eemkit 0.1.0__tar.gz

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  1. eemkit-0.1.0/.gitignore +13 -0
  2. eemkit-0.1.0/CHANGELOG.md +35 -0
  3. eemkit-0.1.0/CITATION.cff +20 -0
  4. eemkit-0.1.0/LICENSE +674 -0
  5. eemkit-0.1.0/PKG-INFO +195 -0
  6. eemkit-0.1.0/README.md +151 -0
  7. eemkit-0.1.0/docs/absorbance.md +61 -0
  8. eemkit-0.1.0/docs/api.md +96 -0
  9. eemkit-0.1.0/docs/app-guide.md +378 -0
  10. eemkit-0.1.0/docs/campaigns.md +70 -0
  11. eemkit-0.1.0/docs/corrections.md +55 -0
  12. eemkit-0.1.0/docs/data_model.md +52 -0
  13. eemkit-0.1.0/docs/gui.md +93 -0
  14. eemkit-0.1.0/docs/img/app/1_project.png +0 -0
  15. eemkit-0.1.0/docs/img/app/2_corrections.png +0 -0
  16. eemkit-0.1.0/docs/img/app/3_indices.png +0 -0
  17. eemkit-0.1.0/docs/img/app/4a_parafac_ranks.png +0 -0
  18. eemkit-0.1.0/docs/img/app/4b_parafac_outliers.png +0 -0
  19. eemkit-0.1.0/docs/img/app/4c_parafac_final.png +0 -0
  20. eemkit-0.1.0/docs/img/app/4d_parafac_by_model.png +0 -0
  21. eemkit-0.1.0/docs/img/app/5a_rivers_time.png +0 -0
  22. eemkit-0.1.0/docs/img/app/5b_rivers_composition.png +0 -0
  23. eemkit-0.1.0/docs/img/app/5c_rivers_tests.png +0 -0
  24. eemkit-0.1.0/docs/img/app/6_export.png +0 -0
  25. eemkit-0.1.0/docs/index.md +80 -0
  26. eemkit-0.1.0/docs/indices.md +29 -0
  27. eemkit-0.1.0/docs/parafac.md +44 -0
  28. eemkit-0.1.0/docs/plotting.md +37 -0
  29. eemkit-0.1.0/docs/quickstart.md +114 -0
  30. eemkit-0.1.0/pyproject.toml +72 -0
  31. eemkit-0.1.0/src/eemkit/__init__.py +51 -0
  32. eemkit-0.1.0/src/eemkit/absorbance.py +216 -0
  33. eemkit-0.1.0/src/eemkit/campaigns.py +276 -0
  34. eemkit-0.1.0/src/eemkit/core/__init__.py +1 -0
  35. eemkit-0.1.0/src/eemkit/core/dataset.py +91 -0
  36. eemkit-0.1.0/src/eemkit/core/grid.py +100 -0
  37. eemkit-0.1.0/src/eemkit/core/history.py +78 -0
  38. eemkit-0.1.0/src/eemkit/corrections/__init__.py +44 -0
  39. eemkit-0.1.0/src/eemkit/corrections/_common.py +58 -0
  40. eemkit-0.1.0/src/eemkit/corrections/blank.py +66 -0
  41. eemkit-0.1.0/src/eemkit/corrections/crop.py +33 -0
  42. eemkit-0.1.0/src/eemkit/corrections/inner_filter.py +123 -0
  43. eemkit-0.1.0/src/eemkit/corrections/raman.py +107 -0
  44. eemkit-0.1.0/src/eemkit/corrections/scatter.py +191 -0
  45. eemkit-0.1.0/src/eemkit/corrections/spectral.py +117 -0
  46. eemkit-0.1.0/src/eemkit/errors.py +37 -0
  47. eemkit-0.1.0/src/eemkit/gui/__init__.py +30 -0
  48. eemkit-0.1.0/src/eemkit/gui/__main__.py +5 -0
  49. eemkit-0.1.0/src/eemkit/gui/campaigns_tab.py +275 -0
  50. eemkit-0.1.0/src/eemkit/gui/common.py +395 -0
  51. eemkit-0.1.0/src/eemkit/gui/corrections_tab.py +334 -0
  52. eemkit-0.1.0/src/eemkit/gui/export_tab.py +137 -0
  53. eemkit-0.1.0/src/eemkit/gui/indices_tab.py +228 -0
  54. eemkit-0.1.0/src/eemkit/gui/main_window.py +258 -0
  55. eemkit-0.1.0/src/eemkit/gui/parafac_tab.py +399 -0
  56. eemkit-0.1.0/src/eemkit/gui/project_tab.py +332 -0
  57. eemkit-0.1.0/src/eemkit/gui/state.py +149 -0
  58. eemkit-0.1.0/src/eemkit/gui/theme.py +125 -0
  59. eemkit-0.1.0/src/eemkit/indices.py +256 -0
  60. eemkit-0.1.0/src/eemkit/io/__init__.py +1 -0
  61. eemkit-0.1.0/src/eemkit/io/_cary_csv.py +174 -0
  62. eemkit-0.1.0/src/eemkit/io/cary60.py +120 -0
  63. eemkit-0.1.0/src/eemkit/io/cary_eclipse.py +140 -0
  64. eemkit-0.1.0/src/eemkit/io/discover.py +176 -0
  65. eemkit-0.1.0/src/eemkit/io/loader.py +158 -0
  66. eemkit-0.1.0/src/eemkit/io/pairing.py +115 -0
  67. eemkit-0.1.0/src/eemkit/parafac/__init__.py +28 -0
  68. eemkit-0.1.0/src/eemkit/parafac/_cp.py +125 -0
  69. eemkit-0.1.0/src/eemkit/parafac/diagnostics.py +56 -0
  70. eemkit-0.1.0/src/eemkit/parafac/export.py +54 -0
  71. eemkit-0.1.0/src/eemkit/parafac/model.py +191 -0
  72. eemkit-0.1.0/src/eemkit/parafac/validation.py +111 -0
  73. eemkit-0.1.0/src/eemkit/pipeline.py +560 -0
  74. eemkit-0.1.0/src/eemkit/plot.py +437 -0
  75. eemkit-0.1.0/tests/conftest.py +142 -0
  76. eemkit-0.1.0/tests/test_absorbance.py +95 -0
  77. eemkit-0.1.0/tests/test_campaigns.py +101 -0
  78. eemkit-0.1.0/tests/test_cary60.py +56 -0
  79. eemkit-0.1.0/tests/test_cary_eclipse.py +112 -0
  80. eemkit-0.1.0/tests/test_corrections.py +284 -0
  81. eemkit-0.1.0/tests/test_dataset.py +99 -0
  82. eemkit-0.1.0/tests/test_grid.py +56 -0
  83. eemkit-0.1.0/tests/test_gui.py +222 -0
  84. eemkit-0.1.0/tests/test_indices.py +112 -0
  85. eemkit-0.1.0/tests/test_pairing.py +61 -0
  86. eemkit-0.1.0/tests/test_parafac.py +144 -0
  87. eemkit-0.1.0/tests/test_pipeline.py +224 -0
  88. eemkit-0.1.0/tests/test_plot.py +115 -0
  89. eemkit-0.1.0/tests/test_real_data.py +52 -0
eemkit-0.1.0/.gitignore ADDED
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+ __pycache__/
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+ *.py[cod]
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+ .pytest_cache/
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+ .ruff_cache/
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+ .coverage
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+ htmlcov/
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+ *.egg-info/
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+ build/
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+ dist/
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+ site/
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+
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+ # paper drafts are kept outside the repository
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+ paper/
eemkit-0.1.0/CHANGELOG.md ADDED
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+ # Changelog
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+
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+ All notable changes are listed here. Versions follow
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+ [semantic versioning](https://semver.org/).
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+
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+ ## 0.1.0 (2026-11-05)
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+
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+ First public release.
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+
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+ * Readers for Agilent Cary Eclipse 3-D EEMs and Cary 60 absorbance CSV files;
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+ folder scan, pairing table draft (always excluded until checked) and
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+ multi-sample `xarray` dataset on common wavelength grids.
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+ * Corrections in an enforced order: instrument spectral correction,
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+ absorbance blank, inner filter, blank subtraction, Raman units, scatter
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+ removal with optional interpolation, crop. Every step is recorded in the
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+ processing history.
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+ * Fluorescence indices (FI, HIX, BIX) and Coble peaks.
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+ * CDOM metrics from the absorbance spectra (`eemkit.absorbance`): a254, a350,
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+ S275–295, S350–400, SR, E2:E3 and SUVA254 (with a DOC column), after a
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+ 680–700 nm baseline correction; low-signal values are left empty with the
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+ reason.
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+ * Non-negative PARAFAC with missing values, random starts, core consistency,
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+ leverage, split-half validation and OpenFluor export.
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+ * Comparison of campaigns, sites and rivers (`eemkit.campaigns`): replicate
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+ means per site and time, design and confounding warnings, Kruskal–Wallis
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+ and Dunn–Holm tests within each group, Spearman correlations with site
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+ position and with covariates, PARAFAC composition; optional site and
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+ covariate tables.
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+ * Publication figures (`eemkit.plot`), including a Cary Eclipse colour scale.
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+ * `eemkit.pipeline`: the whole chain driven by one settings file.
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+ * Desktop application (`eemkit-gui`, PySide6): a sidebar of steps with their
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+ status, light and dark themes, and a "Rivers and dates" page; a
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+ PyInstaller recipe for a stand-alone Windows build, which ships the
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+ licence texts of eemkit, Qt and every bundled package.
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+ * Benchmarked against staRdom 1.1.32 on 205 river-water samples.
eemkit-0.1.0/CITATION.cff ADDED
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+ cff-version: 1.2.0
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+ message: "If you use eemkit, please cite it as below."
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+ title: "eemkit: EEM processing and PARAFAC modelling of dissolved organic matter fluorescence"
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+ type: software
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+ authors:
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+ - family-names: Cirrone
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+ given-names: Riccardo Gaetano
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+ affiliation: University of Siena
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+ version: 0.1.0
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+ date-released: "2026-11-05"
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+ license: GPL-3.0-or-later
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+ repository-code: "https://github.com/LowCostSensor/eemkit"
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+ url: "https://lowcostsensor.github.io/eemkit/"
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+ keywords:
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+ - fluorescence
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+ - excitation-emission matrix
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+ - PARAFAC
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+ - dissolved organic matter
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+ - fDOM
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+ - CDOM