[med-svn] [python-pbcommand] branch upstream updated (3ad18d1 -> 2869178)
Sascha Steinbiss
satta at debian.org
Sun Jan 15 09:57:56 UTC 2017
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satta pushed a change to branch upstream
in repository python-pbcommand.
from 3ad18d1 Imported Upstream version 0.3.22
new 2869178 New upstream version 0.5.3
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:
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(-)
create mode 100644 docs/source/advanced_task_types.rst
create mode 100644 docs/source/api.rst
create mode 100644 docs/source/pbcommand.cli.rst
create mode 100644 docs/source/pbcommand.engine.rst
create mode 100644 docs/source/pbcommand.models.file_types.rst
create mode 100644 docs/source/pbcommand.models.rst
create mode 100644 docs/source/pbcommand.models.rtc.rst
create mode 100644 docs/source/pbcommand.models.task_options.rst
create mode 100644 docs/source/pbcommand.models.tc.rst
create mode 100644 docs/source/pbcommand.models.view_rules.rst
create mode 100644 docs/source/pbcommand.pb_io.pipeline.rst
create mode 100644 docs/source/pbcommand.pb_io.tc.rst
create mode 100644 docs/source/pbcommand.services.rst
create mode 100644 docs/source/pbcommand.utils.rst
create mode 100644 docs/source/report_model.rst
create mode 100644 pacbio-manifest.json
mode change 100755 => 100644 pbcommand/cli/examples/dev_app.py
mode change 100755 => 100644 pbcommand/cli/examples/dev_simple_app.py
mode change 100755 => 100644 pbcommand/cli/utils.py
create mode 100644 pbcommand/models/conditions.py
create mode 100644 pbcommand/pb_io/conditions.py
create mode 100644 pbcommand/schemas/datastore.avsc
create mode 100644 pbcommand/schemas/datastore_view_rules.avsc
create mode 100644 pbcommand/schemas/pipeline_presets.avsc
create mode 100644 pbcommand/schemas/pipeline_template_view_rules.avsc
create mode 100644 pbcommand/schemas/report_spec.avsc
mode change 100755 => 100644 pbcommand/testkit/base_utils.py
delete mode 100644 tests/data/dev_gather_fasta_app_tool_contract.json
create mode 100644 tests/data/example-conditions/reseq-conditions-01.json
create mode 100644 tests/data/example-conditions/reseq-conditions-02.json
create mode 100644 tests/data/example-reports/example_version_1_0_0.json
create mode 100644 tests/data/example-reports/example_with_plot.json
create mode 100644 tests/data/example-reports/test_report.json
create mode 100644 tests/data/example-reports/test_report2.json
delete mode 100644 tests/data/pbcommand.tasks.dev_txt_custom_outs_tool_contract.json
delete mode 100644 tests/data/pbcommand.tasks.dev_txt_hello_tool_contract.json
create mode 100644 tests/data/pipeline-datastore-view-rules/rules_01.json
create mode 100644 tests/data/pipeline-presets/example-pipeline-presets.json
create mode 100644 tests/data/report-specs/report_spec.json
rename tests/data/{ => resolved-tool-contracts}/dev_example_resolved_tool_contract.json (100%)
create mode 100644 tests/data/resolved-tool-contracts/dev_mixed_app_resolved_tool_contract.json
rename tests/data/{ => resolved-tool-contracts}/resolved_contract_01.json (100%)
rename tests/data/{ => resolved-tool-contracts}/resolved_tool_contract_dev_app.json (100%)
rename tests/data/{ => tool-contracts-v1}/dev_example_dev_txt_app_tool_contract.json (52%)
copy tests/data/{ => tool-contracts-v1}/dev_example_tool_contract.json (52%)
create mode 100644 tests/data/tool-contracts-v1/dev_gather_fasta_app_tool_contract.json
create mode 100644 tests/data/tool-contracts-v1/dev_mixed_app_tool_contract.json
rename tests/data/{ => tool-contracts-v1}/dev_scatter_fasta_app_tool_contract.json (54%)
rename tests/data/{dev_example_tool_contract.json => tool-contracts-v1/pbcommand.tasks.dev_app_tool_contract.json} (52%)
rename tests/data/{ => tool-contracts-v1}/pbcommand.tasks.dev_fastq2fasta_tool_contract.json (51%)
rename tests/data/{ => tool-contracts-v1}/pbcommand.tasks.dev_qhello_world_tool_contract.json (54%)
create mode 100644 tests/data/tool-contracts-v1/pbcommand.tasks.dev_txt_custom_outs_tool_contract.json
create mode 100644 tests/data/tool-contracts-v1/pbcommand.tasks.dev_txt_hello_tool_contract.json
create mode 100644 tests/data/tool-contracts/dev_example_dev_txt_app_tool_contract.json
create mode 100644 tests/data/tool-contracts/dev_example_tool_contract.json
create mode 100644 tests/data/tool-contracts/dev_gather_fasta_app_tool_contract.json
create mode 100644 tests/data/tool-contracts/dev_mixed_app_tool_contract.json
create mode 100644 tests/data/tool-contracts/dev_scatter_fasta_app_tool_contract.json
create mode 100644 tests/data/tool-contracts/makefile
create mode 100644 tests/data/tool-contracts/pbcommand.tasks.dev_app_tool_contract.json
create mode 100644 tests/data/tool-contracts/pbcommand.tasks.dev_fastq2fasta_tool_contract.json
create mode 100644 tests/data/tool-contracts/pbcommand.tasks.dev_qhello_world_tool_contract.json
create mode 100644 tests/data/tool-contracts/pbcommand.tasks.dev_txt_custom_outs_tool_contract.json
create mode 100644 tests/data/tool-contracts/pbcommand.tasks.dev_txt_hello_tool_contract.json
create mode 100644 tests/test_models_common_pacbio_options.py
create mode 100644 tests/test_pb_io_conditions.py
create mode 100644 tests/test_pb_io_tool_contract_v1.py
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