Switch default predictor to ensemble, fix download bug, add more imports to...

Switch default predictor to ensemble, fix download bug, add more imports to package-level __init__, update example ipython notebook

.travis.yml

@@ -45,7 +45,7 @@ env:
 script:
   # download data and models, then run tests
   - mhcflurry-downloads fetch
-  - mhcflurry-downloads fetch models_class1_allele_specific_ensemble
+  - mhcflurry-downloads fetch models_class1_allele_specific_single
   - mhcflurry-downloads info  # just to test this command works
   - nosetests test --with-coverage --cover-package=mhcflurry  && ./lint.sh
 after_success:

mhcflurry/__init__.py

@@ -15,6 +15,10 @@
 from .class1_allele_specific.class1_binding_predictor import (
     Class1BindingPredictor)
 from .predict import predict
+
+from .affinity_measurement_dataset import AffinityMeasurementDataset
+from .class1_allele_specific_ensemble import Class1EnsembleMultiAllelePredictor
+from .class1_allele_specific import Class1SingleModelMultiAllelePredictor
 from . import parallelism
 
 __version__ = "0.2.0"
@@ -23,5 +27,8 @@ __all__ = [
     "Class1BindingPredictor",
     "predict",
     "parallelism",
+    "AffinityMeasurementDataset",
+    "Class1EnsembleMultiAllelePredictor",
+    "Class1SingleModelMultiAllelePredictor",
     "__version__",
 ]

mhcflurry/downloads.yml

@@ -22,11 +22,11 @@ releases:
         downloads:
             - name: models_class1_allele_specific_ensemble
               url: http://github.com/hammerlab/mhcflurry/releases/download/0.1.0-alpha1/models_class1_allele_specific_ensemble.tar.bz2
-              default: false
+              default: true
 
             - name: models_class1_allele_specific_single
               url: http://github.com/hammerlab/mhcflurry/releases/download/0.0.8/models_class1_allele_specific_single.no_impute.tar.bz2
-              default: true
+              default: false
 
             - name: data_kim2014
               url: http://github.com/hammerlab/mhcflurry/releases/download/0.0.8/data_kim2014.tar.bz2

mhcflurry/downloads_command.py

@@ -197,7 +197,7 @@ def fetch_subcommand(args):
             logging.debug("Extracting: %s" % names)
             bad_names = [
                 n for n in names
-                if n.strip().startswith("/") or n.strip().startswith(".")
+                if n.strip().startswith("/") or n.strip().startswith("..")
             ]
             if bad_names:
                 raise RuntimeError(

mhcflurry/predict.py

@@ -16,10 +16,11 @@ from collections import OrderedDict
 
 import pandas as pandas
 
-from .class1_allele_specific import class1_single_model_multi_allele_predictor
+from .class1_allele_specific_ensemble import class1_ensemble_multi_allele_predictor
 from .common import normalize_allele_name, UnsupportedAllele
 from .peptide_encoding import encode_peptides
 
+
 def predict(alleles, peptides, predictor=None):
     """
     Make predictions across all combinations of the specified alleles and
@@ -40,7 +41,7 @@ def predict(alleles, peptides, predictor=None):
     encoded_peptides = encode_peptides(peptides)
 
     if predictor is None:
-        predictor = class1_single_model_multi_allele_predictor.get_downloaded_predictor()
+        predictor = class1_ensemble_multi_allele_predictor.get_downloaded_predictor()
     result_dict = OrderedDict([
         ("Allele", []),
         ("Peptide", []),