phasorpy 0.10__tar.gz → 0.12__tar.gz

{phasorpy-0.10 → phasorpy-0.12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phasorpy
-Version: 0.10
+Version: 0.12
 Summary: Analysis of luminescence lifetime and hyperspectral images using the phasor approach
 Author: PhasorPy Contributors
 License-Expression: MIT
@@ -29,7 +29,7 @@ Requires-Dist: matplotlib>=3.9.0
 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: tifffile>=2026.5.2
 Requires-Dist: xarray>=2024.6.0
 Requires-Dist: click
 Requires-Dist: pooch
@@ -37,12 +37,13 @@ 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>=2024.5.24; 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==2026.3.6; (sys_platform == "darwin" and platform_machine == "x86_64") and extra == "all"
+Requires-Dist: brighteyes-mcs-reader>=0.1.0; extra == "all"
+Requires-Dist: imagecodecs==2026.6.6; (sys_platform == "darwin" and platform_machine == "x86_64") 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
@@ -50,6 +51,19 @@ Dynamic: license-file
 PhasorPy is an open-source Python library for the analysis of luminescence
 lifetime and hyperspectral images using the phasor approach.
 
+The phasor approach represents time-resolved and spectral signals as
+phasor coordinates (normalized Fourier coefficients at harmonic frequencies)
+for intuitive visualization and analysis.
+
+PhasorPy enables reproducible phasor-based fluorescence lifetime imaging
+(FLIM) and hyperspectral imaging (HSI) workflows in scientific Python.
+It provides tools to read microscopy data in many file formats and to
+calculate, calibrate, filter, visualize, and interconvert phasor coordinates,
+lifetimes, and signals. Phasor coordinates can be exported to standard
+formats and analyzed through cursor-based region-of-interest selection,
+cluster detection, multi-component unmixing, FRET efficiency and concentration
+estimation.
+
 - [Homepage](https://www.phasorpy.org)
 - [Documentation](https://www.phasorpy.org/docs/stable/)
 - [Source code](https://github.com/phasorpy/phasorpy)

{phasorpy-0.10 → phasorpy-0.12}/README.md

@@ -3,6 +3,19 @@
 PhasorPy is an open-source Python library for the analysis of luminescence
 lifetime and hyperspectral images using the phasor approach.
 
+The phasor approach represents time-resolved and spectral signals as
+phasor coordinates (normalized Fourier coefficients at harmonic frequencies)
+for intuitive visualization and analysis.
+
+PhasorPy enables reproducible phasor-based fluorescence lifetime imaging
+(FLIM) and hyperspectral imaging (HSI) workflows in scientific Python.
+It provides tools to read microscopy data in many file formats and to
+calculate, calibrate, filter, visualize, and interconvert phasor coordinates,
+lifetimes, and signals. Phasor coordinates can be exported to standard
+formats and analyzed through cursor-based region-of-interest selection,
+cluster detection, multi-component unmixing, FRET efficiency and concentration
+estimation.
+
 - [Homepage](https://www.phasorpy.org)
 - [Documentation](https://www.phasorpy.org/docs/stable/)
 - [Source code](https://github.com/phasorpy/phasorpy)

{phasorpy-0.10 → phasorpy-0.12}/docs/_static/switcher.json

@@ -1,15 +1,25 @@
 [
   {
     "name": "dev",
-    "version": "0.11",
+    "version": "0.13",
     "url": "https://www.phasorpy.org/docs/dev/"
   },
   {
-    "name": "0.10 (stable)",
-    "version": "0.10",
+    "name": "0.12 (stable)",
+    "version": "0.12",
     "url": "https://www.phasorpy.org/docs/stable/",
     "preferred": true
   },
+  {
+    "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",

phasorpy-0.12/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-0.12/docs/acknowledgments.rst

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

{phasorpy-0.10 → phasorpy-0.12}/docs/api/index.rst

@@ -5,8 +5,8 @@ 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
-    changes may occur between revisions.
+    PhasorPy is still under active development, and changes in new releases
+    may require updates to existing code.
 
 .. toctree::
     :maxdepth: 3

{phasorpy-0.10 → phasorpy-0.12}/docs/conf.py

@@ -13,6 +13,7 @@ sys.path.insert(0, os.path.dirname(__file__))
 
 # remove the examples header from HTML tutorials
 import sphinx_gallery.gen_rst
+from sphinx_gallery.sorting import ExplicitOrder
 
 sphinx_gallery.gen_rst.EXAMPLE_HEADER = (
     sphinx_gallery.gen_rst.EXAMPLE_HEADER.replace(
@@ -46,7 +47,6 @@ 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',
@@ -63,7 +63,7 @@ exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
 # html_theme = 'sphinx_rtd_theme'
 html_theme = 'pydata_sphinx_theme'
 html_static_path = ['_static']
-html_js_files = ['custom-icons.js']
+html_js_files = [('custom-icons.js', {'defer': 'defer'})]
 html_show_sourcelink = False
 html_sidebars = {'**': ['sidebar-nav-bs']}
 
@@ -130,6 +130,13 @@ sphinx_gallery_conf = {
     'filename_pattern': 'phasorpy_',
     'examples_dirs': '../tutorials',
     'gallery_dirs': 'tutorials',
+    'subsection_order': ExplicitOrder(
+        [
+            '../tutorials/applications',
+            '../tutorials/api',
+            '../tutorials/misc',
+        ]
+    ),
     'reference_url': {'phasorpy': None},
     'matplotlib_animations': True,
     'within_subsection_order': 'conf.TutorialOrder',
@@ -140,9 +147,6 @@ 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."""
@@ -151,22 +155,23 @@ class TutorialOrder:
         'introduction',
         'lifetime_geometry',
         'lfd_workshop',
+        # applications
+        'component_fit',
+        'fret_efficiency',
+        'nadh_fraction',
+        'nadh_concentration',
+        'multidimensional',
         # api
         'io',
+        'lifetime_to_signal',
         'phasor_from_lifetime',
-        'multi_harmonic',
+        'fret',
         'filter',
+        'multi_harmonic',
         'phasorplot',
         'cursor',
         'component',
-        'fret',
-        'lifetime_to_signal',
         'pca',
-        # applications
-        'component_fit',
-        'fret_efficiency',
-        'nadh_concentration',
-        'multidimensional',
         # misc
         'logo',
         'apps',

{phasorpy-0.10 → phasorpy-0.12}/docs/contributing.rst

@@ -4,7 +4,7 @@ Contributing guide
 As a community-maintained project, PhasorPy welcomes contributions in the form
 of bug reports, bug fixes, feature implementations, documentation, datasets,
 and enhancement proposals.
-This document provides information on how to contribute.
+This guide explains how to contribute.
 
 The :doc:`code_of_conduct` applies to everyone participating in the
 PhasorPy community.
@@ -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
@@ -74,13 +74,13 @@ a GitHub repository at
 `https://github.com/phasorpy/phasorpy <https://github.com/phasorpy/phasorpy>`_.
 
 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
+version control system for tracking changes in source code files and for
 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>`_.
 All contributions to the PhasorPy source code and documentation should
-be developed in personal forks/copies of the code, and then submitted as
+be developed in personal forks of the repository, and then submitted as
 `pull requests <https://github.com/phasorpy/phasorpy/pulls>`_ (PRs).
 
 The PhasorPy project loosely follows the
@@ -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>`_
@@ -203,7 +227,6 @@ static type checker::
 
     $ python -m mypy
 
-
 The PhasorPy project follows the Scientific Python
 `SPEC 0 - Minimum Supported Dependencies
 <https://scientific-python.org/specs/spec-0000/>`_ recommendation
@@ -219,7 +242,7 @@ following the `numpydoc
 standard.
 
 Examples in docstrings must run and pass as
-`doctests <https://docs.python.org/3/library/doctest.html>`_ ::
+`doctests <https://docs.python.org/3/library/doctest.html>`_::
 
     $ python -m pytest -v src/phasorpy
 
@@ -232,7 +255,7 @@ to generate the documentation in HTML format published at
 
 Sphinx documentation is written in the
 `reStructuredText <https://docutils.sourceforge.io/rst.html>`_
-markup language in the .rst files in the ``docs`` and ``tutorials`` folders.
+markup language in .rst files in the ``docs`` and ``tutorials`` folders.
 
 All user-facing classes and functions should be included in the
 ``docs/api/*.rst`` files.
@@ -251,8 +274,8 @@ Examples in the .rst files must run and pass as doctests::
 
     $ python -m pytest -v docs
 
-Documentation in HTML format can be built from the docstrings, .rst,
-and tutorial files by running::
+Documentation can be built in HTML format from docstrings, .rst files,
+and tutorials by running::
 
     $ cd docs
     $ make clean
@@ -263,7 +286,7 @@ Then open ``_build/html/index.html`` in a web browser.
 Commit the changes
 ..................
 
-Commit changed and new files to the local repository::
+Commit modified and new files to the local repository::
 
     $ git add phasorpy/new_file.py
     $ git commit -a -m "Summarize changes in 50 characters or less"

{phasorpy-0.10 → phasorpy-0.12}/docs/index.rst

@@ -2,13 +2,13 @@
 PhasorPy documentation
 ======================
 
-Welcome to the documentation of PhasorPy version |version|.
+Welcome to the documentation for PhasorPy version |version|.
 
 PhasorPy is an open-source Python library for the analysis of luminescence
 lifetime and hyperspectral images using the :doc:`phasor_approach`.
 
-Quickstart
-==========
+Project guide
+=============
 
 The :doc:`tutorials/index` demonstrate how to use the library, from simple
 examples to advanced applications.
@@ -16,17 +16,17 @@ examples to advanced applications.
 The :doc:`api/index` contains detailed information about all functions and
 classes of the library.
 
-The :doc:`release/index` list recent bug fixes, feature enhancements, documentation,
-and maintenance changes.
+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`.
@@ -44,7 +44,7 @@ Sample data files used in tutorials and testing are available from the
 Report issues with the code or documentation on the
 `issue tracker on GitHub <https://github.com/phasorpy/phasorpy/issues>`_.
 
-Questions about the usage of the PhasorPy library are answered on the
+Questions about using the PhasorPy library can be asked on the
 `issue tracker on GitHub <https://github.com/phasorpy/phasorpy/issues>`_.
 
 Please cite
@@ -62,8 +62,8 @@ Contents
     api/index
     release/index
     contributing
-    acknowledgments
     license
+    about
 
 Indices and tables
 ------------------