phasorpy 0.7__cp314-cp314-macosx_10_13_x86_64.whl

phasorpy/utils.py

@@ -0,0 +1,172 @@
+"""Utility functions.
+
+The ``phasorpy.utils`` module provides auxiliary and convenience functions
+that do not fit naturally into other modules.
+
+"""
+
+from __future__ import annotations
+
+__all__ = [
+    'logger',
+    'number_threads',
+    'versions',
+]
+
+import logging
+import os
+
+
+def logger() -> logging.Logger:
+    """Return PhasorPy logger instance.
+
+    Returns
+    -------
+    logging.Logger
+        Logger instance for 'phasorpy' namespace.
+
+    Examples
+    --------
+    >>> logger().info('This is a log message')
+
+    """
+    return logging.getLogger('phasorpy')
+
+
+def number_threads(
+    num_threads: int | None = None,
+    max_threads: int | None = None,
+    /,
+) -> int:
+    """Return number of threads for parallel computations across CPU cores.
+
+    This function is used to parse ``num_threads`` parameters.
+
+    Parameters
+    ----------
+    num_threads : int, optional
+        Number of threads to use for parallel computations on CPU cores.
+        If None (default), return 1, disabling multi-threading.
+        If greater than zero, return value up to `max_threads` if set.
+        If zero, return the value of the ``PHASORPY_NUM_THREADS`` environment
+        variable if set, else half the CPU cores up to `max_threads` or 32.
+    max_threads : int, optional
+        Maximum number of threads to return.
+
+    Returns
+    -------
+    int
+        Number of threads for parallel computations.
+
+    Examples
+    --------
+    >>> number_threads()
+    1
+    >>> number_threads(0)  # doctest: +SKIP
+    8  # actual value depends on system
+
+    """
+    if num_threads is None or num_threads < 0:
+        # disable multi-threading by default
+        return 1
+    if num_threads == 0:
+        # return default number of threads
+        if max_threads is None:
+            max_threads = 32
+        else:
+            max_threads = max(max_threads, 1)
+        if 'PHASORPY_NUM_THREADS' in os.environ:
+            return min(
+                max_threads, max(1, int(os.environ['PHASORPY_NUM_THREADS']))
+            )
+        cpu_count: int | None
+        if hasattr(os, 'sched_getaffinity'):
+            cpu_count = len(os.sched_getaffinity(0))
+        else:
+            # sched_getaffinity not available on Windows
+            cpu_count = os.cpu_count()
+        if cpu_count is None:
+            return 1
+        return min(max_threads, max(1, cpu_count // 2))
+    # return num_threads up to max_threads
+    if max_threads is None:
+        return num_threads
+    return min(num_threads, max(max_threads, 1))
+
+
+def versions(
+    *, sep: str = '\n', dash: str = '-', verbose: bool = False
+) -> str:
+    """Return version information for PhasorPy and its dependencies.
+
+    Parameters
+    ----------
+    sep : str, optional
+        Separator between version items. Defaults to newline.
+    dash : str, optional
+        Separator between module name and version. Defaults to dash.
+    verbose : bool, optional
+        Include paths to Python interpreter and modules.
+
+    Returns
+    -------
+    str
+        Formatted string containing version information.
+        Format: ``"<package><dash><version>[<space>(<path>)]<sep>"``
+
+    Examples
+    --------
+    >>> print(versions())  # doctest: +SKIP
+    Python-3.13.5
+    phasorpy-0.6
+    numpy-2.3.1
+    ...
+
+    """
+    import importlib.metadata
+    import os
+    import sys
+
+    if verbose:
+        version_strings = [f'Python{dash}{sys.version}  ({sys.executable})']
+    else:
+        version_strings = [f'Python{dash}{sys.version.split()[0]}']
+
+    for module in (
+        'phasorpy',
+        'numpy',
+        'tifffile',
+        'imagecodecs',
+        'lfdfiles',
+        'sdtfile',
+        'ptufile',
+        'liffile',
+        'matplotlib',
+        'scipy',
+        'skimage',
+        'sklearn',
+        'pandas',
+        'xarray',
+        'click',
+        'pooch',
+    ):
+        try:
+            __import__(module)
+        except ModuleNotFoundError:
+            version_strings.append(f'{module.lower()}{dash}n/a')
+            continue
+        lib = sys.modules[module]
+        try:
+            ver = importlib.metadata.version(module)
+        except importlib.metadata.PackageNotFoundError:
+            ver = getattr(lib, '__version__', 'unknown')
+        ver = f'{module.lower()}{dash}{ver}'
+        if verbose:
+            try:
+                path = getattr(lib, '__file__')
+            except NameError:
+                pass
+            else:
+                ver += f'  ({os.path.dirname(path)})'
+        version_strings.append(ver)
+    return sep.join(version_strings)

phasorpy-0.7.dist-info/METADATA

@@ -0,0 +1,74 @@
+Metadata-Version: 2.4
+Name: phasorpy
+Version: 0.7
+Summary: Analysis of fluorescence lifetime and hyperspectral images using the phasor approach
+Author: PhasorPy Contributors
+License-Expression: 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 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
+Classifier: Programming Language :: Python
+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
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: numpy>=1.26.0
+Requires-Dist: matplotlib>=3.8.0
+Requires-Dist: scipy>=1.11.0
+Requires-Dist: click
+Requires-Dist: pooch
+Requires-Dist: tqdm
+Requires-Dist: scikit-learn>=1.5.0
+Requires-Dist: xarray>=2023.4.0
+Requires-Dist: tifffile>=2024.8.30
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+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>=0.16.0; extra == "docs"
+Requires-Dist: numpydoc; extra == "docs"
+Provides-Extra: all
+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: pawflim; extra == "all"
+Dynamic: license-file
+
+# PhasorPy
+
+PhasorPy is an open-source Python library for the analysis of fluorescence
+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)
+- [Install with pip](https://pypi.org/project/phasorpy/) or [conda](https://anaconda.org/conda-forge/phasorpy).
+- [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/)
+in the form of bug reports, bug fixes, feature implementations, documentation,
+datasets, and enhancement proposals are welcome.
+
+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/).
+
+[![CZI's Essential Open Source Software for Science](https://chanzuckerberg.github.io/open-science/badges/CZI-EOSS.svg)](https://czi.co/EOSS)

phasorpy-0.7.dist-info/RECORD

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phasorpy-0.7.dist-info/WHEEL

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+Tag: cp314-cp314-macosx_10_13_x86_64
+Generator: delocate 0.13.0
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phasorpy-0.7.dist-info/entry_points.txt

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+[console_scripts]
+phasorpy = phasorpy.cli:main

phasorpy-0.7.dist-info/licenses/LICENSE.txt

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2022-2025 PhasorPy Contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

phasorpy-0.7.dist-info/top_level.txt

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+phasorpy