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MANIFEST.in

-include gittaggers.py Makefile
+include gittaggers.py Makefile LICENSE.txt
+include schema_salad/avro/*
 include schema_salad/tests/*
 include schema_salad/tests/test_schema/*.md
 include schema_salad/tests/test_schema/*.yml
 include schema_salad/tests/test_schema/*.cwl
+include schema_salad/tests/foreign/*.cwl
+recursive-include schema_salad/tests/test_real_cwl *
 include schema_salad/metaschema/*
 include schema_salad/tests/docimp/*
 global-exclude *~

Makefile

@@ -15,25 +15,30 @@
 #
 # Contact: common-workflow-language@googlegroups.com
 
-# make pep8 to check for basic Python code compliance
+# make pycodestyle to check for basic Python code compliance
 # make autopep8 to fix most pep8 errors
 # make pylint to check Python code for enhanced compliance including naming
 #  and documentation
 # make coverage-report to check coverage of the python scripts by the tests
 
 MODULE=schema_salad
+PACKAGE=schema-salad
 
-# `SHELL=bash` Will break Titus's laptop, so don't use BASH-isms like
+# `SHELL=bash` doesn't work for some, so don't use BASH-isms like
 # `[[` conditional expressions.
 PYSOURCES=$(wildcard ${MODULE}/**.py tests/*.py) setup.py
-DEVPKGS=pep8 diff_cover autopep8 pylint coverage pep257 pytest flake8
+DEVPKGS=pycodestyle diff_cover autopep8 pylint coverage pep257 pytest flake8
 COVBASE=coverage run --branch --append --source=${MODULE} \
 	--omit=schema_salad/tests/*
 
-VERSION=$(shell git describe --tags --dirty | sed s/v//)
+# Updating the Major & Minor version below?
+# Don't forget to update setup.py as well
+VERSION=3.0.$(shell date +%Y%m%d%H%M%S --utc --date=`git log --first-parent \
+	--max-count=1 --format=format:%cI`)
 
 ## all         : default task
-all: ./setup.py develop
+all:
+	pip install -e .
 
 ## help        : print this help message and exit
 help: Makefile
@@ -54,7 +59,7 @@ 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
@@ -63,25 +68,34 @@ clean: FORCE
 	rm -Rf .coverage
 	rm -f diff-cover.html
 
-## pep8        : check Python code style
-pep8: $(PYSOURCES)
-	pep8 --exclude=_version.py  --show-source --show-pep8 $^ || true
+# Linting and code style related targets
+## sorting imports using isort: https://github.com/timothycrosley/isort
+sort_imports:
+	isort ${MODULE}/*.py ${MODULE}/tests/*.py setup.py
 
-pep8_report.txt: $(PYSOURCES)
-	pep8 --exclude=_version.py $^ > $@ || true
+pep8: pycodestyle
+## pycodestyle        : check Python code style
+pycodestyle: $(PYSOURCES)
+	pycodestyle --exclude=_version.py  --show-source --show-pep8 $^ || true
 
-diff_pep8_report: pep8_report.txt
-	diff-quality --violations=pep8 pep8_report.txt
+pep8_report.txt: pycodestyle_report.txt
+pycodestyle_report.txt: $(PYSOURCES)
+	pycodestyle --exclude=_version.py $^ > $@ || true
 
-## pep257      : check Python code style
-pep257: $(PYSOURCES)
-	pep257 --ignore=D100,D101,D102,D103 $^ || true
+diff_pep8_report: diff_pycodestyle_report
+diff_pycodestyle_report: pycodestyle_report.txt
+	diff-quality --violations=pycodestyle $^
 
-pep257_report.txt: $(PYSOURCES)
-	pep257 setup.py $^ > $@ 2>&1 || true
+pep257: pydocstyle
+## pydocstyle      : check Python code style
+pydocstyle: $(PYSOURCES)
+	pydocstyle --ignore=D100,D101,D102,D103 $^ || true
 
-diff_pep257_report: pep257_report.txt
-	diff-quality --violations=pep8 pep257_report.txt
+pydocstyle_report.txt: $(PYSOURCES)
+	pydocstyle setup.py $^ > $@ 2>&1 || true
+
+diff_pydocstyle_report: pydocstyle_report.txt
+	diff-quality --violations=pycodestyle $^
 
 ## autopep8    : fix most Python code indentation and formatting
 autopep8: $(PYSOURCES)
@@ -95,16 +109,16 @@ format: autopep8
 ## pylint      : run static code analysis on Python code
 pylint: $(PYSOURCES)
 	pylint --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" \
-                $^ || true
+                $^ -j$(nproc)|| true
 
 pylint_report.txt: ${PYSOURCES}
 	pylint --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" \
-		$^ > $@ || true
+		$^ -j$(nproc)> $@ || true
 
 diff_pylint_report: pylint_report.txt
 	diff-quality --violations=pylint pylint_report.txt
 
-.coverage: $(PYSOURCES)
+.coverage: $(PYSOURCES) all
 	rm -f .coverage
 	$(COVBASE) setup.py test
 	$(COVBASE) -m schema_salad.main \
@@ -181,12 +195,12 @@ mypy3: ${PYSOURCES}
 		 --warn-redundant-casts \
 		 schema_salad
 
-jenkins:
+jenkins: FORCE
 	rm -Rf env && virtualenv env
 	. env/bin/activate ; \
 	pip install -U setuptools pip wheel ; \
 	${MAKE} install-dep coverage.html coverage.xml pep257_report.txt \
-		sloccount.sc pep8_report.txt pylint_report.txt
+		sloccount.sc pycodestyle_report.txt pylint_report.txt
 	if ! test -d env3 ; then virtualenv -p python3 env3 ; fi
 	. env3/bin/activate ; \
 	pip install -U setuptools pip wheel ; \
@@ -194,4 +208,22 @@ jenkins:
 	pip install -U -r mypy_requirements.txt ; ${MAKE} mypy2
 	# pip install -U -r mypy_requirements.txt ; ${MAKE} mypy3
 
+release-test: FORCE
+	git diff-index --quiet HEAD -- || ( echo You have uncommited changes, please commit them and try again; false )
+	PYVER=2.7 ./release-test.sh
+	PYVER=3 ./release-test.sh
+
+release: release-test
+	. testenv2.7_2/bin/activate && \
+		testenv2.7_2/src/${PACKAGE}/setup.py sdist bdist_wheel
+	. testenv2.7_2/bin/activate && \
+		pip install twine && \
+		twine upload testenv2.7_2/src/${PACKAGE}/dist/* && \
+		git tag ${VERSION} && git push --tags
+
 FORCE:
+
+# Use this to print the value of a Makefile variable
+# Example `make print-VERSION`
+# From https://www.cmcrossroads.com/article/printing-value-makefile-variable
+print-%  : ; @echo $* = $($*)

PKG-INFO

 Metadata-Version: 1.1
 Name: schema-salad
-Version: 2.6.20171201034858
+Version: 3.0.20181129082112
 Summary: Schema Annotations for Linked Avro Data (SALAD)
-Home-page: https://github.com/common-workflow-language/common-workflow-language
+Home-page: https://github.com/common-workflow-language/schema_salad
 Author: Common workflow language working group
 Author-email: common-workflow-language@googlegroups.com
 License: Apache 2.0
-Download-URL: https://github.com/common-workflow-language/common-workflow-language
-Description-Content-Type: UNKNOWN
+Download-URL: https://github.com/common-workflow-language/schema_salad/releases
 Description: |Build Status| |Build status|
         
         .. |Build Status| image:: https://img.shields.io/travis/common-workflow-language/schema_salad/master.svg?label=unix%20build
            :target: https://travis-ci.org/common-workflow-language/schema_salad
         .. |Build status| image:: https://img.shields.io/appveyor/ci/mr-c/schema-salad/master.svg?label=windows%20build
            :target: https://ci.appveyor.com/project/mr-c/schema-salad/branch/master
+        .. |Code coverage| image:: https://codecov.io/gh/common-workflow-language/schema_salad/branch/master/graph/badge.svg
+           :target: https://codecov.io/gh/common-workflow-language/schema_salad
         
         Schema Salad
         ------------
         
-        Salad is a schema language for describing JSON or YAML structured linked data
-        documents.  Salad is based originally on JSON-LD_ and the Apache Avro_ data
-        serialization system.
-        
-        Salad schema describes rules for preprocessing, structural validation, and link
-        checking for documents described by a Salad schema. Salad features for rich
-        data modeling such as inheritance, template specialization, object identifiers,
-        object references, documentation generation, and transformation to RDF_. Salad
-        provides a bridge between document and record oriented data modeling and the
-        Semantic Web.
+        Salad is a schema language for describing JSON or YAML structured
+        linked data documents.  Salad schema describes rules for
+        preprocessing, structural validation, and hyperlink checking for
+        documents described by a Salad schema. Salad supports rich data
+        modeling with inheritance, template specialization, object
+        identifiers, object references, documentation generation, code
+        generation, and transformation to RDF_. Salad provides a bridge
+        between document and record oriented data modeling and the Semantic
+        Web.
         
         Usage
         -----
@@ -35,14 +35,6 @@ Description: |Build Status| |Build status|
         ::
         
            $ pip install schema_salad
-           $ schema-salad-tool
-           usage: schema-salad-tool [-h] [--rdf-serializer RDF_SERIALIZER]
-                                 [--print-jsonld-context | --print-doc | --print-rdfs | --print-avro | --print-rdf | --print-pre | --print-index | --print-metadata | --version]
-                                 [--strict | --non-strict]
-                                 [--verbose | --quiet | --debug]
-                                 schema [document]
-           $ python
-           >>> import schema_salad
         
         To install from source::
         
@@ -50,6 +42,44 @@ Description: |Build Status| |Build status|
           cd schema_salad
           python setup.py install
         
+        Commands
+        --------
+        
+        Schema salad can be used as a command line tool or imported as a Python module::
+        
+           $ schema-salad-tool
+           usage: schema-salad-tool [-h] [--rdf-serializer RDF_SERIALIZER]
+                                 [--print-jsonld-context | --print-rdfs | --print-avro | --print-rdf | --print-pre | --print-index | --print-metadata | --print-inheritance-dot | --print-fieldrefs-dot | --codegen language | --print-oneline]
+                                 [--strict | --non-strict] [--verbose | --quiet | --debug] [--version]
+                                 [schema] [document]
+        
+           $ python
+           >>> import schema_salad
+        
+        Validate a schema::
+        
+           $ schema-salad-tool myschema.yml
+        
+        Validate a document using a schema::
+        
+           $ schema-salad-tool myschema.yml mydocument.yml
+        
+        Get JSON-LD context::
+        
+           $ schema-salad-tool --print-jsonld-context myschema.yml mydocument.yml
+        
+        Convert a document to JSON-LD::
+        
+           $ schema-salad-tool --print-pre myschema.yml mydocument.yml > mydocument.jsonld
+        
+        Generate Python classes for loading/generating documents described by the schema::
+        
+           $ schema-salad-tool --codegen=python myschema.yml > myschema.py
+        
+        Display inheritance relationship between classes as a graphviz 'dot' file and render as SVG::
+        
+           $ schema-salad-tool --print-inheritance-dot myschema.yml | dot -Tsvg > myschema.svg
+        
         
         Documentation
         -------------
@@ -57,6 +87,7 @@ Description: |Build Status| |Build status|
         See the specification_ and the metaschema_ (salad schema for itself).  For an
         example application of Schema Salad see the Common Workflow Language_.
         
+        
         Rationale
         ---------
         
@@ -101,11 +132,13 @@ Description: |Build Status| |Build status|
 Platform: UNKNOWN
 Classifier: Environment :: Console
 Classifier: Intended Audience :: Science/Research
-Classifier: Operating System :: POSIX :: Linux
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: POSIX
 Classifier: Operating System :: MacOS :: MacOS X
-Classifier: Development Status :: 4 - Beta
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Development Status :: 5 - Production/Stable
 Classifier: Programming Language :: Python :: 2.7
-Classifier: Programming Language :: Python :: 3.3
 Classifier: Programming Language :: Python :: 3.4
 Classifier: Programming Language :: Python :: 3.5
 Classifier: Programming Language :: Python :: 3.6
+Classifier: Programming Language :: Python :: 3.7

README.rst

@@ -4,20 +4,21 @@
    :target: https://travis-ci.org/common-workflow-language/schema_salad
 .. |Build status| image:: https://img.shields.io/appveyor/ci/mr-c/schema-salad/master.svg?label=windows%20build
    :target: https://ci.appveyor.com/project/mr-c/schema-salad/branch/master
+.. |Code coverage| image:: https://codecov.io/gh/common-workflow-language/schema_salad/branch/master/graph/badge.svg
+   :target: https://codecov.io/gh/common-workflow-language/schema_salad
 
 Schema Salad
 ------------
 
-Salad is a schema language for describing JSON or YAML structured linked data
-documents.  Salad is based originally on JSON-LD_ and the Apache Avro_ data
-serialization system.
-
-Salad schema describes rules for preprocessing, structural validation, and link
-checking for documents described by a Salad schema. Salad features for rich
-data modeling such as inheritance, template specialization, object identifiers,
-object references, documentation generation, and transformation to RDF_. Salad
-provides a bridge between document and record oriented data modeling and the
-Semantic Web.
+Salad is a schema language for describing JSON or YAML structured
+linked data documents.  Salad schema describes rules for
+preprocessing, structural validation, and hyperlink checking for
+documents described by a Salad schema. Salad supports rich data
+modeling with inheritance, template specialization, object
+identifiers, object references, documentation generation, code
+generation, and transformation to RDF_. Salad provides a bridge
+between document and record oriented data modeling and the Semantic
+Web.
 
 Usage
 -----
@@ -25,14 +26,6 @@ Usage
 ::
 
    $ pip install schema_salad
-   $ schema-salad-tool
-   usage: schema-salad-tool [-h] [--rdf-serializer RDF_SERIALIZER]
-                         [--print-jsonld-context | --print-doc | --print-rdfs | --print-avro | --print-rdf | --print-pre | --print-index | --print-metadata | --version]
-                         [--strict | --non-strict]
-                         [--verbose | --quiet | --debug]
-                         schema [document]
-   $ python
-   >>> import schema_salad
 
 To install from source::
 
@@ -40,6 +33,44 @@ To install from source::
   cd schema_salad
   python setup.py install
 
+Commands
+--------
+
+Schema salad can be used as a command line tool or imported as a Python module::
+
+   $ schema-salad-tool
+   usage: schema-salad-tool [-h] [--rdf-serializer RDF_SERIALIZER]
+                         [--print-jsonld-context | --print-rdfs | --print-avro | --print-rdf | --print-pre | --print-index | --print-metadata | --print-inheritance-dot | --print-fieldrefs-dot | --codegen language | --print-oneline]
+                         [--strict | --non-strict] [--verbose | --quiet | --debug] [--version]
+                         [schema] [document]
+
+   $ python
+   >>> import schema_salad
+
+Validate a schema::
+
+   $ schema-salad-tool myschema.yml
+
+Validate a document using a schema::
+
+   $ schema-salad-tool myschema.yml mydocument.yml
+
+Get JSON-LD context::
+
+   $ schema-salad-tool --print-jsonld-context myschema.yml mydocument.yml
+
+Convert a document to JSON-LD::
+
+   $ schema-salad-tool --print-pre myschema.yml mydocument.yml > mydocument.jsonld
+
+Generate Python classes for loading/generating documents described by the schema::
+
+   $ schema-salad-tool --codegen=python myschema.yml > myschema.py
+
+Display inheritance relationship between classes as a graphviz 'dot' file and render as SVG::
+
+   $ schema-salad-tool --print-inheritance-dot myschema.yml | dot -Tsvg > myschema.svg
+
 
 Documentation
 -------------
@@ -47,6 +78,7 @@ Documentation
 See the specification_ and the metaschema_ (salad schema for itself).  For an
 example application of Schema Salad see the Common Workflow Language_.
 
+
 Rationale
 ---------
 

debian/changelog

+python-schema-salad (3.0.20181129082112-1) unstable; urgency=medium
+
+  * New upstream release
+  * Now a pure Python3 library
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Thu, 20 Dec 2018 05:37:41 -0800
+
 python-schema-salad (2.6.20171201034858-3) unstable; urgency=medium
 
   * Add missing python-avro dependency

debian/control

@@ -6,32 +6,32 @@ Testsuite: autopkgtest-pkg-python
 Priority: optional
 Build-Depends: debhelper (>= 10),
                dh-python,
-               python,
-               python-all,
-               python-setuptools,
-               python-mistune,
-               python-avro,
-               python-requests,
-               python-yaml,
-               python-rdflib-jsonld,
-               python-rdflib,
-               python-ruamel.yaml,
-               python-typing,
-               python-cachecontrol,
-               python-lockfile,
+               python3,
+               python3-all,
+               python3-setuptools,
+               python3-mistune,
+               python3-requests,
+               python3-yaml,
+               python3-rdflib-jsonld,
+               python3-rdflib,
+               python3-ruamel.yaml,
+               python3-cachecontrol,
+               python3-lockfile,
+               python3-typing-extensions,
                help2man
-Standards-Version: 4.1.3
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/python-schema-salad.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/python-schema-salad.git
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/python-schema-salad
+Vcs-Git: https://salsa.debian.org/med-team/python-schema-salad.git
 Homepage: http://www.commonwl.org
 
-Package: python-schema-salad
+Package: python3-schema-salad
 Architecture: all
-Depends: ${python:Depends},
+Depends: ${python3:Depends},
          ${misc:Depends},
-         python-avro,
          libjs-bootstrap
 Recommends: cwltool
+Breaks: cwltool (<< 1.0.20181128175059)
+Conflicts: python-schema-salad
 Description: Schema Annotations for Linked Avro Data (SALAD)
  Salad is a schema language for describing JSON or YAML structured linked data
  documents. Salad is based originally on JSON-LD and the Apache Avro data

debian/lintian-overrides

+package-contains-documentation-outside-usr-share-doc usr/lib/python3/dist-packages/schema_salad/*

debian/patches/allow_avro_gt_1.8.1.patch

-Description: Allow python-avro >= 1.8.1 (instead of == 1.8.1)
- Otherwise cwltool will fail to build in sid due to asking for exact
- version match
-Author: Andreas Tille <tille@debian.org>
-Last-Update: Fri, 22 Dec 2017 09:00:40 +0100
-
---- a/setup.py
-+++ b/setup.py
-@@ -38,7 +38,7 @@ install_requires = [
-     'six >= 1.8.0']
- 
- extras_require={
--    ':python_version<"3"': ['avro == 1.8.1'],
-+    ':python_version<"3"': ['avro >= 1.8.1'],
-     ':python_version>="3"': ['future', 'avro-cwl == 1.8.4']  # fork of avro for working with python3
- }
- 

debian/patches/avoid_privacy_breach.patch

-Author: Andreas Tille <tille@debian.org>
-Last-Update: Wed, 06 Dec 2017 16:38:46 +0100
-Description: Use locally installed bootstrap.min.css instead of risking
- privacy breach
-
---- a/schema_salad/metaschema/metaschema.html
-+++ b/schema_salad/metaschema/metaschema.html
-@@ -4,7 +4,7 @@
-     <head>
-     <meta charset="UTF-8">
-     <meta name="viewport" content="width=device-width, initial-scale=1.0">
--    <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css">
-+    <link rel="stylesheet" href="file:///usr/share/javascript/bootstrap/css/bootstrap.min.css">
-     <title>Semantic Annotations for Linked Avro Data (SALAD)</title>
-     <style>
-     :target {

debian/patches/exec_cwl

+From: Michael R. Crusoe <michael.crusoe@gmail.com>
+Subject: Add proper "#!" header to all CWL files
+--- schema-salad.orig/schema_salad/tests/foreign/foreign_prop1.cwl
++++ schema-salad/schema_salad/tests/foreign/foreign_prop1.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ doc: |
+   Foreign properties test.  This property is not part of the supplied
+   ontology.  If strict_foreign_properties is true, it should fail.  If
+@@ -7,4 +8,4 @@
+ inputs: []
+ outputs: []
+ baseCommand: echo
+-'edam:has_topic': abc
+\ No newline at end of file
++'edam:has_topic': abc
+--- schema-salad.orig/schema_salad/tests/foreign/foreign_prop2.cwl
++++ schema-salad/schema_salad/tests/foreign/foreign_prop2.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ doc: |
+   Foreign properties test.  If strict_foreign_properties is true, it
+   should fail.  If false, should pass no warnings.
+@@ -8,4 +9,4 @@
+ inputs: []
+ outputs: []
+ baseCommand: echo
+-'edam:has_topic': abc
+\ No newline at end of file
++'edam:has_topic': abc
+--- schema-salad.orig/schema_salad/tests/foreign/foreign_prop3.cwl
++++ schema-salad/schema_salad/tests/foreign/foreign_prop3.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ doc: |
+   Foreign properties test.  Should pass since the edam namespace is declared,
+   the ontology is imported, the property is valid in the ontology, and the
+@@ -11,4 +12,4 @@
+ inputs: []
+ outputs: []
+ baseCommand: echo
+-edam:has_topic: edam:topic_0003
+\ No newline at end of file
++edam:has_topic: edam:topic_0003
+--- schema-salad.orig/schema_salad/tests/foreign/foreign_prop4.cwl
++++ schema-salad/schema_salad/tests/foreign/foreign_prop4.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ doc: |
+   Foreign properties test.  This property is not part of the supplied
+   ontology.  If strict_foreign_properties is true, it should fail.  If
+@@ -11,4 +12,4 @@
+ inputs: []
+ outputs: []
+ baseCommand: echo
+-'edam:fake_property': abc
+\ No newline at end of file
++'edam:fake_property': abc
+--- schema-salad.orig/schema_salad/tests/foreign/foreign_prop5.cwl
++++ schema-salad/schema_salad/tests/foreign/foreign_prop5.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ doc: |
+   Foreign properties test.  The property is supposed to cross
+   reference another concept node, but that node doesn't exist.
+@@ -12,4 +13,4 @@
+ inputs: []
+ outputs: []
+ baseCommand: echo
+-edam:has_topic: abc
+\ No newline at end of file
++edam:has_topic: abc
+--- schema-salad.orig/schema_salad/tests/foreign/foreign_prop6.cwl
++++ schema-salad/schema_salad/tests/foreign/foreign_prop6.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ doc: |
+   Foreign properties test.  The property
+   references a mailto: URI
+@@ -10,4 +11,4 @@
+ inputs: []
+ outputs: []
+ baseCommand: echo
+-edam:has_topic: mailto:test@example.com
+\ No newline at end of file
++edam:has_topic: mailto:test@example.com
+--- schema-salad.orig/schema_salad/tests/foreign/foreign_prop7.cwl
++++ schema-salad/schema_salad/tests/foreign/foreign_prop7.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ doc: |
+   Foreign properties test.  The property
+   reference an unsupported mailto: URI
+@@ -10,4 +11,4 @@
+ inputs: []
+ outputs: []
+ baseCommand: echo
+-edam:has_topic: urn:blurb
+\ No newline at end of file
++edam:has_topic: urn:blurb
+--- schema-salad.orig/schema_salad/tests/test_schema/test1.cwl
++++ schema-salad/schema_salad/tests/test_schema/test1.cwl
+@@ -1 +1,2 @@
+-class: Workflow
+\ No newline at end of file
++#!/usr/bin/env cwl-runner
++class: Workflow
+--- schema-salad.orig/schema_salad/tests/test_schema/test10.cwl
++++ schema-salad/schema_salad/tests/test_schema/test10.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ class: Workflow
+ inputs:
+   foo: string
+@@ -7,4 +8,4 @@
+   step1:
+     scatterMethod: [record]
+     in: []
+-    out: [out]
+\ No newline at end of file
++    out: [out]
+--- schema-salad.orig/schema_salad/tests/test_schema/test11.cwl
++++ schema-salad/schema_salad/tests/test_schema/test11.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ class: Workflow
+ inputs:
+   foo: string
+@@ -7,4 +8,4 @@
+   step1:
+     run: blub.cwl
+     in: []
+-    out: [out]
+\ No newline at end of file
++    out: [out]
+--- schema-salad.orig/schema_salad/tests/test_schema/test12.cwl
++++ schema-salad/schema_salad/tests/test_schema/test12.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ cwlVersion: v1.0
+ class: CommandLineTool
+ baseCommand: echo
+--- schema-salad.orig/schema_salad/tests/test_schema/test13.cwl
++++ schema-salad/schema_salad/tests/test_schema/test13.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ cwlVersion: v1.0
+ class: Workflow
+ inputs:
+@@ -17,4 +18,4 @@
+       id: blah
+       class: CommandLineTool
+       inputs: []
+-      outputs: []
+\ No newline at end of file
++      outputs: []
+--- schema-salad.orig/schema_salad/tests/test_schema/test14.cwl
++++ schema-salad/schema_salad/tests/test_schema/test14.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ cwlVersion: v1.0
+ class: CommandLineTool
+ baseCommand: echo
+--- schema-salad.orig/schema_salad/tests/test_schema/test16.cwl
++++ schema-salad/schema_salad/tests/test_schema/test16.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ cwlVersion: v1.0
+ class: CommandLineTool
+ baseCommand: echo
+--- schema-salad.orig/schema_salad/tests/test_schema/test17.cwl
++++ schema-salad/schema_salad/tests/test_schema/test17.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ class: CommandLineTool
+ cwlVersion: v1.0
+ baseCommand: cowsay
+--- schema-salad.orig/schema_salad/tests/test_schema/test18.cwl
++++ schema-salad/schema_salad/tests/test_schema/test18.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ class: CommandLineTool
+ cwlVersion: v1.0
+ baseCommand: echo
+--- schema-salad.orig/schema_salad/tests/test_schema/test19.cwl
++++ schema-salad/schema_salad/tests/test_schema/test19.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ : aaa
+ cwlVersion: v1.0
+ class: CommandLineTool
+--- schema-salad.orig/schema_salad/tests/test_schema/test2.cwl
++++ schema-salad/schema_salad/tests/test_schema/test2.cwl
+@@ -1 +1,2 @@
+-class: xWorkflow
+\ No newline at end of file
++#!/usr/bin/env cwl-runner
++class: xWorkflow
+--- schema-salad.orig/schema_salad/tests/test_schema/test3.cwl
++++ schema-salad/schema_salad/tests/test_schema/test3.cwl
+@@ -1,6 +1,7 @@
++#!/usr/bin/env cwl-runner
+ class: Workflow
+ inputs:
+   foo: string
+ outputs:
+   bar: xstring
+-steps: []
+\ No newline at end of file
++steps: []
+--- schema-salad.orig/schema_salad/tests/test_schema/test4.cwl
++++ schema-salad/schema_salad/tests/test_schema/test4.cwl
+@@ -1,6 +1,7 @@
++#!/usr/bin/env cwl-runner
+ class: Workflow
+ inputs:
+   foo: string
+ outputs:
+   bar: 12
+-steps: []
+\ No newline at end of file
++steps: []
+--- schema-salad.orig/schema_salad/tests/test_schema/test5.cwl
++++ schema-salad/schema_salad/tests/test_schema/test5.cwl
+@@ -1,6 +1,7 @@
++#!/usr/bin/env cwl-runner
+ class: Workflow
+ inputs:
+   foo: string
+ outputs:
+   bar: string
+-steps: [12]
+\ No newline at end of file
++steps: [12]
+--- schema-salad.orig/schema_salad/tests/test_schema/test6.cwl
++++ schema-salad/schema_salad/tests/test_schema/test6.cwl
+@@ -1,5 +1,6 @@
++#!/usr/bin/env cwl-runner
+ inputs:
+   foo: string
+ outputs:
+   bar: string
+-steps: [12]
+\ No newline at end of file
++steps: [12]
+--- schema-salad.orig/schema_salad/tests/test_schema/test7.cwl
++++ schema-salad/schema_salad/tests/test_schema/test7.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ class: Workflow
+ inputs:
+   foo: string
+@@ -7,4 +8,4 @@
+   step1:
+     scatter_method: blub
+     in: []
+-    out: [out]
+\ No newline at end of file
++    out: [out]
+--- schema-salad.orig/schema_salad/tests/test_schema/test8.cwl
++++ schema-salad/schema_salad/tests/test_schema/test8.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ class: Workflow
+ inputs:
+   foo: string
+@@ -7,4 +8,4 @@
+   step1:
+     scatterMethod: abc
+     in: []
+-    out: [out]
+\ No newline at end of file
++    out: [out]
+--- schema-salad.orig/schema_salad/tests/test_schema/test9.cwl
++++ schema-salad/schema_salad/tests/test_schema/test9.cwl
+@@ -1,3 +1,4 @@
++#!/usr/bin/env cwl-runner
+ class: Workflow
+ inputs:
+   foo: string
+@@ -7,4 +8,4 @@
+   step1:
+     scatterMethod: 12
+     in: []
+-    out: [out]
+\ No newline at end of file
++    out: [out]

debian/patches/series

-avoid_privacy_breach.patch
-allow_avro_gt_1.8.1.patch
+exec_cwl

debian/rules

@@ -8,7 +8,7 @@ export PYBUILD_NAME=schema-salad
 export PYBUILD_DISABLE=test
 
 %:
-	dh $@ --with python2 --buildsystem=pybuild
+	dh $@ --with python3 --buildsystem=pybuild
 
 override_dh_auto_build:
 	dh_auto_build
@@ -16,8 +16,8 @@ override_dh_auto_build:
 		   --version-string=${DEB_VERSION_UPSTREAM} \
 		   --no-discard-stderr \
 		--name="Schema Annotations for Linked Avro Data (SALAD)" \
-		python2\ -m\ schema_salad > debian/schema-salad-tool.1
-	sed -i 's/python2 -m schema_salad/schema-salad-tool/g' \
+		python3\ -m\ schema_salad > debian/schema-salad-tool.1
+	sed -i 's/python3 -m schema_salad/schema-salad-tool/g' \
 		debian/schema-salad-tool.1
 	sed -i 's/__main__.py/schema-salad-tool/g' debian/schema-salad-tool.1
 	sed -i 's/PYTHON/SCHEMA-SALAD-TOOL/g' debian/schema-salad-tool.1
@@ -25,12 +25,17 @@ override_dh_auto_build:
 		   --version-string=${DEB_VERSION_UPSTREAM} \
 		   --no-discard-stderr \
 		--name="Schema Annotations for Linked Avro Data (SALAD)" \
-		python2\ -m\ schema_salad.makedoc > debian/schema-salad-doc.1
-	sed -i 's/python2 -m schema_salad.makedoc/schema-salad-doc/g' \
+		python3\ -m\ schema_salad.makedoc > debian/schema-salad-doc.1
+	sed -i 's/python3 -m schema_salad.makedoc/schema-salad-doc/g' \
 		debian/schema-salad-doc.1
 	sed -i 's/__main__.py/schema-salad-doc/g' debian/schema-salad-doc.1
 	sed -i 's/PYTHON/SCHEMA-SALAD-DOC/g' debian/schema-salad-doc.1
 	find . -name "*.coverage" -delete
 
+override_dh_auto_install:
+	dh_auto_install
+	find debian -name LICENSE -delete
+	find debian -name '*.cwl' -exec chmod a+x {} \;
+
 override_dh_auto_clean:
 	rm -f debian/*.1

gittaggers.py

-from setuptools.command.egg_info import egg_info
 import subprocess
 import time
 
+from setuptools.command.egg_info import egg_info
+
+
 class EggInfoFromGit(egg_info):
     """Tag the build with git commit timestamp.
 
@@ -21,3 +23,4 @@ class EggInfoFromGit(egg_info):
             except (subprocess.CalledProcessError, OSError):
                 pass
         return egg_info.tags(self)
+    vtags = property(tags)

schema_salad.egg-info/PKG-INFO

 Metadata-Version: 1.1
 Name: schema-salad
-Version: 2.6.20171201034858
+Version: 3.0.20181129082112
 Summary: Schema Annotations for Linked Avro Data (SALAD)
-Home-page: https://github.com/common-workflow-language/common-workflow-language
+Home-page: https://github.com/common-workflow-language/schema_salad
 Author: Common workflow language working group
 Author-email: common-workflow-language@googlegroups.com
 License: Apache 2.0
-Download-URL: https://github.com/common-workflow-language/common-workflow-language
-Description-Content-Type: UNKNOWN
+Download-URL: https://github.com/common-workflow-language/schema_salad/releases
 Description: |Build Status| |Build status|
         
         .. |Build Status| image:: https://img.shields.io/travis/common-workflow-language/schema_salad/master.svg?label=unix%20build
            :target: https://travis-ci.org/common-workflow-language/schema_salad
         .. |Build status| image:: https://img.shields.io/appveyor/ci/mr-c/schema-salad/master.svg?label=windows%20build
            :target: https://ci.appveyor.com/project/mr-c/schema-salad/branch/master
+        .. |Code coverage| image:: https://codecov.io/gh/common-workflow-language/schema_salad/branch/master/graph/badge.svg
+           :target: https://codecov.io/gh/common-workflow-language/schema_salad
         
         Schema Salad
         ------------
         
-        Salad is a schema language for describing JSON or YAML structured linked data
-        documents.  Salad is based originally on JSON-LD_ and the Apache Avro_ data
-        serialization system.
-        
-        Salad schema describes rules for preprocessing, structural validation, and link
-        checking for documents described by a Salad schema. Salad features for rich
-        data modeling such as inheritance, template specialization, object identifiers,
-        object references, documentation generation, and transformation to RDF_. Salad
-        provides a bridge between document and record oriented data modeling and the
-        Semantic Web.
+        Salad is a schema language for describing JSON or YAML structured
+        linked data documents.  Salad schema describes rules for
+        preprocessing, structural validation, and hyperlink checking for
+        documents described by a Salad schema. Salad supports rich data
+        modeling with inheritance, template specialization, object
+        identifiers, object references, documentation generation, code
+        generation, and transformation to RDF_. Salad provides a bridge
+        between document and record oriented data modeling and the Semantic
+        Web.
         
         Usage
         -----
@@ -35,14 +35,6 @@ Description: |Build Status| |Build status|
         ::
         
            $ pip install schema_salad
-           $ schema-salad-tool
-           usage: schema-salad-tool [-h] [--rdf-serializer RDF_SERIALIZER]
-                                 [--print-jsonld-context | --print-doc | --print-rdfs | --print-avro | --print-rdf | --print-pre | --print-index | --print-metadata | --version]
-                                 [--strict | --non-strict]
-                                 [--verbose | --quiet | --debug]
-                                 schema [document]
-           $ python
-           >>> import schema_salad
         
         To install from source::
         
@@ -50,6 +42,44 @@ Description: |Build Status| |Build status|
           cd schema_salad
           python setup.py install
         
+        Commands
+        --------
+        
+        Schema salad can be used as a command line tool or imported as a Python module::
+        
+           $ schema-salad-tool
+           usage: schema-salad-tool [-h] [--rdf-serializer RDF_SERIALIZER]
+                                 [--print-jsonld-context | --print-rdfs | --print-avro | --print-rdf | --print-pre | --print-index | --print-metadata | --print-inheritance-dot | --print-fieldrefs-dot | --codegen language | --print-oneline]
+                                 [--strict | --non-strict] [--verbose | --quiet | --debug] [--version]
+                                 [schema] [document]
+        
+           $ python
+           >>> import schema_salad
+        
+        Validate a schema::
+        
+           $ schema-salad-tool myschema.yml
+        
+        Validate a document using a schema::
+        
+           $ schema-salad-tool myschema.yml mydocument.yml
+        
+        Get JSON-LD context::
+        
+           $ schema-salad-tool --print-jsonld-context myschema.yml mydocument.yml
+        
+        Convert a document to JSON-LD::
+        
+           $ schema-salad-tool --print-pre myschema.yml mydocument.yml > mydocument.jsonld
+        
+        Generate Python classes for loading/generating documents described by the schema::
+        
+           $ schema-salad-tool --codegen=python myschema.yml > myschema.py
+        
+        Display inheritance relationship between classes as a graphviz 'dot' file and render as SVG::
+        
+           $ schema-salad-tool --print-inheritance-dot myschema.yml | dot -Tsvg > myschema.svg
+        
         
         Documentation
         -------------
@@ -57,6 +87,7 @@ Description: |Build Status| |Build status|
         See the specification_ and the metaschema_ (salad schema for itself).  For an
         example application of Schema Salad see the Common Workflow Language_.
         
+        
         Rationale
         ---------
         
@@ -101,11 +132,13 @@ Description: |Build Status| |Build status|
 Platform: UNKNOWN
 Classifier: Environment :: Console
 Classifier: Intended Audience :: Science/Research
-Classifier: Operating System :: POSIX :: Linux
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: POSIX
 Classifier: Operating System :: MacOS :: MacOS X
-Classifier: Development Status :: 4 - Beta
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Development Status :: 5 - Production/Stable
 Classifier: Programming Language :: Python :: 2.7
-Classifier: Programming Language :: Python :: 3.3
 Classifier: Programming Language :: Python :: 3.4
 Classifier: Programming Language :: Python :: 3.5
 Classifier: Programming Language :: Python :: 3.6
+Classifier: Programming Language :: Python :: 3.7

schema_salad.egg-info/SOURCES.txt

+LICENSE.txt
 MANIFEST.in
 Makefile
 README.rst
@@ -24,10 +25,13 @@ schema_salad.egg-info/PKG-INFO
 schema_salad.egg-info/SOURCES.txt
 schema_salad.egg-info/dependency_links.txt
 schema_salad.egg-info/entry_points.txt
-schema_salad.egg-info/pbr.json
 schema_salad.egg-info/requires.txt
 schema_salad.egg-info/top_level.txt
 schema_salad.egg-info/zip-safe
+schema_salad/avro/LICENSE
+schema_salad/avro/NOTICE
+schema_salad/avro/__init__.py
+schema_salad/avro/schema.py
 schema_salad/metaschema/field_name.yml
 schema_salad/metaschema/field_name_proc.yml
 schema_salad/metaschema/field_name_schema.yml
@@ -45,9 +49,7 @@ schema_salad/metaschema/map_res.yml
 schema_salad/metaschema/map_res_proc.yml
 schema_salad/metaschema/map_res_schema.yml
 schema_salad/metaschema/map_res_src.yml
-schema_salad/metaschema/metaschema.html
 schema_salad/metaschema/metaschema.yml
-schema_salad/metaschema/metaschema2.yml
 schema_salad/metaschema/metaschema_base.yml
 schema_salad/metaschema/salad.md
 schema_salad/metaschema/typedsl_res.yml
@@ -58,14 +60,11 @@ schema_salad/metaschema/vocab_res.yml
 schema_salad/metaschema/vocab_res_proc.yml
 schema_salad/metaschema/vocab_res_schema.yml
 schema_salad/metaschema/vocab_res_src.yml
-schema_salad/tests/#cg_metaschema.py#
-schema_salad/tests/.coverage
 schema_salad/tests/EDAM.owl
 schema_salad/tests/Process.yml
 schema_salad/tests/__init__.py
+schema_salad/tests/bad_schema.yml
 schema_salad/tests/cwl-pre.yml
-schema_salad/tests/df
-schema_salad/tests/df2
 schema_salad/tests/frag.yml
 schema_salad/tests/hello.txt
 schema_salad/tests/hellofield.yml
@@ -78,9 +77,10 @@ schema_salad/tests/test_cli_args.py
 schema_salad/tests/test_errors.py
 schema_salad/tests/test_examples.py
 schema_salad/tests/test_fetch.py
+schema_salad/tests/test_fp.py
 schema_salad/tests/test_print_oneline.py
+schema_salad/tests/test_real_cwl.py
 schema_salad/tests/test_ref_resolver.py
-schema_salad/tests/test_validate.pyx
 schema_salad/tests/util.py
 schema_salad/tests/docimp/d1.yml
 schema_salad/tests/docimp/d2.md
@@ -88,6 +88,20 @@ schema_salad/tests/docimp/d3.yml
 schema_salad/tests/docimp/d4.yml
 schema_salad/tests/docimp/d5.md
 schema_salad/tests/docimp/dpre.json
+schema_salad/tests/foreign/foreign_prop1.cwl
+schema_salad/tests/foreign/foreign_prop2.cwl
+schema_salad/tests/foreign/foreign_prop3.cwl
+schema_salad/tests/foreign/foreign_prop4.cwl
+schema_salad/tests/foreign/foreign_prop5.cwl
+schema_salad/tests/foreign/foreign_prop6.cwl
+schema_salad/tests/foreign/foreign_prop7.cwl
+schema_salad/tests/test_real_cwl/ICGC-TCGA-PanCancer/PreprocessedFilesType.yaml
+schema_salad/tests/test_real_cwl/ICGC-TCGA-PanCancer/preprocess_util.js
+schema_salad/tests/test_real_cwl/ICGC-TCGA-PanCancer/preprocess_vcf.cwl
+schema_salad/tests/test_real_cwl/ICGC-TCGA-PanCancer/vcf_merge_util.js
+schema_salad/tests/test_real_cwl/h3agatk/GATK-Sub-Workflow-h3abionet-snp.cwl
+schema_salad/tests/test_real_cwl/h3agatk/GATK-complete-WES-Workflow-h3abionet.cwl
+schema_salad/tests/test_real_cwl/topmed/topmed_variant_calling_pipeline.cwl
 schema_salad/tests/test_schema/CommandLineTool.yml
 schema_salad/tests/test_schema/CommonWorkflowLanguage.yml
 schema_salad/tests/test_schema/Process.yml

schema_salad.egg-info/pbr.json

-{"is_release": false, "git_version": "c7f3140"}
\ No newline at end of file

schema_salad.egg-info/requires.txt

 setuptools
 requests>=1.0
-ruamel.yaml<0.15,>=0.12.4
+ruamel.yaml<0.16,>=0.12.4
 rdflib<4.3.0,>=4.2.2
 rdflib-jsonld<0.5.0,>=0.3.0
-mistune<0.8,>=0.7.3
-typing>=3.5.3
+mistune<0.9,>=0.8.1
 CacheControl<0.12,>=0.11.7
 lockfile>=0.9
 six>=1.8.0
+typing-extensions
 
-[:python_version<"3"]
-avro==1.8.1
-
-[:python_version>="3"]
-future
-avro-cwl==1.8.4
+[:python_version<"3.7"]
+typing>=3.6.4

schema_salad/__init__.py

@@ -3,6 +3,7 @@ import logging
 import os
 import sys
 import typing
+import threading
 
 import six
 
@@ -12,21 +13,3 @@ __author__ = 'peter.amstutz@curoverse.com'
 _logger = logging.getLogger("salad")
 _logger.addHandler(logging.StreamHandler())
 _logger.setLevel(logging.INFO)
-
-if six.PY3:
-
-    if onWindows:
-        # create '/tmp' folder if not present
-        # required by autotranslate module
-        # TODO: remove when https://github.com/PythonCharmers/python-future/issues/295
-        # is fixed
-        if not os.path.exists("/tmp"):
-            try:
-                os.makedirs("/tmp")
-            except OSError as exception:
-                _logger.error(u"Cannot create '\\tmp' folder in root needed for",
-                              "'cwltool' Python 3 installation.")
-                exit(1)
-
-    from past import autotranslate  # type: ignore
-    autotranslate(['avro', 'avro.schema'])

schema_salad/__main__.py

+"""Default entry point for the schema-salad module."""
 from __future__ import absolute_import
-from . import main
+
 import sys
-import typing
+
+from . import main
 
 sys.exit(main.main())