Commit d0683b9d authored by Michael R. Crusoe's avatar Michael R. Crusoe 🏳️‍🌈
Browse files

New upstream version 1.0.20180225105849

parent d729dcc9

Makefile

+3 −2
Original line number Diff line number Diff line
@@ -27,7 +27,8 @@ MODULE=cwltool 
# `[[` conditional expressions.

PYSOURCES=$(wildcard ${MODULE}/**.py tests/*.py) setup.py

DEVPKGS=pep8 diff_cover autopep8 pylint coverage pydocstyle flake8 pytest isort mock

DEBDEVPKGS=pep8 python-autopep8 pylint python-coverage pydocstyle sloccount python-flake8 python-mock

DEBDEVPKGS=pep8 python-autopep8 pylint python-coverage pydocstyle sloccount \

	   python-flake8 python-mock shellcheck

VERSION=1.0.$(shell date +%Y%m%d%H%M%S --date=`git log --first-parent \

	--max-count=1 --format=format:%cI`)

mkfile_dir := $(dir $(abspath $(lastword $(MAKEFILE_LIST))))
@@ -56,7 +57,7 @@ install: FORCE 
dist: dist/${MODULE}-$(VERSION).tar.gz



dist/${MODULE}-$(VERSION).tar.gz: $(SOURCES)

	./setup.py sdist

	./setup.py sdist bdist_wheel



## clean       : clean up all temporary / machine-generated files

clean: FORCE

PKG-INFO

+11 −1
Original line number Diff line number Diff line 
Metadata-Version: 1.1

Name: cwltool

Version: 1.0.20180211183944

Version: 1.0.20180225105849

Summary: Common workflow language reference implementation

Home-page: https://github.com/common-workflow-language/cwltool

Author: Common workflow language working group
@@ -149,6 +149,16 @@ Description: ================================================================== 
        

          cwltool --user-space-docker-cmd=dx-docker https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/master/v1.0/v1.0/test-cwl-out2.cwl https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/empty.json

        

        ``cwltool`` can use `Singularity <http://singularity.lbl.gov/>`_ as a Docker container runtime, an experimental feature.

        Singularity will run software containers specified in ``DockerRequirement`` and therefore works with Docker images only,

        native Singularity images are not supported.

        To use Singularity as the Docker container runtime, provide ``--singularity`` command line option to ``cwltool``.

        

        

        .. code:: bash

        

          cwltool --singularity https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/master/v1.0/v1.0/v1.0/cat3-tool-mediumcut.cwl https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/cat-job.json

        

        Tool or workflow loading from remote or local locations

        -------------------------------------------------------

README.rst

+10 −0
Original line number Diff line number Diff line
@@ -139,6 +139,16 @@ or 


  cwltool --user-space-docker-cmd=dx-docker https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/master/v1.0/v1.0/test-cwl-out2.cwl https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/empty.json



``cwltool`` can use `Singularity <http://singularity.lbl.gov/>`_ as a Docker container runtime, an experimental feature.

Singularity will run software containers specified in ``DockerRequirement`` and therefore works with Docker images only,

native Singularity images are not supported.

To use Singularity as the Docker container runtime, provide ``--singularity`` command line option to ``cwltool``.





.. code:: bash



  cwltool --singularity https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/master/v1.0/v1.0/v1.0/cat3-tool-mediumcut.cwl https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/cat-job.json



Tool or workflow loading from remote or local locations

-------------------------------------------------------

cwltool.egg-info/PKG-INFO

+11 −1
Original line number Diff line number Diff line 
Metadata-Version: 1.1

Name: cwltool

Version: 1.0.20180211183944

Version: 1.0.20180225105849

Summary: Common workflow language reference implementation

Home-page: https://github.com/common-workflow-language/cwltool

Author: Common workflow language working group
@@ -149,6 +149,16 @@ Description: ================================================================== 
        

          cwltool --user-space-docker-cmd=dx-docker https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/master/v1.0/v1.0/test-cwl-out2.cwl https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/empty.json

        

        ``cwltool`` can use `Singularity <http://singularity.lbl.gov/>`_ as a Docker container runtime, an experimental feature.

        Singularity will run software containers specified in ``DockerRequirement`` and therefore works with Docker images only,

        native Singularity images are not supported.

        To use Singularity as the Docker container runtime, provide ``--singularity`` command line option to ``cwltool``.

        

        

        .. code:: bash

        

          cwltool --singularity https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/master/v1.0/v1.0/v1.0/cat3-tool-mediumcut.cwl https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/cat-job.json

        

        Tool or workflow loading from remote or local locations

        -------------------------------------------------------

cwltool.egg-info/SOURCES.txt

+13 −0
Original line number Diff line number Diff line
@@ -9,6 +9,7 @@ cwltool/__init__.py 
cwltool/__main__.py

cwltool/argparser.py

cwltool/builder.py

cwltool/command_line_tool.py

cwltool/cwlNodeEngine.js

cwltool/cwlNodeEngineJSConsole.js

cwltool/cwlrdf.py
@@ -16,12 +17,14 @@ cwltool/docker.py 
cwltool/docker_id.py

cwltool/draft2tool.py

cwltool/errors.py

cwltool/executors.py

cwltool/expression.py

cwltool/extensions.yml

cwltool/factory.py

cwltool/flatten.py

cwltool/job.py

cwltool/load_tool.py

cwltool/loghandler.py

cwltool/main.py

cwltool/mutation.py

cwltool/pack.py
@@ -29,6 +32,7 @@ cwltool/pathmapper.py 
cwltool/process.py

cwltool/resolver.py

cwltool/sandboxjs.py

cwltool/singularity.py

cwltool/software_requirements.py

cwltool/stdfsaccess.py

cwltool/update.py
@@ -173,9 +177,11 @@ tests/test_examples.py 
tests/test_ext.py

tests/test_fetch.py

tests/test_http_input.py

tests/test_iwdr.py

tests/test_js_sandbox.py

tests/test_override.py

tests/test_pack.py

tests/test_parallel.py

tests/test_pathmapper.py

tests/test_rdfprint.py

tests/test_relax_path_checks.py
@@ -193,6 +199,7 @@ tests/tmp1/tmp2/tmp3/.gitkeep 
tests/wf/badout1.cwl

tests/wf/badout2.cwl

tests/wf/badout3.cwl

tests/wf/cat-tool.cwl

tests/wf/cat.cwl

tests/wf/count-lines1-wf.cwl

tests/wf/default_path.cwl
@@ -204,12 +211,14 @@ tests/wf/formattest.cwl 
tests/wf/hello-workflow.cwl

tests/wf/hello.txt

tests/wf/hello_single_tool.cwl

tests/wf/iwdr-entry.cwl

tests/wf/js_output.cwl

tests/wf/js_output_workflow.cwl

tests/wf/listing_deep.cwl

tests/wf/listing_none.cwl

tests/wf/listing_shallow.cwl

tests/wf/listing_v1_0.cwl

tests/wf/malformed_outputs.cwl

tests/wf/missing_cwlVersion.cwl

tests/wf/mut.cwl

tests/wf/mut2.cwl
@@ -218,13 +227,17 @@ tests/wf/parseInt-tool.cwl 
tests/wf/revsort-job.json

tests/wf/revsort.cwl

tests/wf/revtool.cwl

tests/wf/scatter-job2.json

tests/wf/scatter-wf4.cwl

tests/wf/scatterfail.cwl

tests/wf/separate_without_prefix.cwl

tests/wf/sorttool.cwl

tests/wf/updatedir.cwl

tests/wf/updatedir_inplace.cwl

tests/wf/updateval.cwl

tests/wf/updateval.py

tests/wf/updateval_inplace.cwl

tests/wf/vf-concat.cwl

tests/wf/wc-job.json

tests/wf/wc-tool.cwl

tests/wf/wffail.cwl