From b241713c0bd12bf01ee81cd8faca4e47dcbc5c97 Mon Sep 17 00:00:00 2001
From: Matthew Dillon <matthewrdillon@gmail.com>
Date: Thu, 20 Apr 2017 14:18:10 -0700
Subject: [PATCH] CI/CD: Support for automation (#42)

To hook up to the new CI/CD system, the following changes were made:

- Added/updated conda recipe
- Every commit is now a version thanks to versioneer
- Removed `install_requires` from `setup.py` (dependencies now handled by conda recipe)
- Standardized travis configuration to use latest development builds of QIIME 2

Pair programmed with: @jairideout, @ebolyen, and @thermokarst
---
 .travis.yml         | 29 +++++++++++++++--------------
 ci/recipe/meta.yaml | 43 +++++++++++++++++++++++++++++++++++++++++++
 setup.py            | 13 ++++---------
 3 files changed, 62 insertions(+), 23 deletions(-)
 create mode 100644 ci/recipe/meta.yaml

diff --git a/.travis.yml b/.travis.yml
index 6e424b4..65801d6 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,24 +1,25 @@
 dist: trusty
 sudo: false
 language: python
-env:
-  - 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:$PATH
+  - export MPLBACKEND='Agg'
+  - wget -q https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+  - export MINICONDA_PREFIX="$HOME/miniconda"
+  - bash miniconda.sh -b -p $MINICONDA_PREFIX
+  - export PATH="$MINICONDA_PREFIX/bin:$PATH"
+  - conda config --set always_yes yes
+  - conda update -q conda
+  - conda info -a
+  - git clone https://github.com/qiime2/q2lint ../q2lint
 install:
-  - conda create --yes -n test-env -c biocore python=$PYTHON_VERSION numpy scikit-bio pytest pytest-cov ipywidgets
+  - conda create -q -n test-env --file https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-conda-linux-64.txt
   - source activate test-env
-  - pip install https://github.com/qiime2/qiime2/archive/master.zip https://github.com/qiime2/q2-types/archive/master.zip https://github.com/qiime2/q2templates/archive/master.zip
-  - pip install flake8 coveralls
-  - pip install .
-  - 'echo "backend: Agg" > matplotlibrc'
-  - git clone https://github.com/qiime2/q2lint
+  - conda install -q pytest-cov
+  - pip install -q flake8 coveralls
+  - python setup.py install
 script:
-  - py.test --cov=q2_demux
   - flake8
-  - python q2lint/q2lint.py
+  - python ../q2lint/q2lint.py
+  - py.test --cov=q2_demux
 after_success:
   - coveralls
diff --git a/ci/recipe/meta.yaml b/ci/recipe/meta.yaml
new file mode 100644
index 0000000..ac19803
--- /dev/null
+++ b/ci/recipe/meta.yaml
@@ -0,0 +1,43 @@
+{% set data = load_setup_py_data() %}
+{% set version = data.get('version') or 'placehold' %}
+{% set release = '.'.join(version.split('.')[:2]) %}
+
+package:
+  name: q2-demux
+  version: {{ version }}
+
+source:
+  path: ../..
+build:
+  script: python setup.py install
+
+requirements:
+  build:
+    - python 3.5*
+    - setuptools
+
+  run:
+    - python 3.5*
+    - setuptools
+    - pandas
+    - numpy
+    - scikit-bio
+    - seaborn
+    - psutil
+    # `ipywidgets` included to avoid ShimWarning from
+    # `seaborn` imports:
+    #  https://github.com/mwaskom/seaborn/issues/874
+    - ipywidgets
+    - qiime2 {{ release }}.*
+    - q2templates {{ release }}.*
+    - q2-types {{ release }}.*
+
+test:
+  imports:
+    - q2_demux
+    - qiime2.plugins.demux
+
+about:
+  home: https://qiime2.org
+  license: BSD-3-Clause
+  license_family: BSD
diff --git a/setup.py b/setup.py
index 43b878f..3a030d2 100644
--- a/setup.py
+++ b/setup.py
@@ -16,13 +16,6 @@
     version=versioneer.get_version(),
     cmdclass=versioneer.get_cmdclass(),
     packages=find_packages(),
-    install_requires=['qiime2 == 2017.3.*', 'q2-types == 2017.3.*',
-                      'q2templates == 2017.3.*', 'numpy', 'pandas',
-                      'scikit-bio', 'seaborn', 'psutil',
-                      # `ipywidgets` included to avoid ShimWarning from
-                      # `seaborn` imports:
-                      #  https://github.com/mwaskom/seaborn/issues/874
-                      'ipywidgets'],
     author="Greg Caporaso",
     author_email="gregcaporaso@gmail.com",
     url="https://qiime2.org",
@@ -33,9 +26,11 @@
         ["q2-demux=q2_demux.plugin_setup:plugin"]
     },
     package_data={
-        'q2_demux.test': ['data/**/*'],
+        'q2_demux.tests': ['data/bad/*',
+                           'data/emp_multiplexed/*',
+                           'data/emp_multiplexed_single_end/*'],
         'q2_demux': ['_summarize/assets/*.html',
                      '_summarize/assets/app/*.js']
     },
-    zip_safe=True,
+    zip_safe=False,
 )