Fix ruff lint failures across pkg/ and tests/

pkg/mybib/arxiv.py

@@ -1,59 +1,59 @@
 """Fetch metadata from arXiv API."""
 
 import sys
-import requests
 import xml.etree.ElementTree as ET
 
+import requests
+
 
 def fetch_arxiv_metadata(arxiv_id: str) -> dict:
     """Fetch metadata from arXiv API.
-    
+
     Args:
         arxiv_id: arXiv identifier (e.g., '2301.00001')
-        
+
     Returns:
         Dictionary with keys: title, authors, journal, year, doi, link
-        
+
     Raises:
         SystemExit: If API call fails or no entry found
     """
     url = f"http://export.arxiv.org/api/query?id_list={arxiv_id}"
     response = requests.get(url)
-    
+
     if response.status_code != 200:
         print(f"Error fetching arxiv metadata: {response.status_code}")
         sys.exit(1)
-    
+
     root = ET.fromstring(response.content)
     ns = {
-        'atom': 'http://www.w3.org/2005/Atom',
-        'arxiv': 'http://arxiv.org/schemas/atom'
+        "atom": "http://www.w3.org/2005/Atom",
+        "arxiv": "http://arxiv.org/schemas/atom",
     }
-    
-    entry = root.find('atom:entry', ns)
+
+    entry = root.find("atom:entry", ns)
     if entry is None:
         print("No entry found for this arxiv ID.")
         sys.exit(1)
-
-    title = entry.find('atom:title', ns).text.strip().replace('\n', ' ')
-    authors = ', '.join(
-        author.find('atom:name', ns).text
-        for author in entry.findall('atom:author', ns)
+
+    title = entry.find("atom:title", ns).text.strip().replace("\n", " ")
+    authors = ", ".join(
+        author.find("atom:name", ns).text for author in entry.findall("atom:author", ns)
     )
-    published = entry.find('atom:published', ns).text
+    published = entry.find("atom:published", ns).text
     year = int(published[:4])
-    
-    doi_elem = entry.find('arxiv:doi', ns)
+
+    doi_elem = entry.find("arxiv:doi", ns)
     doi = doi_elem.text if doi_elem is not None else arxiv_id
-    
-    journal_elem = entry.find('arxiv:journal_ref', ns)
+
+    journal_elem = entry.find("arxiv:journal_ref", ns)
     journal = journal_elem.text if journal_elem is not None else "arXiv"
-    
+
     return {
         "title": title,
         "authors": authors,
         "journal": journal,
         "year": year,
         "doi": doi,
-        "link": f"https://arxiv.org/abs/{arxiv_id}"
+        "link": f"https://arxiv.org/abs/{arxiv_id}",
     }

pkg/mybib/bibtex.py

@@ -5,75 +5,74 @@
 
 def generate_bibtex(df: pd.DataFrame) -> str:
     """Generate BibTeX entries from a DataFrame of references.
-    
+
     Args:
         df: DataFrame with columns: Title, Authors, Journal, Year, DOI, Link
-        
+
     Returns:
         String containing BibTeX formatted entries
     """
     if df.empty:
         return "% No references found\n"
-    
+
     # Handle cases where DataFrame column names might not exactly match
     # Create a mapping of expected columns to actual columns
     col_mapping = {}
-    
+
     for col in df.columns:
         col_lower = col.lower().strip()
-        if col_lower == 'title':
-            col_mapping['title'] = col
-        elif col_lower == 'authors':
-            col_mapping['authors'] = col
-        elif col_lower == 'journal':
-            col_mapping['journal'] = col
-        elif col_lower == 'year':
-            col_mapping['year'] = col
-        elif col_lower == 'doi':
-            col_mapping['doi'] = col
-        elif col_lower == 'link':
-            col_mapping['link'] = col
-        elif col_lower == 'url':
-            col_mapping['link'] = col
-    
+        if col_lower == "title":
+            col_mapping["title"] = col
+        elif col_lower == "authors":
+            col_mapping["authors"] = col
+        elif col_lower == "journal":
+            col_mapping["journal"] = col
+        elif col_lower == "year":
+            col_mapping["year"] = col
+        elif col_lower == "doi":
+            col_mapping["doi"] = col
+        elif col_lower == "link":
+            col_mapping["link"] = col
+        elif col_lower == "url":
+            col_mapping["link"] = col
+
     entries = []
-    
+
     for _, row in df.iterrows():
         # Extract values using mapped column names
-        title = str(row.get(col_mapping.get('title', 'Title'), "")).strip()
-        authors = str(row.get(col_mapping.get('authors', 'Authors'), "")).strip()
-        journal = str(row.get(col_mapping.get('journal', 'Journal'), "")).strip()
-        year = str(row.get(col_mapping.get('year', 'Year'), "")).strip()
-        doi = str(row.get(col_mapping.get('doi', 'DOI'), "")).strip()
-        link = str(row.get(col_mapping.get('link', 'Link'), "")).strip()
-        
+        title = str(row.get(col_mapping.get("title", "Title"), "")).strip()
+        authors = str(row.get(col_mapping.get("authors", "Authors"), "")).strip()
+        journal = str(row.get(col_mapping.get("journal", "Journal"), "")).strip()
+        year = str(row.get(col_mapping.get("year", "Year"), "")).strip()
+        doi = str(row.get(col_mapping.get("doi", "DOI"), "")).strip()
+        link = str(row.get(col_mapping.get("link", "Link"), "")).strip()
+
         # Skip entries with missing critical fields
         if not title:
             continue
-        
+
         # Use DOI as the key, or create one from title if DOI is missing
         if doi and doi != "nan":
             key = doi
         else:
             # Fallback: create key from title
             key = title.lower().replace(" ", "_").replace(":", "")[:30]
-        
+
         # Build BibTeX entry
         entry = f"@article{{{key},\n"
-        entry += f'  title={{{title}}},\n'
-        
+        entry += f"  title={{{title}}},\n"
+
         if authors:
-            entry += f'  author={{{authors}}},\n'
+            entry += f"  author={{{authors}}},\n"
         if journal:
-            entry += f'  journal={{{journal}}},\n'
+            entry += f"  journal={{{journal}}},\n"
         if year and year != "nan":
-            entry += f'  year={{{year}}},\n'
+            entry += f"  year={{{year}}},\n"
         if link and link != "nan":
-            entry += f'  url={{{link}}}\n'
-        
+            entry += f"  url={{{link}}}\n"
+
         entry += "}\n"
-        
+
         entries.append(entry)
-
-    return "\n".join(entries)
 
+    return "\n".join(entries)