phasorpy 0.5__tar.gz → 0.7__tar.gz

{phasorpy-0.5 → phasorpy-0.7}/MANIFEST.in

@@ -14,6 +14,10 @@ recursive-include tutorials *.rst
 exclude *.cmd
 exclude docs/sg_execution_times.rst
 
+include tools/*.py
+include tools/*.sh
+include tools/*.cmd
+
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
 recursive-exclude * *Copy*

{phasorpy-0.5/src/phasorpy.egg-info → phasorpy-0.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phasorpy
-Version: 0.5
+Version: 0.7
 Summary: Analysis of fluorescence lifetime and hyperspectral images using the phasor approach
 Author: PhasorPy Contributors
 License-Expression: MIT
@@ -24,7 +24,7 @@ Classifier: Programming Language :: Python :: 3.13
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
-Requires-Dist: numpy>=1.25.0
+Requires-Dist: numpy>=1.26.0
 Requires-Dist: matplotlib>=3.8.0
 Requires-Dist: scipy>=1.11.0
 Requires-Dist: click
@@ -66,7 +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-0.5 → phasorpy-0.7}/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/).

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{phasorpy-0.5 → phasorpy-0.7}/docs/_static/switcher.json

@@ -1,23 +1,23 @@
 [
   {
     "name": "dev",
-    "version": "0.6",
+    "version": "0.8",
     "url": "https://www.phasorpy.org/docs/dev/"
   },
   {
-    "name": "0.5 (stable)",
-    "version": "0.5",
+    "name": "0.7 (stable)",
+    "version": "0.7",
     "url": "https://www.phasorpy.org/docs/stable/",
     "preferred": true
   },
   {
-    "name": "0.4",
-    "version": "0.4",
-    "url": "https://www.phasorpy.org/docs/v0.4/"
+    "name": "0.6",
+    "version": "0.6",
+    "url": "https://www.phasorpy.org/docs/v0.6/"
   },
   {
-    "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/"
   }
 ]

phasorpy-0.7/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-0.7/docs/api/component.rst

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

phasorpy-0.7/docs/api/cursor.rst

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

phasorpy-0.7/docs/api/experimental.rst

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

{phasorpy-0.5 → phasorpy-0.7}/docs/api/index.rst

@@ -13,12 +13,14 @@ PhasorPy library version |version|.
 
     phasorpy
     phasor
-    cursors
-    components
+    lifetime
+    component
     cluster
+    cursor
     plot
     io
     color
+    experimental
     datasets
     utils
     _utils

phasorpy-0.7/docs/api/lifetime.rst

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

{phasorpy-0.5 → phasorpy-0.7}/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-0.5 → phasorpy-0.7}/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
@@ -59,8 +60,8 @@ html_static_path = ['_static']
 html_js_files = ['custom-icons.js']
 html_show_sourcelink = False
 
-html_logo = '_static/logo.png'
-# html_favicon = ''
+html_logo = '_static/phasorpy_logo.svg'
+html_favicon = '_static/favicon.ico'
 
 pygments_style = 'sphinx'
 
@@ -123,8 +124,43 @@ 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',
+        'filter',
+        'phasorplot',
+        'cursor',
+        'component',
+        'fret',
+        'lifetime_to_signal',
+        'pca',
+        # applications
+        'component_fit',
+        'fret_efficiency',
+        'multidimensional',
+        # misc
+        'phasor_from_signal',
+        'logo',
+    ]
+
+    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-0.5 → phasorpy-0.7}/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-0.5 → phasorpy-0.7}/docs/index.rst

@@ -62,7 +62,6 @@ Contents
     api/index
     release
     contributing
-    code_of_conduct
     acknowledgments
     license
 

{phasorpy-0.5 → phasorpy-0.7}/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.