Revert "Drop Python 3.6" (#1620)

* Revert "Drop Python 3.6"

Ubuntu 18.04 (LTS, supported until April 2023) and Centos 7 are still
on Python 3.6.

This reverts commit 780f64a.

* Review fixes and run 'make sort_imports'

.github/workflows/ci-tests.yml

@@ -24,7 +24,7 @@ jobs:
     strategy:
       matrix:
         py-ver-major: [3]
-        py-ver-minor: [7, 8, 9, 10]
+        py-ver-minor: [6, 7, 8, 9, 10]
         step: [lint, unit, bandit, mypy]
 
     env:

Makefile

@@ -187,7 +187,7 @@ shellcheck: FORCE
 		cwltool-in-docker.sh
 
 pyupgrade: $(PYSOURCES)
-	pyupgrade --exit-zero-even-if-changed --py37-plus $^
+	pyupgrade --exit-zero-even-if-changed --py36-plus $^
 
 release-test: check-python3 FORCE
 	git diff-index --quiet HEAD -- || ( echo You have uncommited changes, please commit them and try again; false )

README.rst

@@ -33,9 +33,9 @@ Quay.io (Docker): |Quay.io Container|
 .. |Total PyPI Downloads| image:: https://static.pepy.tech/personalized-badge/cwltool?period=total&units=international_system&left_color=black&right_color=orange&left_text=Total%20PyPI%20Downloads
    :target: https://pepy.tech/project/cwltool
 
-.. |Conda Version| image:: https://anaconda.org/conda-forge/cwltool/badges/version.svg 
+.. |Conda Version| image:: https://anaconda.org/conda-forge/cwltool/badges/version.svg
    :target: https://anaconda.org/conda-forge/cwltool
-   
+
 .. |Conda Installs| image:: https://anaconda.org/conda-forge/cwltool/badges/downloads.svg
    :target: https://anaconda.org/conda-forge/cwltool
 
@@ -84,7 +84,7 @@ If you encounter an error, first try to update package information by using
    sudo apt-get update
 
 If you are running macOS X or other UNIXes and you want to use packages prepared by the conda-forge project, then
-please follow the install instructions for `conda-forge <https://conda-forge.org/#about>`_ (if you haven't already) and then 
+please follow the install instructions for `conda-forge <https://conda-forge.org/#about>`_ (if you haven't already) and then
 
 .. code:: bash
 
@@ -142,11 +142,11 @@ system link or `another facility <https://wiki.debian.org/DebianAlternatives>`_.
 Recommended Software
 ^^^^^^^^^^^^^^^^^^^^
 
-You may also want to have the following installed: 
+You may also want to have the following installed:
 - `node.js <https://nodejs.org/en/download/>`_
 - Docker, udocker, or Singularity (optional)
 
-Without these, some examples in the CWL tutorials at http://www.commonwl.org/user_guide/ may not work. 
+Without these, some examples in the CWL tutorials at http://www.commonwl.org/user_guide/ may not work.
 
 Run on the command line
 -----------------------

cwltool/argparser.py

@@ -2,6 +2,7 @@
 
 import argparse
 import os
+import urllib
 from typing import (
     Any,
     AnyStr,
@@ -16,7 +17,6 @@
     Union,
     cast,
 )
-import urllib
 
 from schema_salad.ref_resolver import file_uri
 

cwltool/context.py

@@ -4,23 +4,14 @@
 import shutil
 import tempfile
 import threading
-from typing import (
-    IO,
-    TYPE_CHECKING,
-    Any,
-    Callable,
-    Dict,
-    Iterable,
-    List,
-    Optional,
-    TextIO,
-    Union,
-)
+from typing import IO, Any, Callable, Dict, Iterable, List, Optional, TextIO, Union
 
+# move to a regular typing import when Python 3.3-3.6 is no longer supported
 from ruamel.yaml.comments import CommentedMap
 from schema_salad.avro.schema import Names
 from schema_salad.ref_resolver import Loader
 from schema_salad.utils import FetcherCallableType
+from typing_extensions import TYPE_CHECKING
 
 from .builder import Builder
 from .mpi import MpiConfig

cwltool/job.py

@@ -31,6 +31,7 @@
     Union,
     cast,
 )
+
 import psutil
 import shellescape
 from prov.model import PROV

cwltool/provenance.py

@@ -247,22 +247,24 @@ def _valid_orcid(orcid: Optional[str]) -> str:
         "oa:motivatedBy": Dict[str, str],
     },
 )
-
-
-class Aggregate(TypedDict, total=False):
-    uri: Optional[str]
-    bundledAs: Optional[Dict[str, Any]]
-    mediatype: Optional[str]
-    conformsTo: Optional[Union[str, List[str]]]
-    createdOn: Optional[str]
-    createdBy: Optional[Dict[str, str]]
-
-
+Aggregate = TypedDict(
+    "Aggregate",
+    {
+        "uri": Optional[str],
+        "bundledAs": Optional[Dict[str, Any]],
+        "mediatype": Optional[str],
+        "conformsTo": Optional[Union[str, List[str]]],
+        "createdOn": Optional[str],
+        "createdBy": Optional[Dict[str, str]],
+    },
+    total=False,
+)
 # Aggregate.bundledAs is actually type Aggregate, but cyclic definitions are not suported
-class AuthoredBy(TypedDict, total=False):
-    orcid: Optional[str]
-    name: Optional[str]
-    uri: Optional[str]
+AuthoredBy = TypedDict(
+    "AuthoredBy",
+    {"orcid": Optional[str], "name": Optional[str], "uri": Optional[str]},
+    total=False,
+)
 
 
 class ResearchObject:

cwltool/utils.py

@@ -101,13 +101,14 @@
 JSONType = Union[
     Dict[str, JSONAtomType], List[JSONAtomType], str, int, float, bool, None
 ]
-
-
-class WorkflowStateItem(NamedTuple):
-    parameter: CWLObjectType
-    value: Optional[CWLOutputType]
-    success: str
-
+WorkflowStateItem = NamedTuple(
+    "WorkflowStateItem",
+    [
+        ("parameter", CWLObjectType),
+        ("value", Optional[CWLOutputType]),
+        ("success", str),
+    ],
+)
 
 ParametersType = List[CWLObjectType]
 StepType = CWLObjectType  # WorkflowStep

requirements.txt

@@ -12,3 +12,4 @@ coloredlogs
 pydot>=1.4.1
 argcomplete>=1.12.0
 pyparsing != 3.0.2  # breaks --print-dot (pydot) https://github.com/pyparsing/pyparsing/issues/319
+pyparsing < 3;python_version<='3.6'  # breaks --print-dot

setup.py

@@ -120,12 +120,13 @@
         "coloredlogs",
         "pydot >= 1.4.1",
         "pyparsing != 3.0.2",  # breaks --print-dot (pydot) https://github.com/pyparsing/pyparsing/issues/319
+        "pyparsing < 3 ;python_version<='3.6'",  # breaks --print-dot (pydot)
         "argcomplete",
     ],
     extras_require={
         "deps": ["galaxy-tool-util >= 21.1.0"],
     },
-    python_requires=">=3.7, <4",
+    python_requires=">=3.6, <4",
     setup_requires=PYTEST_RUNNER,
     test_suite="tests",
     tests_require=[
@@ -150,6 +151,7 @@
         "Operating System :: POSIX",
         "Operating System :: POSIX :: Linux",
         "Programming Language :: Python :: 3",
+        "Programming Language :: Python :: 3.6",
         "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",

tests/test_stdout_stderr_log_dir.py

@@ -1,5 +1,5 @@
-import os
 import json
+import os
 from pathlib import Path
 
 from cwltool.main import main

tests/util.py

@@ -66,7 +66,8 @@ def env_accepts_null() -> bool:
     if _env_accepts_null is None:
         result = subprocess.run(
             ["env", "-0"],
-            capture_output=True,
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
             encoding="utf-8",
         )
         _env_accepts_null = result.returncode == 0

tox.ini

@@ -1,9 +1,9 @@
 [tox]
 envlist =
-  py3{7,8,9,10}-lint
-  py3{7,8,9,10}-unit
-  py3{7,8,9,10}-bandit
-  py3{7,8,9,10}-mypy
+  py3{6,7,8,9,10}-lint
+  py3{6,7,8,9,10}-unit
+  py3{6,7,8,9,10}-bandit
+  py3{6,7,8,9,10}-mypy
   py39-lintreadme
   py39-shellcheck
   py39-pydocstyle
@@ -16,20 +16,21 @@ testpaths = tests
 
 [gh-actions]
 python =
+  3.6: py36
   3.7: py37
   3.8: py38
   3.9: py39
   3.10: py310
 
 [testenv]
 skipsdist =
-  py3{7,8,9,10}-!{unit,mypy,lintreadme} = True
+  py3{6,7,8,9,10}-!{unit,mypy,lintreadme} = True
 
 description =
-  py3{7,8,9,10}-unit: Run the unit tests
-  py3{7,8,9,10}-lint: Lint the Python code
-  py3{7,8,9,10}-bandit: Search for common security issues
-  py3{7,8,9,10}-mypy: Check for type safety
+  py3{6,7,8,9,10}-unit: Run the unit tests
+  py3{6,7,8,9,10}-lint: Lint the Python code
+  py3{6,7,8,9,10}-bandit: Search for common security issues
+  py3{6,7,8,9,10}-mypy: Check for type safety
   py39-pydocstyle: docstring style checker
   py39-shellcheck: syntax check for shell scripts
   py39-lintreadme: Lint the README.rst→.md conversion
@@ -40,39 +41,39 @@ passenv =
   PROOT_NO_SECCOMP
 
 extras =
-  py3{7,8,9,10}-unit: deps
+  py3{6,7,8,9,10}-unit: deps
 
 deps =
-  py3{7,8,9,10}-{unit,lint,bandit,mypy}: -rrequirements.txt
-  py3{7,8,9,10}-{unit,mypy}: -rtest-requirements.txt
-  py3{7,8,9,10}-lint: -rlint-requirements.txt
-  py3{7,8,9,10}-bandit: bandit
-  py3{7,8,9,10}-bandit: importlib_metadata != 4.8.0
-  py3{7,8,9,10}-mypy: -rmypy-requirements.txt
+  py3{6,7,8,9,10}-{unit,lint,bandit,mypy}: -rrequirements.txt
+  py3{6,7,8,9,10}-{unit,mypy}: -rtest-requirements.txt
+  py3{6,7,8,9,10}-lint: -rlint-requirements.txt
+  py3{6,7,8,9,10}-bandit: bandit
+  py3{6,7,8,9,10}-bandit: importlib_metadata != 4.8.0
+  py3{6,7,8,9,10}-mypy: -rmypy-requirements.txt
   py39-pydocstyle: pydocstyle
   py39-pydocstyle: diff-cover
   py39-lintreadme: twine
   py39-lintreadme: wheel
   py39-lintreadme: readme_renderer[md]
 
 setenv =
-  py3{7,8,9,10}-unit: LC_ALL = C.UTF-8
+  py3{6,7,8,9,10}-unit: LC_ALL = C.UTF-8
 
 commands_pre =
-  py3{7,8,9,10}-unit: python -m pip install -U pip setuptools wheel
+  py3{6,7,8,9,10}-unit: python -m pip install -U pip setuptools wheel
   py39-lintreadme: python setup.py sdist --dist-dir {distdir}
   py39-lintreadme: python setup.py bdist_wheel --dist-dir {distdir}
 
 commands =
-  py3{7,8,9,10}-unit: make coverage-report coverage.xml PYTEST_EXTRA={posargs}
-  py3{7,8,9,10}-bandit: bandit -r cwltool
-  py3{7,8,9,10}-lint: make flake8 format-check
-  py3{7,8,9,10}-mypy: make mypy mypyc PYTEST_EXTRA={posargs}
+  py3{6,7,8,9,10}-unit: make coverage-report coverage.xml PYTEST_EXTRA={posargs}
+  py3{6,7,8,9,10}-bandit: bandit -r cwltool
+  py3{6,7,8,9,10}-lint: make flake8 format-check
+  py3{6,7,8,9,10}-mypy: make mypy mypyc PYTEST_EXTRA={posargs}
   py39-shellcheck: make shellcheck
   py39-pydocstyle: make diff_pydocstyle_report
   py39-lintreadme: twine check {distdir}/*
 
 skip_install =
-  py3{7,8,9,10}-{bandit,lint,mypy,shellcheck,pydocstyle,lintreadme}: true
+  py3{6,7,8,9,10}-{bandit,lint,mypy,shellcheck,pydocstyle,lintreadme}: true
 
 allowlist_externals = make