phasorpy 0.1.dev0__tar.gz → 0.3__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 (111) hide show
  1. {phasorpy-0.1.dev0 → phasorpy-0.3}/LICENSE.txt +21 -21
  2. {phasorpy-0.1.dev0 → phasorpy-0.3}/MANIFEST.in +18 -18
  3. {phasorpy-0.1.dev0 → phasorpy-0.3}/PKG-INFO +78 -78
  4. {phasorpy-0.1.dev0 → phasorpy-0.3}/README.md +23 -23
  5. phasorpy-0.3/docs/_static/custom-icons.js +16 -0
  6. phasorpy-0.3/docs/_static/switcher.json +18 -0
  7. {phasorpy-0.1.dev0 → phasorpy-0.3}/docs/acknowledgments.rst +35 -32
  8. {phasorpy-0.1.dev0 → phasorpy-0.3}/docs/api/_phasorpy.rst +12 -12
  9. {phasorpy-0.1.dev0 → phasorpy-0.3}/docs/api/_utils.rst +9 -9
  10. {phasorpy-0.1.dev0 → phasorpy-0.3}/docs/api/cli.rst +6 -6
  11. {phasorpy-0.1.dev0 → phasorpy-0.3}/docs/api/color.rst +20 -20
  12. {phasorpy-0.1.dev0 → phasorpy-0.3}/docs/api/components.rst +5 -5
  13. {phasorpy-0.1.dev0 → phasorpy-0.3}/docs/api/cursors.rst +5 -5
  14. {phasorpy-0.1.dev0 → phasorpy-0.3}/docs/api/datasets.rst +9 -9
  15. {phasorpy-0.1.dev0 → phasorpy-0.3}/docs/api/index.rst +26 -26
  16. {phasorpy-0.1.dev0 → phasorpy-0.3}/docs/api/io.rst +5 -5
  17. {phasorpy-0.1.dev0 → phasorpy-0.3}/docs/api/phasor.rst +5 -5
  18. {phasorpy-0.1.dev0 → phasorpy-0.3}/docs/api/phasorpy.rst +6 -6
  19. {phasorpy-0.1.dev0 → phasorpy-0.3}/docs/api/plot.rst +5 -5
  20. {phasorpy-0.1.dev0 → phasorpy-0.3}/docs/api/utils.rst +5 -5
  21. {phasorpy-0.1.dev0 → phasorpy-0.3}/docs/code_of_conduct.rst +143 -143
  22. {phasorpy-0.1.dev0 → phasorpy-0.3}/docs/conf.py +146 -121
  23. {phasorpy-0.1.dev0 → phasorpy-0.3}/docs/contributing.rst +292 -292
  24. {phasorpy-0.1.dev0 → phasorpy-0.3}/docs/index.rst +78 -77
  25. {phasorpy-0.1.dev0 → phasorpy-0.3}/docs/license.rst +22 -22
  26. {phasorpy-0.1.dev0 → phasorpy-0.3}/docs/phasor_approach.rst +314 -287
  27. phasorpy-0.3/docs/release.rst +201 -0
  28. {phasorpy-0.1.dev0 → phasorpy-0.3}/pyproject.toml +191 -191
  29. {phasorpy-0.1.dev0 → phasorpy-0.3}/setup.cfg +4 -4
  30. {phasorpy-0.1.dev0 → phasorpy-0.3}/setup.py +53 -53
  31. {phasorpy-0.1.dev0 → phasorpy-0.3}/src/phasorpy/__init__.py +10 -10
  32. {phasorpy-0.1.dev0 → phasorpy-0.3}/src/phasorpy/__main__.py +7 -7
  33. {phasorpy-0.1.dev0 → phasorpy-0.3}/src/phasorpy/_phasorpy.pyx +2161 -1811
  34. {phasorpy-0.1.dev0 → phasorpy-0.3}/src/phasorpy/_typing.py +77 -77
  35. {phasorpy-0.1.dev0 → phasorpy-0.3}/src/phasorpy/_utils.py +454 -441
  36. {phasorpy-0.1.dev0 → phasorpy-0.3}/src/phasorpy/cli.py +87 -87
  37. {phasorpy-0.1.dev0 → phasorpy-0.3}/src/phasorpy/color.py +581 -581
  38. {phasorpy-0.1.dev0 → phasorpy-0.3}/src/phasorpy/components.py +313 -313
  39. {phasorpy-0.1.dev0 → phasorpy-0.3}/src/phasorpy/conftest.py +36 -36
  40. {phasorpy-0.1.dev0 → phasorpy-0.3}/src/phasorpy/cursors.py +502 -502
  41. {phasorpy-0.1.dev0 → phasorpy-0.3}/src/phasorpy/datasets.py +453 -433
  42. {phasorpy-0.1.dev0 → phasorpy-0.3}/src/phasorpy/io.py +1811 -1671
  43. {phasorpy-0.1.dev0 → phasorpy-0.3}/src/phasorpy/phasor.py +3407 -3135
  44. {phasorpy-0.1.dev0 → phasorpy-0.3}/src/phasorpy/plot.py +2078 -2074
  45. phasorpy-0.3/src/phasorpy/utils.py +368 -0
  46. {phasorpy-0.1.dev0 → phasorpy-0.3}/src/phasorpy/version.py +71 -71
  47. {phasorpy-0.1.dev0 → phasorpy-0.3}/src/phasorpy.egg-info/PKG-INFO +78 -78
  48. {phasorpy-0.1.dev0 → phasorpy-0.3}/src/phasorpy.egg-info/SOURCES.txt +4 -23
  49. {phasorpy-0.1.dev0 → phasorpy-0.3}/src/phasorpy.egg-info/not-zip-safe +1 -1
  50. {phasorpy-0.1.dev0 → phasorpy-0.3}/src/phasorpy.egg-info/requires.txt +1 -1
  51. {phasorpy-0.1.dev0 → phasorpy-0.3}/tests/conftest.py +24 -24
  52. {phasorpy-0.1.dev0 → phasorpy-0.3}/tests/test__phasorpy.py +423 -423
  53. {phasorpy-0.1.dev0 → phasorpy-0.3}/tests/test__typing.py +10 -10
  54. {phasorpy-0.1.dev0 → phasorpy-0.3}/tests/test__utils.py +244 -239
  55. {phasorpy-0.1.dev0 → phasorpy-0.3}/tests/test_cli.py +41 -41
  56. {phasorpy-0.1.dev0 → phasorpy-0.3}/tests/test_color.py +39 -39
  57. {phasorpy-0.1.dev0 → phasorpy-0.3}/tests/test_components.py +261 -261
  58. {phasorpy-0.1.dev0 → phasorpy-0.3}/tests/test_cursors.py +478 -478
  59. {phasorpy-0.1.dev0 → phasorpy-0.3}/tests/test_datasets.py +84 -84
  60. {phasorpy-0.1.dev0 → phasorpy-0.3}/tests/test_io.py +791 -762
  61. {phasorpy-0.1.dev0 → phasorpy-0.3}/tests/test_nan.py +406 -376
  62. {phasorpy-0.1.dev0 → phasorpy-0.3}/tests/test_phasor.py +2960 -2408
  63. {phasorpy-0.1.dev0 → phasorpy-0.3}/tests/test_phasorpy.py +18 -18
  64. {phasorpy-0.1.dev0 → phasorpy-0.3}/tests/test_plot.py +527 -527
  65. phasorpy-0.3/tests/test_utils.py +140 -0
  66. {phasorpy-0.1.dev0 → phasorpy-0.3}/tutorials/README.rst +9 -9
  67. {phasorpy-0.1.dev0 → phasorpy-0.3}/tutorials/api/README.rst +4 -4
  68. {phasorpy-0.1.dev0 → phasorpy-0.3}/tutorials/api/phasorpy_components.py +261 -261
  69. {phasorpy-0.1.dev0 → phasorpy-0.3}/tutorials/api/phasorpy_cursors.py +172 -172
  70. {phasorpy-0.1.dev0 → phasorpy-0.3}/tutorials/api/phasorpy_fret.py +234 -234
  71. {phasorpy-0.1.dev0 → phasorpy-0.3}/tutorials/api/phasorpy_lifetime_to_signal.py +195 -195
  72. phasorpy-0.3/tutorials/api/phasorpy_multi-harmonic.py +222 -0
  73. {phasorpy-0.1.dev0 → phasorpy-0.3}/tutorials/api/phasorpy_pca.py +150 -150
  74. {phasorpy-0.1.dev0 → phasorpy-0.3}/tutorials/api/phasorpy_phasor_from_lifetime.py +202 -202
  75. {phasorpy-0.1.dev0 → phasorpy-0.3}/tutorials/api/phasorpy_phasorplot.py +226 -226
  76. {phasorpy-0.1.dev0 → phasorpy-0.3}/tutorials/applications/README.rst +4 -4
  77. {phasorpy-0.1.dev0 → phasorpy-0.3}/tutorials/benchmarks/README.rst +4 -4
  78. {phasorpy-0.1.dev0 → phasorpy-0.3}/tutorials/benchmarks/phasorpy_phasor_from_signal.py +161 -161
  79. {phasorpy-0.1.dev0 → phasorpy-0.3}/tutorials/phasorpy_introduction.py +468 -429
  80. {phasorpy-0.1.dev0 → phasorpy-0.3}/tutorials/phasorpy_lfd_workshop.py +570 -576
  81. phasorpy-0.1.dev0/.codecov.yml +0 -11
  82. phasorpy-0.1.dev0/.github/ISSUE_TEMPLATE/bug_report.md +0 -36
  83. phasorpy-0.1.dev0/.github/dependabot.yml +0 -11
  84. phasorpy-0.1.dev0/.github/pull_request_template.md +0 -24
  85. phasorpy-0.1.dev0/.github/workflows/build_wheels.yml +0 -37
  86. phasorpy-0.1.dev0/.github/workflows/coverage.yml +0 -40
  87. phasorpy-0.1.dev0/.github/workflows/deploy-docs.yml +0 -54
  88. phasorpy-0.1.dev0/.github/workflows/release-pypi.yml +0 -75
  89. phasorpy-0.1.dev0/.github/workflows/run-tests.yml +0 -134
  90. phasorpy-0.1.dev0/.gitignore +0 -203
  91. phasorpy-0.1.dev0/.pre-commit-config.yaml +0 -103
  92. phasorpy-0.1.dev0/CHANGELOG.md +0 -1
  93. phasorpy-0.1.dev0/CODE_OF_CONDUCT.md +0 -1
  94. phasorpy-0.1.dev0/CONTRIBUTING.md +0 -1
  95. phasorpy-0.1.dev0/docs/Makefile +0 -20
  96. phasorpy-0.1.dev0/docs/make.bat +0 -39
  97. phasorpy-0.1.dev0/docs/release.rst +0 -11
  98. phasorpy-0.1.dev0/docs/sg_execution_times.rst +0 -67
  99. phasorpy-0.1.dev0/requirements_dev.txt +0 -63
  100. phasorpy-0.1.dev0/requirements_min.txt +0 -13
  101. phasorpy-0.1.dev0/src/phasorpy/utils.py +0 -68
  102. phasorpy-0.1.dev0/tests/test_utils.py +0 -29
  103. phasorpy-0.1.dev0/tutorials/misc/README.rst +0 -2
  104. phasorpy-0.1.dev0/tutorials/misc/phasorpy_logo.py +0 -23
  105. {phasorpy-0.1.dev0 → phasorpy-0.3}/docs/_static/categorical.png +0 -0
  106. {phasorpy-0.1.dev0 → phasorpy-0.3}/docs/_static/logo.png +0 -0
  107. {phasorpy-0.1.dev0 → phasorpy-0.3}/docs/_static/srgb_spectrum.png +0 -0
  108. {phasorpy-0.1.dev0 → phasorpy-0.3}/src/phasorpy/py.typed +0 -0
  109. {phasorpy-0.1.dev0 → phasorpy-0.3}/src/phasorpy.egg-info/dependency_links.txt +0 -0
  110. {phasorpy-0.1.dev0 → phasorpy-0.3}/src/phasorpy.egg-info/entry_points.txt +0 -0
  111. {phasorpy-0.1.dev0 → phasorpy-0.3}/src/phasorpy.egg-info/top_level.txt +0 -0
@@ -1,21 +1,21 @@
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- MIT License
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-
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- Copyright (c) 2022-2024 PhasorPy Contributors
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-
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- Permission is hereby granted, free of charge, to any person obtaining a copy
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- of this software and associated documentation files (the "Software"), to deal
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- in the Software without restriction, including without limitation the rights
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- to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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- copies of the Software, and to permit persons to whom the Software is
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- furnished to do so, subject to the following conditions:
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-
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- The above copyright notice and this permission notice shall be included in all
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- copies or substantial portions of the Software.
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-
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- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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- IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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- FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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- AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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- LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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- OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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- SOFTWARE.
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+ MIT License
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+
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+ Copyright (c) 2022-2024 PhasorPy Contributors
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+
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+ Permission is hereby granted, free of charge, to any person obtaining a copy
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+ of this software and associated documentation files (the "Software"), to deal
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+ in the Software without restriction, including without limitation the rights
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+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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+ copies of the Software, and to permit persons to whom the Software is
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+ furnished to do so, subject to the following conditions:
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+
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+ The above copyright notice and this permission notice shall be included in all
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+ copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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+ SOFTWARE.
@@ -1,18 +1,18 @@
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- include LICENSE.txt
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- include README.md
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-
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- include tests/*.py
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-
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- include docs/*.py
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- include docs/*.rst
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- include docs/api/*.rst
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- include docs/_static/*.*
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-
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- recursive-include tutorials *.py
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- recursive-include tutorials *.rst
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-
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- exclude *.cmd
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-
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- recursive-exclude * __pycache__
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- recursive-exclude * *.py[co]
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- recursive-exclude * *Copy*
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+ include LICENSE.txt
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+ include README.md
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+
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+ include tests/*.py
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+
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+ include docs/*.py
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+ include docs/*.rst
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+ include docs/api/*.rst
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+ include docs/_static/*.*
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+
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+ recursive-include tutorials *.py
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+ recursive-include tutorials *.rst
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+
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+ exclude *.cmd
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+
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+ recursive-exclude * __pycache__
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+ recursive-exclude * *.py[co]
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+ recursive-exclude * *Copy*
@@ -1,78 +1,78 @@
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- Metadata-Version: 2.1
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- Name: phasorpy
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- Version: 0.1.dev0
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- Summary: Analysis of fluorescence lifetime and hyperspectral images using the phasor approach
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- Author: PhasorPy Contributors
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- License: MIT
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- Project-URL: homepage, https://www.phasorpy.org
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- Project-URL: documentation, https://www.phasorpy.org/docs/stable/
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- Project-URL: download, https://pypi.org/project/phasorpy/#files
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- Project-URL: source, https://github.com/phasorpy/phasorpy
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- Project-URL: tracker, https://github.com/phasorpy/phasorpy/issues
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- Project-URL: release notes, https://www.phasorpy.org/docs/stable/release
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- Classifier: Development Status :: 3 - Alpha
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- Classifier: Intended Audience :: Developers
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- Classifier: Intended Audience :: Science/Research
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- Classifier: License :: OSI Approved :: MIT License
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- Classifier: Programming Language :: Python
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- Classifier: Topic :: Software Development :: Libraries :: Python Modules
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- Classifier: Operating System :: OS Independent
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- Classifier: Programming Language :: Python :: 3
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- Classifier: Programming Language :: Python :: 3 :: Only
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- Classifier: Programming Language :: Python :: 3.10
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- Classifier: Programming Language :: Python :: 3.11
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- Classifier: Programming Language :: Python :: 3.12
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- Classifier: Programming Language :: Python :: 3.13
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- Requires-Python: >=3.10
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- Description-Content-Type: text/markdown
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- License-File: LICENSE.txt
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- Requires-Dist: numpy>=1.24.0
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- Requires-Dist: matplotlib>=3.7.0
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- Requires-Dist: scipy>=1.11.0
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- Requires-Dist: click
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- Requires-Dist: pooch
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- Requires-Dist: tqdm
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- Requires-Dist: xarray>=2023.4.0
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- Requires-Dist: tifffile>=2024.8.30
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- Provides-Extra: docs
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- Requires-Dist: sphinx; extra == "docs"
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- Requires-Dist: sphinx-issues; extra == "docs"
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- Requires-Dist: sphinx_gallery; extra == "docs"
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- Requires-Dist: sphinx-copybutton; extra == "docs"
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- Requires-Dist: sphinx_click; extra == "docs"
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- Requires-Dist: pydata-sphinx-theme; extra == "docs"
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- Requires-Dist: numpydoc; extra == "docs"
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- Provides-Extra: test
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- Requires-Dist: pytest; extra == "test"
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- Requires-Dist: pytest-cov; extra == "test"
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- Requires-Dist: pytest-runner; extra == "test"
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- Provides-Extra: all
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- Requires-Dist: sdtfile>=2024.5.24; extra == "all"
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- Requires-Dist: ptufile>=2024.9.14; extra == "all"
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-
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- # PhasorPy
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-
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- PhasorPy is an open-source Python library for the analysis of fluorescence
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- lifetime and hyperspectral images using the phasor approach.
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-
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- - [Homepage](https://www.phasorpy.org)
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- - [Documentation](https://www.phasorpy.org/docs/stable/)
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- - [Source code](https://github.com/phasorpy/phasorpy)
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- - [Issues and questions](https://github.com/phasorpy/phasorpy/issues)
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- - [Python package](https://pypi.org/project/phasorpy/)
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- - [Data files](https://zenodo.org/communities/phasorpy/)
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-
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- PhasorPy is a community-maintained project.
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- [Contributions](https://www.phasorpy.org/docs/stable/contributing/)
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- in the form of bug reports, bug fixes, feature implementations, documentation,
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- datasets, and enhancement proposals are welcome.
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-
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- This software project is supported in part by the
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- [Essential Open Source Software for Science (EOSS)](https://chanzuckerberg.com/eoss/)
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- program at
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- [Chan Zuckerberg Initiative](https://chanzuckerberg.com/).
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-
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- [![CZI's Essential Open Source Software for Science](https://chanzuckerberg.github.io/open-science/badges/CZI-EOSS.svg)](https://czi.co/EOSS)
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+ Metadata-Version: 2.1
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+ Name: phasorpy
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+ Version: 0.3
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+ Summary: Analysis of fluorescence lifetime and hyperspectral images using the phasor approach
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+ Author: PhasorPy Contributors
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+ License: MIT
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+ Project-URL: Homepage, https://www.phasorpy.org
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+ Project-URL: Documentation, https://www.phasorpy.org/docs/stable/
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+ Project-URL: Download, https://pypi.org/project/phasorpy/#files
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+ Project-URL: Source code, https://github.com/phasorpy/phasorpy
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+ Project-URL: Issue tracker, https://github.com/phasorpy/phasorpy/issues
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+ Project-URL: Release notes, https://www.phasorpy.org/docs/stable/release
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+ Classifier: Development Status :: 3 - Alpha
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+ Classifier: Intended Audience :: Developers
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+ Classifier: Intended Audience :: Science/Research
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+ Classifier: License :: OSI Approved :: MIT License
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+ Classifier: Programming Language :: Python
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+ Classifier: Topic :: Software Development :: Libraries :: Python Modules
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+ Classifier: Operating System :: OS Independent
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+ Classifier: Programming Language :: Python :: 3
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+ Classifier: Programming Language :: Python :: 3 :: Only
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+ Classifier: Programming Language :: Python :: 3.10
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+ Classifier: Programming Language :: Python :: 3.11
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+ Classifier: Programming Language :: Python :: 3.12
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+ Classifier: Programming Language :: Python :: 3.13
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+ Requires-Python: >=3.10
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+ Description-Content-Type: text/markdown
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+ License-File: LICENSE.txt
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+ Requires-Dist: numpy>=1.24.0
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+ Requires-Dist: matplotlib>=3.7.0
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+ Requires-Dist: scipy>=1.11.0
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+ Requires-Dist: click
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+ Requires-Dist: pooch
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+ Requires-Dist: tqdm
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+ Requires-Dist: xarray>=2023.4.0
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+ Requires-Dist: tifffile>=2024.8.30
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+ Provides-Extra: docs
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+ Requires-Dist: sphinx; extra == "docs"
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+ Requires-Dist: sphinx-issues; extra == "docs"
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+ Requires-Dist: sphinx_gallery; extra == "docs"
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+ Requires-Dist: sphinx-copybutton; extra == "docs"
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+ Requires-Dist: sphinx_click; extra == "docs"
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+ Requires-Dist: pydata-sphinx-theme>=0.16.0; extra == "docs"
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+ Requires-Dist: numpydoc; extra == "docs"
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+ Provides-Extra: test
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+ Requires-Dist: pytest; extra == "test"
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+ Requires-Dist: pytest-cov; extra == "test"
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+ Requires-Dist: pytest-runner; extra == "test"
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+ Requires-Dist: pytest-doctestplus; extra == "test"
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+ Requires-Dist: coverage; extra == "test"
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+ Provides-Extra: all
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+ Requires-Dist: lfdfiles>=2024.5.24; extra == "all"
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+ Requires-Dist: sdtfile>=2024.5.24; extra == "all"
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+ Requires-Dist: ptufile>=2024.9.14; extra == "all"
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+
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+ # PhasorPy
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+
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+ PhasorPy is an open-source Python library for the analysis of fluorescence
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+ lifetime and hyperspectral images using the phasor approach.
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+
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+ - [Homepage](https://www.phasorpy.org)
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+ - [Documentation](https://www.phasorpy.org/docs/stable/)
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+ - [Source code](https://github.com/phasorpy/phasorpy)
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+ - [Download releases](https://pypi.org/project/phasorpy/#files)
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+ - [Data files](https://zenodo.org/communities/phasorpy/)
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+ - [Issues and questions](https://github.com/phasorpy/phasorpy/issues)
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+
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+ PhasorPy is a community-maintained project.
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+ [Contributions](https://www.phasorpy.org/docs/stable/contributing/)
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+ in the form of bug reports, bug fixes, feature implementations, documentation,
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+ datasets, and enhancement proposals are welcome.
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+
73
+ This software project is supported in part by the
74
+ [Essential Open Source Software for Science (EOSS)](https://chanzuckerberg.com/eoss/)
75
+ program at
76
+ [Chan Zuckerberg Initiative](https://chanzuckerberg.com/).
77
+
78
+ [![CZI's Essential Open Source Software for Science](https://chanzuckerberg.github.io/open-science/badges/CZI-EOSS.svg)](https://czi.co/EOSS)
@@ -1,23 +1,23 @@
1
- # PhasorPy
2
-
3
- PhasorPy is an open-source Python library for the analysis of fluorescence
4
- lifetime and hyperspectral images using the phasor approach.
5
-
6
- - [Homepage](https://www.phasorpy.org)
7
- - [Documentation](https://www.phasorpy.org/docs/stable/)
8
- - [Source code](https://github.com/phasorpy/phasorpy)
9
- - [Issues and questions](https://github.com/phasorpy/phasorpy/issues)
10
- - [Python package](https://pypi.org/project/phasorpy/)
11
- - [Data files](https://zenodo.org/communities/phasorpy/)
12
-
13
- PhasorPy is a community-maintained project.
14
- [Contributions](https://www.phasorpy.org/docs/stable/contributing/)
15
- in the form of bug reports, bug fixes, feature implementations, documentation,
16
- datasets, and enhancement proposals are welcome.
17
-
18
- This software project is supported in part by the
19
- [Essential Open Source Software for Science (EOSS)](https://chanzuckerberg.com/eoss/)
20
- program at
21
- [Chan Zuckerberg Initiative](https://chanzuckerberg.com/).
22
-
23
- [![CZI's Essential Open Source Software for Science](https://chanzuckerberg.github.io/open-science/badges/CZI-EOSS.svg)](https://czi.co/EOSS)
1
+ # PhasorPy
2
+
3
+ PhasorPy is an open-source Python library for the analysis of fluorescence
4
+ lifetime and hyperspectral images using the phasor approach.
5
+
6
+ - [Homepage](https://www.phasorpy.org)
7
+ - [Documentation](https://www.phasorpy.org/docs/stable/)
8
+ - [Source code](https://github.com/phasorpy/phasorpy)
9
+ - [Download releases](https://pypi.org/project/phasorpy/#files)
10
+ - [Data files](https://zenodo.org/communities/phasorpy/)
11
+ - [Issues and questions](https://github.com/phasorpy/phasorpy/issues)
12
+
13
+ PhasorPy is a community-maintained project.
14
+ [Contributions](https://www.phasorpy.org/docs/stable/contributing/)
15
+ in the form of bug reports, bug fixes, feature implementations, documentation,
16
+ datasets, and enhancement proposals are welcome.
17
+
18
+ This software project is supported in part by the
19
+ [Essential Open Source Software for Science (EOSS)](https://chanzuckerberg.com/eoss/)
20
+ program at
21
+ [Chan Zuckerberg Initiative](https://chanzuckerberg.com/).
22
+
23
+ [![CZI's Essential Open Source Software for Science](https://chanzuckerberg.github.io/open-science/badges/CZI-EOSS.svg)](https://czi.co/EOSS)
@@ -0,0 +1,16 @@
1
+ /*******************************************************************************
2
+ * Set a custom icon for pypi as it's not available in the fa built-in brands
3
+ */
4
+ FontAwesome.library.add(
5
+ (faListOldStyle = {
6
+ prefix: "fa-custom",
7
+ iconName: "pypi",
8
+ icon: [
9
+ 17.313, // viewBox width
10
+ 19.807, // viewBox height
11
+ [], // ligature
12
+ "e001", // unicode codepoint - private use area
13
+ "m10.383 0.2-3.239 1.1769 3.1883 1.1614 3.239-1.1798zm-3.4152 1.2411-3.2362 1.1769 3.1855 1.1614 3.2369-1.1769zm6.7177 0.00281-3.2947 1.2009v3.8254l3.2947-1.1988zm-3.4145 1.2439-3.2926 1.1981v3.8254l0.17548-0.064132 3.1171-1.1347zm-6.6564 0.018325v3.8247l3.244 1.1805v-3.8254zm10.191 0.20931v2.3137l3.1777-1.1558zm3.2947 1.2425-3.2947 1.1988v3.8254l3.2947-1.1988zm-8.7058 0.45739c0.00929-1.931e-4 0.018327-2.977e-4 0.027485 0 0.25633 0.00851 0.4263 0.20713 0.42638 0.49826 1.953e-4 0.38532-0.29327 0.80469-0.65542 0.93662-0.36226 0.13215-0.65608-0.073306-0.65613-0.4588-6.28e-5 -0.38556 0.2938-0.80504 0.65613-0.93662 0.068422-0.024919 0.13655-0.038114 0.20156-0.039466zm5.2913 0.78369-3.2947 1.1988v3.8247l3.2947-1.1981zm-10.132 1.239-3.2362 1.1769 3.1883 1.1614 3.2362-1.1769zm6.7177 0.00213-3.2926 1.2016v3.8247l3.2926-1.2009zm-3.4124 1.2439-3.2947 1.1988v3.8254l3.2947-1.1988zm-6.6585 0.016195v3.8275l3.244 1.1805v-3.8254zm16.9 0.21143-3.2947 1.1988v3.8247l3.2947-1.1981zm-3.4145 1.2411-3.2926 1.2016v3.8247l3.2926-1.2009zm-3.4145 1.2411-3.2926 1.2016v3.8247l3.2926-1.2009zm-3.4124 1.2432-3.2947 1.1988v3.8254l3.2947-1.1988zm-6.6585 0.019027v3.8247l3.244 1.1805v-3.8254zm13.485 1.4497-3.2947 1.1988v3.8247l3.2947-1.1981zm-3.4145 1.2411-3.2926 1.2016v3.8247l3.2926-1.2009zm2.4018 0.38127c0.0093-1.83e-4 0.01833-3.16e-4 0.02749 0 0.25633 0.0085 0.4263 0.20713 0.42638 0.49826 1.97e-4 0.38532-0.29327 0.80469-0.65542 0.93662-0.36188 0.1316-0.65525-0.07375-0.65542-0.4588-1.95e-4 -0.38532 0.29328-0.80469 0.65542-0.93662 0.06842-0.02494 0.13655-0.03819 0.20156-0.03947zm-5.8142 0.86403-3.244 1.1805v1.4201l3.244 1.1805z", // svg path (https://simpleicons.org/icons/pypi.svg)
14
+ ],
15
+ }),
16
+ );
@@ -0,0 +1,18 @@
1
+ [
2
+ {
3
+ "name": "dev",
4
+ "version": "0.4",
5
+ "url": "https://www.phasorpy.org/docs/dev/"
6
+ },
7
+ {
8
+ "name": "0.3 (stable)",
9
+ "version": "0.3",
10
+ "url": "https://www.phasorpy.org/docs/stable/",
11
+ "preferred": true
12
+ },
13
+ {
14
+ "name": "0.2",
15
+ "version": "0.2",
16
+ "url": "https://www.phasorpy.org/docs/v0.2/"
17
+ }
18
+ ]
@@ -1,32 +1,35 @@
1
- Acknowledgments
2
- ===============
3
-
4
- The PhasorPy project is jointly maintained by the
5
- `Advanced Bioimaging Unit <https://pasteur.uy/en/units/advanced-bioimaging>`_
6
- at the University of the Republic and Institut Pasteur de Montevideo and the
7
- `Laboratory for Fluorescence Dynamics <https://www.lfd.uci.edu>`_
8
- at the University of California, Irvine.
9
-
10
- PhasorPy was inspired by the
11
- `Globals for Images · SimFCS <https://www.lfd.uci.edu/globals/>`_ software by
12
- Enrico Gratton.
13
-
14
- This software project is supported in part by the
15
- `Essential Open Source Software for Science (EOSS)
16
- <https://chanzuckerberg.com/eoss/>`_ program at
17
- `Chan Zuckerberg Initiative <https://chanzuckerberg.com/>`_.
18
-
19
- .. _contributors:
20
-
21
- Contributors
22
- ------------
23
-
24
- The following people (in alphabetical order) have contributed to the
25
- development of PhasorPy by providing code, documentation, tutorials,
26
- bug fixes, or expertise:
27
-
28
- - :user:`Christoph Gohlke <cgohlke>`
29
- - Enrico Gratton
30
- - :user:`Leonel Malacrida <lmalacrida>`
31
- - :user:`Bruno Pannunzio <bruno-pannunzio>`
32
- - :user:`Bruno Schüty <schutyb>`
1
+ Acknowledgments
2
+ ===============
3
+
4
+ The PhasorPy project is jointly maintained by the
5
+ `Advanced Bioimaging Unit <https://pasteur.uy/en/units/advanced-bioimaging>`_
6
+ at the University of the Republic and Institut Pasteur de Montevideo and the
7
+ `Laboratory for Fluorescence Dynamics <https://www.lfd.uci.edu>`_
8
+ at the University of California, Irvine.
9
+
10
+ PhasorPy was inspired by the
11
+ `Globals for Images · SimFCS <https://www.lfd.uci.edu/globals/>`_ software by
12
+ Enrico Gratton.
13
+
14
+ This software project is supported in part by the
15
+ `Essential Open Source Software for Science (EOSS)
16
+ <https://chanzuckerberg.com/eoss/>`_ program at
17
+ `Chan Zuckerberg Initiative <https://chanzuckerberg.com/>`_.
18
+
19
+ .. _contributors:
20
+
21
+ Contributors
22
+ ------------
23
+
24
+ The following people (in alphabetical order) have contributed to the
25
+ development of PhasorPy by providing code, documentation, tutorials,
26
+ bug fixes, or expertise:
27
+
28
+ - :user:`Christoph Gohlke <cgohlke>`
29
+ - Enrico Gratton
30
+ - :user:`Leonel Malacrida <lmalacrida>`
31
+ - :user:`Bruno Pannunzio <bruno-pannunzio>`
32
+ - :user:`Bruno Schüty <schutyb>`
33
+
34
+ See also `GitHub contributors
35
+ <https://github.com/phasorpy/phasorpy/graphs/contributors>`_.
@@ -1,12 +1,12 @@
1
- phasorpy._phasorpy
2
- ------------------
3
-
4
- .. note::
5
- This module and its functions are not part of the public interface.
6
- They are intended to facilitate the development of the PhasorPy library.
7
-
8
- .. automodule:: phasorpy._phasorpy
9
- :members:
10
- :undoc-members:
11
- :private-members:
12
- :special-members:
1
+ phasorpy._phasorpy
2
+ ------------------
3
+
4
+ .. note::
5
+ This module and its functions are not part of the public interface.
6
+ They are intended to facilitate the development of the PhasorPy library.
7
+
8
+ .. automodule:: phasorpy._phasorpy
9
+ :members:
10
+ :undoc-members:
11
+ :private-members:
12
+ :special-members:
@@ -1,9 +1,9 @@
1
- phasorpy._utils
2
- ---------------
3
-
4
- .. note::
5
- This module and its functions are not part of the public interface.
6
- They are intended to facilitate the development of the PhasorPy library.
7
-
8
- .. automodule:: phasorpy._utils
9
- :members:
1
+ phasorpy._utils
2
+ ---------------
3
+
4
+ .. note::
5
+ This module and its functions are not part of the public interface.
6
+ They are intended to facilitate the development of the PhasorPy library.
7
+
8
+ .. automodule:: phasorpy._utils
9
+ :members:
@@ -1,6 +1,6 @@
1
- Command line interface
2
- ----------------------
3
-
4
- .. click:: phasorpy.cli:main
5
- :prog: python -m phasorpy
6
- :nested: full
1
+ Command line interface
2
+ ----------------------
3
+
4
+ .. click:: phasorpy.cli:main
5
+ :prog: python -m phasorpy
6
+ :nested: full
@@ -1,20 +1,20 @@
1
- phasorpy.color
2
- --------------
3
-
4
- .. automodule:: phasorpy.color
5
- :members:
6
- :exclude-members: SRGB_SPECTRUM, CATEGORICAL
7
-
8
- .. autodata:: phasorpy.color.CATEGORICAL
9
- :no-value:
10
-
11
- .. image:: ../_static/categorical.png
12
- :alt: phasorpy.color.CATEGORICAL
13
- :align: center
14
-
15
- .. autodata:: phasorpy.color.SRGB_SPECTRUM
16
- :no-value:
17
-
18
- .. image:: ../_static/srgb_spectrum.png
19
- :alt: phasorpy.color.SRGB_SPECTRUM
20
- :align: center
1
+ phasorpy.color
2
+ --------------
3
+
4
+ .. automodule:: phasorpy.color
5
+ :members:
6
+ :exclude-members: SRGB_SPECTRUM, CATEGORICAL
7
+
8
+ .. autodata:: phasorpy.color.CATEGORICAL
9
+ :no-value:
10
+
11
+ .. image:: ../_static/categorical.png
12
+ :alt: phasorpy.color.CATEGORICAL
13
+ :align: center
14
+
15
+ .. autodata:: phasorpy.color.SRGB_SPECTRUM
16
+ :no-value:
17
+
18
+ .. image:: ../_static/srgb_spectrum.png
19
+ :alt: phasorpy.color.SRGB_SPECTRUM
20
+ :align: center
@@ -1,5 +1,5 @@
1
- phasorpy.components
2
- -------------------
3
-
4
- .. automodule:: phasorpy.components
5
- :members:
1
+ phasorpy.components
2
+ -------------------
3
+
4
+ .. automodule:: phasorpy.components
5
+ :members:
@@ -1,5 +1,5 @@
1
- phasorpy.cursors
2
- ----------------
3
-
4
- .. automodule:: phasorpy.cursors
5
- :members:
1
+ phasorpy.cursors
2
+ ----------------
3
+
4
+ .. automodule:: phasorpy.cursors
5
+ :members:
@@ -1,9 +1,9 @@
1
- phasorpy.datasets
2
- -----------------
3
-
4
- .. automodule:: phasorpy.datasets
5
- :members:
6
- :exclude-members: REPOSITORIES
7
-
8
- .. autodata:: phasorpy.datasets.REPOSITORIES
9
- :no-value:
1
+ phasorpy.datasets
2
+ -----------------
3
+
4
+ .. automodule:: phasorpy.datasets
5
+ :members:
6
+ :exclude-members: REPOSITORIES
7
+
8
+ .. autodata:: phasorpy.datasets.REPOSITORIES
9
+ :no-value:
@@ -1,26 +1,26 @@
1
- API reference
2
- =============
3
-
4
- This documents the application programming and command line interfaces of the
5
- PhasorPy library version |version|.
6
-
7
- .. note::
8
- The PhasorPy library is in its early stages of development.
9
- It is not nearly feature complete.
10
- Large, backwards-incompatible changes may occur between revisions.
11
-
12
- .. toctree::
13
- :maxdepth: 3
14
-
15
- phasorpy
16
- phasor
17
- cursors
18
- components
19
- plot
20
- io
21
- color
22
- datasets
23
- utils
24
- _utils
25
- _phasorpy
26
- cli
1
+ API reference
2
+ =============
3
+
4
+ This documents the application programming and command line interfaces of the
5
+ PhasorPy library version |version|.
6
+
7
+ .. note::
8
+ The PhasorPy library is in its early stages of development.
9
+ It is not nearly feature complete.
10
+ Large, backwards-incompatible changes may occur between revisions.
11
+
12
+ .. toctree::
13
+ :maxdepth: 3
14
+
15
+ phasorpy
16
+ phasor
17
+ cursors
18
+ components
19
+ plot
20
+ io
21
+ color
22
+ datasets
23
+ utils
24
+ _utils
25
+ _phasorpy
26
+ cli
@@ -1,5 +1,5 @@
1
- phasorpy.io
2
- -----------
3
-
4
- .. automodule:: phasorpy.io
5
- :members:
1
+ phasorpy.io
2
+ -----------
3
+
4
+ .. automodule:: phasorpy.io
5
+ :members:
@@ -1,5 +1,5 @@
1
- phasorpy.phasor
2
- ---------------
3
-
4
- .. automodule:: phasorpy.phasor
5
- :members:
1
+ phasorpy.phasor
2
+ ---------------
3
+
4
+ .. automodule:: phasorpy.phasor
5
+ :members:
@@ -1,6 +1,6 @@
1
- phasorpy
2
- --------
3
-
4
- .. automodule:: phasorpy
5
- :members:
6
- :special-members: __version__
1
+ phasorpy
2
+ --------
3
+
4
+ .. automodule:: phasorpy
5
+ :members:
6
+ :special-members: __version__
@@ -1,5 +1,5 @@
1
- phasorpy.plot
2
- -------------
3
-
4
- .. automodule:: phasorpy.plot
5
- :members:
1
+ phasorpy.plot
2
+ -------------
3
+
4
+ .. automodule:: phasorpy.plot
5
+ :members:
@@ -1,5 +1,5 @@
1
- phasorpy.utils
2
- --------------
3
-
4
- .. automodule:: phasorpy.utils
5
- :members:
1
+ phasorpy.utils
2
+ --------------
3
+
4
+ .. automodule:: phasorpy.utils
5
+ :members: