Merge pull request #47 from hammerlab/fix-travis

Fix installation of dependencies on Travis using conda

.travis.yml

@@ -7,25 +7,43 @@ 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
+      - tcsh
+      # install pandoc for use with pypandoc for converting the README
+      # from markdown to RST
+      - pandoc
 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:$PATH
-  - conda update --yes conda
+  # Commands below copied from: http://conda.pydata.org/docs/travis.html
+  # We do this conditionally because it saves us some downloading if the
+  # version is the same.
+  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
+      wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh;
+    else
+      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+    fi
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+  # reset the shell's lookup table for program name to path mappings
+  - hash -r
+  - conda config --set always_yes yes --set changeps1 no
+  - conda update -q conda
+  # Useful for debugging any issues with conda
+  - conda info -a
+  # install netmhcbundle
   - git clone https://mhcbundle:$MHC_BUNDLE_PASS@github.com/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
+env:
+  global:
+    # MHC_BUNDLE_PASS
+    - secure: "TIminZrp9m1kMXhemqz8Zx4BjojIoEYZJnNrDrL6T/pKMpP5FQ6sprj8meGfNse4ApRIPmp5lhqxbPOe7Cg7ooetIcORekjRueHwRkYXqgMbgffgZYuEJTAGLKFsBDEXFD1kWT7igmvXFsP1T0bb1TxRPK93Q5G+e1dEAm6Iqwo="
 install:
-  - conda install --yes python=$TRAVIS_PYTHON_VERSION numpy scipy nose pandas matplotlib
+  - >
+      conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION
+      numpy scipy nose pandas matplotlib
+  - source activate test-environment
+  - pip install pypandoc
   - pip install -r requirements.txt
   - pip install .
   - pip install coveralls

README.md

@@ -1,7 +1,7 @@
 [![Build Status](https://travis-ci.org/hammerlab/mhctools.svg?branch=master)](https://travis-ci.org/hammerlab/mhctools) [![Coverage Status](https://coveralls.io/repos/hammerlab/mhctools/badge.svg?branch=master)](https://coveralls.io/r/hammerlab/mhctools?branch=master)
 
 # mhctools
-Python interface to running command-line and web-based MHC binding predictors. 
+Python interface to running command-line and web-based MHC binding predictors.
 
 ## Example
 

mhctools/alleles.py

@@ -171,7 +171,7 @@ def parse_allele_name(name, species_prefix=None):
         3) allele family
         4) allele code
 
-    If species_prefix is provided, that is used instead of getting the species prefix from the name. 
+    If species_prefix is provided, that is used instead of getting the species prefix from the name.
     (And in that case, a species prefix in the name will result in an error being raised.)
 
     For example, in all of the following inputs:
@@ -338,7 +338,6 @@ def compact_allele_name(raw_allele):
     HLA-DPA1*01:05-DPB1*100:01 into DPA10105-DPB110001
     """
     parsed_alleles = parse_classi_or_classii_allele_name(raw_allele)
-    species = parsed_alleles[0].species
     normalized_list = []
     for parsed_allele in parsed_alleles:
         if len(parsed_allele.allele_family) > 0:

mhctools/epitope_collection_builder.py

@@ -102,20 +102,20 @@ def add_binding_prediction(
         source_sequence = str(self.fasta_dictionary[source_sequence_key])
 
         binding_prediction = BindingPrediction(
-                    source_sequence_key=source_sequence_key,
-                    source_sequence=source_sequence,
-                    offset=offset,
-                    allele=normalize_allele_name(allele),
-                    peptide=peptide,
-                    length=len(peptide),
-                    value=ic50,
-                    percentile_rank=rank,
-                    prediction_method_name=self.prediction_method_name,
-                    measure=self.binding_measure)
+            source_sequence_key=source_sequence_key,
+            source_sequence=source_sequence,
+            offset=offset,
+            allele=normalize_allele_name(allele),
+            peptide=peptide,
+            length=len(peptide),
+            value=ic50,
+            percentile_rank=rank,
+            prediction_method_name=self.prediction_method_name,
+            measure=self.binding_measure)
         self.binding_predictions.append(binding_prediction)
 
     def get_collection(self):
         return EpitopeCollection(self.binding_predictions)
 
     def get_dataframe(self):
-        return self.get_collection.dataframe()
+        return self.get_collection().dataframe()

mhctools/iedb.py

@@ -16,7 +16,9 @@
 import logging
 import io
 
+# pylint: disable=import-error
 from six.moves.urllib.request import urlopen, Request
+# pylint: disable=import-error
 from six.moves.urllib.parse import urlencode
 import pandas as pd
 

mhctools/netmhc.py

@@ -17,9 +17,7 @@
 from .base_commandline_predictor import BaseCommandlinePredictor
 from .file_formats import parse_netmhc_stdout
 
-
 class NetMHC(BaseCommandlinePredictor):
-
     def __init__(
             self,
             alleles,

mhctools/netmhcii_pan.py

@@ -20,7 +20,6 @@
 
 
 class NetMHCIIpan(BaseCommandlinePredictor):
-
     def __init__(
             self,
             alleles,

mhctools/process_helpers.py

@@ -18,6 +18,7 @@
 from subprocess import Popen, CalledProcessError
 import time
 
+# pylint: disable=import-error
 from six.moves.queue import Queue
 
 class AsyncProcess(object):
@@ -123,7 +124,7 @@ def add_to_queue(process):
                 # Are there any done processes?
                 to_remove = []
                 for possibly_done in processes.queue:
-                    if possibly_done.poll() != None:
+                    if possibly_done.poll() is not None:
                         possibly_done.wait()
                         to_remove.append(possibly_done)
                 # Remove them from the queue and stop checking
@@ -140,6 +141,7 @@ def add_to_queue(process):
         processes.get().wait()
 
     elapsed_time = time.time() - start_time
-    logging.info("Ran %d commands in %0.4f seconds",
+    logging.info(
+        "Ran %d commands in %0.4f seconds",
         len(multiple_args_dict),
         elapsed_time)