Merge pull request #85 from HIIT/dev

The "Review release" 0.2

.gitignore

@@ -6,8 +6,9 @@ __pycache__/
 *.py[cod]
 *$py.class
 
-# C extensions
+# C/C++ extensions
 *.so
+*.bin
 
 # Distribution / packaging
 .Python

.travis.yml

@@ -1,12 +1,13 @@
 language: python
 python:
   - "3.5"
+cache: pip
 # command to install dependencies
 install:
   - pip install numpy
-  - pip install -e .[dev]
-  - pip install git+https://github.com/dask/dask.git
-  - pip install git+https://github.com/dask/distributed.git
+  - pip install cython
+  - pip install -r requirements-dev.txt
+  - pip install -e .
 # command to run tests
 script:
-  - py.test tests/unit
+  - make test

CONTRIBUTING.rst

@@ -0,0 +1,131 @@
+.. highlight:: shell
+
+============
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every
+little bit helps, and credit will always be given.
+
+You can contribute in many ways:
+
+Types of Contributions
+----------------------
+
+Report Bugs
+~~~~~~~~~~~
+
+Report bugs at https://github.com/HIIT/elfi/issues.
+
+If you are reporting a bug, 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.
+
+Fix Bugs
+~~~~~~~~
+
+Look through the GitHub issues for bugs. Anything tagged with "bug"
+and "help wanted" is open to whoever wants to implement it.
+
+Implement Features
+~~~~~~~~~~~~~~~~~~
+
+Look through the GitHub issues for features. Anything tagged with "enhancement"
+and "help wanted" is open to whoever wants to implement it.
+
+Write Documentation
+~~~~~~~~~~~~~~~~~~~
+
+ELFI could always use more documentation, whether as part of the
+official ELFI docs, in docstrings, or even on the web in blog posts,
+articles, and such.
+
+Submit Feedback
+~~~~~~~~~~~~~~~
+
+The best way to send feedback is to file an issue at https://github.com/HIIT/elfi/issues.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+Get Started!
+------------
+
+Ready to contribute? Here's how to set up `ELFI` for local development.
+
+1. Fork the `elfi` repo on GitHub.
+2. Clone your fork locally::
+
+    $ git clone git@github.com:your_name_here/elfi.git
+
+3. Install your local copy and the development requirements into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development. Due to a bug in the pip installation of GPy numpy needs to be installed manually.::
+
+    $ mkvirtualenv elfi
+    $ cd elfi/
+    $ pip install numpy
+    $ make dev
+
+4. Create a branch for local development::
+
+    $ git checkout -b name-of-your-bugfix-or-feature
+
+   Now you can make your changes locally.
+   
+5. Follow the `Style Guidelines`_
+
+6. When you're done making changes, check that your changes pass flake8 and the tests::
+
+    $ make lint
+    $ make test
+
+  Also make sure that the docstrings of your code are formatted properly::
+
+    $ make docs
+
+7. Commit your changes and push your branch to GitHub::
+
+    $ git add .
+    $ git commit -m "Your detailed description of your changes."
+    $ git push origin name-of-your-bugfix-or-feature
+
+8. Submit a pull request through the GitHub website.
+
+Style Guidelines
+----------------
+
+The projects follows the `Khan Academy Style Guide <https://github.com/Khan/style-guides/blob/master/style/python.md>`_. Except that we use numpy style docstrings instead of Google style docstrings.
+
+See `this example <http://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_numpy.html>`_ for how to format the docstrings.
+
+Additional Style Guidelines
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+- Use the ``.format()`` string method instead of the old percent operator. For more information see `PyFormat <https://pyformat.info/>`_.
+- Use the type hinting syntax suggested `here <https://www.jetbrains.com/help/pycharm/2016.1/type-hinting-in-pycharm.html>`_ in the docstrings.
+
+Pull Request Guidelines
+-----------------------
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include tests.
+2. If the pull request adds functionality, the docs should be updated. Put
+   your new functionality into a function with a docstring, and add the
+   feature to the list in README.rst.
+3. The pull request should work for Python 2.7,  3.5 and later. Check
+   https://travis-ci.org/HIIT/elfi/pull_requests
+   and make sure that the tests pass for all supported Python versions.
+
+Tips
+----
+
+To run a subset of tests::
+
+$ py.test tests.test_elfi
+

Makefile

@@ -0,0 +1,96 @@
+.PHONY: clean clean-test clean-pyc clean-build docs help
+.DEFAULT_GOAL := help
+define BROWSER_PYSCRIPT
+import os, webbrowser, sys
+try:
+	from urllib import pathname2url
+except:
+	from urllib.request import pathname2url
+
+webbrowser.open("file://" + pathname2url(os.path.abspath(sys.argv[1])))
+endef
+export BROWSER_PYSCRIPT
+
+define PRINT_HELP_PYSCRIPT
+import re, sys
+
+for line in sys.stdin:
+	match = re.match(r'^([a-zA-Z_-]+):.*?## (.*)$$', line)
+	if match:
+		target, help = match.groups()
+		print("%-20s %s" % (target, help))
+endef
+export PRINT_HELP_PYSCRIPT
+BROWSER := python -c "$$BROWSER_PYSCRIPT"
+
+help:
+	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
+
+clean: clean-build clean-pyc clean-test ## remove all build, test, coverage and Python artifacts
+
+
+clean-build: ## remove build artifacts
+	rm -fr build/
+	rm -fr dist/
+	rm -fr .eggs/
+	rm -fr docs/_build
+	find . -name '*.egg-info' -exec rm -fr {} +
+	find . -name '*.egg' -exec rm -fr {} +
+
+clean-pyc: ## remove Python file artifacts
+	find . -name '*.pyc' -exec rm -f {} +
+	find . -name '*.pyo' -exec rm -f {} +
+	find . -name '*~' -exec rm -f {} +
+	find . -name '__pycache__' -exec rm -fr {} +
+
+clean-test: ## remove test and coverage artifacts
+	rm -fr .tox/
+	rm -f .coverage
+	rm -fr htmlcov/
+
+lint: ## check style with flake8
+	flake8 elfi tests
+
+test: ## run tests quickly with the default Python
+	py.test
+
+test-all: ## run tests on every Python version with tox
+	tox
+
+coverage: ## check code coverage quickly with the default Python
+	py.test --cov=elfi
+	coverage report -m
+	coverage html
+	$(BROWSER) htmlcov/index.html
+
+docs: ## generate Sphinx HTML documentation, including API docs
+	rm -f docs/elfi.rst
+	rm -f docs/elfi.bo.rst
+	rm -f docs/modules.rst
+	sphinx-apidoc -o docs/ elfi
+	$(MAKE) -C docs clean
+	$(MAKE) -C docs html
+	$(BROWSER) docs/_build/html/index.html
+
+servedocs: docs ## compile the docs watching for changes
+	watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .
+
+# release: clean ## package and upload a release
+# 	python setup.py sdist upload
+# 	python setup.py bdist_wheel upload
+
+dist: clean ## builds source and wheel package
+	python setup.py sdist
+	python setup.py bdist_wheel
+	ls -l dist
+
+install: clean ## install the package to the active Python's site-packages
+	# python setup.py install
+	pip install numpy
+	pip install -e .
+
+dev: install ## install the development requirements to the active Python's site-packages
+	pip install -Ur requirements-dev.txt
+
+clean-notebooks:
+	python notebooks/clean_notebooks.py

README.md

@@ -0,0 +1,60 @@
+ELFI - Engine for Likelihood-Free Inference
+===========================================
+
+<!-- .. image:: https://img.shields.io/pypi/v/elfi.svg
+        :target: https://pypi.python.org/pypi/elfi
+
+.. image:: https://img.shields.io/travis/HIIT/elfi.svg
+        :target: https://travis-ci.com/HIIT/elfi
+
+.. image:: https://readthedocs.org/projects/elfi/badge/?version=latest
+        :target: https://elfi.readthedocs.io/en/latest/?badge=latest
+        :alt: Documentation Status
+ 
+ https://github.com/dwyl/repo-badges
+ -->
+
+[![Build Status](https://travis-ci.com/HIIT/elfi.svg?token=xAu1DN2J4WjCapVWLinn&branch=dev)](https://travis-ci.com/HIIT/elfi)
+
+<img src="https://cloud.githubusercontent.com/assets/1233418/20178983/6e22ee44-a75c-11e6-8345-5934b55b9dc6.png" width="15%" align="right"></img>
+
+ELFI is a statistical software package written in Python for Approximative Bayesian Computation ([ABC](https://en.wikipedia.org/wiki/Approximate_Bayesian_computation)), also known e.g. as likelihood-free inference, simulator-based inference, approximative Bayesian inference etc. This is useful, when the likelihood function is unknown or difficult to evaluate, but a generative simulator model exists.
+
+The probabilistic inference model is defined as a directed acyclic graph, which allows for an intuitive means to describe inherent dependencies in the model. The inference pipeline is automatically parallelized with [Dask](https://dask.pydata.org), which scales well from a desktop up to a cluster environment. The package includes functionality for input/output operations and visualization.
+
+Currently implemented ABC methods:
+- rejection sampler
+- Sequential Monte Carlo sampler
+- [Bayesian Optimization for Likelihood-Free Inference (BOLFI) framework](https://arxiv.org/abs/1501.03291)
+
+See examples under [notebooks](notebooks) to get started.
+
+<!-- ..
+   Installation
+   -------------
+   ::
+
+     pip install elfi
+ -->
+
+Developer installation
+----------------------
+```
+git clone https://github.com/HIIT/elfi.git
+cd elfi
+pip install numpy
+pip install -r requirements-dev.txt
+pip install -e .
+```
+
+It is recommended to create a virtual environment for development before installing.
+
+Virtual environment using Anaconda
+----------------------------------
+Below an example how to create a virtual environment named ``elfi`` using Anaconda:
+
+    conda create -n elfi python=3* scipy
+
+Then activate it:
+
+    source activate elfi