Fix h5pytest

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

@@ -9,7 +9,9 @@ jobs:
   # derived from https://github.com/actions/example-services/blob/master/.github/workflows/postgres-service.yml
   main:
     runs-on: ubuntu-latest
-
+    strategy:
+          matrix:
+            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
@@ -19,21 +21,21 @@ jobs:
         uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
-          python-version: 3.9
+          python-version: ${{ matrix.python-version }}
 
       - name: Basic dependencies install
         shell: bash -l {0}
         run: |
-          conda create --yes -n qiita-files python=3.9 h5py pandas scipy numpy
+          conda create --yes -n qiita-files python=${{ matrix.python-version }} h5py pandas scipy numpy
           conda activate qiita-files
           pip install .
-          pip install sphinx sphinx-bootstrap-theme nose-timer codecov Click
+          pip install sphinx sphinx-bootstrap-theme pytest-cov codecov Click
 
       - name: Main tests
         shell: bash -l {0}
         run: |
           conda activate qiita-files
-          nosetests --with-doctest --with-coverage --cover-package=qiita_files
+          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/parse/workflow.py

@@ -9,7 +9,10 @@
 from copy import deepcopy
 from time import time
 from functools import update_wrapper
-from collections import Iterable
+try:
+    from collections.abc import Iterable
+except ImportError:
+    from collections import Iterable
 from types import MethodType
 
 

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]))

qiita_files/util.py

@@ -10,10 +10,13 @@
 
 import h5py
 
-
-# not present in all 2.x series
-if hasattr(h5py.get_config(), 'default_file_mode'):
-    h5py.get_config().default_file_mode = 'r'
+# deprecated sind h5py 3.3,
+# see https://docs.h5py.org/en/stable/whatsnew/3.6.html
+h5py_version = list(map(int, h5py.__version__.split('.')))
+if h5py_version < [3, 3, 0]:
+    # not present in all 2.x series
+    if hasattr(h5py.get_config(), 'default_file_mode'):
+        h5py.get_config().default_file_mode = 'r'
 
 
 def _is_string_or_bytes(s):

setup.py

@@ -18,8 +18,13 @@
     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
+    Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
+    Programming Language :: Python :: 3.12
     Programming Language :: Python :: Implementation :: CPython
     Operating System :: POSIX :: Linux
     Operating System :: MacOS :: MacOS X