[med-svn] [Git][python-team/packages/python-multipletau][upstream] New upstream version 0.4.1+ds
Alexandre Detiste (@detiste-guest)
gitlab at salsa.debian.org
Sat Jun 29 12:06:43 BST 2024
Alexandre Detiste pushed to branch upstream at Debian Python Team / packages / python-multipletau
Commits:
04e5ef80 by Alexandre Detiste at 2024-06-29T12:55:01+02:00
New upstream version 0.4.1+ds
- - - - -
23 changed files:
- + .github/FUNDING.yml
- + .github/workflows/check.yml
- + .github/workflows/deploy_pypi.yml
- CHANGELOG
- README.rst
- docs/conf.py
- docs/extensions/fancy_include.py
- + docs/extensions/github_changelog.py
- docs/index.rst
- docs/requirements.txt
- multipletau/__init__.py
- − multipletau/_version.py
- multipletau/core.py
- + pyproject.toml
- − setup.py
- + tests/requirements.txt
- tests/test_ac_cc.py
- tests/test_autocorrelate.py
- tests/test_basic.py
- tests/test_compress.py
- tests/test_correlate.py
- tests/test_ref_numpy.py
- tests/test_ret_sum.py
Changes:
=====================================
.github/FUNDING.yml
=====================================
@@ -0,0 +1,2 @@
+github: paulmueller
+liberapay: paulmueller
=====================================
.github/workflows/check.yml
=====================================
@@ -0,0 +1,39 @@
+name: Checks
+
+on:
+ push:
+ pull_request:
+
+jobs:
+ build:
+
+ runs-on: ${{ matrix.os }}
+ strategy:
+ matrix:
+ python-version: ['3.8', '3.11']
+ os: [macos-latest, ubuntu-latest, windows-latest]
+
+ steps:
+ - uses: actions/checkout at v3
+ - name: Set up Python ${{ matrix.python-version }}
+ uses: actions/setup-python at v4
+ with:
+ python-version: ${{ matrix.python-version }}
+ - name: Install dependencies
+ run: |
+ # prerequisites
+ python -m pip install --upgrade pip wheel
+ python -m pip install coverage flake8 pytest
+ # show installed packages
+ pip freeze
+ - name: Install multipletau
+ run: |
+ pip install .
+ - name: Lint with flake8
+ run: |
+ flake8 --exclude _version.py .
+ - name: Test with pytest
+ run: |
+ coverage run --source=multipletau -m pytest tests
+ - name: Upload coverage to Codecov
+ uses: codecov/codecov-action at v3
=====================================
.github/workflows/deploy_pypi.yml
=====================================
@@ -0,0 +1,31 @@
+name: Release to PyPI
+
+on:
+ push:
+ tags:
+ - '*'
+
+jobs:
+ deploy:
+ name: Deploy package to PYPI
+ runs-on: ubuntu-latest
+ strategy:
+ matrix:
+ python-version: ['3.11']
+ steps:
+ - uses: actions/checkout at v3
+ with:
+ fetch-depth: 0
+ - name: Set up Python
+ uses: actions/setup-python at v4
+ with:
+ python-version: ${{ matrix.python-version }}
+ - name: Run build
+ run: pipx run build --sdist --wheel
+ - name: publish
+ env:
+ TWINE_USERNAME: __token__
+ TWINE_PASSWORD: ${{ secrets.PYPI_PWD }}
+ run: |
+ pipx install twine
+ twine upload --skip-existing dist/*
=====================================
CHANGELOG
=====================================
@@ -1,3 +1,11 @@
+0.4.1
+ - docs: remove Python 2 reference
+0.4.0
+ - ref: support NumPy 2
+ - setup: migrate to GitHub Actions
+ - setup: migrate to pyproject.toml
+ - docs: remove dependency on old mock standalone library (#19)
+ - docs: overhaul and add changelog
0.3.3
- fix: add constant `ZERO_CUTOFF` that defines when a trace average is
treated as zero
=====================================
README.rst
=====================================
@@ -10,9 +10,9 @@ correlation on a linear scale such as `numpy.correlate <http://docs.scipy.org/do
Installation
------------
-Multipletau supports Python 2.7 and Python 3.3+ with a common codebase.
-The only requirement for ``multipletau`` is `NumPy <http://www.numpy.org/>`__ (for fast
-operations on arrays). Install multipletau from the Python package index:
+The only requirement for ``multipletau`` is Python 3.x and
+`NumPy <http://www.numpy.org/>`__. Install multipletau from the
+Python package index:
::
@@ -22,7 +22,8 @@ operations on arrays). Install multipletau from the Python package index:
Documentation
-------------
-The documentation, including the reference and examples, is available on `readthedocs.io <https://multipletau.readthedocs.io/en/stable/>`__.
+The documentation, including the reference and examples, is available
+on `readthedocs.io <https://multipletau.readthedocs.io/en/stable/>`__.
Usage
@@ -56,14 +57,14 @@ You can find out what version you are using by typing (in a Python console):
>>> import multipletau
>>> multipletau.__version__
- '0.3.0'
+ '0.4.0'
-.. |PyPI Version| image:: http://img.shields.io/pypi/v/multipletau.svg
+.. |PyPI Version| image:: https://img.shields.io/pypi/v/multipletau.svg
:target: https://pypi.python.org/pypi/multipletau
-.. |Tests Status| image:: http://img.shields.io/travis/FCS-analysis/multipletau.svg?label=tests
- :target: https://travis-ci.org/FCS-analysis/multipletau
+.. |Tests Status| image:: https://img.shields.io/github/actions/workflow/status/FCS-analysis/multipletau/check.yml
+ :target: https://github.com/FCS-analysis/multipletau/actions?query=workflow%3AChecks
.. |Coverage Status| image:: https://img.shields.io/codecov/c/github/FCS-analysis/multipletau/master.svg
:target: https://codecov.io/gh/FCS-analysis/multipletau
.. |Docs Status| image:: https://readthedocs.org/projects/multipletau/badge/?version=latest
=====================================
docs/conf.py
=====================================
@@ -17,12 +17,16 @@
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
-import mock
import os.path as op
import sys
+from unittest import mock
+
+import multipletau
+
+
# include parent directory
pdir = op.dirname(op.dirname(op.abspath(__file__)))
-sys.path.insert(0, pdir)
+sys.path.insert(0, pdir)
# include extenstions
sys.path.append(op.abspath('extensions'))
@@ -41,8 +45,8 @@ description = 'A multiple-tau algorithm for Python/NumPy'
projectname = name
projectdescription = description
-exec(open(op.join(pdir, "multipletau/_version.py")).read())
-release = version #@UndefinedVariable
+
+release = multipletau.__version__
# http://www.sphinx-doc.org/en/stable/ext/autodoc.html#confval-autodoc_member_order
# Order class attributes and functions in separate blocks
@@ -57,7 +61,7 @@ rst_prolog = """
# -- General configuration ------------------------------------------------
# If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
+# needs_sphinx = '1.0'
# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
@@ -70,10 +74,10 @@ extensions = ['sphinx.ext.intersphinx',
'sphinx.ext.viewcode',
'sphinx.ext.napoleon',
'fancy_include',
+ 'github_changelog',
]
-
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
@@ -81,7 +85,7 @@ templates_path = ['_templates']
source_suffix = '.rst'
# The encoding of source files.
-#source_encoding = 'utf-8-sig'
+# source_encoding = 'utf-8-sig'
# The master toctree document.
master_doc = 'index'
@@ -96,121 +100,121 @@ copyright = year+", "+author
#
# The short X.Y version.
# The full version, including alpha/beta/rc tags.
-#release = version
+# release = version
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
-#language = None
+# language = None
# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
-#today = ''
+# today = ''
# Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
+# today_fmt = '%B %d, %Y'
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# The reST default role (used for this markup: `text`) to use for all
# documents.
-#default_role = None
+# default_role = None
# If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
+# add_function_parentheses = True
# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
-#add_module_names = True
+# add_module_names = True
# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
-#show_authors = False
+# show_authors = False
# The name of the Pygments (syntax highlighting) style to use.
-#pygments_style = 'default'
+# pygments_style = 'default'
# A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
+# modindex_common_prefix = []
# If true, keep warnings as "system message" paragraphs in the built documents.
-#keep_warnings = False
+# keep_warnings = False
# -- Options for HTML output ----------------------------------------------
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
-html_theme = 'default'
+html_theme = 'sphinx_rtd_theme'
# Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
+# html_theme_path = []
# The name for this set of Sphinx documents. If None, it defaults to
# "<project> v<release> documentation".
-#html_title = None
+# html_title = None
# A shorter title for the navigation bar. Default is the same as html_title.
-#html_short_title = None
+# html_short_title = None
# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
-#html_logo = None
+# html_logo = None
# The name of an image file (within the static path) to use as favicon of the
# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
-#html_favicon = None
+# html_favicon = None
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
-#html_static_path = ['_static']
+# html_static_path = ['_static']
# Add any extra paths that contain custom files (such as robots.txt or
# .htaccess) here, relative to this directory. These files are copied
# directly to the root of the documentation.
-#html_extra_path = []
+# html_extra_path = []
# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
-#html_last_updated_fmt = '%b %d, %Y'
+# html_last_updated_fmt = '%b %d, %Y'
# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
-#html_use_smartypants = True
+# html_use_smartypants = True
# Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
+# html_sidebars = {}
# Additional templates that should be rendered to pages, maps page names to
# template names.
-#html_additional_pages = {}
+# html_additional_pages = {}
# If false, no module index is generated.
-#html_domain_indices = True
+# html_domain_indices = True
# If false, no index is generated.
-#html_use_index = True
+# html_use_index = True
# If true, the index is split into individual pages for each letter.
-#html_split_index = False
+# html_split_index = False
# If true, links to the reST sources are added to the pages.
-#html_show_sourcelink = True
+# html_show_sourcelink = True
# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
-#html_show_sphinx = True
+# html_show_sphinx = True
# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
-#html_show_copyright = True
+# html_show_copyright = True
# If true, an OpenSearch description file will be output, and all pages will
# contain a <link> tag referring to it. The value of this option must be the
# base URL from which the finished HTML is served.
-#html_use_opensearch = ''
+# html_use_opensearch = ''
# This is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = None
+# html_file_suffix = None
# Output file base name for HTML help builder.
htmlhelp_basename = projectname+'doc'
@@ -219,43 +223,43 @@ htmlhelp_basename = projectname+'doc'
# -- Options for LaTeX output ---------------------------------------------
latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-#'papersize': 'letterpaper',
+ # The paper size ('letterpaper' or 'a4paper').
+ # 'papersize': 'letterpaper',
-# The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
+ # The font size ('10pt', '11pt' or '12pt').
+ # 'pointsize': '10pt',
-# Additional stuff for the LaTeX preamble.
-#'preamble': '',
+ # Additional stuff for the LaTeX preamble.
+ # 'preamble': '',
}
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
# author, documentclass [howto, manual, or own class]).
latex_documents = [
- ('index', projectname+'.tex', projectname+' Documentation',
- author, 'manual'),
+ ('index', projectname+'.tex', projectname+' Documentation',
+ author, 'manual'),
]
# The name of an image file (relative to this directory) to place at the top of
# the title page.
-#latex_logo = None
+# latex_logo = None
# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
-#latex_use_parts = False
+# latex_use_parts = False
# If true, show page references after internal links.
-#latex_show_pagerefs = False
+# latex_show_pagerefs = False
# If true, show URL addresses after external links.
-#latex_show_urls = False
+# latex_show_urls = False
# Documents to append as an appendix to all manuals.
-#latex_appendices = []
+# latex_appendices = []
# If false, no module index is generated.
-#latex_domain_indices = True
+# latex_domain_indices = True
# -- Options for manual page output ---------------------------------------
@@ -268,7 +272,7 @@ man_pages = [
]
# If true, show URL addresses after external links.
-#man_show_urls = False
+# man_show_urls = False
# -- Options for Texinfo output -------------------------------------------
@@ -277,23 +281,23 @@ man_pages = [
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
- ('index', projectname, projectname+' Documentation',
- author, projectname,
- projectdescription,
- 'Numeric'),
+ ('index', projectname, projectname+' Documentation',
+ author, projectname,
+ projectdescription,
+ 'Numeric'),
]
# Documents to append as an appendix to all manuals.
-#texinfo_appendices = []
+# texinfo_appendices = []
# If false, no module index is generated.
-#texinfo_domain_indices = True
+# texinfo_domain_indices = True
# How to display URL addresses: 'footnote', 'no', or 'inline'.
-#texinfo_show_urls = 'footnote'
+# texinfo_show_urls = 'footnote'
# If true, do not generate a @detailmenu in the "Top" node's menu.
-#texinfo_no_detailmenu = False
+# texinfo_no_detailmenu = False
# -----------------------------------------------------------------------------
# intersphinx
=====================================
docs/extensions/fancy_include.py
=====================================
@@ -27,8 +27,7 @@ The directive
will display the doc string formatted with the first line as a
heading, a code block with line numbers, and the image file.
"""
-import io
-import os.path as op
+import pathlib
from docutils.statemachine import ViewList
from docutils.parsers.rst import Directive
@@ -42,13 +41,13 @@ class IncludeDirective(Directive):
def run(self):
path = self.state.document.settings.env.config.fancy_include_path
- full_path = op.join(path, self.arguments[0])
+ path = pathlib.Path(path)
+ full_path = path / self.arguments[0]
- with io.open(full_path, "r") as myfile:
- text = myfile.read()
+ text = full_path.read_text()
# add reference
- name = op.basename(full_path)[:-3]
+ name = full_path.stem
rst = [".. _example_{}:".format(name),
"",
]
@@ -65,18 +64,18 @@ class IncludeDirective(Directive):
# image
for ext in [".png", ".jpg"]:
- image_path = full_path[:-3] + ext
- if op.exists(image_path):
+ image_path = full_path.with_suffix(ext)
+ if image_path.exists():
break
else:
image_path = ""
if image_path:
- rst.append(".. figure:: {}".format(image_path))
+ rst.append(".. figure:: {}".format(image_path.as_posix()))
rst.append("")
# download file
- rst.append(":download:`{}<{}>`".format(
- op.basename(full_path), full_path))
+ rst.append(":download:`{} <{}>`".format(
+ full_path.name, full_path.as_posix()))
# code
rst.append("")
=====================================
docs/extensions/github_changelog.py
=====================================
@@ -0,0 +1,75 @@
+"""Display changelog with links to GitHub issues
+
+Usage
+-----
+The directive
+
+ .. include_changelog:: ../CHANGELOG
+
+adds the content of the changelog file into the current document.
+References to GitHub issues are identified as "(#XY)" (with parentheses
+and hash) and a link is inserted
+
+ https://github.com/RI-imaging/{PROJECT}/issues/{XY}
+
+where PROJECT ist the `project` variable defined in conf.py.
+"""
+import io
+import re
+
+from docutils.statemachine import ViewList
+from docutils.parsers.rst import Directive
+from sphinx.util.nodes import nested_parse_with_titles
+from docutils import nodes
+
+
+class IncludeDirective(Directive):
+ required_arguments = 1
+ optional_arguments = 0
+
+ def run(self):
+ full_path = self.arguments[0]
+ project = self.state.document.settings.env.config.github_project
+
+ def insert_github_link(reobj):
+ line = reobj.string
+ instr = line[reobj.start():reobj.end()]
+ issue = instr.strip("#()")
+ link = "https://github.com/{}/issues/".format(project)
+ rstlink = "(`#{issue} <{link}{issue}>`_)".format(issue=issue,
+ link=link)
+ return rstlink
+
+ with io.open(full_path, "r") as myfile:
+ text = myfile.readlines()
+
+ rst = []
+ for line in text:
+ line = line.strip("\n")
+ if line.startswith(" ") and line.strip().startswith("-"):
+ # list in list:
+ rst.append("")
+ if not line.startswith(" "):
+ rst.append("")
+ line = "version " + line
+ rst.append(line)
+ rst.append("-"*len(line))
+ elif not line.strip():
+ rst.append(line)
+ else:
+ line = re.sub(r"\(#[0-9]*\)", insert_github_link, line)
+ rst.append(line)
+
+ vl = ViewList(rst, "fakefile.rst")
+ # Create a node.
+ node = nodes.section()
+ node.document = self.state.document
+ # Parse the rst.
+ nested_parse_with_titles(self.state, vl, node)
+ return node.children
+
+
+def setup(app):
+ app.add_config_value('github_project', "user/project", 'html')
+ app.add_directive('include_changelog', IncludeDirective)
+ return {'version': '0.1'} # identifies the version of our extension
=====================================
docs/index.rst
=====================================
@@ -17,24 +17,46 @@ Summary:
correlate_numpy
+.. _sec_ac:
+
Autocorrelation
---------------
.. autofunction:: autocorrelate
+
+.. _sec_cc:
+
Cross-correlation
-----------------
.. autofunction:: correlate
+
+.. _sec_cc_numpy:
+
Cross-correlation (NumPy)
-------------------------
.. autofunction:: correlate_numpy
+
+.. _sec_constants:
+
Constants
---------
.. autodata:: multipletau.core.ZERO_CUTOFF
+
+.. _sec_examples:
+
Examples
========
.. fancy_include:: compare_correlation_methods.py
+
+.. _sec_changelog:
+
+Changelog
+=========
+List of changes in-between nanite releases.
+
+.. include_changelog:: ../CHANGELOG
=====================================
docs/requirements.txt
=====================================
@@ -1,2 +1,4 @@
-mock
-sphinx>=1.6.4
+sphinx
+sphinxcontrib.bibtex
+sphinx_rtd_theme
+
=====================================
multipletau/__init__.py
=====================================
@@ -1,8 +1,8 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
u"""
-Multipletau provides a multiple-τ algorithm for Python 2.7 and
-Python 3.x with :py:mod:`numpy` as its sole dependency.
+Multipletau provides a multiple-τ algorithm Python 3.x with
+:py:mod:`numpy` as its sole dependency.
Multiple-τ correlation is computed on a logarithmic scale (less
data points are computed) and is thus much faster than conventional
@@ -23,7 +23,7 @@ Recommended literature
Obtaining multipletau
---------------------
-If you have Python and :py:mod:`numpy` installed, simply run
+If you have Python and :py:mod:`numpy` installed, simply run::
pip install multipletau
@@ -72,7 +72,7 @@ The package is straightforward to use. Here is a quick example:
"""
from .core import autocorrelate, correlate, correlate_numpy # noqa: F401
-from ._version import version as __version__ # noqa: F401
+from ._version import __version__, __version_tuple__ # noqa: F401
__author__ = u"Paul Müller"
__license__ = "BSD (3 clause)"
=====================================
multipletau/_version.py deleted
=====================================
@@ -1,141 +0,0 @@
-#!/usr/bin/env python
-"""Determine package version for git repositories from tags
-
-Each time this file is imported it checks if the ".git" folder is
-present and if so, obtains the version from the git history using
-`git describe`. This information is then stored in the file
-`_version_save.py` which is not versioned by git, but distributed
-along e.g. on PyPI.
-"""
-from __future__ import print_function
-
-# Put the entire script into a `True` statement and add the hint
-# `pragma: no cover` to ignore code coverage here.
-if True: # pragma: no cover
- import imp
- import os
- from os.path import abspath, basename, dirname, join
- import subprocess
- import sys
- import time
- import traceback
- import warnings
-
- def git_describe():
- """
- Return a string describing the version returned by the
- command `git describe --tags HEAD`.
- If it is not possible to determine the correct version,
- then an empty string is returned.
- """
- # Make sure we are in a directory that belongs to the correct
- # repository.
- ourdir = dirname(abspath(__file__))
-
- def _minimal_ext_cmd(cmd):
- # construct minimal environment
- env = {}
- for k in ['SYSTEMROOT', 'PATH']:
- v = os.environ.get(k)
- if v is not None:
- env[k] = v
- # LANGUAGE is used on win32
- env['LANGUAGE'] = 'C'
- env['LANG'] = 'C'
- env['LC_ALL'] = 'C'
- pop = subprocess.Popen(cmd,
- stdout=subprocess.PIPE,
- stderr=subprocess.PIPE,
- env=env)
- out = pop.communicate()[0]
- return out
-
- # change directory
- olddir = abspath(os.curdir)
- os.chdir(ourdir)
-
- try:
- out = _minimal_ext_cmd(['git', 'describe', '--tags', 'HEAD'])
- git_revision = out.strip().decode('ascii')
- except OSError:
- git_revision = ""
-
- # go back to original directory
- os.chdir(olddir)
-
- return git_revision
-
- def load_version(versionfile):
- """load version from version_save.py"""
- longversion = ""
- try:
- _version_save = imp.load_source("_version_save", versionfile)
- longversion = _version_save.longversion
- except BaseException:
- try:
- from ._version_save import longversion
- except BaseException:
- try:
- from _version_save import longversion
- except BaseException:
- pass
-
- return longversion
-
- def save_version(version, versionfile):
- """save version to version_save.py"""
- data = "#!/usr/bin/env python\n" \
- + "# This file was created automatically\n" \
- + "longversion = '{VERSION}'\n"
- try:
- with open(versionfile, "w") as fd:
- fd.write(data.format(VERSION=version))
- except BaseException:
- msg = "Could not write package version to {}.".format(versionfile)
- warnings.warn(msg)
-
- hdir = dirname(abspath(__file__))
- if basename(__file__) == "conf.py" and "name" in locals():
- # This script is executed in conf.py from the docs directory
- versionfile = join(join(join(hdir, ".."),
- name), # noqa: F821
- "_version_save.py")
- else:
- # This script is imported as a module
- versionfile = join(hdir, "_version_save.py")
-
- # Determine the accurate version
- longversion = ""
-
- # 1. git describe
- try:
- # Get the version using `git describe`
- longversion = git_describe()
- except BaseException:
- pass
-
- # 2. previously created version file
- if longversion == "":
- # Either this is this is not a git repository or we are in the
- # wrong git repository.
- # Get the version from the previously generated `_version_save.py`
- longversion = load_version(versionfile)
-
- # 3. last resort: date
- if longversion == "":
- print("Could not determine version. Reason:")
- print(traceback.format_exc())
- ctime = os.stat(__file__)[8]
- longversion = time.strftime("%Y.%m.%d-%H-%M-%S", time.gmtime(ctime))
- print("Using creation time as version: {}".format(longversion))
-
- if not hasattr(sys, 'frozen'):
- # Save the version to `_version_save.py` to allow distribution using
- # `python setup.py sdist`.
- # This is only done if the program is not frozen (with e.g.
- # pyinstaller),
- if longversion != load_version(versionfile):
- save_version(longversion, versionfile)
-
- # PEP 440-conform development version:
- version = ".dev".join(longversion.split("-")[:2])
=====================================
multipletau/core.py
=====================================
@@ -136,7 +136,7 @@ def autocorrelate(a, m=16, deltat=1, normalize=False, copy=True, dtype=None,
Examples
--------
>>> from multipletau import autocorrelate
- >>> autocorrelate(range(42), m=2, dtype=np.float_)
+ >>> autocorrelate(range(42), m=2, dtype=np.float64)
array([[ 0.00000000e+00, 2.38210000e+04],
[ 1.00000000e+00, 2.29600000e+04],
[ 2.00000000e+00, 2.21000000e+04],
@@ -172,9 +172,9 @@ def autocorrelate(a, m=16, deltat=1, normalize=False, copy=True, dtype=None,
copy=copy,
dtype=dtype)
elif dtype.kind != "f":
- warnings.warn("Input dtype is not float; casting to np.float_!",
+ warnings.warn("Input dtype is not float; casting to np.float64!",
DtypeWarning)
- dtype = np.dtype(np.float_)
+ dtype = np.dtype(np.float64)
# If copy is false and dtype is the same as the input array,
# then this line does not have an effect:
@@ -384,7 +384,7 @@ def correlate(a, v, m=16, deltat=1, normalize=False, copy=True, dtype=None,
Examples
--------
>>> from multipletau import correlate
- >>> correlate(range(42), range(1,43), m=2, dtype=np.float_)
+ >>> correlate(range(42), range(1,43), m=2, dtype=np.float64)
array([[ 0.00000000e+00, 2.46820000e+04],
[ 1.00000000e+00, 2.38210000e+04],
[ 2.00000000e+00, 2.29600000e+04],
@@ -421,20 +421,20 @@ def correlate(a, v, m=16, deltat=1, normalize=False, copy=True, dtype=None,
if dtype.kind == "c" or dtype2.kind == "c":
# The user might try to combine complex64 and float128.
warnings.warn(
- "Input dtypes not equal; casting to np.complex_!",
+ "Input dtypes not equal; casting to np.complex128!",
InvalidMWarning)
- dtype = np.dtype(np.complex_)
+ dtype = np.dtype(np.complex128)
else:
- warnings.warn("Input dtypes not equal; casting to np.float_!",
+ warnings.warn("Input dtypes not equal; casting to np.float64!",
InvalidMWarning)
- dtype = np.dtype(np.float_)
+ dtype = np.dtype(np.float64)
else:
dtype = np.dtype(dtype)
if dtype.kind not in ["c", "f"]:
- warnings.warn("Input dtype is not float; casting to np.float_!",
+ warnings.warn("Input dtype is not float; casting to np.float64!",
InvalidMWarning)
- dtype = np.dtype(np.float_)
+ dtype = np.dtype(np.float64)
trace1 = np.array(v, dtype=dtype, copy=copy)
=====================================
pyproject.toml
=====================================
@@ -0,0 +1,47 @@
+[build-system]
+requires = [
+ # for version management
+ "setuptools>=45", "setuptools_scm[toml]>=6.2"
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "multipletau"
+authors = [
+ # In alphabetical order.
+ {name = "André Scholich"},
+ {name = "Alexandre Detiste"},
+ {name = "Chris Lamb"},
+ {name = "Pascal Hebbeker"},
+ {name = "Paul Müller"},
+]
+maintainers = [
+ {name = "Paul Müller", email="dev at craban.de"},
+]
+description = "A multiple-tau algorithm for Python/NumPy"
+readme = "README.rst"
+requires-python = ">=3.6, <4"
+keywords = ["multiple tau",
+ "fluorescence correlation spectroscopy"]
+classifiers = [
+ 'Operating System :: OS Independent',
+ 'Programming Language :: Python :: 3',
+ 'Topic :: Scientific/Engineering :: Visualization',
+ 'Intended Audience :: Science/Research',
+]
+license = {text = "BSD (3 clause)"}
+dependencies = [
+ "numpy>=1.5.1",
+ ]
+dynamic = ["version"]
+
+[project.urls]
+source = "https://github.com/FCS-analysis/multipletau"
+tracker = "https://github.com/FCS-analysis/multipletau/issues"
+documentation = "https://multipletau.readthedocs.io/en/stable/"
+changelog = "https://multipletau.readthedocs.io/en/stable/#changelog"
+
+
+[tool.setuptools_scm]
+write_to = "multipletau/_version.py"
+version_scheme = "post-release"
=====================================
setup.py deleted
=====================================
@@ -1,42 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-from os.path import exists, dirname, realpath
-from setuptools import setup
-import sys
-
-
-author = u"Paul Müller"
-authors = [author]
-description = 'A multiple-tau algorithm for Python/NumPy'
-name = 'multipletau'
-year = "2012"
-
-sys.path.insert(0, realpath(dirname(__file__))+"/"+name)
-from _version import version
-
-
-setup(
- name=name,
- author=author,
- author_email='dev at craban.de',
- url='https://github.com/FCS-analysis/multipletau',
- version=version,
- packages=[name],
- package_dir={name: name},
- license="BSD (3 clause)",
- description=description,
- long_description=open('README.rst').read() if exists('README.rst') else '',
- install_requires=["numpy >= 1.5.1"],
- keywords=["multiple tau", "fluorescence correlation spectroscopy"],
- setup_requires=['pytest-runner'],
- tests_require=["pytest"],
- classifiers= [
- 'Operating System :: OS Independent',
- 'Programming Language :: Python :: 2',
- 'Programming Language :: Python :: 3',
- 'Topic :: Scientific/Engineering :: Visualization',
- 'Intended Audience :: Science/Research'
- ],
- platforms=['ALL']
- )
-
=====================================
tests/requirements.txt
=====================================
@@ -0,0 +1 @@
+pytest
\ No newline at end of file
=====================================
tests/test_ac_cc.py
=====================================
@@ -29,7 +29,7 @@ def test_ac_cc_m():
deltat=1,
normalize=False,
copy=True,
- dtype=np.float_)
+ dtype=np.float64)
res.append(r)
res = np.concatenate(res)
@@ -40,7 +40,7 @@ def test_ac_cc_m():
deltat=1,
normalize=False,
copy=True,
- dtype=np.float_)
+ dtype=np.float64)
rescc.append(r)
# test minimal length of array
multipletau.correlate(a=a[:2*m], v=a[:2*m],
@@ -48,7 +48,7 @@ def test_ac_cc_m():
deltat=1,
normalize=False,
copy=True,
- dtype=np.float_)
+ dtype=np.float64)
rescc = np.concatenate(rescc)
assert np.all(res == rescc)
@@ -68,7 +68,7 @@ def test_ac_cc_normalize():
deltat=1,
normalize=True,
copy=True,
- dtype=np.float_)
+ dtype=np.float64)
res.append(r)
res = np.concatenate(res)
@@ -80,7 +80,7 @@ def test_ac_cc_normalize():
deltat=1,
normalize=True,
copy=True,
- dtype=np.float_)
+ dtype=np.float64)
rescc.append(r)
rescc = np.concatenate(rescc)
@@ -102,7 +102,7 @@ def test_ac_cc_simple():
deltat=1,
normalize=False,
copy=True,
- dtype=np.float_)
+ dtype=np.float64)
rescc.append(r)
rescc = np.concatenate(rescc)
@@ -114,7 +114,7 @@ def test_ac_cc_simple():
deltat=1,
normalize=False,
copy=True,
- dtype=np.float_)
+ dtype=np.float64)
resac.append(r)
resac = np.concatenate(resac)
=====================================
tests/test_autocorrelate.py
=====================================
@@ -48,7 +48,7 @@ def test_ac_copy():
deltat=1,
normalize=True,
copy=True,
- dtype=np.float_)
+ dtype=np.float64)
res1.append(r)
res2 = []
@@ -58,7 +58,7 @@ def test_ac_copy():
deltat=1,
normalize=True,
copy=False,
- dtype=np.float_)
+ dtype=np.float64)
res2.append(r)
# simple test if result is the same
@@ -85,7 +85,7 @@ def test_ac_dtype():
deltat=1,
normalize=True,
copy=True,
- dtype=np.float_)
+ dtype=np.float64)
ri = multipletau.autocorrelate(a=a,
m=16,
@@ -102,9 +102,9 @@ def test_ac_dtype():
dtype=None)
assert ri.dtype == np.dtype(
- np.float_), "if wrong dtype, dtype should default to np.float_"
+ np.float64), "if wrong dtype, dtype should default to np.float64"
assert ri2.dtype == np.dtype(
- np.float_), "if wrong dtype, dtype should default to np.float_"
+ np.float64), "if wrong dtype, dtype should default to np.float64"
assert np.all(
rf == ri), "result should be the same, because input us the same"
assert np.all(
@@ -128,7 +128,7 @@ def test_ac_m():
deltat=1,
normalize=False,
copy=True,
- dtype=np.float_)
+ dtype=np.float64)
res.append(r)
# test minimal length of array
@@ -137,7 +137,7 @@ def test_ac_m():
deltat=1,
normalize=False,
copy=True,
- dtype=np.float_)
+ dtype=np.float64)
res = np.concatenate(res)
# np.save(os.path.dirname(__file__)
@@ -161,35 +161,35 @@ def test_ac_m_wrong():
deltat=1,
normalize=True,
copy=True,
- dtype=np.float_)
+ dtype=np.float64)
r2 = multipletau.autocorrelate(a=a,
m=15,
deltat=1,
normalize=True,
copy=True,
- dtype=np.float_)
+ dtype=np.float64)
r3 = multipletau.autocorrelate(a=a,
m=15.5,
deltat=1,
normalize=True,
copy=True,
- dtype=np.float_)
+ dtype=np.float64)
r4 = multipletau.autocorrelate(a=a,
m=14.5,
deltat=1,
normalize=True,
copy=True,
- dtype=np.float_)
+ dtype=np.float64)
r5 = multipletau.autocorrelate(a=a,
m=16.,
deltat=1,
normalize=True,
copy=True,
- dtype=np.float_)
+ dtype=np.float64)
assert np.all(r1 == r2)
assert np.all(r1 == r3)
assert np.all(r1 == r4)
@@ -210,7 +210,7 @@ def test_ac_normalize():
deltat=1,
normalize=True,
copy=True,
- dtype=np.float_)
+ dtype=np.float64)
res.append(r)
res = np.concatenate(res)
@@ -235,7 +235,7 @@ def test_ac_simple():
deltat=1,
normalize=False,
copy=True,
- dtype=np.float_)
+ dtype=np.float64)
res.append(r)
res = np.concatenate(res)
=====================================
tests/test_basic.py
=====================================
@@ -7,7 +7,7 @@ from multipletau import autocorrelate, correlate
def test_ac():
- ist = autocorrelate(range(42), m=2, dtype=np.float_)
+ ist = autocorrelate(range(42), m=2, dtype=np.float64)
soll = np.array([[0.00000000e+00, 2.38210000e+04],
[1.00000000e+00, 2.29600000e+04],
[2.00000000e+00, 2.21000000e+04],
@@ -17,7 +17,7 @@ def test_ac():
def test_cc():
- ist = correlate(range(42), range(1, 43), m=2, dtype=np.float_)
+ ist = correlate(range(42), range(1, 43), m=2, dtype=np.float64)
soll = np.array([[0.00000000e+00, 2.46820000e+04],
[1.00000000e+00, 2.38210000e+04],
[2.00000000e+00, 2.29600000e+04],
=====================================
tests/test_compress.py
=====================================
@@ -7,7 +7,7 @@ from multipletau import autocorrelate, correlate
def test_ac_compress_average():
- ist = autocorrelate(range(42), m=2, dtype=np.float_, compress="average")
+ ist = autocorrelate(range(42), m=2, dtype=np.float64, compress="average")
soll = np.array([[0.00000000e+00, 2.38210000e+04],
[1.00000000e+00, 2.29600000e+04],
[2.00000000e+00, 2.21000000e+04],
@@ -17,7 +17,7 @@ def test_ac_compress_average():
def test_cc_compress_average():
- ist = correlate(range(42), range(1, 43), m=2, dtype=np.float_,
+ ist = correlate(range(42), range(1, 43), m=2, dtype=np.float64,
compress="average")
soll = np.array([[0.00000000e+00, 2.46820000e+04],
[1.00000000e+00, 2.38210000e+04],
@@ -28,7 +28,7 @@ def test_cc_compress_average():
def test_ac_compress_first():
- ist = autocorrelate(range(42), m=2, dtype=np.float_,
+ ist = autocorrelate(range(42), m=2, dtype=np.float64,
compress="first")
soll = np.array([[0.00000e+00, 2.38210e+04],
[1.00000e+00, 2.29600e+04],
@@ -40,7 +40,7 @@ def test_ac_compress_first():
def test_cc_compress_first():
- ist = correlate(range(42), range(1, 43), m=2, dtype=np.float_,
+ ist = correlate(range(42), range(1, 43), m=2, dtype=np.float64,
compress="first")
soll = np.array([[0.00000e+00, 2.46820e+04],
[1.00000e+00, 2.38210e+04],
@@ -52,7 +52,7 @@ def test_cc_compress_first():
def test_ac_compress_second():
- ist = autocorrelate(range(42), m=2, dtype=np.float_,
+ ist = autocorrelate(range(42), m=2, dtype=np.float64,
compress="second")
soll = np.array([[0.00000e+00, 2.38210e+04],
[1.00000e+00, 2.29600e+04],
@@ -64,7 +64,7 @@ def test_ac_compress_second():
def test_cc_compress_second():
- ist = correlate(range(42), range(1, 43), m=2, dtype=np.float_,
+ ist = correlate(range(42), range(1, 43), m=2, dtype=np.float64,
compress="second")
soll = np.array([[0.00000e+00, 2.46820e+04],
[1.00000e+00, 2.38210e+04],
=====================================
tests/test_correlate.py
=====================================
@@ -84,7 +84,7 @@ def test_cc_dtype():
deltat=1,
normalize=True,
copy=True,
- dtype=np.float_)
+ dtype=np.float64)
ri = multipletau.correlate(a=a,
v=a,
@@ -103,9 +103,9 @@ def test_cc_dtype():
dtype=None)
assert ri.dtype == np.dtype(
- np.float_), "if wrong dtype, dtype should default to np.float_"
+ np.float64), "if wrong dtype, dtype should default to np.float64"
assert ri2.dtype == np.dtype(
- np.float_), "if wrong dtype, dtype should default to np.float_"
+ np.float64), "if wrong dtype, dtype should default to np.float64"
assert np.all(
rf == ri), "result should be the same, because input us the same"
assert np.all(
@@ -126,7 +126,7 @@ def test_cc_dtype2():
deltat=1,
normalize=True,
copy=True)
- assert np.dtype(rf.dtype) == np.dtype(np.complex_)
+ assert np.dtype(rf.dtype) == np.dtype(np.complex128)
rf2 = multipletau.correlate(a=a.real,
v=np.array(a.imag, dtype=np.int_),
@@ -134,7 +134,7 @@ def test_cc_dtype2():
deltat=1,
normalize=True,
copy=True)
- assert np.dtype(rf2.dtype) == np.dtype(np.float_)
+ assert np.dtype(rf2.dtype) == np.dtype(np.float64)
def test_cc_m():
@@ -155,7 +155,7 @@ def test_cc_m():
deltat=1,
normalize=False,
copy=True,
- dtype=np.complex_)
+ dtype=np.complex128)
res.append(r)
# test minimal length of array
@@ -165,7 +165,7 @@ def test_cc_m():
deltat=1,
normalize=False,
copy=True,
- dtype=np.complex_)
+ dtype=np.complex128)
res = np.concatenate(res)
# np.save(os.path.dirname(__file__)
@@ -240,7 +240,7 @@ def test_cc_normalize():
deltat=1,
normalize=True,
copy=True,
- dtype=np.float_)
+ dtype=np.float64)
res.append(r)
res = np.concatenate(res)
# np.save(os.path.dirname(__file__)
@@ -265,7 +265,7 @@ def test_cc_simple():
deltat=1,
normalize=False,
copy=True,
- dtype=np.complex_)
+ dtype=np.complex128)
res.append(r)
res = np.concatenate(res)
@@ -283,7 +283,7 @@ def test_cc_simple():
deltat=1,
normalize=False,
copy=True,
- dtype=np.complex_)
+ dtype=np.complex128)
res2.append(r)
res2 = np.concatenate(res2)
=====================================
tests/test_ref_numpy.py
=====================================
@@ -22,13 +22,13 @@ def test_corresponds_ac():
m=m,
copy=True,
normalize=True,
- dtype=np.float_)
+ dtype=np.float64)
reslin = multipletau.correlate_numpy(a=1*a,
v=1*a,
copy=True,
normalize=True,
- dtype=np.float_)
+ dtype=np.float64)
idx = np.array(restau[:, 0].real, dtype=int)[:m]
@@ -73,13 +73,13 @@ def test_corresponds_ac_first_loop():
m=m,
copy=True,
normalize=False,
- dtype=np.complex_)
+ dtype=np.complex128)
reslin = multipletau.correlate_numpy(a=a,
v=a.imag+1j*a.real,
copy=True,
normalize=False,
- dtype=np.complex_)
+ dtype=np.complex128)
idtau = np.where(restau[:, 0] == m+2)[0][0]
tau3 = restau[idtau, 1] # m+1 initial bins
@@ -102,13 +102,13 @@ def test_corresponds_ac_nonormalize():
m=m,
copy=True,
normalize=False,
- dtype=np.float_)
+ dtype=np.float64)
reslin = multipletau.correlate_numpy(a=1*a,
v=1*a,
copy=True,
normalize=False,
- dtype=np.float_)
+ dtype=np.float64)
idx = np.array(restau[:, 0].real, dtype=int)[:m+1]
@@ -128,13 +128,13 @@ def test_corresponds_cc():
m=m,
copy=True,
normalize=True,
- dtype=np.complex_)
+ dtype=np.complex128)
reslin = multipletau.correlate_numpy(a=a,
v=a.imag+1j*a.real,
copy=True,
normalize=True,
- dtype=np.complex_)
+ dtype=np.complex128)
idx = np.array(restau[:, 0].real, dtype=int)[:m+1]
@@ -154,13 +154,13 @@ def test_corresponds_cc_nonormalize():
m=m,
copy=True,
normalize=False,
- dtype=np.complex_)
+ dtype=np.complex128)
reslin = multipletau.correlate_numpy(a=a,
v=a.imag+1j*a.real,
copy=True,
normalize=False,
- dtype=np.complex_)
+ dtype=np.complex128)
idx = np.array(restau[:, 0].real, dtype=int)[:m+1]
=====================================
tests/test_ret_sum.py
=====================================
@@ -7,7 +7,7 @@ from multipletau import autocorrelate, correlate
def test_ac_return_sum():
- ist, ist_count = autocorrelate(range(42), m=2, dtype=np.float_,
+ ist, ist_count = autocorrelate(range(42), m=2, dtype=np.float64,
ret_sum=True)
soll = np.array([[0.000000e+00, 2.382100e+04],
[1.000000e+00, 2.296000e+04],
@@ -20,7 +20,7 @@ def test_ac_return_sum():
def test_cc_compress_average():
- ist, ist_count = correlate(range(42), range(1, 43), m=2, dtype=np.float_,
+ ist, ist_count = correlate(range(42), range(1, 43), m=2, dtype=np.float64,
ret_sum=True)
soll = np.array([[0.000000e+00, 2.468200e+04],
[1.000000e+00, 2.382100e+04],
View it on GitLab: https://salsa.debian.org/python-team/packages/python-multipletau/-/commit/04e5ef804917708d7b2afb62d2f6b7c10fd73c62
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