CI/CD: Support for automation (#63)

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

.coveragerc

@@ -3,8 +3,12 @@ branch = True
 omit =
     */tests*
     */__init__.py
+    q2_feature_classifier/_version.py
+    versioneer.py
 
 [report]
 omit =
     */tests*
     */__init__.py
+    q2_feature_classifier/_version.py
+    versioneer.py

.gitattributes

@@ -0,0 +1 @@
+q2_feature_classifier/_version.py export-subst

.travis.yml

@@ -1,31 +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:$PATH"
+  - conda config --set always_yes yes
+  - conda update -q conda
+  - conda info -a
+  - git clone https://github.com/qiime2/q2lint ../q2lint
 install:
-  # TODO some of the dependencies here aren't directly required by this
-  # package. For now, install them this way for faster build times. Ultimately
-  # we can let conda do dependency resolution when there are conda packages for
-  # the various QIIME 2 projects. Until then, avoid installing heavyweight
-  # dependencies via pip.
-  - conda create --yes -n test-env -c biocore python=$PYTHON_VERSION scikit-bio jupyter click pytest pytest-cov scikit-learn
+  - 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
-  - conda install --yes -c bioconda blast=2.6.0
-  - conda install --yes -c bioconda vsearch=2.3.2
-  - pip install https://github.com/qiime2/qiime2/archive/master.zip
-  - pip install https://github.com/qiime2/q2-types/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_feature_classifier
   - flake8
-  - python q2lint/q2lint.py
+  - python ../q2lint/q2lint.py
+  - py.test --cov=q2_feature_classifier
 after_success:
   - coveralls

MANIFEST.in

@@ -0,0 +1,2 @@
+include versioneer.py
+include q2_feature_classifier/_version.py

ci/recipe/meta.yaml

@@ -0,0 +1,39 @@
+{% set data = load_setup_py_data() %}
+{% set version = data.get('version') or 'placehold' %}
+{% set release = '.'.join(version.split('.')[:2]) %}
+
+package:
+  name: q2-feature-classifier
+  version: {{ version }}
+
+source:
+  path: ../..
+
+build:
+  script: python setup.py install
+
+requirements:
+  build:
+    - python 3.5*
+    - setuptools
+
+  run:
+    - python 3.5*
+    - setuptools
+    - scikit-learn
+    - scikit-bio
+    - biom-format >=2.1.5,<2.2.0
+    - blast 2.6.0
+    - vsearch
+    - qiime2 {{ release }}.*
+    - q2-types {{ release }}.*
+
+test:
+  imports:
+    - q2_feature_classifier
+    - qiime2.plugins.feature_classifier
+
+about:
+  home: https://qiime2.org
+  license: BSD-3-Clause
+  license_family: BSD

q2_feature_classifier/__init__.py

@@ -7,9 +7,10 @@
 # ----------------------------------------------------------------------------
 
 import importlib
-import pkg_resources
+from ._version import get_versions
 
-__version__ = pkg_resources.get_distribution('q2-feature-classifier').version
+__version__ = get_versions()['version']
+del get_versions
 
 importlib.import_module('q2_feature_classifier.classifier')
 importlib.import_module('q2_feature_classifier._cutter')