Merge pull request #1 from josenavas/initial-commit

Porting code over from qiita

Author: antgonza

.coveragerc

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+# this file is based on the examples provided on scikit-learn's .coveragerc
+
+[run]
+omit =
+    */test*
+    */__init__.py
+source = qiita_files
+branch = True
+include = */qiita_*/*
+
+[report]
+exclude_lines =
+    pragma: no cover
+    def __repr__
+    raise NotImplementedError
+    if __name__ == .__main__.:
+omit =
+    */test*
+    */__init__.py

.travis.yml

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+language: python
+sudo: false
+env:
+    - PYTHON_VERSION=2.7
+    - PYTHON_VERSION=3.5
+before_install:
+  - 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:$PATH
+  # Update conda itself
+  - conda update --yes conda
+install:
+  - travis_retry conda create --yes -n env_name python=$PYTHON_VERSION pip nose flake8 coverage 'h5py>=2.3.1' 'pandas>=0.18' 'scipy>0.13.0' 'numpy>=1.7'
+  - source activate env_name
+  - travis_retry pip install .
+script:
+  - nosetests --with-doctest --with-coverage
+  - flake8 qiita_files setup.py
+after_success:
+  - coveralls

LICENSE

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+Copyright (c) 2013, Qiita development team
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+  Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+  Redistributions in binary form must reproduce the above copyright notice, this
+  list of conditions and the following disclaimer in the documentation and/or
+  other materials provided with the distribution.
+
+  Neither the name of the {organization} nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

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+Qiita Files
+===========
+
+This package defines internal file formats used in Qiita, so the Qiita plugins can manipulate this files.
+
+File formats currently defined:
+    - Demux: Stores QIIME compatible demultiplexed FASTA and FASTQ files