pynumdiff 0.1.2__tar.gz → 0.2__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 (117) hide show
  1. pynumdiff-0.2/.editorconfig +11 -0
  2. pynumdiff-0.2/.github/workflows/release.yml +18 -0
  3. pynumdiff-0.2/.github/workflows/test.yml +25 -0
  4. pynumdiff-0.2/.gitignore +120 -0
  5. pynumdiff-0.2/.pylintrc +621 -0
  6. pynumdiff-0.2/.readthedocs.yaml +16 -0
  7. pynumdiff-0.2/CITATION.cff +33 -0
  8. pynumdiff-0.2/LICENSE.txt +23 -0
  9. pynumdiff-0.2/PKG-INFO +185 -0
  10. pynumdiff-0.2/README.md +147 -0
  11. pynumdiff-0.2/docs/Makefile +20 -0
  12. pynumdiff-0.2/docs/source/LICENSE.rst +27 -0
  13. pynumdiff-0.2/docs/source/basis_fit.rst +5 -0
  14. pynumdiff-0.2/docs/source/code.rst +15 -0
  15. pynumdiff-0.2/docs/source/conf.py +52 -0
  16. pynumdiff-0.2/docs/source/contact.rst +8 -0
  17. pynumdiff-0.2/docs/source/contributing.rst +19 -0
  18. pynumdiff-0.2/docs/source/finite_difference.rst +10 -0
  19. pynumdiff-0.2/docs/source/index.rst +10 -0
  20. pynumdiff-0.2/docs/source/kalman_smooth.rst +12 -0
  21. pynumdiff-0.2/docs/source/linear_model.rst +5 -0
  22. pynumdiff-0.2/docs/source/optimize.rst +5 -0
  23. pynumdiff-0.2/docs/source/polynomial_fit.rst +5 -0
  24. pynumdiff-0.2/docs/source/smooth_finite_difference.rst +5 -0
  25. pynumdiff-0.2/docs/source/total_variation_regularization.rst +13 -0
  26. pynumdiff-0.2/docs/source/utils/evaluate.rst +5 -0
  27. pynumdiff-0.2/docs/source/utils/simulate.rst +5 -0
  28. pynumdiff-0.2/docs/source/utils/utility.rst +5 -0
  29. pynumdiff-0.2/docs/source/utils.rst +9 -0
  30. pynumdiff-0.2/examples/1_basic_tutorial.ipynb +932 -0
  31. pynumdiff-0.2/examples/2a_optimizing_parameters_with_dxdt_known.ipynb +705 -0
  32. pynumdiff-0.2/examples/2b_optimizing_parameters_with_dxdt_unknown.ipynb +734 -0
  33. pynumdiff-0.2/examples/3_automatic_method_suggestion.ipynb +208 -0
  34. pynumdiff-0.2/examples/4_performance_analysis.ipynb +427 -0
  35. pynumdiff-0.2/linting.py +13 -0
  36. pynumdiff-0.2/logo.png +0 -0
  37. pynumdiff-0.2/pynumdiff/README.md +13 -0
  38. pynumdiff-0.2/pynumdiff/__init__.py +11 -0
  39. pynumdiff-0.2/pynumdiff/_version.py +34 -0
  40. pynumdiff-0.2/pynumdiff/basis_fit/__init__.py +5 -0
  41. pynumdiff-0.2/pynumdiff/basis_fit/_basis_fit.py +126 -0
  42. pynumdiff-0.2/pynumdiff/finite_difference/__init__.py +3 -0
  43. pynumdiff-0.2/pynumdiff/finite_difference/_finite_difference.py +118 -0
  44. pynumdiff-0.2/pynumdiff/kalman_smooth/__init__.py +3 -0
  45. pynumdiff-0.2/pynumdiff/kalman_smooth/_kalman_smooth.py +253 -0
  46. pynumdiff-0.2/pynumdiff/linear_model/__init__.py +13 -0
  47. pynumdiff-0.2/pynumdiff/linear_model/_linear_model.py +164 -0
  48. pynumdiff-0.2/pynumdiff/optimize/__init__.py +13 -0
  49. pynumdiff-0.2/pynumdiff/optimize/_optimize.py +262 -0
  50. pynumdiff-0.2/pynumdiff/polynomial_fit/__init__.py +5 -0
  51. pynumdiff-0.2/pynumdiff/polynomial_fit/_polynomial_fit.py +144 -0
  52. pynumdiff-0.2/pynumdiff/smooth_finite_difference/__init__.py +7 -0
  53. pynumdiff-0.2/pynumdiff/smooth_finite_difference/_smooth_finite_difference.py +177 -0
  54. pynumdiff-0.2/pynumdiff/tests/conftest.py +20 -0
  55. pynumdiff-0.2/pynumdiff/tests/test_diff_methods.py +307 -0
  56. pynumdiff-0.2/pynumdiff/tests/test_optimize.py +104 -0
  57. pynumdiff-0.2/pynumdiff/tests/test_utils.py +95 -0
  58. pynumdiff-0.2/pynumdiff/total_variation_regularization/__init__.py +13 -0
  59. pynumdiff-0.1.2/pynumdiff/total_variation_regularization/__chartrand_tvregdiff__.py → pynumdiff-0.2/pynumdiff/total_variation_regularization/_chartrand_tvregdiff.py +12 -12
  60. pynumdiff-0.2/pynumdiff/total_variation_regularization/_total_variation_regularization.py +266 -0
  61. pynumdiff-0.2/pynumdiff/utils/__init__.py +0 -0
  62. pynumdiff-0.2/pynumdiff/utils/evaluate.py +158 -0
  63. pynumdiff-0.2/pynumdiff/utils/old_pi_cruise_control.py +178 -0
  64. pynumdiff-0.2/pynumdiff/utils/simulate.py +335 -0
  65. pynumdiff-0.2/pynumdiff/utils/utility.py +207 -0
  66. pynumdiff-0.2/pynumdiff.egg-info/PKG-INFO +185 -0
  67. pynumdiff-0.2/pynumdiff.egg-info/SOURCES.txt +71 -0
  68. pynumdiff-0.2/pynumdiff.egg-info/requires.txt +20 -0
  69. pynumdiff-0.2/pyproject.toml +57 -0
  70. pynumdiff-0.1.2/PKG-INFO +0 -27
  71. pynumdiff-0.1.2/README.md +0 -219
  72. pynumdiff-0.1.2/pynumdiff/__init__.py +0 -12
  73. pynumdiff-0.1.2/pynumdiff/__version__.py +0 -57
  74. pynumdiff-0.1.2/pynumdiff/finite_difference/__init__.py +0 -5
  75. pynumdiff-0.1.2/pynumdiff/finite_difference/_finite_difference.py +0 -121
  76. pynumdiff-0.1.2/pynumdiff/kalman_smooth/__init__.py +0 -9
  77. pynumdiff-0.1.2/pynumdiff/kalman_smooth/_kalman_smooth.py +0 -646
  78. pynumdiff-0.1.2/pynumdiff/kalman_smooth/_kalman_smooth_old.py +0 -615
  79. pynumdiff-0.1.2/pynumdiff/linear_model/__init__.py +0 -49
  80. pynumdiff-0.1.2/pynumdiff/linear_model/_linear_model.py +0 -633
  81. pynumdiff-0.1.2/pynumdiff/optimize/__init__.py +0 -33
  82. pynumdiff-0.1.2/pynumdiff/optimize/__optimize__.py +0 -144
  83. pynumdiff-0.1.2/pynumdiff/optimize/finite_difference/__finite_difference__.py +0 -35
  84. pynumdiff-0.1.2/pynumdiff/optimize/finite_difference/__init__.py +0 -4
  85. pynumdiff-0.1.2/pynumdiff/optimize/kalman_smooth/__init__.py +0 -6
  86. pynumdiff-0.1.2/pynumdiff/optimize/kalman_smooth/__kalman_smooth__.py +0 -114
  87. pynumdiff-0.1.2/pynumdiff/optimize/linear_model/__init__.py +0 -8
  88. pynumdiff-0.1.2/pynumdiff/optimize/linear_model/__linear_model__.py +0 -184
  89. pynumdiff-0.1.2/pynumdiff/optimize/smooth_finite_difference/__init__.py +0 -9
  90. pynumdiff-0.1.2/pynumdiff/optimize/smooth_finite_difference/__smooth_finite_difference__.py +0 -183
  91. pynumdiff-0.1.2/pynumdiff/optimize/total_variation_regularization/__init__.py +0 -9
  92. pynumdiff-0.1.2/pynumdiff/optimize/total_variation_regularization/__total_variation_regularization__.py +0 -162
  93. pynumdiff-0.1.2/pynumdiff/smooth_finite_difference/__init__.py +0 -10
  94. pynumdiff-0.1.2/pynumdiff/smooth_finite_difference/_smooth_finite_difference.py +0 -350
  95. pynumdiff-0.1.2/pynumdiff/tests/test_finite_difference.py +0 -44
  96. pynumdiff-0.1.2/pynumdiff/tests/test_kalman_smooth.py +0 -58
  97. pynumdiff-0.1.2/pynumdiff/tests/test_linear_model.py +0 -101
  98. pynumdiff-0.1.2/pynumdiff/tests/test_optimize.py +0 -153
  99. pynumdiff-0.1.2/pynumdiff/tests/test_smooth_finite_difference.py +0 -82
  100. pynumdiff-0.1.2/pynumdiff/tests/test_total_variation_regularization.py +0 -117
  101. pynumdiff-0.1.2/pynumdiff/tests/test_utils.py +0 -20
  102. pynumdiff-0.1.2/pynumdiff/total_variation_regularization/__init__.py +0 -36
  103. pynumdiff-0.1.2/pynumdiff/total_variation_regularization/_total_variation_regularization.py +0 -393
  104. pynumdiff-0.1.2/pynumdiff/utils/__init__.py +0 -6
  105. pynumdiff-0.1.2/pynumdiff/utils/_pi_cruise_control.py +0 -65
  106. pynumdiff-0.1.2/pynumdiff/utils/evaluate.py +0 -213
  107. pynumdiff-0.1.2/pynumdiff/utils/old_pi_cruise_control.py +0 -228
  108. pynumdiff-0.1.2/pynumdiff/utils/simulate.py +0 -559
  109. pynumdiff-0.1.2/pynumdiff/utils/utility.py +0 -283
  110. pynumdiff-0.1.2/pynumdiff.egg-info/PKG-INFO +0 -27
  111. pynumdiff-0.1.2/pynumdiff.egg-info/SOURCES.txt +0 -47
  112. pynumdiff-0.1.2/pynumdiff.egg-info/requires.txt +0 -3
  113. pynumdiff-0.1.2/setup.py +0 -30
  114. {pynumdiff-0.1.2 → pynumdiff-0.2}/pynumdiff/tests/__init__.py +0 -0
  115. {pynumdiff-0.1.2 → pynumdiff-0.2}/pynumdiff.egg-info/dependency_links.txt +0 -0
  116. {pynumdiff-0.1.2 → pynumdiff-0.2}/pynumdiff.egg-info/top_level.txt +0 -0
  117. {pynumdiff-0.1.2 → pynumdiff-0.2}/setup.cfg +0 -0
@@ -0,0 +1,11 @@
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+ root = true
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+
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+ [*.py]
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+ indent_style = tab
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+ indent_size = 4
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+ trim_trailing_whitespace = true
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+
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+ [*.ipynb]
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+ indent_style = tab
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+ indent_size = 4
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+ trim_trailing_whitespace = true
@@ -0,0 +1,18 @@
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+ on:
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+ release:
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+ types: [created]
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+ jobs:
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+ deploy-to-pypi:
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+ runs-on: ubuntu-latest
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+ env:
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+ TWINE_USERNAME: __token__
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+ TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
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+ steps:
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+ - uses: actions/checkout@v4
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+ - uses: actions/setup-python@v5
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+ with:
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+ python-version: '3.x'
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+ - run: |
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+ pip install build wheel twine
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+ python -m build
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+ twine upload dist/*
@@ -0,0 +1,25 @@
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+ on:
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+ push:
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+ branches:
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+ - master
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+ pull_request:
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+
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+ jobs:
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+ run-tests:
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+ runs-on: ubuntu-latest
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+ steps:
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+ - uses: actions/checkout@v4
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+ with:
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+ fetch-depth: 0 # important for Coveralls to read commit history
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+ - uses: actions/setup-python@v5
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+ with:
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+ python-version: '3.x'
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+ - name: tests and coverage
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+ run: |
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+ pip install -e .[advanced,dev] coveralls
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+ coverage run --source=pynumdiff --omit='pynumdiff/_version.py' -m pytest -s
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+ coverage xml
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+ - uses: coverallsapp/github-action@v2
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+ with:
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+ format: cobertura
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+ file: coverage.xml
@@ -0,0 +1,120 @@
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+ # Byte-compiled / optimized / DLL files
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+ __pycache__/
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+ *.py[cod]
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+ *$py.class
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+
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+ # C extensions
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+ *.so
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+
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+ # Distribution / packaging
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+ .Python
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+ develop-eggs/
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+ dist/
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+ downloads/
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+ eggs/
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+ .eggs/
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+ lib/
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+ lib64/
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+ parts/
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+ sdist/
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+ var/
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+ wheels/
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+ *.egg-info/
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+ .installed.cfg
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+ *.egg
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+ MANIFEST
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+
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+ # PyInstaller
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+ # Usually these files are written by a python script from a template
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+ # before PyInstaller builds the exe, so as to inject date/other infos into it.
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+ *.manifest
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+ *.spec
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+
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+ # Installer logs
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+ pip-log.txt
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+ pip-delete-this-directory.txt
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+
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+ # Unit test / coverage reports
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+ htmlcov/
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+ .tox/
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+ .coverage
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+ .coverage.*
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+ .cache
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+ nosetests.xml
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+ coverage.xml
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+ *.cover
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+ .hypothesis/
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+ .pytest_cache/
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+
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+ # Translations
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+ *.mo
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+ *.pot
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+
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+ # Django stuff:
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+ *.log
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+ local_settings.py
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+ db.sqlite3
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+
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+ # Flask stuff:
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+ instance/
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+ .webassets-cache
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+
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+ # Scrapy stuff:
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+ .scrapy
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+
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+ # PyBuilder
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+ target/
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+
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+ # Jupyter Notebook
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+ .ipynb_checkpoints
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+
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+ # pyenv
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+ .python-version
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+
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+ # celery beat schedule file
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+ celerybeat-schedule
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+
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+ # SageMath parsed files
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+ *.sage.py
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+
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+ # Environments
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+ .env
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+ .venv
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+ env/
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+ venv/
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+ ENV/
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+ env.bak/
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+ venv.bak/
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+
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+ # Spyder project settings
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+ .spyderproject
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+ .spyproject
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+
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+ # Rope project settings
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+ .ropeproject
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+
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+ # mkdocs documentation
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+ /site
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+
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+ # mypy
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+ .mypy_cache/
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+
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+ # add
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+ *.[oa]
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+ *~
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+ .idea
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+ .DS_Store
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+ *.nc
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+ *.csv
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+ *.mat
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+ .coverage
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+ __pycache__
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+ *.tar
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+ *.tar.gz
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+ *.zip
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+ *.egg-info
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+ dist
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+ *.whl
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+ .vscode
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+ docs/build
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+ pynumdiff/_version.py