Fix duplicate imports in __init__.py generation and resolve linter errors

Refactors `generate_init.py` to track previously imported names, ensuring that symbols exported by multiple modules are only imported once in the package `__init__.py`. This resolves F811 redefinition errors reported by linters.

Changes:
- `generate_init.py`: Added logic to filter out duplicate imports across modules and fixed the appending of import lines.
- `pat2vec/__init__.py`: Regenerated file, removing duplicate imports for `COLUMNS_TO_DROP`, `SEARCH_TERM`, and `filter_annot_dataframe`.
- `pat2vec/pat2vec_search/cogstack_search_methods.py`: Minor formatting fix for `field_list` assignment.

Author: SamoraHunter

generate_init.py

@@ -70,17 +70,24 @@ def generate_init_file_content(package_path="pat2vec"):
         "",
     ]
 
+    imported_names = set()  # Keep track of names we've already imported.
+
     for module, imports in sorted(module_to_imports.items()):
-        if imports:
-            sorted_imports = sorted(imports)
+        unique_imports_for_module = []
+        for name in sorted(imports):
+            if name not in imported_names:
+                unique_imports_for_module.append(name)
+                imported_names.add(name)
+
+        if unique_imports_for_module:
             import_line = f"from {module} import ("
+            output_lines.append(import_line)
 
             wrapper = textwrap.TextWrapper(
                 width=88, initial_indent="    ", subsequent_indent="    "
             )
-            wrapped_imports = wrapper.fill(", ".join(sorted_imports))
+            wrapped_imports = wrapper.fill(", ".join(unique_imports_for_module))
 
-            output_lines.append(import_line)
             output_lines.append(wrapped_imports)
             output_lines.append(")")
 

pat2vec/__init__.py

@@ -59,7 +59,6 @@
     search_diagnostic_orders,
 )
 from .pat2vec_get_methods.get_method_drugs import (
-    COLUMNS_TO_DROP,
     DRUG_FIELDS,
     calculate_drug_features,
     create_drug_features_dataframe,
@@ -81,7 +80,6 @@
     get_current_pat_report_annotations,
 )
 from .pat2vec_get_methods.get_method_smoking import (
-    SEARCH_TERM,
     SMOKING_FIELDS,
     calculate_smoking_features,
     get_smoking,
@@ -92,7 +90,6 @@
     get_current_pat_textual_obs_annotations,
 )
 from .pat2vec_get_methods.get_method_vte_status import (
-    SEARCH_TERM,
     VTE_FIELDS,
     calculate_vte_features,
     get_vte_status,
@@ -399,7 +396,6 @@
     build_merged_bloods,
     build_merged_epr_mct_annot_df,
     build_merged_epr_mct_doc_df,
-    filter_annot_dataframe,
     get_annots_joined_to_docs,
     join_docs_to_annots,
     merge_appointments_csv,