XspecT 0.2.0__tar.gz → 0.2.2__tar.gz

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Files changed (87) hide show
  1. {xspect-0.2.0/src/XspecT.egg-info → xspect-0.2.2}/PKG-INFO +1 -1
  2. {xspect-0.2.0 → xspect-0.2.2}/pyproject.toml +1 -1
  3. {xspect-0.2.0 → xspect-0.2.2/src/XspecT.egg-info}/PKG-INFO +1 -1
  4. {xspect-0.2.0 → xspect-0.2.2}/src/xspect/fastapi.py +6 -2
  5. {xspect-0.2.0 → xspect-0.2.2}/.github/workflows/black.yml +0 -0
  6. {xspect-0.2.0 → xspect-0.2.2}/.github/workflows/docs.yml +0 -0
  7. {xspect-0.2.0 → xspect-0.2.2}/.github/workflows/pylint.yml +0 -0
  8. {xspect-0.2.0 → xspect-0.2.2}/.github/workflows/pypi.yml +0 -0
  9. {xspect-0.2.0 → xspect-0.2.2}/.github/workflows/test.yml +0 -0
  10. {xspect-0.2.0 → xspect-0.2.2}/.gitignore +0 -0
  11. {xspect-0.2.0 → xspect-0.2.2}/LICENSE +0 -0
  12. {xspect-0.2.0 → xspect-0.2.2}/README.md +0 -0
  13. {xspect-0.2.0 → xspect-0.2.2}/docs/Instructions/pictures/About.png +0 -0
  14. {xspect-0.2.0 → xspect-0.2.2}/docs/Instructions/pictures/AddFilter.png +0 -0
  15. {xspect-0.2.0 → xspect-0.2.2}/docs/Instructions/pictures/AddSpecies1.png +0 -0
  16. {xspect-0.2.0 → xspect-0.2.2}/docs/Instructions/pictures/AddSpecies2.png +0 -0
  17. {xspect-0.2.0 → xspect-0.2.2}/docs/Instructions/pictures/BF.png +0 -0
  18. {xspect-0.2.0 → xspect-0.2.2}/docs/Instructions/pictures/ClAssT_Ergebnis1.png +0 -0
  19. {xspect-0.2.0 → xspect-0.2.2}/docs/Instructions/pictures/ClAssT_Ergebnis2.png +0 -0
  20. {xspect-0.2.0 → xspect-0.2.2}/docs/Instructions/pictures/ClAssT_Ergebnis3.png +0 -0
  21. {xspect-0.2.0 → xspect-0.2.2}/docs/Instructions/pictures/ClAssT_Hauptseite.png +0 -0
  22. {xspect-0.2.0 → xspect-0.2.2}/docs/Instructions/pictures/CommandLine_Input.png +0 -0
  23. {xspect-0.2.0 → xspect-0.2.2}/docs/Instructions/pictures/CommandLine_results.png +0 -0
  24. {xspect-0.2.0 → xspect-0.2.2}/docs/Instructions/pictures/CommandLine_whole.png +0 -0
  25. {xspect-0.2.0 → xspect-0.2.2}/docs/Instructions/pictures/How2Use.png +0 -0
  26. {xspect-0.2.0 → xspect-0.2.2}/docs/Instructions/pictures/HowtouseAspecT.png +0 -0
  27. {xspect-0.2.0 → xspect-0.2.2}/docs/Instructions/pictures/XspecT_Ergebnis1.png +0 -0
  28. {xspect-0.2.0 → xspect-0.2.2}/docs/Instructions/pictures/XspecT_Ergebnis2.png +0 -0
  29. {xspect-0.2.0 → xspect-0.2.2}/docs/Instructions/pictures/XspecT_Ergebnis3.png +0 -0
  30. {xspect-0.2.0 → xspect-0.2.2}/docs/Instructions/pictures/XspecT_Ergebnis4.png +0 -0
  31. {xspect-0.2.0 → xspect-0.2.2}/docs/Instructions/pictures/XspecT_Hauptseite.png +0 -0
  32. {xspect-0.2.0 → xspect-0.2.2}/docs/Instructions/pictures/XspecT_Runtime.png +0 -0
  33. {xspect-0.2.0 → xspect-0.2.2}/docs/Instructions/pictures/XspecT_Runtime_Oxa.png +0 -0
  34. {xspect-0.2.0 → xspect-0.2.2}/docs/Instructions/pictures/XspecT_Startseite.png +0 -0
  35. {xspect-0.2.0 → xspect-0.2.2}/docs/Instructions/pictures/change_pw.png +0 -0
  36. {xspect-0.2.0 → xspect-0.2.2}/docs/Instructions/pictures/modify_vecs.png +0 -0
  37. {xspect-0.2.0 → xspect-0.2.2}/docs/Instructions/pictures/secretkey.png +0 -0
  38. {xspect-0.2.0 → xspect-0.2.2}/docs/Makefile +0 -0
  39. {xspect-0.2.0 → xspect-0.2.2}/docs/cli.md +0 -0
  40. {xspect-0.2.0 → xspect-0.2.2}/docs/conf.py +0 -0
  41. {xspect-0.2.0 → xspect-0.2.2}/docs/diagrams/probabilistic_filter_models.md +0 -0
  42. {xspect-0.2.0 → xspect-0.2.2}/docs/img/logo.png +0 -0
  43. {xspect-0.2.0 → xspect-0.2.2}/docs/index.md +0 -0
  44. {xspect-0.2.0 → xspect-0.2.2}/docs/input_data.md +0 -0
  45. {xspect-0.2.0 → xspect-0.2.2}/docs/installation.md +0 -0
  46. {xspect-0.2.0 → xspect-0.2.2}/docs/make.bat +0 -0
  47. {xspect-0.2.0 → xspect-0.2.2}/docs/quickstart.md +0 -0
  48. {xspect-0.2.0 → xspect-0.2.2}/docs/web.md +0 -0
  49. {xspect-0.2.0 → xspect-0.2.2}/setup.cfg +0 -0
  50. {xspect-0.2.0 → xspect-0.2.2}/src/XspecT.egg-info/SOURCES.txt +0 -0
  51. {xspect-0.2.0 → xspect-0.2.2}/src/XspecT.egg-info/dependency_links.txt +0 -0
  52. {xspect-0.2.0 → xspect-0.2.2}/src/XspecT.egg-info/entry_points.txt +0 -0
  53. {xspect-0.2.0 → xspect-0.2.2}/src/XspecT.egg-info/requires.txt +0 -0
  54. {xspect-0.2.0 → xspect-0.2.2}/src/XspecT.egg-info/top_level.txt +0 -0
  55. {xspect-0.2.0 → xspect-0.2.2}/src/xspect/__init__.py +0 -0
  56. {xspect-0.2.0 → xspect-0.2.2}/src/xspect/definitions.py +0 -0
  57. {xspect-0.2.0 → xspect-0.2.2}/src/xspect/download_filters.py +0 -0
  58. {xspect-0.2.0 → xspect-0.2.2}/src/xspect/file_io.py +0 -0
  59. {xspect-0.2.0 → xspect-0.2.2}/src/xspect/main.py +0 -0
  60. {xspect-0.2.0 → xspect-0.2.2}/src/xspect/model_management.py +0 -0
  61. {xspect-0.2.0 → xspect-0.2.2}/src/xspect/models/__init__.py +0 -0
  62. {xspect-0.2.0 → xspect-0.2.2}/src/xspect/models/probabilistic_filter_model.py +0 -0
  63. {xspect-0.2.0 → xspect-0.2.2}/src/xspect/models/probabilistic_filter_svm_model.py +0 -0
  64. {xspect-0.2.0 → xspect-0.2.2}/src/xspect/models/probabilistic_single_filter_model.py +0 -0
  65. {xspect-0.2.0 → xspect-0.2.2}/src/xspect/models/result.py +0 -0
  66. {xspect-0.2.0 → xspect-0.2.2}/src/xspect/pipeline.py +0 -0
  67. {xspect-0.2.0 → xspect-0.2.2}/src/xspect/run.py +0 -0
  68. {xspect-0.2.0 → xspect-0.2.2}/src/xspect/train.py +0 -0
  69. {xspect-0.2.0 → xspect-0.2.2}/src/xspect/train_filter/__init__.py +0 -0
  70. {xspect-0.2.0 → xspect-0.2.2}/src/xspect/train_filter/create_svm.py +0 -0
  71. {xspect-0.2.0 → xspect-0.2.2}/src/xspect/train_filter/extract_and_concatenate.py +0 -0
  72. {xspect-0.2.0 → xspect-0.2.2}/src/xspect/train_filter/html_scrap.py +0 -0
  73. {xspect-0.2.0 → xspect-0.2.2}/src/xspect/train_filter/ncbi_api/__init__.py +0 -0
  74. {xspect-0.2.0 → xspect-0.2.2}/src/xspect/train_filter/ncbi_api/download_assemblies.py +0 -0
  75. {xspect-0.2.0 → xspect-0.2.2}/src/xspect/train_filter/ncbi_api/ncbi_assembly_metadata.py +0 -0
  76. {xspect-0.2.0 → xspect-0.2.2}/src/xspect/train_filter/ncbi_api/ncbi_children_tree.py +0 -0
  77. {xspect-0.2.0 → xspect-0.2.2}/src/xspect/train_filter/ncbi_api/ncbi_taxon_metadata.py +0 -0
  78. {xspect-0.2.0 → xspect-0.2.2}/tests/__init__.py +0 -0
  79. {xspect-0.2.0 → xspect-0.2.2}/tests/conftest.py +0 -0
  80. {xspect-0.2.0 → xspect-0.2.2}/tests/test_file_io.py +0 -0
  81. {xspect-0.2.0 → xspect-0.2.2}/tests/test_model_management.py +0 -0
  82. {xspect-0.2.0 → xspect-0.2.2}/tests/test_model_result.py +0 -0
  83. {xspect-0.2.0 → xspect-0.2.2}/tests/test_pipeline.py +0 -0
  84. {xspect-0.2.0 → xspect-0.2.2}/tests/test_probabilistic_filter_model.py +0 -0
  85. {xspect-0.2.0 → xspect-0.2.2}/tests/test_probabilistic_filter_svm_model.py +0 -0
  86. {xspect-0.2.0 → xspect-0.2.2}/tests/test_probabilistic_single_filter_model.py +0 -0
  87. {xspect-0.2.0 → xspect-0.2.2}/tests/test_train.py +0 -0
{xspect-0.2.0/src/XspecT.egg-info → xspect-0.2.2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: XspecT
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- Version: 0.2.0
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+ Version: 0.2.2
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  Summary: Tool to monitor and characterize pathogens using Bloom filters.
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  License: MIT License
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{xspect-0.2.0 → xspect-0.2.2}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [project]
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  name = "XspecT"
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- version = "0.2.0"
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+ version = "0.2.2"
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  description = "Tool to monitor and characterize pathogens using Bloom filters."
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  readme = {file = "README.md", content-type = "text/markdown"}
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  license = {file = "LICENSE"}
{xspect-0.2.0 → xspect-0.2.2/src/XspecT.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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2
  Name: XspecT
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- Version: 0.2.0
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+ Version: 0.2.2
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  Summary: Tool to monitor and characterize pathogens using Bloom filters.
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  License: MIT License
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{xspect-0.2.0 → xspect-0.2.2}/src/xspect/fastapi.py RENAMED
@@ -27,12 +27,16 @@ def classify(genus: str, file: str, meta: bool = False, step: int = 500):
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  path = get_xspect_upload_path() / file
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  pipeline = Pipeline(genus + " classification", "Test Author", "test@example.com")
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- species_execution = ModelExecution(genus + "-species", sparse_sampling_step=step)
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+ species_execution = ModelExecution(
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+ genus.lower() + "-species", sparse_sampling_step=step
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+ )
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  if meta:
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  species_filtering_step = PipelineStep(
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  StepType.FILTERING, genus, 0.7, species_execution
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  )
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- genus_execution = ModelExecution(genus + "-genus", sparse_sampling_step=step)
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+ genus_execution = ModelExecution(
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+ genus.lower() + "-genus", sparse_sampling_step=step
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+ )
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  genus_execution.add_pipeline_step(species_filtering_step)
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  pipeline.add_pipeline_step(genus_execution)
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  else:
{xspect-0.2.0 → xspect-0.2.2}/.gitignore RENAMED
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{xspect-0.2.0 → xspect-0.2.2}/LICENSE RENAMED
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{xspect-0.2.0 → xspect-0.2.2}/README.md RENAMED
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{xspect-0.2.0 → xspect-0.2.2}/docs/Makefile RENAMED
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{xspect-0.2.0 → xspect-0.2.2}/docs/cli.md RENAMED
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{xspect-0.2.0 → xspect-0.2.2}/docs/conf.py RENAMED
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{xspect-0.2.0 → xspect-0.2.2}/docs/img/logo.png RENAMED
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{xspect-0.2.0 → xspect-0.2.2}/docs/input_data.md RENAMED
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{xspect-0.2.0 → xspect-0.2.2}/docs/installation.md RENAMED
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{xspect-0.2.0 → xspect-0.2.2}/docs/make.bat RENAMED
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{xspect-0.2.0 → xspect-0.2.2}/docs/quickstart.md RENAMED
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{xspect-0.2.0 → xspect-0.2.2}/docs/web.md RENAMED
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{xspect-0.2.0 → xspect-0.2.2}/setup.cfg RENAMED
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{xspect-0.2.0 → xspect-0.2.2}/src/xspect/__init__.py RENAMED
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{xspect-0.2.0 → xspect-0.2.2}/src/xspect/definitions.py RENAMED
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{xspect-0.2.0 → xspect-0.2.2}/src/xspect/file_io.py RENAMED
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{xspect-0.2.0 → xspect-0.2.2}/src/xspect/main.py RENAMED
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{xspect-0.2.0 → xspect-0.2.2}/src/xspect/pipeline.py RENAMED
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{xspect-0.2.0 → xspect-0.2.2}/src/xspect/run.py RENAMED
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{xspect-0.2.0 → xspect-0.2.2}/src/xspect/train.py RENAMED
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{xspect-0.2.0 → xspect-0.2.2}/tests/__init__.py RENAMED
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{xspect-0.2.0 → xspect-0.2.2}/tests/conftest.py RENAMED
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{xspect-0.2.0 → xspect-0.2.2}/tests/test_file_io.py RENAMED
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{xspect-0.2.0 → xspect-0.2.2}/tests/test_pipeline.py RENAMED
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{xspect-0.2.0 → xspect-0.2.2}/tests/test_train.py RENAMED
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