🐛 Fix --version, add enter, parse-resources and version, and fix tests

[shnizzedy]

Fixes

Fixes #22 by @keithcdodd & @shnizzedy
Fixes shnizzedy/cpac#17 by @shnizzedy
Fixes shnizzedy/cpac#25 by @shnizzedy
Related to #26 by @gkiar
Related to #27 by @shnizzedy

Description

• Fixes issue where cpac --version was returning the usage text instead of the version

While I was doing that ☝️, I fixed a few other things that I was touching anyway:

• Adds commands:
  • cpac enter to BASH into a C-PAC container
  • cpac parse-resources to run cpac/helpers/cpac_parse_resources.py directly from cpac
  • cpac version to check the in-container version of C-PAC
• Fixes failing tests
• Updates usage text:
  • supports Singularity 3
  • brief description for each previously undocumented command

Technical details

• In fixing the failing tests here, I discovered --tracking_opt-out isn't being applied to the config commandline utility in C-PAC, so there's some code here to set up the tracking config if it doesn't exist:

  cpac/src/cpac/helpers/cpac_parse_resources.py

  Lines 55 to 69 in 506e8c5

  	def get_or_create_config(udir):
  	"""Function to create a Google Analytics tracking config file.
  	Sourced from https://github.com/FCP-INDI/C-PAC/blob/80424468c7f4e59c102f446b05d4154ec1cd4b2d/CPAC/utils/ga.py#L19-L30
  	""" # noqa: E501 # pylint: disable=line-too-long
  	tracking_path = os.path.join(udir, '.cpac')
  	cparser = configparser.ConfigParser()
  	if os.path.exists(tracking_path):
  	cparser.read(tracking_path)
  	if not cparser.has_section('user'):
  	cparser.read_dict(dict(user=dict(uid=uuid.uuid1().hex,
  	track=True)))
  	with open(tracking_path, 'w+') as fhandle:
  	cparser.write(fhandle)
  	return tracking_path

• This update increases the minimum Python version from 3.6 to 3.7
• 👷 Tests are failing in Singularity on GitHub Actions but passing locally #32

Tests

• cpac/tests/test_cpac_version.py

  Lines 11 to 51 in 506e8c5

  	wrapper_version_string = f'cpac (convenience wrapper) version {__version__}'
  	def startswith_cpac_version(captured):
  	"""Check if captured text starts with cpac version
  	Parameters
  	----------
  	captured : str
  	Returns
  	-------
  	bool
  	"""
  	return captured.out.strip().startswith(wrapper_version_string)
  	@pytest.mark.parametrize('argsep', [' ', '='])
  	def test_cpac_version(argsep, capsys, platform=None, tag=None):
  	r"""Test `cpac version`"""
  	def run_test(argv, platform):
  	with mock.patch.object(sys, 'argv', argv):
  	run()
  	captured = capsys.readouterr()
  	assert startswith_cpac_version(captured)
  	assert 'C-PAC version ' in captured.out
  	if platform is not None:
  	assert platform.title() in captured.out
  	else:
  	assert 'Docker' in captured.out
  	args = set_commandline_args(platform, tag, argsep)
  	argv = 'version'
  	def test_cpac__version(capsys):
  	r"""Test `cpac --version`"""
  	with mock.patch.object(sys, 'argv', ['cpac', '--version']):
  	with pytest.raises(SystemExit):
  	run()
  	captured = capsys.readouterr()
  	assert startswith_cpac_version(captured)

• Updated all failing tests
• I'm not sure how to write tests for enter ― that command opens an interactive prompt in a container.

Checklist

• My pull request has a descriptive title (not a vague title like Update index.md).
• My pull request targets the develop branch of the repository.
• My commit messages follow best practices.
• My code follows the established code style of the repository.
• I added tests for the changes I made (if applicable).
• I updated the changelog.
• I added or updated documentation (if applicable).
• I tried running the project locally and verified that there are no
  visible errors.

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