include_signature=False
+):
+    changed_code = get_changed_code(target_filepath, line_start, include_signature)
+    with open(generated_code_filepath, 'w') as f:
+        f.write(changed_code)
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--target_filepath', type=str, required=True)
+    parser.add_argument('--generated_code_filepath', type=str, required=True)
+    parser.add_argument('--line_start', type=int, required=True)
+    parser.add_argument('--include_signature', action='store_true')
+    args = parser.parse_args()
+    copy_changed_code(
+        args.target_filepath,
+        args.generated_code_filepath,
+        args.line_start,
+        args.include_signature,
+    )