Support for Python 3.12

- Upgrade Pandas to 2.2.2
- Update other dependencies to the latest
- Fix API change with the new pandas version
- Fix unit tests (override addDuration)

Author: pbashyal-nmdp

pyard/data_repository.py

@@ -98,7 +98,7 @@ def generate_ard_mapping(db_connection: sqlite3.Connection, imgt_version) -> ARS
     # filter out the mg with count > 1, leaving only duplicates
     # take the index from the 2d version the data frame, make that a column
     # and turn that into a list
-    multiple_g_list = mg[mg > 1].reset_index()["index"].to_list()
+    multiple_g_list = mg[mg > 1].index.to_list()
 
     # Keep only the alleles that have more than 1 mapping
     dup_g = (
@@ -111,7 +111,7 @@ def generate_ard_mapping(db_connection: sqlite3.Connection, imgt_version) -> ARS
 
     # multiple lgx
     mlgx = df_g_group.drop_duplicates(["2d", "lgx"])["2d"].value_counts()
-    multiple_lgx_list = mlgx[mlgx > 1].reset_index()["index"].to_list()
+    multiple_lgx_list = mlgx[mlgx > 1].index.to_list()
 
     # Keep only the alleles that have more than 1 mapping
     dup_lgx = (

requirements-dev.txt

@@ -1,6 +1,6 @@
-allure-behave==2.9.45
-flake8==4.0.1
+allure-behave==2.13.5
+flake8==7.0.0
 bump2version==1.0.1
-coverage==6.3.2
-wheel==0.38.1
-pre-commit==2.18.1
+coverage==7.5.3
+wheel==0.43.0
+pre-commit==3.7.1

requirements-tests.txt

@@ -1,3 +1,3 @@
 behave==1.2.6
-PyHamcrest==2.0.2
-pytest==7.1.2
+PyHamcrest==2.1.0
+pytest==8.2.2

requirements.txt

@@ -1,3 +1,2 @@
 toml==0.10.2
-numpy==1.24.3
-pandas==1.5.3
+pandas==2.2.2

tests/test_pyard.py

@@ -47,6 +47,9 @@ def setUpClass(cls) -> None:
         cls.db_version = "3440"
         cls.ard = pyard.init(cls.db_version, data_dir="/tmp/py-ard")
 
+    def addDuration(self, test, elapsed):  # Required for Python >= 3.12
+        pass
+
     def test_no_mac(self):
         self.assertEqual(self.ard.redux("A*01:01:01", "G"), "A*01:01:01G")
         self.assertEqual(self.ard.redux("A*01:01:01", "lg"), "A*01:01g")

tests/test_smart_sort.py

@@ -28,6 +28,9 @@ class TestSmartSort(unittest.TestCase):
     def setUp(self) -> None:
         super().setUp()
 
+    def addDuration(self, test, elapsed):  # Required for Python >= 3.12
+        pass
+
     def test_same_comparator(self):
         allele = "HLA-A*01:01"
         self.assertEqual(smart_sort_comparator(allele, allele), 0)