phasorpy 0.11__tar.gz → 0.13__tar.gz

{phasorpy-0.11/src/phasorpy.egg-info → phasorpy-0.13}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phasorpy
-Version: 0.11
+Version: 0.13
 Summary: Analysis of luminescence lifetime and hyperspectral images using the phasor approach
 Author: PhasorPy Contributors
 License-Expression: MIT
@@ -21,14 +21,15 @@ Classifier: Programming Language :: Python :: 3 :: Only
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: 3.14
+Classifier: Programming Language :: Python :: 3.15
 Requires-Python: >=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
 Requires-Dist: numpy>=2.1.0
-Requires-Dist: matplotlib>=3.9.0
-Requires-Dist: pandas>=2.3.0
+Requires-Dist: matplotlib>=3.10.3
+Requires-Dist: pandas>=2.3.2
 Requires-Dist: scikit-learn>=1.5.0
-Requires-Dist: scipy>=1.14.0
+Requires-Dist: scipy>=1.14.1
 Requires-Dist: tifffile>=2026.5.2
 Requires-Dist: xarray>=2024.6.0
 Requires-Dist: click
@@ -37,12 +38,12 @@ Requires-Dist: tqdm
 Provides-Extra: all
 Requires-Dist: czifile>=2026.4.11; extra == "all"
 Requires-Dist: fbdfile>=2025.9.18; extra == "all"
-Requires-Dist: lfdfiles>=2026.4.30; extra == "all"
+Requires-Dist: lfdfiles>=2026.6.24; extra == "all"
 Requires-Dist: liffile>=2025.2.10; extra == "all"
 Requires-Dist: ptufile>=2024.9.14; extra == "all"
 Requires-Dist: sdtfile>=2024.5.24; extra == "all"
 Requires-Dist: pawflim>=1.0.4; extra == "all"
-Requires-Dist: imagecodecs==2026.6.6; (sys_platform == "darwin" and platform_machine == "x86_64") and extra == "all"
+Requires-Dist: brighteyes-mcs-reader>=0.1.0; python_version < "3.15" and extra == "all"
 Dynamic: license-file
 
 # <img src="https://www.phasorpy.org/_static/phasorpy_logo.svg" alt="&#x25CB;" width="48" height="48" align="left"/> PhasorPy

{phasorpy-0.11 → phasorpy-0.13}/docs/_static/switcher.json

@@ -1,23 +1,28 @@
 [
   {
     "name": "dev",
-    "version": "0.12",
+    "version": "0.14",
     "url": "https://www.phasorpy.org/docs/dev/"
   },
   {
-    "name": "0.11 (stable)",
-    "version": "0.11",
+    "name": "0.13 (stable)",
+    "version": "0.13",
     "url": "https://www.phasorpy.org/docs/stable/",
     "preferred": true
   },
+  {
+    "name": "0.12",
+    "version": "0.12",
+    "url": "https://www.phasorpy.org/docs/v0.12/"
+  },
+  {
+    "name": "0.11",
+    "version": "0.11",
+    "url": "https://www.phasorpy.org/docs/v0.11/"
+  },
   {
     "name": "0.10",
     "version": "0.10",
     "url": "https://www.phasorpy.org/docs/v0.10/"
-  },
-  {
-    "name": "0.9",
-    "version": "0.9",
-    "url": "https://www.phasorpy.org/docs/v0.9/"
   }
 ]

phasorpy-0.13/docs/about.rst

@@ -0,0 +1,83 @@
+About PhasorPy
+==============
+
+The PhasorPy project's mission is to advance and democratize phasor analysis
+through the open-source PhasorPy library.
+
+.. _funding:
+
+Founding and funding
+--------------------
+
+The PhasorPy project was established in 2023 by the
+`Advanced Bioimaging Unit <https://www.uba.uy>`_
+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.
+
+The project was supported 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).
+
+Project goals
+-------------
+
+The original goals were to create an open-source Python library based on
+sound software engineering principles, establish a community of users
+and developers, and reimplement core phasor-based functionality of the
+discontinued closed-source
+`Globals for Images - SimFCS <https://www.lfd.uci.edu/globals/>`_
+software by Enrico Gratton.
+
+The current goals are to improve community sustainability and to advance the
+PhasorPy library toward a stable, extensible platform that supports
+large-scale automated workflows, AI-assisted analysis, and robust integration
+with the scientific Python ecosystem, while continuing to serve as a reliable
+base for graphical applications and training resources.
+
+.. _governance:
+
+.. _contributors:
+
+Governance and contributors
+---------------------------
+
+PhasorPy is developed collaboratively by
+`contributors to the PhasorPy repository
+<https://github.com/phasorpy/phasorpy/graphs/contributors?all=1>`_
+and governed by
+`members of the PhasorPy organization
+<https://github.com/orgs/phasorpy/people>`_.
+
+Technical direction is developed through open discussion and
+consensus-building in issues, pull requests, and community meetings.
+Members of the PhasorPy organization make final technical and release
+decisions.
+
+Infrastructure hosting, funded activities, and institutional partnerships are
+coordinated through the `Advanced Bioimaging Unit <https://www.uba.uy>`__.
+
+See the :doc:`Contributing guide <contributing>` to get involved.
+
+Acknowledgments
+---------------
+
+We thank the PhasorPy user community for feedback, bug reports, feature
+suggestions, and data files that have helped improve the library.
+
+We acknowledge the open-source scientific Python ecosystem that PhasorPy
+builds on, including Python, NumPy, SciPy, Matplotlib, and scikit-learn,
+the microscopy file-format stack (including tifffile, ptufile, and related
+tools), and the documentation toolchain based on Sphinx and Sphinx-Gallery.
+
+We also acknowledge GitHub for providing a platform for collaborative
+development and hosting documentation, PyPI and conda-forge for package
+distribution, and Zenodo for hosting sample data.
+
+Citation
+--------
+
+If PhasorPy contributes to research that leads to a publication, please cite
+`doi: 10.5281/zenodo.13862586 <https://doi.org/10.5281/zenodo.13862586>`_.

phasorpy-0.13/docs/acknowledgments.rst

@@ -0,0 +1,3 @@
+:orphan:
+
+See :doc:`about`

{phasorpy-0.11 → phasorpy-0.13}/docs/conf.py

@@ -1,3 +1,7 @@
+# Copyright (c) PhasorPy Contributors
+# SPDX-License-Identifier: MIT
+# See LICENSE.txt file in the project root for details.
+
 """Sphinx build configuration file.
 
 https://www.sphinx-doc.org/en/master/usage/configuration.html
@@ -13,6 +17,8 @@ sys.path.insert(0, os.path.dirname(__file__))
 
 # remove the examples header from HTML tutorials
 import sphinx_gallery.gen_rst
+from docutils import nodes
+from sphinx.application import Sphinx
 from sphinx_gallery.sorting import ExplicitOrder
 
 sphinx_gallery.gen_rst.EXAMPLE_HEADER = (
@@ -47,7 +53,6 @@ extensions = [
     # don't enable intersphinx since tutorials are getting littered with links
     # 'sphinx.ext.intersphinx',
     # 'numpydoc',
-    'sphinx_inline_tabs',
     'sphinx_copybutton',
     'sphinx_click',
     'sphinx_issues',
@@ -148,9 +153,6 @@ sphinx_gallery_conf = {
     # 'backreferences_dir': None,
 }
 
-# TODO: remove MathJax 3 link once scroll bar issue is resolved
-mathjax_path = 'https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js'
-
 
 class TutorialOrder:
     """Order tutorials in gallery subsections."""
@@ -174,6 +176,7 @@ class TutorialOrder:
         'multi_harmonic',
         'phasorplot',
         'cursor',
+        'cluster',
         'component',
         'pca',
         # misc
@@ -210,6 +213,29 @@ intersphinx_mapping = {
 # do not show typehints
 autodoc_typehints = 'none'
 
+# redirect links to defunct websites, for example, to the Web Archive
+link_redirects = {
+    'https://www.lfd.uci.edu': (
+        'https://web.archive.org/web/20260926221331/https://www.lfd.uci.edu'
+    ),
+}
+
+
+def redirect_links(app: Sphinx, doctree: nodes.document) -> None:
+    """Replace URL prefixes in links according to link_redirects."""
+    del app
+    for node in doctree.findall(nodes.reference):
+        refuri = node.get('refuri', '')
+        for old, new in link_redirects.items():
+            if refuri.startswith(old):
+                node['refuri'] = new + refuri[len(old) :]
+                break
+
+
+def setup(app: Sphinx) -> None:
+    """Set up Sphinx app with link redirection."""
+    app.connect('doctree-read', redirect_links)
+
 
 def linkcode_resolve(domain: str, info: dict[str, str]) -> str | None:
     """Return GitHub URL for Python object."""
@@ -235,8 +261,8 @@ def linkcode_resolve(domain: str, info: dict[str, str]) -> str | None:
         except AttributeError:
             return None
 
-    if inspect.isfunction(obj):
-        obj = inspect.unwrap(obj)
+    if inspect.isfunction(obj):  # type: ignore[unreachable]
+        obj = inspect.unwrap(obj)  # type: ignore[unreachable]
     try:
         fn = inspect.getsourcefile(obj)
     except TypeError:

{phasorpy-0.11 → phasorpy-0.13}/docs/contributing.rst

@@ -61,9 +61,9 @@ and include the following items in the bug report:
   output of::
 
     $ python -m phasorpy versions
-    Python-3.14.1
-    phasorpy-0.8
-    numpy-2.3.5
+    Python-3.14.6
+    phasorpy-0.11
+    numpy-2.5.1
     ...
 
 Contribute code or documentation
@@ -88,6 +88,30 @@ The PhasorPy project loosely follows the
 `pyOpenSci <https://www.pyopensci.org/python-package-guide/>`_
 development guidelines.
 
+The PhasorPy project follows and adapts the `SciPy AI policy
+<https://scipy.github.io/devdocs/dev/conduct/ai_policy.html>`_.
+
+Copyright
+.........
+
+All code in PhasorPy is released under the :doc:`license`.
+Contributors license their code under the same license when submitting it
+to PhasorPy's version control repository.
+That means contributors must have the right to submit the code to PhasorPy
+and must comply with the terms of any MIT-compatible open-source license
+associated with submitted code.
+
+Accountability
+..............
+
+Contributors are responsible for all code submitted to the PhasorPy repository.
+They must understand it and be able to explain it, regardless of whether it
+was manually written or AI-generated.
+
+Contributors must disclose whether AI has been used to assist in the
+development of code or documentation. If so, specify the tool(s) used,
+how they were used, and which code or text is AI-generated.
+
 Fork the repository
 ...................
 
@@ -195,7 +219,7 @@ must conform to certain styles, which can be checked and applied with
 
     $ python -m pre_commit run --all-files
 
-User-facing classes and functions must use
+Tests and user-facing classes and functions must use
 `type hints <https://peps.python.org/pep-0484/>`_
 and pass verification with the
 `MyPy <https://mypy.readthedocs.io>`_

{phasorpy-0.11 → phasorpy-0.13}/docs/index.rst

@@ -19,14 +19,14 @@ classes of the library.
 The :doc:`release/index` list recent bug fixes, feature enhancements,
 documentation, and maintenance changes.
 
-The :doc:`contributing` explains how to get support, report bugs,
-submit fixes, and improve the documentation.
+The :doc:`Contributing guide <contributing>` explains how to get support,
+report bugs, submit fixes, and improve the documentation.
 
 The :doc:`code_of_conduct` applies to everyone participating in the
 PhasorPy community.
 
-The :doc:`acknowledgments` list individuals and organizations that
-contributed to the development of PhasorPy.
+The :doc:`About <about>` page describes the project's history, goals,
+funding, and governance.
 
 The PhasorPy library and documentation are released under the permissive
 :doc:`license`.
@@ -62,8 +62,8 @@ Contents
     api/index
     release/index
     contributing
-    acknowledgments
     license
+    about
 
 Indices and tables
 ------------------

{phasorpy-0.11 → phasorpy-0.13}/docs/phasor_approach.rst

@@ -150,16 +150,19 @@ luminescence time-resolved or spectral images:
      - :ref:`PhasorPy <phasorpy>`,
        :ref:`tttrlib <tttrlib>`,
        :ref:`FLIMLib <flimlib>`:sup:`2`,
+       :ref:`PyFLI <pyfli>`:sup:`2`,
        :ref:`BrightEyes <brighteyes>`:sup:`2`,
        :ref:`FLIM_tools <flim_tools>`:sup:`2,4`,
        :ref:`Cell-analysis-tools <cell_analysis_tools>`:sup:`2,4`
    * - **Desktop**
      - :ref:`SimFCS <simfcs>`:sup:`3,4`,
        :ref:`FLIM Playground <flim_playground>`:sup:`1`,
+       :ref:`FLIMKit <flimkit>`:sup:`1`,
        :ref:`FLUTE <flute>`,
        :ref:`FLIMPA <flimpa>`,
        :ref:`GSLab <gslab>`,
        :ref:`AlliGator <alligator>`,
+       :ref:`Spectral Phasors Analysis <spectral_phasors_analysis>`:sup:`2`,
        :ref:`HySP <hysp>`:sup:`3,4`,
        :ref:`FlimFast <flimfast>`:sup:`3,4`
    * - **Napari**
@@ -316,6 +319,22 @@ Details:
   The software is written in Python, is web deployable, and is distributed
   under the MIT license.
 
+-
+  .. _flimkit:
+
+  `FLIMKit <https://github.com/alex1075/FLIMKit>`__
+  is an open-source Python toolkit focused on PTU-based FLIM data. It includes
+  a phasor analysis workflow and is distributed under the MIT license.
+
+-
+  .. _pyfli:
+
+  `PyFLI <https://github.com/vkp217/pyfli-pkg>`__
+  is an open-source Python platform for Fluorescence Lifetime Imaging
+  (FLI) data simulation, processing and visualization, including phasor
+  analysis.
+  The library is distributed under the AGPL-3.0 license.
+
 -
   .. _flim_tools:
 
@@ -333,6 +352,14 @@ Details:
   and correcting phasor coordinates. The library is distributed under the
   BSD license.
 
+-
+  .. _spectral_phasors_analysis:
+
+  `Spectral Phasors Analysis <https://github.com/DBP008/spectral-phasors-analysis>`__
+  is a Python application to explore spectral phasors through simulations and
+  analyze experimental data. The software is distributed under the AGPL-3.0
+  license.
+
 -
   .. _phasor_analysis:
 

{phasorpy-0.11 → phasorpy-0.13}/pyproject.toml

@@ -1,8 +1,8 @@
 [build-system]
 requires = [
-    "setuptools>=68",
+    "setuptools>=77",
     "numpy>=2.1.0",
-    "cython>=3.2.4",
+    "cython>=3.2.9",
 ]
 build-backend = "setuptools.build_meta"
 
@@ -15,11 +15,11 @@ dependencies = [
     # sync with [dependency-groups.run]
     # https://scientific-python.org/specs/spec-0000/
     "numpy>=2.1.0",
-    "matplotlib>=3.9.0",
-    "pandas>=2.3.0",
+    "matplotlib>=3.10.3",
+    "pandas>=2.3.2",
     # "scikit-image>=0.24.0",
     "scikit-learn>=1.5.0",
-    "scipy>=1.14.0",
+    "scipy>=1.14.1",
     "tifffile>=2026.5.2",
     "xarray>=2024.6.0",
     "click",
@@ -39,6 +39,7 @@ classifiers = [
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
     "Programming Language :: Python :: 3.14",
+    "Programming Language :: Python :: 3.15",
 ]
 authors = [{ name = "PhasorPy Contributors" }]
 license = "MIT"
@@ -60,12 +61,13 @@ all = [
     # sync with [dependency-groups.optional]
     "czifile>=2026.4.11",
     "fbdfile>=2025.9.18",
-    "lfdfiles>=2026.4.30",
+    "lfdfiles>=2026.6.24",
     "liffile>=2025.2.10",
     "ptufile>=2024.9.14",
     "sdtfile>=2024.5.24",
     "pawflim>=1.0.4",
-    "imagecodecs==2026.6.6; sys_platform == 'darwin' and platform_machine == 'x86_64'",
+    "brighteyes-mcs-reader>=0.1.0; python_version < '3.15'",
+    # "imagecodecs==2026.6.6; sys_platform == 'darwin' and platform_machine == 'x86_64'",
     # "mkl-fft>=2.1.1",
 ]
 
@@ -73,10 +75,10 @@ all = [
 run = [
     # runtime dependencies; sync with [project.dependencies]
     "numpy>=2.1.0",
-    "matplotlib>=3.10.0",
-    "pandas>=2.3.0",
+    "matplotlib>=3.10.3",
+    "pandas>=2.3.2",
     "scikit-learn>=1.5.0",
-    "scipy>=1.14.0",
+    "scipy>=1.14.1",
     "tifffile>=2026.5.2",
     "xarray>=2024.6.0",
     "click",
@@ -87,12 +89,13 @@ optional = [
     # optional runtime dependencies; sync with [project.optional-dependencies]
     "czifile>=2026.4.11",
     "fbdfile>=2025.9.18",
-    "lfdfiles>=2026.4.30",
+    "lfdfiles>=2026.6.24",
     "liffile>=2025.2.10",
     "ptufile>=2024.9.14",
     "sdtfile>=2024.5.24",
     "pawflim>=1.0.4",
-    "imagecodecs==2026.6.6; sys_platform == 'darwin' and platform_machine == 'x86_64'",
+    "brighteyes-mcs-reader>=0.1.0; python_version < '3.15'",
+    # "imagecodecs==2026.6.6; sys_platform == 'darwin' and platform_machine == 'x86_64'",
 ]
 minimal = [
     # minimal runtime versions for testing against oldest supported versions
@@ -106,15 +109,16 @@ minimal = [
     # optional
     "czifile==2026.4.11; python_version == \"3.12\"",
     "fbdfile==2025.9.18; python_version == \"3.12\"",
-    "lfdfiles==2026.4.30; python_version == \"3.12\"",
+    "lfdfiles==2026.6.24; python_version == \"3.12\"",
     "liffile==2025.2.10; python_version == \"3.12\"",
     "ptufile==2024.9.14; python_version == \"3.12\"",
     "sdtfile==2024.5.24; python_version == \"3.12\"",
     "pawflim==1.0.4; python_version == \"3.12\"",
+    "brighteyes-mcs-reader==0.1.0; python_version == \"3.12\""
 ]
 build = [
     # build requirements
-    "cython>=3.2.4",
+    "cython>=3.2.9",
     "numpy>=2.1.0",
     "abi3audit",
     "build",
@@ -140,7 +144,6 @@ docs = [
     "sphinx",
     "sphinx-copybutton",
     "sphinx-design",
-    "sphinx-inline-tabs",
     "sphinx-issues",
     "sphinx_click",
     "sphinx_gallery",
@@ -148,7 +151,7 @@ docs = [
 lint = [
     # static code analysis requirements
     "autoflake",
-    "black",
+    "black>=26.10.1",
     "blackdoc",
     # "codespell",
     "cython_lint",
@@ -260,9 +263,9 @@ typing-modules = ["_typing"]
 "__init__.py" = ["F401", "F403"]
 "conftest.py" = ["ARG001"]
 "setup.py" = ["T201"]
-"tests/*" = ["ANN", "D", "INP001", "PT011", "SLF001", "S101"]
+"tests/*" = ["INP001", "PT011", "SLF001", "TC001", "PLR0917"]
 "tools/*" = ["ANN", "INP001", "T201"]
-"tutorials/*" = ["ANN", "D", "E402", "INP001", "T201", "S101", "ERA001"]
+"tutorials/*" = ["ANN", "D", "E402", "INP001", "T201", "PLR0917"]
 "docs/conf.py" = ["A001", "ANN204", "D102", "E402", "INP001", "RUF012"]
 
 [tool.ruff.format]
@@ -271,6 +274,9 @@ quote-style = "single"
 [tool.ruff.lint.flake8-quotes]
 inline-quotes = "single"
 
+[tool.ruff.lint.flake8-copyright]
+notice-rgx = "(#\\s*Copyright\\s*\\(c\\)\\s*PhasorPy\\s*Contributors)"
+
 [tool.ruff.lint.pydocstyle]
 convention = "numpy"
 
@@ -305,7 +311,7 @@ disable = [
 
 [tool.black]
 line-length = 79
-target-version = ["py312", "py313", "py314"]
+target-version = ["py312", "py313", "py314", "py315"]
 skip-string-normalization = true
 
 [tool.isort]
@@ -332,7 +338,7 @@ ND2 = "ND2"
 OIF = "OIF"
 
 [tool.mypy]
-packages = ["phasorpy"]
+packages = ["phasorpy", "tests"]
 mypy_path = "$MYPY_CONFIG_FILE_DIR/src"
 plugins = []
 enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]
@@ -341,14 +347,24 @@ warn_unreachable = true
 
 [[tool.mypy.overrides]]
 module = [
+    "_conftest",
     "phasorpy._phasorpy",
+    "setuptools.*",
+    "sphinx_gallery.*",
     "pooch.*",
     "scipy.*",
     "mkl_fft.*",
     "sklearn.*",
+    "h5py.*",
 ]
 ignore_missing_imports = true
 
+[[tool.mypy.overrides]]
+# PyQt6 6.12 stubs contain syntax errors that block mypy
+module = ["PyQt6.*"]
+follow_imports = "skip"
+follow_imports_for_stubs = true
+
 [tool.coverage.run]
 plugins = ["Cython.Coverage"]
 omit = ["conftest.py", "__main__.py"]
@@ -388,7 +404,6 @@ norecursedirs = [
     ".pytest_cache",
     ".ruff_cache",
     ".vscode",
-    "htmlcov",
     "adhoc",
     "build",
     "docs/_build",
@@ -402,29 +417,20 @@ norecursedirs = [
 ]
 
 [tool.cibuildwheel]
-skip = [
-    "cp38*",
-    "cp39*",
-    "cp310*",
-    "cp311*",
-    "cp313*",
-    "cp314-*",
-    "*musllinux*",
-    "*i686*",
-    "*ppc64le*",
-    "*s390x*",
-]
+build = ["cp312-*", "cp314t-*", "cp315t-*"]
+skip = ["*musllinux*", "*i686*", "*ppc64le*", "*s390x*"]
 test-command = "pytest {project}/tests"
-test-skip = ["cp314t*"]
+test-skip = ["cp3*t*"]
 test-requires = [
     # sync with [dependency-groups.optional]
+    "brighteyes-mcs-reader>=0.1.0; python_version < '3.15'",
     "czifile>=2026.4.11",
-    "fbdfile",
-    "lfdfiles",
-    "liffile",
-    "ptufile",
-    "sdtfile",
-    "pawflim",
+    "fbdfile>=2025.9.18",
+    "lfdfiles>=2026.6.24",
+    "liffile>=2025.2.10",
+    "ptufile>=2024.9.14",
+    "sdtfile>=2024.5.24",
+    "pawflim>=1.0.4",
     # sync with [dependency-groups.test]
     "coverage",
     "cython",  # for Cython.Coverage plugin
@@ -434,10 +440,10 @@ test-requires = [
     "pytest-runner",
 ]
 
-[[tool.cibuildwheel.overrides]]
-select = "*-macosx_x86_64"
-inherit.test-requires = "append"
-test-requires = ["imagecodecs==2026.6.6"]
+# [[tool.cibuildwheel.overrides]]
+# select = "*-macosx_x86_64"
+# inherit.test-requires = "append"
+# test-requires = ["imagecodecs==2026.6.6"]
 
 [tool.cibuildwheel.test-environment]
 PHASORPY_DATA_ON_GITHUB = "1"