Merge pull request #41 from Lioscro/update-ci

remove python 3.6 from test matrix and add 3.10 and 3.11

.github/workflows/ci.yml

@@ -5,14 +5,14 @@ on: [push]
 jobs:
   check-code:
     name: Check code quality
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
       - name: Checkout branch
         uses: actions/checkout@master
       - name: Setup python
         uses: actions/setup-python@v1
         with:
-          python-version: '3.8'
+          python-version: '3.9'
           architecture: x64
       - name: Install dependencies
         run: pip install -r dev-requirements.txt
@@ -22,8 +22,8 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python: [3.6, 3.7, 3.8, 3.9]
-        os: [ubuntu-20.04]
+        python: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        os: [ubuntu-22.04]
     name: Test on Python ${{ matrix.python }}
     steps:
       - name: Checkout branch

.pre-commit-config.yaml

@@ -1,13 +1,13 @@
 repos:
-  - repo: https://github.com/pre-commit/mirrors-yapf
-    rev: v0.30.0
+  - repo: https://github.com/google/yapf
+    rev: v0.32.0
     hooks:
       - id: yapf
   - repo: https://github.com/pycqa/flake8
-    rev: 3.9.0
+    rev: 5.0.4
     hooks:
       - id: flake8
   - repo: https://github.com/pycqa/isort
-    rev: 5.10.1
+    rev: 5.12.0
     hooks:
       - id: isort

Makefile

@@ -2,11 +2,10 @@
 
 test:
 	rm -f .coverage
-	nosetests --verbose --with-coverage --cover-package ngs_tools tests/*
+	pytest -v --cov=ngs_tools tests
 
 check:
-	flake8 ngs_tools && echo OK
-	yapf -r --diff ngs_tools && echo OK
+	pre-commit run --all-files
 
 build:
 	python setup.py sdist

dev-requirements.txt

@@ -1,11 +1,12 @@
 bumpversion==0.6.0
-coverage==5.1
-flake8==3.9.0
-nose==1.3.7
-pre-commit==2.4.0
+coverage>=5.1
+flake8==5.0.4
+pre-commit>=2.4.0
+pytest>=7.4.3
+pytest-cov>=4.1.0
 sphinx>=3.3.1
 sphinx-autoapi>=1.5.1
 sphinx_rtd_theme>=0.5.0
 twine>=2.0.0
-wheel==0.34.2
-yapf==0.30.0
+wheel>=0.34.2
+yapf==0.32.0

setup.py

@@ -35,6 +35,9 @@ def read(path):
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
+        'Programming Language :: Python :: 3.10',
+        'Programming Language :: Python :: 3.11',
         'Topic :: Scientific/Engineering :: Bio-Informatics',
         'Topic :: Utilities',
     ],

tests/test_sequence.py

@@ -106,7 +106,7 @@ def test_correct_sequences_to_whitelist(self):
         sequences = ['ACTG', 'ACTT', 'AGCC', 'TTTT']
         qualities = ['AAAA', 'AAAA', 'AAAA', 'AAAA']
         whitelist = ['ACTG', 'TTTN']
-        with mock.patch('ngs_tools.sequence.utils.progress', mixins.tqdm_mock),\
+        with mock.patch('ngs_tools.sequence.utils.progress', mixins.tqdm_mock), \
             mock.patch('ngs_tools.sequence.progress', mixins.tqdm_mock):
             corrections = sequence.correct_sequences_to_whitelist(
                 sequences, qualities, whitelist
@@ -116,7 +116,7 @@ def test_correct_sequences_to_whitelist(self):
     def test_correct_sequences_to_whitelist_simple(self):
         sequences = ['ACTG', 'ACTT', 'AGCC', 'TTTT']
         whitelist = ['ACTG', 'TTTN']
-        with mock.patch('ngs_tools.sequence.utils.progress', mixins.tqdm_mock),\
+        with mock.patch('ngs_tools.sequence.utils.progress', mixins.tqdm_mock), \
             mock.patch('ngs_tools.sequence.progress', mixins.tqdm_mock):
             corrections = sequence.correct_sequences_to_whitelist_simple(
                 sequences, whitelist

tests/test_utils.py

@@ -150,7 +150,7 @@ def test_concatenate_files_as_text(self):
             self.assertEqual(f.read(), 'TEST1\nTEST2\n')
 
     def test_download_file(self):
-        with mock.patch('ngs_tools.utils.urlretrieve') as urlretrieve,\
+        with mock.patch('ngs_tools.utils.urlretrieve') as urlretrieve, \
             mock.patch('ngs_tools.utils.TqdmUpTo', mixins.tqdm_mock):
             path = os.path.join(self.temp_dir, 'test')
             self.assertEqual(path, utils.download_file('remote/path', path))
@@ -162,8 +162,8 @@ def test_download_file(self):
             )
 
     def test_stream_file(self):
-        with mock.patch('ngs_tools.utils.os.mkfifo'),\
-            mock.patch('ngs_tools.utils.urlretrieve') as urlretrieve,\
+        with mock.patch('ngs_tools.utils.os.mkfifo'), \
+            mock.patch('ngs_tools.utils.urlretrieve') as urlretrieve, \
             mock.patch('ngs_tools.utils.threading.Thread') as Thread:
             with utils.stream_file('remote/path', 'local/path') as path:
                 self.assertEqual('local/path', path)
@@ -177,8 +177,8 @@ def test_stream_file(self):
             Thread.return_value.join.assert_called_once()
 
     def test_stream_file_not_supported(self):
-        with mock.patch('ngs_tools.utils.os.mkfifo') as mkfifo,\
-            mock.patch('ngs_tools.utils.urlretrieve'),\
+        with mock.patch('ngs_tools.utils.os.mkfifo') as mkfifo, \
+            mock.patch('ngs_tools.utils.urlretrieve'), \
             mock.patch('ngs_tools.utils.threading.Thread') as Thread:
             mkfifo.side_effect = AttributeError('test')
             with self.assertRaises(OSError):
@@ -187,8 +187,8 @@ def test_stream_file_not_supported(self):
                 Thread.assert_not_called()
 
     def test_stream_file_exception(self):
-        with mock.patch('ngs_tools.utils.os.mkfifo'),\
-            mock.patch('ngs_tools.utils.urlretrieve') as urlretrieve,\
+        with mock.patch('ngs_tools.utils.os.mkfifo'), \
+            mock.patch('ngs_tools.utils.urlretrieve') as urlretrieve, \
             mock.patch('ngs_tools.utils.threading.Thread') as Thread:
             with self.assertRaises(Exception):
                 with utils.stream_file('remote/path', 'local/path') as path: