pkg_resources is deprecated as an API

pyplink/tests/test_pyplink.py

@@ -24,6 +24,7 @@
 # THE SOFTWARE.
 
 
+import atexit
 import os
 import platform
 import random
@@ -32,6 +33,7 @@
 import sys
 import unittest
 import zipfile
+from contextlib import ExitStack
 from io import UnsupportedOperation
 from itertools import zip_longest
 from shutil import which
@@ -40,9 +42,9 @@
 from unittest import mock
 from urllib.request import urlretrieve
 
+import importlib_resources
 import numpy as np
 import pandas as pd
-from pkg_resources import resource_filename
 
 from .. import pyplink
 
@@ -123,19 +125,19 @@ def setUpClass(cls):
         # Creating a temporary directory
         cls.tmp_dir = mkdtemp(prefix="pyplink_test_")
 
+        file_manager = ExitStack()
+        atexit.register(file_manager.close)
+
         # Getting the BED/BIM/FAM files
-        cls.bed = resource_filename(
-            __name__,
-            os.path.join("data", "test_data.bed"),
-        )
-        cls.bim = resource_filename(
-            __name__,
-            os.path.join("data", "test_data.bim"),
-        )
-        cls.fam = resource_filename(
-            __name__,
-            os.path.join("data", "test_data.fam"),
-        )
+        cls.bed = file_manager.enter_context(importlib_resources.as_file(
+            importlib_resources.files(__name__) / "data" / "test_data.bed"
+        )).as_posix()
+        cls.bim = file_manager.enter_context(importlib_resources.as_file(
+            importlib_resources.files(__name__) / "data" / "test_data.bim"
+        )).as_posix()
+        cls.fam = file_manager.enter_context(importlib_resources.as_file(
+            importlib_resources.files(__name__) / "data" / "test_data.fam"
+        )).as_posix()
 
         # Getting the prefix of the files
         cls.prefix = os.path.splitext(cls.bed)[0]

setup.py

@@ -9,17 +9,17 @@
 
 
 import os
-import sys
 from setuptools import setup
 
 
 MAJOR = 1
 MINOR = 3
-MICRO = 7
-VERSION = "{}.{}.{}".format(MAJOR, MINOR, MICRO)
+MICRO = 8
+VERSION = f"{MAJOR}.{MINOR}.{MICRO}b1"
 
 
 def write_version_file(fn=None):
+    """Write the version file."""
     if fn is None:
         fn = os.path.join(
             os.path.dirname(os.path.abspath(__file__)),
@@ -31,30 +31,16 @@ def write_version_file(fn=None):
         'pyplink_version = "{version}"\n'
     )
 
-    a = open(fn, "w")
-    try:
-        a.write(content.format(version=VERSION))
-    finally:
-        a.close()
-
-
-def get_requirements():
-    # Initial requirements
-    requirements = ["numpy >= 1.8.2", "pandas >= 0.17.1"]
-
-    # Checking if python 2 (requires mock)
-    if sys.version_info[0] == 2:
-        requirements.append(["mock >= 2.0.0"])
-
-    return requirements
+    with open(fn, "w") as f:
+        f.write(content.format(version=VERSION))
 
 
 def setup_package():
+    """Setup the package."""
     # Saving the version into a file
     write_version_file()
 
     setup(
-        zip_safe=False,
         name="pyplink",
         version=VERSION,
         description="Python module to read binary Plink files.",
@@ -65,7 +51,11 @@ def setup_package():
         packages=["pyplink", "pyplink.tests"],
         package_data={"pyplink.tests": ["data/*"], },
         test_suite="pyplink.tests.test_suite",
-        install_requires=get_requirements(),
+        install_requires=[
+            "numpy >= 1.8.2",
+            "pandas >= 0.17.1",
+            "importlib_resources >= 5.12.0",
+        ],
         classifiers=["Operating System :: POSIX :: Linux",
                      "Operating System :: MacOS :: MacOS X",
                      "Operating System :: Microsoft",
@@ -82,8 +72,6 @@ def setup_package():
         keywords="bioinformatics format Plink binary",
     )
 
-    return
-
 
 if __name__ == "__main__":
     setup_package()