got rid of six

.github/workflows/tests.yml

@@ -39,10 +39,7 @@ jobs:
         run: |
           echo "Before installing Ensembl releases" && df -h
           pyensembl install --release 75 --species human --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCh37.75/
-          pyensembl install --release 81 --species human --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCh38.81/
-          pyensembl install --release 95 --species human --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCh38.95/
-          pyensembl install --release 95 --species mouse --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCm38.95/
-          pyensembl install --release 102 --species mus_musculus --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCm38.102/
+          pyensembl install --release 102 --species mouse --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCm38.102/
           echo "After installing Ensembl releases" && df -h
       - name: Test with pytest
         run: |

vaxrank/cli.py

@@ -10,7 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import absolute_import, print_function, division
 import sys
 import logging
 import logging.config

vaxrank/core_logic.py

@@ -10,7 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import absolute_import, print_function, division
 
 import logging
 

vaxrank/epitope_prediction.py

@@ -10,7 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import absolute_import, print_function, division
 from collections import OrderedDict
 import traceback
 import logging

vaxrank/gene_pathway_check.py

@@ -10,7 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import absolute_import, print_function, division
 from collections import OrderedDict
 from os.path import join, dirname
 

vaxrank/manufacturability.py

@@ -17,7 +17,6 @@
 For more information see: https://github.com/hammerlab/vaxrank/issues/2
 """
 
-from __future__ import absolute_import, print_function, division
 from collections import namedtuple
 
 # Amino Acid Hydropathy Score

vaxrank/mutant_protein_fragment.py

@@ -10,7 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import absolute_import, print_function, division
 
 import logging
 

vaxrank/reference_proteome.py

@@ -14,7 +14,6 @@
 import os
 import logging
 
-import six
 from datacache import get_data_dir
 import shellinford
 
@@ -31,8 +30,8 @@ def fm_index_path(genome):
     if not os.path.exists(cache_dir):
         os.makedirs(cache_dir)
 
-    return os.path.join(cache_dir, '%s_%d_%d.fm' % (
-        genome.species.latin_name, genome.release, 2 if six.PY2 else 3))
+    return os.path.join(cache_dir, '%s_%d_3.fm' % (
+        genome.species.latin_name, genome.release))
 
 
 def generate_protein_sequences(genome):
@@ -46,12 +45,7 @@ def generate_protein_sequences(genome):
     """
     for t in genome.transcripts():
         if t.is_protein_coding:
-            protein_sequence = t.protein_sequence
-            if six.PY2:
-                # shellinford on PY2 seems to sometimes fail with
-                # unicode strings
-                protein_sequence = protein_sequence.encode("ascii")
-            yield protein_sequence
+            yield t.protein_sequence
 
 
 def load_reference_peptides_index(genome, force_reload=False):

vaxrank/report.py

@@ -13,7 +13,6 @@
 # pylint: disable=abstract-class-instantiated
 # For more details see https://github.com/PyCQA/pylint/issues/3060
 
-from __future__ import absolute_import, division
 from collections import OrderedDict
 from importlib import import_module
 import logging

vaxrank/vaccine_peptide.py

@@ -11,8 +11,6 @@
 # limitations under the License.
 
 
-from __future__ import absolute_import, print_function, division
-
 from operator import attrgetter
 
 import numpy as np

vaxrank/vaxrank_results.py

@@ -10,8 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import absolute_import, print_function, division
-
 from collections import OrderedDict
 
 from serializable import Serializable