Commit 91ec6ace authored by Michael R. Crusoe's avatar Michael R. Crusoe 🏳️‍🌈
Browse files

New upstream version 1.0.20190915164430+dfsg

parent b1cb10cc

Makefile

+4 −10
Original line number Diff line number Diff line
@@ -34,12 +34,6 @@ VERSION=1.0.$(shell TZ=UTC git log --first-parent --max-count=1 \ 
	--format=format:%cd --date=format-local:%Y%m%d%H%M%S)

mkfile_dir := $(dir $(abspath $(lastword $(MAKEFILE_LIST))))

UNAME_S=$(shell uname -s)

ifeq ($(UNAME_S),Linux)

	nproc=$(shell nproc)

endif

ifeq ($(UNAME_S),Darwin)

	nproc=$(shell sysctl -n hw.physicalcpu)

endif



## all         : default task

all:
@@ -120,11 +114,11 @@ format: autopep8 
## pylint      : run static code analysis on Python code

pylint: $(PYSOURCES)

	pylint --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" \

                $^ -j$(nproc)|| true

                $^ -j0|| true



pylint_report.txt: ${PYSOURCES}

	pylint --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" \

		$^ -j$(nproc)> $@ || true

		$^ -j0> $@ || true



diff_pylint_report: pylint_report.txt

	diff-quality --violations=pylint pylint_report.txt
@@ -154,11 +148,11 @@ diff-cover.html: coverage.xml 


## test        : run the ${MODULE} test suite

test: $(pysources)

	python setup.py test --addopts "-n$(nproc) --dist=loadfile"

	python setup.py test --addopts "-n auto --dist=loadfile"



## testcov     : run the ${MODULE} test suite and collect coverage

testcov: $(pysources)

	python setup.py test --addopts "--cov cwltool -n$(nproc) --dist=loadfile"

	python setup.py test --addopts "--cov cwltool -n auto --dist=loadfile"



sloccount.sc: ${PYSOURCES} Makefile

	sloccount --duplicates --wide --details $^ > $@

PKG-INFO

+54 −10
Original line number Diff line number Diff line 
Metadata-Version: 2.1

Name: cwltool

Version: 1.0.20190815141648

Version: 1.0.20190915164430

Summary: Common workflow language reference implementation

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

Author: Common workflow language working group
@@ -13,6 +13,10 @@ Description: ================================================================== 
        

        CWL conformance tests: |Conformance Status| |Linux Status| |Windows Status| |Coverage Status| |Downloads|

        

        |CommandLineTool Support| |DockerRequirement Support| |EnvVarRequirement Support| |ExpressionTool Support| 

        |InitialWorkDirRequirement Support| |InlineJavascriptRequirement Support| |MultipleInputRequirement Support| |Core Support|

        |ResourceRequirement Support| |ScatterRequirement Support| |SchemaDefRequirement Support| |ShellCommandequirement Support|

        |StepInputRequirement Support| |SubWorkflowRequirement Support| |Workflow Support|

        

        .. |Conformance Status| image:: https://ci.commonwl.org/buildStatus/icon?job=cwltool-conformance

           :target: https://ci.commonwl.org/job/cwltool-conformance/
@@ -29,6 +33,52 @@ Description: ================================================================== 
        .. |Downloads| image:: https://pepy.tech/badge/cwltool/month

           :target: https://pepy.tech/project/cwltool

        

        .. |CommandLineTool Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/command_line_tool.json

           :target: https://ci.commonwl.org/job/cwltool-conformance/

        

        .. |DockerRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/docker.json

           :target: https://ci.commonwl.org/job/cwltool-conformance/

        

        .. |EnvVarRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/env_var.json

           :target: https://ci.commonwl.org/job/cwltool-conformance/

        

        .. |ExpressionTool Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/expression_tool.json

           :target: https://ci.commonwl.org/job/cwltool-conformance/

        

        .. |InitialWorkDirRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/initial_work_dir.json

           :target: https://ci.commonwl.org/job/cwltool-conformance/

        

        .. |InlineJavascriptRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/inline_javascript.json

           :target: https://ci.commonwl.org/job/cwltool-conformance/

        

        .. |MultipleInputRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/multiple_input.json

           :target: https://ci.commonwl.org/job/cwltool-conformance/

        

        .. |Core Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/required.json

           :target: https://ci.commonwl.org/job/cwltool-conformance/

        

        .. |ResourceRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/resource.json

           :target: https://ci.commonwl.org/job/cwltool-conformance/

        

        .. |ScatterRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/scatter.json

           :target: https://ci.commonwl.org/job/cwltool-conformance/

        

        .. |SchemaDefRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/schema_def.json

           :target: https://ci.commonwl.org/job/cwltool-conformance/

        

        .. |ShellCommandequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/shell_command.json

           :target: https://ci.commonwl.org/job/cwltool-conformance/

        

        .. |StepInputRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/step_input.json

           :target: https://ci.commonwl.org/job/cwltool-conformance/

        

        .. |SubWorkflowRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/subworkflow.json

           :target: https://ci.commonwl.org/job/cwltool-conformance/

        

        .. |Workflow Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/workflow.json

           :target: https://ci.commonwl.org/job/cwltool-conformance/

        

        

        This is the reference implementation of the Common Workflow Language.  It is

        intended to be feature complete and provide comprehensive validation of CWL

        files as well as provide other tools related to working with CWL.
@@ -53,15 +103,9 @@ Description: ================================================================== 
        

          apt-get install cwltool

        

        For MacOS X, other UNIXes or Windows packages prepared by the Bioconda project. Please follow instructions of Bioconda (https://bioconda.github.io/) for its installation, then perform: 

        

        .. code:: bash

        

          conda install -c bioconda cwltool 

        

        Under the hood, conda setups virtual environments before installing `cwltool` to

        avoid conflicting versions of the same library. When installing cwltool directly,

        it is recommended to do the same manually:

        Otherwise, to

        avoid conflicting versions of the same library,

        it is recommended to do the following:

        

        .. code:: bash

README.rst

+53 −9
Original line number Diff line number Diff line
@@ -4,6 +4,10 @@ Common Workflow Language tool description reference implementation 


CWL conformance tests: |Conformance Status| |Linux Status| |Windows Status| |Coverage Status| |Downloads|



|CommandLineTool Support| |DockerRequirement Support| |EnvVarRequirement Support| |ExpressionTool Support| 

|InitialWorkDirRequirement Support| |InlineJavascriptRequirement Support| |MultipleInputRequirement Support| |Core Support|

|ResourceRequirement Support| |ScatterRequirement Support| |SchemaDefRequirement Support| |ShellCommandequirement Support|

|StepInputRequirement Support| |SubWorkflowRequirement Support| |Workflow Support|



.. |Conformance Status| image:: https://ci.commonwl.org/buildStatus/icon?job=cwltool-conformance

   :target: https://ci.commonwl.org/job/cwltool-conformance/
@@ -20,6 +24,52 @@ CWL conformance tests: |Conformance Status| |Linux Status| |Windows Status| |Cov 
.. |Downloads| image:: https://pepy.tech/badge/cwltool/month

   :target: https://pepy.tech/project/cwltool



.. |CommandLineTool Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/command_line_tool.json

   :target: https://ci.commonwl.org/job/cwltool-conformance/



.. |DockerRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/docker.json

   :target: https://ci.commonwl.org/job/cwltool-conformance/



.. |EnvVarRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/env_var.json

   :target: https://ci.commonwl.org/job/cwltool-conformance/



.. |ExpressionTool Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/expression_tool.json

   :target: https://ci.commonwl.org/job/cwltool-conformance/



.. |InitialWorkDirRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/initial_work_dir.json

   :target: https://ci.commonwl.org/job/cwltool-conformance/



.. |InlineJavascriptRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/inline_javascript.json

   :target: https://ci.commonwl.org/job/cwltool-conformance/



.. |MultipleInputRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/multiple_input.json

   :target: https://ci.commonwl.org/job/cwltool-conformance/



.. |Core Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/required.json

   :target: https://ci.commonwl.org/job/cwltool-conformance/



.. |ResourceRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/resource.json

   :target: https://ci.commonwl.org/job/cwltool-conformance/



.. |ScatterRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/scatter.json

   :target: https://ci.commonwl.org/job/cwltool-conformance/



.. |SchemaDefRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/schema_def.json

   :target: https://ci.commonwl.org/job/cwltool-conformance/



.. |ShellCommandequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/shell_command.json

   :target: https://ci.commonwl.org/job/cwltool-conformance/



.. |StepInputRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/step_input.json

   :target: https://ci.commonwl.org/job/cwltool-conformance/



.. |SubWorkflowRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/subworkflow.json

   :target: https://ci.commonwl.org/job/cwltool-conformance/



.. |Workflow Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/workflow.json

   :target: https://ci.commonwl.org/job/cwltool-conformance/





This is the reference implementation of the Common Workflow Language.  It is

intended to be feature complete and provide comprehensive validation of CWL

files as well as provide other tools related to working with CWL.
@@ -44,15 +94,9 @@ Your operating system may offer cwltool directly. For [Debian](https://tracker.d 


  apt-get install cwltool



For MacOS X, other UNIXes or Windows packages prepared by the Bioconda project. Please follow instructions of Bioconda (https://bioconda.github.io/) for its installation, then perform: 



.. code:: bash



  conda install -c bioconda cwltool 



Under the hood, conda setups virtual environments before installing `cwltool` to

avoid conflicting versions of the same library. When installing cwltool directly,

it is recommended to do the same manually:

Otherwise, to

avoid conflicting versions of the same library,

it is recommended to do the following:



.. code:: bash

cwltool.egg-info/PKG-INFO

+54 −10
Original line number Diff line number Diff line 
Metadata-Version: 2.1

Name: cwltool

Version: 1.0.20190815141648

Version: 1.0.20190915164430

Summary: Common workflow language reference implementation

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

Author: Common workflow language working group
@@ -13,6 +13,10 @@ Description: ================================================================== 
        

        CWL conformance tests: |Conformance Status| |Linux Status| |Windows Status| |Coverage Status| |Downloads|

        

        |CommandLineTool Support| |DockerRequirement Support| |EnvVarRequirement Support| |ExpressionTool Support| 

        |InitialWorkDirRequirement Support| |InlineJavascriptRequirement Support| |MultipleInputRequirement Support| |Core Support|

        |ResourceRequirement Support| |ScatterRequirement Support| |SchemaDefRequirement Support| |ShellCommandequirement Support|

        |StepInputRequirement Support| |SubWorkflowRequirement Support| |Workflow Support|

        

        .. |Conformance Status| image:: https://ci.commonwl.org/buildStatus/icon?job=cwltool-conformance

           :target: https://ci.commonwl.org/job/cwltool-conformance/
@@ -29,6 +33,52 @@ Description: ================================================================== 
        .. |Downloads| image:: https://pepy.tech/badge/cwltool/month

           :target: https://pepy.tech/project/cwltool

        

        .. |CommandLineTool Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/command_line_tool.json

           :target: https://ci.commonwl.org/job/cwltool-conformance/

        

        .. |DockerRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/docker.json

           :target: https://ci.commonwl.org/job/cwltool-conformance/

        

        .. |EnvVarRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/env_var.json

           :target: https://ci.commonwl.org/job/cwltool-conformance/

        

        .. |ExpressionTool Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/expression_tool.json

           :target: https://ci.commonwl.org/job/cwltool-conformance/

        

        .. |InitialWorkDirRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/initial_work_dir.json

           :target: https://ci.commonwl.org/job/cwltool-conformance/

        

        .. |InlineJavascriptRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/inline_javascript.json

           :target: https://ci.commonwl.org/job/cwltool-conformance/

        

        .. |MultipleInputRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/multiple_input.json

           :target: https://ci.commonwl.org/job/cwltool-conformance/

        

        .. |Core Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/required.json

           :target: https://ci.commonwl.org/job/cwltool-conformance/

        

        .. |ResourceRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/resource.json

           :target: https://ci.commonwl.org/job/cwltool-conformance/

        

        .. |ScatterRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/scatter.json

           :target: https://ci.commonwl.org/job/cwltool-conformance/

        

        .. |SchemaDefRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/schema_def.json

           :target: https://ci.commonwl.org/job/cwltool-conformance/

        

        .. |ShellCommandequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/shell_command.json

           :target: https://ci.commonwl.org/job/cwltool-conformance/

        

        .. |StepInputRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/step_input.json

           :target: https://ci.commonwl.org/job/cwltool-conformance/

        

        .. |SubWorkflowRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/subworkflow.json

           :target: https://ci.commonwl.org/job/cwltool-conformance/

        

        .. |Workflow Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/workflow.json

           :target: https://ci.commonwl.org/job/cwltool-conformance/

        

        

        This is the reference implementation of the Common Workflow Language.  It is

        intended to be feature complete and provide comprehensive validation of CWL

        files as well as provide other tools related to working with CWL.
@@ -53,15 +103,9 @@ Description: ================================================================== 
        

          apt-get install cwltool

        

        For MacOS X, other UNIXes or Windows packages prepared by the Bioconda project. Please follow instructions of Bioconda (https://bioconda.github.io/) for its installation, then perform: 

        

        .. code:: bash

        

          conda install -c bioconda cwltool 

        

        Under the hood, conda setups virtual environments before installing `cwltool` to

        avoid conflicting versions of the same library. When installing cwltool directly,

        it is recommended to do the same manually:

        Otherwise, to

        avoid conflicting versions of the same library,

        it is recommended to do the following:

        

        .. code:: bash

cwltool.egg-info/SOURCES.txt

+2 −0
Original line number Diff line number Diff line
@@ -178,6 +178,7 @@ cwltool/schemas/v1.1/salad/schema_salad/metaschema/vocab_res_src.yml 
tests/2.fasta

tests/2.fastq

tests/__init__.py

tests/arg-empty-prefix-separate-false.cwl

tests/bundle-context.jsonld

tests/debian_image_id.cwl

tests/echo-job.yaml
@@ -186,6 +187,7 @@ tests/echo-position-expr.cwl 
tests/echo.cwl

tests/echo_broken_outputs.cwl

tests/env.cwl

tests/env2.cwl

tests/listing-job.yml

tests/listing2-job.yml

tests/non_portable.cwl