From 15c81f88691a6849d77c9fffee30ca915e772024 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Sun, 8 Nov 2020 22:11:45 -0500 Subject: [PATCH 1/3] Rev cwltool. --- lib/galaxy/dependencies/pipfiles/default/Pipfile | 2 +- .../dependencies/pipfiles/default/pinned-requirements.txt | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/lib/galaxy/dependencies/pipfiles/default/Pipfile b/lib/galaxy/dependencies/pipfiles/default/Pipfile index d1012b7b110..fe11e416b89 100644 --- a/lib/galaxy/dependencies/pipfiles/default/Pipfile +++ b/lib/galaxy/dependencies/pipfiles/default/Pipfile @@ -47,7 +47,7 @@ pyuwsgi = "*" pysam = "*" bdbag = "*" bleach = "*" -cwltool = "==1.0.20191225192155" +cwltool = "==2.0.20200312183052" isa-rwval = "*" boltons = "*" Paste = "*" diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt index bc6b194f9a0..7689f34629b 100644 --- a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt @@ -42,7 +42,7 @@ cloudbridge==2.0.0 cmd2==0.8.9 coloredlogs==14.0 cryptography==2.9.2 -cwltool==1.0.20191225192155 +cwltool==2.0.20200312183052 debtcollector==1.22.0 decorator==4.4.2 defusedxml==0.6.0 ; python_version >= '3.0' @@ -161,7 +161,7 @@ ruamel.yaml.clib==0.2.0 ; platform_python_implementation == 'CPython' and python ruamel.yaml==0.16.0 s3transfer==0.2.1 scandir==1.10.0 -schema-salad==4.5.20191229160203 +schema-salad==5.0.20200416112825 setuptools-scm==4.1.2 shellescape==3.4.1 simplejson==3.17.0 From cae46bd415d29003850ce22669163d496db90c84 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Mon, 9 Nov 2020 12:46:23 +0100 Subject: [PATCH 2/3] Rev cwltool with fix for opaque strings --- lib/galaxy/dependencies/pipfiles/default/Pipfile | 2 +- .../dependencies/pipfiles/default/pinned-requirements.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/dependencies/pipfiles/default/Pipfile b/lib/galaxy/dependencies/pipfiles/default/Pipfile index fe11e416b89..4300ab9536c 100644 --- a/lib/galaxy/dependencies/pipfiles/default/Pipfile +++ b/lib/galaxy/dependencies/pipfiles/default/Pipfile @@ -47,7 +47,7 @@ pyuwsgi = "*" pysam = "*" bdbag = "*" bleach = "*" -cwltool = "==2.0.20200312183052" +cwltool = "==3.0.20201109103151" isa-rwval = "*" boltons = "*" Paste = "*" diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt index 7689f34629b..b9e8dc0a4c7 100644 --- a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt @@ -42,7 +42,7 @@ cloudbridge==2.0.0 cmd2==0.8.9 coloredlogs==14.0 cryptography==2.9.2 -cwltool==2.0.20200312183052 +cwltool==3.0.20201109103151 debtcollector==1.22.0 decorator==4.4.2 defusedxml==0.6.0 ; python_version >= '3.0' From 9f4dcc924f90a4e20f0c71076f81ec6ebbce7f00 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Mon, 9 Nov 2020 13:40:17 +0000 Subject: [PATCH 3/3] Update cwltool 3.0.20201109103151 requirements --- .../pipfiles/default/pinned-requirements.txt | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt index b9e8dc0a4c7..154ce9a39d3 100644 --- a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt @@ -3,6 +3,7 @@ adal==1.2.4 amqp==2.6.0 appdirs==1.4.4 +argcomplete==1.12.1 attmap==0.12.11 attrs==19.3.0 azure-common==1.1.14 @@ -113,7 +114,6 @@ parsley==1.3 paste==3.4.1 pastedeploy==2.1.0 pastescript==3.2.0 -pathlib2==2.3.5 ; python_version < '3.6' pbr==5.4.5 prettytable==0.7.2 prov==1.5.1 @@ -123,6 +123,7 @@ pyasn1-modules==0.2.8 pyasn1==0.4.8 pycparser==2.20 pycryptodome==3.9.7 +pydot==1.4.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3' pyeventsystem==0.1.0 pyinotify==0.9.6 ; sys_platform != 'win32' and sys_platform != 'darwin' and sys_platform != 'sunos5' pyjwt==1.7.1 @@ -146,7 +147,7 @@ python3-openid==3.1.0 ; python_version >= '3.0' pytz==2020.1 pyuwsgi==2.0.19.1 pyyaml==5.3.1 -rdflib-jsonld==0.4.0 +rdflib-jsonld==0.5.0 rdflib==4.2.2 refgenconf==0.7.0 repoze.lru==0.7 @@ -158,10 +159,9 @@ rfc3986==1.4.0 routes==2.4.1 rsa==4.6 ; python_version >= '3' ruamel.yaml.clib==0.2.0 ; platform_python_implementation == 'CPython' and python_version < '3.8' -ruamel.yaml==0.16.0 +ruamel.yaml==0.16.5 s3transfer==0.2.1 -scandir==1.10.0 -schema-salad==5.0.20200416112825 +schema-salad==7.0.20200811075006; python_version >= '3.5' setuptools-scm==4.1.2 shellescape==3.4.1 simplejson==3.17.0