From 6c2bee5ea464a6740c7f8c93b3699c6f824a70a4 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Fri, 6 Jul 2018 10:18:52 +0100
Subject: [PATCH] Update cliff and other related dependencies

cliff now has a universal wheel.
Remove unused Pipfile.lock files.
Skip broken lxml 4.2.2, see https://github.com/lxml/lxml/pull/265 .
Fix more oscillating environment markers.
---
 .../pipfiles/default/pinned-requirements.txt  |  40 +-
 .../dependencies/pipfiles/develop/Pipfile     |   2 +-
 .../pipfiles/develop/Pipfile.lock             | 342 ------------------
 .../pipfiles/develop/pinned-requirements.txt  |   6 +-
 .../dependencies/pipfiles/flake8/Pipfile.lock |  73 ----
 lib/galaxy/dependencies/pipfiles/update.sh    |   8 +-
 6 files changed, 30 insertions(+), 441 deletions(-)
 delete mode 100644 lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock
 delete mode 100644 lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock

diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
index 68496c9e3d8..8761b370c63 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
@@ -17,24 +17,24 @@ certifi==2018.4.16
 cffi==1.11.5
 chardet==3.0.4
 cheetah3==3.1.0
-cliff==2.11.0
+cliff==2.13.0; python_version >= '2.6'
 cloudbridge==0.3.3
-cmd2==0.8.4
+cmd2==0.8.8
 contextlib2==0.5.5; python_version < '3.5'
 cryptography==2.2.2
 debtcollector==1.19.0
-decorator==4.2.1
-deprecation==2.0.1
+decorator==4.3.0
+deprecation==2.0.5
 dictobj==0.4
 docopt==0.6.2
 docutils==0.14
-dogpile.cache==0.6.5
+dogpile.cache==0.6.6
 enum34==1.1.6; python_version < '3.4'
 fabric3==1.14.post1
 funcsigs==1.0.2; python_version < '3.3'
 functools32==3.2.3.post2; python_version == '2.7'
 future==0.16.0
-futures==3.2.0; python_version == '2.7' or python_version == '2.6'
+futures==3.2.0; python_version == '2.6' or python_version == '2.7'
 galaxy-sequence-utils==1.1.2
 globus-sdk==1.3.0
 h5py==2.6.0
@@ -46,34 +46,34 @@ jmespath==0.9.3
 jsonpatch==1.23
 jsonpointer==2.0
 jsonschema==2.6.0
-keystoneauth1==3.4.0
+keystoneauth1==3.9.0
 kombu==4.1.0
 mako==1.0.7
 markupsafe==1.0
 mercurial==3.7.3; python_version < '3'
-monotonic==1.4
+monotonic==1.5
 msgpack==0.5.6
-munch==2.3.1
+munch==2.3.2
 netaddr==0.7.19
 netifaces==0.10.7
 nose==1.3.7
 numpy==1.14.2
 oauthlib==2.0.7
-openstacksdk==0.12.0
-os-client-config==1.29.0
+openstacksdk==0.14.0
+os-client-config==1.31.2
 os-service-types==1.2.0
 osc-lib==1.10.0
-oslo.config==6.0.2
+oslo.config==6.3.0
 oslo.i18n==3.20.0
-oslo.serialization==2.25.0
-oslo.utils==3.36.0
+oslo.serialization==2.27.0
+oslo.utils==3.36.3
 packaging==17.1
 paramiko==2.4.1
 parsley==1.3
 paste==2.0.3
 pastedeploy==1.5.2
 pastescript==2.0.2
-pbr==4.0.4
+pbr==4.1.0
 positional==1.2.1
 prettytable==0.7.2
 psutil==5.4.3
@@ -88,10 +88,10 @@ pyjwt==1.6.1
 pykwalify==1.6.1
 pynacl==1.2.1
 pyparsing==2.2.0
-pyperclip==1.6.0
+pyperclip==1.6.2
 pysam==0.14.1
 python-cinderclient==2.0.1
-python-dateutil==2.7.2
+python-dateutil==2.7.3
 python-genomespaceclient==0.2
 python-glanceclient==2.6.0
 python-keystoneclient==3.10.0
@@ -100,7 +100,7 @@ python-neutronclient==6.1.0
 python-novaclient==7.0.0
 python-openid==2.2.5
 python-swiftclient==3.3.0
-pytz==2018.4
+pytz==2018.5
 pyyaml==3.12
 repoze.lru==0.7
 requests-oauthlib==0.8.0
@@ -110,7 +110,7 @@ requestsexceptions==1.4.0
 retrying==1.3.3
 rfc3986==1.1.0
 routes==2.4.1
-simplejson==3.13.2
+simplejson==3.16.0
 six==1.11.0
 social-auth-core==1.5.0
 sqlalchemy-migrate==0.11.0
@@ -118,7 +118,7 @@ sqlalchemy-utils==0.33.2
 sqlalchemy==1.2.6
 sqlparse==0.2.4
 stevedore==1.28.0
-subprocess32==3.5.0; python_version < '3.0'
+subprocess32==3.5.2; python_version < '3.0'
 svgwrite==1.1.12
 tempita==0.5.2
 tzlocal==1.5.1
diff --git a/lib/galaxy/dependencies/pipfiles/develop/Pipfile b/lib/galaxy/dependencies/pipfiles/develop/Pipfile
index a5faf8865d6..dd036046343 100644
--- a/lib/galaxy/dependencies/pipfiles/develop/Pipfile
+++ b/lib/galaxy/dependencies/pipfiles/develop/Pipfile
@@ -21,6 +21,6 @@ watchdog = "*"
 pygithub3 = {version = "*", markers = "python_version < '3'"}
 Sphinx = "<1.7"  # Docs do not build with sphinx 1.7 for some reason, can't find issue.
 sphinx_rtd_theme = "*"
-lxml = "*"
+lxml = "!=4.2.2"
 recommonmark = "*"
 nodeenv = "*"
diff --git a/lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock b/lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock
deleted file mode 100644
index ac05e1f1a72..00000000000
--- a/lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock
+++ /dev/null
@@ -1,342 +0,0 @@
-{
-    "_meta": {
-        "hash": {
-            "sha256": "58ed0af0f529ee3e95e4106050c9e712d08d981684ffe21c57d334e3f688b7fe"
-        },
-        "pipfile-spec": 6,
-        "requires": {},
-        "sources": [
-            {
-                "name": "galaxy",
-                "url": "https://wheels.galaxyproject.org/simple",
-                "verify_ssl": true
-            },
-            {
-                "name": "pypi",
-                "url": "https://pypi.python.org/simple",
-                "verify_ssl": true
-            }
-        ]
-    },
-    "default": {
-        "alabaster": {
-            "hashes": [
-                "sha256:674bb3bab080f598371f4443c5008cbfeb1a5e622dd312395d2d82af2c54c456",
-                "sha256:b63b1f4dc77c074d386752ec4a8a7517600f6c0db8cd42980cae17ab7b3275d7"
-            ],
-            "version": "==0.7.11"
-        },
-        "argh": {
-            "hashes": [
-                "sha256:a9b3aaa1904eeb78e32394cd46c6f37ac0fb4af6dc488daa58971bdc7d7fcaf3",
-                "sha256:e9535b8c84dc9571a48999094fda7f33e63c3f1b74f3e5f3ac0105a58405bb65"
-            ],
-            "version": "==0.26.2"
-        },
-        "babel": {
-            "hashes": [
-                "sha256:6778d85147d5d85345c14a26aada5e478ab04e39b078b0745ee6870c2b5cf669",
-                "sha256:8cba50f48c529ca3fa18cf81fa9403be176d374ac4d60738b839122dfaaa3d23"
-            ],
-            "version": "==2.6.0"
-        },
-        "certifi": {
-            "hashes": [
-                "sha256:13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7",
-                "sha256:9fa520c1bacfb634fa7af20a76bcbd3d5fb390481724c597da32c719a7dca4b0"
-            ],
-            "version": "==2018.4.16"
-        },
-        "chardet": {
-            "hashes": [
-                "sha256:84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae",
-                "sha256:84d8ecaf41275e791dd748e7f7999520e60914f8754969396b1f7cfba20b241d",
-                "sha256:fc323ffcaeaed0e0a02bf4d117757b98aed530d9ed4531e3e15460124c106691"
-            ],
-            "version": "==3.0.4"
-        },
-        "commonmark": {
-            "hashes": [
-                "sha256:34d73ec8085923c023930dfc0bcd1c4286e28a2a82de094bb72fabcc0281cbe5"
-            ],
-            "version": "==0.5.4"
-        },
-        "docutils": {
-            "hashes": [
-                "sha256:02aec4bd92ab067f6ff27a38a38a41173bf01bed8f89157768c1573f53e474a6",
-                "sha256:51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274",
-                "sha256:7a4bd47eaf6596e1295ecb11361139febe29b084a87bf005bf899f9a42edc3c6"
-            ],
-            "version": "==0.14"
-        },
-        "funcsigs": {
-            "hashes": [
-                "sha256:330cc27ccbf7f1e992e69fef78261dc7c6569012cf397db8d3de0234e6c937ca",
-                "sha256:a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50"
-            ],
-            "markers": "python_version < '3.3'",
-            "version": "==1.0.2"
-        },
-        "idna": {
-            "hashes": [
-                "sha256:156a6814fb5ac1fc6850fb002e0852d56c0c8d2531923a51032d1b70760e186e",
-                "sha256:684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16"
-            ],
-            "version": "==2.7"
-        },
-        "imagesize": {
-            "hashes": [
-                "sha256:3620cc0cadba3f7475f9940d22431fc4d407269f1be59ec9b8edcca26440cf18",
-                "sha256:5b326e4678b6925158ccc66a9fa3122b6106d7c876ee32d7de6ce59385b96315"
-            ],
-            "version": "==1.0.0"
-        },
-        "jinja2": {
-            "hashes": [
-                "sha256:74c935a1b8bb9a3947c50a54766a969d4846290e1e788ea44c1392163723c3bd",
-                "sha256:f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4"
-            ],
-            "version": "==2.10"
-        },
-        "lxml": {
-            "hashes": [
-                "sha256:01b194561b6a25d94b1267b785d6ec67eec6b62cce2591f3096de98ec22a704b",
-                "sha256:10ad7277b618b9a0bafed7ddf73af6d9c9b3de8d42cbb881859d611d54de665c",
-                "sha256:1fc9e6adc16c0cab2596de5cd7adc5988635ec1e2dcae367e2a2009302ae89b3",
-                "sha256:34cb8e68be4403d01a84f5dd5b9a089ddaedf28a3e9ff259708d88f9a60e2b7e",
-                "sha256:36a47fb5d99f7827cb478cc71f907b728304ead3b12b0eb1a102199a0a0bf8a7",
-                "sha256:37cda88cf6082fd9d78988156140a5922d4b296577b5ff83f72116c4061d7304",
-                "sha256:39e80bafa7be141ff2d0bb8ed1652b9ac326573bf0e6678770d729adbd9d2670",
-                "sha256:4211c2ff1a465d9bafc671715d40695bfeb59065005a8b565069b4ab3faba5d9",
-                "sha256:473ad409306e83dca68632bf29e1b40592b159af86318410ac42e8054f2904b8",
-                "sha256:482da759ec33fb78e3781d1c59aafa39a83265bbc796967f830d64d08f7212ad",
-                "sha256:48cccd8ba29c4cc967cb0e3317c5931e0f0ade1692895da6ba9a5a31410d75af",
-                "sha256:4b487bf101ce0217afcc3eb661713b32f10d30f1cac1e9d966f0a988ea8a389c",
-                "sha256:512f1b88f46ef1e55cb05150b8e7029be1c10995c3531d6c1205afa8b61d8996",
-                "sha256:73e23a2dd19d8f3c012cf6d3b221b32bf2254de49dfed449b2b87dd8fa56611e",
-                "sha256:810934dddb01a797fcd8ec9d9e981b8ebc7738ae1a5bbd2c90c7cdae5435609e",
-                "sha256:82f278cd24da1b8a98df89de38946d67381a00e39adef768fd302dc8f4e1c383",
-                "sha256:852d077b69432ad3c2ee622d4a82588fc32c8f260d41ce1a34207e60213b04a1",
-                "sha256:8eee7864ea7882512bada274c2a58997a09fa8da5f8a31e298ebf7226df0cf75",
-                "sha256:967ac7c857b4c67dbc906e2c7d81f89c14ea84d63adf4e95c6a1c9ed1bec2d77",
-                "sha256:a8b8c161d9dab9e884f99e7d898f6e06db547a3a0398962b55de96130b6da777",
-                "sha256:a9368022ca262fd15625f365b557d66ce0743bc1e1901d85dfe1af9836f01713",
-                "sha256:ab5ab5df9589a4538c238cf3711978419562ccf9c72efc06fb2f5e3833b7e0f4",
-                "sha256:be1d3c858071d552aab304742726ea1b3a46f21761f2c2a7afa93a37e57597f5",
-                "sha256:bea02d0662709d905bc18402ad4b84c5a6dc72d9d86dbbe9958eadf3d158e63b",
-                "sha256:d06bbb503f9e41c836a1941d163469b6df2f77f004bff609849f58ed52fa2ad4",
-                "sha256:d2965ef3521bcc3c82bd218a44f4c1f2630c127b5e1f35da50cb360e872bc3af",
-                "sha256:d78d58d934a3c2f39daaf89aad5e71551ff75550cf4820020ad6ae29f1b82cc9"
-            ],
-            "index": "galaxy",
-            "version": "==4.2.2"
-        },
-        "markupsafe": {
-            "hashes": [
-                "sha256:160c289726ad7eb6707dd242214423344f0403bf944cd2eea63ee6bb77da480b",
-                "sha256:180787f23e03012c9648f4e1fa7cc58075e32389884b3879f9a7046c6a0bd7cf",
-                "sha256:23823274546fdd18afba43a40b6338909430357013cd5ef631b4d1e6061a6778",
-                "sha256:5ecf3cf8c99fab514009be2fbcc009883fb435aaf1b86ef1d64d34865589be06",
-                "sha256:a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665",
-                "sha256:eb9bc9e50a570ab5d11b72356c6e453cd02a9984dfaf5fd5fba6ca7125a024b4"
-            ],
-            "version": "==1.0"
-        },
-        "mock": {
-            "hashes": [
-                "sha256:5ce3c71c5545b472da17b72268978914d0252980348636840bd34a00b5cc96c1",
-                "sha256:b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba"
-            ],
-            "index": "galaxy",
-            "version": "==2.0.0"
-        },
-        "nodeenv": {
-            "hashes": [
-                "sha256:0611c726af1b252908646787f4d49811aa69cd92ec19644ded06ad9d3162f88e"
-            ],
-            "index": "galaxy",
-            "version": "==1.3.1"
-        },
-        "nose": {
-            "hashes": [
-                "sha256:9ff7c6cc443f8c51994b34a667bbcf45afd6d945be7477b52e97516fd17c53ac",
-                "sha256:c5a2d5584c1c3198373cbb5bba8b28cc96c094009f9839c166d1c4e623b2dcbe",
-                "sha256:dadcddc0aefbf99eea214e0f1232b94f2fa9bd98fa8353711dacb112bfcbbb2a",
-                "sha256:f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98",
-                "sha256:f36054c5786e84ff6b131f3249a3cce82787f1a930ab053287c0edaa9f840d0f"
-            ],
-            "version": "==1.3.7"
-        },
-        "nosehtml": {
-            "hashes": [
-                "sha256:3572c2aa4a4ab285dfc4eaa3bd6bdb599d4b808060f6effc03c672b41f9ea1eb",
-                "sha256:405992a3f489f1b85ada11e35a29ecb28343738ec3c7c6a0efb71bed2271375b"
-            ],
-            "index": "galaxy",
-            "version": "==0.4.5"
-        },
-        "pathtools": {
-            "hashes": [
-                "sha256:7c35c5421a39bb82e58018febd90e3b6e5db34c5443aaaf742b3f33d4655f1c0"
-            ],
-            "version": "==0.1.2"
-        },
-        "pbr": {
-            "hashes": [
-                "sha256:3747c6f017f2dc099986c325239661948f9f5176f6880d9fdef164cb664cd665",
-                "sha256:a9c27eb8f0e24e786e544b2dbaedb729c9d8546342b5a6818d8eda098ad4340d"
-            ],
-            "version": "==4.0.4"
-        },
-        "pygithub3": {
-            "hashes": [
-                "sha256:5669a4cdbf4b3192716442e2224db45ecd1639e42f990739ddfa8f2ca3f7ba87"
-            ],
-            "index": "galaxy",
-            "markers": "python_version < '3'",
-            "version": "==0.5.1"
-        },
-        "pygments": {
-            "hashes": [
-                "sha256:78f3f434bcc5d6ee09020f92ba487f95ba50f1e3ef83ae96b9d5ffa1bab25c5d",
-                "sha256:dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc"
-            ],
-            "version": "==2.2.0"
-        },
-        "pytz": {
-            "hashes": [
-                "sha256:65ae0c8101309c45772196b21b74c46b2e5d11b6275c45d251b150d5da334555",
-                "sha256:c06425302f2cf668f1bba7a0a03f3c1d34d4ebeef2c72003da308b3947c7f749"
-            ],
-            "version": "==2018.4"
-        },
-        "pyyaml": {
-            "hashes": [
-                "sha256:0c507b7f74b3d2dd4d1322ec8a94794927305ab4cebbe89cc47fe5e81541e6e8",
-                "sha256:16b20e970597e051997d90dc2cddc713a2876c47e3d92d59ee198700c5427736",
-                "sha256:3262c96a1ca437e7e4763e2843746588a965426550f3797a79fca9c6199c431f",
-                "sha256:326420cbb492172dec84b0f65c80942de6cedb5233c413dd824483989c000608",
-                "sha256:443530519821618ba9951b49dbba639310d0d65045b131b97b3e507c31e9f8be",
-                "sha256:4474f8ea030b5127225b8894d626bb66c01cda098d47a2b0d3429b6700af9fd8",
-                "sha256:592766c6303207a20efc445587778322d7f73b161bd994f227adaa341ba212ab",
-                "sha256:5ac82e411044fb129bae5cfbeb3ba626acb2af31a8d17d175004b70862a741a7",
-                "sha256:5f84523c076ad14ff5e6c037fe1c89a7f73a3e04cf0377cb4d017014976433f3",
-                "sha256:75e1cadefb2dea453f59d128beea1558351f675a85798a05320a4e6be8247a99",
-                "sha256:76f1b008856a3eaa5592d8ed9331a8207006a8feea1e835806ac86deb046267a",
-                "sha256:827dc04b8fa7d07c44de11fabbc888e627fa8293b695e0f99cb544fdfa1bf0d1",
-                "sha256:b4c423ab23291d3945ac61346feeb9a0dc4184999ede5e7c43e1ffb975130ae6",
-                "sha256:bb38f36943c97a5cb28da50728bcfe10b632d3fd0e3f90c7c6e80b0d86ca790c",
-                "sha256:bc6bced57f826ca7cb5125a10b23fd0f2fff3b7c4701d64c439a300ce665fff8",
-                "sha256:c01b880ec30b5a6e6aa67b09a2fe3fb30473008c85cd6a67359a1b15ed6d83a4",
-                "sha256:ca233c64c6e40eaa6c66ef97058cdc80e8d0157a443655baa1b2966e812807ca",
-                "sha256:e58e31a0859b07d01a8ade5cd5864233d09ce033bb7da9e46f01c82da8b953e6",
-                "sha256:e863072cdf4c72eebf179342c94e6989c67185842d9997960b3e69290b2fa269"
-            ],
-            "version": "==3.12"
-        },
-        "recommonmark": {
-            "hashes": [
-                "sha256:6e29c723abcf5533842376d87c4589e62923ecb6002a8e059eb608345ddaff9d",
-                "sha256:cd8bf902e469dae94d00367a8197fb7b81fcabc9cfb79d520e0d22d0fbeaa8b7"
-            ],
-            "index": "galaxy",
-            "version": "==0.4.0"
-        },
-        "requests": {
-            "hashes": [
-                "sha256:63b52e3c866428a224f97cab011de738c36aec0185aa91cfacd418b5d58911d1",
-                "sha256:ec22d826a36ed72a7358ff3fe56cbd4ba69dd7a6718ffd450ff0e9df7a47ce6a"
-            ],
-            "version": "==2.19.1"
-        },
-        "selenium": {
-            "hashes": [
-                "sha256:6f4c7727d44034b8d635d7cf1c3377f76efc95e192ed5cfb97e0057fe5a92d44",
-                "sha256:f35bb209cab740c195276a323c1b750dbcfdb9f6983e7d6e3abba9cd8838f355"
-            ],
-            "index": "galaxy",
-            "version": "==3.13.0"
-        },
-        "six": {
-            "hashes": [
-                "sha256:70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9",
-                "sha256:832dc0e10feb1aa2c68dcc57dbb658f1c7e65b9b61af69048abc87a2db00a0eb"
-            ],
-            "version": "==1.11.0"
-        },
-        "snowballstemmer": {
-            "hashes": [
-                "sha256:919f26a68b2c17a7634da993d91339e288964f93c274f1343e3bbbe2096e1128",
-                "sha256:9f3bcd3c401c3e862ec0ebe6d2c069ebc012ce142cce209c098ccb5b09136e89"
-            ],
-            "version": "==1.2.1"
-        },
-        "sphinx": {
-            "hashes": [
-                "sha256:832bed0dc6099c2abca957d90ff55bc1a6ec4425c13fc144adbae68a970e3775",
-                "sha256:d5b91b4dad56ffc9f19425ebaa7bc23290a0a2e9035781d5bc54822384663277"
-            ],
-            "index": "galaxy",
-            "version": "==1.6.7"
-        },
-        "sphinx-rtd-theme": {
-            "hashes": [
-                "sha256:aa3e190392e963551432de7df24b8a5fbe5b71a2f4fcd9d5b75808b52ad999e5",
-                "sha256:de88d637a60371d4f923e06b79c4ba260490c57d2ab5a8316942ab5d9a6ce1bf"
-            ],
-            "index": "galaxy",
-            "version": "==0.4.0"
-        },
-        "sphinxcontrib-websupport": {
-            "hashes": [
-                "sha256:68ca7ff70785cbe1e7bccc71a48b5b6d965d79ca50629606c7861a21b206d9dd",
-                "sha256:9de47f375baf1ea07cdb3436ff39d7a9c76042c10a769c52353ec46e4e8fc3b9"
-            ],
-            "version": "==1.1.0"
-        },
-        "testfixtures": {
-            "hashes": [
-                "sha256:7e4df89a8bf8b8905464160f08aff131a36f0b33654fe4f9e4387afe546eae25",
-                "sha256:bcadbad77526cc5fc38bfb2ab80da810d7bde56ffe4c7fdb8e2bba122ded9620"
-            ],
-            "index": "galaxy",
-            "version": "==6.2.0"
-        },
-        "twill": {
-            "hashes": [
-                "sha256:05a673498be25d5e6292559f47cbf1b7b424e1d7c454f36efc3cc6324ee0bfc1",
-                "sha256:7809e4509e8c333c21581245494109eee18d2a9dd377c54f5050bbfa009d28c2",
-                "sha256:d2df51cc4eca5a6dec0a2af3817b236655558deff9542fc3d7653d16c8d5ba7e"
-            ],
-            "index": "galaxy",
-            "markers": "python_version < '3'",
-            "version": "==0.9.1"
-        },
-        "typing": {
-            "hashes": [
-                "sha256:3a887b021a77b292e151afb75323dea88a7bc1b3dfa92176cff8e44c8b68bddf",
-                "sha256:b2c689d54e1144bbcfd191b0832980a21c2dbcf7b5ff7a66248a60c90e951eb8",
-                "sha256:d400a9344254803a2368533e4533a4200d21eb7b6b729c173bc38201a74db3f2"
-            ],
-            "markers": "python_version < '3.5'",
-            "version": "==3.6.4"
-        },
-        "urllib3": {
-            "hashes": [
-                "sha256:a68ac5e15e76e7e5dd2b8f94007233e01effe3e50e8daddf69acfd81cb686baf",
-                "sha256:b5725a0bd4ba422ab0e66e89e030c806576753ea3ee08554382c14e685d117b5"
-            ],
-            "version": "==1.23"
-        },
-        "watchdog": {
-            "hashes": [
-                "sha256:06a7f94de694d5e8fe2bc077e7530fa7c87163cd90c8c1f38a7dcc6fe550104d",
-                "sha256:36f1cb5c72ffa5ecf92e35f936b293f3d04dffbe2b55567fbca6bdea1ee84cb4",
-                "sha256:7e65882adb7746039b6f3876ee174952f8eaaa34491ba34333ddf1fe35de4162"
-            ],
-            "index": "galaxy",
-            "version": "==0.8.3"
-        }
-    },
-    "develop": {}
-}
diff --git a/lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt
index 9db61e9a804..5947b7302a0 100644
--- a/lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt
@@ -11,17 +11,17 @@ funcsigs==1.0.2; python_version < '3.3'
 idna==2.7
 imagesize==1.0.0
 jinja2==2.10
-lxml==4.2.1
+lxml==4.2.3
 markupsafe==1.0
 mock==2.0.0
 nodeenv==1.3.1
 nose==1.3.7
 nosehtml==0.4.5
 pathtools==0.1.2
-pbr==4.0.4
+pbr==4.1.0
 pygithub3==0.5.1; python_version < '3'
 pygments==2.2.0
-pytz==2018.4
+pytz==2018.5
 pyyaml==3.12
 recommonmark==0.4.0
 requests==2.19.1
diff --git a/lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock b/lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock
deleted file mode 100644
index fa89efcdb0b..00000000000
--- a/lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock
+++ /dev/null
@@ -1,73 +0,0 @@
-{
-    "_meta": {
-        "hash": {
-            "sha256": "68f35c8c353b79ccfd80ad884f83009e2b196c6fe761fa91b01f3d3c6804bb93"
-        },
-        "pipfile-spec": 6,
-        "requires": {},
-        "sources": [
-            {
-                "name": "pypi",
-                "url": "https://pypi.python.org/simple",
-                "verify_ssl": true
-            }
-        ]
-    },
-    "default": {
-        "configparser": {
-            "hashes": [
-                "sha256:5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a"
-            ],
-            "markers": "python_version < '3.2'",
-            "version": "==3.5.0"
-        },
-        "enum34": {
-            "hashes": [
-                "sha256:2d81cbbe0e73112bdfe6ef8576f2238f2ba27dd0d55752a776c41d38b7da2850",
-                "sha256:644837f692e5f550741432dd3f223bbb9852018674981b1664e5dc339387588a",
-                "sha256:6bd0f6ad48ec2aa117d3d141940d484deccda84d4fcd884f5c3d93c23ecd8c79",
-                "sha256:8ad8c4783bf61ded74527bffb48ed9b54166685e4230386a9ed9b1279e2df5b1"
-            ],
-            "markers": "python_version < '3.4'",
-            "version": "==1.1.6"
-        },
-        "flake8": {
-            "hashes": [
-                "sha256:7253265f7abd8b313e3892944044a365e3f4ac3fcdcfb4298f55ee9ddf188ba0",
-                "sha256:c7841163e2b576d435799169b78703ad6ac1bbb0f199994fc05f700b2a90ea37"
-            ],
-            "index": "pypi",
-            "version": "==3.5.0"
-        },
-        "flake8-import-order": {
-            "hashes": [
-                "sha256:40d2a39ed91e080f3285f4c16256b252d7c31070e7f11b7854415bb9f924ea81",
-                "sha256:68d430781a9ef15c85a0121500cf8462f1a4bc7672acb2a32bfdbcab044ae0b7"
-            ],
-            "index": "pypi",
-            "version": "==0.17.1"
-        },
-        "mccabe": {
-            "hashes": [
-                "sha256:ab8a6258860da4b6677da4bd2fe5dc2c659cff31b3ee4f7f5d64e79735b80d42",
-                "sha256:dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f"
-            ],
-            "version": "==0.6.1"
-        },
-        "pycodestyle": {
-            "hashes": [
-                "sha256:682256a5b318149ca0d2a9185d365d8864a768a28db66a84a2ea946bcc426766",
-                "sha256:6c4245ade1edfad79c3446fadfc96b0de2759662dc29d07d80a6f27ad1ca6ba9"
-            ],
-            "version": "==2.3.1"
-        },
-        "pyflakes": {
-            "hashes": [
-                "sha256:08bd6a50edf8cffa9fa09a463063c425ecaaf10d1eb0335a7e8b1401aef89e6f",
-                "sha256:8d616a382f243dbf19b54743f280b80198be0bca3a5396f1d2e1fca6223e8805"
-            ],
-            "version": "==1.6.0"
-        }
-    },
-    "develop": {}
-}
diff --git a/lib/galaxy/dependencies/pipfiles/update.sh b/lib/galaxy/dependencies/pipfiles/update.sh
index 4d8bb0bad49..21678dcac59 100755
--- a/lib/galaxy/dependencies/pipfiles/update.sh
+++ b/lib/galaxy/dependencies/pipfiles/update.sh
@@ -34,17 +34,21 @@ ENVS="develop
 flake8
 default"
 
+export PIPENV_IGNORE_VIRTUALENVS=1
 for env in $ENVS; do
     cd "$THIS_DIRECTORY/$env"
-    pipenv lock
+    pipenv lock -v
     # Strip out hashes and trailing whitespace for unhashed version
     # of this requirements file, needed for pipenv < 11.1.2
     pipenv lock -r | sed -e 's/--hash[^[:space:]]*//g' -e 's/[[:space:]]*$//' > pinned-requirements.txt
     # Fix oscillating environment markers
     sed -i.orig -e "s/^cffi==\([^;]\+\).*$/cffi==\1/" \
+                -e "s/^cmd2==\([^;]\+\).*$/cmd2==\1/" \
                 -e "s/^enum34==\([^;]\+\).*$/enum34==\1; python_version < '3.4'/" \
                 -e "s/^funcsigs==\([^;]\+\).*$/funcsigs==\1; python_version < '3.3'/" \
-                -e "s/^py2-ipaddress==\([^;]\+\).*$/py2-ipaddress==\1; python_version < '3'/" pinned-requirements.txt
+                -e "s/^futures==\([^;]\+\).*$/futures==\1; python_version == '2.6' or python_version == '2.7'/" \
+                -e "s/^py2-ipaddress==\([^;]\+\).*$/py2-ipaddress==\1; python_version < '3'/" \
+                -e "s/^subprocess32==\([^;]\+\).*$/subprocess32==\1; python_version < '3.0'/" pinned-requirements.txt
 done
 
 if [ "$commit" -eq "1" ];