[med-svn] [python-pbcommand] 03/03: Merge tag 'upstream/0.5.3'
Sascha Steinbiss
satta at debian.org
Sun Jan 15 09:57:56 UTC 2017
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satta pushed a commit to branch master
in repository python-pbcommand.
commit e1a2eaa419c497019b31476b5b73429e7f4fca7f
Merge: 24ebb07 2869178
Author: Sascha Steinbiss <satta at debian.org>
Date: Sun Jan 15 09:49:47 2017 +0000
Merge tag 'upstream/0.5.3'
Upstream version 0.5.3
Makefile | 18 +-
README.md | 110 ++++-
REQUIREMENTS.txt | 4 +-
REQUIREMENTS_TEST.txt | 9 +-
circle.yml | 2 +-
docs/source/advanced_task_types.rst | 128 ++++++
docs/source/api.rst | 40 ++
docs/source/commandline_interface.rst | 95 ++--
docs/source/conf.py | 11 +-
docs/source/index.rst | 3 +
docs/source/pbcommand.cli.rst | 8 +
docs/source/pbcommand.engine.rst | 9 +
docs/source/pbcommand.models.file_types.rst | 11 +
docs/source/pbcommand.models.rst | 11 +
docs/source/pbcommand.models.rtc.rst | 11 +
docs/source/pbcommand.models.task_options.rst | 11 +
docs/source/pbcommand.models.tc.rst | 11 +
docs/source/pbcommand.models.view_rules.rst | 11 +
docs/source/pbcommand.pb_io.pipeline.rst | 9 +
docs/source/pbcommand.pb_io.tc.rst | 9 +
docs/source/pbcommand.services.rst | 8 +
docs/source/pbcommand.utils.rst | 9 +
docs/source/report_model.rst | 192 ++++++++
docs/source/services.rst | 43 +-
pacbio-manifest.json | 11 +
pbcommand/__init__.py | 2 +-
pbcommand/cli/core.py | 6 +-
pbcommand/cli/examples/dev_app.py | 0
pbcommand/cli/examples/dev_gather_fasta_app.py | 7 +-
pbcommand/cli/examples/dev_mixed_app.py | 30 +-
pbcommand/cli/examples/dev_quick_hello_world.py | 25 +-
pbcommand/cli/examples/dev_scatter_fasta_app.py | 17 +-
pbcommand/cli/examples/dev_simple_app.py | 0
pbcommand/cli/quick.py | 81 +++-
pbcommand/cli/utils.py | 0
pbcommand/engine/runner.py | 7 +-
pbcommand/interactive_resolver.py | 27 +-
pbcommand/models/__init__.py | 12 +-
pbcommand/models/common.py | 481 ++++++++++++++++++++-
pbcommand/models/conditions.py | 32 ++
pbcommand/models/parser.py | 232 +++++-----
pbcommand/models/report.py | 460 ++++++++++++++++++--
pbcommand/models/tool_contract.py | 75 +++-
pbcommand/pb_io/__init__.py | 8 +-
pbcommand/pb_io/common.py | 113 ++++-
pbcommand/pb_io/conditions.py | 53 +++
pbcommand/pb_io/report.py | 39 +-
pbcommand/pb_io/tool_contract_io.py | 55 ++-
pbcommand/resolver.py | 40 +-
pbcommand/schemas/__init__.py | 31 +-
pbcommand/schemas/datastore.avsc | 89 ++++
pbcommand/schemas/datastore_view_rules.avsc | 56 +++
pbcommand/schemas/pbreport.avsc | 56 ++-
pbcommand/schemas/pipeline_presets.avsc | 44 ++
.../schemas/pipeline_template_view_rules.avsc | 50 +++
pbcommand/schemas/report_spec.avsc | 248 +++++++++++
pbcommand/schemas/resolved_tool_contract.avsc | 15 +-
pbcommand/schemas/tool_contract.avsc | 93 +++-
pbcommand/services/cli.py | 205 ++++++++-
pbcommand/services/models.py | 14 +-
pbcommand/services/service_access_layer.py | 102 ++++-
pbcommand/services/utils.py | 6 +-
pbcommand/testkit/base_utils.py | 0
pbcommand/testkit/core.py | 2 +-
pbcommand/utils.py | 92 ++--
pbcommand/validators.py | 53 ++-
setup.py | 1 -
tests/base_utils.py | 19 +
tests/data/dev_gather_fasta_app_tool_contract.json | 37 --
.../example-conditions/reseq-conditions-01.json | 24 +
.../example-conditions/reseq-conditions-02.json | 24 +
.../example-reports/example_version_1_0_0.json | 31 ++
tests/data/example-reports/example_with_plot.json | 24 +
tests/data/example-reports/overview.json | 3 +-
tests/data/example-reports/test_report.json | 40 ++
tests/data/example-reports/test_report2.json | 72 +++
...nd.tasks.dev_txt_custom_outs_tool_contract.json | 44 --
...bcommand.tasks.dev_txt_hello_tool_contract.json | 44 --
.../pipeline-datastore-view-rules/rules_01.json | 20 +
.../pipeline-presets/example-pipeline-presets.json | 17 +
tests/data/report-specs/report_spec.json | 114 +++++
.../dev_example_resolved_tool_contract.json | 0
.../dev_mixed_app_resolved_tool_contract.json | 28 ++
.../resolved_contract_01.json | 0
.../resolved_tool_contract_dev_app.json | 0
.../dev_example_dev_txt_app_tool_contract.json | 72 +--
.../dev_example_tool_contract.json | 72 +--
.../dev_gather_fasta_app_tool_contract.json | 37 ++
.../dev_mixed_app_tool_contract.json | 224 ++++++++++
.../dev_scatter_fasta_app_tool_contract.json | 72 +--
.../pbcommand.tasks.dev_app_tool_contract.json} | 72 +--
...ommand.tasks.dev_fastq2fasta_tool_contract.json | 100 ++---
...mmand.tasks.dev_qhello_world_tool_contract.json | 74 ++--
...nd.tasks.dev_txt_custom_outs_tool_contract.json | 44 ++
...bcommand.tasks.dev_txt_hello_tool_contract.json | 44 ++
.../dev_example_dev_txt_app_tool_contract.json | 50 +++
.../tool-contracts/dev_example_tool_contract.json | 50 +++
.../dev_gather_fasta_app_tool_contract.json | 38 ++
.../dev_mixed_app_tool_contract.json | 102 +++++
.../dev_scatter_fasta_app_tool_contract.json | 50 +++
tests/data/tool-contracts/makefile | 4 +
.../pbcommand.tasks.dev_app_tool_contract.json | 50 +++
...ommand.tasks.dev_fastq2fasta_tool_contract.json | 53 +++
...mmand.tasks.dev_qhello_world_tool_contract.json | 46 ++
...nd.tasks.dev_txt_custom_outs_tool_contract.json | 45 ++
...bcommand.tasks.dev_txt_hello_tool_contract.json | 45 ++
tests/test_e2e_example_apps.py | 65 ++-
tests/test_load_resolved_tool_contract.py | 6 +-
tests/test_models_common_pacbio_options.py | 167 +++++++
tests/test_models_report.py | 221 ++++++++--
tests/test_models_report_attribute.py | 7 -
tests/test_parsers.py | 25 ++
tests/test_pb_io_conditions.py | 48 ++
tests/test_pb_io_report.py | 3 +
tests/test_pb_io_tool_contract.py | 10 +-
tests/test_pb_io_tool_contract_v1.py | 36 ++
tests/test_resolver.py | 69 ++-
tests/test_schema_validation.py | 69 ++-
tests/test_utils.py | 23 +-
tox.ini | 2 +-
120 files changed, 5450 insertions(+), 929 deletions(-)
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