Merge pull request #1178 from pysam-developers/update-release-notes

updated release notes

Author: AndreasHeger

.python-version

@@ -0,0 +1,2 @@
+3.6
+3.11

NEWS

@@ -5,18 +5,27 @@ http://pysam.readthedocs.io/en/latest/release.html
 Release notes
 =============
 
-Release 1.0.0?
-==============
-
-* python 2.7 support has been removed. The minimum python version is now 3.2 with
-  versions 3.6-3.11 tested.
-
 Release 0.21.0
 ==============
 
-This release wraps htslib/bcftools version 1.17 and samtools version 1.17.
-
-* [
+This release wraps htslib/samtools/bcftools version 1.17.
+
+Pysam is now compatible with Python 3.11. We have removed python 2.x
+support. Pysam is tested with python versions 3.6 to 3.11.
+
+* [#1175] VariantHeader.new_record: set start/stop before alleles
+* [#1173] Add multiple build improvements in htscodecs on multi-arch macOS
+* [#1148] Ignore CIGAR-less reads in find_introns.
+* [#1172] Add new `samtools cram-size` and `samtools reset` commands
+* [#1169] Fix CRAM index-related crash when using the musl C standard library.
+* [#1168] Add a minimal pyproject.toml for PEP517.
+* [#1158] Fix type hints and add FastqProxy type hints.
+* [#1147] Py3.11 compatibility, get shared object suffix from EXT_SUFFIX.
+* [#1143] Add mypy symbols for samtools and bcftools.
+* [#1155] Fix pysam.index() when using recent `samtools index` options.
+* [#1151] Test suite py3.11 compatibility, work around failing test case.
+* [#1149] MacOS universal build compatibility.
+* [#1146] Fix build when CFLAGS/etc environment variables are set.
 
 Release 0.20.0
 ==============

pyproject.toml

@@ -2,11 +2,11 @@
 name = "pysam"
 description = "pysam - a python module for reading, manipulating and writing genomic data sets."
 license = { text = "MIT License" }
-version = "0.20.0"
+version = "0.21.0"
 authors = [
  { name = "Andreas Heger", email = "[email protected]"}
 ]
-requires-python = ">=3.8"
+requires-python = ">=3.6"
 
 dynamic = [
     "classifiers",
@@ -19,5 +19,5 @@ dependencies = [
 
 
 [build-system]
-requires = ["setuptools>=61.0", "wheel", "Cython>=0.29.30,<3.0"]
+requires = ["setuptools>=59.0", "wheel", "Cython>=0.29.30,<3.0"]
 build-backend = "setuptools.build_meta:__legacy__"

tests/compile_test.py

@@ -8,7 +8,7 @@
 
 # clean up previous compilation
 import os
-import unittest
+import pytest
 import pysam
 from TestUtils import make_data_files, BAM_DATADIR, TABIX_DATADIR
 
@@ -24,31 +24,29 @@ def setUpModule():
 except OSError:
     pass
 
-import pyximport
-pyximport.install(build_in_temp=False)
-import _compile_test
+NO_PYXIMPORT = False
+try:
+    import pyximport
+    pyximport.install(build_in_temp=False)
+    import _compile_test
+except:
+    NO_PYXIMPORT = True
 
 
-class BAMTest(unittest.TestCase):
+@pytest.mark.skipif(NO_PYXIMPORT, reason="no pyximport")
+def test_bam():
 
     input_filename = os.path.join(BAM_DATADIR, "ex1.bam")
-
-    def testCount(self):
-
-        nread = _compile_test.testCountBAM(
-            pysam.Samfile(self.input_filename))
-        self.assertEqual(nread, 3270)
+    nread = _compile_test.testCountBAM(
+        pysam.Samfile(input_filename))
+    assert nread == 3270
 
 
-class GTFTest(unittest.TestCase):
+@pytest.mark.skipif(NO_PYXIMPORT, reason="no pyximport")
+def test_gtf():
 
     input_filename = os.path.join(TABIX_DATADIR, "example.gtf.gz")
 
-    def testCount(self):
-        nread = _compile_test.testCountGTF(
-            pysam.Tabixfile(self.input_filename))
-        self.assertEqual(nread, 237)
-
-
-if __name__ == "__main__":
-    unittest.main()
+    nread = _compile_test.testCountGTF(
+        pysam.Tabixfile(input_filename))
+    assert nread == 237

tox.ini

@@ -0,0 +1,8 @@
+# content of: tox.ini , put in same dir as setup.py
+[tox]
+envlist = py36 py311
+
+[testenv]
+deps = pytest       # install pytest in the virtualenv where commands will be executed
+commands =
+    pytest tests