normi 0.1.0__tar.gz

normi-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2023 Biomolecular Dynamics
+
+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.

normi-0.1.0/MANIFEST.in

@@ -0,0 +1 @@
+include extra-requirements.txt

normi-0.1.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: normi
+Version: 0.1.0
+Summary: Estimator for Normalized Mutual Information
+Home-page: https://github.com/moldyn/NorMI
+Author: braniii
+License: MIT License
+Project-URL: Documentation, https://moldyn.github.io/NorMI
+Project-URL: Source Code, https://github.com/moldyn/NorMI
+Project-URL: Changelog, https://moldyn.github.io/NorMI/changelog
+Project-URL: Bug Tracker, https://github.com/moldyn/NorMI/issues
+Keywords: normalized mutual information,mutual information,Kraskov Estimator,KSG Estimator
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Intended Audience :: Science/Research
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.21.0
+Requires-Dist: scipy
+Requires-Dist: click>=8.0.0
+Requires-Dist: beartype>=0.10.4
+Requires-Dist: tqdm
+Requires-Dist: scikit-learn>=1.0.0
+Requires-Dist: typing_extensions>=3.9.0; python_version < "3.9"
+Provides-Extra: testing
+Requires-Dist: pytest-cov; extra == "testing"
+Requires-Dist: pytest-rerunfailures; extra == "testing"
+Requires-Dist: flake8; extra == "testing"
+Requires-Dist: pytest; extra == "testing"
+Provides-Extra: coding
+Requires-Dist: wemake-python-styleguide; extra == "coding"
+Provides-Extra: docs
+Requires-Dist: mkdocs-click; extra == "docs"
+Requires-Dist: mkdocstrings; extra == "docs"
+Requires-Dist: mkdocs-section-index; extra == "docs"
+Requires-Dist: mkdocs-gen-files; extra == "docs"
+Requires-Dist: mkdocs-literate-nav; extra == "docs"
+Requires-Dist: mkdocstrings-python; extra == "docs"
+Requires-Dist: mkdocs-material; extra == "docs"
+Provides-Extra: all
+Requires-Dist: mkdocs-click; extra == "all"
+Requires-Dist: pytest-rerunfailures; extra == "all"
+Requires-Dist: flake8; extra == "all"
+Requires-Dist: pytest-cov; extra == "all"
+Requires-Dist: pytest; extra == "all"
+Requires-Dist: mkdocstrings; extra == "all"
+Requires-Dist: wemake-python-styleguide; extra == "all"
+Requires-Dist: mkdocs-section-index; extra == "all"
+Requires-Dist: mkdocs-gen-files; extra == "all"
+Requires-Dist: mkdocs-literate-nav; extra == "all"
+Requires-Dist: mkdocstrings-python; extra == "all"
+Requires-Dist: mkdocs-material; extra == "all"
+
+<div align="center">
+  <!--
+  
+  <img class="lightmode" style="width: 400px;" src="https://github.com/moldyn/normi/blob/main/docs/logo_large_light.svg?raw=true#gh-light-mode-only" />
+  -->
+
+  <p>
+    <a href="https://github.com/wemake-services/wemake-python-styleguide" alt="wemake-python-styleguide">
+        <img src="https://img.shields.io/badge/style-wemake-000000.svg" /></a>
+    <a href="https://beartype.rtfd.io" alt="bear-ified">
+        <img src="https://raw.githubusercontent.com/beartype/beartype-assets/main/badge/bear-ified.svg" /></a>
+    <a href="https://pypi.org/project/normi" alt="PyPI">
+        <img src="https://img.shields.io/pypi/v/normi" /></a>
+    <a href="https://anaconda.org/conda-forge/normi" alt="conda version">
+	<img src="https://img.shields.io/conda/vn/conda-forge/normi" /></a>
+    <a href="https://pepy.tech/project/normi" alt="Downloads">
+        <img src="https://static.pepy.tech/badge/normi" /></a>
+    <a href="https://github.com/moldyn/normi/actions/workflows/pytest.yml" alt="GitHub Workflow Status">
+        <img src="https://img.shields.io/github/actions/workflow/status/moldyn/normi/pytest.yml?branch=main"></a>
+    <a href="https://codecov.io/gh/moldyn/normi" alt="Code coverage">
+        <img src="https://codecov.io/gh/moldyn/normi/branch/main/graph/badge.svg?token=KNWDAUXIGI" /></a>
+    <a href="https://github.com/moldyn/normi/actions/workflows/codeql.yml" alt="CodeQL">
+        <img src="https://github.com/moldyn/normi/actions/workflows/codeql.yml/badge.svg?branch=main" /></a>
+    <a href="https://img.shields.io/pypi/pyversions/normi" alt="PyPI - Python Version">
+        <img src="https://img.shields.io/pypi/pyversions/normi" /></a>
+    <a href="https://moldyn.github.io/normi" alt="Docs">
+        <img src="https://img.shields.io/badge/MkDocs-Documentation-brightgreen" /></a>
+    <a href="https://github.com/moldyn/normi/blob/main/LICENSE" alt="License">
+        <img src="https://img.shields.io/github/license/moldyn/normi" /></a>
+  </p>
+
+  <p>
+    <a href="https://moldyn.github.io/normi">Docs</a> •
+    <a href="#features">Features</a> •
+    <a href="#installation">Installation</a> •
+    <a href="#usage">Usage</a> •
+    <a href="https://moldyn.github.io/normi/faq">FAQ</a>
+  </p>
+</div>
+
+# NorMI: Nonparametric Normalized Mutual Information Estimator Based on $k$-NN Statistics
+This software provides an extension to the Kraskov-Estimator to allow normalizing the mutual information.
+
+The method will be published soon as:
+> **Adaptive Entropy-Based Normalization for (High-Dimensional) Mutual Information**
+> D. Nagel, G. Diez, and G. Stock,  
+
+If you use this software package, please cite the above mentioned paper.
+
+## Features
+- Intuitive usage via [module](#module---inside-a-python-script) and via [CI](#ci---usage-directly-from-the-command-line)
+- Sklearn-style API for fast integration into your Python workflow
+- No magic, only a  single parameter which can be optimized via cross-validation
+- Extensive [documentation](https://moldyn.github.io/normi) and detailed discussion in publication
+
+## Installation
+<!--
+The package is called `normi` and is available via [PyPI](https://pypi.org/project/normi) or [conda](https://anaconda.org/conda-forge/normi). To install it, simply call:
+```bash
+python3 -m pip install --upgrade normi
+```
+or
+```
+conda install -c conda-forge normi
+```
+or for the latest dev version
+-->
+The package is not yet published and only available directly from github
+```bash
+# via ssh key
+python3 -m pip install git+ssh://git@github.com/moldyn/normi.git
+
+# or via password-based login
+python3 -m pip install git+https://github.com/moldyn/normi.git
+```
+
+### Shell Completion
+Using the `bash`, `zsh` or `fish` shell click provides an easy way to provide shell completion, checkout the [docs](https://click.palletsprojects.com/en/8.0.x/shell-completion).
+In the case of bash you need to add following line to your `~/.bashrc`
+```bash
+eval "$(_NORMALIZED_MI_COMPLETE=bash_source normi)"
+```
+
+## Usage
+In general one can call the module directly by its entry point `$ normi` or by calling the module `$ python -m normi`. The latter method is preferred to ensure using the desired python environment. For enabling the shell completion, the entry point needs to be used.
+
+### CI - Usage Directly from the Command Line
+The module brings a rich CI using [click](https://click.palletsprojects.com).
+Each module and submodule contains a detailed help, which can be accessed by
+...
+
+tba
+
+### Module - Inside a Python Script
+```python
+from normi import NormalizedMI
+
+# Load file
+# X is np.ndarray of shape (n_samples, n_features)
+
+nmi = NormalizedMI()
+nmi.fit(X)
+...
+```

normi-0.1.0/README.md

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+<div align="center">
+  <!--
+  <img class="darkmode" style="width: 400px;" src="https://github.com/moldyn/normi/blob/main/docs/logo_large_dark.svg?raw=true#gh-dark-mode-only" />
+  <img class="lightmode" style="width: 400px;" src="https://github.com/moldyn/normi/blob/main/docs/logo_large_light.svg?raw=true#gh-light-mode-only" />
+  -->
+
+  <p>
+    <a href="https://github.com/wemake-services/wemake-python-styleguide" alt="wemake-python-styleguide">
+        <img src="https://img.shields.io/badge/style-wemake-000000.svg" /></a>
+    <a href="https://beartype.rtfd.io" alt="bear-ified">
+        <img src="https://raw.githubusercontent.com/beartype/beartype-assets/main/badge/bear-ified.svg" /></a>
+    <a href="https://pypi.org/project/normi" alt="PyPI">
+        <img src="https://img.shields.io/pypi/v/normi" /></a>
+    <a href="https://anaconda.org/conda-forge/normi" alt="conda version">
+	<img src="https://img.shields.io/conda/vn/conda-forge/normi" /></a>
+    <a href="https://pepy.tech/project/normi" alt="Downloads">
+        <img src="https://static.pepy.tech/badge/normi" /></a>
+    <a href="https://github.com/moldyn/normi/actions/workflows/pytest.yml" alt="GitHub Workflow Status">
+        <img src="https://img.shields.io/github/actions/workflow/status/moldyn/normi/pytest.yml?branch=main"></a>
+    <a href="https://codecov.io/gh/moldyn/normi" alt="Code coverage">
+        <img src="https://codecov.io/gh/moldyn/normi/branch/main/graph/badge.svg?token=KNWDAUXIGI" /></a>
+    <a href="https://github.com/moldyn/normi/actions/workflows/codeql.yml" alt="CodeQL">
+        <img src="https://github.com/moldyn/normi/actions/workflows/codeql.yml/badge.svg?branch=main" /></a>
+    <a href="https://img.shields.io/pypi/pyversions/normi" alt="PyPI - Python Version">
+        <img src="https://img.shields.io/pypi/pyversions/normi" /></a>
+    <a href="https://moldyn.github.io/normi" alt="Docs">
+        <img src="https://img.shields.io/badge/MkDocs-Documentation-brightgreen" /></a>
+    <a href="https://github.com/moldyn/normi/blob/main/LICENSE" alt="License">
+        <img src="https://img.shields.io/github/license/moldyn/normi" /></a>
+  </p>
+
+  <p>
+    <a href="https://moldyn.github.io/normi">Docs</a> •
+    <a href="#features">Features</a> •
+    <a href="#installation">Installation</a> •
+    <a href="#usage">Usage</a> •
+    <a href="https://moldyn.github.io/normi/faq">FAQ</a>
+  </p>
+</div>
+
+# NorMI: Nonparametric Normalized Mutual Information Estimator Based on $k$-NN Statistics
+This software provides an extension to the Kraskov-Estimator to allow normalizing the mutual information.
+
+The method will be published soon as:
+> **Adaptive Entropy-Based Normalization for (High-Dimensional) Mutual Information**
+> D. Nagel, G. Diez, and G. Stock,  
+
+If you use this software package, please cite the above mentioned paper.
+
+## Features
+- Intuitive usage via [module](#module---inside-a-python-script) and via [CI](#ci---usage-directly-from-the-command-line)
+- Sklearn-style API for fast integration into your Python workflow
+- No magic, only a  single parameter which can be optimized via cross-validation
+- Extensive [documentation](https://moldyn.github.io/normi) and detailed discussion in publication
+
+## Installation
+<!--
+The package is called `normi` and is available via [PyPI](https://pypi.org/project/normi) or [conda](https://anaconda.org/conda-forge/normi). To install it, simply call:
+```bash
+python3 -m pip install --upgrade normi
+```
+or
+```
+conda install -c conda-forge normi
+```
+or for the latest dev version
+-->
+The package is not yet published and only available directly from github
+```bash
+# via ssh key
+python3 -m pip install git+ssh://git@github.com/moldyn/normi.git
+
+# or via password-based login
+python3 -m pip install git+https://github.com/moldyn/normi.git
+```
+
+### Shell Completion
+Using the `bash`, `zsh` or `fish` shell click provides an easy way to provide shell completion, checkout the [docs](https://click.palletsprojects.com/en/8.0.x/shell-completion).
+In the case of bash you need to add following line to your `~/.bashrc`
+```bash
+eval "$(_NORMALIZED_MI_COMPLETE=bash_source normi)"
+```
+
+## Usage
+In general one can call the module directly by its entry point `$ normi` or by calling the module `$ python -m normi`. The latter method is preferred to ensure using the desired python environment. For enabling the shell completion, the entry point needs to be used.
+
+### CI - Usage Directly from the Command Line
+The module brings a rich CI using [click](https://click.palletsprojects.com).
+Each module and submodule contains a detailed help, which can be accessed by
+...
+
+tba
+
+### Module - Inside a Python Script
+```python
+from normi import NormalizedMI
+
+# Load file
+# X is np.ndarray of shape (n_samples, n_features)
+
+nmi = NormalizedMI()
+nmi.fit(X)
+...
+```

normi-0.1.0/extra-requirements.txt

@@ -0,0 +1,14 @@
+# Extra requirements
+# package[version_required]: tag1, tag2, ...
+flake8:                       testing
+wemake-python-styleguide:     coding
+pytest:                       testing
+pytest-cov:                   testing
+pytest-rerunfailures:         testing
+mkdocs-material:              docs
+mkdocstrings:                 docs
+mkdocstrings-python:          docs
+mkdocs-literate-nav:          docs
+mkdocs-gen-files:             docs
+mkdocs-section-index:         docs
+mkdocs-click:                 docs

normi-0.1.0/setup.cfg

@@ -0,0 +1,44 @@
+[tool:pytest]
+addopts = 
+	--strict-markers
+	--doctest-modules
+	--reruns 5
+	--reruns-delay 1
+	--cov-report=term-missing
+	--cov=src/normi tests/
+
+[flake8]
+format = wemake
+show-source = True
+statistics = True
+doctests = True
+max-complexity = 10
+count = True
+dictionaries = en_US, python, technical
+spellcheck-targets = comments
+rst-roles = class, func, ref
+rst-directives = todo
+ignore = 
+	S101, C101, N, DAR401, DAR402, W504,
+	WPS306, WPS352, WPS120, WPS111, WPS305, WPS326, WPS115
+exclude = .git, src/*/__pycache__, docs, build, dist
+per-file-ignores = 
+	src/*/__init__.py:F401, F403, D104, D400, E501
+	setup.py:D100
+	tests/*.py:WPS, DAR101, DAR201
+
+[isort]
+include_trailing_comma = true
+multi_line_output = 3
+line_length = 79
+skip = src/*/__init__.py
+
+[darglint]
+strictness = short
+docstring_style = numpy
+ignore_regex = ^_(.*)
+
+[egg_info]
+tag_build = 
+tag_date = 0
+

normi-0.1.0/setup.py

@@ -0,0 +1,113 @@
+# -*- coding: utf-8 -*-
+import pathlib
+import sys
+from collections import defaultdict
+
+import setuptools
+
+# check for python version
+if sys.version_info < (3, 8):
+    raise SystemExit('Python 3.8+ is required!')
+
+
+def get_extra_requirements(path, add_all=True):
+    """Parse extra-requirements file."""
+    with open(path) as depfile:
+        extra_deps = defaultdict(set)
+        for line in depfile:
+            if not line.startswith('#'):
+                if ':' not in line:
+                    raise ValueError(
+                        f'Dependency in {path} not correct formatted: {line}',
+                    )
+                dep, tags = line.split(':')
+                tags = {tag.strip() for tag in tags.split(',')}
+                for tag in tags:
+                    extra_deps[tag].add(dep)
+
+        # add tag `all` at the end
+        if add_all:
+            extra_deps['all'] = {
+                tag for tags in extra_deps.values() for tag in tags
+            }
+
+    return extra_deps
+
+
+def remove_gh_dark_mode_only_tags(text, tag='#gh-dark-mode-only'):
+    """Remove recursively all """
+    idx = text.find(tag)
+    if idx < 0:
+        return text
+
+    idx_tag_end = text.find('>', idx)
+    idx_tag_start = text.rfind('<', 0, idx)
+    return remove_gh_dark_mode_only_tags(
+        text[:idx_tag_start] + text[idx_tag_end + 1:], tag,
+    )
+
+
+# The directory containing this file
+HERE = pathlib.Path(__file__).parent
+
+# The text of the README file
+README = remove_gh_dark_mode_only_tags(
+    (HERE / 'README.md').read_text(),
+)
+
+# This call to setup() does all the work
+setuptools.setup(
+    name='normi',
+    version='0.1.0',
+    description='Estimator for Normalized Mutual Information',
+    long_description=README,
+    long_description_content_type='text/markdown',
+    keywords=[
+        'normalized mutual information',
+        'mutual information',
+        'Kraskov Estimator',
+        'KSG Estimator',
+    ],
+    author='braniii',
+    url='https://github.com/moldyn/NorMI',
+    license='MIT License',
+    classifiers=[
+        'License :: OSI Approved :: MIT License',
+        'Intended Audience :: Science/Research',
+        'Natural Language :: English',
+        'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
+        'Programming Language :: Python :: 3.10',
+        'Programming Language :: Python :: 3.11',
+        'Topic :: Scientific/Engineering :: Bio-Informatics',
+        'Topic :: Scientific/Engineering :: Information Analysis',
+        'Topic :: Scientific/Engineering :: Physics',
+        'Topic :: Software Development :: Libraries :: Python Modules',
+    ],
+    project_urls={
+        'Documentation': 'https://moldyn.github.io/NorMI',
+        'Source Code': 'https://github.com/moldyn/NorMI',
+        'Changelog': 'https://moldyn.github.io/NorMI/changelog',
+        'Bug Tracker': 'https://github.com/moldyn/NorMI/issues',
+    },
+    package_dir={'': 'src'},
+    packages=setuptools.find_packages(where='src'),
+    include_package_data=True,
+    python_requires='>=3.8',
+    entry_points={
+        'console_scripts': [
+            'normi = normi.__main__:main',
+        ],
+    },
+    install_requires=[
+        'numpy>=1.21.0',
+        'scipy',
+        'click>=8.0.0',
+        'beartype>=0.10.4',
+        'tqdm',
+        'scikit-learn>=1.0.0',
+        'typing_extensions>=3.9.0;python_version<"3.9"',
+    ],
+    extras_require=get_extra_requirements('extra-requirements.txt'),
+)

normi-0.1.0/src/normi/__init__.py

@@ -0,0 +1,11 @@
+# -*- coding: utf-8 -*-
+"""Normalized mutual information"""
+__all__ = ['NormalizedMI']
+
+NORMS = {'joint', 'geometric', 'arithmetic', 'min', 'max'}
+INVMEASURES = {'radius', 'volume', 'kraskov'}
+
+from ._estimators import NormalizedMI
+
+
+__version__ = '0.1.0'

normi-0.1.0/src/normi/__main__.py

@@ -0,0 +1,130 @@
+"""CLI of normalized-mi.
+
+MIT License
+Copyright (c) 2023, Daniel Nagel
+All rights reserved.
+
+"""
+import click
+import numpy as np
+
+from normi import INVMEASURES, NORMS, NormalizedMI, __version__
+from normi._utils import savetxt
+
+# setup matplotlibs rcParam
+
+PRECISION = ['half', 'single', 'double']
+PRECISION_TO_DTYPE = {
+    'half': np.float16,
+    'single': np.float32,
+    'double': np.float64,
+}
+
+HELP_STR = f"""Normalized MI v{__version__}
+
+\b
+Estimating the normalized mutual information based on k-nn statistics.
+Copyright (c) 2023, Daniel Nagel
+"""
+
+
+@click.command(
+    help='Estimating NMI matrix of coordinates.',
+    no_args_is_help=True,
+)
+@click.option(
+    '-i',
+    '--input',
+    'input_file',
+    required=True,
+    type=click.Path(exists=True),
+    help=(
+        'Path to input file. Needs to be of shape (n_samples, n_features).'
+        ' All command lines need to start with "#". By default np.float16'
+        ' is used for the datatype.'
+    ),
+)
+@click.option(
+    '-o',
+    '--output',
+    'output_basename',
+    required=True,
+    type=click.Path(),
+    help=(
+        'Path to output basename. Will be a matrix of shape (n_features, '
+        'n_features).'
+    ),
+)
+@click.option(
+    '--norm',
+    default='joint',
+    show_default=True,
+    type=click.Choice(NORMS, case_sensitive=False),
+    help='Normalization method of the mutual information.',
+)
+@click.option(
+    '--inv-measure',
+    default='radius',
+    show_default=True,
+    type=click.Choice(INVMEASURES, case_sensitive=False),
+    help='Invariant measure to rescale the entropies.',
+)
+@click.option(
+    '--n-dims',
+    default=1,
+    show_default=True,
+    type=click.IntRange(min=1),
+    help=(
+        'Dimension of each feature. Assumes the first nth colums belong to the'
+        ' first feature.'
+    ),
+)
+@click.option(
+    '--precision',
+    default='single',
+    show_default=True,
+    type=click.Choice(PRECISION, case_sensitive=True),
+    help=(
+        'Precision used for calculation. Lower precision reduces memory '
+        'impact but may lead to overflow errors.'
+    ),
+)
+@click.option(
+    '-v',
+    '--verbose',
+    is_flag=True,
+    help='Activate verbose mode.',
+)
+def main(
+    input_file, output_basename, norm, inv_measure, n_dims, precision, verbose,
+):
+    # load file
+    if verbose:
+        click.echo(f'\nNormalized MI\n~~~ Load file: {input_file}')
+    features = np.loadtxt(input_file, dtype=PRECISION_TO_DTYPE[precision])
+
+    if verbose:
+        click.echo('~~~ Initialize class')
+    nmi = NormalizedMI(
+        normalize_method=norm,
+        invariant_measure=inv_measure,
+        verbose=verbose,
+        n_dims=n_dims,
+    )
+    if verbose:
+        click.echo('~~~ Fit class')
+    nmi.fit(features)
+
+    # save results
+    if verbose:
+        click.echo(f'~~~ Save files: {output_basename}.nmi/.mi/.hxy/.hx/.hy')
+    kwargs = {'fmt': '%.5f'}
+    savetxt(f'{output_basename}.nmi', nmi.nmi_, **kwargs)
+    savetxt(f'{output_basename}.mi', nmi.mi_, **kwargs)
+    savetxt(f'{output_basename}.hx', nmi.hx_, **kwargs)
+    savetxt(f'{output_basename}.hy', nmi.hy_, **kwargs)
+    savetxt(f'{output_basename}.hxy', nmi.hxy_, **kwargs)
+
+
+if __name__ == '__main__':
+    main()