From 0353a5aa9c44602e6b55e79866ceef07470644ae Mon Sep 17 00:00:00 2001 From: Jai Ram Rideout Date: Mon, 15 Sep 2014 10:33:11 -0700 Subject: [PATCH 1/3] add vi .swp files to .gitignore --- .gitignore | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.gitignore b/.gitignore index 51cbe85..7487fc0 100644 --- a/.gitignore +++ b/.gitignore @@ -52,3 +52,5 @@ coverage.xml # Sphinx documentation docs/_build/ +# vi +.*.swp From 0e96e211fceb5740f9e2bad4a58e2a97a150da9b Mon Sep 17 00:00:00 2001 From: Jai Ram Rideout Date: Mon, 15 Sep 2014 10:45:39 -0700 Subject: [PATCH 2/3] Update README.md with more info about metoo --- README.md | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 65a2336..f25135b 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,14 @@ -notqiime -======== +metoo +===== -QIIME: The next generation +*Staging ground for QIIME 2 development* + +This repository serves as a staging ground for the next major version of +[QIIME](http://qiime.org/) (i.e., QIIME 2), which will be a complete redesign +and reimplementation of the package. + +**Note:** This repository exists mainly for developers and is not intended for +users or production. It will be transitioned to the canonical QIIME repo +([biocore/qiime](https://github.com/biocore/qiime)) when the package is ready +to be released. This package is under active development and all functionality +should be treated as **pre-alpha**. From 7a74f1c880591b56045b77e7cc96666bb6c501b6 Mon Sep 17 00:00:00 2001 From: Jai Ram Rideout Date: Mon, 15 Sep 2014 13:17:37 -0700 Subject: [PATCH 3/3] TST: add travis-ci and coveralls Fixes #1. --- .coveragerc | 21 +++++++++++++++++++++ .travis.yml | 15 +++++++++++++++ README.md | 4 +++- licenses/burrito.txt | 27 +++++++++++++++++++++++++++ licenses/scikit-bio.txt | 27 +++++++++++++++++++++++++++ metoo/__init__.py | 0 6 files changed, 93 insertions(+), 1 deletion(-) create mode 100644 .coveragerc create mode 100644 .travis.yml create mode 100644 licenses/burrito.txt create mode 100644 licenses/scikit-bio.txt create mode 100644 metoo/__init__.py diff --git a/.coveragerc b/.coveragerc new file mode 100644 index 0000000..0004eef --- /dev/null +++ b/.coveragerc @@ -0,0 +1,21 @@ +# Taken and modified from https://github.com/biocore/burrito +# this file is based on the examples provided in scikit-bio's .coveragerc + +[run] +omit = + */tests* + */__init__.py +source = metoo +branch = True +include = */metoo/* + +[report] +exclude_lines = + pragma: no cover + def __repr__ + raise NotImplementedError + if __name__ == .__main__.: +omit = + */tests* + */__init__.py + diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 0000000..dc9ccdc --- /dev/null +++ b/.travis.yml @@ -0,0 +1,15 @@ +# Taken and modified from https://github.com/biocore/burrito +# Check on http://lint.travis-ci.org/ after modifying it! +language: python +python: + - "2.7" + - "3.3" + - "3.4" +install: + - pip install nose pep8 flake8 coveralls +script: + - nosetests --with-coverage + - pep8 metoo + - flake8 metoo +after_success: + - coveralls diff --git a/README.md b/README.md index f25135b..0f0c155 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,8 @@ metoo ===== +[![Build Status](https://travis-ci.org/biocore/metoo.png?branch=master)](https://travis-ci.org/biocore/metoo) [![Coverage Status](https://coveralls.io/repos/biocore/metoo/badge.png)](https://coveralls.io/r/biocore/metoo) + *Staging ground for QIIME 2 development* This repository serves as a staging ground for the next major version of @@ -8,7 +10,7 @@ This repository serves as a staging ground for the next major version of and reimplementation of the package. **Note:** This repository exists mainly for developers and is not intended for -users or production. It will be transitioned to the canonical QIIME repo +production. It will be transitioned to the canonical QIIME repo ([biocore/qiime](https://github.com/biocore/qiime)) when the package is ready to be released. This package is under active development and all functionality should be treated as **pre-alpha**. diff --git a/licenses/burrito.txt b/licenses/burrito.txt new file mode 100644 index 0000000..bdbcede --- /dev/null +++ b/licenses/burrito.txt @@ -0,0 +1,27 @@ +Copyright (c) 2014, burrito 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 names burrito or biocore 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. diff --git a/licenses/scikit-bio.txt b/licenses/scikit-bio.txt new file mode 100644 index 0000000..68bfae3 --- /dev/null +++ b/licenses/scikit-bio.txt @@ -0,0 +1,27 @@ +Copyright (c) 2013--, scikit-bio 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 names scikit-bio, skbio, or biocore 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. diff --git a/metoo/__init__.py b/metoo/__init__.py new file mode 100644 index 0000000..e69de29