phasorpy 0.4__tar.gz → 0.6__tar.gz

{phasorpy-0.4 → phasorpy-0.6}/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-0.4/src/phasorpy.egg-info → phasorpy-0.6}/PKG-INFO

@@ -1,9 +1,9 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: phasorpy
-Version: 0.4
+Version: 0.6
 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
@@ -42,17 +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>=2025.1.30; extra == "all"
+Requires-Dist: liffile>=2025.2.10; extra == "all"
+Requires-Dist: pawflim; extra == "all"
+Dynamic: license-file
 
 # PhasorPy
 
@@ -71,7 +66,7 @@ PhasorPy is a community-maintained project.
 in the form of bug reports, bug fixes, feature implementations, documentation,
 datasets, and enhancement proposals are welcome.
 
-This software project is supported in part by the
+This software project was supported in part by the
 [Essential Open Source Software for Science (EOSS)](https://chanzuckerberg.com/eoss/)
 program at
 [Chan Zuckerberg Initiative](https://chanzuckerberg.com/).

{phasorpy-0.4 → phasorpy-0.6}/README.md

@@ -15,7 +15,7 @@ PhasorPy is a community-maintained project.
 in the form of bug reports, bug fixes, feature implementations, documentation,
 datasets, and enhancement proposals are welcome.
 
-This software project is supported in part by the
+This software project was supported in part by the
 [Essential Open Source Software for Science (EOSS)](https://chanzuckerberg.com/eoss/)
 program at
 [Chan Zuckerberg Initiative](https://chanzuckerberg.com/).

{phasorpy-0.4 → phasorpy-0.6}/docs/_static/switcher.json

@@ -1,23 +1,23 @@
 [
   {
     "name": "dev",
-    "version": "0.5",
+    "version": "0.7",
     "url": "https://www.phasorpy.org/docs/dev/"
   },
   {
-    "name": "0.4 (stable)",
-    "version": "0.4",
+    "name": "0.6 (stable)",
+    "version": "0.6",
     "url": "https://www.phasorpy.org/docs/stable/",
     "preferred": true
   },
   {
-    "name": "0.3",
-    "version": "0.3",
-    "url": "https://www.phasorpy.org/docs/v0.3/"
+    "name": "0.5",
+    "version": "0.5",
+    "url": "https://www.phasorpy.org/docs/v0.5/"
   },
   {
-    "name": "0.2",
-    "version": "0.2",
-    "url": "https://www.phasorpy.org/docs/v0.2/"
+    "name": "0.4",
+    "version": "0.4",
+    "url": "https://www.phasorpy.org/docs/v0.4/"
   }
 ]

phasorpy-0.6/docs/acknowledgments.rst

@@ -0,0 +1,42 @@
+Acknowledgments
+===============
+
+The PhasorPy project was established by the
+`Advanced Bioimaging Unit <https://pasteur.uy/en/units/advanced-bioimaging>`_
+at the University of the Republic and Institut Pasteur de Montevideo and the
+`Laboratory for Fluorescence Dynamics <https://www.lfd.uci.edu>`_
+at the University of California, Irvine.
+
+PhasorPy was inspired by the
+`Globals for Images · SimFCS <https://www.lfd.uci.edu/globals/>`_ software by
+Enrico Gratton.
+
+This software project was supported in part by the
+`Essential Open Source Software for Science (EOSS)
+<https://chanzuckerberg.com/eoss/>`_ program at
+`Chan Zuckerberg Initiative <https://chanzuckerberg.com/>`_
+(grant number 2022-252604, 2022-2024).
+
+.. _contributors:
+
+Contributors
+------------
+
+PhasorPy is developed by `contributors to the PhasorPy repository
+<https://github.com/phasorpy/phasorpy/graphs/contributors>`_
+and
+`members of the PhasorPy organization
+<https://github.com/orgs/phasorpy/people>`_.
+
+User Community
+--------------
+
+Many thanks to the PhasorPy user community for their feedback, bug reports,
+feature suggestions, and data files that have helped improve the library.
+
+Citation
+--------
+
+If PhasorPy contributes to a project that leads to a publication,
+please cite
+`doi: 10.5281/zenodo.13862586 <https://doi.org/10.5281/zenodo.13862586>`_.

phasorpy-0.6/docs/api/cluster.rst

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

phasorpy-0.6/docs/api/experimental.rst

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

{phasorpy-0.4 → phasorpy-0.6}/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
@@ -16,9 +15,11 @@ PhasorPy library version |version|.
     phasor
     cursors
     components
+    cluster
     plot
     io
     color
+    experimental
     datasets
     utils
     _utils

{phasorpy-0.4 → phasorpy-0.6}/docs/code_of_conduct.rst

@@ -1,3 +1,5 @@
+:orphan:
+
 Code of conduct
 ===============
 
@@ -68,9 +70,8 @@ Enforcement
 -----------
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
-reported to the community leader responsible for enforcement:
-
-- `Leonel Malacrida <conduct@phasorpy.org>`_
+reported to `<conduct@phasorpy.org>`_ and `PhasorPy organization members
+<https://github.com/orgs/phasorpy/people>`_.
 
 All complaints will be reviewed and investigated promptly and fairly.
 

{phasorpy-0.4 → phasorpy-0.6}/docs/conf.py

@@ -2,9 +2,10 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 # pylint: skip-file
 
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('../src/'))
+import os
+import sys
+
+sys.path.insert(0, os.path.dirname(__file__))
 
 # remove the examples header from HTML tutorials
 import sphinx_gallery.gen_rst
@@ -123,8 +124,41 @@ sphinx_gallery_conf = {
     'gallery_dirs': 'tutorials',
     'reference_url': {'phasorpy': None},
     'matplotlib_animations': True,
+    'within_subsection_order': 'conf.TutorialOrder',
 }
 
+
+class TutorialOrder:
+    """Order tutorials in gallery subsections."""
+
+    tutorials = [
+        'introduction',
+        'lifetime_geometry',
+        'lfd_workshop',
+        # api
+        'io',
+        'phasor_from_lifetime',
+        'multi-harmonic',
+        'filtering',
+        'phasorplot',
+        'cursors',
+        'components',
+        'fret',
+        'lifetime_to_signal',
+        'pca',
+        # applications
+        'component_fit',
+        'fret_efficiency',
+        # benchmarks
+        'phasor_from_signal',
+    ]
+
+    def __init__(self, srcdir: str): ...
+
+    def __call__(self, filename: str) -> int:
+        return self.tutorials.index(filename[9:-3])
+
+
 copybutton_prompt_text = (
     r'>>> |\.\.\. |\$ |In \[\d*\]: | {2,5}\.\.\.: | {5,8}: '
 )

{phasorpy-0.4 → phasorpy-0.6}/docs/contributing.rst

@@ -61,9 +61,9 @@ and include the following items in the bug report:
   of::
 
     $ python -m phasorpy versions
-    Python 3.11.4 ...
-    phasorpy 0.1.dev ...
-    numpy 1.25.2
+    Python-3.13.3
+    phasorpy-0.5
+    numpy-2.2.6
     ...
 
 Contribute code or documentation
@@ -289,4 +289,6 @@ and must pass before code or documentation can be accepted.
 Other PhasorPy developers will review the pull request to check and help
 to improve its implementation, documentation, and style.
 
-Pull requests must be approved by a core team member before merging.
+Pull requests must be approved by a
+`PhasorPy organization member <https://github.com/orgs/phasorpy/people>`_
+before merging.

{phasorpy-0.4 → phasorpy-0.6}/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
@@ -67,7 +62,6 @@ Contents
     api/index
     release
     contributing
-    code_of_conduct
     acknowledgments
     license
 

{phasorpy-0.4 → phasorpy-0.6}/docs/phasor_approach.rst

@@ -200,8 +200,8 @@ approach to analyze fluorescence time-resolved or spectral images:
   microscopy written in MATLAB by Alexander Vallmitjana, released under
   the CC BY 4.0 license.
 
-- `AlliGator <https://alligator-distribution.readthedocs.io>`_
-  is a free, closed-source software for fluorescence lifetime image data
+- `AlliGator <https://github.com/smXplorer/AlliGator>`_
+  is an open-source software for fluorescence lifetime image data
   analysis using the phasor approach and standard nonlinear fitting.
   The software is written in LabVIEW for Windows by Xavier Michalet.
 

{phasorpy-0.4 → phasorpy-0.6}/docs/release.rst

@@ -6,15 +6,131 @@ 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.
+
+0.6 (2025.6.22)
+---------------
+
+This is the sixth alpha release of the PhasorPy library.
+It contains several bug fixes, improvements, and breaking changes.
+
+The new ``phasor_component_fit`` function fits fractions of multiple
+components to phasor coordinates.
+The ``phasor_nearest_neighbor`` function returns nearest neighbors in phasor
+coordinates.
+The ``phasor_to_normal_lifetime`` function returns single lifetimes closest
+to phasor coordinates.
+The ``phasor_semicircle_intersect`` function returns intersections of lines
+with the universal semicircle.
+
+The ``LifetimePlots`` class interactively plots lifetimes in the time domain,
+frequency domain, and phasor plot. It can be invoked from the command line
+with ``python -m phasorpy lifetime``.
+
+The ``two_fractions_from_phasor`` and ``graphical_component_analysis``
+functions are renamed to ``phasor_component_fraction`` and
+``phasor_component_graphical``, respectively.
+The ``versions`` function has moved to the ``phasorpy.utils`` namespace.
+The ``spectral_vector_denoise``, ``anscombe_transform``, and
+``anscombe_transform_inverse`` functions have moved to the
+``phasorpy.experimental`` namespace.
+
+Functions in the ``io`` module now return only the first channel by default.
+
+Three new tutorials are added: "Geometrical interpretation of lifetimes",
+"Multi-component fit", and "FRET efficiency image".
+This release supports Python 3.11 to 3.13.
+
+What's Changed
+..............
+
+* Bump version by @cgohlke in https://github.com/phasorpy/phasorpy/pull/221
+* Bump pypa/cibuildwheel from 2.23.2 to 2.23.3 in the github-actions group by @dependabot in https://github.com/phasorpy/phasorpy/pull/223
+* Update description of AlliGator software by @cgohlke in https://github.com/phasorpy/phasorpy/pull/225
+* Cython 3.1.0 is released by @cgohlke in https://github.com/phasorpy/phasorpy/pull/226
+* Add phasor_to_normal_lifetime function by @cgohlke in https://github.com/phasorpy/phasorpy/pull/228
+* Read first channel from files by default by @cgohlke in https://github.com/phasorpy/phasorpy/pull/229
+* Update acknowledgments by @cgohlke in https://github.com/phasorpy/phasorpy/pull/230
+* Use importlib to get package versions by @cgohlke in https://github.com/phasorpy/phasorpy/pull/231
+* Use Windows Server 2022 in GitHub Actions by @cgohlke in https://github.com/phasorpy/phasorpy/pull/232
+* Add tutorial about geometrical interpretation of lifetimes by @cgohlke in https://github.com/phasorpy/phasorpy/pull/233
+* Update reference phasor_from_signal benchmark results by @cgohlke in https://github.com/phasorpy/phasorpy/pull/234
+* Sort clusters returned by phasor_cluster_gmm by @cgohlke in https://github.com/phasorpy/phasorpy/pull/236
+* Reorganize io module by @cgohlke in https://github.com/phasorpy/phasorpy/pull/235
+* Update pre-commit configuration by @cgohlke in https://github.com/phasorpy/phasorpy/pull/237
+* Fix test failing with numpy 2.3.0 by @cgohlke in https://github.com/phasorpy/phasorpy/pull/239
+* Add phasor_component_fit function by @cgohlke in https://github.com/phasorpy/phasorpy/pull/238
+* Rename functions in components module by @cgohlke in https://github.com/phasorpy/phasorpy/pull/240
+* Add phasor_semicircle_intersect function by @cgohlke in https://github.com/phasorpy/phasorpy/pull/241
+* Add private helper functions to mask universal semicircle by @cgohlke in https://github.com/phasorpy/phasorpy/pull/242
+* Add private _distance_from_semicircle function by @cgohlke in https://github.com/phasorpy/phasorpy/pull/244
+* Reorganize plot module by @cgohlke in https://github.com/phasorpy/phasorpy/pull/245
+* Add interactive LifetimePlots class by @cgohlke in https://github.com/phasorpy/phasorpy/pull/247
+* Reorganize version, utils, and experimental modules by @cgohlke in https://github.com/phasorpy/phasorpy/pull/248
+* Add phasor_nearest_neighbor function by @bruno-pannunzio in https://github.com/phasorpy/phasorpy/pull/243
+* Release v0.6 by @cgohlke in https://github.com/phasorpy/phasorpy/pull/244
+
+**Full Changelog**: https://github.com/phasorpy/phasorpy/compare/v0.5...v0.6
+
+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.
+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
@@ -42,7 +158,6 @@ What's Changed
 
 **Full Changelog**: https://github.com/phasorpy/phasorpy/compare/v0.3...v0.4
 
-
 0.3 (2024.12.16)
 ----------------
 

{phasorpy-0.4 → phasorpy-0.6}/pyproject.toml

@@ -2,7 +2,7 @@
 requires = [
     "setuptools>=68",
     "numpy",
-    "Cython>=3.0.11",
+    "cython>=3.1.0",
 ]
 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"
@@ -66,28 +65,19 @@ 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>=2025.1.30",
+    "liffile>=2025.2.10",
+    "pawflim",
 ]
 
 [tool.setuptools]
-package-dir = { "" = "src" }
-packages = ["phasorpy"]
-license-files = ["LICENSE.txt"]
 zip-safe = false
 
 [tool.setuptools.dynamic]
-version = { attr = "phasorpy.version.__version__" }
+version = { attr = "phasorpy.__version__" }
 
 [tool.setuptools.package-data]
 phasorpy = ["py.typed"]
@@ -123,7 +113,7 @@ disable = [
 
 [tool.black]
 line-length = 79
-target-version = ["py310"]
+target-version = ["py311"]
 skip-string-normalization = true
 
 [tool.isort]
@@ -143,14 +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"
@@ -187,6 +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", "liffile", "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"

phasorpy-0.6/src/phasorpy/__init__.py

@@ -0,0 +1,9 @@
+"""PhasorPy package."""
+
+from __future__ import annotations
+
+__all__ = ['__version__']
+
+
+__version__ = '0.6'
+"""PhasorPy version string."""