Commit 0e389f5c authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 3.20.0

parent 46d02fb7

.gitignore

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@@ -10,7 +10,8 @@ __pycache__ 
.idea/

/test-report.xml

/test-report-*.xml

/venv/

venv/

v3nv/

tmp/

/src/toil/test/cwl/spec

/cwltool_deps/
@@ -18,3 +19,4 @@ tmp/ 
/docker/Dockerfile

/docker/toil-*.tar.gz

/src/toil/version.py

.coverage*

.gitlab-ci.yml

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before_script:

  - docker info

  - cat /etc/hosts

after_script:

  # We need to clean up any files that Toil may have made via Docker that

  # aren't deletable by the Gitlab user. If we don't do this, Gitlab will try

  # and clean them up before running the next job on the runner, fail, and fail

  # that next job.

  - pwd

  - sudo rm -rf tmp





stages:

  - test





py2-job:

  stage: test

  script:

    - pwd

    - virtualenv -p python2.7 venv && . venv/bin/activate && make prepare && make develop extras=[all] && pip install htcondor && PYTHONIOENCODING=utf-8 make test



py3-job:

  stage: test

  script:

    - pwd

    - virtualenv -p python3.6 venv && . venv/bin/activate && make prepare && make develop extras=[all] && pip install htcondor && PYTHONIOENCODING=utf-8 make test

.travis.yml

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language: python

python:

  - "3.5"

  - "3.6"

  - "2.7"

install:

  - make prepare

  - make develop extras=[aws,google] # adding extras to avoid import errors

script:

  - TOIL_TEST_QUICK=True make test_offline

env:

  # Necessary to get boto to work in Travis's Ubuntu Precise

  # environment (see #2498). Consider removing this if/when we

  # transition to the Xenial environment.

  - BOTO_CONFIG=/dev/null

Makefile

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@@ -90,8 +90,8 @@ help: 


# This Makefile uses bash features like printf and <()

SHELL=bash

python=python2.7

pip=pip2.7

python=python

pip=pip

tests=src

tests_local=src/toil/test

# do slightly less than travis timeout of 10 min.
@@ -267,8 +267,7 @@ check_build_reqs: 




prepare: check_venv

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

		pytest-timeout==1.2.0 cwltest

	$(pip) install mock==1.0.1 pytest==4.3.1 pytest-cov==2.6.1 stubserver==1.0.1 pytest-timeout==1.3.3 cwltest





check_venv:

README.rst

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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,

Toil is a scalable, efficient, cross-platform (Linux & macOS) pipeline management system,

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

programming.



Our next scheduled release is May 24, 2019.



* Check the `website`_ for a description of Toil and its features.

* Full documentation for the latest stable release can be found at

  `Read the Docs`_.