virtool-workflow 6.0.0a5__tar.gz → 6.0.0a7__tar.gz

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Files changed (45) hide show
  1. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/PKG-INFO +4 -2
  2. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/pyproject.toml +5 -4
  3. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/pytest_plugin/data.py +1 -1
  4. virtool_workflow-6.0.0a7/virtool_workflow/pytest_plugin/utils.py +9 -0
  5. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/LICENSE +0 -0
  6. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/README.md +0 -0
  7. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/__init__.py +0 -0
  8. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/analysis/__init__.py +0 -0
  9. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/analysis/fastqc.py +0 -0
  10. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/analysis/skewer.py +0 -0
  11. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/analysis/trimming.py +0 -0
  12. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/analysis/utils.py +0 -0
  13. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/api/__init__.py +0 -0
  14. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/api/acquire.py +0 -0
  15. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/api/client.py +0 -0
  16. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/api/utils.py +0 -0
  17. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/cli.py +0 -0
  18. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/data/__init__.py +0 -0
  19. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/data/analyses.py +0 -0
  20. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/data/hmms.py +0 -0
  21. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/data/indexes.py +0 -0
  22. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/data/jobs.py +0 -0
  23. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/data/ml.py +0 -0
  24. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/data/samples.py +0 -0
  25. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/data/subtractions.py +0 -0
  26. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/data/uploads.py +0 -0
  27. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/decorators.py +0 -0
  28. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/errors.py +0 -0
  29. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/files.py +0 -0
  30. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/hooks.py +0 -0
  31. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/pytest_plugin/__init__.py +0 -0
  32. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/pytest_plugin/subprocess.py +0 -0
  33. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/runtime/__init__.py +0 -0
  34. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/runtime/config.py +0 -0
  35. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/runtime/discover.py +0 -0
  36. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/runtime/events.py +0 -0
  37. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/runtime/hook.py +0 -0
  38. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/runtime/path.py +0 -0
  39. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/runtime/ping.py +0 -0
  40. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/runtime/redis.py +0 -0
  41. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/runtime/run.py +0 -0
  42. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/runtime/run_subprocess.py +0 -0
  43. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/runtime/sentry.py +0 -0
  44. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/utils.py +0 -0
  45. {virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/workflow.py +0 -0
{virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: virtool-workflow
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- Version: 6.0.0a5
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+ Version: 6.0.0a7
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  Summary: A framework for developing bioinformatics workflows for Virtool.
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  Home-page: https://github.com/virtool/virtool-workflow
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  License: MIT
@@ -13,11 +13,13 @@ Classifier: Topic :: Software Development :: Libraries
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  Requires-Dist: aiofiles (>=0.7.0,<0.8.0)
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  Requires-Dist: aiohttp (>=3.8.1,<4.0.0)
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  Requires-Dist: aioredis (==1.3.1)
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+ Requires-Dist: biopython (>=1.81,<2.0)
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  Requires-Dist: click (>=8.1.7,<9.0.0)
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  Requires-Dist: orjson (>=3.9.9,<4.0.0)
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+ Requires-Dist: pydantic-factories (>=1.17.3,<2.0.0)
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  Requires-Dist: pyfixtures (>=1.0.0,<2.0.0)
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  Requires-Dist: sentry-sdk (>=1.5.7,<2.0.0)
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- Requires-Dist: virtool-core (>=8.0.0,<9.0.0)
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+ Requires-Dist: virtool-core (>=10.0.1,<11.0.0)
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  Project-URL: Repository, https://github.com/virtool/virtool-workflow
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  Description-Content-Type: text/markdown
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{virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [tool.poetry]
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  name = "virtool-workflow"
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- version = "6.0.0-alpha.5"
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+ version = "6.0.0-alpha.7"
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  description = "A framework for developing bioinformatics workflows for Virtool."
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  authors = ["Ian Boyes", "Blake Smith", "Ryan Fang"]
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  license = "MIT"
@@ -19,11 +19,14 @@ python = "~3.10"
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  click = "^8.1.7"
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  aiohttp = "^3.8.1"
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  aiofiles = "^0.7.0"
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- virtool-core = "^8.0.0"
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+ virtool-core = "^10.0.1"
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  aioredis = "1.3.1"
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  sentry-sdk = "^1.5.7"
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  pyfixtures = "^1.0.0"
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  orjson = "^3.9.9"
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+ biopython = "^1.81"
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+ pydantic-factories = "^1.17.3"
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+
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  [tool.poetry.scripts]
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  run-workflow = "virtool_workflow.cli:cli_main"
@@ -36,11 +39,9 @@ pytest-mock = "^3.10.0"
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  pre-commit = "^2.18.1"
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  sphinx = "^4.0.2"
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  syrupy = "^3.0.5"
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- pydantic-factories = "^1.17.3"
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  sphinx-autobuild = "^2021.3.14"
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  sphinx-nameko-theme = "^0.0.3"
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  pytest-structlog = "^0.6"
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- biopython = "^1.81"
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  sphinx-toolbox = "^3.5.0"
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  [tool.pytest.ini_options]
{virtool_workflow-6.0.0a5 → virtool_workflow-6.0.0a7}/virtool_workflow/pytest_plugin/data.py RENAMED
@@ -19,7 +19,7 @@ from virtool_core.models.subtraction import (
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  SubtractionFile,
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  )
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- from tests.fixtures.api.utils import SUBTRACTION_FILENAMES
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+ from virtool_workflow.pytest_plugin.utils import SUBTRACTION_FILENAMES
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  @dataclass
virtool_workflow-6.0.0a7/virtool_workflow/pytest_plugin/utils.py ADDED
@@ -0,0 +1,9 @@
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+ SUBTRACTION_FILENAMES = (
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+ "subtraction.fa.gz",
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+ "subtraction.1.bt2",
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+ "subtraction.2.bt2",
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+ "subtraction.3.bt2",
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+ "subtraction.4.bt2",
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+ "subtraction.rev.1.bt2",
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+ "subtraction.rev.2.bt2",
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+ )