phasorpy 0.8__tar.gz → 0.10__tar.gz

{phasorpy-0.8 → phasorpy-0.10}/LICENSE.txt

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2022-2025 PhasorPy Contributors
+Copyright (c) 2022-2026 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
@@ -9,8 +9,8 @@ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 copies of the Software, and to permit persons to whom the Software is
 furnished to do so, subject to the following conditions:
 
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
 
 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,

{phasorpy-0.8/src/phasorpy.egg-info → phasorpy-0.10}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: phasorpy
-Version: 0.8
-Summary: Analysis of fluorescence lifetime and hyperspectral images using the phasor approach
+Version: 0.10
+Summary: Analysis of luminescence lifetime and hyperspectral images using the phasor approach
 Author: PhasorPy Contributors
 License-Expression: MIT
 Project-URL: Homepage, https://www.phasorpy.org
@@ -10,7 +10,7 @@ Project-URL: Download, https://pypi.org/project/phasorpy/#files
 Project-URL: Source code, https://github.com/phasorpy/phasorpy
 Project-URL: Issue tracker, https://github.com/phasorpy/phasorpy/issues
 Project-URL: Release notes, https://www.phasorpy.org/docs/stable/release
-Classifier: Development Status :: 3 - Alpha
+Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
 Classifier: Programming Language :: Python
@@ -24,35 +24,30 @@ Classifier: Programming Language :: Python :: 3.14
 Requires-Python: >=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
-Requires-Dist: numpy>=2.0.0
+Requires-Dist: numpy>=2.1.0
 Requires-Dist: matplotlib>=3.9.0
-Requires-Dist: scipy>=1.13.0
+Requires-Dist: pandas>=2.3.0
+Requires-Dist: scikit-learn>=1.5.0
+Requires-Dist: scipy>=1.14.0
+Requires-Dist: tifffile>=2024.8.30
+Requires-Dist: xarray>=2024.6.0
 Requires-Dist: click
 Requires-Dist: pooch
 Requires-Dist: tqdm
-Requires-Dist: scikit-learn>=1.5.0
-Requires-Dist: xarray>=2024.6.0
-Requires-Dist: tifffile>=2024.8.30
-Provides-Extra: docs
-Requires-Dist: sphinx; extra == "docs"
-Requires-Dist: sphinx-issues; extra == "docs"
-Requires-Dist: sphinx_gallery; extra == "docs"
-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: all
+Requires-Dist: czifile>=2026.4.11; extra == "all"
+Requires-Dist: fbdfile>=2025.9.18; 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: fbdfile>=2025.9.18; extra == "all"
-Requires-Dist: pawflim; 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==2026.3.6; (sys_platform == "darwin" and platform_machine == "x86_64") and extra == "all"
 Dynamic: license-file
 
-# PhasorPy
+# <img src="https://www.phasorpy.org/_static/phasorpy_logo.svg" alt="&#x25CB;" width="48" height="48" align="left"/> PhasorPy
 
-PhasorPy is an open-source Python library for the analysis of fluorescence
+PhasorPy is an open-source Python library for the analysis of luminescence
 lifetime and hyperspectral images using the phasor approach.
 
 - [Homepage](https://www.phasorpy.org)
@@ -62,6 +57,9 @@ lifetime and hyperspectral images using the phasor approach.
 - [Data files](https://zenodo.org/communities/phasorpy/)
 - [Issues and questions](https://github.com/phasorpy/phasorpy/issues)
 
+Please cite [doi: 10.5281/zenodo.13862586](https://doi.org/10.5281/zenodo.13862586)
+if PhasorPy contributes to research that leads to a publication.
+
 PhasorPy is a community-maintained project.
 [Contributions](https://www.phasorpy.org/docs/stable/contributing/)
 in the form of bug reports, bug fixes, feature implementations, documentation,

{phasorpy-0.8 → phasorpy-0.10}/README.md

@@ -1,6 +1,6 @@
-# PhasorPy
+# <img src="https://www.phasorpy.org/_static/phasorpy_logo.svg" alt="&#x25CB;" width="48" height="48" align="left"/> PhasorPy
 
-PhasorPy is an open-source Python library for the analysis of fluorescence
+PhasorPy is an open-source Python library for the analysis of luminescence
 lifetime and hyperspectral images using the phasor approach.
 
 - [Homepage](https://www.phasorpy.org)
@@ -10,6 +10,9 @@ lifetime and hyperspectral images using the phasor approach.
 - [Data files](https://zenodo.org/communities/phasorpy/)
 - [Issues and questions](https://github.com/phasorpy/phasorpy/issues)
 
+Please cite [doi: 10.5281/zenodo.13862586](https://doi.org/10.5281/zenodo.13862586)
+if PhasorPy contributes to research that leads to a publication.
+
 PhasorPy is a community-maintained project.
 [Contributions](https://www.phasorpy.org/docs/stable/contributing/)
 in the form of bug reports, bug fixes, feature implementations, documentation,

phasorpy-0.10/docs/_static/switcher.json

@@ -0,0 +1,18 @@
+[
+  {
+    "name": "dev",
+    "version": "0.11",
+    "url": "https://www.phasorpy.org/docs/dev/"
+  },
+  {
+    "name": "0.10 (stable)",
+    "version": "0.10",
+    "url": "https://www.phasorpy.org/docs/stable/",
+    "preferred": true
+  },
+  {
+    "name": "0.9",
+    "version": "0.9",
+    "url": "https://www.phasorpy.org/docs/v0.9/"
+  }
+]

{phasorpy-0.8 → phasorpy-0.10}/docs/acknowledgments.rst

@@ -3,12 +3,12 @@ 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
+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
+`Globals for Images - SimFCS <https://www.lfd.uci.edu/globals/>`_ software by
 Enrico Gratton.
 
 This software project was supported in part by the
@@ -22,7 +22,8 @@ This software project was supported in part by the
 Contributors
 ------------
 
-PhasorPy is developed by `contributors to the PhasorPy repository
+PhasorPy is developed by
+`contributors to the PhasorPy repository
 <https://github.com/phasorpy/phasorpy/graphs/contributors>`_
 and
 `members of the PhasorPy organization
@@ -37,6 +38,5 @@ 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
+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-0.8 → phasorpy-0.10}/docs/api/cli.rst

@@ -1,4 +1,4 @@
-Command line interface
+Command-line interface
 ----------------------
 
 .. click:: phasorpy.cli:main

{phasorpy-0.8 → phasorpy-0.10}/docs/api/index.rst

@@ -1,8 +1,8 @@
 API reference
 =============
 
-This documents the application programming and command line interfaces of the
-PhasorPy library version |version|.
+This documents the application programming and command-line interfaces of
+the PhasorPy library version |version|.
 
 .. note::
     The PhasorPy library is still under construction. Backwards-incompatible

{phasorpy-0.8 → phasorpy-0.10}/docs/conf.py

@@ -1,5 +1,9 @@
-# Configuration file for the Sphinx documentation builder.
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
+"""Sphinx build configuration file.
+
+https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+"""
+
 # pylint: skip-file
 
 import os
@@ -19,7 +23,7 @@ sphinx_gallery.gen_rst.EXAMPLE_HEADER = (
 # project information
 
 project = 'PhasorPy'
-copyright = '2022-2025 PhasorPy Contributors'
+copyright = '2022-2026 PhasorPy Contributors'
 author = 'PhasorPy Contributors'
 
 import phasorpy
@@ -31,6 +35,7 @@ version_match = version.split('.dev')[0].split('.rc')[0]
 # general configuration
 
 extensions = [
+    'sphinx.ext.mathjax',
     'sphinx.ext.napoleon',
     'sphinx.ext.autodoc',
     'sphinx.ext.autosummary',
@@ -60,6 +65,7 @@ html_theme = 'pydata_sphinx_theme'
 html_static_path = ['_static']
 html_js_files = ['custom-icons.js']
 html_show_sourcelink = False
+html_sidebars = {'**': ['sidebar-nav-bs']}
 
 html_title = f'PhasorPy {version} documentation'
 html_logo = '_static/phasorpy_logo.svg'
@@ -134,6 +140,9 @@ 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."""
@@ -156,10 +165,12 @@ class TutorialOrder:
         # applications
         'component_fit',
         'fret_efficiency',
+        'nadh_concentration',
         'multidimensional',
         # misc
-        'phasor_from_signal',
         'logo',
+        'apps',
+        'phasor_from_signal',
     ]
 
     def __init__(self, srcdir: str): ...
@@ -234,7 +245,7 @@ def linkcode_resolve(domain: str, info: dict[str, str]) -> str | None:
     except (OSError, TypeError):
         lineno = None
 
-    linespec = f"#L{lineno:d}-L{lineno + len(source) - 1:d}" if lineno else ''
+    linespec = f'#L{lineno:d}-L{lineno + len(source) - 1:d}' if lineno else ''
 
     startdir = Path(phasorpy.__file__).parent.parent
     try:
@@ -242,10 +253,7 @@ def linkcode_resolve(domain: str, info: dict[str, str]) -> str | None:
     except ValueError:
         return None
 
-    if '.dev' in version or '.rc' in version:
-        tag = 'main'
-    else:
-        tag = f'v{version}'
+    tag = 'main' if '.dev' in version or '.rc' in version else f'v{version}'
     return (
         f'https://github.com/phasorpy/phasorpy/blob/{tag}/src/{fn}{linespec}'
     )

{phasorpy-0.8 → phasorpy-0.10}/docs/contributing.rst

@@ -6,7 +6,7 @@ of bug reports, bug fixes, feature implementations, documentation, datasets,
 and enhancement proposals.
 This document provides information on how to contribute.
 
-The :doc:`code_of_conduct` should be honored by everyone participating in the
+The :doc:`code_of_conduct` applies to everyone participating in the
 PhasorPy community.
 
 Ask for help
@@ -24,8 +24,8 @@ To suggest a new feature or other improvement to the PhasorPy library, open a
 Share data files
 ----------------
 
-The PhasorPy project strives to support reading image and metadata from many
-time-resolved and hyperspectral file formats used in bio-imaging.
+The PhasorPy project strives to support reading images and metadata from many
+time-resolved and hyperspectral file formats used in bioimaging.
 Consider sharing datasets for testing and use in tutorials, preferably with the
 `PhasorPy community on Zenodo <https://zenodo.org/communities/phasorpy/>`_.
 
@@ -36,8 +36,8 @@ To report a bug in the PhasorPy library, please open a
 `GitHub issue <https://github.com/phasorpy/phasorpy/issues>`_
 and include the following items in the bug report:
 
-- A minimal, self-contained Python code reproducing the problem.
-  Format the code using markdown, for example::
+- A minimal, self-contained Python script reproducing the problem.
+  Format the code as a Python code block, for example::
 
     ```Python
     import phasorpy
@@ -54,16 +54,16 @@ and include the following items in the bug report:
   or shared via cloud storage, preferably on
   `Zenodo.org <https://zenodo.org/communities/phasorpy/>`_.
 
-- An explanation why the current behavior is wrong and what is expected
+- An explanation of why the current behavior is wrong and what is expected
   instead.
 
-- Information how PhasorPy was installed (pip, conda, or other) and the output
-  of::
+- Information on how PhasorPy was installed (pip, conda, or other) and the
+  output of::
 
     $ python -m phasorpy versions
-    Python-3.13.3
-    phasorpy-0.5
-    numpy-2.2.6
+    Python-3.14.1
+    phasorpy-0.8
+    numpy-2.3.5
     ...
 
 Contribute code or documentation
@@ -75,7 +75,7 @@ a GitHub repository at
 
 The repository is based on `git <https://git-scm.com/>`_, a distributed
 version control software for tracking changes in the source code files and for
-coordinating work among programmers who are collaboratively developing.
+coordinating work among programmers collaboratively developing the code.
 
 PhasorPy uses GitHub's `fork and pull collaborative development model
 <https://docs.github.com/en/pull-requests/collaborating-with-pull-requests>`_.
@@ -91,7 +91,7 @@ development guidelines.
 Fork the repository
 ...................
 
-To work on the PhasorPy source code, fork the repository by pressing the
+To work with the PhasorPy source code, fork the repository by pressing the
 "Fork" button at
 `https://github.com/phasorpy/phasorpy <https://github.com/phasorpy/phasorpy>`_.
 
@@ -105,14 +105,15 @@ There are now two remote repositories:
 ``upstream``, which refers to the PhasorPy repository, and
 ``origin``, which refers to the personal fork.
 
-Instead of using the git command line application, you may find
+Instead of using the git command-line application, you may find
 `GitHub Desktop <https://desktop.github.com>`_ easier to use.
 
 Create a development environment
 ................................
 
-A Python compatible C compiler is required for developing the PhasorPy
-library. For example, `Visual Studio <https://visualstudio.microsoft.com/>`_,
+A C compiler compatible with the Python distribution is required for
+developing the PhasorPy library. For example,
+`Visual Studio <https://visualstudio.microsoft.com/>`_,
 `Xcode <https://developer.apple.com/xcode/>`_, or gcc.
 
 To work with the PhasorPy source code, it is recommended to set up a Python
@@ -124,7 +125,8 @@ following from within the local phasorpy repository::
     $ mkdir -p ~/pyenv/phasorpy-dev
     $ python -m venv ~/pyenv/phasorpy-dev
     $ source ~/pyenv/phasorpy-dev/bin/activate
-    $ pip install -r requirements_dev.txt
+    $ pip install --upgrade pip
+    $ pip install --upgrade --group dev
     $ pip install -e .
 
 Verify that the development environment is working by running the tests::
@@ -152,7 +154,7 @@ For example::
 This changes the local repository to the "new-feature-branch" branch.
 Keep any changes in this branch specific to one bug or feature.
 
-To update this branch with latest code from the PhasorPy repository,
+To update this branch with the latest code from the PhasorPy repository,
 retrieve the changes from the main branch, make a backup of the feature
 branch, and perform a rebase::
 
@@ -161,16 +163,16 @@ branch, and perform a rebase::
     $ git branch new-feature-branch-backup new-feature-branch
     $ git rebase upstream/main
 
-This replays local commits at the "new-feature-branch" branch on top
+This replays local commits on the "new-feature-branch" branch on top
 of the latest PhasorPy upstream main branch.
-Merge-conflicts need to be resolved before submitting a pull request.
+Merge conflicts need to be resolved before submitting a pull request.
 
 Tests
 .....
 
 PhasorPy includes a `pytest <https://docs.pytest.org/>`_ based suite of
-unit tests in the ``tests`` folder. All classes and functions must be tested
-thorougly.
+unit tests in the ``tests`` folder. All user-facing classes and functions
+should be covered by tests.
 
 Run the unit tests in the development environment::
 
@@ -188,7 +190,7 @@ Code standards
 ..............
 
 All the PhasorPy source code, including tutorials and docstring examples,
-must conform to certain styles, which can be and applied with
+must conform to certain styles, which can be checked and applied with
 `pre-commit <https://pre-commit.com/>`_::
 
     $ python -m pre_commit run --all-files
@@ -203,7 +205,7 @@ static type checker::
 
 
 The PhasorPy project follows the Scientific Python
-`SPEC 0 — Minimum Supported Dependencies
+`SPEC 0 - Minimum Supported Dependencies
 <https://scientific-python.org/specs/spec-0000/>`_ recommendation
 for Python, NumPy, and other dependencies.
 
@@ -221,7 +223,7 @@ Examples in docstrings must run and pass as
 
     $ python -m pytest -v src/phasorpy
 
-Examples in docstrings are meant to illustrate mere usage, not to
+Examples in docstrings are meant to illustrate basic usage, not to
 provide a testing framework.
 
 PhasorPy uses `Sphinx <https://www.sphinx-doc.org>`_
@@ -235,13 +237,15 @@ markup language in the .rst files in the ``docs`` and ``tutorials`` folders.
 All user-facing classes and functions should be included in the
 ``docs/api/*.rst`` files.
 
-Any changes should be mentioned in the release notes (``docs/release.rst``).
+Any changes should be mentioned in the release notes
+(``docs/release/index.rst``).
 
 New features or important usage information should be covered in the
 tutorials. Tutorials are included in the documentation via the
 `Sphinx-Gallery <https://sphinx-gallery.github.io>`_
 extension, which builds an HTML gallery of examples from the set of Python
 scripts in the ``tutorials`` folder.
+Avoid large external datasets or long-running computations.
 
 Examples in the .rst files must run and pass as doctests::
 
@@ -253,7 +257,8 @@ and tutorial files by running::
     $ cd docs
     $ make clean
     $ make html
-    $ open _build/html/index.html
+
+Then open ``_build/html/index.html`` in a web browser.
 
 Commit the changes
 ..................
@@ -274,11 +279,9 @@ on GitHub::
 
     $ git push origin new-feature-branch
 
-Open the personal fork on GitHub::
-
-    $ open https://github.com/your-user-name/phasorpy.git
-
-Click the green "pull request" button on the "new-feature-branch" branch.
+Then navigate to the personal fork on GitHub at
+``https://github.com/your-user-name/phasorpy`` and click the green
+"pull request" button on the "new-feature-branch" branch.
 
 Review the pull request checklist for recommendations.
 
@@ -287,7 +290,7 @@ All tests are automatically run via
 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.
+improve its implementation, documentation, and style.
 
 Pull requests must be approved by a
 `PhasorPy organization member <https://github.com/orgs/phasorpy/people>`_

{phasorpy-0.8 → phasorpy-0.10}/docs/index.rst

@@ -4,26 +4,26 @@ PhasorPy documentation
 
 Welcome to the documentation of PhasorPy version |version|.
 
-PhasorPy is an open-source Python library for the analysis of fluorescence
+PhasorPy is an open-source Python library for the analysis of luminescence
 lifetime and hyperspectral images using the :doc:`phasor_approach`.
 
 Quickstart
 ==========
 
-The :doc:`tutorials/index` demonstrate the use of the library, from simple
+The :doc:`tutorials/index` demonstrate how to use the library, from simple
 examples to advanced applications.
 
 The :doc:`api/index` contains detailed information about all functions and
 classes of the library.
 
-The :doc:`release` list recent bug fixes, feature enhancements, documentation
+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 bug fixes, or improve documentation.
+submit fixes, and improve the documentation.
 
-The :doc:`code_of_conduct` should be honored by everyone participating in
-the PhasorPy community.
+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.
@@ -48,8 +48,8 @@ Questions about the usage of the PhasorPy library are answered on the
 `issue tracker on GitHub <https://github.com/phasorpy/phasorpy/issues>`_.
 
 Please cite
-`doi: 10.5281/zenodo.13862587 <https://doi.org/10.5281/zenodo.13862587>`_
-if PhasorPy contributes to a project that leads to a publication.
+`doi: 10.5281/zenodo.13862586 <https://doi.org/10.5281/zenodo.13862586>`_
+if PhasorPy contributes to research that leads to a publication.
 
 Contents
 ========
@@ -60,7 +60,7 @@ Contents
     phasor_approach
     tutorials/index
     api/index
-    release
+    release/index
     contributing
     acknowledgments
     license

phasorpy-0.10/docs/license.rst

@@ -0,0 +1,5 @@
+MIT License
+===========
+
+.. literalinclude:: ../LICENSE.txt
+   :language: text