[med-svn] [Git][med-team/python-pyfaidx][upstream] New upstream version 0.8.0
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sat Jan 13 16:44:45 GMT 2024
Étienne Mollier pushed to branch upstream at Debian Med / python-pyfaidx
Commits:
3eadce6c by Étienne Mollier at 2024-01-13T17:33:26+01:00
New upstream version 0.8.0
- - - - -
6 changed files:
- .coveragerc
- dev-requirements.txt
- pyfaidx/__init__.py
- pyproject.toml
- tests/test_Fasta_synchronization.py
- tests/test_feature_indexing.py
Changes:
=====================================
.coveragerc
=====================================
@@ -5,8 +5,6 @@ omit =
*/lib_pypy/_*.py
*/site-packages/ordereddict.py
*/site-packages/nose/*
- */site-packages/six/*
- */unittest2/*
[paths]
source =
=====================================
dev-requirements.txt
=====================================
@@ -1,8 +1,6 @@
-six
pytest
pytest-cov
setuptools
-mock
cython
# pysam
requests
=====================================
pyfaidx/__init__.py
=====================================
@@ -3,8 +3,6 @@
Fasta file -> Faidx -> Fasta -> FastaRecord -> Sequence
"""
-from __future__ import division
-
import datetime
import os
import re
@@ -13,7 +11,7 @@ import sys
import shutil
import warnings
from collections import namedtuple
-from itertools import islice
+from itertools import islice, zip_longest
from math import ceil
from os.path import getmtime
from tempfile import TemporaryFile
@@ -24,13 +22,7 @@ try:
except ImportError: #python < 3.8
from importlib_metadata import version
-from six import PY2, PY3, integer_types, string_types
-from six.moves import zip_longest
-
-try:
- from collections import OrderedDict
-except ImportError: #python 2.6
- from ordereddict import OrderedDict
+from collections import OrderedDict
try:
import fsspec
@@ -39,9 +31,6 @@ except ImportError:
__version__ = version("pyfaidx")
-if sys.version_info > (3, ):
- buffer = memoryview
-
dna_bases = re.compile(r'([ACTGNactgnYRWSKMDVHBXyrwskmdvhbx]+)')
class KeyFunctionError(ValueError):
@@ -99,8 +88,8 @@ class Sequence(object):
self.start = start
self.end = end
self.comp = comp
- assert isinstance(name, string_types)
- assert isinstance(seq, string_types)
+ assert isinstance(name, str)
+ assert isinstance(seq, str)
def __getitem__(self, n):
""" Returns a sliced version of Sequence
@@ -180,7 +169,7 @@ class Sequence(object):
end = self_start + slice_stop + correction_factor
return self.__class__(self.name, self.seq[n], start, end,
self.comp)
- elif isinstance(n, integer_types):
+ elif isinstance(n, int):
if n < 0:
n = len(self) + n
if self.start:
@@ -455,7 +444,7 @@ class Faidx(object):
try:
key_fn_test = self.key_function(
"TestingReturnType of_key_function")
- if not isinstance(key_fn_test, string_types):
+ if not isinstance(key_fn_test, str):
raise KeyFunctionError(
"key_function argument should return a string, not {0}".
format(type(key_fn_test)))
@@ -482,9 +471,9 @@ class Faidx(object):
self.lock = Lock()
self.buffer = dict((('seq', None), ('name', None), ('start', None),
('end', None)))
- if not read_ahead or isinstance(read_ahead, integer_types):
+ if not read_ahead or isinstance(read_ahead, int):
self.read_ahead = read_ahead
- elif not isinstance(read_ahead, integer_types):
+ elif not isinstance(read_ahead, int):
raise ValueError("read_ahead value must be int, not {0}".format(
type(read_ahead)))
@@ -923,7 +912,7 @@ class FastaRecord(object):
start = len(self) + start
return self._fa.get_seq(self.name, start + 1, stop)[::step]
- elif isinstance(n, integer_types):
+ elif isinstance(n, int):
if n < 0:
n = len(self) + n
return self._fa.get_seq(self.name, n + 1, n + 1)
@@ -1034,7 +1023,7 @@ class FastaRecord(object):
'shape': (len(self), ),
'typestr': '|S1',
'version': 3,
- 'data': buffer(str(self).encode('ascii'))
+ 'data': memoryview(str(self).encode('ascii'))
}
@@ -1065,7 +1054,7 @@ class MutableFastaRecord(FastaRecord):
start = len(self) + start
self._fa.faidx.to_file(self.name, start + 1, stop, value)
- elif isinstance(n, integer_types):
+ elif isinstance(n, int):
if n < 0:
n = len(self) + n
return self._fa.faidx.to_file(self.name, n + 1, n + 1, value)
@@ -1126,7 +1115,7 @@ class Fasta(object):
def __getitem__(self, rname):
"""Return a chromosome by its name, or its numerical index."""
- if isinstance(rname, integer_types):
+ if isinstance(rname, int):
rname = next(islice(self.records.keys(), rname, None))
try:
return self.records[rname]
@@ -1353,13 +1342,9 @@ invalid_characters_set = set(
chr(x) for x in range(256) if chr(x) not in complement_map[0])
invalid_characters_string = ''.join(invalid_characters_set)
-if PY3:
- complement_table = str.maketrans(complement_map[0], complement_map[1],
- invalid_characters_string)
- translate_arguments = (complement_table, )
-elif PY2:
- complement_table = string.maketrans(complement_map[0], complement_map[1])
- translate_arguments = (complement_table, invalid_characters_string)
+complement_table = str.maketrans(complement_map[0], complement_map[1],
+ invalid_characters_string)
+translate_arguments = (complement_table, )
def complement(seq):
=====================================
pyproject.toml
=====================================
@@ -27,7 +27,6 @@ classifiers = [
"Topic :: Scientific/Engineering :: Bio-Informatics"
]
dependencies = [
- "six",
"setuptools",
"importlib_metadata"
]
=====================================
tests/test_Fasta_synchronization.py
=====================================
@@ -1,9 +1,6 @@
import os
import pytest
-try:
- from collections import OrderedDict
-except ImportError: #python 2.6
- from ordereddict import OrderedDict
+from collections import OrderedDict
import threading
from pyfaidx import Fasta
import random
=====================================
tests/test_feature_indexing.py
=====================================
@@ -1,3 +1,4 @@
+import builtins
import os
import pytest
from os.path import getmtime
@@ -7,12 +8,7 @@ import time
import platform
import shutil
-try:
- from unittest import mock
-except ImportError:
- import mock
-
-import six.moves.builtins as builtins
+from unittest import mock
path = os.path.dirname(__file__)
os.chdir(path)
@@ -268,7 +264,7 @@ def test_build_issue_96_fail_build_faidx(remove_index):
opened_files.append(f)
return f
- with mock.patch('six.moves.builtins.open', side_effect=test_open):
+ with mock.patch('builtins.open', side_effect=test_open):
try:
Faidx(fasta_path)
remove_index.assertFail(
@@ -305,7 +301,7 @@ def test_build_issue_96_fail_read_malformed_index_duplicate_key(remove_index):
opened_files.append(f)
return f
- with mock.patch('six.moves.builtins.open', side_effect=test_open):
+ with mock.patch('builtins.open', side_effect=test_open):
try:
Faidx(fasta_path)
remove_index.assertFail(
View it on GitLab: https://salsa.debian.org/med-team/python-pyfaidx/-/commit/3eadce6c2fa66ccd54e2ed7e371e065b639f143d
--
View it on GitLab: https://salsa.debian.org/med-team/python-pyfaidx/-/commit/3eadce6c2fa66ccd54e2ed7e371e065b639f143d
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