License checker extensions

[netsettler]

Some additions to license checkers.

• New license framework for R (tentatively implemented)
• New license framework for Conda (tentatively implemented)
• Much new license metadata
• New script run-license-checker for people to use this without installing it in code.

Having done this, though, we removed the scan2-pipeline policy definition because it can now be modularly added elsewhere, in that code. Such a definition can be added in an external module and then invoked interactively by:

run-license-checker scan2-pipeline --policy-dir <dir>

or from code by:

from dcicutils.license_utils import LicenseCheckerRegistry
Scan2PipelineLicenseChecker = LicenseCheckerRegistry.lookup_checker('scan2-pipeline', policy_dir=<policy-dir>)
Scan2PIpelineLicenseChecker.validate()

Note that if the conda checkers do not run, you may be in the wrong directory or Conda may not have set its CONDA_PREFIX environment variable. You can specify the directory by:

from dcicutils.license_utils import LicenseCheckerRegistry, LicenseOptions
Scan2PipelineLicenseChecker = LicenseCheckerRegistry.lookup_checker('scan2-pipeline', policy_dir="<policy-dir>")
with LicenseOptions.selected_options(conda_prefix="<conda-dir>"):
    Scan2PIpelineLicenseChecker.validate()

or you can override the search for Conda's CONDA_PREFIX environment variable by setting the CONDA_LICENSE_CHECKER_PREFIX environment variable, which can be used to override CONDA_PREFIX.

[coveralls]

Pull Request Test Coverage Report for Build 6354777482

• 254 of 331 (76.74%) changed or added relevant lines in 3 files are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage decreased (-0.1%) to 77.659%

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Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
dcicutils/license_utils.py	240	317	75.71%
<!--	Total:	254	331	76.74%	-->

Totals
Change from base Build 6240767306:	-0.1%
Covered Lines:	8478
Relevant Lines:	10917

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💛 - Coveralls