1 get sequences and metadata

.travis.yml

@@ -2,22 +2,30 @@ language: python
 env:
   - PYTHON_VERSION=2.7
 before_install:
-  - wget http://repo.continuum.io/miniconda/Miniconda3-3.7.3-Linux-x86_64.sh -O miniconda.sh
+  - 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:$PATH
-  # Update conda itself
-  - conda update --yes conda
+  - export PATH=/home/travis/miniconda3/bin:$TRAVIS_BUILD_DIR/scripts:$PATH
+  - export AG_TESTING='True'
 install:
-  - conda create --yes -n env_name python=$PYTHON_VERSION pip nose numpy scipy matplotlib pandas>=0.15 flake8 statsmodels lxml h5py>=2.3.1 
+  - conda create --yes -n env_name python=$PYTHON_VERSION pip nose numpy=1.9.2 scipy matplotlib pandas>=0.15 flake8 statsmodels lxml h5py>=2.3.1 notebook 
   - source activate env_name
   # upgrade click, older versions of click do not have __version__
   - pip install -U click
-  - pip install scikit-bio==0.2.3 biom-format colorbrewer
+  - pip install scikit-bio==0.2.3 biom-format colorbrewer seaborn click
+  - pip install qiime runipy ipymd
 script:
+  - source activate env_name
+  - export PYTHONPATH=$TRAVIS_BUILD_DIR:$PYTHONPATH
   - nosetests --with-doctest
   - flake8 americangut/*.py
   - flake8 scripts/*.py scripts/ag
-  # The test code contains a LOT of non-flake8 lines, mostly due to expected
-  # data
-  #- flake8 tests/*
+  - ipymd --from markdown --to notebook ipynb/primary-processing/*.md
+  - runipy ipynb/primary-processing/1-get_sequences_and_metadata.ipynb
+  # runipy ipynb/primary-processing/2-filter_sequences_for_blooms.ipynb
+  # runipy ipynb/primary-processing/3-pick_otus.ipynb
+  # runipy ipynb/primary-processing/4-prepare_metaanalyses.ipynb
+  # runipy ipynb/primary-processing/5-alpha_diversity.ipynb
+  # runipy ipynb/primary-processing/6-beta-diversity.ipynb
+  # runipy ipynb/primary-processing/7-taxonomy-summaries.ipynb
+  # runipy ipynb/primary-processing/7.5-collapse_samples.ipynb

americangut/__init__.py

@@ -0,0 +1,8 @@
+import os
+
+WORKING_DIR = 'agp_processing'
+if not os.path.exists(WORKING_DIR):
+    os.mkdir(WORKING_DIR)
+
+
+__all__ = ['WORKING_DIR']