Merge pull request #1026 from jmchilton/drop_python_2

Drop Python 2 Support

Author: nsoranzo

CONTRIBUTING.rst

@@ -106,7 +106,7 @@ Before you submit a pull request, check that it meets these guidelines:
 
 1. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring.
-2. The pull request should work for Python 2.7 and >=3.5. Check
+2. The pull request should work for Python >=3.5. Check
    https://travis-ci.org/galaxyproject/planemo/pull_requests
    and make sure that the tests pass for all supported Python versions.
 
@@ -118,7 +118,7 @@ To run a subset of tests::
     % make tox ENV=py37-unit ARGS='--tests tests/test_shed_upload.py'
 
 This will use Tox_ to run the specified tests using Python 3.7. ``ENV`` here
-can be used to specify different Python version (e.g. ``py27`` and
+can be used to specify different Python version (e.g. ``py35`` or
 ``py37``).
 
 Even more granularity is also possible by specifying specific test methods.::
@@ -138,7 +138,7 @@ Tox_ itself is configured to wrap nose_. One can skip Tox_ and run
 
 ::
 
-    nosetests tests/test_shed_upload.py
+    pytest tests/test_shed_upload.py
 
 Tox_
 ~~~~~~~~~~~
@@ -147,22 +147,24 @@ Tox_ is a tool to automate testing across different Python versions. The
 ``tox`` executable can be supplied with a ``-e`` argument to specify a
 testing environment. Planemo defines the following environments:
 
-``py27-lint``
-    Lint the planemo code using Python 2.7.
-
 ``py37-lint``
-    Lint the planemo code using Python 3.7 (also ensures valid Python 3
-    syntax).
+    Lint the planemo code using Python 3.7..
+
+``py37-lint_docs``
+    Lint the docs reStructuredText.
 
-``py37-lint_readme``
-    Lint the README reStructuredText.
+``py37-lint_docstrings``
+    Lint the project Python docstrings (doesn't pass currently).
 
-``py27-unit``
-    Run planemo tests in Python 2.7.
+``py35-unit-quick``
+    Run the fastest unit tests (with least external dependencies) on Python 3.5.
 
-``py37-unit``
-    Run planemo tests in Python 3.7.
+``py36-unit-nonredundant-noclientbuild-gx-2005``
+    Run tests that are marked as targeting a Galaxy branch and test against Galaxy 20.05.
+    Skip tests that are marked as redundant or that require a Galaxy client build.
 
+``py37-unit-gx-dev``
+    Run tests that are marked as targeting a Galaxy branch and test against Galaxy's dev branch.
 
 Pre-commit Hooks
 ~~~~~~~~~~~~~~~~~~~~~

planemo/options.py

@@ -159,7 +159,7 @@ def galaxy_python_version():
         '--galaxy_python_version',
         use_global_config=True,
         default=None,
-        type=click.Choice(['2', '2.7', '3', '3.5', '3.6', '3.7', '3.8']),
+        type=click.Choice(['3', '3.5', '3.6', '3.7', '3.8']),
         help="Python version to start Galaxy under",
     )
 

requirements.txt

@@ -7,8 +7,8 @@ cwltool==1.0.20191225192155
 docutils
 ephemeris>=0.10.3
 galaxy-containers
-galaxy-tool-util>=20.5.0.dev1
-galaxy-util>=20.1.0.dev0  # temporarily needed because this is a pre-release and https://github.com/pypa/pip/issues/988
+galaxy-tool-util>=20.5.0
+galaxy-util>=20.5.0
 glob2
 gxformat2>=0.8.0
 jinja2

setup.py

@@ -10,8 +10,8 @@
 except ImportError:
     from distutils.core import setup
 
-if sys.version_info < (2, 7):
-    sys.stderr.write("ERROR: planemo requires at least Python Version 2.7\n")
+if sys.version_info < (3, 5):
+    sys.stderr.write("ERROR: planemo requires at least Python Version 3.5\n")
     sys.exit(1)
 
 # Allow installer to turn off dependency on lxml by setting the environment variable
@@ -91,14 +91,11 @@ def get_var(var_name):
 if os.path.exists("requirements.txt"):
     with open("requirements.txt") as fh:
         requirements = [r for r in fh.read().split("\n") if ";" not in r]
-    with open("requirements.txt") as fh:
-        py27_requirements = [r.split(";", 1)[0].strip() for r in fh.read().split("\n") if ";" in r]
     if not PLANEMO_REQUIRE_LXML:
         requirements.remove("lxml")
 else:
     # In tox, it will cover them anyway.
     requirements = []
-    py27_requirements = []
 
 test_requirements = [
     # TODO: put package test requirements here
@@ -120,9 +117,6 @@ def get_var(var_name):
     package_dir=PACKAGE_DIR,
     include_package_data=True,
     install_requires=requirements,
-    extras_require={
-        ':python_version=="2.7"': py27_requirements,
-    },
     license="AFL",
     zip_safe=False,
     keywords='planemo',
@@ -136,8 +130,6 @@ def get_var(var_name):
         'Topic :: Software Development :: Code Generators',
         'Topic :: Software Development :: Testing',
         'Natural Language :: English',
-        "Programming Language :: Python :: 2",
-        'Programming Language :: Python :: 2.7',
         "Programming Language :: Python :: 3",
         'Programming Language :: Python :: 3.5',
         'Programming Language :: Python :: 3.6',

tests/test_cmd_serve.py

@@ -45,7 +45,6 @@ def setUp(self):
         self._serve_artifact = os.path.join(TEST_REPOS_DIR, "single_tool", "cat.xml")
 
     @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
-    @skip_if_environ("PLANEMO_SKIP_PYTHON2")
     @mark.tests_galaxy_branch
     def test_serve(self):
         extra_args = [
@@ -54,7 +53,6 @@ def test_serve(self):
         self._launch_thread_and_wait(self._run, extra_args)
 
     @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
-    @skip_if_environ("PLANEMO_SKIP_PYTHON3")
     @skip_if_environ("PLANEMO_SKIP_GALAXY_CLIENT_TESTS")
     @skip_unless_executable("python3")
     def test_serve_client_python3(self):

tox.ini

@@ -45,9 +45,6 @@ setenv =
     noshed: PLANEMO_SKIP_SHED_TESTS=1
     quick: PLANEMO_SKIP_SLOW_TESTS=1
     quick: PLANEMO_SKIP_GALAXY_TESTS=1
-    py27-unit: PLANEMO_SKIP_PYTHON3=1
-    !py27-unit: PLANEMO_SKIP_PYTHON2=1
-    !py27-unit: PLANEMO_DEFAULT_PYTHON_VERSION=3
     master: PLANEMO_TEST_GALAXY_BRANCH=master
     dev: PLANEMO_TEST_GALAXY_BRANCH=dev
     2005: PLANEMO_TEST_GALAXY_BRANCH=release_20.05