Merge 5d0d743 into 982d467

.travis.yml

@@ -11,24 +11,21 @@ before_install:
   - chmod +x miniconda.sh
   - ./miniconda.sh -b
   - export PATH=/home/travis/miniconda3/bin:$PATH
-  # Update conda itself
   - conda update --yes conda
-  # Useful for debugging any issues with conda
   - conda info -a
 install:
-  - conda create --yes -n test_env python=$PYVERSION
-  - conda install --yes -n test_env --file ci/conda_requirements.txt -c biocore
-  - conda install --yes -n test_env cython
-  - source activate test_env
+  - wget -q https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py36-linux-conda.yml
+  - conda env create -q -n test-env --file qiime2-latest-py36-linux-conda.yml
+  - conda install --yes -n test-env --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 .
   - sudo pip install flake8
   - sudo pip install nose
   - sudo pip install coveralls
-before_script:
-  - flake8 . 
 script:
-  - source activate test_env
+  - source activate test-env
   - nosetests -v deicode --with-coverage --cover-package=deicode
 after_success:
   - coveralls

COPYING.txt

@@ -23,9 +23,7 @@ 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
+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

@@ -1,35 +1,35 @@
-[![Build Status](https: // travis - ci.org / biocore / DEICODE.svg?branch=master)](https: // travis - ci.org / biocore / DEICODE)
-[![Coverage Status](https: // coveralls.io / repos / github / biocore / DEICODE / badge.svg?branch=master)](https: // coveralls.io / github / biocore / DEICODE?branch=master)
+[![Build Status](https://travis-ci.org/biocore/DEICODE.svg?branch=master)](https://travis-ci.org/biocore/DEICODE)
+[![Coverage Status](https://coveralls.io/repos/github/biocore/DEICODE/badge.svg?branch=master)](https://coveralls.io/github/biocore/DEICODE?branch=master)
 
-Deicode is a tool box for running Robust Aitchison PCA on sparse compositional omics datasets, linking specific features to beta - diversity ordination.
+DEICODE is a tool box for running Robust Aitchison PCA on sparse compositional omics datasets, linking specific features to beta-diversity ordination. 
 
-# Installation
+## Installation
 
 To install the most up to date version of deicode, run the following command
 
-# pip (only supported for Qiime >= 2018.8)
-pip install deicode
+    # pip (only supported for Qiime >= 2018.8)
+    pip install deicode
 
-# conda (only supported for Qiime >= 2019.1)
-conda install - c conda - forge deicode
+    # conda (only supported for Qiime >= 2019.1)
+    conda install -c conda-forge deicode 
 
-**Note**: that deicode is not compatible with python 2, and is compatible with Python 3.4 or later. deicode is currently in alpha. We are actively developing it, and backward - incompatible interface changes may arise.
+**Note**: that deicode is not compatible with python 2, and is compatible with Python 3.4 or later. deicode is currently in alpha. We are actively developing it, and backward-incompatible interface changes may arise.
 
-# Qiime2 tutorial
+## Qiime2 tutorial
 
-**Note**: the official plugin docs and tutorial can be found[here](https: // library.qiime2.org / plugins / q2 - deicode).
+**Note**: the official plugin docs and tutorial can be found [here](https://library.qiime2.org/plugins/q2-deicode).
 
-* [Sleep Apnea Biplots](https: // github.com / biocore / DEICODE / blob / master / ipynb / sleep_apnea / SleepApnea - qiime2 - tutorial.md)
+* [Sleep Apnea Biplots](https://github.com/biocore/DEICODE/blob/master/ipynb/sleep_apnea/SleepApnea-qiime2-tutorial.md)
 
-# Other Resources
+## Other Resources
 
-* [What is Robust Aitchison RPCA](https: // github.com / biocore / DEICODE / blob / master / ipynb / introduction.ipynb)
+* [What is Robust Aitchison RPCA](https://github.com/biocore/DEICODE/blob/master/ipynb/introduction.ipynb)
 
-- The code for OptSpace was translated to python from a[MATLAB package](http: // swoh.web.engr.illinois.edu / software / optspace / code.html) maintained by Sewoong Oh(UIUC).
-- Transforms and PCoA: [Scikit - bio](http: // scikit - bio.org)
-- Data For Examples: [Qiita](https: // qiita.ucsd.edu /)
+- The code for OptSpace was translated to python from a [MATLAB package](http://swoh.web.engr.illinois.edu/software/optspace/code.html) maintained by Sewoong Oh (UIUC).
+- Transforms and PCoA : [Scikit-bio](http://scikit-bio.org)
+- Data For Examples : [Qiita](https://qiita.ucsd.edu/)
 
 #### Simulation and Benchmarking
 
-* [simulations](https: // github.com / biocore / DEICODE / tree / master / benchmarking / simulations)
-* [case studies](https: // github.com / biocore / DEICODE / tree / master / benchmarking / case_studies)
+* [simulations](https://github.com/biocore/DEICODE/tree/master/benchmarking/simulations)
+* [case studies](https://github.com/biocore/DEICODE/tree/master/benchmarking/case_studies)

deicode/__init__.py

@@ -8,4 +8,4 @@
 #
 # ----------------------------------------------------------------------------
 
-__version__ = "0.1.4"
+__version__ = "0.1.5"

deicode/q2/_method.py

@@ -9,8 +9,9 @@ def rpca(table: biom.Table,
          rank: int=3,
          min_sample_count: int=500,
          min_feature_count: int=10,
-         iterations: int=5) -> tuple([skbio.OrdinationResults,
-                                      skbio.DistanceMatrix]):
+         iterations: int=5) -> (
+         skbio.OrdinationResults,
+         skbio.DistanceMatrix):
     """ Runs RPCA with an rclr preprocessing step"""
 
     # filter sample to min depth

deicode/q2/plugin_setup.py

@@ -21,7 +21,7 @@
 plugin = qiime2.plugin.Plugin(
     name='deicode',
     version=__version__,
-    website="https://github.com/cameronmartino/DEICODE",
+    website="https://github.com/biocore/DEICODE",
     # citations=[citations['martino-unpublished']],
     short_description=('Plugin for Robust Aitchison PCA:'
                        'compositional biplots from sparse count data.'),
@@ -46,18 +46,18 @@
         'table': 'Input table of counts.',
     },
     parameter_descriptions={
-        'rank': ('The underlying low-rank',
+        'rank': ('The underlying low-rank'
                  ' structure (suggested: 1 < rank < 10)'),
-        'min_sample_count': ('Minimum sum cutoff of',
+        'min_sample_count': ('Minimum sum cutoff of'
                              ' sample across all features'),
-        'min_feature_count': ('Minimum sum cutoff of',
+        'min_feature_count': ('Minimum sum cutoff of'
                               ' features across all samples'),
         'iterations': ('The number of iterations to optomize the solution'
                        ' (suggested to below 100, beware of overfitting)'),
     },
     output_descriptions={
         'biplot': ('A biplot of the (Robust Aitchison) RPCA feature loadings'),
-        'distance_matrix': ('The Aitchison distance of',
+        'distance_matrix': ('The Aitchison distance of'
                             'the sample loadings from RPCA.')
     },
     name='(Robust Aitchison) RPCA Biplot',