phasorpy 0.6__tar.gz → 0.8__tar.gz

{phasorpy-0.6 → phasorpy-0.8}/MANIFEST.in

@@ -1,19 +1,22 @@
 include LICENSE.txt
 include README.md
 
-include tests/*.py
-
 include docs/*.py
 include docs/*.rst
 include docs/api/*.rst
 include docs/_static/*.*
 
+recursive-include tests *.py
 recursive-include tutorials *.py
 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-0.6/src/phasorpy.egg-info → phasorpy-0.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phasorpy
-Version: 0.6
+Version: 0.8
 Summary: Analysis of fluorescence lifetime and hyperspectral images using the phasor approach
 Author: PhasorPy Contributors
 License-Expression: MIT
@@ -18,20 +18,20 @@ Classifier: Topic :: Software Development :: Libraries :: Python Modules
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3 :: Only
-Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
-Requires-Python: >=3.11
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: >=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
-Requires-Dist: numpy>=1.25.0
-Requires-Dist: matplotlib>=3.8.0
-Requires-Dist: scipy>=1.11.0
+Requires-Dist: numpy>=2.0.0
+Requires-Dist: matplotlib>=3.9.0
+Requires-Dist: scipy>=1.13.0
 Requires-Dist: click
 Requires-Dist: pooch
 Requires-Dist: tqdm
 Requires-Dist: scikit-learn>=1.5.0
-Requires-Dist: xarray>=2023.4.0
+Requires-Dist: xarray>=2024.6.0
 Requires-Dist: tifffile>=2024.8.30
 Provides-Extra: docs
 Requires-Dist: sphinx; extra == "docs"
@@ -46,6 +46,7 @@ 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"
 Dynamic: license-file
 

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{phasorpy-0.6 → phasorpy-0.8}/docs/_static/switcher.json

@@ -1,23 +1,23 @@
 [
   {
     "name": "dev",
-    "version": "0.7",
+    "version": "0.9",
     "url": "https://www.phasorpy.org/docs/dev/"
   },
   {
-    "name": "0.6 (stable)",
-    "version": "0.6",
+    "name": "0.8 (stable)",
+    "version": "0.8",
     "url": "https://www.phasorpy.org/docs/stable/",
     "preferred": true
   },
   {
-    "name": "0.5",
-    "version": "0.5",
-    "url": "https://www.phasorpy.org/docs/v0.5/"
+    "name": "0.7",
+    "version": "0.7",
+    "url": "https://www.phasorpy.org/docs/v0.7/"
   },
   {
-    "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/"
   }
 ]

phasorpy-0.8/docs/api/_phasorpy.rst

@@ -0,0 +1,8 @@
+phasorpy._phasorpy
+------------------
+
+.. automodule:: phasorpy._phasorpy
+    :members:
+    :undoc-members:
+    :private-members:
+    :special-members:

phasorpy-0.8/docs/api/_utils.rst

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

phasorpy-0.8/docs/api/component.rst

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

phasorpy-0.8/docs/api/cursor.rst

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

phasorpy-0.8/docs/api/filter.rst

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

{phasorpy-0.6 → phasorpy-0.8}/docs/api/index.rst

@@ -13,9 +13,11 @@ PhasorPy library version |version|.
 
     phasorpy
     phasor
-    cursors
-    components
+    lifetime
+    filter
+    component
     cluster
+    cursor
     plot
     io
     color

phasorpy-0.8/docs/api/lifetime.rst

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

{phasorpy-0.6 → phasorpy-0.8}/docs/conf.py

@@ -26,7 +26,7 @@ import phasorpy
 
 version = phasorpy.__version__
 release = phasorpy.__version__
-version_match = version.replace('.dev', '').replace('.rc', '')
+version_match = version.split('.dev')[0].split('.rc')[0]
 
 # general configuration
 
@@ -35,7 +35,8 @@ extensions = [
     'sphinx.ext.autodoc',
     'sphinx.ext.autosummary',
     'sphinx.ext.doctest',
-    'sphinx.ext.viewcode',
+    # 'sphinx.ext.viewcode',  # include source code in documentation
+    'sphinx.ext.linkcode',  # link to source code on GitHub
     'sphinx.ext.todo',
     # don't enable intersphinx since tutorials are getting littered with links
     # 'sphinx.ext.intersphinx',
@@ -60,8 +61,9 @@ html_static_path = ['_static']
 html_js_files = ['custom-icons.js']
 html_show_sourcelink = False
 
-html_logo = '_static/logo.png'
-# html_favicon = ''
+html_title = f'PhasorPy {version} documentation'
+html_logo = '_static/phasorpy_logo.svg'
+html_favicon = '_static/favicon.ico'
 
 pygments_style = 'sphinx'
 
@@ -125,6 +127,11 @@ sphinx_gallery_conf = {
     'reference_url': {'phasorpy': None},
     'matplotlib_animations': True,
     'within_subsection_order': 'conf.TutorialOrder',
+    'show_memory': False,
+    'show_api_usage': False,
+    'remove_config_comments': True,
+    # 'min_reported_time': 0.5,
+    # 'backreferences_dir': None,
 }
 
 
@@ -138,19 +145,21 @@ class TutorialOrder:
         # api
         'io',
         'phasor_from_lifetime',
-        'multi-harmonic',
-        'filtering',
+        'multi_harmonic',
+        'filter',
         'phasorplot',
-        'cursors',
-        'components',
+        'cursor',
+        'component',
         'fret',
         'lifetime_to_signal',
         'pca',
         # applications
         'component_fit',
         'fret_efficiency',
-        # benchmarks
+        'multidimensional',
+        # misc
         'phasor_from_signal',
+        'logo',
     ]
 
     def __init__(self, srcdir: str): ...
@@ -174,7 +183,69 @@ intersphinx_mapping = {
     'skimage': ('https://scikit-image.org/docs/stable/', None),
 }
 
-intersphinx_disabled_reftypes = ['*']
+# limit intersphinx linking to avoid "littering" tutorials
+# disable doc links but allow function links
+# intersphinx_disabled_reftypes = ['std:doc']
 
 # do not show typehints
 autodoc_typehints = 'none'
+
+
+def linkcode_resolve(domain: str, info: dict[str, str]) -> str | None:
+    """Return GitHub URL for Python object."""
+    # adapted from
+    # https://github.com/matplotlib/matplotlib/blob/main/doc/conf.py
+    import inspect
+    from pathlib import Path
+
+    if domain != 'py':
+        return None
+
+    modname = info['module']
+    fullname = info['fullname']
+
+    submod = sys.modules.get(modname)
+    if submod is None:
+        return None
+
+    obj = submod
+    for part in fullname.split('.'):
+        try:
+            obj = getattr(obj, part)
+        except AttributeError:
+            return None
+
+    if inspect.isfunction(obj):
+        obj = inspect.unwrap(obj)
+    try:
+        fn = inspect.getsourcefile(obj)
+    except TypeError:
+        fn = None
+    if not fn or fn.endswith('__init__.py'):
+        try:
+            fn = inspect.getsourcefile(sys.modules[obj.__module__])
+        except (TypeError, AttributeError, KeyError):
+            fn = None
+    if not fn:
+        return None
+
+    try:
+        source, lineno = inspect.getsourcelines(obj)
+    except (OSError, TypeError):
+        lineno = None
+
+    linespec = f"#L{lineno:d}-L{lineno + len(source) - 1:d}" if lineno else ''
+
+    startdir = Path(phasorpy.__file__).parent.parent
+    try:
+        fn = os.path.relpath(fn, start=startdir).replace(os.path.sep, '/')
+    except ValueError:
+        return None
+
+    if '.dev' in version or '.rc' in version:
+        tag = 'main'
+    else:
+        tag = f'v{version}'
+    return (
+        f'https://github.com/phasorpy/phasorpy/blob/{tag}/src/{fn}{linespec}'
+    )

{phasorpy-0.6 → phasorpy-0.8}/docs/phasor_approach.rst

@@ -166,12 +166,20 @@ approach to analyze fluorescence time-resolved or spectral images:
   images using the phasor approach. The software is distributed under an
   unknown license and was last updated in 2013.
 
+-
+  .. _napari_phasors:
+
+  `Napari-phasors <https://github.com/napari-phasors/napari-phasors>`_
+  is a napari plugin for phasor analysis based on PhasorPy.
+  The plugin is distributed under the BSD-3-Clause license.
+
 -
   .. _napari_flim_phasor_plotter:
 
   `Napari-flim-phasor-plotter <https://github.com/zoccoler/napari-flim-phasor-plotter>`_
   is a napari plugin to interactively load and show raw FLIM single images
   and series and generate phasor plots.
+  The plugin is distributed under the BSD-3-Clause license.
 
 -
   .. _napari_live_flim:
@@ -263,6 +271,13 @@ approach to analyze fluorescence time-resolved or spectral images:
   "instant FLIM" system. It supports image segmentation based on phasor plot
   regions of interest and K-means clustering.
 
+  .. _cell_analysis_tools:
+
+- `Cell-analysis-tools <https://github.com/skalalab/cell-analysis-tools>`_
+  is an open-source Python library for the analysis of single cell imaging
+  data, including phasor analysis of FLIM data.
+  The library is distributed under the GPL v3.
+
 -
   .. _flim_studio: