[med-svn] [cwltool] branch master updated (a4a66a7 -> 26c8c52)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Fri Aug 11 11:45:41 UTC 2017
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch master
in repository cwltool.
from a4a66a7 Policy, rdflib dep, RRID -> SciCrunch
new 67bf19a New upstream version 1.0.20170803160545
new 26c8c52 new upstream release
The 2 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 | 23 +-
Makefile | 51 +-
PKG-INFO | 448 ++++++++++++++-
README.rst | 415 +++++++++++++-
cwltool.egg-info/PKG-INFO | 448 ++++++++++++++-
cwltool.egg-info/SOURCES.txt | 77 ++-
cwltool.egg-info/requires.txt | 16 +-
cwltool.py | 2 +
cwltool/__init__.py | 1 +
cwltool/__main__.py | 4 +-
cwltool/builder.py | 68 ++-
cwltool/cwlNodeEngine.js | 6 +-
cwltool/cwlrdf.py | 26 +-
cwltool/docker.py | 40 +-
cwltool/{docker_uid.py => docker_id.py} | 39 +-
cwltool/draft2tool.py | 392 ++++++++-----
cwltool/errors.py | 1 +
cwltool/expression.py | 74 ++-
cwltool/extensions.yml | 36 ++
cwltool/factory.py | 25 +-
cwltool/flatten.py | 1 +
cwltool/job.py | 381 ++++++++-----
cwltool/load_tool.py | 198 ++++---
cwltool/main.py | 619 ++++++++++++++-------
cwltool/mutation.py | 69 +++
cwltool/pack.py | 144 +++--
cwltool/pathmapper.py | 179 +++---
cwltool/process.py | 412 +++++++++-----
cwltool/resolver.py | 32 +-
cwltool/sandboxjs.py | 249 +++++++--
cwltool/schemas/draft-3/Workflow.yml | 1 +
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 +
.../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 | 45 +-
cwltool/update.py | 70 ++-
cwltool/utils.py | 158 +++++-
cwltool/workflow.py | 506 ++++++++++++-----
debian/changelog | 8 +-
debian/patches/older-rdflib | 11 +
debian/patches/series | 1 +
ez_setup.py | 391 -------------
gittaggers.py | 4 +-
setup.cfg | 13 +-
setup.py | 71 ++-
tests/2.fasta | 11 +
tests/2.fastq | 12 +
tests/__init__.py | 0
tests/echo-cwlrun-job.yaml | 6 +
tests/echo-job.yaml | 5 +
tests/echo.cwl | 15 +
tests/listing-job.yml | 3 +
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_js_sandbox.py | 35 ++
tests/test_pack.py | 35 ++
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/wf/badout1.cwl | 13 +
tests/wf/badout2.cwl | 13 +
tests/wf/badout3.cwl | 13 +
tests/wf/cat.cwl | 6 +
tests/wf/default_path.cwl | 11 +
tests/wf/echo.cwl | 24 +
tests/wf/empty.ttl | 0
tests/wf/expect_packed.cwl | 130 +++++
tests/wf/hello.txt | 6 +
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/missing_cwlVersion.cwl | 31 ++
tests/wf/mut.cwl | 16 +
tests/wf/mut2.cwl | 19 +
tests/wf/mut3.cwl | 21 +
tests/wf/revsort-job.json | 6 +
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/wffail.cwl | 38 ++
tests/wf/wrong_cwlVersion.cwl | 32 ++
125 files changed, 6963 insertions(+), 1707 deletions(-)
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/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
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
create mode 100644 debian/patches/older-rdflib
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/echo-cwlrun-job.yaml
create mode 100644 tests/echo-job.yaml
create mode 100644 tests/echo.cwl
create mode 100644 tests/listing-job.yml
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_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/wf/badout1.cwl
create mode 100644 tests/wf/badout2.cwl
create mode 100644 tests/wf/badout3.cwl
create mode 100644 tests/wf/cat.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/expect_packed.cwl
create mode 100644 tests/wf/hello.txt
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/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/revsort-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/wffail.cwl
create mode 100644 tests/wf/wrong_cwlVersion.cwl
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