extend tests to py2.7 (#15)

* extend tests to py2.7

* also remove --cov for old py27

* fix import for py27

* try to fix syntax for py27

* some additional work to function with old python 2.7 and also slightly more modern python 3.x

* more elegant conversion

* remove leftover

* make import StringIO compatible

Author: sjanssen2

.github/workflows/qiita-plugin-ci.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
           matrix:
-            python-version: ["3.5", "3.6", "3.9", "3.10", "3.11", "3.12"]
+            python-version: ["2.7", "3.5", "3.6", "3.9", "3.10", "3.11", "3.12"]
     steps:
       # Downloads a copy of the code in your repository before running CI tests
       - name: Check out repository code
@@ -35,7 +35,7 @@ jobs:
         shell: bash -l {0}
         run: |
           conda activate qiita-files
-          pytest --doctest-modules --cov=qiita_files `if (( $(echo "${{ matrix.python-version }} > 3.6" | bc -l) )); then echo "--cov-report=lcov"; else echo ""; fi`
+          pytest --doctest-modules `if (( $(echo "${{ matrix.python-version }} > 3.6" | bc -l) )); then echo "--cov-report=lcov --cov=qiita_files"; else echo ""; fi`
 
   lint:
     runs-on: ubuntu-latest

qiita_files/parse/fastq.py

@@ -8,7 +8,10 @@
 
 import numpy as np
 from qiita_files.util import open_file
-from itertools import zip_longest
+try:
+    from itertools import zip_longest
+except ImportError:
+    from itertools import izip_longest as zip_longest
 
 
 def _ascii_to_phred(s, offset):

qiita_files/parse/tests/test_fastq.py

@@ -155,7 +155,7 @@ class ParseFastqTestsInputIsFileNames(FileData, ParseFastqTests, TestCase):
 }
 
 
-FASTQ_EXAMPLE = rb"""@GAPC_0015:6:1:1259:10413#0/1
+FASTQ_EXAMPLE = r"""@GAPC_0015:6:1:1259:10413#0/1
 AACACCAAACTTCTCCACCACGTGAGCTACAAAAG
 +GAPC_0015:6:1:1259:10413#0/1
 ````Y^T]`]c^cabcacc`^Lb^ccYT\T\Y\WF
@@ -194,26 +194,26 @@ class ParseFastqTestsInputIsFileNames(FileData, ParseFastqTests, TestCase):
 @GAPC_0015:6:1:1317:3403#0/1
 TTGTTTCCACTTGGTTGATTTCACCCCTGAGTTTG
 +GAPC_0015:6:1:1317:3403#0/1
-\\\ZTYTSaLbb``\_UZ_bbcc`cc^[ac\a\Tc"""
+\\\ZTYTSaLbb``\_UZ_bbcc`cc^[ac\a\Tc""".encode("utf-8")
 
 
-FASTQ_EXAMPLE_2 = rb"""@GAPC_0017:6:1:1259:10413#0/1
+FASTQ_EXAMPLE_2 = r"""@GAPC_0017:6:1:1259:10413#0/1
 AACACCAAACTTCTCCACCACGTGAGCTACAAAAG
 +GAPC_0015:6:1:1259:10413#0/1
 ````Y^T]`]c^cabcacc`^Lb^ccYT\T\Y\WF
 @GAPC_0015:6:1:1283:11957#0/1
 TATGTATATATAACATATACATATATACATACATA
 +GAPC_0015:6:1:1283:11957#0/1
 ]KZ[PY]_[YY^```ac^\\`bT``c`\aT``bbb
-"""
+""".encode("utf-8")
 
 
-FASTQ_EXAMPLE_3 = rb"""@GAPC_0017:6:1:1259:10413#0/1
+FASTQ_EXAMPLE_3 = r"""@GAPC_0017:6:1:1259:10413#0/1
 AACACCAAACTTCTCCACCACGTGAGCTACAAAAG
 +GAPC_0015:6:1:1259:10413#0/1
 ````Y^T]`]c^cabcacc`^Lb^ccYT\T\Y\WF
 @GAPC_0015:6:1:1283:11957#0/1
-"""
+""".encode("utf-8")
 
 
 if __name__ == "__main__":

qiita_files/parse/tests/test_iterator.py

@@ -276,61 +276,61 @@ def test_fastq_gen(self):
         self.assertEqual(obs3, exp3)
 
 
-fasta1 = rb""">1
+fasta1 = r""">1
 aattggcc
 >2
 aattaatt
-"""
+""".encode("utf-8")
 
-fasta2 = rb""">3
+fasta2 = r""">3
 atat
-"""
+""".encode("utf-8")
 
-fasta3 = rb""">4
+fasta3 = r""">4
 attatt
 >5
 ggccc
-"""
+""".encode("utf-8")
 
-qual1 = rb""">1
+qual1 = r""">1
 1 2 3 4 5 6 7 8
 >2
 8 7 6 5 4 3 2 1
-"""
+""".encode("utf-8")
 
-qual2 = rb""">3
+qual2 = r""">3
 1 2 3 4
-"""
+""".encode("utf-8")
 
-qual3 = rb""">4
+qual3 = r""">4
 1 2 3 4 5 6
 >5
 1 2 3 4 5
-"""
+""".encode("utf-8")
 
-qual_bad_val = rb""">3
+qual_bad_val = r""">3
 1 2
-"""
+""".encode("utf-8")
 
-qual_bad_id = rb""">asdasd
+qual_bad_id = r""">asdasd
 1 2 3 4
-"""
+""".encode("utf-8")
 
-fastq1 = rb"""@1
+fastq1 = r"""@1
 atat
 +
 ABCD
 @2
 atgc
 +
 BCDE
-"""
+""".encode("utf-8")
 
-fastq2 = rb"""@3
+fastq2 = r"""@3
 taa
 +
 EFG
-"""
+""".encode("utf-8")
 
 
 if __name__ == '__main__':

qiita_files/tests/test_util.py

@@ -8,11 +8,16 @@
 # -----------------------------------------------------------------------------
 
 import os
+import sys
 from unittest import TestCase, main
 import tempfile
 
 import h5py
-from io import StringIO, BytesIO
+if sys.version_info[0] == 2:
+    from StringIO import StringIO
+else:
+    from io import StringIO
+from io import BytesIO
 
 from qiita_files.util import (open_file, _is_string_or_bytes)
 
@@ -25,7 +30,7 @@ class TestFilePathOpening(TestCase):
     """Tests adapted from scikit-bio's skbio.io.util tests"""
     def test_is_string_or_bytes(self):
         self.assertTrue(_is_string_or_bytes('foo'))
-        self.assertTrue(_is_string_or_bytes(u'foo'))
+        self.assertTrue(_is_string_or_bytes(u'foo'.encode("utf-8")))
         self.assertTrue(_is_string_or_bytes(b'foo'))
         self.assertFalse(_is_string_or_bytes(StringIO('bar')))
         self.assertFalse(_is_string_or_bytes([1]))

setup.py

@@ -18,6 +18,7 @@
     Topic :: Software Development :: Libraries :: Application Frameworks
     Topic :: Software Development :: Libraries :: Python Modules
     Programming Language :: Python
+    Programming Language :: Python :: 2.7
     Programming Language :: Python :: 3.5
     Programming Language :: Python :: 3.6
     Programming Language :: Python :: 3.9