Add Python packaging framework

This was based on the cookiecutter template ionelmc/pylibrary,
but simplified!

.bumpversion.cfg

@@ -0,0 +1,20 @@
+[bumpversion]
+current_version = 0.1.0
+commit = True
+tag = True
+
+[bumpversion:file:setup.py]
+search = version='{current_version}'
+replace = version='{new_version}'
+
+[bumpversion:file:README.rst]
+search = v{current_version}.
+replace = v{new_version}.
+
+[bumpversion:file:docs/conf.py]
+search = version = release = '{current_version}'
+replace = version = release = '{new_version}'
+
+[bumpversion:file:tlo/__init__.py]
+search = __version__ = '{current_version}'
+replace = __version__ = '{new_version}'

.coveragerc

@@ -0,0 +1,15 @@
+[paths]
+source =
+   tlo
+
+[run]
+branch = true
+source =
+    tlo
+    tests
+parallel = true
+
+[report]
+show_missing = true
+precision = 2
+omit = *migrations*

.editorconfig

@@ -0,0 +1,13 @@
+# see http://editorconfig.org
+root = true
+
+[*]
+end_of_line = lf
+trim_trailing_whitespace = true
+insert_final_newline = true
+indent_style = space
+indent_size = 4
+charset = utf-8
+
+[*.{bat,cmd,ps1}]
+end_of_line = crlf

.travis.yml

@@ -0,0 +1,34 @@
+language: python
+sudo: false
+cache: pip
+env:
+  global:
+    - LD_PRELOAD=/lib/x86_64-linux-gnu/libSegFault.so
+    - SEGFAULT_SIGNALS=all
+  matrix:
+    - TOXENV=check
+    - TOXENV=docs
+matrix:
+  include:
+    - python: '3.6'
+      env:
+        - TOXENV=py36,report
+before_install:
+  - python --version
+  - uname -a
+  - lsb_release -a
+install:
+  - pip install tox
+  - virtualenv --version
+  - easy_install --version
+  - pip --version
+  - tox --version
+script:
+  - tox -v
+after_failure:
+  - more .tox/log/* | cat
+  - more .tox/*/log/* | cat
+notifications:
+  email:
+    on_success: never
+    on_failure: always

MANIFEST.in

@@ -0,0 +1,15 @@
+graft docs
+graft src
+graft ci
+graft tests
+
+include .bumpversion.cfg
+include .coveragerc
+include .cookiecutterrc
+include .editorconfig
+
+include README.rst
+
+include tox.ini .travis.yml
+
+global-exclude *.py[cod] __pycache__ *.so *.dylib

README.rst

@@ -0,0 +1,66 @@
+========
+Overview
+========
+
+.. start-badges
+
+.. image:: https://travis-ci.com/UCL/TLOmodel.svg?branch=master
+    :alt: Travis-CI Build Status
+    :target: https://travis-ci.com/UCL/TLOmodel
+
+.. end-badges
+
+Thanzi la Onse Epidemiology Model
+=================================
+
+This is the main software framework for epidemiology and health system modelling in the Thanzi la Onse project.
+
+See https://www.york.ac.uk/igdc/research/thanzi-la-onse/ for more about the project.
+
+Installation
+============
+
+To get started quickly, we recommend using Anaconda Python, and installing within a fresh environment.
+
+::
+
+    conda create -n tlo python=3.6 virtualenv
+    source activate tlo
+    pip install -r requirements/dev.txt
+    pip install -e .
+
+This will install the software in 'editable' mode, so any changes you make to the source will immediately be reflected.
+After the initial install, each time you wish to use the model simply activate the environment::
+
+    source activate tlo
+
+Documentation
+=============
+
+To build the documentation, activate your environment as above then run::
+
+    tox -e docs
+
+Development
+===========
+
+To run all the tests run::
+
+    tox
+
+Note, to combine test coverage data from all the tox environments run:
+
+.. list-table::
+    :widths: 10 90
+    :stub-columns: 1
+
+    - - Windows
+      - ::
+
+            set PYTEST_ADDOPTS=--cov-append
+            tox
+
+    - - Other
+      - ::
+
+            PYTEST_ADDOPTS=--cov-append tox

docs/authors.rst

@@ -0,0 +1,5 @@
+
+Authors
+=======
+
+* Jonathan Cooper - http://iris.ucl.ac.uk/iris/browse/profile?upi=JCOOP83

docs/conf.py

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+# -*- coding: utf-8 -*-
+from __future__ import unicode_literals
+
+import os
+
+
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.coverage',
+    'sphinx.ext.doctest',
+    'sphinx.ext.extlinks',
+    'sphinx.ext.ifconfig',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.todo',
+    'sphinx.ext.viewcode',
+]
+if os.getenv('SPELLCHECK'):
+    extensions += 'sphinxcontrib.spelling',
+    spelling_show_suggestions = True
+    spelling_lang = 'en_GB'
+
+source_suffix = '.rst'
+master_doc = 'index'
+project = 'TLOmodel'
+year = '2018'
+author = 'Jonathan Cooper'
+copyright = '{0}, {1}'.format(year, author)
+version = release = '0.1.0'
+
+pygments_style = 'trac'
+templates_path = ['.']
+extlinks = {
+    'issue': ('https://github.com/UCL/TLOmodel/issues/%s', '#'),
+    'pr': ('https://github.com/UCL/TLOmodel/pull/%s', 'PR #'),
+}
+# on_rtd is whether we are on readthedocs.org
+on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
+
+if not on_rtd:  # only set the theme if we're building docs locally
+    html_theme = 'sphinx_rtd_theme'
+
+html_use_smartypants = True
+html_last_updated_fmt = '%b %d, %Y'
+html_split_index = False
+html_sidebars = {
+    '**': ['searchbox.html', 'globaltoc.html', 'sourcelink.html'],
+}
+html_short_title = '%s-%s' % (project, version)
+
+napoleon_use_ivar = True
+napoleon_use_rtype = False
+napoleon_use_param = False

docs/contributing.rst

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+============
+Contributing
+============
+
+We'll flesh out the guidelines here further as the project gets going!
+
+Bug reports
+===========
+
+When `reporting a bug <https://github.com/UCL/TLOmodel/issues>`_ please include:
+
+    * Your operating system name and version.
+    * Any details about your local setup that might be helpful in troubleshooting.
+    * Detailed steps to reproduce the bug.
+
+Development
+===========
+
+To set up `TLOmodel` for local development:
+
+1. Fork `TLOmodel <https://github.com/UCL/TLOmodel>`_
+   (look for the "Fork" button).
+   If you have write access to this main repository, you can skip this step and clone
+   it directly in step 2.
+2. Clone your fork locally::
+
+    git clone [email protected]:your_name_here/TLOmodel.git
+
+3. Create a branch for local development::
+
+    git checkout -b name-of-your-bugfix-or-feature
+
+   Now you can make your changes locally.
+
+4. When you're done making changes, run all the checks, doc builder and spell checker with `tox <http://tox.readthedocs.io/en/latest/install.html>`_ one command::
+
+    tox
+
+5. Commit your changes and push your branch to GitHub::
+
+    git add .
+    git commit  # Write a description of your changes in the editor and save
+    git push origin name-of-your-bugfix-or-feature
+
+6. Submit a pull request through the GitHub website.
+
+Pull Request Guidelines
+-----------------------
+
+If you need some code review or feedback while you're developing the code just make the pull request.
+
+For merging, you should:
+
+1. Include passing tests (run ``tox``) [1]_.
+2. Update documentation when there's new API, functionality etc.
+3. Add a note to ``CHANGELOG.rst`` about the changes.
+4. Add yourself to ``AUTHORS.rst``.
+
+.. [1] If you don't have all the necessary python versions available locally you can rely on Travis - it will
+       `run the tests <https://travis-ci.com/UCL/TLOmodel/pull_requests>`_ for each change you add in the pull request.
+
+       It will be slower though ...
+
+Tips
+----
+
+To run a subset of tests::
+
+    tox -e py36 -- pytest -k test_myfeature
+
+To run all the test environments in *parallel* (you need to ``pip install detox``)::
+
+    detox

docs/index.rst

@@ -0,0 +1,21 @@
+========
+Contents
+========
+
+.. toctree::
+   :maxdepth: 2
+
+   readme
+   installation
+   usage
+   reference/index
+   contributing
+   authors
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+

docs/installation.rst

@@ -0,0 +1,17 @@
+============
+Installation
+============
+
+To get started quickly, we recommend using Anaconda Python, and installing within a fresh environment.
+
+::
+
+    conda create -n tlo python=3.6 virtualenv
+    source activate tlo
+    pip install -r requirements/dev.txt
+    pip install -e .
+
+This will install the software in 'editable' mode, so any changes you make to the source will immediately be reflected.
+After the initial install, each time you wish to use the model simply activate the environment::
+
+    source activate tlo

docs/readme.rst

@@ -0,0 +1 @@
+.. include:: ../README.rst

docs/reference/index.rst

@@ -0,0 +1,7 @@
+Reference
+=========
+
+.. toctree::
+    :glob:
+
+    tlo*

docs/reference/tlo.rst

@@ -0,0 +1,9 @@
+tlo
+===
+
+.. testsetup::
+
+    from tlo import *
+
+.. automodule:: tlo
+    :members:

docs/requirements.txt

@@ -0,0 +1,3 @@
+sphinx>=1.3
+sphinx-rtd-theme
+-e .

docs/spelling_wordlist.txt

@@ -0,0 +1,11 @@
+builtin
+builtins
+classmethod
+staticmethod
+classmethods
+staticmethods
+args
+kwargs
+callstack
+Changelog
+Indices

docs/usage.rst

@@ -0,0 +1,9 @@
+=====
+Usage
+=====
+
+To use TLOmodel in a project::
+
+	import tlo
+
+More to come...