Merge schema salad commit '7ea7dcf92e5782c4aca844f1e98d2d9550e07aae' …

…into v1.0-errata

v1.0/salad/.gitignore

@@ -2,3 +2,11 @@
 .eggs
 *.egg-info/
 *pyc
+
+build/
+dist/
+ruamel
+typeshed/2and3/ruamel/yaml
+# virtualenv 
+venv/
+.cache/

v1.0/salad/.travis.yml

@@ -1,20 +1,16 @@
+sudo: false
 language: python
-python: 2.7
+python:
+  - 2.7
+  - 3.3
+  - 3.4
+  - 3.5
+  - 3.6
 os:
   - linux
-env:
-  - TOX_ENV=py27-lint
-  - TOX_ENV=py27-unit
-  - TOX_ENV=py34-mypy
-#  - TOX_ENV=py34-lint
-#  - TOX_ENV=py33-lint
-#  - TOX_ENV=py34-unit
-#  - TOX_ENV=py33-unit
 
 install:
-  - pip install tox
-
-script: tox -e $TOX_ENV
-
+  - pip install tox-travis
+script: tox
 notifications:
   email: false

v1.0/salad/MANIFEST.in

@@ -1 +1,8 @@
-include gittaggers.py ez_setup.py
+include gittaggers.py Makefile
+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/metaschema/*
+global-exclude *~
+global-exclude *.pyc

v1.0/salad/Makefile

@@ -26,7 +26,9 @@ MODULE=schema_salad
 # `SHELL=bash` Will break Titus's laptop, so don't use BASH-isms like
 # `[[` conditional expressions.
 PYSOURCES=$(wildcard ${MODULE}/**.py tests/*.py) setup.py
-DEVPKGS=pep8 diff_cover autopep8 pylint coverage pep257
+DEVPKGS=pep8 diff_cover autopep8 pylint coverage pep257 pytest flake8
+COVBASE=coverage run --branch --append --source=${MODULE} \
+	--omit=schema_salad/tests/*
 
 VERSION=$(shell git describe --tags --dirty | sed s/v//)
 
@@ -46,7 +48,7 @@ install-dependencies:
 
 ## install     : install the ${MODULE} module and schema-salad-tool
 install: FORCE
-	./setup.py build install
+	pip install .
 
 ## dist        : create a module package for distribution
 dist: dist/${MODULE}-$(VERSION).tar.gz
@@ -103,37 +105,31 @@ diff_pylint_report: pylint_report.txt
 	diff-quality --violations=pylint pylint_report.txt
 
 .coverage: $(PYSOURCES)
-	coverage run --branch --source=${MODULE} setup.py test
-	coverage run --append --branch --source=${MODULE} \
-		-m schema_salad.main \
+	rm -f .coverage
+	$(COVBASE) setup.py test
+	$(COVBASE) -m schema_salad.main \
 		--print-jsonld-context schema_salad/metaschema/metaschema.yml \
 		> /dev/null
-	coverage run --append --branch --source=${MODULE} \
-		-m schema_salad.main \
+	$(COVBASE) -m schema_salad.main \
 		--print-rdfs schema_salad/metaschema/metaschema.yml \
 		> /dev/null
-	coverage run --append --branch --source=${MODULE} \
-		-m schema_salad.main \
+	$(COVBASE) -m schema_salad.main \
 		--print-avro schema_salad/metaschema/metaschema.yml \
 		> /dev/null
-	coverage run --append --branch --source=${MODULE} \
-		-m schema_salad.main \
+	$(COVBASE) -m schema_salad.main \
 		--print-rdf schema_salad/metaschema/metaschema.yml \
 		> /dev/null
-	coverage run --append --branch --source=${MODULE} \
-		-m schema_salad.main \
+	$(COVBASE) -m schema_salad.main \
 		--print-pre schema_salad/metaschema/metaschema.yml \
 		> /dev/null
-	coverage run --append --branch --source=${MODULE} \
-		-m schema_salad.main \
+	$(COVBASE) -m schema_salad.main \
 		--print-index schema_salad/metaschema/metaschema.yml \
 		> /dev/null
-	coverage run --append --branch --source=${MODULE} \
-		-m schema_salad.main \
+	$(COVBASE) -m schema_salad.main \
 		--print-metadata schema_salad/metaschema/metaschema.yml \
 		> /dev/null
-	coverage run --append --branch --source=${MODULE} \
-		-m schema_salad.makedoc schema_salad/metaschema/metaschema.yml \
+	$(COVBASE) -m schema_salad.makedoc \
+		schema_salad/metaschema/metaschema.yml \
 		> /dev/null
 
 coverage.xml: .coverage
@@ -169,17 +165,33 @@ list-author-emails:
 	@echo 'name, E-Mail Address'
 	@git log --format='%aN,%aE' | sort -u | grep -v 'root'
 
-mypy: ${PYSOURCES}
-	MYPYPATH=typeshed/2.7 mypy --py2 --disallow-untyped-calls schema_salad
+mypy2: ${PYSOURCES}
+	rm -Rf typeshed/2and3/ruamel/yaml
+	ln -s $(shell python -c 'from __future__ import print_function; import ruamel.yaml; import os.path; print(os.path.dirname(ruamel.yaml.__file__))') \
+		typeshed/2and3/ruamel/
+	MYPYPATH=$MYPYPATH:typeshed/2.7:typeshed/2and3 mypy --py2 --disallow-untyped-calls \
+		 --warn-redundant-casts \
+		 schema_salad
+
+mypy3: ${PYSOURCES}
+	rm -Rf typeshed/2and3/ruamel/yaml
+	ln -s $(shell python -c 'from __future__ import print_function; import ruamel.yaml; import os.path; print(os.path.dirname(ruamel.yaml.__file__))') \
+		typeshed/2and3/ruamel/
+	MYPYPATH=$MYPYPATH:typeshed/3:typeshed/2and3 mypy --disallow-untyped-calls \
+		 --warn-redundant-casts \
+		 schema_salad
 
 jenkins:
-	if ! test -d env ; then virtualenv env ; fi
+	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
 	if ! test -d env3 ; then virtualenv -p python3 env3 ; fi
 	. env3/bin/activate ; \
-	pip install -U mypy-lang; ${MAKE} mypy
+	pip install -U setuptools pip wheel ; \
+	${MAKE} install-dep ; \
+	pip install -U -r mypy_requirements.txt ; ${MAKE} mypy2
+	# pip install -U -r mypy_requirements.txt ; ${MAKE} mypy3
 
 FORCE:

v1.0/salad/README.rst

@@ -27,6 +27,13 @@ Usage
    $ python
    >>> import schema_salad
 
+To install from source::
+
+  git clone https://github.com/common-workflow-language/schema_salad 
+  cd schema_salad 
+  python setup.py install
+ 
+
 Documentation
 -------------
 

v1.0/salad/mypy.ini

@@ -0,0 +1,2 @@
+[mypy-ruamel.*]
+ignore_errors = True

v1.0/salad/mypy_requirements.txt

@@ -0,0 +1 @@
+mypy==0.511 ;  python_version>="3"

v1.0/salad/release-test.sh

@@ -0,0 +1,69 @@
+#!/bin/bash
+
+set -e
+set -x
+
+package=schema-salad
+module=schema_salad
+repo=https://github.com/common-workflow-language/schema_salad.git
+run_tests="py.test --pyarg ${module}"
+pipver=8.0.1 # minimum required version of pip
+setupver=20.10.1 # minimum required version of setuptools
+
+rm -Rf testenv? || /bin/true
+
+export HEAD=`git rev-parse HEAD`
+virtualenv testenv1
+virtualenv testenv2
+virtualenv testenv3
+virtualenv testenv4
+
+# First we test the head
+source testenv1/bin/activate
+rm testenv1/lib/python-wheels/setuptools* \
+	&& pip install --force-reinstall -U pip==${pipver} \
+        && pip install setuptools==${setupver} wheel
+make install-dependencies
+make test
+pip uninstall -y ${package} || true; pip uninstall -y ${package} || true; make install
+mkdir testenv1/not-${module}
+# if there is a subdir named '${module}' py.test will execute tests
+# there instead of the installed module's tests
+pushd testenv1/not-${module}; ../bin/${run_tests}; popd
+
+
+# Secondly we test via pip
+
+cd testenv2
+source bin/activate
+rm lib/python-wheels/setuptools* \
+	&& pip install --force-reinstall -U pip==${pipver} \
+        && pip install setuptools==${setupver} wheel
+pip install -e git+${repo}@${HEAD}#egg=${package}
+cd src/${package}
+make install-dependencies
+make dist
+make test
+cp dist/${package}*tar.gz ../../../testenv3/
+pip uninstall -y ${package} || true; pip uninstall -y ${package} || true; make install
+cd ../.. # no subdir named ${proj} here, safe for py.testing the installed module
+bin/${run_tests}
+
+# Is the distribution in testenv2 complete enough to build another
+# functional distribution?
+
+cd ../testenv3/
+source bin/activate
+rm lib/python-wheels/setuptools* \
+	&& pip install --force-reinstall -U pip==${pipver} \
+        && pip install setuptools==${setupver} wheel
+pip install ${package}*tar.gz
+pip install pytest
+mkdir out
+tar --extract --directory=out -z -f ${package}*.tar.gz
+cd out/${package}*
+make dist
+make test
+pip uninstall -y ${package} || true; pip uninstall -y ${package} || true; make install
+mkdir ../not-${module}
+pushd ../not-${module} ; ../../bin/${run_tests}; popd

v1.0/salad/requirements.txt

@@ -1,9 +1,10 @@
-requests
-ruamel.yaml
-rdflib >= 4.1.
-rdflib-jsonld >= 0.3.0
-mistune
-typing ; python_version>="2.7"
-avro ; python_version<"3"
-avro-python3 ; python_version>="3"
-
+typing==3.5.3
+avro-cwl ; python_version>="3"
+future ; python_version>="3"
+avro==1.8.1 ; python_version<"3"
+ruamel.yaml>=0.12.4, <0.15
+rdflib==4.2.2
+rdflib-jsonld==0.4.0
+mistune==0.7.3
+CacheControl==0.11.7
+lockfile==0.12.2

v1.0/salad/schema_salad/__init__.py

@@ -1,3 +1,4 @@
+from __future__ import absolute_import
 import logging
 import sys
 import typing

v1.0/salad/schema_salad/__main__.py

@@ -1,3 +1,4 @@
+from __future__ import absolute_import
 from . import main
 import sys
 import typing