Merge branch 'develop'

.bumpversion.cfg

@@ -0,0 +1,9 @@
+[bumpversion]
+current_version = 0.2.0
+
+[bumpversion:file:setup.py]
+
+[bumpversion:file:src/imfusion/__init__.py]
+search = __version__ = '{current_version}'
+replace = __version__ = '{new_version}'
+

.coveragerc

@@ -0,0 +1,5 @@
+[run]
+source = pybiomart
+
+[report]
+omit = pybiomart/_version.py

.gitattributes

@@ -0,0 +1 @@
+pybiomart/_version.py export-subst

.gitignore

@@ -3,3 +3,11 @@ __pycache__
 pybiomart.egg-info
 *.pyc
 dist
+.coverage
+.DS_Store
+.cache
+htmlcov
+RELEASE-VERSION
+docs/_build
+.vscode
+.tox

.travis.yml

@@ -0,0 +1,33 @@
+language: python
+
+python:
+    # We don't actually use the Travis Python, but this keeps it organized.
+    - '2.7'
+    - '3.4'
+    - '3.5'
+
+install:
+    - sudo apt-get update
+
+    - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+    - bash miniconda.sh -b -p $HOME/miniconda
+    - export PATH="$HOME/miniconda/bin:$PATH"
+    - hash -r
+    - conda config --set always_yes yes --set changeps1 no
+    - conda update -q conda
+
+    # Useful for debugging any issues with conda.
+    - conda info -a
+
+    # Create conda environment.
+    - conda create -q -n test python=$TRAVIS_PYTHON_VERSION
+    - source activate test
+
+    # Install with test dependencies.
+    - pip install .[dev]
+
+
+script: py.test --cov pybiomart --cov-report term-missing
+
+after_success:
+    - coveralls

AUTHORS.rst

@@ -0,0 +1,13 @@
+=======
+Credits
+=======
+
+Development Lead
+----------------
+
+* Julian de Ruiter <julianderuiter@gmail.com>
+
+Contributors
+------------
+
+None yet. Why not be the first?

CONTRIBUTING.rst

@@ -0,0 +1,100 @@
+.. highlight:: shell
+
+============
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every
+little bit helps, and credit will always be given.
+
+Types of Contributions
+----------------------
+
+Report Bugs
+~~~~~~~~~~~
+
+Report bugs at https://github.com/jrderuiter/pybiomart/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
+~~~~~~~~~~~~~~~~~~~
+
+pybiomart could always use more documentation, whether as part of the
+official pybiomart 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/jrderuiter/pybiomart/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 `pybiomart` for local development.
+
+1. Fork the `pybiomart` repo on GitHub.
+2. Clone your fork locally::
+
+    $ git clone git@github.com:your_name_here/pybiomart.git
+
+3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
+
+    $ mkvirtualenv pybiomart
+    $ cd pybiomart/
+    $ python setup.py develop
+
+4. Create a branch for local development::
+
+    $ git checkout -b name-of-your-bugfix-or-feature
+
+   Now you can make your changes locally.
+
+5. When you're done making changes, check that your changes pass the tests::
+
+    $ python setup.py test or py.test
+
+6. 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
+
+7. Submit a pull request through the GitHub website.
+
+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, 3.4 and 3.5. Check
+   https://travis-ci.org/jrderuiter/pybiomart/pull_requests
+   and make sure that the tests pass for all supported Python versions.

HISTORY.rst

@@ -0,0 +1,17 @@
+=======
+History
+=======
+
+0.2.0 (2017-05-10)
+------------------
+
+- Fixed Python 2.7 bug encountered when parsing XML.
+- Dropped versioneer for bumpversion.
+- Refactored unit tests.
+- Added tox for testing against multiple pythons.
+- Updated documentation.
+
+0.1.0
+------------------
+
+* Intial release.

LICENSE.txt → LICENSE

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2015 Julian de Ruiter
+Copyright (c) 2015-2017 Julian de Ruiter
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

MANIFEST.IN

@@ -1 +1,13 @@
-include RELEASE-VERSION
+
+include AUTHORS.rst
+
+include CONTRIBUTING.rst
+include HISTORY.rst
+include LICENSE
+include README.rst
+
+recursive-include tests *
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+
+recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif

Makefile

@@ -0,0 +1,87 @@
+.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/
+	find . -name '*.egg-info' -exec rm -fr {} +
+	find . -name '*.egg' -exec rm -f {} +
+
+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 -f .coverage
+	rm -fr htmlcov/
+
+lint: ## check style with flake8
+	pylint src/genemap tests
+
+test: clean-pyc ## run tests quickly with the default Python
+	py.test tests
+
+tox: clean
+	docker run -v `pwd`:/app -t -i themattrix/tox-base
+
+coverage: ## check code coverage quickly with the default Python
+	py.test tests --cov=geneviz --cov-report=html
+	$(BROWSER) htmlcov/index.html
+
+docs: ## generate and serve Sphinx documentation
+	rm -rf docs/_build
+	sphinx-autobuild docs docs/_build
+
+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
+
+gh-pages:
+	git checkout gh-pages
+	find ./* -not -path '*/\.*' -prune -exec rm -r "{}" \;
+	git checkout develop docs Makefile src AUTHORS.rst CONTRIBUTING.rst HISTORY.rst README.rst
+	git reset HEAD
+	(cd docs && make html)
+	mv -fv docs/_build/html/* ./
+	rm -rf docs Makefile src AUTHORS.rst CONTRIBUTING.rst HISTORY.rst README.rst
+	touch .nojekyll
+	git add -A
+	git commit -m "Generated gh-pages for `git log develop -1 --pretty=short --abbrev-commit`" && git push origin gh-pages ; git checkout develop

README.rst

@@ -1,14 +1,25 @@
 PyBiomart
 =========
 
-PyBiomart is a Python library that provides an easy interface to
-databases implementing the BioMart software suite
-(http://www.biomart.org).
+.. image:: https://travis-ci.org/jrderuiter/pybiomart.svg?branch=develop
+    :target: https://travis-ci.org/jrderuiter/pybiomart
+
+.. image:: https://coveralls.io/repos/github/jrderuiter/pybiomart/badge.svg?branch=develop
+    :target: https://coveralls.io/github/jrderuiter/pybiomart?branch=develop
+
+A simple and pythonic biomart interface for Python.
+
+The intent of pybiomart is to provide a simple interface to biomart, which can be used to easily query biomart databases from Python. In this sense, pybiomart aims to provide functionality similar to packages such as biomaRt (which provides access to biomart from R).
+
+Documentation
+-------------
+
+Documentation is available at: `https://jrderuiter.github.io/pybiomart <https://jrderuiter.github.io/pybiomart>`_.
 
 Examples
 --------
 
-Retrieving and querying a dataset using the server interace:
+Retrieving and querying a dataset using the server interface:
 
 .. code:: python
 
@@ -18,7 +29,7 @@ Retrieving and querying a dataset using the server interace:
 
     dataset = (server.marts['ENSEMBL_MART_ENSEMBL']
                      .datasets['hsapiens_gene_ensembl'])
-                     
+
     dataset.query(attributes=['ensembl_gene_id', 'external_gene_name'],
                   filters={'chromosome_name': ['1','2']})
 
@@ -30,24 +41,10 @@ Retrieving a dataset directly with known dataset name:
 
     dataset = Dataset(name='hsapiens_gene_ensembl',
                       host='http://www.ensembl.org')
-                      
+
     dataset.query(attributes=['ensembl_gene_id', 'external_gene_name'],
                   filters={'chromosome_name': ['1','2']})
 
-Dependencies
-------------
-
--  Python 3.3+, Python 2.7 (legacy Python)
--  requests, requests-cache
--  pandas
-
-Installation
-------------
-
-.. code:: {bash}
-
-    pip install git+git://github.com/jrderuiter/pybiomart.git#egg=pybiomart
-
 License
 -------