Update type hints for new beautifulsoup4 (#335)

src/pyobo/sources/bigg/bigg_compartment.py

@@ -62,9 +62,11 @@ def get_compartments(*, force: bool = False, version: str | None = None) -> dict
     """Get a dictionary of BiGG compartments."""
     rv = {}
     soup = get_soup(DATA_URL)
-    table = soup.find(**{"class": "myTable"})
-    for row in table.findAll("tr"):
-        cells = list(row.findAll("td"))
+    table = soup.find(**{"class": "myTable"})  # type:ignore[arg-type]
+    if table is None:
+        raise ValueError
+    for row in table.find_all("tr"):  # type:ignore[attr-defined]
+        cells = list(row.find_all("td"))
         if not cells:
             continue
         identifier_cell, name_cell = cells

src/pyobo/sources/omim_ps.py

@@ -11,7 +11,6 @@
     "OMIMPSGetter",
 ]
 
-
 logger = logging.getLogger(__name__)
 PREFIX = "omim.ps"
 URL = "https://omim.org/phenotypicSeriesTitles/all"
@@ -25,8 +24,16 @@ class OMIMPSGetter(Obo):
     def iter_terms(self, force: bool = False) -> Iterable[Term]:
         """Iterate over terms in the ontology."""
         soup = get_soup(URL, user_agent="Mozilla/5.0")
-        rows = soup.find(id="mimContent").find("table").find("tbody").find_all("tr")
-        for row in rows:
+        content = soup.find(id="mimContent")
+        if content is None:
+            raise ValueError
+        table = content.find("table")  # type:ignore[attr-defined]
+        if table is None:
+            raise ValueError
+        tbody = table.find("tbody")
+        if tbody is None:
+            raise ValueError
+        for row in tbody.find_all("tr"):
             anchor = row.find("td").find("a")
             name = anchor.text.strip()
             identifier = anchor.attrs["href"][len("/phenotypicSeries/") :]

src/pyobo/sources/umls/get_synonym_types.py

@@ -26,7 +26,11 @@ def get_umls_synonyms(*, refresh: bool = False) -> Mapping[str, str]:
     res = requests.get(ABBREVIATIONS_URL, timeout=5)
     soup = BeautifulSoup(res.text, features="html.parser")
     table = soup.find(id="mrdoc_TTY")
-    body = table.find("tbody")
+    if table is None:
+        raise ValueError
+    body = table.find("tbody")  # type:ignore[attr-defined]
+    if body is None:
+        raise ValueError
     rv = {}
     for row in body.find_all("tr"):
         left, right = row.find_all("td")