[med-svn] [cwltool] branch upstream updated (9bbeaa5 -> d2d28ba)
Andreas Tille
tille at debian.org
Sun Dec 18 07:35:15 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository cwltool.
from 9bbeaa5 Imported Upstream version 1.0.20160504183010
new d2d28ba New upstream version 1.0.20161207161158
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
MANIFEST.in | 2 +-
Makefile | 161 ++++
PKG-INFO | 44 +-
README.rst | 38 +-
cwltool.egg-info/PKG-INFO | 44 +-
cwltool.egg-info/SOURCES.txt | 74 +-
cwltool.egg-info/entry_points.txt | 1 -
cwltool.egg-info/pbr.json | 1 +
cwltool.egg-info/requires.txt | 13 +-
cwltool/builder.py | 126 +--
cwltool/cwlNodeEngine.js | 13 +
cwltool/cwlrdf.py | 60 +-
cwltool/cwltest.py | 210 -----
cwltool/docker.py | 30 +-
cwltool/docker_uid.py | 16 +-
cwltool/draft2tool.py | 449 ++++++-----
cwltool/errors.py | 3 +
cwltool/expression.py | 240 +++---
cwltool/factory.py | 21 +-
cwltool/job.py | 365 ++++++---
cwltool/load_tool.py | 250 ++++++
cwltool/main.py | 811 ++++++++++---------
cwltool/pack.py | 82 ++
cwltool/pathmapper.py | 264 +++++--
cwltool/process.py | 505 +++++++++---
cwltool/resolver.py | 30 +
cwltool/sandboxjs.py | 197 ++---
.../{cwl-avro.yml => CommonWorkflowLanguage.yml} | 457 ++++++-----
cwltool/schemas/draft-3/Process.yml | 20 +-
cwltool/schemas/draft-3/README.md | 5 +-
cwltool/schemas/draft-3/UserGuide.yml | 859 ++++++++++++++++++++
cwltool/schemas/draft-3/Workflow.yml | 4 +-
.../salad/schema_salad/metaschema/metaschema.yml | 4 +-
cwltool/schemas/draft-3/userguide-intro.md | 21 +-
.../CommandLineTool-standalone.yml | 0
.../schemas/{draft-3 => v1.0}/CommandLineTool.yml | 661 +++++++++++-----
.../{draft-3 => v1.0}/CommonWorkflowLanguage.yml | 0
cwltool/schemas/v1.0/Process.yml | 743 ++++++++++++++++++
cwltool/schemas/{draft-3 => v1.0}/README.md | 4 +-
cwltool/schemas/v1.0/UserGuide.yml | 869 +++++++++++++++++++++
cwltool/schemas/{draft-3 => v1.0}/Workflow.yml | 313 +++++---
cwltool/schemas/{draft-3 => v1.0}/concepts.md | 138 ++--
cwltool/schemas/{draft-3 => v1.0}/contrib.md | 8 +-
cwltool/schemas/{draft-3 => v1.0}/intro.md | 4 +-
cwltool/schemas/{draft-3 => v1.0}/invocation.md | 20 +-
.../salad/schema_salad/metaschema/field_name.yml | 0
.../schema_salad/metaschema/field_name_proc.yml | 0
.../schema_salad/metaschema/field_name_schema.yml | 0
.../schema_salad/metaschema/field_name_src.yml | 0
.../salad/schema_salad/metaschema/ident_res.yml | 0
.../schema_salad/metaschema/ident_res_proc.yml | 0
.../schema_salad/metaschema/ident_res_schema.yml | 0
.../schema_salad/metaschema/ident_res_src.yml | 0
.../schema_salad/metaschema/import_include.md | 64 ++
.../salad/schema_salad/metaschema/link_res.yml | 0
.../schema_salad/metaschema/link_res_proc.yml | 0
.../schema_salad/metaschema/link_res_schema.yml | 0
.../salad/schema_salad/metaschema/link_res_src.yml | 0
.../salad/schema_salad/metaschema/metaschema.yml | 270 ++-----
.../schema_salad/metaschema/metaschema_base.yml | 164 ++++
.../salad/schema_salad/metaschema/salad.md | 0
.../salad/schema_salad/metaschema/vocab_res.yml | 0
.../schema_salad/metaschema/vocab_res_proc.yml | 0
.../schema_salad/metaschema/vocab_res_schema.yml | 0
.../schema_salad/metaschema/vocab_res_src.yml | 0
cwltool/schemas/v1.0/userguide-intro.md | 28 +
.../CommandLineTool-standalone.yml | 0
.../{draft-3 => v1.1.0-dev1}/CommandLineTool.yml | 715 ++++++++++++-----
.../CommonWorkflowLanguage.yml | 0
cwltool/schemas/v1.1.0-dev1/Process.yml | 749 ++++++++++++++++++
cwltool/schemas/{draft-3 => v1.1.0-dev1}/README.md | 4 +-
cwltool/schemas/v1.1.0-dev1/UserGuide.yml | 869 +++++++++++++++++++++
.../schemas/{draft-3 => v1.1.0-dev1}/Workflow.yml | 328 +++++---
.../schemas/{draft-3 => v1.1.0-dev1}/concepts.md | 143 ++--
.../schemas/{draft-3 => v1.1.0-dev1}/contrib.md | 8 +-
cwltool/schemas/{draft-3 => v1.1.0-dev1}/intro.md | 4 +-
.../schemas/{draft-3 => v1.1.0-dev1}/invocation.md | 20 +-
.../salad/schema_salad/metaschema/field_name.yml | 0
.../schema_salad/metaschema/field_name_proc.yml | 0
.../schema_salad/metaschema/field_name_schema.yml | 0
.../schema_salad/metaschema/field_name_src.yml | 0
.../salad/schema_salad/metaschema/ident_res.yml | 0
.../schema_salad/metaschema/ident_res_proc.yml | 0
.../schema_salad/metaschema/ident_res_schema.yml | 0
.../schema_salad/metaschema/ident_res_src.yml | 0
.../schema_salad/metaschema/import_include.md | 64 ++
.../salad/schema_salad/metaschema/link_res.yml | 0
.../schema_salad/metaschema/link_res_proc.yml | 0
.../schema_salad/metaschema/link_res_schema.yml | 0
.../salad/schema_salad/metaschema/link_res_src.yml | 0
.../salad/schema_salad/metaschema/metaschema.yml | 270 ++-----
.../schema_salad/metaschema/metaschema_base.yml | 164 ++++
.../salad/schema_salad/metaschema/salad.md | 0
.../salad/schema_salad/metaschema/vocab_res.yml | 0
.../schema_salad/metaschema/vocab_res_proc.yml | 0
.../schema_salad/metaschema/vocab_res_schema.yml | 0
.../schema_salad/metaschema/vocab_res_src.yml | 0
cwltool/schemas/v1.1.0-dev1/userguide-intro.md | 28 +
cwltool/stdfsaccess.py | 30 +-
cwltool/update.py | 291 +++++--
cwltool/utils.py | 2 +-
cwltool/workflow.py | 413 +++++-----
ez_setup.py | 259 +++---
setup.cfg | 5 +-
setup.py | 37 +-
105 files changed, 9941 insertions(+), 3168 deletions(-)
create mode 100644 Makefile
create mode 100644 cwltool.egg-info/pbr.json
create mode 100755 cwltool/cwlNodeEngine.js
delete mode 100755 cwltool/cwltest.py
create mode 100644 cwltool/load_tool.py
create mode 100644 cwltool/pack.py
create mode 100644 cwltool/resolver.py
copy cwltool/schemas/draft-2/{cwl-avro.yml => CommonWorkflowLanguage.yml} (90%)
copy cwltool/schemas/{draft-3 => v1.0}/CommandLineTool-standalone.yml (100%)
copy cwltool/schemas/{draft-3 => v1.0}/CommandLineTool.yml (52%)
copy cwltool/schemas/{draft-3 => v1.0}/CommonWorkflowLanguage.yml (100%)
create mode 100644 cwltool/schemas/v1.0/Process.yml
copy cwltool/schemas/{draft-3 => v1.0}/README.md (92%)
create mode 100644 cwltool/schemas/v1.0/UserGuide.yml
copy cwltool/schemas/{draft-3 => v1.0}/Workflow.yml (67%)
copy cwltool/schemas/{draft-3 => v1.0}/concepts.md (79%)
copy cwltool/schemas/{draft-3 => v1.0}/contrib.md (70%)
copy cwltool/schemas/{draft-3 => v1.0}/intro.md (88%)
copy cwltool/schemas/{draft-3 => v1.0}/invocation.md (91%)
copy cwltool/schemas/{draft-3 => v1.0}/salad/schema_salad/metaschema/field_name.yml (100%)
copy cwltool/schemas/{draft-3 => v1.0}/salad/schema_salad/metaschema/field_name_proc.yml (100%)
copy cwltool/schemas/{draft-3 => v1.0}/salad/schema_salad/metaschema/field_name_schema.yml (100%)
copy cwltool/schemas/{draft-3 => v1.0}/salad/schema_salad/metaschema/field_name_src.yml (100%)
copy cwltool/schemas/{draft-3 => v1.0}/salad/schema_salad/metaschema/ident_res.yml (100%)
copy cwltool/schemas/{draft-3 => v1.0}/salad/schema_salad/metaschema/ident_res_proc.yml (100%)
copy cwltool/schemas/{draft-3 => v1.0}/salad/schema_salad/metaschema/ident_res_schema.yml (100%)
copy cwltool/schemas/{draft-3 => v1.0}/salad/schema_salad/metaschema/ident_res_src.yml (100%)
copy cwltool/schemas/{draft-3 => v1.0}/salad/schema_salad/metaschema/import_include.md (63%)
copy cwltool/schemas/{draft-3 => v1.0}/salad/schema_salad/metaschema/link_res.yml (100%)
copy cwltool/schemas/{draft-3 => v1.0}/salad/schema_salad/metaschema/link_res_proc.yml (100%)
copy cwltool/schemas/{draft-3 => v1.0}/salad/schema_salad/metaschema/link_res_schema.yml (100%)
copy cwltool/schemas/{draft-3 => v1.0}/salad/schema_salad/metaschema/link_res_src.yml (100%)
copy cwltool/schemas/{draft-3 => v1.0}/salad/schema_salad/metaschema/metaschema.yml (60%)
create mode 100644 cwltool/schemas/v1.0/salad/schema_salad/metaschema/metaschema_base.yml
copy cwltool/schemas/{draft-3 => v1.0}/salad/schema_salad/metaschema/salad.md (100%)
copy cwltool/schemas/{draft-3 => v1.0}/salad/schema_salad/metaschema/vocab_res.yml (100%)
copy cwltool/schemas/{draft-3 => v1.0}/salad/schema_salad/metaschema/vocab_res_proc.yml (100%)
copy cwltool/schemas/{draft-3 => v1.0}/salad/schema_salad/metaschema/vocab_res_schema.yml (100%)
copy cwltool/schemas/{draft-3 => v1.0}/salad/schema_salad/metaschema/vocab_res_src.yml (100%)
create mode 100644 cwltool/schemas/v1.0/userguide-intro.md
copy cwltool/schemas/{draft-3 => v1.1.0-dev1}/CommandLineTool-standalone.yml (100%)
copy cwltool/schemas/{draft-3 => v1.1.0-dev1}/CommandLineTool.yml (50%)
copy cwltool/schemas/{draft-3 => v1.1.0-dev1}/CommonWorkflowLanguage.yml (100%)
create mode 100644 cwltool/schemas/v1.1.0-dev1/Process.yml
copy cwltool/schemas/{draft-3 => v1.1.0-dev1}/README.md (92%)
create mode 100644 cwltool/schemas/v1.1.0-dev1/UserGuide.yml
copy cwltool/schemas/{draft-3 => v1.1.0-dev1}/Workflow.yml (66%)
copy cwltool/schemas/{draft-3 => v1.1.0-dev1}/concepts.md (78%)
copy cwltool/schemas/{draft-3 => v1.1.0-dev1}/contrib.md (70%)
copy cwltool/schemas/{draft-3 => v1.1.0-dev1}/intro.md (88%)
copy cwltool/schemas/{draft-3 => v1.1.0-dev1}/invocation.md (91%)
copy cwltool/schemas/{draft-3 => v1.1.0-dev1}/salad/schema_salad/metaschema/field_name.yml (100%)
copy cwltool/schemas/{draft-3 => v1.1.0-dev1}/salad/schema_salad/metaschema/field_name_proc.yml (100%)
copy cwltool/schemas/{draft-3 => v1.1.0-dev1}/salad/schema_salad/metaschema/field_name_schema.yml (100%)
copy cwltool/schemas/{draft-3 => v1.1.0-dev1}/salad/schema_salad/metaschema/field_name_src.yml (100%)
copy cwltool/schemas/{draft-3 => v1.1.0-dev1}/salad/schema_salad/metaschema/ident_res.yml (100%)
copy cwltool/schemas/{draft-3 => v1.1.0-dev1}/salad/schema_salad/metaschema/ident_res_proc.yml (100%)
copy cwltool/schemas/{draft-3 => v1.1.0-dev1}/salad/schema_salad/metaschema/ident_res_schema.yml (100%)
copy cwltool/schemas/{draft-3 => v1.1.0-dev1}/salad/schema_salad/metaschema/ident_res_src.yml (100%)
copy cwltool/schemas/{draft-3 => v1.1.0-dev1}/salad/schema_salad/metaschema/import_include.md (63%)
copy cwltool/schemas/{draft-3 => v1.1.0-dev1}/salad/schema_salad/metaschema/link_res.yml (100%)
copy cwltool/schemas/{draft-3 => v1.1.0-dev1}/salad/schema_salad/metaschema/link_res_proc.yml (100%)
copy cwltool/schemas/{draft-3 => v1.1.0-dev1}/salad/schema_salad/metaschema/link_res_schema.yml (100%)
copy cwltool/schemas/{draft-3 => v1.1.0-dev1}/salad/schema_salad/metaschema/link_res_src.yml (100%)
copy cwltool/schemas/{draft-3 => v1.1.0-dev1}/salad/schema_salad/metaschema/metaschema.yml (60%)
create mode 100644 cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/metaschema_base.yml
copy cwltool/schemas/{draft-3 => v1.1.0-dev1}/salad/schema_salad/metaschema/salad.md (100%)
copy cwltool/schemas/{draft-3 => v1.1.0-dev1}/salad/schema_salad/metaschema/vocab_res.yml (100%)
copy cwltool/schemas/{draft-3 => v1.1.0-dev1}/salad/schema_salad/metaschema/vocab_res_proc.yml (100%)
copy cwltool/schemas/{draft-3 => v1.1.0-dev1}/salad/schema_salad/metaschema/vocab_res_schema.yml (100%)
copy cwltool/schemas/{draft-3 => v1.1.0-dev1}/salad/schema_salad/metaschema/vocab_res_src.yml (100%)
create mode 100644 cwltool/schemas/v1.1.0-dev1/userguide-intro.md
mode change 100644 => 100755 ez_setup.py
mode change 100644 => 100755 setup.py
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