Merge pull request #25 from hammerlab/travis

Add Travis to mhctools

.travis.yml

@@ -0,0 +1,39 @@
+sudo: false  # Use container-based infrastructure
+language: python
+python:
+  - "2.7"
+  - "3.4"
+addons:
+  apt:
+    packages:
+      # Needed for NetMHC
+      tcsh
+env:
+  global:
+    # MHC_BUNDLE_PASS
+    - secure: "TIminZrp9m1kMXhemqz8Zx4BjojIoEYZJnNrDrL6T/pKMpP5FQ6sprj8meGfNse4ApRIPmp5lhqxbPOe7Cg7ooetIcORekjRueHwRkYXqgMbgffgZYuEJTAGLKFsBDEXFD1kWT7igmvXFsP1T0bb1TxRPK93Q5G+e1dEAm6Iqwo="
+# Setup anaconda for easily running scipy on Travis; see https://gist.github.com/dan-blanchard/7045057
+before_install:
+  - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
+  - chmod +x miniconda.sh
+  - ./miniconda.sh -b
+  - export PATH=/home/travis/miniconda/bin:$PATH
+  - conda update --yes conda
+  - git clone https://mhcbundle:[email protected]/hammerlab/netmhc-bundle.git
+  - export NETMHC_BUNDLE_HOME=$PWD/netmhc-bundle
+  - mkdir tmp
+  - export NETMHC_BUNDLE_TMPDIR=$PWD/tmp
+  - export PATH=$PATH:$NETMHC_BUNDLE_HOME/bin
+install:
+  - conda install --yes python=$TRAVIS_PYTHON_VERSION numpy scipy nose pandas
+  - pip install -r requirements.txt
+  - pip install .
+script: nosetests test && ./lint.sh
+deploy:
+  provider: pypi
+  user: hammerlab
+  password: # See http://docs.travis-ci.com/user/encryption-keys/
+    secure: "gJSWl4PLXKtVc2ERwbzfd4qKk9Yy4T8dpfR7Q89VLVXTd7Tv1SsEknShJZUFaCPN85aYFcAWsoOI6vSlBSdXeTONU/pmPgcWOLfiErsgCqUs6qq7edOhrtOS307SREX4oF6AF2iyJduWAF4NPq+9IoJUROIiB4u5qeUtWfVu2Eo="
+  on:
+    tags: true
+    branch: master

README.md

@@ -1,3 +1,5 @@
+[![Build Status](https://travis-ci.org/hammerlab/mhctools.svg?branch=master)](https://travis-ci.org/hammerlab/mhctools)
+
 # mhctools
 Python interface to running command-line and web-based MHC binding predictors. 
 

lint.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+set -o errexit
+
+find mhctools test -name '*.py' \
+  | xargs pylint \
+  --errors-only \
+  --disable=print-statement
+
+echo 'Passes pylint check'

mhctools/base_commandline_predictor.py

@@ -86,6 +86,7 @@ def _determine_valid_alleles(command, supported_allele_flag):
                         logging.info("Skipping allele %s: %s" % (
                             line, error))
                         continue
+            return valid_alleles
         except:
             logging.warning(
                 "Failed to run %s %s",

mhctools/common.py

@@ -16,6 +16,7 @@
 
 # Python3 doesn't have a unicode classes
 try:
+    # pylint: disable=undefined-variable
     string_classes = (unicode, str)
 except NameError:
     string_classes = (str,)

mhctools/epitope_collection.py

@@ -58,7 +58,7 @@ def strong_binders_by_rank(self, max_rank=2.0):
 
     def groupby(self, key_fn):
         groups = defaultdict(list)
-        for binding_prediction in self.binding_predictions:
+        for binding_prediction in self.elements:
             key = key_fn(binding_prediction)
             groups[key].append(binding_prediction)
         # want to create an EpitopeCollection for each group

mhctools/iedb.py

@@ -75,6 +75,11 @@ def _parse_iedb_response(response):
     if len(response) == 0:
         raise ValueError("Empty response from IEDB!")
     df = pd.read_csv(io.BytesIO(response), delim_whitespace=True, header=0)
+
+    # pylint doesn't realize that df is a DataFrame, so tell is
+    assert type(df) == pd.DataFrame
+    df = pd.DataFrame(df)
+
     if len(df) == 0:
         raise ValueError(
             "No binding predictions in response from IEDB: %s" % (response,))

pylintrc

@@ -0,0 +1,4 @@
+[TYPECHECK]
+# Without ignoring this, we get errors like:
+# E:249,20: Module 'numpy' has no 'nan' member (no-member)
+ignored-modules = numpy

requirements.txt

@@ -1,4 +1,6 @@
-numpy==1.7
-pandas==0.13.1
-varcode >=0.3.17
-six >= 1.9.0
+numpy>=1.7
+pandas>=0.13.1
+varcode>=0.3.17
+six>=1.9.0
+pylint>=1.4.4
+nose>=1.3.6

setup.py

@@ -37,7 +37,7 @@
 if __name__ == '__main__':
     setup(
         name='mhctools',
-        version="0.1.3",
+        version="0.1.4",
         description="Python interface to running command-line and web-based MHC binding predictors",
         author="Alex Rubinsteyn",
         author_email="alex {dot} rubinsteyn {at} mssm {dot} edu",
@@ -55,8 +55,8 @@
         install_requires=[
             'numpy>=1.7',
             'pandas>=0.13.1',
-            'varcode >=0.3.17',
-            'six >=1.9.0'
+            'varcode>=0.3.17',
+            'six>=1.9.0'
         ],
         long_description=readme,
         packages=['mhctools'],

test/test_known_epitopes.py

@@ -18,6 +18,7 @@
 import mhctools
 
 mhc_classes = [
+    mhctools.NetMHCcons,
     mhctools.NetMHCpan,
     mhctools.NetMHCcons,
     mhctools.NetMHC,