Merge branch 'master' into 13823-bionic

refs #13823

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

diff --cc build/build.list
index b1253c9b6c7ed54f931a86255fbacec641785bf8,5196e9c64d47a70601e1c816ce81abc7b1ced7ef..f2197ecdbb62e2795bf176c650871812602673a0
--- 1/build/build.list
--- 2/build/build.list
+++ b/build/build.list
@@@ -8,31 -8,31 +8,31 @@@ debian8,debian9,ubuntu1404,ubuntu1604,u
  debian8,debian9,ubuntu1404,centos7|oauth2client|1.5.2|2|python|all
  debian8,debian9,ubuntu1404,centos7|pyasn1|0.1.7|2|python|all
  debian8,debian9,ubuntu1404,centos7|pyasn1-modules|0.0.5|2|python|all
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|rsa|3.4.2|2|python|all
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|uritemplate|3.0.0|2|python|all
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|httplib2|0.9.2|3|python|all
 -debian8,debian9,centos7|ws4py|0.3.5|2|python|all
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|rsa|3.4.2|2|python|all
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|uritemplate|3.0.0|2|python|all
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|httplib2|0.9.2|3|python|all
 +debian8,debian9,centos7|ws4py|0.4.2|2|python|all
  debian8,debian9,centos7|pykka|1.2.1|2|python|all
  debian8,debian9,ubuntu1404,centos7|six|1.10.0|2|python|all
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|ciso8601|1.0.6|3|python|amd64
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|ciso8601|1.0.6|3|python|amd64
  debian8,debian9,centos7|pycrypto|2.6.1|3|python|amd64
 -debian8,debian9,ubuntu1404,ubuntu1604|backports.ssl_match_hostname|3.5.0.1|2|python|all
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|llfuse|1.2|3|python|amd64
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804|backports.ssl_match_hostname|3.5.0.1|2|python|all
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|llfuse|1.2|3|python|amd64
  debian8,debian9,ubuntu1404,centos7|pycurl|7.19.5.3|3|python|amd64
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|pyyaml|3.12|2|python|amd64
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|rdflib|4.2.2|2|python|all
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|pyyaml|3.12|2|python|amd64
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|rdflib|4.2.2|2|python|all
  debian8,debian9,ubuntu1404,centos7|shellescape|3.4.1|2|python|all
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|mistune|0.7.3|2|python|all
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|typing|3.6.4|2|python|all
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|avro|1.8.1|2|python|all
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|mistune|0.7.3|2|python|all
- debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|typing|3.5.3.0|2|python|all
++debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|typing|3.6.4|2|python|all
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|avro|1.8.1|2|python|all
  debian8,debian9,ubuntu1404,centos7|ruamel.ordereddict|0.4.9|2|python|amd64
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|cachecontrol|0.11.7|2|python|all
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|pathlib2|2.3.2|2|python|all
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|scandir|1.7|2|python|all
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|docker-py|1.7.2|2|python3|all
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|cachecontrol|0.11.7|2|python|all
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|pathlib2|2.3.2|2|python|all
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|scandir|1.7|2|python|all
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|docker-py|1.7.2|2|python3|all
  debian8,debian9,centos7|six|1.10.0|2|python3|all
  debian8,debian9,ubuntu1404,centos7|requests|2.12.4|2|python3|all
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|websocket-client|0.37.0|2|python3|all
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|websocket-client|0.37.0|2|python3|all
  ubuntu1404|requests|2.4.3|2|python|all
  centos7|contextlib2|0.5.4|2|python|all
  centos7|isodate|0.5.4|2|python|all
@@@ -40,9 -40,11 +40,11 @@@ centos7|python-daemon|2.1.2|1|python|al
  centos7|pbr|0.11.1|2|python|all
  centos7|pyparsing|2.1.10|2|python|all
  centos7|keepalive|0.5|2|python|all
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|lockfile|0.12.2|2|python|all|--epoch 1
 -debian8,debian9,ubuntu1404,ubuntu1604,centos7|subprocess32|3.5.1|2|python|all
 -all|ruamel.yaml|0.14.12|2|python|amd64|--python-setup-py-arguments --single-version-externally-managed
+ centos7|networkx|1.11|0|python|all
+ centos7|psutil|5.0.1|0|python|all
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|lockfile|0.12.2|2|python|all|--epoch 1
 +debian8,debian9,ubuntu1404,ubuntu1604,ubuntu1804,centos7|subprocess32|3.5.1|2|python|all
 +centos7,debian8,debian9,ubuntu1404,ubuntu1604|ruamel.yaml|0.15.34|1|python|amd64|--python-setup-py-arguments --single-version-externally-managed
  all|cwltest|1.0.20180518074130|4|python|all|--depends 'python-futures >= 3.0.5' --depends 'python-subprocess32 >= 3.5.0'
  all|junit-xml|1.8|3|python|all
  all|rdflib-jsonld|0.4.0|2|python|all

diff --cc build/package-build-dockerfiles/Makefile
index b7f5aa5534eb45d4fc1ff419b80aaf60c464e042,f19f17fc0ebc1f432b022b874f68645b1da1d2ff..9dc536bf1eb919a7d334d3d18061db3dfd8c90d7
--- 1/build/package-build-dockerfiles/Makefile
--- 2/build/package-build-dockerfiles/Makefile
+++ b/build/package-build-dockerfiles/Makefile
@@@ -2,7 -2,7 +2,7 @@@
  #
  # SPDX-License-Identifier: AGPL-3.0
  
- all: centos7/generated debian8/generated debian9/generated ubuntu1204/generated ubuntu1404/generated ubuntu1604/generated ubuntu1804/generated
 -all: centos7/generated debian8/generated debian9/generated ubuntu1404/generated ubuntu1604/generated
++all: centos7/generated debian8/generated debian9/generated ubuntu1404/generated ubuntu1604/generated ubuntu1804/generated
  
  centos7/generated: common-generated-all
        test -d centos7/generated || mkdir centos7/generated

diff --cc build/run-library.sh
Simple merge

diff --cc sdk/cwl/setup.py
index 1205ba4fdc68774b42d04081ab9ad6e1b8533673,3b4dfbe99111972e638ae19ac40813d065f6d2d4..e452ce26440da32cdf3732cdc8f43f271600b432
--- 1/sdk/cwl/setup.py
--- 2/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@@ -33,10 -33,10 +33,10 @@@ setup(name='arvados-cwl-runner'
        # Note that arvados/build/run-build-packages.sh looks at this
        # file to determine what version of cwltool and schema-salad to build.
        install_requires=[
-           'cwltool==1.0.20180615183820',
-           'schema-salad==2.7.20180501211602',
-           'typing >= 3.5.3',
+           'cwltool==1.0.20180806194258',
+           'schema-salad==2.7.20180719125426',
+           'typing >= 3.6.4',
 -          'ruamel.yaml >=0.13.11, <0.15',
 +          'ruamel.yaml >=0.13.11, <0.16',
            'arvados-python-client>=1.1.4.20180607143841',
            'setuptools',
            'ciso8601 >=1.0.6, <2.0.0',