Merge pull request #117 from HIIT/optional_imports

Optional imports + version numbering + PyPI

.gitattributes

@@ -0,0 +1 @@
+.ipynb linguist-documentation

.travis.yml

@@ -7,7 +7,7 @@ install:
   - pip install numpy
   - pip install cython
   - pip install -r requirements-dev.txt
-  - pip install -e .
+  - pip install -e .[nosql]
 # command to run tests
 script:
   - make test

CHANGELOG.md

@@ -1,7 +1,13 @@
 # Change Log
 
-## 0.2.2 - 0.3
+0.3.1 (2017-01-31)
+------------------
+- Clean up requirements
+- Set graphviz and unqlite optional
+- PyPI release (pip install elfi)
 
+0.2.2 - 0.3
+-----------
 - The inference problem is now contained in an Inference Task object.
 - SMC-ABC has been reimplemented.
 - Results from inference are now contained in a Result object.

README.md

@@ -1,21 +1,10 @@
 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.org/HIIT/elfi.svg?branch=master)](https://travis-ci.org/HIIT/elfi)
+[![Code Health](https://landscape.io/github/HIIT/elfi/master/landscape.svg?style=flat)](https://landscape.io/github/HIIT/elfi/master)
 [![Documentation Status](https://readthedocs.org/projects/elfi/badge/?version=latest)](http://elfi.readthedocs.io/en/latest/?badge=latest)
+[![Gitter chat](https://badges.gitter.im/HIIT/elfi.svg)](https://gitter.im/HIIT/elfi?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
 
 <img src="https://cloud.githubusercontent.com/assets/1233418/20178983/6e22ee44-a75c-11e6-8345-5934b55b9dc6.png" width="15%" align="right"></img>
 
@@ -28,37 +17,33 @@ Currently implemented ABC methods:
 - sequential Monte Carlo sampler
 - [Bayesian Optimization for Likelihood-Free Inference (BOLFI) framework](http://jmlr.csail.mit.edu/papers/v17/15-017.html)
 
-See examples under [notebooks](notebooks) to get started. Full documentation can be found at http://elfi.readthedocs.io/. Limited user-support may be asked from elfi-support.at.hiit.fi.
+See examples under [notebooks](notebooks) to get started. Full documentation can be found at http://elfi.readthedocs.io/. Limited user-support may be asked from elfi-support.at.hiit.fi, but the [Gitter chat](https://gitter.im/HIIT/elfi?utm_source=share-link&utm_medium=link&utm_campaign=share-link) is preferable.
 
-<!-- ..
-   Installation
-   -------------
-   ::
-
-     pip install elfi
- -->
-
-Developer installation
-----------------------
-ELFI is currently tested only with Python 3.5. If you are new to Python, perhaps the simplest way to install it is [Anaconda](https://www.continuum.io/downloads).
 
-Currently we recommend using Distributed 1.14.3.
+Installation
+------------
 ```
-git clone https://github.com/HIIT/elfi.git
-cd elfi
-pip install numpy
-pip install -r requirements-dev.txt
-pip install -e .
+pip install elfi
 ```
 
-It is recommended to create a virtual environment for development before installing.
+ELFI is currently tested only with Python 3.5. If you are new to Python, perhaps the simplest way to install it is [Anaconda](https://www.continuum.io/downloads).
+
+Currently it is required to use Distributed 1.14.3.
 
 Virtual environment using Anaconda
 ----------------------------------
-Below an example how to create a virtual environment named ``elfi`` using Anaconda:
-
-    conda create -n elfi python=3* scipy
+If you want to create a virtual environment before installing, you can do so with Anaconda:
 
-Then activate it:
+```
+conda create -n elfi python=3.5 scipy
+source activate elfi
+pip install elfi
+```
 
-    source activate elfi
+Potential problems with installation
+------------------------------------
+ELFI depends on several other Python packages, which have their own dependencies. Resolving these may sometimes go wrong:
+- If you receive an error about missing `numpy`, please install it first.
+- If you receive an error about `yaml.load`, install `pyyaml`.
+- On OS X with Anaconda virtual environment say `conda install python.app` and then use `pythonw` instead of `python`.
+- Note that ELFI currently supports Python 3.5 only, although 3.x may work as well.

docs/installation.rst

@@ -4,25 +4,43 @@
 Installation
 ============
 
+To install ELFI, run this command in your terminal:
 
-.. Stable release
-.. --------------
+    pip install elfi
 
-.. To install ELFI, run this command in your terminal:
+If you don't have `pip`_ installed, this `Python installation guide`_ can guide
+you through the process.
 
-.. .. code-block:: console
+.. _pip: https://pip.pypa.io
+.. _Python installation guide: http://docs.python-guide.org/en/latest/starting/installation/
 
-..     $ pip install elfi
 
-.. This is the preferred method to install ELFI, as it will always install the most recent stable release.
+ELFI is currently tested only with Python 3.5. If you are new to Python, perhaps the simplest way to install it is Anaconda_
 
-.. If you don't have `pip`_ installed, this `Python installation guide`_ can guide
-.. you through the process.
+.. _Anaconda: https://www.continuum.io/downloads
 
-.. .. _pip: https://pip.pypa.io
-.. .. _Python installation guide: http://docs.python-guide.org/en/latest/starting/installation/
+Currently it is required to use Distributed 1.14.3.
 
 
+Virtual environment using Anaconda
+----------------------------------
+
+If you want to create a virtual environment before installing, you can do so with Anaconda:
+
+    conda create -n elfi python=3.5 scipy
+    source activate elfi
+    pip install elfi
+
+
+Potential problems with installation
+------------------------------------
+
+ELFI depends on several other Python packages, which have their own dependencies. Resolving these may sometimes go wrong:
+* If you receive an error about missing `numpy`, please install it first.
+* If you receive an error about `yaml.load`, install `pyyaml`.
+* On OS X with Anaconda virtual environment say `conda install python.app` and then use `pythonw` instead of `python`.
+* Note that ELFI currently supports Python 3.5 only, although 3.x may work as well.
+
 From sources
 ------------
 
@@ -46,6 +64,5 @@ Once you have a copy of the source, you can install it with:
 
     $ python setup.py install
 
-
 .. _Github repo: https://github.com/HIIT/elfi
 .. _tarball: https://github.com/HIIT/elfi/tarball/master

docs/readme.rst

@@ -19,9 +19,10 @@ Currently implemented ABC methods:
 
 GitHub page: https://github.com/HIIT/elfi
 
-See examples under the notebooks_ directory to get started. Limited user-support may be asked from elfi-support.at.hiit.fi.
+See examples under the notebooks_ directory to get started. Limited user-support may be asked from elfi-support.at.hiit.fi, but the `Gitter chat`_ is preferable.
 
 .. _notebooks: https://github.com/HIIT/elfi/tree/master/notebooks
+.. _Gitter chat: https://gitter.im/HIIT/elfi?utm_source=share-link&utm_medium=link&utm_campaign=share-link
 
 Licenses:
 

elfi/__init__.py

@@ -12,4 +12,6 @@
 
 __author__ = 'ELFI authors'
 __email__ = 'elfi-support@hiit.fi'
-__version__ = '0.3_dev'
+
+# make sure __version_ is on the last non-empty line (read by setup.py)
+__version__ = '0.3.1'

elfi/storage.py

@@ -16,7 +16,6 @@
 from elfi.utils import to_slice, get_key_slice, get_key_id, get_named_item, make_key
 import elfi.env as env
 
-from unqlite import UnQLite
 
 logger = logging.getLogger(__name__)
 
@@ -545,6 +544,12 @@ class UnQLiteDatabase():
     """
 
     def __init__(self, location=None):
+
+        try:
+            from unqlite import UnQLite
+        except ImportError:
+            raise ImportError("The unqlite library is required for this feature.")
+
         self.location = location
         if type(self.location) == str and len(self.location) > 0:
             logger.debug("Connecting to database at {}".format(os.path.abspath(location)))

elfi/visualization.py

@@ -1,4 +1,3 @@
-from graphviz import Digraph
 import numpy as np
 import matplotlib.pyplot as plt
 from collections import OrderedDict
@@ -10,6 +9,8 @@ def draw_model(discrepancy_node, draw_constants=False, filename=None):
     """
     Return a GraphViz dot representation of the model.
 
+    Requires the optional 'graphviz' library.
+
     Parameters
     ----------
     discrepancy_node : Node
@@ -20,6 +21,10 @@ def draw_model(discrepancy_node, draw_constants=False, filename=None):
         If given, save the dot file into the given filename, trying to guess the type.
         For example: 'mymodel.png'.
     """
+    try:
+        from graphviz import Digraph
+    except ImportError:
+        raise ImportError("The graphviz library is required for this feature.")
 
     # gather the set of nodes, excluding Constants
     nodes = discrepancy_node.component

setup.cfg

@@ -1,5 +1,5 @@
 [wheel]
-universal = 1
+universal = 0
 
 [flake8]
 exclude = .git,
@@ -18,3 +18,6 @@ multi_line_output = 0
 [tool:pytest]
 addopts = --doctest-modules
 testpaths = elfi tests
+
+[zest.releaser]
+python-file-with-version = elfi/__init__.py

setup.py

@@ -1,49 +1,53 @@
 import os
-from setuptools import setup
+from setuptools import setup, find_packages
 from io import open
 
-with open('README.md', 'r', encoding='utf-8') as f:
+
+with open('docs/readme.rst', 'r', encoding='utf-8') as f:
     long_description = f.read()
 
+packages = ['elfi'] + ['elfi.' + p for p in find_packages('elfi')]
+
 requirements = [
-                'toolz>=0.8',
                 'distributed==1.14.3',
-                'graphviz>=0.5',
-                'cairocffi>=0.7',
                 'dask>=0.11.1',
-                'sobol_seq>=0.1.2',
                 'numpy>=1.8',
                 'scipy>=0.16.1',
-                'Cython>=0.25.1',
                 'matplotlib>=1.1',
-                'GPy>=1.0.9',
-                'unqlite>=0.6.0'
+                'GPy>=1.0.9'
                 ]
 
+optionals = {
+    'doc': ['Sphinx'],
+    'nosql': ['unqlite>=0.6.0'],
+    'graphviz': ['graphviz>=0.5']
+}
+
+# read version number
+__version__ = open('elfi/__init__.py').readlines()[-1].split(' ')[-1].strip().strip("'\"")
+
 setup(
     name='elfi',
-    packages=['elfi'],
-    version='0.2.x_dev',
+    keywords='abc likelihood-free statistics',
+    packages=packages,
+    version=__version__,
     author='HIIT',
     author_email='elfi-support@hiit.fi',
-    url='https://github.com/HIIT/elfi',
+    url='http://elfi.readthedocs.io',
 
     install_requires=requirements,
-
-    extras_require={
-        'doc': ['Sphinx'],
-    },
+    extras_require=optionals,
 
     description='Modular ABC inference framework for python',
     long_description=long_description,
 
-    license='BSD3',
+    license='BSD',
 
-    classifiers=['Programming Language :: Python',
+    classifiers=['Programming Language :: Python :: 3.5',
                  'Topic :: Scientific/Engineering',
                  'Topic :: Scientific/Engineering :: Bio-Informatics',
-                 'Programming Language :: Python :: 3'
                  'Operating System :: OS Independent',
-                 'Development Status :: 2 - Pre-Alpha',
+                 'Development Status :: 3 - Alpha',
                  'Intended Audience :: Science/Research',
-                 'License :: OSI Approved :: BSD3 License'])
+                 'License :: OSI Approved :: BSD License'],
+    zip_safe = False)