pyNexafs 0.1.0b1__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 (108) hide show
  1. pynexafs-0.1.0b1/.github/workflows/linting.yml +47 -0
  2. pynexafs-0.1.0b1/.github/workflows/semver.yml +249 -0
  3. pynexafs-0.1.0b1/.github/workflows/test.yml +62 -0
  4. pynexafs-0.1.0b1/.gitignore +166 -0
  5. pynexafs-0.1.0b1/.pre-commit-config.yaml +67 -0
  6. pynexafs-0.1.0b1/.readthedocs.yaml +42 -0
  7. pynexafs-0.1.0b1/LICENSE +21 -0
  8. pynexafs-0.1.0b1/PKG-INFO +39 -0
  9. pynexafs-0.1.0b1/README.rst +69 -0
  10. pynexafs-0.1.0b1/docs/CHANGELOG.rst +50 -0
  11. pynexafs-0.1.0b1/docs/conf.py +158 -0
  12. pynexafs-0.1.0b1/docs/examples/example_MEX2.ipynb +724 -0
  13. pynexafs-0.1.0b1/docs/source/_static/index.css +8 -0
  14. pynexafs-0.1.0b1/docs/source/_templates/custom_class_template.rst +32 -0
  15. pynexafs-0.1.0b1/docs/source/_templates/custom_module_template.rst +66 -0
  16. pynexafs-0.1.0b1/docs/source/api.rst +13 -0
  17. pynexafs-0.1.0b1/docs/source/examples.rst +301 -0
  18. pynexafs-0.1.0b1/docs/source/index.rst +48 -0
  19. pynexafs-0.1.0b1/docs/source/install.rst +57 -0
  20. pynexafs-0.1.0b1/docs/source/support.rst +19 -0
  21. pynexafs-0.1.0b1/pyNexafs/__init__.py +15 -0
  22. pynexafs-0.1.0b1/pyNexafs/__main__.py +52 -0
  23. pynexafs-0.1.0b1/pyNexafs/gui/__init__.py +1 -0
  24. pynexafs-0.1.0b1/pyNexafs/gui/data_browser.py +92 -0
  25. pynexafs-0.1.0b1/pyNexafs/gui/icons/flaticon/normalization.png +0 -0
  26. pynexafs-0.1.0b1/pyNexafs/gui/icons/flaticon/normalization_b&w.png +0 -0
  27. pynexafs-0.1.0b1/pyNexafs/gui/icons/normalisation.pdn +0 -0
  28. pynexafs-0.1.0b1/pyNexafs/gui/icons/normalisation.png +0 -0
  29. pynexafs-0.1.0b1/pyNexafs/gui/icons/normalisation2_dark.pdn +0 -0
  30. pynexafs-0.1.0b1/pyNexafs/gui/icons/normalisation2_dark.png +0 -0
  31. pynexafs-0.1.0b1/pyNexafs/gui/icons/normalisation2_light.pdn +0 -0
  32. pynexafs-0.1.0b1/pyNexafs/gui/icons/normalisation2_light.png +0 -0
  33. pynexafs-0.1.0b1/pyNexafs/gui/qant_converter.py +69 -0
  34. pynexafs-0.1.0b1/pyNexafs/gui/widgets/__init__.py +3 -0
  35. pynexafs-0.1.0b1/pyNexafs/gui/widgets/converter.py +931 -0
  36. pynexafs-0.1.0b1/pyNexafs/gui/widgets/fileloader.py +511 -0
  37. pynexafs-0.1.0b1/pyNexafs/gui/widgets/fitting/nexafs_fits.py +64 -0
  38. pynexafs-0.1.0b1/pyNexafs/gui/widgets/graphing/__init__.py +1 -0
  39. pynexafs-0.1.0b1/pyNexafs/gui/widgets/graphing/matplotlib/graphs.py +209 -0
  40. pynexafs-0.1.0b1/pyNexafs/gui/widgets/graphing/matplotlib/styling.py +176 -0
  41. pynexafs-0.1.0b1/pyNexafs/gui/widgets/graphing/matplotlib/widgets.py +1092 -0
  42. pynexafs-0.1.0b1/pyNexafs/gui/widgets/graphing/plotly_graphs.py +35 -0
  43. pynexafs-0.1.0b1/pyNexafs/gui/widgets/io/__init__.py +0 -0
  44. pynexafs-0.1.0b1/pyNexafs/gui/widgets/io/dir_selection.py +221 -0
  45. pynexafs-0.1.0b1/pyNexafs/gui/widgets/io/fileviewer.py +2227 -0
  46. pynexafs-0.1.0b1/pyNexafs/gui/widgets/normaliser.py.old +806 -0
  47. pynexafs-0.1.0b1/pyNexafs/gui/widgets/reducer.py +554 -0
  48. pynexafs-0.1.0b1/pyNexafs/gui/widgets/viewer.py +463 -0
  49. pynexafs-0.1.0b1/pyNexafs/nexafs/__init__.py +26 -0
  50. pynexafs-0.1.0b1/pyNexafs/nexafs/fitting/functions.py +108 -0
  51. pynexafs-0.1.0b1/pyNexafs/nexafs/normalisation/__init__.py +30 -0
  52. pynexafs-0.1.0b1/pyNexafs/nexafs/normalisation/norm_settings.py +1120 -0
  53. pynexafs-0.1.0b1/pyNexafs/nexafs/normalisation/scan_normalised.py +1598 -0
  54. pynexafs-0.1.0b1/pyNexafs/nexafs/scan.py +845 -0
  55. pynexafs-0.1.0b1/pyNexafs/parsers/__init__.py +29 -0
  56. pynexafs-0.1.0b1/pyNexafs/parsers/_base.py +2268 -0
  57. pynexafs-0.1.0b1/pyNexafs/parsers/au/__init__.py +14 -0
  58. pynexafs-0.1.0b1/pyNexafs/parsers/au/aus_sync/MEX1.py +786 -0
  59. pynexafs-0.1.0b1/pyNexafs/parsers/au/aus_sync/MEX1_relabels.py +131 -0
  60. pynexafs-0.1.0b1/pyNexafs/parsers/au/aus_sync/MEX2.py +1156 -0
  61. pynexafs-0.1.0b1/pyNexafs/parsers/au/aus_sync/MEX2_relabels.py +300 -0
  62. pynexafs-0.1.0b1/pyNexafs/parsers/au/aus_sync/SXR.py +461 -0
  63. pynexafs-0.1.0b1/pyNexafs/parsers/au/aus_sync/__init__.py +11 -0
  64. pynexafs-0.1.0b1/pyNexafs/resources.py +18 -0
  65. pynexafs-0.1.0b1/pyNexafs/utils/__init__.py +18 -0
  66. pynexafs-0.1.0b1/pyNexafs/utils/decorators.py +226 -0
  67. pynexafs-0.1.0b1/pyNexafs/utils/mda.py +1264 -0
  68. pynexafs-0.1.0b1/pyNexafs/utils/reduction.py +680 -0
  69. pynexafs-0.1.0b1/pyNexafs/utils/sizes.py +42 -0
  70. pynexafs-0.1.0b1/pyNexafs.egg-info/PKG-INFO +39 -0
  71. pynexafs-0.1.0b1/pyNexafs.egg-info/SOURCES.txt +106 -0
  72. pynexafs-0.1.0b1/pyNexafs.egg-info/dependency_links.txt +1 -0
  73. pynexafs-0.1.0b1/pyNexafs.egg-info/requires.txt +4 -0
  74. pynexafs-0.1.0b1/pyNexafs.egg-info/top_level.txt +2 -0
  75. pynexafs-0.1.0b1/pyproject.toml +229 -0
  76. pynexafs-0.1.0b1/setup.cfg +4 -0
  77. pynexafs-0.1.0b1/tests/parsers/au/test_parser_au-MEX1.py +0 -0
  78. pynexafs-0.1.0b1/tests/parsers/au/test_parser_au-MEX2.py +97 -0
  79. pynexafs-0.1.0b1/tests/parsers/au/test_parser_au-SXR.py +0 -0
  80. pynexafs-0.1.0b1/tests/test_data/au/MEX1/MEX1_40747.mda +0 -0
  81. pynexafs-0.1.0b1/tests/test_data/au/MEX1/MEX1_40747_processed.asc +307 -0
  82. pynexafs-0.1.0b1/tests/test_data/au/MEX1/MEX1_40747_processed.xdi +229 -0
  83. pynexafs-0.1.0b1/tests/test_data/au/MEX2/2024-03/MEX2_5640.mda +0 -0
  84. pynexafs-0.1.0b1/tests/test_data/au/MEX2/2024-03/MEX2_5640_processed.xdi +273 -0
  85. pynexafs-0.1.0b1/tests/test_data/au/MEX2/2024-03/MEX2_5641.mda +0 -0
  86. pynexafs-0.1.0b1/tests/test_data/au/MEX2/2024-03/MEX2_5641_processed.xdi +273 -0
  87. pynexafs-0.1.0b1/tests/test_data/au/MEX2/2024-03/MEX2_5642.mda +0 -0
  88. pynexafs-0.1.0b1/tests/test_data/au/MEX2/2024-03/MEX2_5642_processed.xdi +273 -0
  89. pynexafs-0.1.0b1/tests/test_data/au/MEX2/2025-03/MEX2_13366.mda +0 -0
  90. pynexafs-0.1.0b1/tests/test_data/au/MEX2/2025-03/MEX2_13366_processed.xdi +557 -0
  91. pynexafs-0.1.0b1/tests/test_data/au/MEX2/2025-03/MEX2_13385.mda +0 -0
  92. pynexafs-0.1.0b1/tests/test_data/au/MEX2/2025-03/MEX2_13385_processed.xdi +557 -0
  93. pynexafs-0.1.0b1/tests/test_data/au/MEX2/2025-03/MEX2_13386.mda +0 -0
  94. pynexafs-0.1.0b1/tests/test_data/au/MEX2/2025-03/MEX2_13386_processed.xdi +557 -0
  95. pynexafs-0.1.0b1/tests/test_data/au/SXR/sxr129598.asc +871 -0
  96. pynexafs-0.1.0b1/tests/test_data/au/SXR/sxr129598.mda +0 -0
  97. pynexafs-0.1.0b1/tests/test_data/au/SXR/sxr129930.asc +571 -0
  98. pynexafs-0.1.0b1/tests/test_data/au/SXR/sxr129930.mda +0 -0
  99. pynexafs-0.1.0b1/tests/test_data/au/SXR/sxr129931.asc +571 -0
  100. pynexafs-0.1.0b1/tests/test_data/au/SXR/sxr129931.mda +0 -0
  101. pynexafs-0.1.0b1/tests/test_data/au/SXR/sxr129932.asc +571 -0
  102. pynexafs-0.1.0b1/tests/test_data/au/SXR/sxr129932.mda +0 -0
  103. pynexafs-0.1.0b1/tests/test_data/au/SXR/sxr129933.asc +571 -0
  104. pynexafs-0.1.0b1/tests/test_data/au/SXR/sxr129933.mda +0 -0
  105. pynexafs-0.1.0b1/tests/test_data/au/SXR/sxr129934.asc +571 -0
  106. pynexafs-0.1.0b1/tests/test_data/au/SXR/sxr129934.mda +0 -0
  107. pynexafs-0.1.0b1/tests/test_parser_base.py +499 -0
  108. pynexafs-0.1.0b1/tests/test_scan.py +11 -0
@@ -0,0 +1,47 @@
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+ name: Linting 📜 (NumpyDoc, Ruff & Black)
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+ run-name: ${{ github.actor }} - Linting 📜 (NumpyDoc, Ruff & Black)
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+
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+ concurrency:
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+ group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}-linting
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+ cancel-in-progress: true
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+
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+ on:
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+ push:
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+ pull_request:
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+ branches:
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+ - main
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+
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+ jobs:
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+ build:
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+ runs-on: ${{ matrix.os }}-latest
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+ strategy:
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+ matrix:
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+ os: [Ubuntu]
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+ python-version: ["3.13", "3.12", "3.11"]
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+ include:
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+ - os: Windows
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+ python-version: "3.13"
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+ - os: macOS
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+ python-version: "3.13"
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+ steps:
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+ - uses: actions/checkout@v4
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+ - name: Set up Python ${{ matrix.python-version }}
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+ uses: actions/setup-python@v5
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+ with:
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+ python-version: ${{ matrix.python-version }}
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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 numpydoc black ruff
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+
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+ - name: Analysing the code with Ruff
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+ run: |
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+ ruff check
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+
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+ - name: Analysing the code with black
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+ run: |
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+ black --check .
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+
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+ - name: Analysing the code with numpydoc
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+ run: | # Exclude test and gui files.
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+ numpydoc lint --config . $(git ls-files -- '*.py' ':!:*tests/*' ':!:*gui/*')
@@ -0,0 +1,249 @@
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+ # Based on Python Semantic Release (PSR) and PYPI (Python Package Index) as of July-2025
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+ # [1] https://python-semantic-release.readthedocs.io/en/stable/configuration/automatic-releases/github-actions.html#examples
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+ # [2] https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
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+
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+ name: Python 🐍 Semantic Versioning
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+ run-name: ${{ github.actor }} - Python 🐍 Semantic Versioning
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+
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+ concurrency:
9
+ group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.ref_name }}-release
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+ cancel-in-progress: false
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+
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+ on:
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+ workflow_dispatch:
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+ inputs:
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+ prerelease:
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+ description: 'Run as a prerelease?'
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+ required: true
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+ type: boolean
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+ default: true
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+ prerelease_token:
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+ description: 'Token for prerelease'
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+ required: false
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+ type: choice
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+ options:
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+ - alpha
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+ - beta
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+ - rc
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+ default: 'beta'
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+ push:
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+
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+ permissions:
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+ contents: read
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+
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+ jobs:
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+ semver-release:
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+ name: Run Python 🐍 Semantic Version to stamp distribution 📦
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+ # Only run this job on the master account.
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+ runs-on: ubuntu-latest
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+ # defaults: # https://github.com/actions/upload-artifact/issues/232#issuecomment-1065422577
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+ # run:
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+ # working-directory: ./pyNexafs
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+ permissions:
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+ contents: write
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+ outputs:
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+ released: ${{ steps.is_released.outputs.released }}
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+
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+ steps:
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+ - name: Use workflow inputs for pre-release
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+ shell: bash
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+ if: ${{ github.event == 'workflow_dispatch' }}
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+ run: |
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+ echo "prerelease=${{ github.event.inputs.prerelease }}" >> $GITHUB_ENV
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+ echo "prerelease_token=${{ github.event.inputs.prerelease_token }}" >> $GITHUB_ENV
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+ - name: Set default value for pre-release
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+ shell: bash
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+ if: ${{ github.event != 'workflow_dispatch' }}
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+ run: |
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+ echo "prerelease=true" >> $GITHUB_ENV
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+ echo "prerelease_token=beta" >> $GITHUB_ENV
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+ - name: Display pre-release input
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+ shell: bash
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+ run: |
63
+ echo "Python SemVer pre-release?: $prerelease"
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+ # Note: We checkout the repository at the branch that triggered the workflow
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+ # with the entire history to ensure to match PSR's release branch detection
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+ # and history evaluation.
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+ # However, we forcefully reset the branch to the workflow sha because it is
68
+ # possible that the branch was updated while the workflow was running. This
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+ # prevents accidentally releasing un-evaluated changes.
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+ - name: Setup | Checkout Repository on Release Branch
71
+ uses: actions/checkout@v4
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+ with:
73
+ ref: ${{ github.ref_name }}
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+ fetch-depth: 0
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+
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+ - name: Setup | Force release branch to be at workflow sha
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+ run: |
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+ git reset --hard ${{ github.sha }}
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+
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+ - name: Evaluate | Verify upstream has NOT changed
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+ # Last chance to abort before causing an error as another PR/push was applied to
82
+ # the upstream branch while this workflow was running. This is important
83
+ # because we are committing a version change (--commit). You may omit this step
84
+ # if you have 'commit: false' in your configuration.
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+ #
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+ # You may consider moving this to a repo script and call it from this step instead
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+ # of writing it in-line.
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+ shell: bash
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+ run: |
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+ set +o pipefail
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+
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+ UPSTREAM_BRANCH_NAME="$(git status -sb | head -n 1 | cut -d' ' -f2 | grep -E '\.{3}' | cut -d'.' -f4)"
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+ printf '%s\n' "Upstream branch name: $UPSTREAM_BRANCH_NAME"
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+
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+ set -o pipefail
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+
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+ if [ -z "$UPSTREAM_BRANCH_NAME" ]; then
98
+ printf >&2 '%s\n' "::error::Unable to determine upstream branch name!"
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+ exit 1
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+ fi
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+
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+ git fetch "${UPSTREAM_BRANCH_NAME%%/*}"
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+
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+ if ! UPSTREAM_SHA="$(git rev-parse "$UPSTREAM_BRANCH_NAME")"; then
105
+ printf >&2 '%s\n' "::error::Unable to determine upstream branch sha!"
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+ exit 1
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+ fi
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+
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+ HEAD_SHA="$(git rev-parse HEAD)"
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+
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+ if [ "$HEAD_SHA" != "$UPSTREAM_SHA" ]; then
112
+ printf >&2 '%s\n' "[HEAD SHA] $HEAD_SHA != $UPSTREAM_SHA [UPSTREAM SHA]"
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+ printf >&2 '%s\n' "::error::Upstream has changed, aborting release..."
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+ exit 1
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+ fi
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+
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+ printf '%s\n' "Verified upstream branch has not changed, continuing with release..."
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+
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+ # - name: Delete Previous | Distribution Artifacts
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+ # uses: actions/delete-artifact@v4 ???
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+ # with:
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+ # name: distribution-artifacts
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+ # path: dist
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+ - name: Action | Semantic Version Release
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+ id: release
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+ # Adjust tag with desired version if applicable.
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+ # https://python-semantic-release.readthedocs.io/en/stable/configuration/automatic-releases/github-actions.html
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+ uses: python-semantic-release/python-semantic-release@v10.2.0
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+ with:
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+ github_token: ${{ secrets.GITHUB_TOKEN }}
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+ git_committer_name: "github-actions"
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+ git_committer_email: "actions@users.noreply.github.com"
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+ build: true
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+ prerelease: ${{ env.prerelease == 'true' }}
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+ prerelease_token: ${{ env.prerelease_token }}
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+ changelog: true
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+ verbosity: 2
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+ no_operation_mode: ${{ github.repository_owner != 'xraysoftmat'}}
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+
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+ - name: Env | Check if released and log conditionals
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+ id: is_released
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+ run: |
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+ echo "Success: ${{ steps.release.outcome }} ; ${{ steps.release.outcome == 'success' }}"
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+ echo "Ownership: ${{ github.repository_owner }} ; ${{ github.repository_owner == 'xraysoftmat' }}"
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+ echo "Released: ${{ steps.release.outputs.released }}"
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+ echo "Branch: ${{ github.ref }}; ${{ github.ref == 'refs/heads/main' }}"
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+ echo "released=${{ steps.release.outcome && github.ref == 'refs/heads/main' && steps.release.outputs.released && github.repository_owner == 'xraysoftmat' && steps.release.outcome == 'success' }}" >> "$GITHUB_OUTPUT"
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+
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+ - name: Display | Release Information
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+ if: |
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+ success() && steps.is_released.outputs.released
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+ run: |
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+ echo "Process Release: ${{ steps.is_released.outputs.released }}"
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+ echo "Release Tag: ${{ steps.release.outputs.tag }}"
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+ echo "Release Version: ${{ steps.release.outputs.version }}"
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+ echo "Release Branch: ${{ github.ref_name }}"
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+ echo "Release Prerelease: ${{ env.prerelease }}"
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+
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+ - name: Publish | Upload to GitHub Release Assets
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+ uses: python-semantic-release/publish-action@v10.2.0
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+ if: |
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+ success() && steps.is_released.outputs.released == 'true'
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+ with:
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+ github_token: ${{ secrets.GITHUB_TOKEN }}
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+ tag: ${{ steps.release.outputs.tag }}
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+
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+ - name: Upload | Distribution Artifacts
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+ uses: actions/upload-artifact@v4
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+ if: |
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+ success() && steps.is_released.outputs.released == 'true'
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+ with:
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+ name: distribution-artifacts
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+ path: ./dist
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+ overwrite: true
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+ if-no-files-found: error
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+
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+ - name: Publish | Upload to GitHub Release Assets
178
+ uses: python-semantic-release/publish-action@v10.2.0
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+ if: |
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+ success() && steps.is_released.outputs.released == 'true'
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+ with:
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+ github_token: ${{ secrets.GITHUB_TOKEN }}
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+ tag: ${{ steps.release.outputs.tag }}
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+
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+ pypi-deploy:
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+ # 1. Separate out the deploy step from the publish step to run each step at
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+ # the least amount of token privilege
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+ # 2. Also, deployments can fail, and its better to have a separate job if you need to retry
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+ # and it won't require reversing the release.
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+ name: Publish Python 🐍 distribution 📦 release to PyPI
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+ runs-on: ubuntu-latest
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+ needs: semver-release # match the job name above
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+ if: |
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+ success() && needs.semver-release.outputs.released == 'true'
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+ defaults:
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+ run:
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+ working-directory: ./pyNexafs
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+ # Only run this job on the master account, only publish to PyPI on tag pushes
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+ permissions:
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+ contents: read
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+ id-token: write
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+
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+ environment:
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+ name: pypi
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+ url: https://pypi.org/p/pyNexafs
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+
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+ steps:
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+ - name: Setup | Download Build Artifacts
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+ uses: actions/download-artifact@v4
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+ id: artifact-download
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+ with:
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+ name: distribution-artifacts # Match the name used in the upload step
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+ path: pyNexafs/dist # Match the path used in the upload step
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+
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+ - name: Publish package distribution 📦 to PyPI
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+ uses: pypa/gh-action-pypi-publish@release/v1
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+ with:
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+ packages-dir: pyNexafs/dist
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+
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+
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+ ### Not currently using TestPyPI, but can be enabled if needed.
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+ # testpypi-deploy:
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+ # name: Publish Python 🐍 distribution 📦 to TestPyPI
224
+ # runs-on: ubuntu-latest
225
+ # # Only run this job on the master account, only publish to TestPyPI on tag pushes
226
+ # needs: semver-release # match the job name above
227
+ # if: |
228
+ # success() && needs.semver-release.outputs.released == 'true'
229
+ # environment:
230
+ # name: testpypi
231
+ # url: https://test.pypi.org/p/pyNexafs
232
+
233
+ # permissions:
234
+ # contents: read
235
+ # id-token: write # IMPORTANT: mandatory for trusted publishing
236
+
237
+ # steps:
238
+ # - name: Setup | Download Build Artifacts
239
+ # uses: actions/download-artifact@v4
240
+ # id: artifact-download
241
+ # with:
242
+ # name: distribution-artifacts # Match the name used in the upload step
243
+ # path: pyNexafs/dist # Match the path used in the upload step
244
+
245
+ # - name: Publish distribution 📦 to TestPyPI
246
+ # uses: pypa/gh-action-pypi-publish@release/v1
247
+ # with:
248
+ # repository-url: https://test.pypi.org/legacy/
249
+ # packages-dir: pyNexafs/dist
@@ -0,0 +1,62 @@
1
+ name: Tests 🔧 (PyTest, Coveralls)
2
+ run-name: ${{ github.actor }} - Tests 🔧 (PyTest, Coveralls)
3
+
4
+ concurrency:
5
+ group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}-tests
6
+ cancel-in-progress: true
7
+
8
+ on:
9
+ push:
10
+ pull_request:
11
+ branches:
12
+ - main
13
+
14
+ jobs:
15
+ test:
16
+ runs-on: ${{ matrix.os }}-latest
17
+ strategy:
18
+ matrix:
19
+ os: [Ubuntu]
20
+ python-version: ["3.13", "3.12", "3.11"]
21
+ # sphinx-version:
22
+ # ["sphinx==6.0", "sphinx==6.2", "sphinx==7.0", "sphinx>=7.3"]
23
+ include:
24
+ - os: Windows
25
+ python-version: "3.13"
26
+ - os: MacOS
27
+ python-version: "3.13"
28
+ # sphinx-version: "sphinx" # version shouldn't really matter here
29
+ defaults:
30
+ run:
31
+ shell: bash -eo pipefail {0} # Fail on any error (-e), fail on any failed command in a pipeline.
32
+ steps:
33
+ - uses: actions/checkout@v4
34
+
35
+ - name: Python setup
36
+ uses: actions/setup-python@v5
37
+ with:
38
+ python-version: ${{ matrix.python-version }}
39
+
40
+ - name: Setup environment
41
+ run: |
42
+ python -m pip install --upgrade pip wheel setuptools uv
43
+ python -m pip install coveralls
44
+ python -m pip list
45
+ # python -m pip install ${{ matrix.sphinx-version }}
46
+
47
+ - name: Install
48
+ run: |
49
+ uv pip install . --group dev --group docs --system
50
+ pip list
51
+ # system is used to install the package globally in the test environment.
52
+
53
+ - name: Run test suite
54
+ run: |
55
+ pytest -v --pyargs .
56
+
57
+ - name: Test coverage
58
+ run: |
59
+ coverage run --source=pyNexafs -m pytest tests/
60
+ coveralls
61
+ env:
62
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -0,0 +1,166 @@
1
+ # Byte-compiled / optimized / DLL files
2
+ __pycache__/
3
+ *.py[cod]
4
+ *$py.class
5
+
6
+ # C extensions
7
+ *.so
8
+
9
+ # Distribution / packaging
10
+ .Python
11
+ build/
12
+ develop-eggs/
13
+ dist/
14
+ downloads/
15
+ eggs/
16
+ .eggs/
17
+ lib/
18
+ lib64/
19
+ parts/
20
+ sdist/
21
+ var/
22
+ wheels/
23
+ share/python-wheels/
24
+ *.egg-info/
25
+ .installed.cfg
26
+ *.egg
27
+ MANIFEST
28
+
29
+ # PyInstaller
30
+ # Usually these files are written by a python script from a template
31
+ # before PyInstaller builds the exe, so as to inject date/other infos into it.
32
+ *.manifest
33
+ *.spec
34
+
35
+ # Installer logs
36
+ pip-log.txt
37
+ pip-delete-this-directory.txt
38
+
39
+ # Unit test / coverage reports
40
+ htmlcov/
41
+ .tox/
42
+ .nox/
43
+ .coverage
44
+ .coverage.*
45
+ .cache
46
+ nosetests.xml
47
+ coverage.xml
48
+ *.cover
49
+ *.py,cover
50
+ .hypothesis/
51
+ .pytest_cache/
52
+ cover/
53
+
54
+ # Translations
55
+ *.mo
56
+ *.pot
57
+
58
+ # Django stuff:
59
+ *.log
60
+ local_settings.py
61
+ db.sqlite3
62
+ db.sqlite3-journal
63
+
64
+ # Flask stuff:
65
+ instance/
66
+ .webassets-cache
67
+
68
+ # Scrapy stuff:
69
+ .scrapy
70
+
71
+ # Sphinx documentation
72
+ docs/_build/
73
+
74
+ # PyBuilder
75
+ .pybuilder/
76
+ target/
77
+
78
+ # Jupyter Notebook
79
+ .ipynb_checkpoints
80
+
81
+ # IPython
82
+ profile_default/
83
+ ipython_config.py
84
+
85
+ # pyenv
86
+ # For a library or package, you might want to ignore these files since the code is
87
+ # intended to run in multiple environments; otherwise, check them in:
88
+ # .python-version
89
+
90
+ # pipenv
91
+ # According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
92
+ # However, in case of collaboration, if having platform-specific dependencies or dependencies
93
+ # having no cross-platform support, pipenv may install dependencies that don't work, or not
94
+ # install all needed dependencies.
95
+ #Pipfile.lock
96
+
97
+ # poetry
98
+ # Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
99
+ # This is especially recommended for binary packages to ensure reproducibility, and is more
100
+ # commonly ignored for libraries.
101
+ # https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
102
+ #poetry.lock
103
+
104
+ # pdm
105
+ # Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
106
+ #pdm.lock
107
+ # pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
108
+ # in version control.
109
+ # https://pdm.fming.dev/#use-with-ide
110
+ .pdm.toml
111
+
112
+ # PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
113
+ __pypackages__/
114
+
115
+ # Celery stuff
116
+ celerybeat-schedule
117
+ celerybeat.pid
118
+
119
+ # SageMath parsed files
120
+ *.sage.py
121
+
122
+ # Environments
123
+ .env
124
+ .venv
125
+ env/
126
+ venv/
127
+ ENV/
128
+ env.bak/
129
+ venv.bak/
130
+
131
+ # Spyder project settings
132
+ .spyderproject
133
+ .spyproject
134
+
135
+ # Rope project settings
136
+ .ropeproject
137
+
138
+ # mkdocs documentation
139
+ /site
140
+
141
+ # mypy
142
+ .mypy_cache/
143
+ .dmypy.json
144
+ dmypy.json
145
+
146
+ # Pyre type checker
147
+ .pyre/
148
+
149
+ # pytype static type analyzer
150
+ .pytype/
151
+
152
+ # Cython debug symbols
153
+ cython_debug/
154
+
155
+ # PyCharm
156
+ # JetBrains specific template is maintained in a separate JetBrains.gitignore that can
157
+ # be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
158
+ # and can be added to the global gitignore or merged into this file. For a more nuclear
159
+ # option (not recommended) you can uncomment the following to ignore the entire idea folder.
160
+ #.idea/
161
+
162
+ # Datafiles
163
+ .asc
164
+
165
+ tests/archive*
166
+ .vscode*
@@ -0,0 +1,67 @@
1
+ ### `Pre-commit` module configuration file
2
+ # Can be installed using `pip install pre-commit`
3
+ # The pre-commit hooks can then be installed using:
4
+ # >>> pre-commit install --hook-type pre-commit --hook-type commit-msg --hook-type pre-push
5
+ # All checks are run by default when `git <action>` is run for the given hook, i.e. commit.
6
+
7
+ repos:
8
+ # Pre-commit hooks for basic Python processing
9
+ - repo: https://github.com/pre-commit/pre-commit-hooks
10
+ rev: v5.0.0
11
+ hooks:
12
+ - id: check-added-large-files
13
+ exclude: '^tests/test_data/.*\.mda$'
14
+ - id: check-toml
15
+ - id: check-yaml
16
+ - id: end-of-file-fixer
17
+ - id: mixed-line-ending
18
+ - id: trailing-whitespace
19
+ exclude: '^tests/test_data/.*$'
20
+
21
+ # Ruff - for linting and formatting
22
+ - repo: https://github.com/astral-sh/ruff-pre-commit
23
+ # Ruff version.
24
+ rev: v0.12.7
25
+ hooks:
26
+ # Run the linter.
27
+ - id: ruff-check
28
+ args: [ --fix ]
29
+ # Run the formatter.
30
+ - id: ruff-format
31
+
32
+ # Black - for standard code formatting
33
+ - repo: https://github.com/psf/black
34
+ rev: 24.10.0
35
+ hooks:
36
+ - id: black
37
+ # extend-exclude: '^tests/test_data/.*$'
38
+
39
+ # NumPyDoc - for docstring validation
40
+ - repo: https://github.com/numpy/numpydoc
41
+ rev: v1.8.0
42
+ hooks:
43
+ - id: numpydoc-validation
44
+ exclude: '^test.*$'
45
+
46
+ # Python Semantic Release & commitizen - for automatic versioning
47
+ # NOTE: The `pre-commit install` has a default hook-type of [pre-commit], but not [pre-push] or [commit-msg].
48
+ # To install these hooks, you also need to run
49
+ # >>> pre-commit install --hook-type pre-commit --hook-type commit-msg --hook-type pre-push
50
+ - repo: https://github.com/commitizen-tools/commitizen
51
+ rev: v4.8.3
52
+ hooks:
53
+ - id: commitizen
54
+ stages: [commit-msg]
55
+ - id: commitizen-branch
56
+ stages: [pre-push]
57
+
58
+ # Use "pre-commit install --hook-type commit-msg" to install, pre-commit install doesn't work.
59
+ - repo: https://github.com/opensource-nepal/commitlint
60
+ rev: v1.3.0
61
+ hooks:
62
+ - id: commitlint
63
+ stages: [commit-msg]
64
+ # args: [--config-path, .github/commitlint.yml]
65
+ additional_dependencies:
66
+ - commitlint
67
+ - commitizen
@@ -0,0 +1,42 @@
1
+ # .readthedocs.yaml
2
+ # Read the Docs configuration file
3
+ # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
4
+
5
+ # Required
6
+ version: 2
7
+
8
+ # python:
9
+ # install:
10
+ # - method: pip
11
+ # path: .
12
+ # extra_requirements:
13
+ # - docs
14
+
15
+ # Set the OS, Python version and other tools you might need
16
+ build:
17
+ os: ubuntu-lts-latest
18
+ tools:
19
+ python: "3.13"
20
+ # You can also specify other tool versions:
21
+ # nodejs: "19"
22
+ # rust: "1.64"
23
+ # golang: "1.19"
24
+ jobs:
25
+ install:
26
+ - pip install --group 'docs'
27
+
28
+ # Build documentation in the "docs/" directory with Sphinx
29
+ sphinx:
30
+ configuration: docs/conf.py
31
+
32
+ # Optionally build your docs in additional formats such as PDF and ePub
33
+ formats:
34
+ - pdf
35
+ # - epub
36
+
37
+ # Optional but recommended, declare the Python requirements required
38
+ # to build your documentation
39
+ # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
40
+ # python:
41
+ # install:
42
+ # - requirements: docs/requirements.txt
@@ -0,0 +1,21 @@
1
+ MIT License
2
+
3
+ Copyright (c) 2025 Matt Gebert
4
+
5
+ Permission is hereby granted, free of charge, to any person obtaining a copy
6
+ of this software and associated documentation files (the "Software"), to deal
7
+ in the Software without restriction, including without limitation the rights
8
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
9
+ copies of the Software, and to permit persons to whom the Software is
10
+ furnished to do so, subject to the following conditions:
11
+
12
+ The above copyright notice and this permission notice shall be included in all
13
+ copies or substantial portions of the Software.
14
+
15
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21
+ SOFTWARE.
@@ -0,0 +1,39 @@
1
+ Metadata-Version: 2.4
2
+ Name: pyNexafs
3
+ Version: 0.1.0b1
4
+ Summary: A package for processing and analysing NEXAFS data.
5
+ Author-email: Matthew Gebert <matthew.gebert@monash.edu>
6
+ Maintainer-email: Matthew Gebert <matthew.gebert@monash.edu>
7
+ License: MIT License
8
+
9
+ Copyright (c) 2025 Matt Gebert
10
+
11
+ Permission is hereby granted, free of charge, to any person obtaining a copy
12
+ of this software and associated documentation files (the "Software"), to deal
13
+ in the Software without restriction, including without limitation the rights
14
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
15
+ copies of the Software, and to permit persons to whom the Software is
16
+ furnished to do so, subject to the following conditions:
17
+
18
+ The above copyright notice and this permission notice shall be included in all
19
+ copies or substantial portions of the Software.
20
+
21
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
22
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
23
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
24
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
25
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
26
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
27
+ SOFTWARE.
28
+
29
+ Project-URL: code, https://github.com/xraysoftmat/pyNexafs
30
+ Project-URL: documentation, https://pyNexafs.readthedocs.io/en/latest/
31
+ Keywords: NEXAFS,XANES,Near,Edge,X-ray,Absorption,Fine,Structure,Spectroscopy,Optical Data,XAS,Synchrotron
32
+ Requires-Python: >=3.11
33
+ Description-Content-Type: text/markdown
34
+ License-File: LICENSE
35
+ Requires-Dist: numpy
36
+ Requires-Dist: overrides
37
+ Requires-Dist: scipy
38
+ Requires-Dist: xdrlib3
39
+ Dynamic: license-file