New upstream version 3.18.0

__pycache__

.eggs/

.cache/

.pytest_cache/

.idea/

/test-report.xml

/test-report-*.xml

/venv/

tmp/

/src/toil/test/cwl/spec

/cwltool_deps/

/docs/generated_rst/

The 'develop' target creates an editable install of Toil and its runtime requirements in the

current virtualenv. The install is called 'editable' because changes to the source code

immediately affect the virtualenv. Set the 'extras' variable to ensure that the 'develop' target

installs support for extras. Consult setup.py for the list of supported extras. To install Toil

in develop mode with all extras, run

installs support for extras; some tests require extras to be installed. Consult setup.py for the

list of supported extras. To install Toil in develop mode with all extras, run

	make develop extras=[all]

The 'docs' target uses Sphinx to create HTML documentation in the docs/_build directory

Targets are provided to run Toil's tests. Note that these targets do *not* automatically install

Toil's dependencies; it is recommended to 'make develop' before running any of them.

The 'test' target runs Toil's unit tests serially with pytest. It will run some docker tests and

setup. If you wish to avoid this, use the 'test_offline' target instead. Note: this target does not

capture output from the terminal. For any of the test targets, set the 'tests' variable to run a

	make test tests=src/toil/test/sort/sortTest.py::SortTest::testSort

The 'test_offline' target is similar to 'test' but it skips the docker dependent tests and their

setup.

setup. It can also be used to invoke individual tests, e.g.

    make test_offline tests_local=src/toil/test/sort/sortTest.py::SortTest::testSort

The 'integration_test_local' target runs toil's integration tests. These are more thorough but also

more costly than the regular unit tests. For the AWS integration tests to run, the environment

# The auto-deployment test needs the docker appliance

test: check_venv check_build_reqs docker

	TOIL_APPLIANCE_SELF=$(docker_registry)/$(docker_base_name):$(docker_tag) \

	    $(python) -m pytest $(pytest_args_local) $(tests)

	    $(python) -m pytest --cov=toil $(pytest_args_local) $(tests)

# For running integration tests locally in series (uses the -s argument for pyTest)

integration_test_local: check_venv check_build_reqs sdist push_docker

prepare: check_venv

	$(pip) install sphinx==1.5.5 mock==1.0.1 pytest==2.8.3 stubserver==1.0.1 \

	$(pip) install sphinx==1.5.5 mock==1.0.1 pytest==3.6.2 stubserver==1.0.1 \

		pytest-timeout==1.2.0 cwltest

check_venv:

	@$(python) -c 'import sys; sys.exit( int( not (hasattr(sys, "real_prefix") or ( hasattr(sys, "base_prefix") and sys.base_prefix != sys.prefix ) ) ) )' \

	@$(python) -c 'import sys, os; sys.exit( int( 0 if "VIRTUAL_ENV" in os.environ else 1 ) )' \

		|| ( printf "$(red)A virtualenv must be active.$(normal)\n" ; false )

.. image:: https://badge.waffle.io/BD2KGenomics/toil.svg?label=ready&title=Ready

   :target: https://waffle.io/BD2KGenomics/toil

   :alt: 'Stories in Ready'

ATTENTION: Toil has moved from https://github.com/BD2KGenomics/toil to https://github.com/DataBiosphere/toil as of July 5th, 2018.

Toil is a scalable, efficient, cross-platform pipeline management system,

written entirely in Python, and designed around the principles of functional

* Google Groups discussion `forum`_ and videochat `invite list`_.

.. _website: http://toil.ucsc-cgl.org/

.. _Read the Docs: http://toil.readthedocs.org/

.. _Read the Docs: https://toil.readthedocs.io/en/latest

.. _forum: https://groups.google.com/forum/#!forum/toil-community

.. _invite list: https://groups.google.com/forum/#!forum/toil-community-videochats

.. _blog: https://toilpipelines.wordpress.com/

from __future__ import absolute_import

from six.moves import xrange

from argparse import ArgumentParser

import os

import logging

|                        | deleted until all associated nodes have been       |

|                        | terminated.                                        |

+------------------------+----------------------------------------------------+

| TOIL_AZURE_ZONE        | A specified region for provisioning instances.     |

+------------------------+----------------------------------------------------+

| TOIL_SLURM_ARGS        | Arguments for sbatch for the slurm batch system.   |

|                        | Do not pass CPU or memory specifications here.     |

|                        | Instead, define resource requirements for the job. |