DiagnoseHarmonisation 1.0.0.post6__tar.gz

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Files changed (76) hide show
  1. diagnoseharmonisation-1.0.0.post6/.gitattributes +2 -0
  2. diagnoseharmonisation-1.0.0.post6/.github/workflows/deploy-docs.yml +34 -0
  3. diagnoseharmonisation-1.0.0.post6/.gitignore +80 -0
  4. diagnoseharmonisation-1.0.0.post6/DiagnoseHarmonisation/DiagnosticFunctions.py +1817 -0
  5. diagnoseharmonisation-1.0.0.post6/DiagnoseHarmonisation/DiagnosticFunctionsLong.py +1818 -0
  6. diagnoseharmonisation-1.0.0.post6/DiagnoseHarmonisation/DiagnosticReport.py +2177 -0
  7. diagnoseharmonisation-1.0.0.post6/DiagnoseHarmonisation/HarmonisationFunctions.py +989 -0
  8. diagnoseharmonisation-1.0.0.post6/DiagnoseHarmonisation/LoggingTool.py +365 -0
  9. diagnoseharmonisation-1.0.0.post6/DiagnoseHarmonisation/PlotDiagnosticResults.py +3174 -0
  10. diagnoseharmonisation-1.0.0.post6/DiagnoseHarmonisation/PowerAnalysis.py +117 -0
  11. diagnoseharmonisation-1.0.0.post6/DiagnoseHarmonisation/SaveDiagnosticResults.py +131 -0
  12. diagnoseharmonisation-1.0.0.post6/DiagnoseHarmonisation/Simulator.py +248 -0
  13. diagnoseharmonisation-1.0.0.post6/DiagnoseHarmonisation/__init__.py +0 -0
  14. diagnoseharmonisation-1.0.0.post6/DiagnoseHarmonisation/_version.py +115 -0
  15. diagnoseharmonisation-1.0.0.post6/DiagnoseHarmonisation/cli.py +279 -0
  16. diagnoseharmonisation-1.0.0.post6/DiagnoseHarmonisation/temp.py +0 -0
  17. diagnoseharmonisation-1.0.0.post6/DiagnoseHarmonisation.egg-info/PKG-INFO +191 -0
  18. diagnoseharmonisation-1.0.0.post6/DiagnoseHarmonisation.egg-info/SOURCES.txt +74 -0
  19. diagnoseharmonisation-1.0.0.post6/DiagnoseHarmonisation.egg-info/dependency_links.txt +1 -0
  20. diagnoseharmonisation-1.0.0.post6/DiagnoseHarmonisation.egg-info/entry_points.txt +2 -0
  21. diagnoseharmonisation-1.0.0.post6/DiagnoseHarmonisation.egg-info/requires.txt +29 -0
  22. diagnoseharmonisation-1.0.0.post6/DiagnoseHarmonisation.egg-info/top_level.txt +1 -0
  23. diagnoseharmonisation-1.0.0.post6/LICENSE +21 -0
  24. diagnoseharmonisation-1.0.0.post6/PKG-INFO +191 -0
  25. diagnoseharmonisation-1.0.0.post6/README.md +127 -0
  26. diagnoseharmonisation-1.0.0.post6/docs/Theory.md +87 -0
  27. diagnoseharmonisation-1.0.0.post6/docs/api/DiagnosticFunctions.md +9 -0
  28. diagnoseharmonisation-1.0.0.post6/docs/api/DiagnosticFunctionsLong.md +9 -0
  29. diagnoseharmonisation-1.0.0.post6/docs/api/DiagnosticReport.md +9 -0
  30. diagnoseharmonisation-1.0.0.post6/docs/api/HarmonisationFunctions.md +9 -0
  31. diagnoseharmonisation-1.0.0.post6/docs/api/LoggingTool.md +9 -0
  32. diagnoseharmonisation-1.0.0.post6/docs/api/PlotDiagnosticResults.md +9 -0
  33. diagnoseharmonisation-1.0.0.post6/docs/api/index.md +17 -0
  34. diagnoseharmonisation-1.0.0.post6/docs/getting_started.md +57 -0
  35. diagnoseharmonisation-1.0.0.post6/docs/index.md +31 -0
  36. diagnoseharmonisation-1.0.0.post6/docs/simulator.md +10 -0
  37. diagnoseharmonisation-1.0.0.post6/docs/terminal.md +30 -0
  38. diagnoseharmonisation-1.0.0.post6/mkdocs.yml +35 -0
  39. diagnoseharmonisation-1.0.0.post6/pyproject.toml +73 -0
  40. diagnoseharmonisation-1.0.0.post6/requirements.txt +12 -0
  41. diagnoseharmonisation-1.0.0.post6/setup.cfg +4 -0
  42. diagnoseharmonisation-1.0.0.post6/tests/.DS_Store +0 -0
  43. diagnoseharmonisation-1.0.0.post6/tests/TestTool.py +0 -0
  44. diagnoseharmonisation-1.0.0.post6/tests/__init__.py +0 -0
  45. diagnoseharmonisation-1.0.0.post6/tests/__pycache__/TestTool.cpython-312-pytest-8.4.1.pyc +0 -0
  46. diagnoseharmonisation-1.0.0.post6/tests/__pycache__/__init__.cpython-312.pyc +0 -0
  47. diagnoseharmonisation-1.0.0.post6/tests/__pycache__/__init__.cpython-313.pyc +0 -0
  48. diagnoseharmonisation-1.0.0.post6/tests/__pycache__/test_CohensD.cpython-312-pytest-8.4.1.pyc +0 -0
  49. diagnoseharmonisation-1.0.0.post6/tests/__pycache__/test_CohensD.cpython-313-pytest-9.0.1.pyc +0 -0
  50. diagnoseharmonisation-1.0.0.post6/tests/__pycache__/test_ComBat.cpython-313-pytest-9.0.1.pyc +0 -0
  51. diagnoseharmonisation-1.0.0.post6/tests/__pycache__/test_DiagnosticFunctions.cpython-312-pytest-8.4.1.pyc +0 -0
  52. diagnoseharmonisation-1.0.0.post6/tests/__pycache__/test_DiagnosticFunctions.cpython-313-pytest-9.0.1.pyc +0 -0
  53. diagnoseharmonisation-1.0.0.post6/tests/__pycache__/test_DiagnosticReport.cpython-312-pytest-8.4.1.pyc +0 -0
  54. diagnoseharmonisation-1.0.0.post6/tests/__pycache__/test_DiagnosticReport.cpython-313-pytest-8.3.4.pyc +0 -0
  55. diagnoseharmonisation-1.0.0.post6/tests/__pycache__/test_DiagnosticReport.cpython-313-pytest-9.0.1.pyc +0 -0
  56. diagnoseharmonisation-1.0.0.post6/tests/__pycache__/test_Mahalanobis.cpython-313-pytest-9.0.1.pyc +0 -0
  57. diagnoseharmonisation-1.0.0.post6/tests/__pycache__/test_PcaCorr.cpython-312-pytest-8.4.1.pyc +0 -0
  58. diagnoseharmonisation-1.0.0.post6/tests/__pycache__/test_PcaCorr.cpython-313-pytest-9.0.1.pyc +0 -0
  59. diagnoseharmonisation-1.0.0.post6/tests/__pycache__/test_PowerAnalysis.cpython-313-pytest-9.0.1.pyc +0 -0
  60. diagnoseharmonisation-1.0.0.post6/tests/__pycache__/test_VarianceRatio.cpython-313-pytest-9.0.1.pyc +0 -0
  61. diagnoseharmonisation-1.0.0.post6/tests/__pycache__/test_combat.cpython-312-pytest-8.4.1.pyc +0 -0
  62. diagnoseharmonisation-1.0.0.post6/tests/__pycache__/test_mahalanobis.cpython-312-pytest-8.4.1.pyc +0 -0
  63. diagnoseharmonisation-1.0.0.post6/tests/__pycache__/test_run_longitudinal.cpython-313-pytest-9.0.1.pyc +0 -0
  64. diagnoseharmonisation-1.0.0.post6/tests/__pycache__/test_variance_ratio.cpython-312-pytest-8.4.1.pyc +0 -0
  65. diagnoseharmonisation-1.0.0.post6/tests/onharmony.csv +181 -0
  66. diagnoseharmonisation-1.0.0.post6/tests/test_CohensD.py +33 -0
  67. diagnoseharmonisation-1.0.0.post6/tests/test_DiagnosticReport.py +395 -0
  68. diagnoseharmonisation-1.0.0.post6/tests/test_VarianceRatio.py +25 -0
  69. diagnoseharmonisation-1.0.0.post6/tests/test_combat.py +50 -0
  70. diagnoseharmonisation-1.0.0.post6/tests/test_covbat.py +171 -0
  71. diagnoseharmonisation-1.0.0.post6/tests/test_frobenius.py +169 -0
  72. diagnoseharmonisation-1.0.0.post6/tests/test_lme.py +45 -0
  73. diagnoseharmonisation-1.0.0.post6/tests/test_mahalanobis.py +45 -0
  74. diagnoseharmonisation-1.0.0.post6/tests/test_missing.py +135 -0
  75. diagnoseharmonisation-1.0.0.post6/tests/test_tool_longitudinal.py +38 -0
  76. diagnoseharmonisation-1.0.0.post6/tests/test_umap.py +238 -0
@@ -0,0 +1,2 @@
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+ # Auto detect text files and perform LF normalization
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+ * text=auto
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+ name: Build and deploy MkDocs site
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+
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+ on:
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+ push:
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+ branches:
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+ - main # change if your main branch is named 'master' or other
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+
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+ permissions:
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+ contents: write # required so gh-pages branch can be updated
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+
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+ jobs:
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+ deploy:
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+ runs-on: ubuntu-latest
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+ steps:
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+ - name: Check out repository
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+ uses: actions/checkout@v4
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+
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+ - name: Set up Python
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+ uses: actions/setup-python@v4
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+ with:
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+ python-version: '3.10'
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+
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+ - name: Install dependencies
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+ run: |
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+ python -m pip install --upgrade pip
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+ pip install mkdocs mkdocs-material mkdocstrings[python]
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+
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+ - name: Build site
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+ run: mkdocs build
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+
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+ - name: Deploy to GitHub Pages
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+ run: mkdocs gh-deploy --force
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+ env:
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+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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+ # Compiled source #
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+ ###################
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+ *.com
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+ *.class
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+ *.dll
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+ *.exe
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+ *.o
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+ *.so
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+
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+ # Packages #
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+ ############
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+ # it's better to unpack these files and commit the raw source
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+ # git has its own built in compression methods
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+ *.7z
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+ *.dmg
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+ *.gz
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+ *.iso
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+ *.jar
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+ *.rar
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+ *.tar
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+ *.zip
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+ umap*
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+ memory*
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+
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+ # Logs and databases #
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+ ######################
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+ *.log
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+ *.sql
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+ *.sqlite
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+
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+ # Python
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+ ####################
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+ __pycache__/
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+ *.py[cod]
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+ *.egg-info/
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+ build/
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+ dist/
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+ .venv/
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+ venv/
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+ .env
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+ .pytest_cache/
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+ requirements.txt
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+ site/
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+ /site/
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+ history/
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+ /history/
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+ .history/
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+ /.history/
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+ /__pycache__/
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+ *__pycache__/
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+
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+ # macOS
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+ ########
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+ .DS_Store
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+ ._*
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+ .AppleDouble/
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+ .LSOverride
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+
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+ # Pytest outputs
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+ ################
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+ .coverage
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+ htmlcov/
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+ .tox/
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+ .cache/
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+ */__pycache__/
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+ tests/__pycache__/
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+ */tests/__pycache__/
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+
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+ # OS generated files #
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+ ######################
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+ .DS_Store
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+ .DS_Store?
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+ ._*
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+ .Spotlight-V100
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+ .Trashes
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+ ehthumbs.db
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+ Thumbs.db
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+ tests/__pycache__/__init__.cpython-313.pyc
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+ tests/__pycache__/test_DiagnosticReport.cpython-313-pytest-9.0.1.pyc
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+ .DS_Store