First commit of sphinx docs and some community tools

CODE_OF_CONDUCT.md

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+# Contributor Covenant 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, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, 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 project team at [email protected]. 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][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq

CONTRIBUTING.md

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+## How to contribute to the Lifemapper Client Library
+
+#### You found a bug
+
+* Check that it hasn't already be reported by searching our GitHub issues [Issues](https://github.com/lifemapper/lm_client/issues).
+
+* If you're unable to find an open issue addressing the problem, [open a new one](https://github.com/lifemapper/lm_client/issues/new?assignees=cjgrady&template=bug_report.md). Be sure to include a **title and clear description**, as much relevant information as possible, and a **code sample** or an **executable test case** demonstrating the expected behavior that is not occurring.
+
+
+#### You wrote a patch for a bug
+
+* Open a new GitHub pull request with the patch.
+
+* Ensure the pull request description clearly describes the problem and solution. Include the relevant issue number if applicable.
+
+* Before submitting, check that your patch follows our coding and testing conventions
+
+
+#### You want to add new functinoality
+
+* [Submit a new GitHub issue](https://github.com/lifemapper/lm_client/issues/new?assignees=&template=feature_request.md) and suggest your analysis.  We want to make sure that it fits before you spend time coding it.
+
+* Write your code and tests following our coding and testing conventions.
+
+* Submit a pull request
+
+
+#### Coding conventions
+
+* We Use [PEP8](https://www.python.org/dev/peps/pep-0008/)
+
+* Doc strings should follow [Google Style Guidelines](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html)
+
+* We use [pytest](https://docs.pytest.org/en/latest/) style tests
+
+* Use pytest with coverage and pep8 to determine if test code is adequate.  At this time, we support Python 2.7 and multiple versions of Python 3.
+
+```
+$ py.test tests/ --pep8 lm_client -v --cov lm_client --cov-report term-missing
+
+$ py.test-3 tests/ --pep8 lm_client -v --cov lm_client --cov-report term-missing
+```
+
+#### You want to update documentation
+
+* Update the documentation in a new branch
+
+* If you update in-line documentation, make sure to rebuild the API doc RST files
+
+```
+$ sphinx-apidoc -o ./_sphinx_config/source ./lm_client/
+```
+
+* If you edit any RST docs (or update API docs), rebuild the html pages
+
+```
+$ sphinx-build -b html ./_sphinx_config/ ./docs/sphinx/
+```
+
+* Open and submit a new pull request for your updates
+
+Thanks!
+
+Lifemapper Team

README.md

@@ -1,2 +1,30 @@
-lm_client
-=========
+# Lifemapper Client Library
+
+![Latest release](https://img.shields.io/github/release/lifemapper/lm_client.svg)
+[![Build Status](https://travis-ci.org/lifemapper/lm_client.svg?branch=master)](https://travis-ci.org/lifemapper/lm_client)
+[![Coverage Status](https://coveralls.io/repos/github/lifemapper/lm_client/badge.svg?branch=master)](https://coveralls.io/github/lifemapper/lm_client?branch=master)
+![License Badge](https://img.shields.io/github/license/lifemapper/lm_client.svg)
+
+The Lifemapper Client Library is an pen source project designed to provide
+access to Lifemapper web services.
+
+![Lifemapper](https://biotaphy.github.io/analyses/sphinx/_images/lm_logo.png)
+
+
+## Install
+
+Installation help can be found at https://lifemapper.github.io/lm_client/sphinx/pages/installation.html
+
+## Getting help
+
+A this time, the easiest way to get help is to [file a bug report](https://github.com/lifemapper/lm_client/issues/new?labels=&template=bug_report.md&title=).
+
+## Contributing
+
+Did you find a bug?  Do you have an idea for an analysis?  Do you want to write
+some documentation?  Head over to [our contributing page](CONTRIBUTING.md)
+for more information about how you can help out.
+
+## License
+
+The BiotaPhy analyses repository is released under the [GPL 3.0 License](LICENSE).

_sphinx_config/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = LifemapperClientLibrary
+SOURCEDIR     = .
+BUILDDIR      = ../docs/sphinx
+
+# 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)

_sphinx_config/conf.py

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+# -*- coding: utf-8 -*-
+#
+# Lifemapper Client Library documentation build configuration file, created by
+# sphinx-quickstart on Wed Apr  3 16:15:12 2019.
+#
+# 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.
+
+# 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.
+#
+import os
+import sys
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.doctest',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.todo',
+    'sphinx.ext.coverage',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.githubpages',
+    'sphinx.ext.napoleon']
+
+# 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.
+project = u'Lifemapper Client Library'
+copyright = u'2019, Lifemapper Team'
+author = u'Lifemapper Team'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = u'1.0.0'
+# The full version, including alpha/beta/rc tags.
+release = u'1.0.0'
+
+# 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 = None
+
+# 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 = ['_build', 'Thumbs.db', '.DS_Store']
+
+# 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 = False
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'classic'
+
+# 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 = {
+    '**': [
+        'relations.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 = 'LifemapperClientLibrarydoc'
+
+
+# -- 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, 'LifemapperClientLibrary.tex', u'Lifemapper Client Library Documentation',
+     u'Lifemapper Team', '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, 'lifemapperclientlibrary', u'Lifemapper Client Library 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, 'LifemapperClientLibrary', u'Lifemapper Client Library Documentation',
+     author, 'LifemapperClientLibrary', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'https://docs.python.org/': None}