Skip to content

Commit 2ad8000

Browse files
holtgreweholtgrewe
committed
chore: remove Python 3.6 tests
1 parent 83f8b2a commit 2ad8000

9 files changed

Lines changed: 184 additions & 562 deletions

‎setup.py‎

Lines changed: 0 additions & 80 deletions
This file was deleted.

‎tests/test_header.py‎

Lines changed: 44 additions & 110 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,6 @@
11
# -*- coding: utf-8 -*-
22
"""Tests for vcfpy.header"""
33

4-
import sys
54
import warnings
65

76
import pytest
@@ -141,24 +140,14 @@ def test_header_alt_allele_header_line():
141140
line3 = header.AltAlleleHeaderLine.from_mapping({"ID": "DUP", "Description": "duplication"})
142141
assert line1 == line2
143142
assert line1 != line3
144-
if sys.version_info < (3, 6):
145-
assert str(line1) == (
146-
"""AltAlleleHeaderLine('ALT', '<ID=DEL,Description="deletion">', """
147-
"""OrderedDict([('ID', 'DEL'), ('Description', 'deletion')]))"""
148-
)
149-
assert repr(line1) == (
150-
"""AltAlleleHeaderLine('ALT', '<ID=DEL,Description="deletion">', """
151-
"""OrderedDict([('ID', 'DEL'), ('Description', 'deletion')]))"""
152-
)
153-
else:
154-
assert (
155-
str(line1) == "AltAlleleHeaderLine('ALT', '<ID=DEL,Description=\"deletion\">', "
156-
"{'ID': 'DEL', 'Description': 'deletion'})"
157-
)
158-
assert (
159-
repr(line1) == "AltAlleleHeaderLine('ALT', '<ID=DEL,Description=\"deletion\">', "
160-
"{'ID': 'DEL', 'Description': 'deletion'})"
161-
)
143+
assert (
144+
str(line1) == "AltAlleleHeaderLine('ALT', '<ID=DEL,Description=\"deletion\">', "
145+
"{'ID': 'DEL', 'Description': 'deletion'})"
146+
)
147+
assert (
148+
repr(line1) == "AltAlleleHeaderLine('ALT', '<ID=DEL,Description=\"deletion\">', "
149+
"{'ID': 'DEL', 'Description': 'deletion'})"
150+
)
162151
assert line1.value == '<ID=DEL,Description="deletion">'
163152
assert line1.serialize() == '##ALT=<ID=DEL,Description="deletion">'
164153
with pytest.raises(TypeError):
@@ -171,17 +160,8 @@ def test_header_contig_header_line():
171160
line3 = header.ContigHeaderLine.from_mapping({"ID": "2", "length": 123})
172161
assert line1 == line2
173162
assert line1 != line3
174-
if sys.version_info < (3, 6):
175-
assert (
176-
str(line1) == "ContigHeaderLine('contig', '<ID=1,length=234>', OrderedDict([('ID', '1'), ('length', 234)]))"
177-
)
178-
assert (
179-
repr(line1)
180-
== "ContigHeaderLine('contig', '<ID=1,length=234>', OrderedDict([('ID', '1'), ('length', 234)]))"
181-
)
182-
else:
183-
assert str(line1) == "ContigHeaderLine('contig', '<ID=1,length=234>', {'ID': '1', 'length': 234})"
184-
assert repr(line1) == "ContigHeaderLine('contig', '<ID=1,length=234>', {'ID': '1', 'length': 234})"
163+
assert str(line1) == "ContigHeaderLine('contig', '<ID=1,length=234>', {'ID': '1', 'length': 234})"
164+
assert repr(line1) == "ContigHeaderLine('contig', '<ID=1,length=234>', {'ID': '1', 'length': 234})"
185165
assert line1.value == "<ID=1,length=234>"
186166
assert line1.serialize() == "##contig=<ID=1,length=234>"
187167
with pytest.raises(TypeError):
@@ -194,24 +174,14 @@ def test_header_filter_header_line():
194174
line3 = header.FilterHeaderLine.from_mapping({"ID": "q30", "Description": "Phred score <30"})
195175
assert line1 == line2
196176
assert line1 != line3
197-
if sys.version_info < (3, 6):
198-
assert (
199-
str(line1) == "FilterHeaderLine('FILTER', '<ID=PASS,Description=\"All filters passed\">', "
200-
"OrderedDict([('ID', 'PASS'), ('Description', 'All filters passed')]))"
201-
)
202-
assert (
203-
repr(line1) == "FilterHeaderLine('FILTER', '<ID=PASS,Description=\"All filters passed\">', "
204-
"OrderedDict([('ID', 'PASS'), ('Description', 'All filters passed')]))"
205-
)
206-
else:
207-
assert (
208-
str(line1) == "FilterHeaderLine('FILTER', '<ID=PASS,Description=\"All filters passed\">', "
209-
"{'ID': 'PASS', 'Description': 'All filters passed'})"
210-
)
211-
assert (
212-
repr(line1) == "FilterHeaderLine('FILTER', '<ID=PASS,Description=\"All filters passed\">', "
213-
"{'ID': 'PASS', 'Description': 'All filters passed'})"
214-
)
177+
assert (
178+
str(line1) == "FilterHeaderLine('FILTER', '<ID=PASS,Description=\"All filters passed\">', "
179+
"{'ID': 'PASS', 'Description': 'All filters passed'})"
180+
)
181+
assert (
182+
repr(line1) == "FilterHeaderLine('FILTER', '<ID=PASS,Description=\"All filters passed\">', "
183+
"{'ID': 'PASS', 'Description': 'All filters passed'})"
184+
)
215185
assert line1.value == '<ID=PASS,Description="All filters passed">'
216186
assert line1.serialize() == '##FILTER=<ID=PASS,Description="All filters passed">'
217187
with pytest.raises(TypeError):
@@ -224,24 +194,12 @@ def test_header_pedigree_header_line():
224194
line3 = header.PedigreeHeaderLine.from_mapping({"ID": "father"})
225195
assert line1 == line2
226196
assert line1 != line3
227-
if sys.version_info < (3, 6):
228-
assert (
229-
str(line1) == "PedigreeHeaderLine('PEDIGREE', '<ID=child,Father=father>', "
230-
"OrderedDict([('ID', 'child'), ('Father', 'father')]))"
231-
)
232-
assert (
233-
repr(line1) == "PedigreeHeaderLine('PEDIGREE', '<ID=child,Father=father>', "
234-
"OrderedDict([('ID', 'child'), ('Father', 'father')]))"
235-
)
236-
else:
237-
assert (
238-
str(line1)
239-
== "PedigreeHeaderLine('PEDIGREE', '<ID=child,Father=father>', {'ID': 'child', 'Father': 'father'})"
240-
)
241-
assert (
242-
repr(line1)
243-
== "PedigreeHeaderLine('PEDIGREE', '<ID=child,Father=father>', {'ID': 'child', 'Father': 'father'})"
244-
)
197+
assert (
198+
str(line1) == "PedigreeHeaderLine('PEDIGREE', '<ID=child,Father=father>', {'ID': 'child', 'Father': 'father'})"
199+
)
200+
assert (
201+
repr(line1) == "PedigreeHeaderLine('PEDIGREE', '<ID=child,Father=father>', {'ID': 'child', 'Father': 'father'})"
202+
)
245203
assert line1.value == "<ID=child,Father=father>"
246204
assert line1.serialize() == "##PEDIGREE=<ID=child,Father=father>"
247205
with pytest.raises(TypeError):
@@ -254,12 +212,8 @@ def test_header_sample_header_line():
254212
line3 = header.SampleHeaderLine.from_mapping({"ID": "sample2"})
255213
assert line1 == line2
256214
assert line1 != line3
257-
if sys.version_info < (3, 6):
258-
assert str(line1) == "SampleHeaderLine('SAMPLE', '<ID=sample1>', OrderedDict([('ID', 'sample1')]))"
259-
assert repr(line1) == "SampleHeaderLine('SAMPLE', '<ID=sample1>', OrderedDict([('ID', 'sample1')]))"
260-
else:
261-
assert str(line1) == "SampleHeaderLine('SAMPLE', '<ID=sample1>', {'ID': 'sample1'})"
262-
assert repr(line1) == "SampleHeaderLine('SAMPLE', '<ID=sample1>', {'ID': 'sample1'})"
215+
assert str(line1) == "SampleHeaderLine('SAMPLE', '<ID=sample1>', {'ID': 'sample1'})"
216+
assert repr(line1) == "SampleHeaderLine('SAMPLE', '<ID=sample1>', {'ID': 'sample1'})"
263217
assert line1.value == "<ID=sample1>"
264218
assert line1.serialize() == "##SAMPLE=<ID=sample1>"
265219
with pytest.raises(TypeError):
@@ -278,26 +232,16 @@ def test_header_info_header_line():
278232
)
279233
assert line1 == line2
280234
assert line1 != line3
281-
if sys.version_info < (3, 6):
282-
assert (
283-
str(line1) == "InfoHeaderLine('INFO', '<ID=SVTYPE,Number=1,Type=String>', "
284-
"OrderedDict([('ID', 'SVTYPE'), ('Number', 1), ('Type', 'String')]))"
285-
)
286-
assert (
287-
repr(line1) == "InfoHeaderLine('INFO', '<ID=SVTYPE,Number=1,Type=String>', "
288-
"OrderedDict([('ID', 'SVTYPE'), ('Number', 1), ('Type', 'String')]))"
289-
)
290-
else:
291-
assert (
292-
str(line1)
293-
== "InfoHeaderLine('INFO', '<ID=SVTYPE,Number=1,Type=String,Description=\"Type of structural variant\">', "
294-
"{'ID': 'SVTYPE', 'Number': 1, 'Type': 'String', 'Description': 'Type of structural variant'})"
295-
)
296-
assert (
297-
repr(line1)
298-
== "InfoHeaderLine('INFO', '<ID=SVTYPE,Number=1,Type=String,Description=\"Type of structural variant\">', "
299-
"{'ID': 'SVTYPE', 'Number': 1, 'Type': 'String', 'Description': 'Type of structural variant'})"
300-
)
235+
assert (
236+
str(line1)
237+
== "InfoHeaderLine('INFO', '<ID=SVTYPE,Number=1,Type=String,Description=\"Type of structural variant\">', "
238+
"{'ID': 'SVTYPE', 'Number': 1, 'Type': 'String', 'Description': 'Type of structural variant'})"
239+
)
240+
assert (
241+
repr(line1)
242+
== "InfoHeaderLine('INFO', '<ID=SVTYPE,Number=1,Type=String,Description=\"Type of structural variant\">', "
243+
"{'ID': 'SVTYPE', 'Number': 1, 'Type': 'String', 'Description': 'Type of structural variant'})"
244+
)
301245
assert line1.value == '<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">'
302246
assert line1.serialize() == '##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">'
303247
with pytest.raises(TypeError):
@@ -316,24 +260,14 @@ def test_header_format_header_line():
316260
)
317261
assert line1 == line2
318262
assert line1 != line3
319-
if sys.version_info < (3, 6):
320-
assert (
321-
str(line1) == "FormatHeaderLine('FORMAT', '<ID=AD,Number=R,Type=Integer>', "
322-
"OrderedDict([('ID', 'AD'), ('Number', 'R'), ('Type', 'Integer')]))"
323-
)
324-
assert (
325-
repr(line1) == "FormatHeaderLine('FORMAT', '<ID=AD,Number=R,Type=Integer>', "
326-
"OrderedDict([('ID', 'AD'), ('Number', 'R'), ('Type', 'Integer')]))"
327-
)
328-
else:
329-
assert (
330-
str(line1) == "FormatHeaderLine('FORMAT', '<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths\">', "
331-
"{'ID': 'AD', 'Number': 'R', 'Type': 'Integer', 'Description': 'Allelic depths'})"
332-
)
333-
assert (
334-
repr(line1) == "FormatHeaderLine('FORMAT', '<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths\">', "
335-
"{'ID': 'AD', 'Number': 'R', 'Type': 'Integer', 'Description': 'Allelic depths'})"
336-
)
263+
assert (
264+
str(line1) == "FormatHeaderLine('FORMAT', '<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths\">', "
265+
"{'ID': 'AD', 'Number': 'R', 'Type': 'Integer', 'Description': 'Allelic depths'})"
266+
)
267+
assert (
268+
repr(line1) == "FormatHeaderLine('FORMAT', '<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths\">', "
269+
"{'ID': 'AD', 'Number': 'R', 'Type': 'Integer', 'Description': 'Allelic depths'})"
270+
)
337271
assert line1.value == '<ID=AD,Number=R,Type=Integer,Description="Allelic depths">'
338272
assert line1.serialize() == '##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths">'
339273
with pytest.raises(TypeError):

‎tests/test_parser_parse_header.py‎

Lines changed: 4 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,6 @@
22
"""Test parsing of full VCF header"""
33

44
import io
5-
import sys
65
import warnings
76

87
import pytest
@@ -48,18 +47,10 @@ def test_parse_header(medium_header):
4847
assert len(header.lines) == 18
4948
EXPECTED = "HeaderLine('fileformat', 'VCFv4.3')"
5049
assert str(header.lines[0]) == EXPECTED
51-
if sys.version_info < (3, 6):
52-
EXPECTED = (
53-
"FormatHeaderLine('FORMAT', '<ID=HQ,Number=2,Type=Integer,"
54-
"Description=\"Haplotype Quality\">', OrderedDict([('ID', 'HQ'), "
55-
"('Number', 2), ('Type', 'Integer'), ('Description', "
56-
"'Haplotype Quality')]))"
57-
)
58-
else:
59-
EXPECTED = (
60-
"FormatHeaderLine('FORMAT', '<ID=HQ,Number=2,Type=Integer,Description=\"Haplotype Quality\">', "
61-
"{'ID': 'HQ', 'Number': 2, 'Type': 'Integer', 'Description': 'Haplotype Quality'})"
62-
)
50+
EXPECTED = (
51+
"FormatHeaderLine('FORMAT', '<ID=HQ,Number=2,Type=Integer,Description=\"Haplotype Quality\">', "
52+
"{'ID': 'HQ', 'Number': 2, 'Type': 'Integer', 'Description': 'Haplotype Quality'})"
53+
)
6354
assert str(header.lines[-1]) == EXPECTED
6455
assert header.samples.names == ["NA00001", "NA00002", "NA00003"]
6556

0 commit comments

Comments
 (0)