[med-svn] [cwltool] branch upstream updated (1c49ced -> 29cb30f)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Fri Aug 11 12:07:37 UTC 2017
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch upstream
in repository cwltool.
from 1c49ced New upstream version 1.0.20170114120503
adds cd43a05 New upstream version 1.0.20170803160545
adds 29cb30f New upstream version 1.0.20170810192106
No new revisions were added by this update.
Summary of changes:
MANIFEST.in | 23 +-
Makefile | 51 +-
PKG-INFO | 448 ++++++++++++++-
README.rst | 415 +++++++++++++-
cwltool.egg-info/PKG-INFO | 448 ++++++++++++++-
cwltool.egg-info/SOURCES.txt | 105 +++-
cwltool.egg-info/pbr.json | 1 +
cwltool.egg-info/requires.txt | 14 +-
cwltool.py | 2 +
cwltool/__init__.py | 1 +
cwltool/__main__.py | 4 +-
cwltool/builder.py | 100 +++-
cwltool/cwlNodeEngine.js | 6 +-
cwltool/cwlrdf.py | 26 +-
cwltool/docker.py | 40 +-
cwltool/{docker_uid.py => docker_id.py} | 39 +-
cwltool/draft2tool.py | 446 ++++++++++-----
cwltool/errors.py | 1 +
cwltool/expression.py | 93 +--
cwltool/extensions.yml | 36 ++
cwltool/factory.py | 25 +-
cwltool/flatten.py | 1 +
cwltool/job.py | 386 ++++++++-----
cwltool/load_tool.py | 198 ++++---
cwltool/main.py | 621 ++++++++++++++-------
cwltool/mutation.py | 69 +++
cwltool/pack.py | 149 +++--
cwltool/pathmapper.py | 197 +++++--
cwltool/process.py | 413 +++++++++-----
cwltool/resolver.py | 32 +-
cwltool/sandboxjs.py | 261 +++++++--
cwltool/schemas/draft-3/Workflow.yml | 1 +
cwltool/schemas/draft-3/index.md | 0
cwltool/schemas/v1.0/CommandLineTool.yml | 50 +-
cwltool/schemas/v1.0/Process.yml | 190 ++++++-
cwltool/schemas/v1.0/UserGuide.yml | 148 ++++-
cwltool/schemas/v1.0/Workflow.yml | 68 ++-
cwltool/schemas/v1.0/concepts.md | 4 +-
.../v1.0/salad/schema_salad/metaschema/map_res.yml | 36 ++
.../salad/schema_salad/metaschema/map_res_proc.yml | 12 +
.../schema_salad/metaschema/map_res_schema.yml | 30 +
.../salad/schema_salad/metaschema/map_res_src.yml | 8 +
.../salad/schema_salad/metaschema/metaschema.yml | 13 +
.../metaschema/{metaschema.yml => metaschema2.yml} | 4 +-
.../schema_salad/metaschema/metaschema_base.yml | 7 +
.../v1.0/salad/schema_salad/metaschema/salad.md | 19 +-
.../salad/schema_salad/metaschema/typedsl_res.yml | 33 ++
.../schema_salad/metaschema/typedsl_res_proc.yml | 26 +
.../schema_salad/metaschema/typedsl_res_schema.yml | 17 +
.../schema_salad/metaschema/typedsl_res_src.yml | 9 +
cwltool/schemas/v1.1.0-dev1/CommandLineTool.yml | 10 +-
cwltool/schemas/v1.1.0-dev1/Process.yml | 18 +-
cwltool/schemas/v1.1.0-dev1/UserGuide.yml | 28 +-
cwltool/schemas/v1.1.0-dev1/Workflow.yml | 21 +-
cwltool/schemas/v1.1.0-dev1/concepts.md | 4 +-
cwltool/software_requirements.py | 122 ++++
cwltool/stdfsaccess.py | 47 +-
cwltool/update.py | 70 ++-
cwltool/utils.py | 158 +++++-
cwltool/workflow.py | 506 ++++++++++++-----
ez_setup.py | 391 -------------
gittaggers.py | 4 +-
setup.cfg | 12 +-
setup.py | 73 ++-
tests/2.fasta | 11 +
tests/2.fastq | 12 +
tests/__init__.py | 0
tests/cat.cwl | 8 +
tests/cat2.cwl | 9 +
tests/echo-cwlrun-job.yaml | 6 +
tests/echo-job.yaml | 5 +
tests/echo.cwl | 15 +
tests/env.cwl | 5 +
tests/item1.yml | 3 +
tests/listing-job.yml | 3 +
tests/output.txt | 16 +
tests/random_lines.cwl | 29 +
tests/random_lines_job.json | 8 +
tests/random_lines_mapping.cwl | 29 +
tests/seqtk_seq.cwl | 24 +
tests/seqtk_seq_job.json | 6 +
tests/seqtk_seq_with_docker.cwl | 26 +
tests/seqtk_seq_wrong_name.cwl | 27 +
tests/test_bad_outputs_wf.cwl | 33 ++
tests/test_check.py | 22 +
tests/test_cwl_version.py | 14 +
tests/test_default_path.py | 15 +
tests/test_deps_env_resolvers_conf.yml | 3 +
tests/test_deps_env_resolvers_conf_rewrite.yml | 3 +
tests/test_deps_mapping.yml | 6 +
tests/test_docker_warning.py | 25 +
tests/test_examples.py | 520 +++++++++++++++++
tests/test_ext.py | 149 +++++
tests/test_fetch.py | 54 ++
tests/test_http_input.py | 26 +
tests/test_js_sandbox.py | 35 ++
tests/test_pack.py | 62 ++
tests/test_pathmapper.py | 56 ++
tests/test_relax_path_checks.py | 46 ++
tests/test_toolargparse.py | 117 ++++
tests/tmp1/tmp2/tmp3/.gitkeep | 0
tests/util.py | 19 +
tests/value | 1 +
tests/wf/4c637b77-8130-4158-807c-ccc78ea7b563 | 1 +
tests/wf/badout1.cwl | 13 +
tests/wf/badout2.cwl | 13 +
tests/wf/badout3.cwl | 13 +
tests/wf/c5b8320e-6e31-4bbb-8453-03b054b3254e | 1 +
tests/wf/cat.cwl | 6 +
tests/wf/conditional.cwl | 22 +
tests/wf/default_path.cwl | 11 +
tests/wf/echo.cwl | 24 +
tests/wf/empty.ttl | 0
tests/wf/emptyscatter.cwl | 18 +
tests/wf/emptyscatter.yml | 1 +
tests/wf/expect_packed.cwl | 130 +++++
tests/wf/foo1.txt | 1 +
tests/wf/foo3.txt | 1 +
tests/wf/fooa.txt | 1 +
tests/wf/foob.txt | 1 +
tests/wf/foofoo5.txt.txt | 1 +
tests/wf/hello-workflow.cwl | 38 ++
tests/wf/hello.txt | 6 +
tests/wf/hello_single_tool.cwl | 9 +
tests/wf/listing_deep.cwl | 12 +
tests/wf/listing_none.cwl | 12 +
tests/wf/listing_shallow.cwl | 12 +
tests/wf/listing_v1_0.cwl | 7 +
tests/wf/loop.cwl | 36 ++
tests/wf/missing_cwlVersion.cwl | 31 +
tests/wf/mut.cwl | 16 +
tests/wf/mut2.cwl | 19 +
tests/wf/mut3.cwl | 21 +
tests/wf/output.txt | 16 +
tests/wf/revsort-job.json | 6 +
tests/wf/revsort-ovr2-job.json | 15 +
tests/wf/revsort.cwl | 68 +++
tests/wf/revtool.cwl | 39 ++
tests/wf/scatterfail.cwl | 39 ++
tests/wf/sorttool.cwl | 35 ++
tests/wf/updatedir.cwl | 16 +
tests/wf/updatedir_inplace.cwl | 20 +
tests/wf/updateval.cwl | 20 +
tests/wf/updateval.py | 6 +
tests/wf/updateval_inplace.cwl | 24 +
tests/wf/value | 1 +
tests/wf/wffail.cwl | 38 ++
tests/wf/whale.txt | 16 +
tests/wf/wrong_cwlVersion.cwl | 32 ++
tests/writeable.cwl | 11 +
150 files changed, 7382 insertions(+), 1735 deletions(-)
create mode 100644 cwltool.egg-info/pbr.json
rename cwltool/{docker_uid.py => docker_id.py} (72%)
create mode 100644 cwltool/extensions.yml
create mode 100644 cwltool/mutation.py
create mode 100644 cwltool/schemas/draft-3/index.md
create mode 100644 cwltool/schemas/v1.0/salad/schema_salad/metaschema/map_res.yml
create mode 100644 cwltool/schemas/v1.0/salad/schema_salad/metaschema/map_res_proc.yml
create mode 100644 cwltool/schemas/v1.0/salad/schema_salad/metaschema/map_res_schema.yml
create mode 100644 cwltool/schemas/v1.0/salad/schema_salad/metaschema/map_res_src.yml
copy cwltool/schemas/v1.0/salad/schema_salad/metaschema/{metaschema.yml => metaschema2.yml} (99%)
create mode 100644 cwltool/schemas/v1.0/salad/schema_salad/metaschema/typedsl_res.yml
create mode 100644 cwltool/schemas/v1.0/salad/schema_salad/metaschema/typedsl_res_proc.yml
create mode 100644 cwltool/schemas/v1.0/salad/schema_salad/metaschema/typedsl_res_schema.yml
create mode 100644 cwltool/schemas/v1.0/salad/schema_salad/metaschema/typedsl_res_src.yml
create mode 100644 cwltool/software_requirements.py
delete mode 100755 ez_setup.py
create mode 100644 tests/2.fasta
create mode 100644 tests/2.fastq
create mode 100644 tests/__init__.py
create mode 100644 tests/cat.cwl
create mode 100644 tests/cat2.cwl
create mode 100644 tests/echo-cwlrun-job.yaml
create mode 100644 tests/echo-job.yaml
create mode 100644 tests/echo.cwl
create mode 100644 tests/env.cwl
create mode 100644 tests/item1.yml
create mode 100644 tests/listing-job.yml
create mode 100644 tests/output.txt
create mode 100644 tests/random_lines.cwl
create mode 100644 tests/random_lines_job.json
create mode 100644 tests/random_lines_mapping.cwl
create mode 100644 tests/seqtk_seq.cwl
create mode 100644 tests/seqtk_seq_job.json
create mode 100644 tests/seqtk_seq_with_docker.cwl
create mode 100644 tests/seqtk_seq_wrong_name.cwl
create mode 100644 tests/test_bad_outputs_wf.cwl
create mode 100644 tests/test_check.py
create mode 100644 tests/test_cwl_version.py
create mode 100644 tests/test_default_path.py
create mode 100644 tests/test_deps_env_resolvers_conf.yml
create mode 100644 tests/test_deps_env_resolvers_conf_rewrite.yml
create mode 100644 tests/test_deps_mapping.yml
create mode 100644 tests/test_docker_warning.py
create mode 100644 tests/test_examples.py
create mode 100644 tests/test_ext.py
create mode 100644 tests/test_fetch.py
create mode 100644 tests/test_http_input.py
create mode 100644 tests/test_js_sandbox.py
create mode 100644 tests/test_pack.py
create mode 100644 tests/test_pathmapper.py
create mode 100644 tests/test_relax_path_checks.py
create mode 100644 tests/test_toolargparse.py
create mode 100644 tests/tmp1/tmp2/tmp3/.gitkeep
create mode 100644 tests/util.py
create mode 100644 tests/value
create mode 100644 tests/wf/4c637b77-8130-4158-807c-ccc78ea7b563
create mode 100644 tests/wf/badout1.cwl
create mode 100644 tests/wf/badout2.cwl
create mode 100644 tests/wf/badout3.cwl
create mode 100644 tests/wf/c5b8320e-6e31-4bbb-8453-03b054b3254e
create mode 100644 tests/wf/cat.cwl
create mode 100644 tests/wf/conditional.cwl
create mode 100644 tests/wf/default_path.cwl
create mode 100644 tests/wf/echo.cwl
create mode 100644 tests/wf/empty.ttl
create mode 100644 tests/wf/emptyscatter.cwl
create mode 100644 tests/wf/emptyscatter.yml
create mode 100644 tests/wf/expect_packed.cwl
create mode 100644 tests/wf/foo1.txt
create mode 100644 tests/wf/foo3.txt
create mode 100644 tests/wf/fooa.txt
create mode 100644 tests/wf/foob.txt
create mode 100644 tests/wf/foofoo5.txt.txt
create mode 100644 tests/wf/hello-workflow.cwl
create mode 100644 tests/wf/hello.txt
create mode 100644 tests/wf/hello_single_tool.cwl
create mode 100644 tests/wf/listing_deep.cwl
create mode 100644 tests/wf/listing_none.cwl
create mode 100644 tests/wf/listing_shallow.cwl
create mode 100644 tests/wf/listing_v1_0.cwl
create mode 100644 tests/wf/loop.cwl
create mode 100644 tests/wf/missing_cwlVersion.cwl
create mode 100644 tests/wf/mut.cwl
create mode 100644 tests/wf/mut2.cwl
create mode 100644 tests/wf/mut3.cwl
create mode 100644 tests/wf/output.txt
create mode 100644 tests/wf/revsort-job.json
create mode 100644 tests/wf/revsort-ovr2-job.json
create mode 100644 tests/wf/revsort.cwl
create mode 100644 tests/wf/revtool.cwl
create mode 100644 tests/wf/scatterfail.cwl
create mode 100644 tests/wf/sorttool.cwl
create mode 100644 tests/wf/updatedir.cwl
create mode 100644 tests/wf/updatedir_inplace.cwl
create mode 100644 tests/wf/updateval.cwl
create mode 100644 tests/wf/updateval.py
create mode 100644 tests/wf/updateval_inplace.cwl
create mode 100644 tests/wf/value
create mode 100644 tests/wf/wffail.cwl
create mode 100644 tests/wf/whale.txt
create mode 100644 tests/wf/wrong_cwlVersion.cwl
create mode 100644 tests/writeable.cwl
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