msreport 0.0.32__tar.gz → 0.0.33__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (104) hide show
  1. msreport-0.0.33/.gitignore +125 -0
  2. msreport-0.0.33/CHANGELOG.md +706 -0
  3. {msreport-0.0.32 → msreport-0.0.33}/PKG-INFO +153 -154
  4. {msreport-0.0.32 → msreport-0.0.33}/README.md +1 -1
  5. msreport-0.0.33/msreport/__init__.py +20 -0
  6. {msreport-0.0.32 → msreport-0.0.33}/msreport/analyze.py +414 -39
  7. {msreport-0.0.32 → msreport-0.0.33}/msreport/plot/distribution.py +3 -3
  8. {msreport-0.0.32 → msreport-0.0.33}/msreport/plot/multivariate.py +0 -1
  9. msreport-0.0.33/msreport/plot/style_sheets/_all_relevant_styles.md +594 -0
  10. {msreport-0.0.32 → msreport-0.0.33}/msreport/qtable.py +3 -2
  11. {msreport-0.0.32 → msreport-0.0.33}/msreport/reader.py +9 -1
  12. {msreport-0.0.32 → msreport-0.0.33}/msreport/rinterface/limma.py +68 -3
  13. {msreport-0.0.32 → msreport-0.0.33}/msreport/rinterface/rscripts/limma.R +79 -18
  14. {msreport-0.0.32 → msreport-0.0.33}/pyproject.toml +28 -31
  15. msreport-0.0.33/tests/_OLD_testdata/.gitignore +1 -0
  16. msreport-0.0.33/tests/_OLD_testdata/common/table.txt +6 -0
  17. msreport-0.0.33/tests/_OLD_testdata/fragpipe/SampleA_1/ion.tsv +1022 -0
  18. msreport-0.0.33/tests/_OLD_testdata/fragpipe/SampleA_1/peptide.tsv +1021 -0
  19. msreport-0.0.33/tests/_OLD_testdata/fragpipe/SampleA_1/protein.tsv +403 -0
  20. msreport-0.0.33/tests/_OLD_testdata/fragpipe/SampleA_1/psm.tsv +551 -0
  21. msreport-0.0.33/tests/_OLD_testdata/fragpipe/SampleB_1/ion.tsv +1083 -0
  22. msreport-0.0.33/tests/_OLD_testdata/fragpipe/SampleB_1/peptide.tsv +1083 -0
  23. msreport-0.0.33/tests/_OLD_testdata/fragpipe/SampleB_1/protein.tsv +562 -0
  24. msreport-0.0.33/tests/_OLD_testdata/fragpipe/SampleB_1/psm.tsv +918 -0
  25. msreport-0.0.33/tests/_OLD_testdata/fragpipe/combined_ion.tsv +1121 -0
  26. msreport-0.0.33/tests/_OLD_testdata/fragpipe/combined_modified_peptide.tsv +1121 -0
  27. msreport-0.0.33/tests/_OLD_testdata/fragpipe/combined_peptide.tsv +1120 -0
  28. msreport-0.0.33/tests/_OLD_testdata/fragpipe/combined_protein.tsv +679 -0
  29. msreport-0.0.33/tests/_OLD_testdata/maxquant/evidence.txt +1523 -0
  30. msreport-0.0.33/tests/_OLD_testdata/maxquant/peptides.txt +1143 -0
  31. msreport-0.0.33/tests/_OLD_testdata/maxquant/proteinGroups.txt +667 -0
  32. msreport-0.0.33/tests/_OLD_testdata/spectronaut/table_spectronaut_style_tag.txt +6 -0
  33. msreport-0.0.33/tests/test_aggregate/test_condense.py +419 -0
  34. msreport-0.0.33/tests/test_aggregate/test_pivot.py +168 -0
  35. msreport-0.0.33/tests/test_aggregate/test_summarize.py +188 -0
  36. {msreport-0.0.32 → msreport-0.0.33}/tests/test_analyze.py +55 -4
  37. msreport-0.0.33/tests/test_normalize/test_categorical_normalizer.py +144 -0
  38. msreport-0.0.33/tests/test_normalize/test_normalize.py +241 -0
  39. msreport-0.0.33/tests/test_reader/test_fragpipe.py +386 -0
  40. msreport-0.0.33/tests/test_reader/test_maxquant.py +106 -0
  41. msreport-0.0.33/tests/test_reader/test_reader_functions.py +557 -0
  42. msreport-0.0.33/tests/test_reader/test_resultreader.py +128 -0
  43. msreport-0.0.33/tests/test_reader/test_spectronaut.py +24 -0
  44. msreport-0.0.33/tests/testdata/common/table.txt +6 -0
  45. msreport-0.0.33/tests/testdata/fragpipe/SampleA_1/ion.tsv +21 -0
  46. msreport-0.0.33/tests/testdata/fragpipe/SampleA_1/peptide.tsv +21 -0
  47. msreport-0.0.33/tests/testdata/fragpipe/SampleA_1/protein.tsv +21 -0
  48. msreport-0.0.33/tests/testdata/fragpipe/SampleA_1/psm.tsv +21 -0
  49. msreport-0.0.33/tests/testdata/fragpipe/SampleB_1/ion.tsv +21 -0
  50. msreport-0.0.33/tests/testdata/fragpipe/SampleB_1/peptide.tsv +21 -0
  51. msreport-0.0.33/tests/testdata/fragpipe/SampleB_1/protein.tsv +21 -0
  52. msreport-0.0.33/tests/testdata/fragpipe/SampleB_1/psm.tsv +21 -0
  53. msreport-0.0.33/tests/testdata/fragpipe/combined_ion.tsv +21 -0
  54. msreport-0.0.33/tests/testdata/fragpipe/combined_modified_peptide.tsv +21 -0
  55. msreport-0.0.33/tests/testdata/fragpipe/combined_peptide.tsv +21 -0
  56. msreport-0.0.33/tests/testdata/fragpipe/combined_protein.tsv +21 -0
  57. msreport-0.0.33/tests/testdata/fragpipe/fragpipe-files.fp-manifest +2 -0
  58. msreport-0.0.33/tests/testdata/maxquant/evidence.txt +21 -0
  59. msreport-0.0.33/tests/testdata/maxquant/peptides.txt +21 -0
  60. msreport-0.0.33/tests/testdata/maxquant/proteinGroups.txt +21 -0
  61. msreport-0.0.33/tests/testdata/spectronaut/ConditionSetup.tsv +3 -0
  62. msreport-0.0.33/tests/testdata/spectronaut/table_spectronaut_style_tag.txt +6 -0
  63. msreport-0.0.32/msreport/__init__.py +0 -11
  64. msreport-0.0.32/msreport.egg-info/PKG-INFO +0 -154
  65. msreport-0.0.32/msreport.egg-info/SOURCES.txt +0 -51
  66. msreport-0.0.32/msreport.egg-info/dependency_links.txt +0 -1
  67. msreport-0.0.32/msreport.egg-info/requires.txt +0 -30
  68. msreport-0.0.32/msreport.egg-info/top_level.txt +0 -1
  69. msreport-0.0.32/setup.cfg +0 -4
  70. msreport-0.0.32/setup.py +0 -3
  71. {msreport-0.0.32 → msreport-0.0.33}/LICENSE.txt +0 -0
  72. {msreport-0.0.32 → msreport-0.0.33}/msreport/aggregate/__init__.py +0 -0
  73. {msreport-0.0.32 → msreport-0.0.33}/msreport/aggregate/condense.py +0 -0
  74. {msreport-0.0.32 → msreport-0.0.33}/msreport/aggregate/pivot.py +0 -0
  75. {msreport-0.0.32 → msreport-0.0.33}/msreport/aggregate/summarize.py +0 -0
  76. {msreport-0.0.32 → msreport-0.0.33}/msreport/errors.py +0 -0
  77. {msreport-0.0.32 → msreport-0.0.33}/msreport/export.py +0 -0
  78. {msreport-0.0.32 → msreport-0.0.33}/msreport/fasta.py +0 -0
  79. {msreport-0.0.32 → msreport-0.0.33}/msreport/helper/__init__.py +0 -0
  80. {msreport-0.0.32 → msreport-0.0.33}/msreport/helper/calc.py +0 -0
  81. {msreport-0.0.32 → msreport-0.0.33}/msreport/helper/maxlfq.py +0 -0
  82. {msreport-0.0.32 → msreport-0.0.33}/msreport/helper/table.py +0 -0
  83. {msreport-0.0.32 → msreport-0.0.33}/msreport/helper/temp.py +0 -0
  84. {msreport-0.0.32 → msreport-0.0.33}/msreport/impute.py +0 -0
  85. {msreport-0.0.32 → msreport-0.0.33}/msreport/isobar.py +0 -0
  86. {msreport-0.0.32 → msreport-0.0.33}/msreport/normalize.py +0 -0
  87. {msreport-0.0.32 → msreport-0.0.33}/msreport/peptidoform.py +0 -0
  88. {msreport-0.0.32 → msreport-0.0.33}/msreport/plot/__init__.py +0 -0
  89. {msreport-0.0.32 → msreport-0.0.33}/msreport/plot/_partial_plots.py +0 -0
  90. {msreport-0.0.32 → msreport-0.0.33}/msreport/plot/comparison.py +0 -0
  91. {msreport-0.0.32 → msreport-0.0.33}/msreport/plot/quality.py +0 -0
  92. {msreport-0.0.32 → msreport-0.0.33}/msreport/plot/style.py +0 -0
  93. {msreport-0.0.32 → msreport-0.0.33}/msreport/plot/style_sheets/msreport-notebook.mplstyle +0 -0
  94. {msreport-0.0.32 → msreport-0.0.33}/msreport/plot/style_sheets/seaborn-whitegrid.mplstyle +0 -0
  95. {msreport-0.0.32 → msreport-0.0.33}/msreport/rinterface/__init__.py +0 -0
  96. {msreport-0.0.32 → msreport-0.0.33}/msreport/rinterface/rinstaller.py +0 -0
  97. {msreport-0.0.32 → msreport-0.0.33}/tests/test_export.py +0 -0
  98. {msreport-0.0.32 → msreport-0.0.33}/tests/test_helper.py +0 -0
  99. {msreport-0.0.32 → msreport-0.0.33}/tests/test_impute.py +0 -0
  100. {msreport-0.0.32 → msreport-0.0.33}/tests/test_isobar.py +0 -0
  101. {msreport-0.0.32 → msreport-0.0.33}/tests/test_maxlfq.py +0 -0
  102. {msreport-0.0.32 → msreport-0.0.33}/tests/test_peptidoform.py +0 -0
  103. {msreport-0.0.32 → msreport-0.0.33}/tests/test_plot.py +0 -0
  104. {msreport-0.0.32 → msreport-0.0.33}/tests/test_qtable.py +0 -0
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+ # Byte-compiled / optimized / DLL files
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+ __pycache__/
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+ # before PyInstaller builds the exe, so as to inject date/other infos into it.
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