phasorpy 0.1.dev0__tar.gz → 0.2__tar.gz

{phasorpy-0.1.dev0 → phasorpy-0.2}/.codecov.yml

@@ -1,11 +1,11 @@
-codecov:
-  notify:
-    require_ci_to_pass: false
-    after_n_builds: 1
-coverage:
-  status:
-    project:
-      default:
-        threshold: 0.1%
-        informational: true
-comment: off
+codecov:
+  notify:
+    require_ci_to_pass: false
+    after_n_builds: 1
+coverage:
+  status:
+    project:
+      default:
+        threshold: 0.1%
+        informational: true
+comment: off

{phasorpy-0.1.dev0 → phasorpy-0.2}/.github/dependabot.yml

@@ -1,11 +1,11 @@
-version: 2
-
-updates:
-  - package-ecosystem: "github-actions"
-    directory: "/"
-    schedule:
-      interval: "monthly"
-    groups:
-      github-actions:
-        patterns:
-          - "*"
+version: 2
+
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    groups:
+      github-actions:
+        patterns:
+          - "*"

phasorpy-0.2/.github/pull_request_template.md

@@ -0,0 +1,15 @@
+## Description
+
+...
+
+## Checklist
+
+- [ ] The pull request title and description are concise.
+- [ ] Related issues are linked in the description.
+- [ ] New dependencies are explained.
+- [ ] The source code and documentation can be distributed under the [MIT license](https://www.phasorpy.org/docs/stable/license/).
+- [ ] The source code adheres to [code standards](https://www.phasorpy.org/docs/stable/contributing/#code-standards).
+- [ ] New classes, functions, and features are thoroughly [tested](https://www.phasorpy.org/docs/stable/contributing/#tests).
+- [ ] New, user-facing classes, functions, and features are [documented](https://www.phasorpy.org/docs/stable/contributing/#documentation).
+- [ ] New features are covered in tutorials.
+- [ ] No files other than source code, documentation, and project settings are added to the repository.

phasorpy-0.2/.github/workflows/build_sdist.yml

@@ -0,0 +1,77 @@
+name: Build sdist
+
+on:
+  push:
+    tags:
+      - "*"
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  build_artifacts:
+    name: Build sdist
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+          fetch-depth: 0
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: Install PyBuild
+        run: |
+          python -m pip install -U build
+      - name: Build sdist
+        run: |
+          python -m build --sdist .
+      - uses: actions/upload-artifact@v4
+        with:
+          name: sdist
+          path: dist
+
+  test_artifacts:
+    name: Test sdist
+    needs: [build_artifacts]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: sdist
+          path: dist
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - run: |
+          ls
+          ls dist
+          python -m pip install -U twine setuptools build wheel numpy Cython
+          python -m twine check dist/*
+          python -m pip install --upgrade --no-build-isolation --no-cache-dir --no-deps --pre --no-index --find-links=dist phasorpy
+          python -c"from phasorpy import __version__;print(__version__)"
+
+# Upload sdist and wheels manually for now
+#
+#  upload_artifacts:
+#    name: Upload release to PyPI
+#    needs: [test_artifacts]
+#    runs-on: ubuntu-latest
+#    environment:
+#      name: pypi
+#      url: https://pypi.org/p/phasorpy
+#    permissions:
+#      id-token: write
+#    if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
+#    steps:
+#      - uses: actions/download-artifact@v4
+#        with:
+#          name: releases
+#          path: dist
+#      - uses: pypa/gh-action-pypi-publish@release/v1

{phasorpy-0.1.dev0 → phasorpy-0.2}/.github/workflows/build_wheels.yml

@@ -12,7 +12,6 @@ on:
   workflow_dispatch:
 
 env:
-  CIBW_TEST_SKIP: "cp313*"
   MPLBACKEND: agg
 
 jobs:
@@ -21,16 +20,23 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-22.04, macos-12, windows-2019]
+        os: [ubuntu-22.04, macos-13, windows-2019]
     steps:
       - uses: actions/checkout@v4
-      - uses: pypa/cibuildwheel@v2.20.0
+      # - name: Set up QEMU
+      #   if: runner.os == 'Linux'
+      #   uses: docker/setup-qemu-action@v3
+      #   with:
+      #     platforms: all
+      - uses: pypa/cibuildwheel@v2.21.3
         env:
-          # CIBW_ENVIRONMENT: "PIP_PRE=1"
-          CIBW_BUILD_VERBOSITY: 2
+          # Building and testing manylinux2014_aarch64 too is slow.
+          # See https://github.com/phasorpy/phasorpy/pull/135
+          # CIBW_ARCHS_LINUX: x86_64 aarch64
           CIBW_ARCHS_LINUX: auto
           CIBW_ARCHS_MACOS: x86_64 arm64
           CIBW_ARCHS_WINDOWS: AMD64 ARM64
+          CIBW_BUILD_VERBOSITY: 2
       - uses: actions/upload-artifact@v4
         with:
           path: ./wheelhouse/*.whl

{phasorpy-0.1.dev0 → phasorpy-0.2}/.github/workflows/run-tests.yml

@@ -55,7 +55,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ["windows-2019", "macos-12"]
+        os: ["windows-2019", "macos-13"]
         python-version: ["3.10"]
         # 3.12 tested with cibuildwheel
     steps:
@@ -84,10 +84,10 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu-22.04", "windows-2019", "macos-12"]
+        os: ["ubuntu-22.04", "windows-2019", "macos-13"]
     steps:
       - uses: actions/checkout@v4
-      - uses: pypa/cibuildwheel@v2.20.0
+      - uses: pypa/cibuildwheel@v2.21.3
         env:
           # CIBW_ENVIRONMENT: "PIP_PRE=1"
           CIBW_BUILD_VERBOSITY: 3
@@ -98,6 +98,34 @@ jobs:
           path: ./wheelhouse/*.whl
           name: wheels-${{ matrix.os }}
 
+  # Building and testing manylinux2014_aarch64 too is slow.
+  # See https://github.com/phasorpy/phasorpy/pull/135
+  #
+  #  build_wheels_arm64:
+  #    name: Test Linux on AArch64
+  #    runs-on: ${{ matrix.os }}
+  #    strategy:
+  #      fail-fast: false
+  #      matrix:
+  #        os: ["ubuntu-latest"]
+  #    steps:
+  #      - uses: actions/checkout@v4
+  #      - name: Set up QEMU
+  #        if: runner.os == 'Linux'
+  #        uses: docker/setup-qemu-action@v3
+  #        with:
+  #          platforms: all
+  #      - uses: pypa/cibuildwheel@v2.21.3
+  #        env:
+  #          CIBW_ARCHS_LINUX: aarch64
+  #          CIBW_BUILD_VERBOSITY: 2
+  #          CIBW_BUILD: "cp311*"
+  #          CIBW_SKIP: "*musllinux*"
+  #      - uses: actions/upload-artifact@v4
+  #        with:
+  #          path: ./wheelhouse/*.whl
+  #          name: wheels-aarch64
+
   static_analysis:
     name: Static code analysis
     runs-on: "ubuntu-latest"

{phasorpy-0.1.dev0 → phasorpy-0.2}/PKG-INFO

@@ -1,15 +1,15 @@
 Metadata-Version: 2.1
 Name: phasorpy
-Version: 0.1.dev0
+Version: 0.2
 Summary: Analysis of fluorescence lifetime and hyperspectral images using the phasor approach
 Author: PhasorPy Contributors
 License: MIT
-Project-URL: homepage, https://www.phasorpy.org
-Project-URL: documentation, https://www.phasorpy.org/docs/stable/
-Project-URL: download, https://pypi.org/project/phasorpy/#files
-Project-URL: source, https://github.com/phasorpy/phasorpy
-Project-URL: tracker, https://github.com/phasorpy/phasorpy/issues
-Project-URL: release notes, https://www.phasorpy.org/docs/stable/release
+Project-URL: Homepage, https://www.phasorpy.org
+Project-URL: Documentation, https://www.phasorpy.org/docs/stable/
+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: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
@@ -40,7 +40,7 @@ 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; extra == "docs"
+Requires-Dist: pydata-sphinx-theme>=0.16.0; extra == "docs"
 Requires-Dist: numpydoc; extra == "docs"
 Provides-Extra: test
 Requires-Dist: pytest; extra == "test"
@@ -61,9 +61,9 @@ lifetime and hyperspectral images using the phasor approach.
 - [Homepage](https://www.phasorpy.org)
 - [Documentation](https://www.phasorpy.org/docs/stable/)
 - [Source code](https://github.com/phasorpy/phasorpy)
-- [Issues and questions](https://github.com/phasorpy/phasorpy/issues)
-- [Python package](https://pypi.org/project/phasorpy/)
+- [Download releases](https://pypi.org/project/phasorpy/#files)
 - [Data files](https://zenodo.org/communities/phasorpy/)
+- [Issues and questions](https://github.com/phasorpy/phasorpy/issues)
 
 PhasorPy is a community-maintained project.
 [Contributions](https://www.phasorpy.org/docs/stable/contributing/)

{phasorpy-0.1.dev0 → phasorpy-0.2}/README.md

@@ -6,9 +6,9 @@ lifetime and hyperspectral images using the phasor approach.
 - [Homepage](https://www.phasorpy.org)
 - [Documentation](https://www.phasorpy.org/docs/stable/)
 - [Source code](https://github.com/phasorpy/phasorpy)
-- [Issues and questions](https://github.com/phasorpy/phasorpy/issues)
-- [Python package](https://pypi.org/project/phasorpy/)
+- [Download releases](https://pypi.org/project/phasorpy/#files)
 - [Data files](https://zenodo.org/communities/phasorpy/)
+- [Issues and questions](https://github.com/phasorpy/phasorpy/issues)
 
 PhasorPy is a community-maintained project.
 [Contributions](https://www.phasorpy.org/docs/stable/contributing/)

phasorpy-0.2/docs/_static/custom-icons.js

@@ -0,0 +1,16 @@
+/*******************************************************************************
+ * Set a custom icon for pypi as it's not available in the fa built-in brands
+ */
+FontAwesome.library.add(
+  (faListOldStyle = {
+    prefix: "fa-custom",
+    iconName: "pypi",
+    icon: [
+      17.313, // viewBox width
+      19.807, // viewBox height
+      [], // ligature
+      "e001", // unicode codepoint - private use area
+      "m10.383 0.2-3.239 1.1769 3.1883 1.1614 3.239-1.1798zm-3.4152 1.2411-3.2362 1.1769 3.1855 1.1614 3.2369-1.1769zm6.7177 0.00281-3.2947 1.2009v3.8254l3.2947-1.1988zm-3.4145 1.2439-3.2926 1.1981v3.8254l0.17548-0.064132 3.1171-1.1347zm-6.6564 0.018325v3.8247l3.244 1.1805v-3.8254zm10.191 0.20931v2.3137l3.1777-1.1558zm3.2947 1.2425-3.2947 1.1988v3.8254l3.2947-1.1988zm-8.7058 0.45739c0.00929-1.931e-4 0.018327-2.977e-4 0.027485 0 0.25633 0.00851 0.4263 0.20713 0.42638 0.49826 1.953e-4 0.38532-0.29327 0.80469-0.65542 0.93662-0.36226 0.13215-0.65608-0.073306-0.65613-0.4588-6.28e-5 -0.38556 0.2938-0.80504 0.65613-0.93662 0.068422-0.024919 0.13655-0.038114 0.20156-0.039466zm5.2913 0.78369-3.2947 1.1988v3.8247l3.2947-1.1981zm-10.132 1.239-3.2362 1.1769 3.1883 1.1614 3.2362-1.1769zm6.7177 0.00213-3.2926 1.2016v3.8247l3.2926-1.2009zm-3.4124 1.2439-3.2947 1.1988v3.8254l3.2947-1.1988zm-6.6585 0.016195v3.8275l3.244 1.1805v-3.8254zm16.9 0.21143-3.2947 1.1988v3.8247l3.2947-1.1981zm-3.4145 1.2411-3.2926 1.2016v3.8247l3.2926-1.2009zm-3.4145 1.2411-3.2926 1.2016v3.8247l3.2926-1.2009zm-3.4124 1.2432-3.2947 1.1988v3.8254l3.2947-1.1988zm-6.6585 0.019027v3.8247l3.244 1.1805v-3.8254zm13.485 1.4497-3.2947 1.1988v3.8247l3.2947-1.1981zm-3.4145 1.2411-3.2926 1.2016v3.8247l3.2926-1.2009zm2.4018 0.38127c0.0093-1.83e-4 0.01833-3.16e-4 0.02749 0 0.25633 0.0085 0.4263 0.20713 0.42638 0.49826 1.97e-4 0.38532-0.29327 0.80469-0.65542 0.93662-0.36188 0.1316-0.65525-0.07375-0.65542-0.4588-1.95e-4 -0.38532 0.29328-0.80469 0.65542-0.93662 0.06842-0.02494 0.13655-0.03819 0.20156-0.03947zm-5.8142 0.86403-3.244 1.1805v1.4201l3.244 1.1805z", // svg path (https://simpleicons.org/icons/pypi.svg)
+    ],
+  }),
+);

phasorpy-0.2/docs/_static/switcher.json

@@ -0,0 +1,13 @@
+[
+  {
+    "name": "dev",
+    "version": "0.3",
+    "url": "https://www.phasorpy.org/docs/dev/"
+  },
+  {
+    "name": "0.2 (stable)",
+    "version": "0.2",
+    "url": "https://www.phasorpy.org/docs/stable/",
+    "preferred": true
+  }
+]

{phasorpy-0.1.dev0 → phasorpy-0.2}/docs/acknowledgments.rst

@@ -30,3 +30,6 @@ bug fixes, or expertise:
 - :user:`Leonel Malacrida <lmalacrida>`
 - :user:`Bruno Pannunzio <bruno-pannunzio>`
 - :user:`Bruno Schüty <schutyb>`
+
+See also `GitHub contributors
+<https://github.com/phasorpy/phasorpy/graphs/contributors>`_.

{phasorpy-0.1.dev0 → phasorpy-0.2}/docs/conf.py

@@ -25,6 +25,7 @@ import phasorpy
 
 version = phasorpy.__version__
 release = phasorpy.__version__
+version_match = version.replace('.dev', '').replace('.rc', '')
 
 # general configuration
 
@@ -55,6 +56,7 @@ 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_show_sourcelink = False
 
 html_logo = '_static/logo.png'
@@ -71,6 +73,7 @@ napoleon_use_param = True
 
 html_theme_options = {
     'logo': {
+        # 'text': f'PhasorPy {version}',
         'text': 'PhasorPy',
         'alt_text': 'PhasorPy',
         # 'image_dark': '_static/logo-dark.svg',
@@ -78,17 +81,39 @@ html_theme_options = {
     'header_links_before_dropdown': 4,
     'show_nav_level': 2,
     'navigation_with_keys': False,
+    # 'collapse_navigation': True,
+    'navbar_align': 'content',  # [left, content, right]
+    'navbar_persistent': [],
+    # 'navbar_center': [],  # , 'version-switcher', 'navbar-nav'
+    'navbar_end': [
+        'search-button',
+        'version-switcher',
+        'theme-switcher',
+        'navbar-icon-links',
+    ],
+    'switcher': {
+        'version_match': version_match,
+        'json_url': 'https://www.phasorpy.org/docs/dev/_static/switcher.json',
+    },
+    # 'check_switcher': False,
+    'show_version_warning_banner': True,
     'icon_links': [
+        {
+            'name': 'Home',
+            'url': 'https://www.phasorpy.org',
+            'icon': 'fa fa-home',
+        },
+        {
+            'name': 'PyPI',
+            'url': 'https://pypi.org/project/phasorpy/',
+            'icon': 'fa-custom fa-pypi',
+            'type': 'fontawesome',
+        },
         {
             'name': 'GitHub',
             'url': 'https://github.com/phasorpy/phasorpy',
             'icon': 'fa-brands fa-github',
         },
-        # {
-        #     'name': 'PyPI',
-        #     'url': 'https://pypi.org/project/phasorpy/',
-        #     'icon': 'fa-custom fa-pypi',
-        # },
     ],
 }
 

{phasorpy-0.1.dev0 → phasorpy-0.2}/docs/contributing.rst

@@ -1,5 +1,5 @@
-Contributing
-============
+Contributing guide
+==================
 
 As a community-maintained project, PhasorPy welcomes contributions in the form
 of bug reports, bug fixes, feature implementations, documentation, datasets,

{phasorpy-0.1.dev0 → phasorpy-0.2}/docs/index.rst

@@ -15,9 +15,6 @@ lifetime and hyperspectral images using the :doc:`phasor_approach`.
 Quickstart
 ==========
 
-The PhasorPy library and documentation are released under the permissive
-:doc:`license`.
-
 The :doc:`tutorials/index` demonstrate the use the library, from simple
 examples to advanced applications.
 
@@ -27,46 +24,50 @@ classes of the library.
 The :doc:`release` list recent bug fixes, feature enhancements, documentation
 and maintenance changes.
 
-The :doc:`contributing` guidelines explain how to get support, report bugs,
+The :doc:`contributing` explains how to get support, report bugs,
 submit bug fixes, or improve documentation.
 
 The :doc:`code_of_conduct` should be honored by everyone participating in
 the PhasorPy community.
 
+The :doc:`acknowledgments` list individuals and organizations that
+contributed to the development of PhasorPy.
+
+The PhasorPy library and documentation are released under the permissive
+:doc:`license`.
+
 The library's source code and documentation are maintained in the
 `PhasorPy repository on GitHub <https://github.com/phasorpy/phasorpy>`_.
 
+Releases can be downloaded and installed from the
+`PhasorPy project on PyPI <https://pypi.org/project/phasorpy/>`_.
+
 Sample data files used in tutorials and testing are available from the
 `PhasorPy community on Zenodo <https://zenodo.org/communities/phasorpy>`_.
 
-Please report issues with the code or documentation on 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
 `issue tracker on GitHub <https://github.com/phasorpy/phasorpy/issues>`_.
 
-The :doc:`acknowledgments` list individuals and organizations that
-contributed to the development of PhasorPy.
-
-Please cite the PhasorPy library as:
-
-.. todo::
-
-    Create DOI at zenodo.org.
+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.
 
 Contents
 ========
 
 .. toctree::
-    :maxdepth: 1
+    :maxdepth: 2
 
     phasor_approach
     tutorials/index
     api/index
-    contributing
     release
-    acknowledgments
+    contributing
     code_of_conduct
+    acknowledgments
     license
 
 Indices and tables

{phasorpy-0.1.dev0 → phasorpy-0.2}/docs/phasor_approach.rst

@@ -188,13 +188,18 @@ approach to analyze fluorescence time-resolved or spectral images:
 - `FLUTE <https://github.com/LaboratoryOpticsBiosciences/FLUTE>`_,
   the Fluorescence Lifetime Ultimate Explorer, is an open-source Python GUI
   for interactive phasor analysis of FLIM data developed by Chiara Stringari
-  and others. The software is distributed under the GPL license.
+  and others. The software is distributed under the BSD-3-Clause license.
 
 - `FLIMPA <https://github.com/SofiaKapsiani/FLIMPA>`_
   is an open-source GUI software designed for the phasor plot analysis of
   raw TCSPC-FLIM data. The software is written in Python and distributed
   under the BSD-3-Clause license.
 
+- `AlliGator <https://alligator-distribution.readthedocs.io>`_
+  is a free, closed-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.
+
 - `FLIM_tools <https://github.com/jayunruh/FLIM_tools>`_
   is an open-source Python library for linear unmixing and phasor tools for
   FLIM analysis developed by Jay Unruh. The library is distributed under
@@ -214,6 +219,13 @@ approach to analyze fluorescence time-resolved or spectral images:
   segmentation, pH correlation, nanoscale effects, and precise quantification.
   The notebook is distributed under CC BY-NC 4.0.
 
+-
+  .. _phasorplots_for_dummies:
+
+  `PhasorPlots for dummies <https://github.com/Jalink-lab/phasor-plots>`_
+  is a Jupyter notebook to teach the analysis of FLIM/FRET by phasor plots.
+  The notebook is implemented in R and licensed under the GPL v3.
+
 - `FLIMLib <https://flimlib.github.io>`_ is an exponential curve fitting
   library used for Fluorescent Lifetime Imaging (FLIM). It includes a function
   to calculate phasor coordinates from time-resolved signals.
@@ -280,6 +292,10 @@ approach to analyze fluorescence time-resolved or spectral images:
   image analysis and visualization, including phasor plots, in conjunction
   with the FLIMera wide-field camera.
 
+- `LIFA <https://lambertinstruments.com/lifa-software>`_
+  is a commercial software by Lambert Instruments to record and analyze
+  fluorescence lifetime images, integrating all Lambert hardware.
+
 - `FlimFast <https://www.cgohlke.com/flimfast/>`_
   was a research-grade Windows desktop software for frequency-domain,
   full-field, fluorescence lifetime imaging at video rate, developed by