moose-classifier 0.15__tar.gz → 1.0__tar.gz

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Files changed (87) hide show
  1. moose_classifier-1.0/.github/workflows/publish-pypi.yml +39 -0
  2. moose_classifier-0.15/.github/workflows/unnittests.yml → moose_classifier-1.0/.github/workflows/unittests.yml +1 -2
  3. {moose_classifier-0.15 → moose_classifier-1.0}/.gitignore +1 -0
  4. {moose_classifier-0.15/src/moose_classifier.egg-info → moose_classifier-1.0}/PKG-INFO +1 -1
  5. {moose_classifier-0.15 → moose_classifier-1.0}/src/classify.py +4 -8
  6. {moose_classifier-0.15 → moose_classifier-1.0/src/moose_classifier.egg-info}/PKG-INFO +1 -1
  7. {moose_classifier-0.15 → moose_classifier-1.0}/src/moose_classifier.egg-info/SOURCES.txt +2 -1
  8. moose_classifier-1.0/testfiles/TestClassify/test01/details.csv.bz2 +0 -0
  9. moose_classifier-1.0/testfiles/TestClassify/test02/details.csv.bz2 +0 -0
  10. moose_classifier-1.0/testfiles/TestClassify/test03/details.csv.bz2 +0 -0
  11. moose_classifier-1.0/testfiles/TestClassify/test06/details.csv.bz2 +0 -0
  12. moose_classifier-1.0/testfiles/TestClassify/test14/details.csv.bz2 +0 -0
  13. moose_classifier-1.0/testfiles/TestClassify/test15/details.csv.bz2 +0 -0
  14. moose_classifier-1.0/testfiles/TestClassify/test16/details.csv.bz2 +0 -0
  15. moose_classifier-0.15/testfiles/TestClassify/test01/details.csv.bz2 +0 -0
  16. moose_classifier-0.15/testfiles/TestClassify/test02/details.csv.bz2 +0 -0
  17. moose_classifier-0.15/testfiles/TestClassify/test03/details.csv.bz2 +0 -0
  18. moose_classifier-0.15/testfiles/TestClassify/test06/details.csv.bz2 +0 -0
  19. moose_classifier-0.15/testfiles/TestClassify/test14/details.csv.bz2 +0 -0
  20. moose_classifier-0.15/testfiles/TestClassify/test15/details.csv.bz2 +0 -0
  21. moose_classifier-0.15/testfiles/TestClassify/test16/details.csv.bz2 +0 -0
  22. {moose_classifier-0.15 → moose_classifier-1.0}/README.md +0 -0
  23. {moose_classifier-0.15 → moose_classifier-1.0}/pyproject.toml +0 -0
  24. {moose_classifier-0.15 → moose_classifier-1.0}/requirements.txt +0 -0
  25. {moose_classifier-0.15 → moose_classifier-1.0}/setup.cfg +0 -0
  26. {moose_classifier-0.15 → moose_classifier-1.0}/sphinx/Makefile +0 -0
  27. {moose_classifier-0.15 → moose_classifier-1.0}/sphinx/classifier.rst +0 -0
  28. {moose_classifier-0.15 → moose_classifier-1.0}/sphinx/conf.py +0 -0
  29. {moose_classifier-0.15 → moose_classifier-1.0}/sphinx/index.rst +0 -0
  30. {moose_classifier-0.15 → moose_classifier-1.0}/sphinx/make.bat +0 -0
  31. {moose_classifier-0.15 → moose_classifier-1.0}/sphinx/modules.rst +0 -0
  32. {moose_classifier-0.15 → moose_classifier-1.0}/src/lineages.py +0 -0
  33. {moose_classifier-0.15 → moose_classifier-1.0}/src/moose_classifier.egg-info/dependency_links.txt +0 -0
  34. {moose_classifier-0.15 → moose_classifier-1.0}/src/moose_classifier.egg-info/entry_points.txt +0 -0
  35. {moose_classifier-0.15 → moose_classifier-1.0}/src/moose_classifier.egg-info/requires.txt +0 -0
  36. {moose_classifier-0.15 → moose_classifier-1.0}/src/moose_classifier.egg-info/top_level.txt +0 -0
  37. {moose_classifier-0.15 → moose_classifier-1.0}/src/version.py +0 -0
  38. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/blast.csv.bz2 +0 -0
  39. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/blast_3strepto.csv +0 -0
  40. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/blast_extrafields.csv.bz2 +0 -0
  41. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/map.csv.bz2 +0 -0
  42. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/map_single.csv.bz2 +0 -0
  43. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/seq_info.csv.bz2 +0 -0
  44. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/taxonomy.csv.bz2 +0 -0
  45. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test01/classifications.csv.bz2 +0 -0
  46. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test02/classifications.csv.bz2 +0 -0
  47. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test02/map_single.csv.bz2 +0 -0
  48. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test03/classifications.csv.bz2 +0 -0
  49. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test06/classifications.csv.bz2 +0 -0
  50. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test06/map.csv.bz2 +0 -0
  51. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test07/blast.csv.bz2 +0 -0
  52. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test07/classifications.csv.bz2 +0 -0
  53. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test07/details.csv.bz2 +0 -0
  54. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test07/map.csv.bz2 +0 -0
  55. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test07/seq_info.csv.bz2 +0 -0
  56. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test07/taxonomy.csv.bz2 +0 -0
  57. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test08/classifications.csv.bz2 +0 -0
  58. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test08/details.csv.bz2 +0 -0
  59. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test09/blast.csv.bz2 +0 -0
  60. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test09/classifications.csv.bz2 +0 -0
  61. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test09/details.csv.bz2 +0 -0
  62. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test09/map.csv.bz2 +0 -0
  63. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test10/classifications.csv.bz2 +0 -0
  64. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test10/details.csv.bz2 +0 -0
  65. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test11/blast.csv.bz2 +0 -0
  66. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test11/classifications.csv.bz2 +0 -0
  67. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test11/details.csv.bz2 +0 -0
  68. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test11/seq_info.csv.bz2 +0 -0
  69. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test11/taxonomy.csv.bz2 +0 -0
  70. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test12/map_single.csv.bz2 +0 -0
  71. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test13/blast.csv.bz2 +0 -0
  72. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test13/classifications.csv.bz2 +0 -0
  73. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test13/seq_info.csv.bz2 +0 -0
  74. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test13/weights.csv.bz2 +0 -0
  75. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test14/classifications.csv.bz2 +0 -0
  76. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test15/classifications.csv.bz2 +0 -0
  77. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test16/classifications.csv.bz2 +0 -0
  78. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test17/classifications.csv.bz2 +0 -0
  79. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test17/details.csv.bz2 +0 -0
  80. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test18/classifications.csv.bz2 +0 -0
  81. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/test18/details.csv.bz2 +0 -0
  82. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/TestClassify/weights.csv.bz2 +0 -0
  83. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/rank_thresholds.csv +0 -0
  84. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/rrnDB_16S_copy_num.csv.bz2 +0 -0
  85. {moose_classifier-0.15 → moose_classifier-1.0}/testfiles/taxonomy.csv.bz2 +0 -0
  86. {moose_classifier-0.15 → moose_classifier-1.0}/tests/__init__.py +0 -0
  87. {moose_classifier-0.15 → moose_classifier-1.0}/tests/test_classify.py +0 -0
moose_classifier-1.0/.github/workflows/publish-pypi.yml ADDED
@@ -0,0 +1,39 @@
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+ ---
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+ name: Publish to PyPI
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+
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+ on:
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+ release:
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+ types: [published]
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+ workflow_dispatch:
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+
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+ jobs:
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+ test:
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+ uses: ./.github/workflows/unittests.yml
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+
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+ publish:
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+ needs: test
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+ runs-on: ubuntu-latest
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+ environment: pypi
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+ permissions:
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+ id-token: write
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+
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+ steps:
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+ - name: Checkout tag
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+ uses: actions/checkout@v4
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+ with:
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+ ref: ${{ github.ref }}
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+ fetch-depth: 0
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+
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+ - name: Set up Python
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+ uses: actions/setup-python@v5
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+ with:
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+ python-version: '3.12'
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+
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+ - name: Install build
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+ run: python -m pip install build
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+
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+ - name: Build package
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+ run: python -m build
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+
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+ - name: Publish to PyPI
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+ uses: pypa/gh-action-pypi-publish@release/v1
moose_classifier-0.15/.github/workflows/unnittests.yml → moose_classifier-1.0/.github/workflows/unittests.yml RENAMED
@@ -5,8 +5,7 @@ on:
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  branches: [ master ]
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  pull_request:
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  branches: [ master ]
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- schedule:
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- - cron: '0 6 * * 1' # 6am Monday
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+ workflow_call:
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  jobs:
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  build:
{moose_classifier-0.15 → moose_classifier-1.0}/.gitignore RENAMED
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  dist
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  *.egg-info
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  test_output
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+ .venv/
{moose_classifier-0.15/src/moose_classifier.egg-info → moose_classifier-1.0}/PKG-INFO RENAMED
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  Metadata-Version: 2.4
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  Name: moose_classifier
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- Version: 0.15
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+ Version: 1.0
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  Summary: Alignment based taxonomic classifier
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  Author: Chris Rosenthal
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  Author-email: crosenth@gmail.com
{moose_classifier-0.15 → moose_classifier-1.0}/src/classify.py RENAMED
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  """sort details for consistency and ease of viewing.
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  [no blast results] may have irregular aligns.columns
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  """
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- aligns = aligns.sort_values(by=details_cols)
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+ aligns = aligns.sort_values(
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+ by=['specimen', 'assignment_id', 'weight', 'pident', 'tax_name'],
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+ ascending=[True, True, False, False, True]
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+ )
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  aligns.to_csv(
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  args.details_out,
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  '--rank-thresholds',
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  metavar='',
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  help='Columns [tax_id,ranks...] [%(default)s]')
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- selection_parser.add_argument(
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- '--top-n-pct',
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- metavar='',
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- default=25,
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- type=float,
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- help=('top percent hits sorted by pident, evalue '
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- 'or bitscore per taxonomy group'))
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  assignment_parser = parser.add_argument_group('assignment options')
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  assignment_parser.add_argument(
{moose_classifier-0.15 → moose_classifier-1.0/src/moose_classifier.egg-info}/PKG-INFO RENAMED
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  Metadata-Version: 2.4
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  Name: moose_classifier
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- Version: 0.15
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+ Version: 1.0
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  Summary: Alignment based taxonomic classifier
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  Author: Chris Rosenthal
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  Author-email: crosenth@gmail.com
{moose_classifier-0.15 → moose_classifier-1.0}/src/moose_classifier.egg-info/SOURCES.txt RENAMED
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  README.md
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  pyproject.toml
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  requirements.txt
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- .github/workflows/unnittests.yml
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+ .github/workflows/publish-pypi.yml
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+ .github/workflows/unittests.yml
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  sphinx/Makefile
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  sphinx/classifier.rst
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  sphinx/conf.py