phasorpy 0.3__tar.gz → 0.5__tar.gz

{phasorpy-0.3 → phasorpy-0.5}/LICENSE.txt

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2022-2024 PhasorPy Contributors
+Copyright (c) 2022-2025 PhasorPy Contributors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

{phasorpy-0.3 → phasorpy-0.5}/MANIFEST.in

@@ -12,6 +12,7 @@ recursive-include tutorials *.py
 recursive-include tutorials *.rst
 
 exclude *.cmd
+exclude docs/sg_execution_times.rst
 
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]

{phasorpy-0.3/src/phasorpy.egg-info → phasorpy-0.5}/PKG-INFO

@@ -1,9 +1,9 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: phasorpy
-Version: 0.3
+Version: 0.5
 Summary: Analysis of fluorescence lifetime and hyperspectral images using the phasor approach
 Author: PhasorPy Contributors
-License: MIT
+License-Expression: MIT
 Project-URL: Homepage, https://www.phasorpy.org
 Project-URL: Documentation, https://www.phasorpy.org/docs/stable/
 Project-URL: Download, https://pypi.org/project/phasorpy/#files
@@ -13,25 +13,24 @@ Project-URL: Release notes, https://www.phasorpy.org/docs/stable/release
 Classifier: Development Status :: 3 - Alpha
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3 :: Only
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
-Requires-Python: >=3.10
+Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
-Requires-Dist: numpy>=1.24.0
-Requires-Dist: matplotlib>=3.7.0
+Requires-Dist: numpy>=1.25.0
+Requires-Dist: matplotlib>=3.8.0
 Requires-Dist: scipy>=1.11.0
 Requires-Dist: click
 Requires-Dist: pooch
 Requires-Dist: tqdm
+Requires-Dist: scikit-learn>=1.5.0
 Requires-Dist: xarray>=2023.4.0
 Requires-Dist: tifffile>=2024.8.30
 Provides-Extra: docs
@@ -42,16 +41,13 @@ Requires-Dist: sphinx-copybutton; extra == "docs"
 Requires-Dist: sphinx_click; extra == "docs"
 Requires-Dist: pydata-sphinx-theme>=0.16.0; extra == "docs"
 Requires-Dist: numpydoc; extra == "docs"
-Provides-Extra: test
-Requires-Dist: pytest; extra == "test"
-Requires-Dist: pytest-cov; extra == "test"
-Requires-Dist: pytest-runner; extra == "test"
-Requires-Dist: pytest-doctestplus; extra == "test"
-Requires-Dist: coverage; extra == "test"
 Provides-Extra: all
 Requires-Dist: lfdfiles>=2024.5.24; extra == "all"
 Requires-Dist: sdtfile>=2024.5.24; extra == "all"
 Requires-Dist: ptufile>=2024.9.14; extra == "all"
+Requires-Dist: liffile>=2025.2.10; extra == "all"
+Requires-Dist: pawflim; extra == "all"
+Dynamic: license-file
 
 # PhasorPy
 
@@ -61,7 +57,7 @@ lifetime and hyperspectral images using the phasor approach.
 - [Homepage](https://www.phasorpy.org)
 - [Documentation](https://www.phasorpy.org/docs/stable/)
 - [Source code](https://github.com/phasorpy/phasorpy)
-- [Download releases](https://pypi.org/project/phasorpy/#files)
+- [Install with pip](https://pypi.org/project/phasorpy/) or [conda](https://anaconda.org/conda-forge/phasorpy).
 - [Data files](https://zenodo.org/communities/phasorpy/)
 - [Issues and questions](https://github.com/phasorpy/phasorpy/issues)
 

{phasorpy-0.3 → phasorpy-0.5}/README.md

@@ -6,7 +6,7 @@ lifetime and hyperspectral images using the phasor approach.
 - [Homepage](https://www.phasorpy.org)
 - [Documentation](https://www.phasorpy.org/docs/stable/)
 - [Source code](https://github.com/phasorpy/phasorpy)
-- [Download releases](https://pypi.org/project/phasorpy/#files)
+- [Install with pip](https://pypi.org/project/phasorpy/) or [conda](https://anaconda.org/conda-forge/phasorpy).
 - [Data files](https://zenodo.org/communities/phasorpy/)
 - [Issues and questions](https://github.com/phasorpy/phasorpy/issues)
 

phasorpy-0.5/docs/_static/switcher.json

@@ -0,0 +1,23 @@
+[
+  {
+    "name": "dev",
+    "version": "0.6",
+    "url": "https://www.phasorpy.org/docs/dev/"
+  },
+  {
+    "name": "0.5 (stable)",
+    "version": "0.5",
+    "url": "https://www.phasorpy.org/docs/stable/",
+    "preferred": true
+  },
+  {
+    "name": "0.4",
+    "version": "0.4",
+    "url": "https://www.phasorpy.org/docs/v0.4/"
+  },
+  {
+    "name": "0.3",
+    "version": "0.3",
+    "url": "https://www.phasorpy.org/docs/v0.3/"
+  }
+]

{phasorpy-0.3 → phasorpy-0.5}/docs/acknowledgments.rst

@@ -25,6 +25,7 @@ The following people (in alphabetical order) have contributed to the
 development of PhasorPy by providing code, documentation, tutorials,
 bug fixes, or expertise:
 
+- :user:`Rodrigo Blanco <R-Blanco802>`
 - :user:`Christoph Gohlke <cgohlke>`
 - Enrico Gratton
 - :user:`Leonel Malacrida <lmalacrida>`

phasorpy-0.5/docs/api/cluster.rst

@@ -0,0 +1,5 @@
+phasorpy.cluster
+----------------
+
+.. automodule:: phasorpy.cluster
+    :members:

{phasorpy-0.3 → phasorpy-0.5}/docs/api/index.rst

@@ -5,9 +5,8 @@ This documents the application programming and command line interfaces of the
 PhasorPy library version |version|.
 
 .. note::
-    The PhasorPy library is in its early stages of development.
-    It is not nearly feature complete.
-    Large, backwards-incompatible changes may occur between revisions.
+    The PhasorPy library is still under construction. Backwards-incompatible
+    changes may occur between revisions.
 
 .. toctree::
     :maxdepth: 3
@@ -16,6 +15,7 @@ PhasorPy library version |version|.
     phasor
     cursors
     components
+    cluster
     plot
     io
     color

{phasorpy-0.3 → phasorpy-0.5}/docs/conf.py

@@ -18,7 +18,7 @@ sphinx_gallery.gen_rst.EXAMPLE_HEADER = (
 # project information
 
 project = 'PhasorPy'
-copyright = '2022-2024 PhasorPy Contributors'
+copyright = '2022-2025 PhasorPy Contributors'
 author = 'PhasorPy Contributors'
 
 import phasorpy

{phasorpy-0.3 → phasorpy-0.5}/docs/index.rst

@@ -7,15 +7,10 @@ Welcome to the documentation of PhasorPy version |version|.
 PhasorPy is an open-source Python library for the analysis of fluorescence
 lifetime and hyperspectral images using the :doc:`phasor_approach`.
 
-.. note::
-    The PhasorPy library is in its early stages of development.
-    It is not nearly feature complete.
-    Large, backwards-incompatible changes may occur between revisions.
-
 Quickstart
 ==========
 
-The :doc:`tutorials/index` demonstrate the use the library, from simple
+The :doc:`tutorials/index` demonstrate the use of the library, from simple
 examples to advanced applications.
 
 The :doc:`api/index` contains detailed information about all functions and
@@ -40,7 +35,8 @@ The library's source code and documentation are maintained in the
 `PhasorPy repository on GitHub <https://github.com/phasorpy/phasorpy>`_.
 
 Releases can be downloaded and installed from the
-`PhasorPy project on PyPI <https://pypi.org/project/phasorpy/>`_.
+`PhasorPy project on PyPI <https://pypi.org/project/phasorpy/>`_
+or `conda-forge <https://anaconda.org/conda-forge/phasorpy>`_.
 
 Sample data files used in tutorials and testing are available from the
 `PhasorPy community on Zenodo <https://zenodo.org/communities/phasorpy>`_.

{phasorpy-0.3 → phasorpy-0.5}/docs/license.rst

@@ -1,7 +1,7 @@
 MIT License
 ===========
 
-Copyright © 2022-2024 :ref:`PhasorPy Contributors <contributors>`
+Copyright © 2022-2025 :ref:`PhasorPy Contributors <contributors>`
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the “Software”), to deal

{phasorpy-0.3 → phasorpy-0.5}/docs/release.rst

@@ -6,18 +6,102 @@ a release. It includes descriptions of bug fixes, feature enhancements,
 documentation and maintenance changes.
 
 .. note::
-    The PhasorPy library is in its early stages of development.
-    It is not nearly feature complete.
-    Large, backwards-incompatible changes may occur between revisions.
+    The PhasorPy library is still under construction. Backwards-incompatible
+    changes may occur between revisions.
+
+0.5 (2025.4.11)
+---------------
+
+This is the fifth alpha release of the PhasorPy library.
+It contains several bug fixes and improvements.
+The new ``phasor_cluster_gmm`` function finds clusters in phasor coordinates
+using a Gaussian mixture model.
+The ``phasor_filter_pawflim`` function applies a wavelet filter using the
+pawFLIM library.
+This release supports Python 3.11 to 3.13. Python 3.10 is no longer supported.
+
+What's Changed
+..............
+
+* Bump version by @cgohlke in https://github.com/phasorpy/phasorpy/pull/183
+* Bug Fix for phasor_calibrate when skipping axes with harmonic axis by @bruno-pannunzio in https://github.com/phasorpy/phasorpy/pull/185
+* Fixes for liffile 2025.2.6 by @cgohlke in https://github.com/phasorpy/phasorpy/pull/184
+* Fix phasor_normalize with numpy 1.24 by @cgohlke in https://github.com/phasorpy/phasorpy/pull/186
+* Add pawFLIM wavelet filter for phasor coordinates by @bruno-pannunzio in https://github.com/phasorpy/phasorpy/pull/167
+* Add dataset from zenodo.org/records/14860228 by @cgohlke in https://github.com/phasorpy/phasorpy/pull/187
+* Improve support for Leica image files by @cgohlke in https://github.com/phasorpy/phasorpy/pull/188
+* Remove notes about early stage of development by @cgohlke in https://github.com/phasorpy/phasorpy/pull/189
+* Add plot_histograms function by @cgohlke in https://github.com/phasorpy/phasorpy/pull/191
+* Fix NaN padding in phasor_to_simfcs_referenced by @cgohlke in https://github.com/phasorpy/phasorpy/pull/192
+* Return more metadata from IFLI and FBD readers by @cgohlke in https://github.com/phasorpy/phasorpy/pull/193
+* Add more formats to file I/O tutorial by @cgohlke in https://github.com/phasorpy/phasorpy/pull/194
+* Fix module attribute of functions in phasorpy.io by @cgohlke in https://github.com/phasorpy/phasorpy/pull/195
+* Add plot_image helper function by @cgohlke in https://github.com/phasorpy/phasorpy/pull/196
+* Add section on other means to IO tutorial by @cgohlke in https://github.com/phasorpy/phasorpy/pull/197
+* Bump pypa/cibuildwheel from 2.22.0 to 2.23.0 in the github-actions group by @dependabot in https://github.com/phasorpy/phasorpy/pull/198
+* Improve IO tutorial by @cgohlke in https://github.com/phasorpy/phasorpy/pull/199
+* Fix minor issues found by GitHub Copilot by @cgohlke in https://github.com/phasorpy/phasorpy/pull/202
+* Move parse_skip_axis function to _utils module by @cgohlke in https://github.com/phasorpy/phasorpy/pull/203
+* Fix new mypy errors with numpy 2.2.4 by @cgohlke in https://github.com/phasorpy/phasorpy/pull/204
+* Raise minimum requirements by @cgohlke in https://github.com/phasorpy/phasorpy/pull/208
+* Add phasor_cluster_gmm function by @R-Blanco802 in https://github.com/phasorpy/phasorpy/pull/201
+* Require scikit-learn>=1.5.0 by @cgohlke in https://github.com/phasorpy/phasorpy/pull/209
+* Support routing channels in signal_from_sdt by @cgohlke in https://github.com/phasorpy/phasorpy/pull/210
+* Improve tests and documentation of phasor_cluster_gmm by @cgohlke in https://github.com/phasorpy/phasorpy/pull/211
+* Ignore PhasorPlot.contour cmap if colors is set by @cgohlke in https://github.com/phasorpy/phasorpy/pull/213
+* Bump pypa/cibuildwheel from 2.23.1 to 2.23.2 in the github-actions group by @dependabot in https://github.com/phasorpy/phasorpy/pull/214
+* Update Ubuntu version by @cgohlke in https://github.com/phasorpy/phasorpy/pull/219
+* Require Cython>=3.1.0b1 by @cgohlke in https://github.com/phasorpy/phasorpy/pull/216
+* Add PTU file exported from FLIM_testdata.lif with photon filter by @cgohlke in https://github.com/phasorpy/phasorpy/pull/217
+* Fix multi-channel FLIM LABS files containing single-channel phasors by @cgohlke in https://github.com/phasorpy/phasorpy/pull/218
+* Release v0.5 by @cgohlke in https://github.com/phasorpy/phasorpy/pull/220
+
+## New Contributors
+* @R-Blanco802 made their first contribution in https://github.com/phasorpy/phasorpy/pull/201
+
+**Full Changelog**: https://github.com/phasorpy/phasorpy/compare/v0.4...v0.5
+
+0.4 (2025.1.30)
+---------------
+
+This is the fourth alpha release of the PhasorPy library.
+It contains several bug fixes and many improvements, mostly to the
+``phasorpy.io`` module.
+File reader functions are now named ``signal_from_*`` or ``phasor_from_*``
+and have a more consistent API.
+Point mode PTU files, LIF files containing phasor coordinates or hyperspectral
+signals, and FLIM LABS JSON files are supported.
+PhasorPy releases are now available on conda-forge.
+This release supports Python 3.10 to 3.13.
+
+What's Changed
+..............
+
+* Bump version by @cgohlke in https://github.com/phasorpy/phasorpy/pull/163
+* Support labelled signal axes by @cgohlke in https://github.com/phasorpy/phasorpy/pull/166
+* Update copyright year by @cgohlke in https://github.com/phasorpy/phasorpy/pull/168
+* Return array coordinates from files in normal units by @cgohlke in https://github.com/phasorpy/phasorpy/pull/169
+* Document availability on conda-forge by @cgohlke in https://github.com/phasorpy/phasorpy/pull/170
+* Fix RST code is two backticks by @cgohlke in https://github.com/phasorpy/phasorpy/pull/171
+* Support reading point mode PTU files by @cgohlke in https://github.com/phasorpy/phasorpy/pull/172
+* Fix phasor_calibrate for handling higher harmonics than size of first dimension of reference_real by @bruno-pannunzio in https://github.com/phasorpy/phasorpy/pull/176
+* Improve io module by @cgohlke in https://github.com/phasorpy/phasorpy/pull/177
+* Add support for Leica LIF files by @cgohlke in https://github.com/phasorpy/phasorpy/pull/178
+* Add support for new FLIM LABS JSON format by @cgohlke in https://github.com/phasorpy/phasorpy/pull/179
+* Reformat with black 25.1 by @cgohlke in https://github.com/phasorpy/phasorpy/pull/180
+* Release v0.4 by @cgohlke in https://github.com/phasorpy/phasorpy/pull/181
+* Fixes for liffile 2025.1.30 by @cgohlke in https://github.com/phasorpy/phasorpy/pull/182
+
+**Full Changelog**: https://github.com/phasorpy/phasorpy/compare/v0.3...v0.4
 
 0.3 (2024.12.16)
 ----------------
 
 This is the third alpha release of the PhasorPy library.
-It fixes the averaging of phasor coordinates in the `phasor_center` and
-`phasor_calibrate` functions, replaces the `phasor_filter` function
-with `phasor_filter_median`, adds support for multiple harmonics to
-`phasor_threshold`, and adds the `real_imspector_tiff` function to read
+It fixes the averaging of phasor coordinates in the ``phasor_center`` and
+``phasor_calibrate`` functions, replaces the ``phasor_filter`` function
+with ``phasor_filter_median``, adds support for multiple harmonics to
+``phasor_threshold``, and adds the ``read_imspector_tiff`` function to read
 ImSpector FLIM TIFF files. This release supports Python 3.10 to 3.13.
 
 What's Changed

{phasorpy-0.3 → phasorpy-0.5}/pyproject.toml

@@ -2,7 +2,7 @@
 requires = [
     "setuptools>=68",
     "numpy",
-    "Cython>=3.0.11",
+    "cython>=3.1.0b1",
 ]
 build-backend = "setuptools.build_meta"
 
@@ -14,36 +14,35 @@ dynamic = ["version"]
 dependencies = [
     # sync with requirements_min.txt
     # https://scientific-python.org/specs/spec-0000/
-    "numpy>=1.24.0",
-    "matplotlib>=3.7.0",
+    "numpy>=1.25.0",
+    "matplotlib>=3.8.0",
     "scipy>=1.11.0",
     "click",
     "pooch",
     "tqdm",
-    # "scikit-image>=0.20.0",
-    # "scikit-learn>=1.2.2",
-    # "pandas>=2.0.0",
+    "scikit-learn>=1.5.0",
+    # "scikit-image>=0.21.0",
+    # "pandas>=2.1.0",
     "xarray>=2023.4.0",
     "tifffile>=2024.8.30",
 ]
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 classifiers = [
     "Development Status :: 3 - Alpha",
     "Intended Audience :: Developers",
     "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: MIT License",
     "Programming Language :: Python",
     "Topic :: Software Development :: Libraries :: Python Modules",
     "Operating System :: OS Independent",
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3 :: Only",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
 ]
 authors = [{ name = "PhasorPy Contributors" }]
-license = { text = "MIT" }
+license = "MIT"
+license-files = ["LICENSE.txt"]
 
 [project.urls]
 Homepage = "https://www.phasorpy.org"
@@ -66,23 +65,15 @@ docs = [
     "pydata-sphinx-theme>=0.16.0",
     "numpydoc",
 ]
-test = [
-    "pytest",
-    "pytest-cov",
-    "pytest-runner",
-    "pytest-doctestplus",
-    "coverage",
-]
 all = [
     "lfdfiles>=2024.5.24",
     "sdtfile>=2024.5.24",
     "ptufile>=2024.9.14",
+    "liffile>=2025.2.10",
+    "pawflim",
 ]
 
 [tool.setuptools]
-package-dir = { "" = "src" }
-packages = ["phasorpy"]
-license-files = ["LICENSE.txt"]
 zip-safe = false
 
 [tool.setuptools.dynamic]
@@ -122,7 +113,7 @@ disable = [
 
 [tool.black]
 line-length = 79
-target-version = ["py310"]
+target-version = ["py311"]
 skip-string-normalization = true
 
 [tool.isort]
@@ -142,14 +133,15 @@ strict = true
 warn_unreachable = true
 
 [[tool.mypy.overrides]]
-module = ["phasorpy._phasorpy", "pooch.*", "scipy.*", "mkl_fft.*"]
+module = ["phasorpy._phasorpy", "pooch.*", "scipy.*", "mkl_fft.*", "sklearn.*"]
 ignore_missing_imports = true
 
 [tool.coverage.run]
 plugins = ["Cython.Coverage"]
+omit = ["conftest.py", "__main__.py"]
 
 [tool.coverage.report]
-exclude_lines = ["pragma: no cover", "pragma: ${PY_MAJOR_VERSION} no cover"]
+exclude_lines = ["if TYPE_CHECKING:", "plot.show()", "pragma: no cover", "pragma: ${PY_MAJOR_VERSION} no cover"]
 
 [tool.coverage.html]
 directory = "_htmlcov"
@@ -159,7 +151,7 @@ minversion = "7"
 log_cli_level = "INFO"
 # filterwarnings = ["error"]  # breaks debugging tests in VSCode (Sept. 2024)
 xfail_strict = true
-addopts = "-rfEXs --strict-config --strict-markers --doctest-modules --doctest-glob=*.py --doctest-glob=*.rst"
+addopts = "-rfEXs --strict-config --strict-markers --doctest-modules --doctest-glob=*.py --doctest-glob=*.rst --ignore=src/phasorpy/_io.py"
 doctest_optionflags = [
     "NORMALIZE_WHITESPACE",
     "ELLIPSIS",
@@ -186,6 +178,6 @@ norecursedirs = [
 ]
 
 [tool.cibuildwheel]
-skip = "pp* cp37* cp38* cp39* *musllinux* *i686 *ppc64le *s390x cp39*win*arm64 cp310*win*arm64"
-test-requires = ["lfdfiles", "sdtfile", "ptufile", "pytest", "pytest-cov", "pytest-runner", "pytest-doctestplus", "coverage"]
+skip = "pp* cp37* cp38* cp39* cp310* *musllinux* *i686 *ppc64le *s390x cp39*win*arm64"
+test-requires = ["scikit-learn", "lfdfiles", "sdtfile", "ptufile", "liffile", "pawflim", "pytest", "pytest-cov", "pytest-runner", "pytest-doctestplus", "coverage"]
 test-command = "pytest {project}/tests"