Update Python version handling and add tests. Fixes #27.

- Refactor version retrieval in simplesam.py and pileup.py to use importlib.metadata.
- Update GitHub Actions workflow to test against newer Python versions and exclude certain versions on macOS.
- Add test for version import functionality.

Author: mdshw5

.github/workflows/tests.yml

@@ -12,19 +12,29 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     strategy:
+      fail-fast: false
+      max-parallel: 10
       matrix:
-        python: [3.6.15, 3.7.12, 3.8.12, 3.9.10, 3.10.2]
+        python-version: ['3.13', '3.12', '3.11', '3.10', '3.9']
         os: [ubuntu-latest, macos-latest]
+        exclude:
+          # mac os: exclude all but the last two (available) python releases
+          - os: macos-latest
+            python-version: 3.11
+          - os: macos-latest
+            python-version: 3.10
+          - os: macos-latest
+            python-version: 3.9
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v2.3.1
+        uses: actions/checkout@v3.1.0
         with:
           persist-credentials: false
           fetch-depth: 0
 
-      - name: Setup Python
-        uses: actions/setup-python@v2
+      - name: Setup python
+        uses: actions/setup-python@v4.3.0
         with:
           python-version: ${{ matrix.python }}
 

scripts/pileup.py

@@ -2,7 +2,11 @@
 
 import sys
 import argparse
-import pkg_resources
+try:
+    from importlib.metadata import version
+except ImportError:
+    import pkg_resources
+    version = lambda name: pkg_resources.get_distribution(name).version
 from collections import deque
 from collections import Counter
 from collections import OrderedDict
@@ -80,7 +84,7 @@ def pileup(args):
 
 def main():
 	parser = argparse.ArgumentParser(prog='pileup', description="generate a simple pileup-like file from a sorted/indexed BAM file")
-	parser.add_argument('--version', action='version', version="%(prog)s version {0}".format(pkg_resources.get_distribution("simplesam").version))
+	parser.add_argument('--version', action='version', version="%(prog)s version {0}".format(version("simplesam")))
 
 	parser.add_argument('bam', type=argparse.FileType('r'), help="sorted/indexed BAM file ")
 	parser.add_argument('pileup', type=argparse.FileType('w'), help="pileup output file")

simplesam.py

@@ -20,14 +20,18 @@
 from io import TextIOWrapper
 import re
 from six import PY3, string_types
-from pkg_resources import get_distribution
+try:
+    from importlib.metadata import version
+except ImportError:
+    from pkg_resources import get_distribution
+    version = lambda name: get_distribution(name).version
 
 try:
     from multiprocessing.dummy.connection import Connection
 except ImportError: #python2
     from _multiprocessing import Connection
 
-__version__ = get_distribution("simplesam").version
+__version__ = version("simplesam")
 
 class DefaultOrderedDict(OrderedDict):
     def __init__(self, default, items=[]):

tests/__init__.py

@@ -0,0 +1,9 @@
+import simplesam
+
+
+def test_version_import():
+    """Test that simplesam can be imported and has a version."""
+    # This test ensures that the version retrieval works without pkg_resources errors
+    assert hasattr(simplesam, '__version__')
+    assert isinstance(simplesam.__version__, str)
+    assert len(simplesam.__version__) > 0