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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cwltool.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit