fix merge

.github/workflows/black.yml

@@ -1,6 +1,6 @@
 name: Lint
 
-on: [push, pull_request]
+on: [pull_request]
 
 jobs:
   lint:

.github/workflows/run-pytest.yml

@@ -1,18 +1,18 @@
 name: Run pytests
 
 on:
-  push:
-    branches: [master, dev]
   pull_request:
     branches: [master, dev]
-
+  workflow_dispatch:
+    inputs: null
+
 jobs:
   pytest:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8, 3.9]
-        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        os: [ubuntu-latest]
 
     steps:
       - uses: actions/checkout@v2
@@ -22,10 +22,10 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install dev dependancies
+      - name: Install dev dependencies
         run: if [ -f requirements/requirements-dev.txt ]; then pip install -r requirements/requirements-dev.txt; fi
 
-      - name: Install test dependancies
+      - name: Install test dependencies
         run: if [ -f requirements/requirements-test.txt ]; then pip install -r requirements/requirements-test.txt; fi
 
       - name: Install package

docs/changelog.md

@@ -5,6 +5,11 @@
 
 - [pipestat](http://pipestat.databio.org/en/latest/) support 
 
+## [0.12.3] -- 2022-01-25
+
+### Fixed
+- A few bugs with compatibility with Python version 3.9
+
 ## [0.12.2] -- 2021-12-20
 
 ### Fixed

pypiper/manager.py

@@ -20,7 +20,8 @@
 import sys
 import time
 import warnings
-from collections import Iterable
+
+from collections.abc import Iterable
 from hashlib import md5
 
 import __main__

pypiper/ngstk.py

@@ -2000,7 +2000,8 @@ def get_read_type(self, bam_file, n=10):
         :param int n: Number of lines to read from bam file.
         :return str, int: tuple of read type and read length
         """
-        from collections import Counter
+
+        from collections.abc import Counter
 
         try:
             p = subprocess.Popen(

pypiper/pipeline.py

@@ -4,12 +4,8 @@
 import glob
 import os
 import sys
-from collections import OrderedDict
 
-if sys.version_info < (3, 3):
-    from collections import Iterable, Mapping
-else:
-    from collections.abc import Iterable, Mapping
+from collections.abc import Iterable, Mapping
 
 from .exceptions import (
     IllegalPipelineDefinitionError,
@@ -412,10 +408,11 @@ def _is_unordered(collection):
         illogical to investigate whether it's ordered.
     """
     if not isinstance(collection, Iterable):
-        raise TypeError("Non-iterable alleged collection: {}".format(type(collection)))
-    return isinstance(collection, set) or (
-        isinstance(collection, dict) and not isinstance(collection, OrderedDict)
-    )
+        raise TypeError("Non-iterable alleged collection: {}".
+                        format(type(collection)))
+
+
+    return isinstance(collection, set) or isinstance(collection, dict)
 
 
 def _parse_stage_spec(stage_spec):

pypiper/utils.py

@@ -3,7 +3,8 @@
 import os
 import re
 import sys
-from collections import Iterable, Mapping, Sequence
+
+from collections.abc import Iterable, Mapping, Sequence
 from shlex import split
 from subprocess import PIPE
 
@@ -854,10 +855,7 @@ def _determine_args(argument_groups, arguments, use_all_args=False):
     :return set[str]: Collection of (unique) argument names to add to a parser.
     """
 
-    if sys.version_info < (3, 3):
-        from collections import Iterable
-    else:
-        from collections.abc import Iterable
+    from collections.abc import Iterable
 
     from logmuse import LOGGING_CLI_OPTDATA
 

requirements/requirements-test.txt

@@ -0,0 +1,15 @@
+mock==2.0.0
+<<<<<<< HEAD:requirements/reqs-test.txt
+pytest>=4.6.9
+pytest-cov>=2.8.1
+hypothesis==4.38.0
+coveralls
+veracitools
+=======
+pytest>=4.2.1
+hypothesis
+coveralls>=1.1
+pytest-cov==2.6.1
+veracitools
+pytest-remotedata
+>>>>>>> master:requirements/requirements-test.txt

setup.py

@@ -7,19 +7,12 @@
 
 try:
     from setuptools import setup
-
-    if sys.version_info < (2, 7):
-        extra['install_requires'] = ['argparse']
 except ImportError:
     from distutils.core import setup
 
-    if sys.version_info < (2, 7):
-        extra["dependencies"] = ["argparse"]
-
-
 def read_reqs_file(reqs_name):
     """Read requirements file for given requirements group."""
-    path_reqs_file = os.path.join("requirements", "reqs-{}.txt".format(reqs_name))
+    path_reqs_file = os.path.join("requirements", "requirements-{}.txt".format(reqs_name))
     with open(path_reqs_file, "r") as reqs_file:
         return [
             pkg.rstrip() for pkg in reqs_file.readlines() if not pkg.startswith("#")