Initial commit

.gitignore

@@ -0,0 +1,49 @@
+# Temporary files
+*~
+\#*#
+
+*.py[cod]
+
+# C extensions
+*.so
+
+# Packages
+*.egg
+*.egg-info
+dist
+build
+eggs
+parts
+bin
+var
+sdist
+develop-eggs
+.installed.cfg
+lib
+lib64
+__pycache__
+
+# Installer logs
+pip-log.txt
+
+# Unit test / coverage reports
+.coverage
+.tox
+nosetests.xml
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# vi
+.*.swp
+
+# Sphinx builds
+doc/source/generated
+
+# OSX files
+.DS_Store

.travis.yml

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+Check on http://lint.travis-ci.org/ after modifying it!
+sudo: false
+language: python
+env:
+  - PYVERSION=3.5 USE_CYTHON=TRUE
+before_install:
+  - "export DISPLAY=:99.0"
+  - "sh -e /etc/init.d/xvfb start"
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+  - chmod +x miniconda.sh
+  - ./miniconda.sh -b
+  - export PATH=/home/travis/miniconda3/bin:$PATH
+  # Update conda itself
+  - conda update --yes conda
+  # Useful for debugging any issues with conda
+install:
+  - conda create --yes -n test_env python=$PYVERSION --file ci/conda_requirements.txt -c biocore
+  - conda install --yes -n test_env cython
+  - source activate test_env
+  - pip install -r ci/pip_requirements.txt
+  - pip install -e .
+  - ./scripts/run_the_ipys.sh ipynb/
+script:
+  - make all
+notifications:
+  webhooks:
+    on_success: change
+    on_failure: always

Makefile

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+.DEFAULT_GOAL := help
+
+TEST_COMMAND = nosetests --with-doctest
+
+help:
+	@echo 'Use "make test" to run all the unit tests and docstring tests.'
+	@echo 'Use "make pep8" to validate PEP8 compliance.'
+	@echo 'Use "make html" to create html documentation with sphinx'
+	@echo 'Use "make all" to run all the targets listed above.'
+test:
+	$(TEST_COMMAND)
+pep8:
+	flake8 gneiss setup.py
+
+all: pep8 test

README.md

@@ -1 +1,5 @@
-# gneiss
+# gneiss
+
+Canonically pronouced *nice*
+
+A compositional statistics and visualization toolbox

ci/conda_requirements.txt

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+pip
+nose
+pep8
+flake8
+IPython<4.0.0
+notebook
+scikit-bio

ci/pip_requirements.txt

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+coveralls
+ete3

setup.py

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+#!/usr/bin/env python
+
+# ----------------------------------------------------------------------------
+# Copyright (c) 2016--, gneiss development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+# ----------------------------------------------------------------------------
+
+import re
+import ast
+import os
+
+from setuptools import find_packages, setup
+from setuptools.command.build_ext import build_ext as _build_ext
+
+
+class build_ext(_build_ext):
+    def finalize_options(self):
+        _build_ext.finalize_options(self)
+        # Prevent numpy from thinking it is still in its setup process:
+        __builtins__.__NUMPY_SETUP__ = False
+        import numpy
+        self.include_dirs.append(numpy.get_include())
+# Dealing with Cython
+USE_CYTHON = os.environ.get('USE_CYTHON', False)
+ext = '.pyx' if USE_CYTHON else '.c'
+
+extensions = [
+]
+
+if USE_CYTHON:
+    from Cython.Build import cythonize
+    extensions = cythonize(extensions)
+
+classes = """
+    Development Status :: 0 - pre-alpha
+    License :: OSI Approved :: BSD License
+    Topic :: Software Development :: Libraries
+    Topic :: Scientific/Engineering
+    Topic :: Scientific/Engineering :: Bio-Informatics
+    Programming Language :: Python :: 2
+    Programming Language :: Python :: 2 :: Only
+    Operating System :: Unix
+    Operating System :: POSIX
+    Operating System :: MacOS :: MacOS X
+"""
+classifiers = [s.strip() for s in classes.split('\n') if s]
+
+description = ('Compositional data analysis tools and visualizations')
+
+with open('README.md') as f:
+    long_description = f.read()
+
+
+# version parsing from __init__ pulled from Flask's setup.py
+# https://github.com/mitsuhiko/flask/blob/master/setup.py
+_version_re = re.compile(r'__version__\s+=\s+(.*)')
+
+with open('gneiss/__init__.py', 'rb') as f:
+    hit = _version_re.search(f.read().decode('utf-8')).group(1)
+    version = str(ast.literal_eval(hit))
+
+setup(name='gneiss',
+      version=version,
+      license='BSD',
+      description=description,
+      long_description=long_description,
+      author="gneiss development team",
+      author_email="jamietmorton@gmail.com",
+      maintainer="gneiss development team",
+      maintainer_email="jamietmorton@gmail.com",
+      packages=find_packages(),
+      setup_requires=['numpy >= 1.9.2'],
+      ext_modules=extensions,
+      cmdclass={'build_ext': build_ext},
+      install_requires=[
+          'IPython >= 3.2.0',
+          'matplotlib >= 1.4.3',
+          'numpy >= 1.9.2',
+          'pandas >= 0.18.0',
+          'scipy >= 0.15.1',
+          'nose >= 1.3.7',
+          'scikit-bio>=0.4.2',
+          'ete3',
+      ],
+      classifiers=classifiers,
+      package_data={
+          }
+      )