pseudopeople 0.1.0__tar.gz

pseudopeople-0.1.0/CHANGELOG.rst

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+**0.1.0 - 03/23/23**
+
+ - Initial release
+ - Implemented generate_decennial_census with missing data noise function
+ - Implemented custom user configuration override

pseudopeople-0.1.0/CODE_OF_CONDUCT.rst

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+Code of Conduct
+===============
+
+Our Pledge
+----------
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, gender identity and expression, level of experience,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+Our Standards
+-------------
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+- Using welcoming and inclusive language
+- Being respectful of differing viewpoints and experiences
+- Gracefully accepting constructive criticism
+- Focusing on what is best for the community
+- Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+- The use of sexualized language or imagery and unwelcome sexual attention or
+  advances
+- Trolling, insulting/derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+- Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+Our Responsibilities
+--------------------
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers 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, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+Scope
+-----
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+Enforcement
+-----------
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the current maintainer (found in this repositories AUTHORS.md). All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+Attribution
+-----------
+
+This Code of Conduct is adapted from the `Contributor Covenant`_, version 1.4,
+available at `version`_.
+
+.. _Contributor Covenant: http://contributor-covenant.org
+.. _version: http://contributor-covenant.org/version/1/4/

pseudopeople-0.1.0/CONTRIBUTING.rst

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+Contributing
+============
+
+When contributing to this repository, please first discuss the change you wish to make via issue,
+email, or any other method with the owners of this repository before making a change.
+
+Please note we have a code of conduct, please follow it in all your interactions with the project.
+
+Submitting Changes
+------------------
+
+- Always make a new branch for your work.
+- Patches should be small to facilitate easier review. Sometimes this will result in many small
+  PRs to land a single large feature.
+- Larger changes should be discussed in the project's GitHub issues page.
+- New features and significant bug fixes should be documented in the changelog.
+- You must have legal permission to distribute any code you contribute to ``pseudopeople``, and it
+  must be available under the BSD-3 license.
+

pseudopeople-0.1.0/LICENSE

@@ -0,0 +1,28 @@
+BSD 3-Clause License
+
+Copyright (c) 2023, Institute for Health Metrics and Evaluation
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. 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.
+
+3. Neither the name of the copyright holder 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 COPYRIGHT HOLDER 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.

pseudopeople-0.1.0/MANIFEST.in

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+include AUTHORS.rst
+include CHANGELOG.rst
+include CODE_OF_CONDUCT.rst
+include CONTRIBUTING.rst
+include LICENSE.txt
+include README.rst
+
+recursive-include docs *
+prune docs/_build
+
+recursive-include src/pseudopeople *.py *.yaml
+recursive-include tests *.py *txt *.yaml

pseudopeople-0.1.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: pseudopeople
+Version: 0.1.0
+Summary: pseudopeople is package which adds noise to simulated census-scale data using standard scientific Python tools.
+Home-page: https://github.com/ihmeuw/pseudopeople
+Author: The pseudopeople developers
+Author-email: vivarium.dev@gmail.com
+License: BSD-3-Clause
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Education
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
+Classifier: Natural Language :: English
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Operating System :: POSIX
+Classifier: Operating System :: POSIX :: BSD
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Topic :: Education
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Artificial Life
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Classifier: Topic :: Software Development :: Libraries
+Provides-Extra: docs
+Provides-Extra: test
+Provides-Extra: interactive
+Provides-Extra: dev
+License-File: LICENSE
+
+============
+Pseudopeople
+============
+
+Pseudopeople is a package intended to add configurable noise to a simulated
+census-scale data-set written using standard scientific Python tools.
+
+**Pseudopeople requires Python 3.7-3.10 to run**
+
+You can install ``pseudopeople`` from PyPI with pip:
+
+  ``> pip install pseudopeople``
+
+or build it from source with
+
+  ``> git clone https://github.com/ihmeuw/pseudopeople.git``
+
+  ``> cd pseudopeople``
+
+  ``> python setup.py install``
+
+This will make the ``pseudopeople`` library available to python and install a
+command-line executable called ``...`` that you can use to verify your
+installation with
+
+  ``> ... test``

pseudopeople-0.1.0/README.rst

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+============
+Pseudopeople
+============
+
+Pseudopeople is a package intended to add configurable noise to a simulated
+census-scale data-set written using standard scientific Python tools.
+
+**Pseudopeople requires Python 3.7-3.10 to run**
+
+You can install ``pseudopeople`` from PyPI with pip:
+
+  ``> pip install pseudopeople``
+
+or build it from source with
+
+  ``> git clone https://github.com/ihmeuw/pseudopeople.git``
+
+  ``> cd pseudopeople``
+
+  ``> python setup.py install``
+
+This will make the ``pseudopeople`` library available to python and install a
+command-line executable called ``...`` that you can use to verify your
+installation with
+
+  ``> ... test``

pseudopeople-0.1.0/docs/Makefile

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+# Minimal makefile for Sphinx documentation
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = pseudopeople
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+clean:
+	rm -rf build/*

pseudopeople-0.1.0/docs/nitpick-exceptions

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+# pandas
+py:class pandas.core.indexes.base.Index
+py:class pandas.core.indexes.multi.MultiIndex
+py:class pandas._libs.tslibs.timestamps.Timestamp
+py:class pandas._libs.tslibs.timedeltas.Timedelta
+py:class pandas.core.frame.DataFrame
+py:class pandas.core.series.Series
+py:class pandas.core.generic.PandasObject

pseudopeople-0.1.0/docs/source/_static/style.css

@@ -0,0 +1,3 @@
+.wy-nav-content {
+    max-width: 1000px !important;
+}

pseudopeople-0.1.0/docs/source/_templates/layout.html

@@ -0,0 +1,4 @@
+{% extends "!layout.html" %}
+{% block extrahead %}
+    <link href="{{ pathto("_static/style.css", True) }}" rel="stylesheet" type="text/css">
+{% endblock %}

pseudopeople-0.1.0/docs/source/api_reference/index.rst

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+API Reference
+=============
+
+.. automodule:: pseudopeople
+
+.. toctree::
+   :maxdepth: 2
+   :glob:
+
+   *

pseudopeople-0.1.0/docs/source/api_reference/interface.rst

@@ -0,0 +1 @@
+.. automodule:: pseudopeople.interface

pseudopeople-0.1.0/docs/source/concepts/configuration.rst

@@ -0,0 +1,16 @@
+.. _configuration_concept:
+
+========================
+The Configuration System
+========================
+
+.. contents::
+   :depth: 2
+   :local:
+   :backlinks: none
+
+Outline
+-------
+ - Configuration is hierarchical
+ - Configuration sources and priorities
+ - Specifying defaults.

pseudopeople-0.1.0/docs/source/concepts/forms.rst

@@ -0,0 +1,33 @@
+.. _forms_concept:
+
+===============
+     Forms
+===============
+
+.. contents::
+   :depth: 2
+   :local:
+   :backlinks: none
+
+
+
+
+What is a form?
+---------------
+
+A form in the Pseudopeople framework is analogous to a dataset representing
+a census survey or tax document.  The types of forms that are compatible with
+the Pseudopeople framework include:
+
+.. list-table:: **Types of Forms**
+   :header-rows: 1
+   :widths: 20
+
+   * - Name
+   * - | Decennial census
+   * - | American communities survey
+   * - | Current population survey
+   * - | Women, infrants, and children survey
+   * - | Social security
+   * - | Tax W2 and 1099 forms
+   * - | Tax 1040 form

pseudopeople-0.1.0/docs/source/concepts/index.rst

@@ -0,0 +1,13 @@
+.. _concepts_main:
+
+========
+Concepts
+========
+Here we cover several core conceptual topics related to working with
+the Pseudopeople framework.
+
+.. toctree::
+   :glob:
+   :maxdepth: 1
+
+   *

pseudopeople-0.1.0/docs/source/concepts/noise_functions.rst

@@ -0,0 +1,42 @@
+.. _noise_functions_concept:
+
+=================
+ Noise Functions
+=================
+
+.. contents::
+   :depth: 2
+   :local:
+   :backlinks: none
+
+
+
+
+What is a noise function?
+-------------------------
+
+A noise function is ultimately where the configuration (add link) provided is
+applied to the raw data which is then noised or altered and returned to the user
+in a state where real world data error have been added to each form (add link).
+Noise functions will be applied to datasets by column or by row.  There are
+several noise functions that are applied to the raw data which include:
+
+.. list-table:: **Noise Functions**
+   :header-rows: 1
+   :widths: 20
+
+   * - Name
+   * - | Omission
+   * - | Duplications
+   * - | Missing data
+   * - | Incorrect selection
+   * - | Copy from within household
+   * - | Month and day swaps (applies to dates only)
+   * - | Zip Code Miswriting (applies to Zip Code only)
+   * - | Age Miswriting (applies to age only)
+   * - | Numeric miswriting
+   * - | Nicknames
+   * - | Fake names
+   * - | Phonetic errors
+   * - | OCR (optical character recognition)
+   * - | Typographic

pseudopeople-0.1.0/docs/source/conf.py

@@ -0,0 +1,254 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# 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.
+from pathlib import Path
+
+from docutils.nodes import Text
+from sphinx.ext.intersphinx import missing_reference
+
+import pseudopeople
+
+base_dir = Path(pseudopeople.__file__).parent
+
+about = {}
+with (base_dir / "__about__.py").open() as f:
+    exec(f.read(), about)
+
+sys.path.insert(0, str(Path("..").resolve()))
+
+# -- Project information -----------------------------------------------------
+
+project = about["__title__"]
+copyright = f'2023, {about["__author__"]}'
+author = about["__author__"]
+
+# The short X.Y version.
+version = about["__version__"]
+# The full version, including alpha/beta/rc tags.
+release = about["__version__"]
+
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+
+needs_sphinx = "4.0"
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.doctest",
+    "sphinx.ext.todo",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+    "sphinx_click.ext",
+    "matplotlib.sphinxext.plot_directive",
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = ".rst"
+
+# The master toctree document.
+master_doc = "index"
+
+# General information about the project.
+
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = "en"
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = "sphinx"
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True
+
+
+# -- 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_path = ["_theme"]
+html_theme = "sphinx_rtd_theme"
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# 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"]
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# This is required for the alabaster theme
+# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
+html_sidebars = {
+    "**": [
+        "globaltoc.html",  # needs 'show_related': True theme option to display
+        "searchbox.html",
+    ]
+}
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = f'{about["__title__"]}doc'
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# 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 = [
+    (
+        master_doc,
+        f'{about["__title__"]}.tex',
+        f'{about["__title__"]} Documentation',
+        about["__author__"],
+        "manual",
+    ),
+]
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, f'{about["__title__"]}', f'{about["__title__"]} Documentation', [author], 1)
+]
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (
+        master_doc,
+        f'{about["__title__"]}',
+        f'{about["__title__"]} Documentation',
+        author,
+        f'{about["__title__"]}',
+        about["__summary__"],
+        "Miscellaneous",
+    ),
+]
+
+# Other docs we can link to
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3.8", None),
+    "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
+    "tables": ("https://www.pytables.org/", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "networkx": ("https://networkx.org/documentation/stable/", None),
+}
+
+
+# -- Autodoc configuration ------------------------------------------------
+
+autodoc_default_options = {
+    # Automatically document members (e.g. classes in a module,
+    # methods in a class, etc.)
+    "members": True,
+    # Order of items documented is determined by the order
+    # of appearance in the source code
+    "member-order": "bysource",
+    # Generate docs even if an item has no docstring.
+    "undoc-members": True,
+    # Don't document things with a leading underscore.
+    "private-members": False,
+}
+# Display type hints in the description instead of the signature.
+autodoc_typehints = "description"
+
+
+# -- nitpicky mode --------------------------------------------------------
+# Ensures that all references in the docs resolve.
+
+nitpicky = True
+
+nitpick_ignore = []
+for line in open("../nitpick-exceptions"):
+    if line.strip() == "" or line.startswith("#"):
+        continue
+    dtype, target = line.split(None, 1)
+    target = target.strip()
+    nitpick_ignore.append((dtype, target))
+
+
+# Fix sphinx warnings when for literal Ellipses in type hints.
+def setup(app):
+    app.connect("missing-reference", __sphinx_issue_8127)
+
+
+def __sphinx_issue_8127(app, env, node, contnode):
+    reftarget = node.get("reftarget", None)
+    if reftarget == "..":
+        node["reftype"] = "data"
+        node["reftarget"] = "Ellipsis"
+        text_node = next(iter(contnode.traverse(lambda n: n.tagname == "#text")))
+        replacement_node = Text("...", "")
+        if text_node.parent is not None:
+            text_node.parent.replace(text_node, replacement_node)
+        else:  # e.g. happens in rtype fields
+            contnode = replacement_node
+        return missing_reference(app, env, node, contnode)

pseudopeople-0.1.0/docs/source/glossary.rst

@@ -0,0 +1,22 @@
+.. _glossary:
+
+========
+Glossary
+========
+
+.. glossary::
+
+    Configuration
+        The configuration is a set of parameters that will define the level for each
+        noise type in a ConfigTree object.
+
+    Forms
+        Forms are analogous to a dataset that will be noised and returned to the
+        user with errors in the data at a level provided by the configuration.
+        The noised datasets will be output in the format of different census and
+        tax forms.
+
+    Noise functions
+        Functions that will be applied to forms at a row or column level to apply
+        errors or mistakes in the data to replicate realistic challenges in personal
+        record linkage.