phasorpy 0.1__tar.gz

phasorpy-0.1/LICENSE.txt

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2022-2024 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-0.1/MANIFEST.in

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+include LICENSE.txt
+include README.md
+
+include tests/*.py
+
+include docs/*.py
+include docs/*.rst
+include docs/api/*.rst
+include docs/_static/*.*
+
+recursive-include tutorials *.py
+recursive-include tutorials *.rst
+
+exclude *.cmd
+
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+recursive-exclude * *Copy*

phasorpy-0.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: phasorpy
+Version: 0.1
+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 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: License :: OSI Approved :: MIT License
+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 :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: numpy>=1.24.0
+Requires-Dist: matplotlib>=3.7.0
+Requires-Dist: scipy>=1.11.0
+Requires-Dist: click
+Requires-Dist: pooch
+Requires-Dist: tqdm
+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; extra == "docs"
+Requires-Dist: numpydoc; extra == "docs"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: pytest-runner; extra == "test"
+Requires-Dist: pytest-doctestplus; extra == "test"
+Requires-Dist: coverage; extra == "test"
+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"
+
+# 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)
+- [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/)
+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
+[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-0.1/README.md

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+# 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)
+- [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/)
+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
+[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-0.1/docs/_static/custom-icons.js

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+/*******************************************************************************
+ * 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-0.1/docs/acknowledgments.rst

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+Acknowledgments
+===============
+
+The PhasorPy project is jointly maintained 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 is supported in part by the
+`Essential Open Source Software for Science (EOSS)
+<https://chanzuckerberg.com/eoss/>`_ program at
+`Chan Zuckerberg Initiative <https://chanzuckerberg.com/>`_.
+
+.. _contributors:
+
+Contributors
+------------
+
+The following people (in alphabetical order) have contributed to the
+development of PhasorPy by providing code, documentation, tutorials,
+bug fixes, or expertise:
+
+- :user:`Christoph Gohlke <cgohlke>`
+- Enrico Gratton
+- :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/docs/api/_phasorpy.rst

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+phasorpy._phasorpy
+------------------
+
+.. note::
+    This module and its functions are not part of the public interface.
+    They are intended to facilitate the development of the PhasorPy library.
+
+.. automodule:: phasorpy._phasorpy
+    :members:
+    :undoc-members:
+    :private-members:
+    :special-members:

phasorpy-0.1/docs/api/_utils.rst

@@ -0,0 +1,9 @@
+phasorpy._utils
+---------------
+
+.. note::
+    This module and its functions are not part of the public interface.
+    They are intended to facilitate the development of the PhasorPy library.
+
+.. automodule:: phasorpy._utils
+    :members:

phasorpy-0.1/docs/api/cli.rst

@@ -0,0 +1,6 @@
+Command line interface
+----------------------
+
+.. click:: phasorpy.cli:main
+   :prog: python -m phasorpy
+   :nested: full

phasorpy-0.1/docs/api/color.rst

@@ -0,0 +1,20 @@
+phasorpy.color
+--------------
+
+.. automodule:: phasorpy.color
+    :members:
+    :exclude-members: SRGB_SPECTRUM, CATEGORICAL
+
+.. autodata:: phasorpy.color.CATEGORICAL
+   :no-value:
+
+.. image:: ../_static/categorical.png
+  :alt: phasorpy.color.CATEGORICAL
+  :align: center
+
+.. autodata:: phasorpy.color.SRGB_SPECTRUM
+   :no-value:
+
+.. image:: ../_static/srgb_spectrum.png
+  :alt: phasorpy.color.SRGB_SPECTRUM
+  :align: center

phasorpy-0.1/docs/api/components.rst

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

phasorpy-0.1/docs/api/cursors.rst

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

phasorpy-0.1/docs/api/datasets.rst

@@ -0,0 +1,9 @@
+phasorpy.datasets
+-----------------
+
+.. automodule:: phasorpy.datasets
+    :members:
+    :exclude-members: REPOSITORIES
+
+.. autodata:: phasorpy.datasets.REPOSITORIES
+   :no-value:

phasorpy-0.1/docs/api/index.rst

@@ -0,0 +1,26 @@
+API reference
+=============
+
+This documents the application programming and command line interfaces of the
+PhasorPy library version |version|.
+
+.. note::
+    The PhasorPy library is in its early stages of development.
+    It is not nearly feature complete.
+    Large, backwards-incompatible changes may occur between revisions.
+
+.. toctree::
+    :maxdepth: 3
+
+    phasorpy
+    phasor
+    cursors
+    components
+    plot
+    io
+    color
+    datasets
+    utils
+    _utils
+    _phasorpy
+    cli

phasorpy-0.1/docs/api/io.rst

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

phasorpy-0.1/docs/api/phasor.rst

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

phasorpy-0.1/docs/api/phasorpy.rst

@@ -0,0 +1,6 @@
+phasorpy
+--------
+
+.. automodule:: phasorpy
+    :members:
+    :special-members: __version__

phasorpy-0.1/docs/api/plot.rst

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

phasorpy-0.1/docs/api/utils.rst

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

phasorpy-0.1/docs/code_of_conduct.rst

@@ -0,0 +1,143 @@
+Code of conduct
+===============
+
+The PhasorPy project adopts the `Contributor Covenant Code of Conduct
+<https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>`_.
+
+Our Pledge
+----------
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socioeconomic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+Our Standards
+-------------
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+- Demonstrating empathy and kindness toward other people
+- Being respectful of differing opinions, viewpoints, and experiences
+- Giving and gracefully accepting constructive feedback
+- Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+- Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+- The use of sexualized language or imagery, and sexual attention or advances
+  of any kind
+- Trolling, insulting or derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+- Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+Enforcement Responsibilities
+----------------------------
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for
+moderation decisions when appropriate.
+
+Scope
+-----
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail
+address, posting via an official social media account, or acting as an
+appointed representative at an online or offline event.
+
+Enforcement
+-----------
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leader responsible for enforcement:
+
+- `Leonel Malacrida <conduct@phasorpy.org>`_
+
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+Enforcement Guidelines
+----------------------
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+1. Correction
+.............
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+2. Warning
+..........
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+3. Temporary Ban
+................
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+4. Permanent Ban
+................
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+Attribution
+-----------
+
+This Code of Conduct is adapted from the `Contributor Covenant
+<https://www.contributor-covenant.org>`_, version 2.1, available at
+https://www.contributor-covenant.org/version/2/1/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by `Mozilla's code of conduct
+enforcement ladder <https://github.com/mozilla/diversity>`_.
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

phasorpy-0.1/docs/conf.py

@@ -0,0 +1,123 @@
+# Configuration file for the Sphinx documentation builder.
+# 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/'))
+
+# remove the examples header from HTML tutorials
+import sphinx_gallery.gen_rst
+
+sphinx_gallery.gen_rst.EXAMPLE_HEADER = (
+    sphinx_gallery.gen_rst.EXAMPLE_HEADER.replace(
+        '.. only:: html', '.. only:: xml'
+    )
+)
+
+# project information
+
+project = 'PhasorPy'
+copyright = '2022-2024 PhasorPy Contributors'
+author = 'PhasorPy Contributors'
+
+import phasorpy
+
+version = phasorpy.__version__
+release = phasorpy.__version__
+
+# general configuration
+
+extensions = [
+    'sphinx.ext.napoleon',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.doctest',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.todo',
+    # don't enable intersphinx since tutorials are getting littered with links
+    # 'sphinx.ext.intersphinx',
+    # 'numpydoc',
+    'sphinx_inline_tabs',
+    'sphinx_copybutton',
+    'sphinx_click',
+    'sphinx_issues',
+    'sphinx_gallery.gen_gallery',
+    'pytest_doctestplus.sphinx.doctestplus',
+]
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# options for HTML output
+
+# html_theme = 'alabaster'
+# 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'
+# html_favicon = ''
+
+pygments_style = 'sphinx'
+
+# extension configurations
+
+napoleon_google_docstring = False
+napoleon_numpy_docstring = True
+todo_include_todos = True
+napoleon_use_param = True
+
+html_theme_options = {
+    'logo': {
+        'text': 'PhasorPy',
+        'alt_text': 'PhasorPy',
+        # 'image_dark': '_static/logo-dark.svg',
+    },
+    'header_links_before_dropdown': 4,
+    'show_nav_level': 2,
+    'navigation_with_keys': False,
+    'icon_links': [
+        {
+            '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',
+            'type': 'fontawesome',
+        },
+    ],
+}
+
+sphinx_gallery_conf = {
+    'filename_pattern': 'phasorpy_',
+    'examples_dirs': '../tutorials',
+    'gallery_dirs': 'tutorials',
+    'reference_url': {'phasorpy': None},
+    'matplotlib_animations': True,
+}
+
+copybutton_prompt_text = (
+    r'>>> |\.\.\. |\$ |In \[\d*\]: | {2,5}\.\.\.: | {5,8}: '
+)
+copybutton_prompt_is_regexp = True
+
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/3/', None),
+    'numpy': ('https://numpy.org/doc/stable/', None),
+    'matplotlib': ('https://matplotlib.org/stable/', None),
+    'scipy': ('https://docs.scipy.org/doc/scipy/reference/', None),
+    'pandas': ('https://pandas.pydata.org/docs/', None),
+    'sklearn': ('https://scikit-learn.org/stable/', None),
+    'skimage': ('https://scikit-image.org/docs/stable/', None),
+}
+
+intersphinx_disabled_reftypes = ['*']
+
+# do not show typehints
+autodoc_typehints = 'none'