phasorpy 0.9__tar.gz → 0.10__tar.gz

{phasorpy-0.9 → phasorpy-0.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phasorpy
-Version: 0.9
+Version: 0.10
 Summary: Analysis of luminescence lifetime and hyperspectral images using the phasor approach
 Author: PhasorPy Contributors
 License-Expression: MIT
@@ -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
@@ -24,26 +24,28 @@ 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: pandas>=2.2.0
+Requires-Dist: pandas>=2.3.0
 Requires-Dist: scikit-learn>=1.5.0
-Requires-Dist: scipy>=1.13.0
+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
 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: 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"
 Dynamic: license-file
 
-# <img src="docs/_static/phasorpy_logo.svg" alt="PhasorPy" width="48" height="48" align="left"> 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 luminescence
 lifetime and hyperspectral images using the phasor approach.

{phasorpy-0.9 → phasorpy-0.10}/README.md

@@ -1,4 +1,4 @@
-# <img src="docs/_static/phasorpy_logo.svg" alt="PhasorPy" width="48" height="48" align="left"> 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 luminescence
 lifetime and hyperspectral images using the phasor approach.

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-0.9 → phasorpy-0.10}/docs/acknowledgments.rst

@@ -8,7 +8,7 @@ at the University of the Republic and Institut Pasteur de Montevideo, and the
 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

{phasorpy-0.9 → phasorpy-0.10}/docs/conf.py

@@ -65,6 +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'
@@ -164,6 +165,7 @@ class TutorialOrder:
         # applications
         'component_fit',
         'fret_efficiency',
+        'nadh_concentration',
         'multidimensional',
         # misc
         'logo',

{phasorpy-0.9 → phasorpy-0.10}/docs/contributing.rst

@@ -205,7 +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.
 

{phasorpy-0.9 → phasorpy-0.10}/docs/phasor_approach.rst

@@ -1,14 +1,14 @@
 Phasor approach
 ===============
 
-“The phasor approach to fluorescence lifetime imaging, and more recently
+"The phasor approach to fluorescence lifetime imaging, and more recently
 hyperspectral fluorescence imaging, has increased the use of these
 techniques, and improved the ease and intuitiveness of the data analysis.
 The fit-free nature of the phasor plots increases the speed of the analysis
 and reduces the dimensionality, optimization of data handling and storage.
-The reciprocity principle between the real and imaginary space—where the
+The reciprocity principle between the real and imaginary space--where the
 phasor and the pixel that the phasor originated from are linked and can be
-converted from one another—has helped the expansion of this method.
+converted from one another--has helped the expansion of this method.
 The phasor coordinates calculated from a pixel, where multiple fluorescent
 species are present, depends on the phasor positions of those components.
 The relative positions are governed by the linear combination properties of
@@ -21,7 +21,7 @@ the total fluorescence from that image pixel.
 The higher the fractional intensity contribution of a vertex, the closer is
 the resultant phasor. The linear additivity in the phasor space can be
 exploited to obtain the fractional intensity contribution from multiple
-species and quantify their contribution.”
+species and quantify their contribution."
 (quoted from :ref:`Malacrida et al., 2021 <malacrida-2021>`)
 
 The following resources provide an overview of the history, theory,
@@ -168,7 +168,8 @@ approach to analyze fluorescence time-resolved or spectral images:
      - :ref:`Napari-phasors <napari_phasors>`,
        :ref:`Napari-flim-phasor-plotter <napari_flim_phasor_plotter>`,
        :ref:`Napari-live-flim <napari_live_flim>`,
-       :ref:`FLOPA <flopa>`
+       :ref:`FLOPA <flopa>`,
+       :ref:`FLIMari <flimari>`
    * - **ImageJ**
      - :ref:`Spectral/Time Gated Phasor PlugIns <phasor_plugins>`
    * - **Matlab**
@@ -189,7 +190,7 @@ Details:
 -
   .. _simfcs:
 
-  `Globals for Images · SimFCS <https://www.lfd.uci.edu/globals/>`__
+  `Globals for Images - SimFCS <https://www.lfd.uci.edu/globals/>`__
   is a free, closed-source, Windows desktop application for fluorescence image
   analysis, visualization, simulation, and acquisition.
   The software was developed by Enrico Gratton during 1998-2022 at the
@@ -228,6 +229,14 @@ Details:
   is a napari plugin for FLIM data opening, processing and analysis.
   The plugin is distributed under the GPLv3 license.
 
+-
+
+  .. _flimari:
+
+  `FLIMari <https://github.com/GuangchenW/FLIMari>`__
+  is a napari plugin for FLIM analysis. It provides an interactive,
+  phasor-based lifetime visualization and analysis pipeline.
+  The plugin is distributed under the MIT license.
 -
   .. _hysp:
 
@@ -314,9 +323,9 @@ Details:
 -
   .. _phasor_plugins:
 
-  `Spectral Phasor PlugIn <http://spechron.com/Spectral%20Phasor-Download.aspx>`__
+  `Spectral Phasor PlugIn <https://web.archive.org/web/20250621131318/http://spechron.com/Spectral%20Phasor-Introduction.aspx>`__
   and
-  `Time Gated Phasor PlugIn <http://spechron.com/Time%20gated%20Phasor-Download.aspx>`__
+  `Time Gated Phasor PlugIn <https://web.archive.org/web/20240910041344/http://spechron.com/Time%20gated%20Phasor%20Introduction.aspx>`__
   are open-source ImageJ plugins by Farzad Fereidouni, which provide
   visualization, segmentation, and unmixing of time-resolved and spectral
   images using the phasor approach. The software is distributed under an

{phasorpy-0.9 → phasorpy-0.10}/pyproject.toml

@@ -1,8 +1,8 @@
 [build-system]
 requires = [
     "setuptools>=68",
-    "numpy>=2.0.0",
-    "cython>=3.2.2",
+    "numpy>=2.1.0",
+    "cython>=3.2.4",
 ]
 build-backend = "setuptools.build_meta"
 
@@ -14,12 +14,12 @@ dynamic = ["version"]
 dependencies = [
     # sync with [dependency-groups.run]
     # https://scientific-python.org/specs/spec-0000/
-    "numpy>=2.0.0",
+    "numpy>=2.1.0",
     "matplotlib>=3.9.0",
-    "pandas>=2.2.0",
-    # "scikit-image>=0.23.0",
+    "pandas>=2.3.0",
+    # "scikit-image>=0.24.0",
     "scikit-learn>=1.5.0",
-    "scipy>=1.13.0",
+    "scipy>=1.14.0",
     "tifffile>=2024.8.30",
     "xarray>=2024.6.0",
     "click",
@@ -28,7 +28,7 @@ dependencies = [
 ]
 requires-python = ">=3.12"
 classifiers = [
-    "Development Status :: 3 - Alpha",
+    "Development Status :: 4 - Beta",
     "Intended Audience :: Developers",
     "Intended Audience :: Science/Research",
     "Programming Language :: Python",
@@ -58,23 +58,25 @@ phasorpy = "phasorpy.cli:main"
 [project.optional-dependencies]
 all = [
     # sync with [dependency-groups.optional]
+    "czifile>=2026.4.11",
     "fbdfile>=2025.9.18",
     "lfdfiles>=2024.5.24",
     "liffile>=2025.2.10",
     "ptufile>=2024.9.14",
     "sdtfile>=2024.5.24",
     "pawflim>=1.0.4",
+    "imagecodecs==2026.3.6; sys_platform == 'darwin' and platform_machine == 'x86_64'",
     # "mkl-fft>=2.1.1",
 ]
 
 [dependency-groups]
 run = [
     # runtime dependencies; sync with [project.dependencies]
-    "numpy>=2.0.0",
-    "matplotlib>=3.9.0",
-    "pandas>=2.2.0",
+    "numpy>=2.1.0",
+    "matplotlib>=3.10.0",
+    "pandas>=2.3.0",
     "scikit-learn>=1.5.0",
-    "scipy>=1.13.0",
+    "scipy>=1.14.0",
     "tifffile>=2024.8.30",
     "xarray>=2024.6.0",
     "click",
@@ -83,23 +85,26 @@ run = [
 ]
 optional = [
     # optional runtime dependencies; sync with [project.optional-dependencies]
+    "czifile>=2026.4.11",
     "fbdfile>=2025.9.18",
     "lfdfiles>=2024.5.24",
     "liffile>=2025.2.10",
     "ptufile>=2024.9.14",
     "sdtfile>=2024.5.24",
     "pawflim>=1.0.4",
+    "imagecodecs==2026.3.6; sys_platform == 'darwin' and platform_machine == 'x86_64'",
 ]
 minimal = [
     # minimal runtime versions for testing against oldest supported versions
-    "numpy==2.0.2; python_version == \"3.12\"",
-    "matplotlib==3.9.4; python_version == \"3.12\"",
-    "pandas==2.2.3; python_version == \"3.12\"",
+    "numpy==2.1.0; python_version == \"3.12\"",
+    "matplotlib==3.10.3; python_version == \"3.12\"",
+    "pandas==2.3.2; python_version == \"3.12\"",
     "scikit-learn==1.5.0; python_version == \"3.12\"",
-    "scipy==1.13.1; python_version == \"3.12\"",
+    "scipy==1.14.1; python_version == \"3.12\"",
     "tifffile==2024.8.30; python_version == \"3.12\"",
     "xarray==2024.6.0; python_version == \"3.12\"",
     # optional
+    "czifile==2026.4.11; python_version == \"3.12\"",
     "fbdfile==2025.9.18; python_version == \"3.12\"",
     "lfdfiles==2024.5.24; python_version == \"3.12\"",
     "liffile==2025.2.10; python_version == \"3.12\"",
@@ -109,8 +114,8 @@ minimal = [
 ]
 build = [
     # build requirements
-    "cython>=3.2.2",
-    "numpy>=2.0.0",
+    "cython>=3.2.4",
+    "numpy>=2.1.0",
     "abi3audit",
     "build",
     "cibuildwheel",
@@ -174,6 +179,10 @@ version = { attr = "phasorpy.__version__" }
 [tool.setuptools.package-data]
 phasorpy = ["py.typed"]
 
+[tool.check-unicode]
+allow-codepoints = ["U+00B0", "U+00F6", "U+039B", "U+03BB"]
+check-confusables = true
+
 [tool.ruff]
 line-length = 79
 exclude = [
@@ -295,7 +304,7 @@ disable = [
 
 [tool.black]
 line-length = 79
-target-version = ["py312", "py313"]
+target-version = ["py312", "py313", "py314"]
 skip-string-normalization = true
 
 [tool.isort]
@@ -355,6 +364,7 @@ directory = "_htmlcov"
 
 [tool.pytest.ini_options]
 minversion = "7"
+log_level = "INFO"
 log_cli_level = "INFO"
 # filterwarnings = ["error"]  # breaks debugging tests in VSCode (Sept. 2024)
 xfail_strict = true
@@ -406,6 +416,7 @@ test-command = "pytest {project}/tests"
 test-skip = ["cp314t*"]
 test-requires = [
     # sync with [dependency-groups.optional]
+    "czifile>=2026.4.11",
     "fbdfile",
     "lfdfiles",
     "liffile",
@@ -421,6 +432,11 @@ test-requires = [
     "pytest-runner",
 ]
 
+[[tool.cibuildwheel.overrides]]
+select = "*-macosx_x86_64"
+inherit.test-requires = "append"
+test-requires = ["imagecodecs==2026.3.6"]
+
 [tool.cibuildwheel.test-environment]
 PHASORPY_DATA_ON_GITHUB = "1"
 SKIP_FETCH = "1"

{phasorpy-0.9 → phasorpy-0.10}/src/phasorpy/__init__.py

@@ -5,5 +5,5 @@ from __future__ import annotations
 __all__ = ['__version__']
 
 
-__version__ = '0.9'
+__version__ = '0.10'
 """PhasorPy version string."""