fix: remove versioneer Python 3.12 compatibility

examples/vcf_from_scratch.py

@@ -2,10 +2,7 @@
 # -*- coding: utf-8 -*-
 """Create VCF from scratch using vcfpy."""
 
-import argparse
-import itertools
 import sys
-import time
 
 import vcfpy
 

requirements/dev.txt

@@ -7,6 +7,7 @@
 
 # Fancier output for py.test and dependencies
 pytest-sugar >=0.8.0
+pytest-cov
 termcolor >=1.1.0
 
 # Sphinx and dependencies

setup.cfg

@@ -7,7 +7,6 @@ exclude =
     .tox
     docs/
     vcfpy/__init__.py
-    versioneer.py
 ignore = E203, E266, E501, W503
 max-line-length = 80
 max-complexity = 18
@@ -21,16 +20,3 @@ pep8ignore =
     examples/*.py E501
 	tests/*.py E501
 	vcfpy/*.py F401
-
-
-# See the docstring in versioneer.py for instructions. Note that you must
-# re-run 'versioneer.py setup' after changing this section, and commit the
-# resulting files.
-
-[versioneer]
-VCS = git
-style = pep440
-versionfile_source = vcfpy/_version.py
-versionfile_build = vcfpy/_version.py
-tag_prefix = v
-parentdir_prefix = vcfpy

setup.py

@@ -7,8 +7,6 @@
 
 from setuptools import setup
 
-import versioneer
-
 
 def parse_requirements(path):
     """Parse ``requirements.txt`` at ``path``."""
@@ -43,14 +41,19 @@ def parse_requirements(path):
 
 test_requirements = parse_requirements("requirements/test.txt")
 
+package_root = os.path.abspath(os.path.dirname(__file__))
+version = {}
+with open(os.path.join(package_root, "vcfpy/_version.py")) as fp:
+    exec(fp.read(), version)
+version = version["__version__"]
+
 setup(
     name="vcfpy",
-    version=versioneer.get_version(),
-    cmdclass=versioneer.get_cmdclass(),
+    version=version,
     description=("Python 3 VCF library with good support for both reading and writing"),
     long_description=readme + "\n\n" + history,
     author="Manuel Holtgrewe",
-    author_email="manuel.holtgrewe@bihealth.de",
+    author_email="manuel.holtgrewe@bih-charite.de",
     url="https://github.com/bihealth/vcfpy",
     packages=["vcfpy"],
     package_dir={"vcfpy": "vcfpy"},
@@ -65,11 +68,11 @@ def parse_requirements(path):
         "License :: OSI Approved :: MIT License",
         "Natural Language :: English",
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.6",
-        "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
     ],
     test_suite="tests",
     tests_require=test_requirements,

tests/test_context_manager.py

@@ -85,7 +85,7 @@ def test_reader_fetch():
 
 
 def test_writer(header_samples, tmpdir_factory):
-    O = vcfpy.OrderedDict
+    OD = vcfpy.OrderedDict
     # open temporary file and setup the Writer with header
     path = tmpdir_factory.mktemp("write_header").join("out.vcf")
     header, _ = header_samples
@@ -98,12 +98,12 @@ def test_writer(header_samples, tmpdir_factory):
         [record.Substitution(record.SNV, "T")],
         None,
         [],
-        O(),
+        OD(),
         ["GT"],
         [
-            record.Call("NA00001", O(GT="0/1")),
-            record.Call("NA00002", O(GT="0/0")),
-            record.Call("NA00003", O(GT="1/1")),
+            record.Call("NA00001", OD(GT="0/1")),
+            record.Call("NA00002", OD(GT="0/0")),
+            record.Call("NA00003", OD(GT="1/1")),
         ],
     )
     # open writer

tests/test_parser_helpers.py

@@ -1,8 +1,6 @@
 # -*- coding: utf-8 -*-
 """Test for the helper routines in the vcfpy.parser module"""
 
-import pytest
-
 from vcfpy import parser
 
 __author__ = "Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>"

tests/test_parser_parse_header_lines.py

@@ -4,8 +4,6 @@
 
 import sys
 
-import pytest
-
 from vcfpy import header
 from vcfpy import parser
 

tests/test_parser_warnings.py

@@ -20,7 +20,6 @@ def test_header_checker_missing_fileformat():
     lines = [header.HeaderLine("key", "value")]
     hdr = header.Header(lines=lines, samples=header.SamplesInfos(["NA001"]))
     # setup HeaderChecker
-    stream = io.StringIO()
     checker = parser.HeaderChecker()
     # execute
     with pytest.raises(exceptions.InvalidHeaderException):

tests/test_reader_nosample.py

@@ -1,13 +1,12 @@
 # -*- coding: utf-8 -*-
 """Tests for reading with file without samples"""
 
-from io import StringIO
 import textwrap
 
 import vcfpy
 
 
-def test_reading_parse_nosample(tmpdir, nosample_vcf_file):
+def test_reading_parse_nosample_read_only(tmpdir, nosample_vcf_file):
     """Test reading of VCF file without any samples."""
     # Perform record-wise copying, saving results in records
     records = []
@@ -18,7 +17,7 @@ def test_reading_parse_nosample(tmpdir, nosample_vcf_file):
     assert len(records) == 5
 
 
-def test_reading_parse_nosample(tmpdir, nosample_vcf_file):
+def test_reading_parse_nosample_also_write(tmpdir, nosample_vcf_file):
     """Read VCF file without samples, write file with samples."""
     # Perform record-wise copying, saving results in records
     path_out = tmpdir.mkdir("output").join("output.vcf")

tests/test_vcfs_from_the_wild.py

@@ -56,3 +56,4 @@
 def test_read_vcfs_from_the_wild(filename):
     path = os.path.join(os.path.dirname(__file__), "vcfs_from_the_wild", filename)
     r = reader.Reader.from_path(path)
+    _ = r

tests/test_write_bgzf.py

@@ -62,7 +62,7 @@ def check_file(path, line):
 
 
 def test_write_minimal_record_writer_from_path(header_samples, tmpdir_factory):
-    O = vcfpy.OrderedDict
+    OD = vcfpy.OrderedDict
     # open temporary file and setup the Writer with header
     path = tmpdir_factory.mktemp("write_header").join("out.vcf.gz")
     header, _ = header_samples
@@ -76,12 +76,12 @@ def test_write_minimal_record_writer_from_path(header_samples, tmpdir_factory):
         [record.Substitution(record.SNV, "T")],
         None,
         [],
-        O(),
+        OD(),
         ["GT"],
         [
-            record.Call("NA00001", O(GT="0/1")),
-            record.Call("NA00002", O(GT="0/0")),
-            record.Call("NA00003", O(GT="1/1")),
+            record.Call("NA00001", OD(GT="0/1")),
+            record.Call("NA00002", OD(GT="0/0")),
+            record.Call("NA00003", OD(GT="1/1")),
         ],
     )
     # write out the record, close file to ensure flushing to disk
@@ -93,7 +93,7 @@ def test_write_minimal_record_writer_from_path(header_samples, tmpdir_factory):
 
 
 def test_write_minimal_record_writer_from_stream_path(header_samples, tmpdir_factory):
-    O = vcfpy.OrderedDict
+    OD = vcfpy.OrderedDict
     # open temporary file and setup the Writer with header
     path = tmpdir_factory.mktemp("write_header").join("out.vcf.gz")
     header, _ = header_samples
@@ -108,12 +108,12 @@ def test_write_minimal_record_writer_from_stream_path(header_samples, tmpdir_fac
             [record.Substitution(record.SNV, "T")],
             None,
             [],
-            O(),
+            OD(),
             ["GT"],
             [
-                record.Call("NA00001", O(GT="0/1")),
-                record.Call("NA00002", O(GT="0/0")),
-                record.Call("NA00003", O(GT="1/1")),
+                record.Call("NA00001", OD(GT="0/1")),
+                record.Call("NA00002", OD(GT="0/0")),
+                record.Call("NA00003", OD(GT="1/1")),
             ],
         )
         # write out the record, close file to ensure flushing to disk
@@ -125,7 +125,7 @@ def test_write_minimal_record_writer_from_stream_path(header_samples, tmpdir_fac
 
 
 def test_write_minimal_record_writer_from_stream_use_bgzf(header_samples, tmpdir_factory):
-    O = vcfpy.OrderedDict
+    OD = vcfpy.OrderedDict
     # open temporary file and setup the Writer with header
     path = tmpdir_factory.mktemp("write_header").join("out.vcf.gz")
     header, samples = header_samples
@@ -140,12 +140,12 @@ def test_write_minimal_record_writer_from_stream_use_bgzf(header_samples, tmpdir
             [record.Substitution(record.SNV, "T")],
             None,
             [],
-            O(),
+            OD(),
             ["GT"],
             [
-                record.Call("NA00001", O(GT="0/1")),
-                record.Call("NA00002", O(GT="0/0")),
-                record.Call("NA00003", O(GT="1/1")),
+                record.Call("NA00001", OD(GT="0/1")),
+                record.Call("NA00002", OD(GT="0/0")),
+                record.Call("NA00003", OD(GT="1/1")),
             ],
         )
         # write out the record, close file to ensure flushing to disk

tests/test_write_record.py

@@ -47,7 +47,7 @@ def header_samples():
 
 
 def test_write_minimal_record(header_samples, tmpdir_factory):
-    O = vcfpy.OrderedDict
+    OD = vcfpy.OrderedDict
     # open temporary file and setup the Writer with header
     path = tmpdir_factory.mktemp("write_header").join("out.vcf")
     header, _ = header_samples
@@ -61,12 +61,12 @@ def test_write_minimal_record(header_samples, tmpdir_factory):
         [record.Substitution(record.SNV, "T")],
         None,
         [],
-        O(),
+        OD(),
         ["GT"],
         [
-            record.Call("NA00001", O(GT="0/1")),
-            record.Call("NA00002", O(GT="0/0")),
-            record.Call("NA00003", O(GT="1/1")),
+            record.Call("NA00001", OD(GT="0/1")),
+            record.Call("NA00002", OD(GT="0/0")),
+            record.Call("NA00003", OD(GT="1/1")),
         ],
     )
     # write out the record, close file to ensure flushing to disk
@@ -80,8 +80,7 @@ def test_write_minimal_record(header_samples, tmpdir_factory):
 
 
 def test_write_annotated_record(header_samples, tmpdir_factory):
-    O = vcfpy.OrderedDict
-    S = record.Substitution
+    OD = vcfpy.OrderedDict
     # open temporary file and setup the Writer with header
     path = tmpdir_factory.mktemp("write_annotated_record").join("out.vcf")
     header, _ = header_samples
@@ -95,12 +94,12 @@ def test_write_annotated_record(header_samples, tmpdir_factory):
         [record.Substitution(record.SNV, "T"), record.Substitution(record.SNV, "G")],
         50,
         ["PASS"],
-        O([("DP", 93), ("AF", [0.3, 0.2]), ("DB", True)]),
+        OD([("DP", 93), ("AF", [0.3, 0.2]), ("DB", True)]),
         ["GT", "DP", "GQ", "HQ"],
         [
-            record.Call("NA00001", O(GT="0/1", DP=30, GQ=40, HQ=[1, 2])),
-            record.Call("NA00002", O(GT="0/2", DP=31, GQ=41, HQ=[3, 4])),
-            record.Call("NA00003", O(GT="1/2", DP=32, GQ=42, HQ=[5, 6])),
+            record.Call("NA00001", OD(GT="0/1", DP=30, GQ=40, HQ=[1, 2])),
+            record.Call("NA00002", OD(GT="0/2", DP=31, GQ=41, HQ=[3, 4])),
+            record.Call("NA00003", OD(GT="1/2", DP=32, GQ=42, HQ=[5, 6])),
         ],
     )
     # write out the record, close file to ensure flushing to disk
@@ -114,8 +113,7 @@ def test_write_annotated_record(header_samples, tmpdir_factory):
 
 
 def test_write_record_with_escaping(header_samples, tmpdir_factory):
-    O = vcfpy.OrderedDict
-    S = record.Substitution
+    OD = vcfpy.OrderedDict
     # open temporary file and setup the Writer with header
     path = tmpdir_factory.mktemp("write_header").join("out.vcf")
     header, _ = header_samples
@@ -129,12 +127,12 @@ def test_write_record_with_escaping(header_samples, tmpdir_factory):
         [record.Substitution(record.SNV, "T")],
         None,
         [],
-        O([("ANNO", ["Here,are%some chars", "%25"])]),
+        OD([("ANNO", ["Here,are%some chars", "%25"])]),
         ["GT", "FT"],
         [
-            record.Call("NA00001", O(GT="0/1", FT=["%25", "FOO"])),
-            record.Call("NA00002", O(GT="0/0", FT=[])),
-            record.Call("NA00003", O(GT="1/1", FT=[])),
+            record.Call("NA00001", OD(GT="0/1", FT=["%25", "FOO"])),
+            record.Call("NA00002", OD(GT="0/0", FT=[])),
+            record.Call("NA00003", OD(GT="1/1", FT=[])),
         ],
     )
     # write out the record, close file to ensure flushing to disk
@@ -151,13 +149,13 @@ def test_write_record_with_escaping(header_samples, tmpdir_factory):
 
 
 def test_write_record_no_samples(tmpdir_factory):
-    O = vcfpy.OrderedDict
+    OD = vcfpy.OrderedDict
     # Create header without samples
     hdr = header.Header(
         lines=[header.HeaderLine("fileformat", "VCFv4.0")], samples=header.SamplesInfos([])
     )
     # construct record to write out from scratch
-    r = record.Record("20", 100, [], "C", [record.Substitution(record.SNV, "T")], None, [], O())
+    r = record.Record("20", 100, [], "C", [record.Substitution(record.SNV, "T")], None, [], OD())
     # Write out header and record
     path = tmpdir_factory.mktemp("write_header").join("out.vcf")
     w = writer.Writer.from_path(path, hdr)

tests/test_writer_write_subset.py

@@ -4,7 +4,7 @@
 """
 
 
-from vcfpy import Reader, Writer, Header, SamplesInfos, Call, UnparsedCall
+from vcfpy import Reader, Writer, Header, SamplesInfos
 
 
 def test_reading_and_write_subset_of_samples(

vcfpy/__init__.py

@@ -47,7 +47,4 @@
 
 from .writer import Writer
 
-from ._version import get_versions
-
-__version__ = get_versions()["version"]
-del get_versions
+from ._version import __version__