├── .gitignore ├── .travis.yml ├── AUTHORS.rst ├── CONTRIBUTING.rst ├── HISTORY.rst ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.rst ├── docs ├── Makefile ├── authors.rst ├── conf.py ├── contributing.rst ├── history.rst ├── index.rst ├── installation.rst ├── make.bat └── usage.rst ├── popgen ├── __init__.py └── popgen.py ├── requirements.txt ├── setup.cfg ├── setup.py ├── test ├── __init__.py └── test_popgen.py └── tox.ini /.gitignore: -------------------------------------------------------------------------------- 1 | *.py[cod] 2 | 3 | # C extensions 4 | *.so 5 | 6 | # Packages 7 | *.egg 8 | *.egg-info 9 | dist 10 | build 11 | eggs 12 | parts 13 | bin 14 | var 15 | sdist 16 | develop-eggs 17 | .installed.cfg 18 | lib 19 | lib64 20 | 21 | # Installer logs 22 | pip-log.txt 23 | 24 | # Unit test / coverage reports 25 | .coverage 26 | .tox 27 | nosetests.xml 28 | 29 | # Translations 30 | *.mo 31 | 32 | # Mr Developer 33 | .mr.developer.cfg 34 | .project 35 | .pydevproject 36 | 37 | # Complexity 38 | output/*.html 39 | output/*/index.html 40 | 41 | # Sphinx 42 | docs/_build -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 1 | # Config file for automatic testing at travis-ci.org 2 | 3 | language: python 4 | 5 | python: 6 | - "3.3" 7 | - "2.7" 8 | - "2.6" 9 | - "pypy" 10 | 11 | # command to install dependencies, e.g. pip install -r requirements.txt --use-mirrors 12 | install: 13 | - pip install -r requirements.txt 14 | 15 | # command to run tests, e.g. python setup.py test 16 | script: 17 | - py.test -------------------------------------------------------------------------------- /AUTHORS.rst: -------------------------------------------------------------------------------- 1 | ======= 2 | Credits 3 | ======= 4 | 5 | Development Lead 6 | ---------------- 7 | 8 | * Karthik Konduri 9 | 10 | Contributors 11 | ------------ 12 | 13 | None yet. Why not be the first? -------------------------------------------------------------------------------- /CONTRIBUTING.rst: -------------------------------------------------------------------------------- 1 | ============ 2 | Contributing 3 | ============ 4 | 5 | Contributions are welcome, and they are greatly appreciated! Every 6 | little bit helps, and credit will always be given. 7 | 8 | You can contribute in many ways: 9 | 10 | Types of Contributions 11 | ---------------------- 12 | 13 | Report Bugs 14 | ~~~~~~~~~~~ 15 | 16 | Report bugs at https://github.com/karthikcharan83/popgen/issues. 17 | 18 | If you are reporting a bug, please include: 19 | 20 | * Your operating system name and version. 21 | * Any details about your local setup that might be helpful in troubleshooting. 22 | * Detailed steps to reproduce the bug. 23 | 24 | Fix Bugs 25 | ~~~~~~~~ 26 | 27 | Look through the GitHub issues for bugs. Anything tagged with "bug" 28 | is open to whoever wants to implement it. 29 | 30 | Implement Features 31 | ~~~~~~~~~~~~~~~~~~ 32 | 33 | Look through the GitHub issues for features. Anything tagged with "feature" 34 | is open to whoever wants to implement it. 35 | 36 | Write Documentation 37 | ~~~~~~~~~~~~~~~~~~~ 38 | 39 | Synthetic Population Generator .20 could always use more documentation, whether as part of the 40 | official Synthetic Population Generator .20 docs, in docstrings, or even on the web in blog posts, 41 | articles, and such. 42 | 43 | Submit Feedback 44 | ~~~~~~~~~~~~~~~ 45 | 46 | The best way to send feedback is to file an issue at https://github.com/karthikcharan83/popgen/issues. 47 | 48 | If you are proposing a feature: 49 | 50 | * Explain in detail how it would work. 51 | * Keep the scope as narrow as possible, to make it easier to implement. 52 | * Remember that this is a volunteer-driven project, and that contributions 53 | are welcome :) 54 | 55 | Get Started! 56 | ------------ 57 | 58 | Ready to contribute? Here's how to set up `popgen` for 59 | local development. 60 | 61 | 1. Fork_ the `popgen` repo on GitHub. 62 | 2. Clone your fork locally:: 63 | 64 | $ git clone git@github.com:your_name_here/popgen.git 65 | 66 | 3. Create a branch for local development:: 67 | 68 | $ git checkout -b name-of-your-bugfix-or-feature 69 | 70 | Now you can make your changes locally. 71 | 72 | 4. When you're done making changes, check that your changes pass style and unit 73 | tests, including testing other Python versions with tox:: 74 | 75 | $ tox 76 | 77 | To get tox, just pip install it. 78 | 79 | 5. Commit your changes and push your branch to GitHub:: 80 | 81 | $ git add . 82 | $ git commit -m "Your detailed description of your changes." 83 | $ git push origin name-of-your-bugfix-or-feature 84 | 85 | 6. Submit a pull request through the GitHub website. 86 | 87 | .. _Fork: https://github.com/Nekroze/popgen/fork 88 | 89 | Pull Request Guidelines 90 | ----------------------- 91 | 92 | Before you submit a pull request, check that it meets these guidelines: 93 | 94 | 1. The pull request should include tests. 95 | 2. If the pull request adds functionality, the docs should be updated. Put 96 | your new functionality into a function with a docstring, and add the 97 | feature to the list in README.rst. 98 | 3. The pull request should work for Python 2.6, 2.7, and 3.3, and for PyPy. 99 | Check https://travis-ci.org/karthikcharan83/popgen 100 | under pull requests for active pull requests or run the ``tox`` command and 101 | make sure that the tests pass for all supported Python versions. 102 | 103 | 104 | Tips 105 | ---- 106 | 107 | To run a subset of tests:: 108 | 109 | $ py.test test/test_popgen.py -------------------------------------------------------------------------------- /HISTORY.rst: -------------------------------------------------------------------------------- 1 | .. :changelog: 2 | 3 | History 4 | ------- 5 | 6 | 2.0 (2014-12-12) 7 | ++++++++++++++++++ 8 | 9 | * First release on PyPI. -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | The MIT License (MIT) 2 | 3 | Copyright (c) 2014 Karthik Konduri 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy of 6 | this software and associated documentation files (the "Software"), to deal in 7 | the Software without restriction, including without limitation the rights to 8 | use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of 9 | the Software, and to permit persons to whom the Software is furnished to do so, 10 | subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS 17 | FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR 18 | COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER 19 | IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN 20 | CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- 1 | include AUTHORS.rst 2 | include CONTRIBUTING.rst 3 | include HISTORY.rst 4 | include LICENSE 5 | include README.rst -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- 1 | .PHONY: help clean clean-pyc clean-build list test test-all coverage docs release sdist 2 | 3 | help: 4 | @echo "clean-build - remove build artifacts" 5 | @echo "clean-pyc - remove Python file artifacts" 6 | @echo "lint - check style with flake8" 7 | @echo "test - run tests quickly with the default Python" 8 | @echo "testall - run tests on every Python version with tox" 9 | @echo "coverage - check code coverage quickly with the default Python" 10 | @echo "docs - generate Sphinx HTML documentation, including API docs" 11 | @echo "release - package and upload a release" 12 | @echo "sdist - package" 13 | 14 | clean: clean-build clean-pyc 15 | 16 | clean-build: 17 | rm -fr build/ 18 | rm -fr dist/ 19 | rm -fr *.egg-info 20 | 21 | clean-pyc: 22 | find . -name '*.pyc' -exec rm -f {} + 23 | find . -name '*.pyo' -exec rm -f {} + 24 | find . -name '*~' -exec rm -f {} + 25 | 26 | lint: 27 | flake8 popgen test 28 | 29 | test: 30 | py.test 31 | 32 | test-all: 33 | tox 34 | 35 | coverage: 36 | coverage run --source popgen setup.py test 37 | coverage report -m 38 | coverage html 39 | open htmlcov/index.html 40 | 41 | docs: 42 | rm -f docs/popgen.rst 43 | rm -f docs/modules.rst 44 | sphinx-apidoc -o docs/ popgen 45 | $(MAKE) -C docs clean 46 | $(MAKE) -C docs html 47 | open docs/_build/html/index.html 48 | 49 | release: clean 50 | python setup.py sdist upload 51 | python setup.py bdist_wheel upload 52 | 53 | sdist: clean 54 | python setup.py sdist 55 | python setup.py bdist_wheel upload 56 | ls -l dist -------------------------------------------------------------------------------- /README.rst: -------------------------------------------------------------------------------- 1 | ============================= 2 | Synthetic Population Generator .20 3 | ============================= 4 | 5 | .. image:: https://badge.fury.io/py/popgen.png 6 | :target: http://badge.fury.io/py/popgen 7 | 8 | .. image:: https://travis-ci.org/karthikcharan83/popgen.png?branch=master 9 | :target: https://travis-ci.org/karthikcharan83/popgen 10 | 11 | .. image:: https://pypip.in/d/popgen/badge.png 12 | :target: https://pypi.python.org/pypi/popgen 13 | 14 | 15 | Synthetic Population Generator 2.0 16 | 17 | 18 | Features 19 | -------- 20 | 21 | * TODO 22 | -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- 1 | # Makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line. 5 | SPHINXOPTS = 6 | SPHINXBUILD = sphinx-build 7 | PAPER = 8 | BUILDDIR = _build 9 | 10 | # User-friendly check for sphinx-build 11 | ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1) 12 | $(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/) 13 | endif 14 | 15 | # Internal variables. 16 | PAPEROPT_a4 = -D latex_paper_size=a4 17 | PAPEROPT_letter = -D latex_paper_size=letter 18 | ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . 19 | # the i18n builder cannot share the environment and doctrees with the others 20 | I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . 21 | 22 | .PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext 23 | 24 | help: 25 | @echo "Please use \`make ' where is one of" 26 | @echo " html to make standalone HTML files" 27 | @echo " dirhtml to make HTML files named index.html in directories" 28 | @echo " singlehtml to make a single large HTML file" 29 | @echo " pickle to make pickle files" 30 | @echo " json to make JSON files" 31 | @echo " htmlhelp to make HTML files and a HTML help project" 32 | @echo " qthelp to make HTML files and a qthelp project" 33 | @echo " devhelp to make HTML files and a Devhelp project" 34 | @echo " epub to make an epub" 35 | @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" 36 | @echo " latexpdf to make LaTeX files and run them through pdflatex" 37 | @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx" 38 | @echo " text to make text files" 39 | @echo " man to make manual pages" 40 | @echo " texinfo to make Texinfo files" 41 | @echo " info to make Texinfo files and run them through makeinfo" 42 | @echo " gettext to make PO message catalogs" 43 | @echo " changes to make an overview of all changed/added/deprecated items" 44 | @echo " xml to make Docutils-native XML files" 45 | @echo " pseudoxml to make pseudoxml-XML files for display purposes" 46 | @echo " linkcheck to check all external links for integrity" 47 | @echo " doctest to run all doctests embedded in the documentation (if enabled)" 48 | 49 | clean: 50 | rm -rf $(BUILDDIR)/* 51 | 52 | html: 53 | $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html 54 | @echo 55 | @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." 56 | 57 | dirhtml: 58 | $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml 59 | @echo 60 | @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." 61 | 62 | singlehtml: 63 | $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml 64 | @echo 65 | @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." 66 | 67 | pickle: 68 | $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle 69 | @echo 70 | @echo "Build finished; now you can process the pickle files." 71 | 72 | json: 73 | $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json 74 | @echo 75 | @echo "Build finished; now you can process the JSON files." 76 | 77 | htmlhelp: 78 | $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp 79 | @echo 80 | @echo "Build finished; now you can run HTML Help Workshop with the" \ 81 | ".hhp project file in $(BUILDDIR)/htmlhelp." 82 | 83 | qthelp: 84 | $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp 85 | @echo 86 | @echo "Build finished; now you can run "qcollectiongenerator" with the" \ 87 | ".qhcp project file in $(BUILDDIR)/qthelp, like this:" 88 | @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/complexity.qhcp" 89 | @echo "To view the help file:" 90 | @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/complexity.qhc" 91 | 92 | devhelp: 93 | $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp 94 | @echo 95 | @echo "Build finished." 96 | @echo "To view the help file:" 97 | @echo "# mkdir -p $$HOME/.local/share/devhelp/complexity" 98 | @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/complexity" 99 | @echo "# devhelp" 100 | 101 | epub: 102 | $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub 103 | @echo 104 | @echo "Build finished. The epub file is in $(BUILDDIR)/epub." 105 | 106 | latex: 107 | $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex 108 | @echo 109 | @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." 110 | @echo "Run \`make' in that directory to run these through (pdf)latex" \ 111 | "(use \`make latexpdf' here to do that automatically)." 112 | 113 | latexpdf: 114 | $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex 115 | @echo "Running LaTeX files through pdflatex..." 116 | $(MAKE) -C $(BUILDDIR)/latex all-pdf 117 | @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." 118 | 119 | latexpdfja: 120 | $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex 121 | @echo "Running LaTeX files through platex and dvipdfmx..." 122 | $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja 123 | @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." 124 | 125 | text: 126 | $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text 127 | @echo 128 | @echo "Build finished. The text files are in $(BUILDDIR)/text." 129 | 130 | man: 131 | $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man 132 | @echo 133 | @echo "Build finished. The manual pages are in $(BUILDDIR)/man." 134 | 135 | texinfo: 136 | $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo 137 | @echo 138 | @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." 139 | @echo "Run \`make' in that directory to run these through makeinfo" \ 140 | "(use \`make info' here to do that automatically)." 141 | 142 | info: 143 | $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo 144 | @echo "Running Texinfo files through makeinfo..." 145 | make -C $(BUILDDIR)/texinfo info 146 | @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo." 147 | 148 | gettext: 149 | $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale 150 | @echo 151 | @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." 152 | 153 | changes: 154 | $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes 155 | @echo 156 | @echo "The overview file is in $(BUILDDIR)/changes." 157 | 158 | linkcheck: 159 | $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck 160 | @echo 161 | @echo "Link check complete; look for any errors in the above output " \ 162 | "or in $(BUILDDIR)/linkcheck/output.txt." 163 | 164 | doctest: 165 | $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest 166 | @echo "Testing of doctests in the sources finished, look at the " \ 167 | "results in $(BUILDDIR)/doctest/output.txt." 168 | 169 | xml: 170 | $(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml 171 | @echo 172 | @echo "Build finished. The XML files are in $(BUILDDIR)/xml." 173 | 174 | pseudoxml: 175 | $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml 176 | @echo 177 | @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml." -------------------------------------------------------------------------------- /docs/authors.rst: -------------------------------------------------------------------------------- 1 | .. include:: ../AUTHORS.rst -------------------------------------------------------------------------------- /docs/conf.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | # 3 | # complexity documentation build configuration file, created by 4 | # sphinx-quickstart on Tue Jul 9 22:26:36 2013. 5 | # 6 | # This file is execfile()d with the current directory set to its containing dir. 7 | # 8 | # Note that not all possible configuration values are present in this 9 | # autogenerated file. 10 | # 11 | # All configuration values have a default; values that are commented out 12 | # serve to show the default. 13 | 14 | import sys, os 15 | 16 | # If extensions (or modules to document with autodoc) are in another directory, 17 | # add these directories to sys.path here. If the directory is relative to the 18 | # documentation root, use os.path.abspath to make it absolute, like shown here. 19 | #sys.path.insert(0, os.path.abspath('.')) 20 | 21 | cwd = os.getcwd() 22 | parent = os.path.dirname(cwd) 23 | sys.path.insert(0, parent) 24 | 25 | import popgen 26 | 27 | # -- General configuration ----------------------------------------------------- 28 | 29 | # If your documentation needs a minimal Sphinx version, state it here. 30 | #needs_sphinx = '1.0' 31 | 32 | # Add any Sphinx extension module names here, as strings. They can be extensions 33 | # coming with Sphinx (named 'sphinx.ext.*') or your custom ones. 34 | extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode'] 35 | 36 | # Add any paths that contain templates here, relative to this directory. 37 | templates_path = ['_templates'] 38 | 39 | # The suffix of source filenames. 40 | source_suffix = '.rst' 41 | 42 | # The encoding of source files. 43 | #source_encoding = 'utf-8-sig' 44 | 45 | # The master toctree document. 46 | master_doc = 'index' 47 | 48 | # General information about the project. 49 | project = u'Synthetic Population Generator .20' 50 | copyright = u'2014, Karthik Konduri' 51 | 52 | # The version info for the project you're documenting, acts as replacement for 53 | # |version| and |release|, also used in various other places throughout the 54 | # built documents. 55 | # 56 | # The short X.Y version. 57 | version = popgen.__version__ 58 | # The full version, including alpha/beta/rc tags. 59 | release = popgen.__version__ 60 | 61 | # The language for content autogenerated by Sphinx. Refer to documentation 62 | # for a list of supported languages. 63 | #language = None 64 | 65 | # There are two options for replacing |today|: either, you set today to some 66 | # non-false value, then it is used: 67 | #today = '' 68 | # Else, today_fmt is used as the format for a strftime call. 69 | #today_fmt = '%B %d, %Y' 70 | 71 | # List of patterns, relative to source directory, that match files and 72 | # directories to ignore when looking for source files. 73 | exclude_patterns = ['_build'] 74 | 75 | # The reST default role (used for this markup: `text`) to use for all documents. 76 | #default_role = None 77 | 78 | # If true, '()' will be appended to :func: etc. cross-reference text. 79 | #add_function_parentheses = True 80 | 81 | # If true, the current module name will be prepended to all description 82 | # unit titles (such as .. function::). 83 | #add_module_names = True 84 | 85 | # If true, sectionauthor and moduleauthor directives will be shown in the 86 | # output. They are ignored by default. 87 | #show_authors = False 88 | 89 | # The name of the Pygments (syntax highlighting) style to use. 90 | pygments_style = 'sphinx' 91 | 92 | # A list of ignored prefixes for module index sorting. 93 | #modindex_common_prefix = [] 94 | 95 | # If true, keep warnings as "system message" paragraphs in the built documents. 96 | #keep_warnings = False 97 | 98 | 99 | # -- Options for HTML output --------------------------------------------------- 100 | 101 | # The theme to use for HTML and HTML Help pages. See the documentation for 102 | # a list of builtin themes. 103 | html_theme = 'default' 104 | 105 | # Theme options are theme-specific and customize the look and feel of a theme 106 | # further. For a list of options available for each theme, see the 107 | # documentation. 108 | #html_theme_options = {} 109 | 110 | # Add any paths that contain custom themes here, relative to this directory. 111 | #html_theme_path = [] 112 | 113 | # The name for this set of Sphinx documents. If None, it defaults to 114 | # " v documentation". 115 | #html_title = None 116 | 117 | # A shorter title for the navigation bar. Default is the same as html_title. 118 | #html_short_title = None 119 | 120 | # The name of an image file (relative to this directory) to place at the top 121 | # of the sidebar. 122 | #html_logo = None 123 | 124 | # The name of an image file (within the static path) to use as favicon of the 125 | # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 126 | # pixels large. 127 | #html_favicon = None 128 | 129 | # Add any paths that contain custom static files (such as style sheets) here, 130 | # relative to this directory. They are copied after the builtin static files, 131 | # so a file named "default.css" will overwrite the builtin "default.css". 132 | html_static_path = ['_static'] 133 | 134 | # If not '', a 'Last updated on:' timestamp is inserted at every page bottom, 135 | # using the given strftime format. 136 | #html_last_updated_fmt = '%b %d, %Y' 137 | 138 | # If true, SmartyPants will be used to convert quotes and dashes to 139 | # typographically correct entities. 140 | #html_use_smartypants = True 141 | 142 | # Custom sidebar templates, maps document names to template names. 143 | #html_sidebars = {} 144 | 145 | # Additional templates that should be rendered to pages, maps page names to 146 | # template names. 147 | #html_additional_pages = {} 148 | 149 | # If false, no module index is generated. 150 | #html_domain_indices = True 151 | 152 | # If false, no index is generated. 153 | #html_use_index = True 154 | 155 | # If true, the index is split into individual pages for each letter. 156 | #html_split_index = False 157 | 158 | # If true, links to the reST sources are added to the pages. 159 | #html_show_sourcelink = True 160 | 161 | # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. 162 | #html_show_sphinx = True 163 | 164 | # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. 165 | #html_show_copyright = True 166 | 167 | # If true, an OpenSearch description file will be output, and all pages will 168 | # contain a tag referring to it. The value of this option must be the 169 | # base URL from which the finished HTML is served. 170 | #html_use_opensearch = '' 171 | 172 | # This is the file name suffix for HTML files (e.g. ".xhtml"). 173 | #html_file_suffix = None 174 | 175 | # Output file base name for HTML help builder. 176 | htmlhelp_basename = 'popgendoc' 177 | 178 | 179 | # -- Options for LaTeX output -------------------------------------------------- 180 | 181 | latex_elements = { 182 | # The paper size ('letterpaper' or 'a4paper'). 183 | #'papersize': 'letterpaper', 184 | 185 | # The font size ('10pt', '11pt' or '12pt'). 186 | #'pointsize': '10pt', 187 | 188 | # Additional stuff for the LaTeX preamble. 189 | #'preamble': '', 190 | } 191 | 192 | # Grouping the document tree into LaTeX files. List of tuples 193 | # (source start file, target name, title, author, documentclass [howto/manual]). 194 | latex_documents = [ 195 | ('index', 'popgen.tex', u'Synthetic Population Generator .20 Documentation', 196 | u'Karthik Konduri', 'manual'), 197 | ] 198 | 199 | # The name of an image file (relative to this directory) to place at the top of 200 | # the title page. 201 | #latex_logo = None 202 | 203 | # For "manual" documents, if this is true, then toplevel headings are parts, 204 | # not chapters. 205 | #latex_use_parts = False 206 | 207 | # If true, show page references after internal links. 208 | #latex_show_pagerefs = False 209 | 210 | # If true, show URL addresses after external links. 211 | #latex_show_urls = False 212 | 213 | # Documents to append as an appendix to all manuals. 214 | #latex_appendices = [] 215 | 216 | # If false, no module index is generated. 217 | #latex_domain_indices = True 218 | 219 | 220 | # -- Options for manual page output -------------------------------------------- 221 | 222 | # One entry per manual page. List of tuples 223 | # (source start file, name, description, authors, manual section). 224 | man_pages = [ 225 | ('index', 'popgen', u'Synthetic Population Generator .20 Documentation', 226 | [u'Karthik Konduri'], 1) 227 | ] 228 | 229 | # If true, show URL addresses after external links. 230 | #man_show_urls = False 231 | 232 | 233 | # -- Options for Texinfo output ------------------------------------------------ 234 | 235 | # Grouping the document tree into Texinfo files. List of tuples 236 | # (source start file, target name, title, author, 237 | # dir menu entry, description, category) 238 | texinfo_documents = [ 239 | ('index', 'popgen', u'Synthetic Population Generator .20 Documentation', 240 | u'Karthik Konduri', 'popgen', 'One line description of project.', 241 | 'Miscellaneous'), 242 | ] 243 | 244 | # Documents to append as an appendix to all manuals. 245 | #texinfo_appendices = [] 246 | 247 | # If false, no module index is generated. 248 | #texinfo_domain_indices = True 249 | 250 | # How to display URL addresses: 'footnote', 'no', or 'inline'. 251 | #texinfo_show_urls = 'footnote' 252 | 253 | # If true, do not generate a @detailmenu in the "Top" node's menu. 254 | #texinfo_no_detailmenu = False -------------------------------------------------------------------------------- /docs/contributing.rst: -------------------------------------------------------------------------------- 1 | .. include:: ../CONTRIBUTING.rst -------------------------------------------------------------------------------- /docs/history.rst: -------------------------------------------------------------------------------- 1 | .. include:: ../HISTORY.rst -------------------------------------------------------------------------------- /docs/index.rst: -------------------------------------------------------------------------------- 1 | .. complexity documentation master file, created by 2 | sphinx-quickstart on Tue Jul 9 22:26:36 2013. 3 | You can adapt this file completely to your liking, but it should at least 4 | contain the root `toctree` directive. 5 | 6 | .. include:: ../README.rst 7 | 8 | Contents: 9 | ========= 10 | 11 | .. toctree:: 12 | :maxdepth: 2 13 | 14 | installation 15 | usage 16 | contributing 17 | authors 18 | history 19 | 20 | Feedback 21 | ======== 22 | 23 | If you have any suggestions or questions about **Synthetic Population Generator .20** feel free to email me 24 | at karthik.charan@gmail.com. 25 | 26 | If you encounter any errors or problems with **Synthetic Population Generator .20**, please let me know! 27 | Open an Issue at the GitHub http://github.com/karthikcharan83/popgen main repository. -------------------------------------------------------------------------------- /docs/installation.rst: -------------------------------------------------------------------------------- 1 | ============ 2 | Installation 3 | ============ 4 | 5 | At the command line either via easy_install or pip:: 6 | 7 | $ easy_install popgen 8 | $ pip install popgen 9 | 10 | Or, if you have virtualenvwrapper installed:: 11 | 12 | $ mkvirtualenv popgen 13 | $ pip install popgen -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- 1 | @ECHO OFF 2 | 3 | REM Command file for Sphinx documentation 4 | 5 | if "%SPHINXBUILD%" == "" ( 6 | set SPHINXBUILD=sphinx-build 7 | ) 8 | set BUILDDIR=_build 9 | set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% . 10 | set I18NSPHINXOPTS=%SPHINXOPTS% . 11 | if NOT "%PAPER%" == "" ( 12 | set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS% 13 | set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS% 14 | ) 15 | 16 | if "%1" == "" goto help 17 | 18 | if "%1" == "help" ( 19 | :help 20 | echo.Please use `make ^` where ^ is one of 21 | echo. html to make standalone HTML files 22 | echo. dirhtml to make HTML files named index.html in directories 23 | echo. singlehtml to make a single large HTML file 24 | echo. pickle to make pickle files 25 | echo. json to make JSON files 26 | echo. htmlhelp to make HTML files and a HTML help project 27 | echo. qthelp to make HTML files and a qthelp project 28 | echo. devhelp to make HTML files and a Devhelp project 29 | echo. epub to make an epub 30 | echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter 31 | echo. text to make text files 32 | echo. man to make manual pages 33 | echo. texinfo to make Texinfo files 34 | echo. gettext to make PO message catalogs 35 | echo. changes to make an overview over all changed/added/deprecated items 36 | echo. xml to make Docutils-native XML files 37 | echo. pseudoxml to make pseudoxml-XML files for display purposes 38 | echo. linkcheck to check all external links for integrity 39 | echo. doctest to run all doctests embedded in the documentation if enabled 40 | goto end 41 | ) 42 | 43 | if "%1" == "clean" ( 44 | for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i 45 | del /q /s %BUILDDIR%\* 46 | goto end 47 | ) 48 | 49 | 50 | %SPHINXBUILD% 2> nul 51 | if errorlevel 9009 ( 52 | echo. 53 | echo.The 'sphinx-build' command was not found. Make sure you have Sphinx 54 | echo.installed, then set the SPHINXBUILD environment variable to point 55 | echo.to the full path of the 'sphinx-build' executable. Alternatively you 56 | echo.may add the Sphinx directory to PATH. 57 | echo. 58 | echo.If you don't have Sphinx installed, grab it from 59 | echo.http://sphinx-doc.org/ 60 | exit /b 1 61 | ) 62 | 63 | if "%1" == "html" ( 64 | %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html 65 | if errorlevel 1 exit /b 1 66 | echo. 67 | echo.Build finished. The HTML pages are in %BUILDDIR%/html. 68 | goto end 69 | ) 70 | 71 | if "%1" == "dirhtml" ( 72 | %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml 73 | if errorlevel 1 exit /b 1 74 | echo. 75 | echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml. 76 | goto end 77 | ) 78 | 79 | if "%1" == "singlehtml" ( 80 | %SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml 81 | if errorlevel 1 exit /b 1 82 | echo. 83 | echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml. 84 | goto end 85 | ) 86 | 87 | if "%1" == "pickle" ( 88 | %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle 89 | if errorlevel 1 exit /b 1 90 | echo. 91 | echo.Build finished; now you can process the pickle files. 92 | goto end 93 | ) 94 | 95 | if "%1" == "json" ( 96 | %SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json 97 | if errorlevel 1 exit /b 1 98 | echo. 99 | echo.Build finished; now you can process the JSON files. 100 | goto end 101 | ) 102 | 103 | if "%1" == "htmlhelp" ( 104 | %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp 105 | if errorlevel 1 exit /b 1 106 | echo. 107 | echo.Build finished; now you can run HTML Help Workshop with the ^ 108 | .hhp project file in %BUILDDIR%/htmlhelp. 109 | goto end 110 | ) 111 | 112 | if "%1" == "qthelp" ( 113 | %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp 114 | if errorlevel 1 exit /b 1 115 | echo. 116 | echo.Build finished; now you can run "qcollectiongenerator" with the ^ 117 | .qhcp project file in %BUILDDIR%/qthelp, like this: 118 | echo.^> qcollectiongenerator %BUILDDIR%\qthelp\complexity.qhcp 119 | echo.To view the help file: 120 | echo.^> assistant -collectionFile %BUILDDIR%\qthelp\complexity.ghc 121 | goto end 122 | ) 123 | 124 | if "%1" == "devhelp" ( 125 | %SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp 126 | if errorlevel 1 exit /b 1 127 | echo. 128 | echo.Build finished. 129 | goto end 130 | ) 131 | 132 | if "%1" == "epub" ( 133 | %SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub 134 | if errorlevel 1 exit /b 1 135 | echo. 136 | echo.Build finished. The epub file is in %BUILDDIR%/epub. 137 | goto end 138 | ) 139 | 140 | if "%1" == "latex" ( 141 | %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex 142 | if errorlevel 1 exit /b 1 143 | echo. 144 | echo.Build finished; the LaTeX files are in %BUILDDIR%/latex. 145 | goto end 146 | ) 147 | 148 | if "%1" == "latexpdf" ( 149 | %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex 150 | cd %BUILDDIR%/latex 151 | make all-pdf 152 | cd %BUILDDIR%/.. 153 | echo. 154 | echo.Build finished; the PDF files are in %BUILDDIR%/latex. 155 | goto end 156 | ) 157 | 158 | if "%1" == "latexpdfja" ( 159 | %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex 160 | cd %BUILDDIR%/latex 161 | make all-pdf-ja 162 | cd %BUILDDIR%/.. 163 | echo. 164 | echo.Build finished; the PDF files are in %BUILDDIR%/latex. 165 | goto end 166 | ) 167 | 168 | if "%1" == "text" ( 169 | %SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text 170 | if errorlevel 1 exit /b 1 171 | echo. 172 | echo.Build finished. The text files are in %BUILDDIR%/text. 173 | goto end 174 | ) 175 | 176 | if "%1" == "man" ( 177 | %SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man 178 | if errorlevel 1 exit /b 1 179 | echo. 180 | echo.Build finished. The manual pages are in %BUILDDIR%/man. 181 | goto end 182 | ) 183 | 184 | if "%1" == "texinfo" ( 185 | %SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo 186 | if errorlevel 1 exit /b 1 187 | echo. 188 | echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo. 189 | goto end 190 | ) 191 | 192 | if "%1" == "gettext" ( 193 | %SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale 194 | if errorlevel 1 exit /b 1 195 | echo. 196 | echo.Build finished. The message catalogs are in %BUILDDIR%/locale. 197 | goto end 198 | ) 199 | 200 | if "%1" == "changes" ( 201 | %SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes 202 | if errorlevel 1 exit /b 1 203 | echo. 204 | echo.The overview file is in %BUILDDIR%/changes. 205 | goto end 206 | ) 207 | 208 | if "%1" == "linkcheck" ( 209 | %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck 210 | if errorlevel 1 exit /b 1 211 | echo. 212 | echo.Link check complete; look for any errors in the above output ^ 213 | or in %BUILDDIR%/linkcheck/output.txt. 214 | goto end 215 | ) 216 | 217 | if "%1" == "doctest" ( 218 | %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest 219 | if errorlevel 1 exit /b 1 220 | echo. 221 | echo.Testing of doctests in the sources finished, look at the ^ 222 | results in %BUILDDIR%/doctest/output.txt. 223 | goto end 224 | ) 225 | 226 | if "%1" == "xml" ( 227 | %SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml 228 | if errorlevel 1 exit /b 1 229 | echo. 230 | echo.Build finished. The XML files are in %BUILDDIR%/xml. 231 | goto end 232 | ) 233 | 234 | if "%1" == "pseudoxml" ( 235 | %SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml 236 | if errorlevel 1 exit /b 1 237 | echo. 238 | echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml. 239 | goto end 240 | ) 241 | 242 | :end -------------------------------------------------------------------------------- /docs/usage.rst: -------------------------------------------------------------------------------- 1 | ======== 2 | Usage 3 | ======== 4 | 5 | To use Synthetic Population Generator .20 in a project:: 6 | 7 | import popgen -------------------------------------------------------------------------------- /popgen/__init__.py: -------------------------------------------------------------------------------- 1 | __author__ = 'Karthik Konduri' 2 | __email__ = 'karthik.charan@gmail.com' 3 | __version__ = '2.0' 4 | -------------------------------------------------------------------------------- /popgen/popgen.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/foss-transportationmodeling/popgen/1af734cd1bf5b5d8179065713472b53e44946afa/popgen/popgen.py -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | wheel>=0.22 -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- 1 | [wheel] 2 | universal = 1 -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import os 4 | import sys 5 | 6 | try: 7 | from setuptools import setup 8 | except ImportError: 9 | from distutils.core import setup 10 | 11 | 12 | if sys.argv[-1] == 'publish': 13 | os.system('python setup.py sdist upload') 14 | sys.exit() 15 | 16 | readme = open('README.rst').read() 17 | doclink = """ 18 | Documentation 19 | ------------- 20 | 21 | The full documentation is at http://popgen.rtfd.org.""" 22 | history = open('HISTORY.rst').read().replace('.. :changelog:', '') 23 | 24 | setup( 25 | name='popgen', 26 | version='2.0', 27 | description='Synthetic Population Generator 2.0', 28 | long_description=readme + '\n\n' + doclink + '\n\n' + history, 29 | author='Karthik Konduri', 30 | author_email='karthik.charan@gmail.com', 31 | url='https://github.com/karthikcharan83/popgen', 32 | packages=[ 33 | 'popgen', 34 | ], 35 | package_dir={'popgen': 'popgen'}, 36 | include_package_data=True, 37 | install_requires=[ 38 | ], 39 | license='MIT', 40 | zip_safe=False, 41 | keywords='popgen', 42 | classifiers=[ 43 | 'Development Status :: 2 - Pre-Alpha', 44 | 'Intended Audience :: Developers', 45 | 'License :: OSI Approved :: MIT License', 46 | 'Natural Language :: English', 47 | 'Programming Language :: Python :: 2', 48 | 'Programming Language :: Python :: 2.6', 49 | 'Programming Language :: Python :: 2.7', 50 | 'Programming Language :: Python :: 3', 51 | 'Programming Language :: Python :: 3.3', 52 | 'Programming Language :: Python :: Implementation :: PyPy', 53 | ], 54 | ) -------------------------------------------------------------------------------- /test/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/foss-transportationmodeling/popgen/1af734cd1bf5b5d8179065713472b53e44946afa/test/__init__.py -------------------------------------------------------------------------------- /test/test_popgen.py: -------------------------------------------------------------------------------- 1 | """ 2 | Tests for `popgen` module. 3 | """ 4 | import pytest 5 | from popgen import popgen 6 | 7 | 8 | class TestPopgen(object): 9 | 10 | @classmethod 11 | def setup_class(cls): 12 | pass 13 | 14 | def test_something(self): 15 | pass 16 | 17 | @classmethod 18 | def teardown_class(cls): 19 | pass -------------------------------------------------------------------------------- /tox.ini: -------------------------------------------------------------------------------- 1 | [tox] 2 | envlist = py26, py27, py33, style, docs 3 | 4 | [testenv] 5 | setenv = 6 | PYTHONPATH = {toxinidir}:{toxinidir}/popgen 7 | deps = 8 | -r{toxinidir}/requirements.txt 9 | pytest 10 | commands = 11 | py.test --basetemp={envtmpdir} 12 | 13 | [testenv:style] 14 | deps = 15 | -r{toxinidir}/requirements.txt 16 | flake8 17 | commands = 18 | python setup.py flake8 19 | 20 | [testenv:docs] 21 | changedir=docs/ 22 | deps = 23 | -r{toxinidir}/requirements.txt 24 | sphinx 25 | commands = 26 | sphinx-build -b linkcheck ./ _build/ 27 | sphinx-build -b html ./ _build/ --------------------------------------------------------------------------------