biolearn 0.0.0__tar.gz

biolearn-0.0.0/.binder/postBuild

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+#!/bin/bash
+
+# Adapted from scikit-learn
+# https://github.com/scikit-learn/scikit-learn/blob/main/.binder/
+
+set -e
+
+# This script is called in a binder context. When this script is called, we are
+# inside a git checkout of the omicslearn/omicslearn repo. This script is
+# generating notebooks from the omicslearn python examples.
+
+if [[ ! -f /.dockerenv ]]; then
+    echo "This script was written for repo2docker and is supposed to run inside a docker container."
+    echo "Exiting because this script can delete data if run outside of a docker container."
+    exit 1
+fi
+
+# Back up content we need from the nilearn repo
+TMP_CONTENT_DIR=/tmp/bio-learn
+mkdir -p $TMP_CONTENT_DIR
+cp -r examples .binder $TMP_CONTENT_DIR
+# delete everything in current directory including dot files and dot folders
+find . -delete
+
+# Generate notebooks and remove other files from examples folder
+GENERATED_NOTEBOOKS_DIR=.generated-notebooks
+cp -r $TMP_CONTENT_DIR/examples $GENERATED_NOTEBOOKS_DIR
+
+find $GENERATED_NOTEBOOKS_DIR -name '*.py' -exec sphx_glr_python_to_jupyter.py '{}' +
+NON_NOTEBOOKS=$(find $GENERATED_NOTEBOOKS_DIR -type f | grep -v '\.ipynb')
+rm -f $NON_NOTEBOOKS
+
+# Put the .binder folder back (may be useful for debugging purposes)
+mv $TMP_CONTENT_DIR/.binder .
+# Final clean up
+rm -rf $TMP_CONTENT_DIR
+
+# This is for compatibility with binder sphinx-gallery integration: this makes
+# sure that the binder links generated by sphinx-gallery are correct even tough
+# the repo we use for binder (nilearn/nilearn) is not the repo of the
+# generated doc (nilearn/nilearn.github.io)
+mkdir notebooks
+ln -s ../$GENERATED_NOTEBOOKS_DIR notebooks/auto_examples

biolearn-0.0.0/.binder/requirements.txt

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+.[plotting,plotly]
+sphinx-gallery

biolearn-0.0.0/.binder/runtime.txt

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+python - 3.10

biolearn-0.0.0/.coveragerc

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+[run]
+branch = True
+parallel = True
+omit =
+    */biolearn/tests/*
+    */biolearn/*/tests/*

biolearn-0.0.0/.flake8

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+[flake8]
+max-line-length = 100
+exclude = .git,__pycache__,doc/,docs/,build/,dist/,archive/
+per-file-ignores =
+  __init__.py:F401

biolearn-0.0.0/.gitignore

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+*.pyc
+
+# ignore python type annotation stubs for now
+*.pyi
+.pytest_cache
+
+# Mac OS X
+.DS_Store
+
+# IDE related
+.idea/
+.vscode/
+
+# build related
+biolearn.egg-info/
+build
+dist/
+biolearn/_version.py
+
+# coverage
+.coverage
+coverage
+nosetests_coverage/
+
+# documentation
+doc/_build
+doc/auto_examples
+doc/modules/generated

biolearn-0.0.0/AUTHORS.rst

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+.. -*- mode: rst -*-
+
+.. include:: changes/names.rst
+
+====
+Team
+====
+
+This work is made available by a community of people, which
+originated from
+the :BoA:`Biomarkers of Aging Consortium <>`
+
+.. _core_devs:
+
+Core developers
+...............
+
+The biolearn core developers are:
+
+* `Mahdi Moqri`_
+* `Martin Perez-Guevara`_
+* `Seth Paulson`_
+
+Other contributors
+..................
+
+Special thanks to scientific and executive members of the :BoA:`Biomarkers of Aging Consortium <>`

biolearn-0.0.0/LICENSE

@@ -0,0 +1,34 @@
+License for biolearn
+=====================
+
+New BSD License
+
+Copyright (c) 2007 - 2022 The omicslearn developers.
+All rights reserved.
+
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+  a. Redistributions of source code must retain the above copyright notice,
+     this list of conditions and the following disclaimer.
+  b. Redistributions in binary form must reproduce the above copyright
+     notice, this list of conditions and the following disclaimer in the
+     documentation and/or other materials provided with the distribution.
+  c. Neither the name of the omicslearn developers nor the names of
+     its contributors may be used to endorse or promote products
+     derived from this software without specific prior written
+     permission.
+
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGE.

biolearn-0.0.0/Makefile

@@ -0,0 +1,24 @@
+# simple makefile to simplify repetitive build env management tasks under posix
+# CAREFUL: several commands are not compatible with Windows shell
+
+PYTHON ?= python
+
+all: clean test
+
+clean-pyc:
+	find . -name "*.pyc" | xargs rm -f
+	find . -name "__pycache__" | xargs rm -rf
+
+clean-build:
+	rm -rf build
+
+clean: clean-build clean-pyc
+
+test-code:
+	python -m pytest --pyargs biolearn --cov=biolearn
+
+test-coverage:
+	rm -rf coverage .coverage
+	pytest --pyargs biolearn --showlocals --cov=biolearn --cov-report=html:coverage
+
+test: test-code

biolearn-0.0.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: biolearn
+Version: 0.0.0
+Summary: Machine learning for biomarkers computing
+Author: Biolearn developers
+Maintainer-email: Martin Perez-Guevara <mperezguevara@gmail.com>
+License: new BSD
+License-File: AUTHORS.rst
+License-File: LICENSE
+Keywords: biomarker
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: C
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Software Development
+Requires-Python: >=3.10
+Requires-Dist: numpy>=1.19.0
+Provides-Extra: dev
+Requires-Dist: biolearn[doc,plotting,test]; extra == 'dev'
+Provides-Extra: doc
+Requires-Dist: biolearn[plotting]; extra == 'doc'
+Requires-Dist: black; extra == 'doc'
+Requires-Dist: coverage; extra == 'doc'
+Requires-Dist: flake8; extra == 'doc'
+Requires-Dist: flake8-docstrings; extra == 'doc'
+Requires-Dist: furo; extra == 'doc'
+Requires-Dist: memory-profiler; extra == 'doc'
+Requires-Dist: mkl; extra == 'doc'
+Requires-Dist: myst-parser; extra == 'doc'
+Requires-Dist: numpydoc; extra == 'doc'
+Requires-Dist: sphinx; extra == 'doc'
+Requires-Dist: sphinx-copybutton; extra == 'doc'
+Requires-Dist: sphinx-design; extra == 'doc'
+Requires-Dist: sphinx-gallery; extra == 'doc'
+Requires-Dist: sphinxcontrib-bibtex; extra == 'doc'
+Requires-Dist: sphinxext-opengraph; extra == 'doc'
+Provides-Extra: plotting
+Requires-Dist: matplotlib>=3.3.0; extra == 'plotting'
+Provides-Extra: test
+Requires-Dist: coverage; extra == 'test'
+Requires-Dist: pytest-cov; extra == 'test'
+Requires-Dist: pytest>=6.0.0; extra == 'test'
+Description-Content-Type: text/x-rst
+
+Biolearn
+========
+
+Biolearn leverages the `scikit-learn <https://scikit-learn.org>`_ Python toolbox for biomarkers analysis
+
+Important links
+===============
+
+- Official source code repo: https://github.com/bio-learn/biolearn/
+- HTML documentation (stable release): https://bio-learn.github.io/
+
+Install
+=======
+
+Latest release
+--------------
+
+**1. Setup a virtual environment**
+
+We recommend that you install ``biolearn`` in a virtual Python environment.
+In linux as example you can create one with venv:
+
+.. code-block:: bash
+
+    python3 -m venv bioenv
+    source bioenv/bin/activate
+
+After you can install the package in the activated virtual environment:
+
+.. code-block:: bash
+
+    pip install -U biolearn
+
+Development version
+-------------------
+
+Please find all development setup instructions in the
+`contribution guide <https://bio-learn.github.io/stable/development.html#setting-up-your-environment>`_.
+
+Check installation
+------------------
+
+Try importing biolearn in a python / iPython session:
+
+.. code-block:: python
+
+    import biolearn
+
+If no error is raised, you have installed biolearn correctly.
+
+Discord server
+==============
+
+The biolearn team has a discord server to answer questions,
+discuss feature requests, or have any biolearn related discussions.
+
+For more information and ways to engage with the biolearn team see
+`How to get help <https://bio-learn.github.io/stable/development.html#how-to-get-help>`_.
+
+Dependencies
+============
+
+The required dependencies to use the software are listed in the file `pyproject.toml <https://github.com/bio-learn/biolearn/blob/main/pyproject.toml>`_.
+
+If you are using biolearn plotting functionalities or running the examples, matplotlib >= 3.3.0 is required.
+
+Some plotting functions in biolearn support both matplotlib and plotly as plotting engines.
+
+If you want to run the tests, you need pytest >= 6.0.0 and pytest-cov for coverage reporting.
+
+Development
+===========
+
+Detailed instructions on how to contribute are available at
+http://bio-learn.github.io/stable/development.html

biolearn-0.0.0/README.rst

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+Biolearn
+========
+
+Biolearn leverages the `scikit-learn <https://scikit-learn.org>`_ Python toolbox for biomarkers analysis
+
+Important links
+===============
+
+- Official source code repo: https://github.com/bio-learn/biolearn/
+- HTML documentation (stable release): https://bio-learn.github.io/
+
+Install
+=======
+
+Latest release
+--------------
+
+**1. Setup a virtual environment**
+
+We recommend that you install ``biolearn`` in a virtual Python environment.
+In linux as example you can create one with venv:
+
+.. code-block:: bash
+
+    python3 -m venv bioenv
+    source bioenv/bin/activate
+
+After you can install the package in the activated virtual environment:
+
+.. code-block:: bash
+
+    pip install -U biolearn
+
+Development version
+-------------------
+
+Please find all development setup instructions in the
+`contribution guide <https://bio-learn.github.io/stable/development.html#setting-up-your-environment>`_.
+
+Check installation
+------------------
+
+Try importing biolearn in a python / iPython session:
+
+.. code-block:: python
+
+    import biolearn
+
+If no error is raised, you have installed biolearn correctly.
+
+Discord server
+==============
+
+The biolearn team has a discord server to answer questions,
+discuss feature requests, or have any biolearn related discussions.
+
+For more information and ways to engage with the biolearn team see
+`How to get help <https://bio-learn.github.io/stable/development.html#how-to-get-help>`_.
+
+Dependencies
+============
+
+The required dependencies to use the software are listed in the file `pyproject.toml <https://github.com/bio-learn/biolearn/blob/main/pyproject.toml>`_.
+
+If you are using biolearn plotting functionalities or running the examples, matplotlib >= 3.3.0 is required.
+
+Some plotting functions in biolearn support both matplotlib and plotly as plotting engines.
+
+If you want to run the tests, you need pytest >= 6.0.0 and pytest-cov for coverage reporting.
+
+Development
+===========
+
+Detailed instructions on how to contribute are available at
+http://bio-learn.github.io/stable/development.html

biolearn-0.0.0/biolearn/__init__.py

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+try:
+    from ._version import __version__  # noqa: F401
+except ImportError:
+    __version__ = "0+unknown"
+
+# list all submodules available in omicslearn and version
+__all__ = [
+    "__version__",
+]

biolearn-0.0.0/biolearn/_utils/__init__.py

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+from .docs import fill_doc
+
+__all__ = ['fill_doc']