Adding tox config

.github/workflows/check.yml

@@ -0,0 +1,48 @@
+name: check
+on:
+  pull_request:
+
+concurrency:
+  group: check-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    name: test ${{ matrix.py }} - ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        os:
+          - Ubuntu
+          - MacOs
+        py:
+          - 3.11
+          - '3.10'
+          - 3.9
+    steps:
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+      - uses: actions/checkout@v4
+      - name: Install tox and dev dependencies
+        run: python -m pip install -r dev-requirements.txt
+      - name: Setup Micromamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          micromamba-version: "latest"
+      - name: Pick environment to run
+        run: |
+          import subprocess; import json; import os
+          major, minor, impl = json.loads(subprocess.check_output(["python", "-c", "import json; import sys; import platform; print(json.dumps([sys.version_info[0], sys.version_info[1], platform.python_implementation()]));"], universal_newlines=True))
+          with open(os.environ['GITHUB_ENV'], 'a') as file_handler:
+                file_handler.write('TOXENV=' + ("py" if impl == "CPython" else "pypy") + ("{}{}".format(major, minor) if impl == "CPython" else "3") + "\n")
+        shell: python
+      - name: Setup test suite
+        run: tox -vv --notest
+      - name: Run test suite
+        run: tox --skip-pkg-install
+        env:
+          CI_RUN: "yes"
+          DIFF_AGAINST: HEAD

MANIFEST.in

@@ -0,0 +1,7 @@
+include README.md
+graft ShortSeq
+prune ShortSeq/tests/testdata/
+prune *.egg-info/
+prune **/__pycache__
+global-exclude .DS_Store
+global-exclude *.so

ShortSeq/__init__.pxd

@@ -1,6 +1,6 @@
 from .short_seq cimport *
-from .fast_read cimport *
-from .short_seq_util cimport *
 from .short_seq_var cimport *
 from .short_seq_128 cimport *
 from .short_seq_64 cimport *
+from .fast_read cimport *
+from .util cimport *

ShortSeq/short_seq.pxd

@@ -9,11 +9,13 @@ from cpython.unicode cimport PyUnicode_AsASCIIString
 
 from libcpp.vector cimport vector
 
-from .short_seq_util cimport *
 from .short_seq_var cimport *
 from .short_seq_128 cimport *
 from .short_seq_64 cimport *
 from .fast_read cimport *
+from .util cimport *
+
+from ShortSeq import MAX_64_NT, MAX_128_NT, MAX_VAR_NT
 
 """
 Private dictionary fast-path methods not currently offered by the Cython wrapper

ShortSeq/short_seq_128.pxd

@@ -1,4 +1,4 @@
-from .short_seq_util cimport *
+from .util cimport *
 
 # Constants
 cdef size_t MIN_128_NT

ShortSeq/short_seq_64.pxd

@@ -1,4 +1,4 @@
-from .short_seq_util cimport *
+from .util cimport *
 
 # Constants
 cdef size_t MIN_64_NT

ShortSeq/short_seq_var.pxd

@@ -1,4 +1,4 @@
-from .short_seq_util cimport *
+from .util cimport *
 from cpython.mem cimport PyObject_Calloc, PyObject_Free
 from libc.math cimport ceil
 from libc.string cimport memcmp

ShortSeq/tests/unit_tests_main.py

@@ -1,7 +1,4 @@
 import unittest
-import time
-
-from pympler.asizeof import asizeof
 
 from ShortSeq import ShortSeq, ShortSeq64, ShortSeq128, ShortSeqVar
 from ShortSeq import MIN_VAR_NT, MAX_VAR_NT, MIN_64_NT, MAX_64_NT, MIN_128_NT, MAX_128_NT
@@ -158,16 +155,6 @@ def test_slice(self):
             self.assertEqual(sq[i:], sample[i:])
             self.assertEqual(sq[-i:], sample[-i:])
 
-    def test_gzip_size_comparison(self):
-        sample = rand_sequence(MAX_64_NT, no_range=True)
-        import gzip
-
-        gz_bytes = gzip.compress(sample.encode())
-        print(asizeof(gz_bytes))
-        print(asizeof(sample.encode()))
-        print(asizeof(ShortSeq.from_str(sample)))
-
-
 
 class ShortSeqVarTests(unittest.TestCase):
     """These tests address the variable length ShortSeq variant (ShortSeqVar)"""

ShortSeq/umi/umi.pxd

@@ -1,4 +1,4 @@
-from ShortSeq.short_seq_util cimport *
+from ShortSeq.util cimport *
 from cpython.mem cimport PyObject_Calloc, PyObject_Free
 from cpython.exc cimport PyErr_NoMemory
 from libc.math cimport ceil, floor

ShortSeq/short_seq_util.pxd → ShortSeq/util.pxd

@@ -44,6 +44,7 @@ For SIMD operations.
 cdef extern from "x86intrin.h" nogil:
     uint64_t _pext_u64 (uint64_t __X, uint64_t __Y)
     uint32_t _pext_u32 (uint32_t __X, uint32_t __Y)
+    uint64_t _popcnt64(uint64_t __X)
 
 """
 A little bit of hackery to allow fast access to the packed hash field of both

dev-requirements.txt

@@ -0,0 +1,3 @@
+tox<4
+tox-conda
+cython

setup.py

@@ -7,7 +7,7 @@
 URL = 'https://github.com/AlexTate/ShortSeq'
 AUTHOR = 'Alex Tate'
 PLATFORM = 'Unix'
-REQUIRES_PYTHON = '>=3.10.0'
+REQUIRES_PYTHON = '>3.8, <3.12'
 VERSION = '0.0.1'
 
 
@@ -33,8 +33,8 @@
               sources=['ShortSeq/short_seq_64.pyx'],
               extra_compile_args=short_seq_common_compile_args,
               language='c++'),
-    Extension("ShortSeq.short_seq_util",
-              sources=['ShortSeq/short_seq_util.pyx'],
+    Extension("ShortSeq.util",
+              sources=['ShortSeq/util.pyx'],
               extra_compile_args=short_seq_common_compile_args,
               language='c++'),
     Extension("ShortSeq.fast_read",
@@ -54,6 +54,7 @@
     description=DESCRIPTION,
     include_package_data=True,
     packages=find_namespace_packages(),
+    python_requires=REQUIRES_PYTHON,
     zip_safe=False,
     ext_modules=cythonize(
         extensions,

tox.ini

@@ -0,0 +1,18 @@
+[tox]
+envlist = ShortSeq-dev-py3{9,10,11}
+minversion = 3.27.1
+requires = tox-conda
+
+[testenv]
+deps = -rrequirements.txt
+conda_channels = conda-forge
+changedir = {envtmpdir} ; prevent unittest from importing module from the CWD
+commands =
+    python --version
+    python -m unittest ShortSeq.tests.unit_tests_main
+
+[gh]
+python =
+    3.11: py311
+    3.10: py310
+    3.9: py39