minor

gseapy/base.py

@@ -732,7 +732,7 @@ def enrichment_score(
         # Test whether each element of a 1-D array is also present in a second array
         # It's more intuitive here than original enrichment_score source code.
         # use .astype to covert bool to integer
-        tag_indicator = np.in1d(gene_list, gene_set, assume_unique=True).astype(
+        tag_indicator = np.isin(gene_list, gene_set, assume_unique=True).astype(
             int
         )  # notice that the sign is 0 (no tag) or 1 (tag)
 

gseapy/msigdb.py

@@ -10,11 +10,20 @@ def __init__(self, dbver: str = "2023.1.Hs"):
         dbver: MSIGDB version number. default: 2023.1.Hs
         """
         self.url = "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/"
-        self._pattern = re.compile("(\w.+)\.(v\d.+)\.(entrez|symbols)\.gmt")
+        self._pattern = re.compile(r"(\w.+)\.(v\d.+)\.(entrez|symbols)\.gmt")
         self._db_version = self._get_db_version()
+        if self._db_version is None:
+            raise Exception("Failed to fetch available MSIGDB versions")
         self.categoires = self.list_category(dbver)
 
     def _get_db_version(self):
+        """
+        Get all available MSIGDB versions
+
+        Return:
+            A pd.DataFrame of all available MSIGDB versions.
+            If failed to fetch, return None.
+        """
         resp = requests.get(self.url)
         if resp.ok:
             d = pd.read_html(resp.text)[0]
@@ -48,6 +57,13 @@ def get_gmt(
 
     def list_dbver(self):
         # self._db_version.columns = ["dbver", "date"]
+        """
+        Return a pd.DataFrame of all available MSIGDB versions
+
+        Return:
+            A pd.DataFrame of all available MSIGDB versions.
+            If failed to fetch, return None.
+        """
         return self._db_version
 
     def list_category(self, dbver: str = "2023.1.Hs"):
@@ -66,6 +82,13 @@ def list_category(self, dbver: str = "2023.1.Hs"):
         return None
 
     def list_gmt(self, db: str):
+        """
+        list all gmt files in MSIGDB database.
+
+        :param db: MSIGDB version number. default: 2023.1.Hs
+        :return: a pandas DataFrame object
+        """
+
         url = self.url + db
         resp = requests.get(url)
         if resp.ok: